appendices - link.springer.com978-3-540-77587-4/1.pdf · appendices (editor’s note: the following...

Part 7

Appendices

Appendices

(Editor’s note: the following is a compendium of literature resources suggested by some of the

authors of this Handbook. It cannot be, and does not pretend to be, comprehensive or

balanced, but rather it is provided as an aid for digging deeper into the various components

of the subject.)

LITERATURE RESOURCES

General Texts

Anthony C (1982) The Biochemistry of Methylotrophs. London: Academic Press.

Atlas RM, Philp JC (2005) Bioremediation: Applied Microbial Solutions for Real-World

Environmental Cleanup. Washington, DC: ASM Press.

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Olah GA, Molnar A (2003) Hydrocarbon Chemistry, 2nd ed. New York: Wiley.

Ollivier B, Magot M (2005) Petroleum Microbiology. Washington, DC: ASM Press.

TPH Working Group Series, Volumes 1–5 (1997–99). Amherst, MA: Amherst Scientific

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Microbiol Mol Biol Rev 67: 503–549.

Vandecasteele J-P (2008) Petroleum Microbiology. IPF Publications.

Vazquez-Duhalt R, Quintero-Ramirez R (2004) Petroleum Biotechnology – Studies in Surface

Science and Catalysis, Vol 151. Amsterdam: Elsevier.

Wang Z, Stout SA (2007) Oil Spill Environmental Forensics. New York: Academic Press.

Section Relevant Texts

Volume 1

Hydrocarbons in the Environment

Analytical Methods and Data Bases

Chernushevich IV, Loboda AV, Thomson BA (2001) An introduction to quadrupole/time-of-

flight mass spectrometry. J Mass Spectrom 36: 849–865.

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products. Anal Bioanal Chem 389: 1341–1363.

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mining organic compounds bound residues in soil and sediment. Environ Poll 108: 19–43.

K. N. Timmis (ed.), Handbook of Hydrocarbon and Lipid Microbiology, DOI 10.1007/978-3-540-77587-4_363,# Springer-Verlag Berlin Heidelberg, 2010

4612 Appendices

Schmidt TC, Zwank L, Elsner M, Berg M, Meckenstock RU, Haderlein SB (2004) Compound-

specific stable isotope analysis of organic contaminants in natural environments: a critical

review of the state of art, prospects, and future challenges. J Bioanal Chem 378: 283–300.

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Appendices 4613

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Lipids and Membranes

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4614 Appendices

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Wax Esters

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Appendices 4615

Waltermann M, Steinbuchel A (2005) Neutral lipid bodies in prokaryotes: recent insights into

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4616 Appendices

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Volume 2

Aerobic Degradation of Hydrocarbons

Biochemistry

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Genetics

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4618 Appendices

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Thompson LS, Saunders E, Buchan A (2007) Ecological genomics of marine Roseobacters.


Moran MA, Buchan A, Gonzalez JM, Heidelberg JF, Whitman WB, Kiene RP, et al. (2004)

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Nature 432: 910–913.

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Throne-Holst M, Wentzel A, Ellingsen TE, Kotlar HK, Zotchev SB (2007) Identification of

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Wood AP, Aurikko JP, Kelly DP (2004) A challenge for 21st century molecular biology and

biochemistry: what are the causes of obligate autotrophy and methanotrophy? FEMS

Microbiol Rev 28: 335–352.

Yuste L, Rojo F (2001) Role of the crc gene in catabolic repression of the Pseudomonas putida

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Appendices 4619

Lipolytic Enzymes

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de Pascale D, Cusano AM, Autore F, Parrilli E, di Prisco G, Marino G, Tutino ML (2008) The

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311–323.

Hemilae H, Koivula TT, Palva I (1994) Hormonesensitive lipase is closely related to several

bacterial proteins, and distantly related to acetylcholinesterase and lipoprotein lipase: identi-

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Loveless BJ, Saier MH Jr. (1997) A novel family of channel-forming, autotransporting,

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large beta-roll sandwich are revealed by the crystal structure of extracellular lipase from

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structure and function of a new family of hydrolases. Structure 8: 373–383.

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Gonzalez L, Derewenda ZS (1998) Structure of a microbial homologue of mammalian

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Anaerobic Degradation of Hydrocarbons

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WEB RESOURCES

Hydrocarbons (Lawrence P. Wackett)

Introduction

Hydrocarbons of diverse types are produced by microbes. The microbes are marine, freshwater

and terrestrial species. Web resources that cover this area principally focus on the type of

compound produced: hydrocarbons, waxes, oils, or fuel molecules. With intense current

interest in biofuels, web resources that deal with this topic are likely to expand dramatically.

Websites that cover microbial hydrocarbons, oils and waxes are largely designed to cover some

specific aspect of these compounds; either their catabolism (UM-BBD), their chemical proper-

ties (Cyberlipid website), or their production as fuels (BioFuels Database). These and other

websites are compiled in >Table 1. Since the taxonomy of microbial hydrocarbon production

is broad, there are no single comprehensive resources, that the author is aware of, that

deals specifically with microbial hydrocarbon biosynthesis. The closest resource is the

. Table 1

Web resources for hydrocarbons and fuels from microbes (see also Chapter 29, Volume 3)

Web resource Information provided URL

UM-BBD functional

groups

Types of hydrocarbons

metabolized by microbes

http://umbbd.msi.umn.edu/search/

FG_image_map.html

Non-methane

hydrocarbons

Report on production by marine

plankton

http://web.mit.edu/afs/athena.mit.edu/

org/c/cgcs/www/MIT_CGCS_Rpt66.html

Cyberlipids: Waxes Excellent overview on biological

waxes

http://www.cyberlipid.org/wax/

wax0001.htm

Cyberlipids:

Hydrocarbons

Excellent overview on

biohydrocarbons

http://www.cyberlipid.org/simple/

simp0002.htm

American Oil

Chemist’s Society

Fats, oils and surfactants http://www.aocs.org/

ABC’s of biofuel Department of Energy tutorial

on biofuels

http://www1.eere.energy.gov/biomass/

abcs_biofuels.html

Joint BioEnergy

Institute

Cellulosic ethanol; other

renewable energy

http://jbei.lbl.gov

Great Lakes

Bioenergy Research

Center


renewable energy

http://www.greatlakesbioenergy.org

BioEnergy Science

Center


renewable energy

http://www.bioenergycenter.org

Alternative fuels

data center

Alternative fuels: ethanol,

hydrogen, methane, propane,

biodiesel

http://www.eere.energy.gov/afdc/

Oil from microalgae Hydrocarbons, esters and ethers

from algae

http://www.fao.org/docrep/w7241e/

w7241e0h.htm

Oil from algae Links to info on algal oils http://www.oilgae.com

4634 Appendices

BioFuels Database (> Table 1). The BioFuels Database has pages that deal specifically with the

biosynthesis of specific types of hydrocarbons. The hydrocarbon classes currently covered

include alkanes, alkenes and isoprenoid compounds. Within the class of alkenes for example,

the database covers the formation of ethene, isobutene, 1-alkenes and long-chain internal

alkenes. If a user wishes to learn about hydrocarbon catabolism, particularly aromatic hydro-

carbons, the UM-BBD would be the best resource. The UM-BBD can be searched, or there are

extensive lists of:

1. organisms and their respective biodegradative pathways,

http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=allmicros, or

2. compounds degraded,

http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=allcomps

It is expected that web resources covering the microbial production, degradation, and uses

of hydrocarbons will expand in the coming years as this topic becomes increasingly important

to society.

http://umbbd.msi.umn.edu/servlets/pageservlet?ptype = allmicros,

http://umbbd.msi.umn.edu/servlets/pageservlet?ptype = allcomps

http://umbbd.msi.umn.edu/search/FG_image_map.html

http://umbbd.msi.umn.edu/search/FG_image_map.html

http://web.mit.edu/afs/athena.mit.edu/org/c/cgcs/www/MIT_CGCS_Rpt66.html

http://web.mit.edu/afs/athena.mit.edu/org/c/cgcs/www/MIT_CGCS_Rpt66.html

http://www.cyberlipid.org/wax/wax0001.htm

http://www.cyberlipid.org/wax/wax0001.htm

http://www.cyberlipid.org/simple/simp0002.htm

http://www.cyberlipid.org/simple/simp0002.htm

http://www.aocs.org/

http://www1.eere.energy.gov/biomass/abcs_biofuels.html

http://www1.eere.energy.gov/biomass/abcs_biofuels.html

http://jbei.lbl.gov

http://www.greatlakesbioenergy.org

http://www.bioenergycenter.org

http://www.eere.energy.gov/afdc/

http://www.fao.org/docrep/w7241e/w7241e0h.htm

http://www.fao.org/docrep/w7241e/w7241e0h.htm

http://www.oilgae.com

Appendices 4635

Additional Author Recommended Websites

� Stable Isotopes in Understanding Origin and Degradation Processes of Petroleum:

www.epa.gov/ada

� Biocatalysis/Biodegradation Database: http://umbbd.msi.umn.edu

� Flux-related metabolic network descriptions: http://jjj.bio.vu.nl/index.html

� Greenhouse gases, climate change and energy:

www.eia.doe.gov/bookshelf/brochures/greenhouse/Chapter1.htm

� Belching ruminants, a minor player in atmospheric methane:

http://www-naweb.iaea.org/nafa/aph/stories/2008-atmospheric-methane.html

� Human oral microbiome database: http://www.homd.org

� Trimethylaminuria:

http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=gene&part=trimethylaminuria

� Volatiles and disease diagnosis. (Note by Don Kelly: In addition to the discussion of

the olfactory skills of dogs, described in the text, searching the internet with terms such

as ‘‘dogs and cancer detection’’ reveals numerous examples of canine detection of skin

and other cancers. Other diseases seem amenable to detection by animals: in particular

‘HeroRats’ (the Giant Gambian pouched rat, Cricetomys gambianus), originally trained to

detect landmines, can detect the presence (by sniffing) of volatiles from tuberculosis

bacteria in sputum samplesmore than 100 times faster than standard laboratory procedures

for diagnosis. Using relevant search words reveals a huge media coverage of this topic,

including current work in New Zealand):

http://www.otago.ac.nz/news/news/2008/20–03–08_press_release.html

� Directed Evolution

Computational tools for improving randomized protein libraries:

http://guinevere.otago.ac.nz/stats.html

CASTER: Tool for Combinatorial Active-Site Saturation Test (CAST) to change substrate

acceptance/enantioselectivity:

http://www.mpi-muelheim.mpg.de/kofo/institut/arbeitsbereiche/reetz/englisch/reetz_

research1.html

MAP: Tool for the statistical analysis of current random mutagenesis methods for directed

protein evolution:

http://map.iu-bremen.de/MAP.html

In silico mutagenesis: A primer selection tool designed for sequence scanning applications

used in directed evolution experiments:

http://www.insilico.uni-duesseldorf.de/mutagenesisindex.html

� Community profiling

T-RFLP wikipedia website:

http://en.wikipedia.org/wiki/Terminal_restriction_fragment_length_polymorphism

T-Align website:

http://inismor.ucd.ie/�talign/index.html

RDP website:

http://rdp8.cme.msu.edu/html/TAP-trflp.html

Restriction Enzyme Picker website: REPK

http://rocaplab.ocean.washington.edu/tools/repk

Petroleum oil supply depletion: www.odac-info.org,

http://www.aspo-ireland.org/

http://www.epa.gov/ada

http://umbbd.msi.umn.edu

http://jjj.bio.vu.nl/index.html

http://www.eia.doe.gov/bookshelf/brochures/greenhouse/Chapter1.htm

http://www-naweb.iaea.org/nafa/aph/stories/2008-atmospheric-methane.html

http://www.homd.org

http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book = gene&part = trimethylaminuria

http://www.otago.ac.nz/news/news/2008/20–03–08_press_release.html

http://guinevere.otago.ac.nz/stats.html

http://www.mpi-muelheim.mpg.de/kofo/institut/arbeitsbereiche/reetz/englisch/reetz_research1.html

http://www.mpi-muelheim.mpg.de/kofo/institut/arbeitsbereiche/reetz/englisch/reetz_research1.html

http://map.iu-bremen.de/MAP.html

http://www.insilico.uni-duesseldorf.de/mutagenesisindex.html

http://en.wikipedia.org/wiki/Terminal_restriction_fragment_length_polymorphism

http://inismor.ucd.ie/&sim;talign/index.html

http://inismor.ucd.ie/&sim;talign/index.html

http://rdp8.cme.msu.edu/html/TAP-trflp.html

http://rocaplab.ocean.washington.edu/tools/repk

http://www.odac-info.org

http://www.aspo-ireland.org/

4636 Appendices

VIDEO RESOURCES

Petroleum production and contamination:

www.black-tides.com

Bioremediation:

www.learningagents.ca/MEIA

www.youtube.com/watch?v=MT0qY3_n1kI&fmt=18

http://esd.lbl.gov/people/thazen/Videos/MMO%20Movie.mpg

RT PCR:

http://www.bio.davidson.edu/courses/Immunology/Flash/RT_PCR.html

TaqMan PCR:

http://www.vetscite.org/issue1/tools/leute_2_0800.htm

http://www.black-tides.com

http://www.learningagents.ca/MEIA

http://www.youtube.com/watch?v = MT0qY3_n1kI&fmt = 18

http://esd.lbl.gov/people/thazen/Videos/MMO&percnt;20Movie.mpg

http://www.bio.davidson.edu/courses/Immunology/Flash/RT_PCR.html

http://www.vetscite.org/issue1/tools/leute_2_0800.htm

Subject Index

Subject Index

AAAA+ central domain, 1132

Abiotic factors, 287

Abioticially transformation processes, 305

Abiotic methane, 195

Absorption, 1448, 1470

Accessibility, 1084, 1086, 1091, 1093

Accidental oil spills, 1889, 1900

Acclimation, 2635

Accretionary margins, 189, 191

Acenaphthene, 2080, 2090

Acenaphthylene, 280, 2090

Acetagenesis, 2894

Acetals, 27, 28, 35, 38

Acetate, 115–120, 122, 619–622, 641–644, 649, 696, 697,

700, 701, 1650–1657, 3122, 3123

Acetate activation, 1652

Acetate fermentation pathway, 629

Acetate kinase, 360, 362

Acetate Switch, 1650, 1656–1657

Acetatoclastic methanogens, 2212

Acetic acid, 3208

Aceticlastic methanogenesis, 116–119, 153

Aceticlastic pathway, 358, 359, 891, 2236, 2240

Acetobacter, 135–138

Acetoclastic, 620–622

Acetoclastic and hydrogenotrophic methanogens,

3913, 3915

Acetoclastic methanogenesis, 659, 3915

Acetogenesis, 621

Acetohalobium arabaticum, 674

Acetone, 3168, 3174

Acetonitrile, 31

Acetotrophic methanogenesis, 494–495

Acetotrophic substrates, 116

Acetyl carrier

– acyl carrier protein (ACP), 1653, 1665

– fermentation, 1653, 1654

Acetyl-CoA (Acetyl-coenzyme A), 116, 148, 150, 151,

153, 918–920, 1650, 3281, 3282, 3284, 3285, 3288

Acetyl coenzyme A carboxylase (ACC), 510, 514, 516–517

Acetyl coenzyme A synthetase, 360

Acetylene, 14, 1663–1666

Acholeplasma laidlawii, 420–422

Acid/base reactions, 28

Acidification, 3091, 3092

Acidimicrobiales, 1823

Acidiphilium, 1924, 1926, 1928

Acidisphaera, 1924, 1927, 1928

Acidithiobacillus, 2278, 2282, 2285, 3092

K. N. Timmis (ed.), Handbook of Hydrocarbon and Lipid Mi# Springer-Verlag Berlin Heidelberg, 2010

Acidity, 25–28

Acid mine drainage, 2278, 2280–2286

Acidocella, 1926–1929

Acidogenesis, 2632

Acidophiles, 2282, 2283, 2285, 2287, 3837

Acidophilic methanotrophs, 2182, 2183,

2185–2190, 3347

Acidosphaera, 1926, 1928

Acidotolerant methanogens, 631

Acidovorax, 1716, 1720

Acid precipitation, 3691, 3708–3709

Acid rain, 3088, 3091, 3093

Acid sphingomyelinase, 3181, 3182

Acinetobacter, 528, 533, 1799–1802, 1907, 1910, 1915,

1917, 2365, 2415, 2774, 3204, 3690

Acinetobacter baumannii, 1632, 1802

Acinetobacter baylyi, 801, 1062

Acinetobacter calcoaceticus, 1802, 1803, 2885, 2886

Acinetobacter calcoaceticus HO1-N, 791

Acinetobacter calcoaceticus RAG-1, 1617–1619

Acinetobacter M1, 789

Acinetobacter radioresistens, 1803, 3032–3034

Acinetobacter radioresistens KA53, 1509

Acinetobacter RAG-1, 1509

Acinetobacter sp., 1503, 1508, 1509, 1626, 1629,

1630, 1632

Acinetobacter sp. DSM17874, 790

Acinetobacter sp. EB104, 789

Acinetobacter sp. M1, 789–792

Acinetobacter sp. strain M-1, 1148, 1151

Acinetobacter venetianus VE-C3, 1617, 1618

Acinetobacteria, 1370, 1375

Acne, 3215–3224

Acoustic surveys, 2722

AcrAB-TolC multidrug efflux system, 1587

Acridine orange direct counts (AODC), 4524

Acrylate pathway, 3121

Acrylnitrile, 31

Acryloyl-CoA pathway, 3280

Actinobacteria, 1672, 1681, 1821–1832, 1841,

1947–1948

Actinomycetales, 1823–1824

Actinomycetes, 1167, 3832

Actinopolyspora, 1941, 1947

Activated sludge, 2402–2408

Activated sludge inoculation, 1809

Active layer, 2174

Active site, 1084–1086, 1089, 1090, 1092, 1094

Active transport, 1549, 1551, 1552

Activity-based assays, 4303–4306

crobiology, DOI 10.1007/978-3-540-77587-4_364,

4640 Subject Index

Activity mining, 4565, 4566, 4568, 4571, 4576

Acyclic terpene utilization (atu), 959

Acylated homoserine lactones (AHLs), 390–392

Acyl-based signaling molecules, 391

Acyl carrier protein (ACP), 388–392, 410–412, 510,

512–514, 1653, 1665

Acyl-CoA dependent steryl ester synthases, 540

Acyl-CoA dependent triacylglycerol synthesis,

474–476, 478

Acyl-CoA independent triacylglycerol synthesis,

474, 475

Acyl-Coenzyme A (Acyl-CoA), 528, 533–534

Acylglycerols, 2849

Acyl halides, 28

Acyltransferases, 389–392, 510, 511, 528, 533, 534

Acyl-wax ester synthase, 1291

Adamantane, 8, 11

Adaptive mechanism, 1606, 1607, 1612

Addition to fumarate, 1013, 1016–1017, 1019, 1021

σ-Adducts, 985Adenosine–5’-phosphosulfate reductase (aps), 2762

Adenosylhopane, 286

Adenylate cyclase, 4408, 4414, 4415, 4417, 4418

Adenylate energy charge (EC), 1622

3’ Adenylation

– inserts, 3982

– purified PCR products, 3981–3982

Adhesions, 697, 1292, 1295, 1481–1483, 1494–1496,

1516, 1519, 3219, 3221, 3222, 3632, 3634–3636, 3638

Adhesion to hydrocarbons, 4074, 4075

Adjuvant(s), 3312–3325, 3384

Adsorption, 298, 309, 1448, 1470, 1476

Advection, 206, 209

Aerobic, 936–938, 942

Aerobic alkane biodegradation, 2414–2415

Aerobic bacteria, 1840, 1841, 1844, 2131

Aerobic conditions, 2343, 2345

Aerobic desaturation, 389

Aerobic methane oxidizing bacteria, 1953–1964

Aerobic methanotrophic, 2182

Aerobic microbial community, 4293

Aerobic oxidation, 737–738

Aerobic PAH degradation, 2415–2416

Aerobic respiration, 2475–2477, 2479, 3656, 3657

Aerobic saprotrophic bacteria, 2745

Aerobic treatment, 2396

Aerolysin, alpha-hemolysin, 426

Aeromonas hydrophila, 1111

Aerosols, 3093

Affinity, 4232, 4236, 4239

– copurification, 4419, 4420, 4423–4424

– purification, 4408, 4409, 4419–4425

Afipia, 3831, 3834

Agar plate assays, 2863

Agar shake tubes, 3805, 3806, 3808, 3818

Agricultural/natural soils subjected to inundation, 636

Agrobacterium tumefaciens, 2579

Agrochemicals, 305, 307

AHL sysnthase, 390, 392

Airplanes, 3473, 3474, 3485

a-la-carte fatty acids, 2847, 2849, 2855

Alanylphosphatidylglycerol, 399

Alasan, 1508, 1509, 1802, 3032–3033

Alaska, 2502

Albedo, 3089, 3093, 3348

Alcaligenes, 1800

Alcanivoraceae, 1738–1740

Alcanivorax, 1737–1747, 1943, 1944, 2345, 2415, 2419,

2623, 2625, 2626

Alcanivorax borkumensis, 530, 782, 1144, 1149–1151,

1266–1287, 1507, 1738, 1740, 1741, 1743–1745, 1944,

4266, 4274–4276

– metabolism and transport, 1274–1275

– vs. related species, 1269–1271

Alcanivorax borkumensis SK2, 789–791, 2688

Alcanivorax borkumensis SK2 genome, 4275, 4276

Alcanivorone, 1745, 1746

Alcohol dehydrogenase (ADH), 791, 792

Alcohols, 24–28, 31, 33, 35, 41, 2804–2805, 2807

Alcoholysis, 2828, 2837

Aldehydes, 9, 17, 27, 28, 35, 41, 784, 789, 791–793

Alessandro Volta, 694

Algae, 2829–2830, 2832, 2837, 3022–3025,

3027, 3028

– Botryococcus braunii, 2818, 2820–2824

Algaenan, 40

Alginate, 2772

Alicycliphilus strain BC, 938, 942

Alicyclobacillus, 134, 136, 138

Aliphatic, 935–943

Aliphatic hydrocarbons, 2619, 2690, 2693, 2694

Alkaline, 1932–1935

Alkalinity, 647, 648

Alkaliphile, 1932, 1933, 1935

Alkaliphilic, 1291, 1932–1935

Alkaliphilic methanogens, 647

Alkaliphilic Methylobacter, 3837

Alkalitolerant, 1800, 1932–1935

Alkane degradation, 1136, 1271–1272, 1890, 1891,

2690, 2691

Alkane degrader, 941

Alkane degraders, 4161, 4163–4164, 4171

Alkane-degrading, 2365

Alkane-degrading enzymes, 2689

Alkane hydrolases, 2689, 2693, 2694

Alkane hydroxylase (AlkB), 1751, 1801

Alkane hydroxylases, 785–790, 792, 793, 1005, 1144,

1146, 1148–1151, 1339–1342, 2688–2690

Alkane metabolism, 1291–1292

Alkane monooxygenase, 1902, 1916, 1917

Alkane monooxygenase (AlkBGT), 2881–2884

Alkane monooxygenase gene homologs, 1916

Subject Index 4641

Alkane oxidizers, 2208

Alkanes, 370–372, 610, 611, 984, 988, 990, 993–995, 997,

998, 1001–1005, 1142–1146, 1148–1151, 1505–1507,

1509, 1510, 1514–1518, 1520–1524, 1537, 1548–1551,

1650, 1652, 1720, 1855, 1924, 1926–1928, 2035–2042,

2688–2694, 2806, 3098, 3099, 3101–3103, 3108, 3744

– assimilating bacteria, 3778

n-Alkanes, 7–10, 12, 13, 42, 43, 45, 53, 105, 106, 108, 303,

2163, 2165, 2166, 2344, 3910, 3914

Alkane-utilizing bacteria, 1809

Alkanindiges, 1799–1802

Alkanols, 460, 461, 464

n-Alkan-1-ols, 310

alkB, 994, 1145, 1148–1151, 1293

alkB1, 2689, 2692, 2694, 2695

alkB2, 2690

alkB alkane hydroxylase, 787, 788

alkB family, 786–789

alkB gene(s), 1891, 2414, 2415, 2419

Alkenes, 13–18, 42, 45, 53, 370, 372, 610, 611, 984, 994,

1003, 2010–2011, 2035, 2042

AlkG rubredoxin, 788

Alkines, 13–16

AlkL, 1548, 1551

alkS/alkB1 genomic regions, 1743

Alkylated DBT, 2788, 4557

Alkylbenzenes, 19, 42

Alkylcatechols, 1074

Alkyl-enzyme intermediate, 1082, 1084–1086

Alkyl halides, 702

Alkylperoxo, 1073

Alkylpyrone, 404, 405, 520, 521, 523, 524

Alkylquinone, 522, 523

Alkyl radicals, 12, 13, 272, 274, 275

Alkylresorcinol, 404, 405, 520–524

Alkylresorcinol methyl ether, 522

Alkyl-substituted PAH, 285

Alkylsuccinate adduct, 1046

Alkynes, 2011

Allergic effects, MWF, 3306

Allochthonous emissions, 311

Allochthonous microbes, 2734

Allochthonous substances, 300

AlmA, 789, 790

Alpha-helix, 427–429

Alpha hemolysin, 426, 430, 431

Alphaproteobacteria, 1708–1714, 2342, 3831, 3832

Alpine, 2323–2324

Alpine habitats, 1908, 1913, 1914

Alpine soils, 1901, 1902, 1904, 1907, 1908, 1914, 1917

Alteration, 100, 105–108

Alternaria brassicola, 3262

Alternative sources, 2996, 2997

Alteromonadaceae, 1726

American petroleum institute (API) gravity, 43, 44

Amides, 28, 31, 35

Amine borates, 2645, 2647

Amines, 28, 29, 31, 33, 35, 41, 2774

Amino acids, 28, 31, 32, 36, 300, 301

Amino acid sequence, 3689, 3698–3700

Amino-allyl coupling, 4371

Aminobenzoyl-CoA oxygenase, 1370

l-Aminocyclopropane-l-carboxylic acid, 3014

4-Amino-4-deoxy-L-arabinose (L-Ara4N), 412–414

Aminopentanetetrols, 584

Aminophenol 1,6-dioxygenase, 1365–1367

Ammonia, 2758

Ammonia flush, 2648

Ammonia monooxygenase (AMO), 2512

Ammonium mineral salts (AMS) medium, 3834

Ammonium sulphate precipitation, 3692

Amorphous Fe(III)-oxide stock, 3865

Amphipathic helices, 428, 429

Amplicons digestion, 4117–4119

Amplification, 4040–4043, 4047, 4048

Amsel criteria, 3231

Anabolism, 732, 739

Anaerobes, 2263, 2268

Anaerobic, 618–623, 682, 685, 687–690, 936–938,

2164–2170, 2611–2613, 3098, 3100–3102, 3106, 3107

Anaerobic agar plates, 3806–3807

Anaerobic and aerobic oxidation, 3061

Anaerobic aquifers, 308

Anaerobic bag, 3807

Anaerobic cabinet, 3805, 3807

Anaerobic carboxylation, 1021

Anaerobic chamber, 3428, 3432, 3436–3438

Anaerobic C-H oxyfunctionalization, 2887

Anaerobic culturing, 3857–3858

Anaerobic degradation, 909–922, 957–961

– Aromatoleum aromaticum, 4390–4392

– aryl-and alkylsuccinate synthases, 4390

– oil, 3907

– processes, 4294

Anaerobic degradation of hydrocarbons, 1011–1021,

1901, 1915

Anaerobic digesters, 2403, 2406

Anaerobic digestion, 2810–2811, 2814

Anaerobic digestion of biomass, 2892, 2893

Anaerobic food chain, 3454

Anaerobic fungi, 699, 701

Anaerobic hydrocarbon degradation, 2416–2417

Anaerobic hydrocarbon degraders, 1997–2015

Anaerobic hydrocarbon metabolism, 1012

Anaerobic hydroxylation, 1013–1016

Anaerobic jar, 3805, 3807

Anaerobic methane oxidation, 672, 674, 2187,

2233–2242, 3830, 3838, 3841

Anaerobic methanotrophs (ANME), 2007, 2008,

2026, 2030, 2194, 3801, 3817, 3821–3823

Anaerobic microorganisms, 3787–3798

Anaerobic nitrate-reducing conditions, 1719

4642 Subject Index

Anaerobic oxidation, 738–739

Anaerobic oxidation of methane (AOM), 890, 896–904,

984, 999, 2025–2027, 2029–2030, 2194–2196, 2198,

2199, 2232–2243, 3448, 3811

Anaerobic oxidation processes, 4510, 4515

Anaerobic protists, 713–714

Anaerobic treatment, 2632, 2634, 2635

Anaerobic tubes, 3804–3807

Anaerobic utilization, 2050–2060

Anaeromyxobacter dehalogenans, 4315, 4322, 4323

Anaerovibrio, 2248, 2250

Anaerovibrio lipolytica, 2248, 3116

Anaerovibrio lipolyticus, 2249, 2250

Analysis of oils, 3575–3582

Analysis of variance (ANOVA) test, 4361

Analytical techniques, 3726, 3739

Ancient seeps, 194, 195, 197–198

Anderson–Schulz–Flory distribution, 222

Angular oxygenation, 2148

Aniline dioxygenase, 1376, 1377

Anilines, 31, 1720

Animal health, 3160, 3163

ANME, 151, 152, 2194, 2195, 2197–2199, 3079–3083

ANME–1, 671, 674, 890, 891, 896–898, 900, 902, 2025,

2027–2029, 2232, 2233, 2239, 2240, 2242

ANME–1b, 674

ANME–2, 890, 891, 896, 897, 900, 902, 2232, 2233, 2239,

2240, 2242

ANME–3, 890, 891, 900, 2233, 2240, 2242

Annotation, 4265–4277

Anoxic, 2294–2296, 2300–2302, 2610, 2613

Anoxic chamber, 3788

Anoxic conditions, 2343, 2345, 2346, 3788–3796

Anoxic freshwater lakes, 115

Anoxic portions of animal digestive tracts, 636, 637, 642

Anoxic sediments, 2024

Anoxic waterlogged soils, 627–628

ant, 2793, 2794

Antagonistic microorganisms, 4169

Antarctic, 3233, 3831, 3837

Anthracene, 1800, 2080, 2082, 2088, 2089, 2091, 2093,

2095, 2098–2100, 3922

Anthranilate, 2793, 2794, 2799

Anthranilate dioxygenase, 1375–1377

2,6-Anthraquinone disulfonate (AQDS), 3859

Anthrax toxin, 432

Anthrone assay, 3710, 3720

Anthropogenic, 280, 281, 285, 287–288, 290

Anthropogenic contaminants, 300, 306, 310, 312

Anthropogenic impact, 305

Anthropogenic marker, 305

Anthropogenic perturbations, 280

Anthropogenic pollutants, 298

Anthropogenic pollution, 307

Anthropogenic sources, 270

Anthroposphere, 302

Anti-aging products, 3390–3391

Antibacterial agents, 392

Antibiosis, 2557–2558

Antibiotic, 3218, 3224

Antibiotic analogues, 2907

Antibiotic resistance, 3236

Antibiotic resistance markers, 4251

Antibiotic resistant bacteria, 1631

Antibiotic tolerance, 3191

Antibodies, 2700–2707, 4192

Antibody labeling, 4066–4067, 4069

Antibody microarrays, 2700–2708

Antibody production, 2702–2703

Antifungal metabolites, 3462

Antigen-antibody, 4064

Antigen-delivery system, 3312, 3313, 3325

Antigenic determinant, 2703

Anti-microbial, 3161

Antimicrobial and/or antiviral activities, 2974

Antiperspirants, 3388–3399

AntR, 2793, 2794

Antrim Shale, 668

AOM. See Anaerobic oxidation of methane (AOM)

AOM-activity, 193, 194

AOM-carbonates, 198

AOM-consortia, 188, 193, 194

Apigenin, 3264

Apocrine glands, 3205, 3207

Apoptosis, 3172

Applications, 942–943, 2115, 2968, 2969, 2971–2976,

3376, 3377

Applied biosystems SOLiD, 4270

AP-1 transcription factor, 3253

APWmedium, 3861, 3864

Aquatic ecosystems, 298

Aquatic food chain, 4500, 4505

Aquatic metagenome, 4347–4351

Aquatic organic matter, 298

Aquatic sediments, 636

Aquatic systems, 298, 300, 309, 310

Aqueous methane, 761–762

Aqueous solubility, 41, 44–46

Aquifers, 2465–2470, 2584–2588, 2593, 2594,

2610–2614

Arabian Gulf, 1932, 1940

AraC, 1241

AraC family, 1133

Arachidonic acid, 3025, 3247, 3251, 3253

AraC XylS, 1240

AraC XylS type transcriptional regulators, 1241–1242

ARB, 3913

Arbitrary PCR, 3962

Archaea, 452–457, 618–620, 622, 694–698, 1942, 1943,

1945, 1948, 2779

Archaea-Deltaproteobacteria, 3841

Archaea in terrestrial environments, 284

Subject Index 4643

Archaeal hydrocarbon degradation, 1683

Archaeoglobus, 2207, 2209, 2212, 2719

Archaeol, 452, 455, 457, 2027

Archaetidic acid, 452, 455

Archaetidylglycerophosphate, 455

Archaetidyl-myo-inositol, 457

Archaetidylserine, 455

Archiving, 4347–4351

Arcobacter, 2168

Arctic, 656–661

Arctic permafrost, 2174–2177, 3342, 3347

Arene-cis-dihydrodiols, 801, 842

Arene oxides, 2084

Arenes, 370, 610

Are1p, 540

Are2p, 540

Arginine fermentation, 1789

ArnA, 413

ArnB, 413

ArnC, 413

ArnD, 413

ArnE, 413

ArnF, 413

ArnT, 413

Aromatic, 935–943, 2162, 2163, 2165, 2166

Aromatic compounds, 1347, 1349, 1652–1653

Aromatic dioxygenase genes, 1917

Aromatic hydrocarbon degradation, 1783, 1784

Aromatic hydrocarbons, 298, 303, 307, 311, 799–830,

2344, 2619

Aromaticity, 18, 19, 29, 40, 235

Aromatic ring hydroxylating dioxygenase (ARHDs),

1250

Aromatics, 1356–1392, 2768, 2776

Aromatization, 286

Aromatoleum aromaticum, 1016, 4390–4391

Array design, 2679, 2680

Array detector, 4556

Arrayer, 4065, 4066, 4069, 4070

Arrays, 4040, 4041, 4044–4048

Arrhenius relationships, 1090

Arrhenius-type relationship, 647

Artemisinin, 2945

Arthrobacter, 1549, 1854–1862, 1908, 1910

Arthrobacter Keyseri, 804

Ascomycetes, 1926

Ascomycota, 2067–2070, 2085, 2227, 2228

Ash layers, 192

Aspergillosis, 3286

Aspergillus fumigatus, 3284, 3286–3287

Aspergillus nidulans, 3284

Asphaltenes, 52, 2768, 2779, 2781, 2782,

2789, 3576

Assaying Fe(III)/Fe(II), 3866–3867

Assays, 2930, 2934, 2936

Assessing the oil volume at sea, 3480

Assessment, 3603–3610

1’Atalante, 670, 671

1’Atalante basin, 671

Atmosphere, 3088, 3089, 3091, 3093, 3094

Atmospheric alkanes, 272–275

Atmospheric aromatic VOCs, 276

Atmospheric carbon dioxide, 3343–3344

Atmospheric chemistry, 3594

Atmospheric methane, 3344–3345, 3841

Atmospheric methane consumption, 2189

Atmospheric OVOCs, 276–277

Atmospheric photochemistry, 270

Atmospheric pressure ionization (API), 53, 55,

58, 62

Atmospheric residence times of VOCs, 272

Atmospheric temperature, 3340–3343

Atom orbitals, 6

Atopobium, 3232

Atoppers, 3788, 3790, 3791, 3793–3796, 3798

ATP, growth yields, 736, 748

ATP synthase, 362, 364, 365

Atrazine, 1226–1227, 1229

Attractant compounds, 3207

Authigenic carbonates, 3062

Autochthonous material, 298, 300

Automated sample extraction, 2708

Automatic instrumentation, 2708

Autonomous underwater vehicles (AUVs), 3445

– submersible, 3421

Autoradiography, 4162, 4166–4169

Autothonous immissions, 311

Autotransporter, 4587–4598

Autoxidation, 310

Azoarcus evansii, 949

Azoarcus species, 2004, 2005, 2012

Azoarcus, 1716–1717, 1719

Azotobacter, 1663, 1665, 1666, 2502

Azotobacter vinelandii, 447–448

BB12, 1020, 3280–3282, 3289

Baboon, 698

Baby smell, 3205, 3211

BACCAardI, 4270

BAC clones, 4267, 4268, 4275

Bacilli, 1364, 1381, 1382

Bacillus, 122, 512, 515, 1888–1891, 1933, 1943,

1944, 1947, 3204, 3205, 3208, 3209,

3689–3691, 3701

Bacillus krulwichiae, 1947

Bacillus licheniformis, 1508

Bacillus lipopeptides, 3691, 3701

Bacillus mojavensis, 1508, 2732

Bacillus sp., 1503, 1508, 1510

Bacillus subtilis, 523, 1508, 1656, 2132, 2136, 2770

Back-arc basins, 1983

4644 Subject Index

Background, 4066, 4068–4070

– fluorescence, 4134

– signal, 4045

Bacteria, 460–470, 2768, 2770, 2772, 2774, 2777, 2779,

2781, 2782, 3180–3182, 3270, 3273–3275, 3280, 3282,

3287–3289

– functions, 4105

– inoculum, 3464, 3468

– population, 3462, 3469

– scatter, 4109, 4111, 4112

Bacterial adenylate cyclase two-hybrid (BACTH) system,

4414, 4415, 4417, 4419

Bacterial aerobic hydrocarbon degradation, 4294

Bacterial artificial chromosomes, 4348

Bacterial catabolic pathways, 2578, 2579

Bacterial cellulose, 2973, 2974

Bacterial communities, 2342, 2343, 4052

Bacterial diversity, 2306, 2327

Bacterial diversity, MWF, 2372–2374

Bacterial lipases, 3242–3245

Bacterial/microbial adhesion to hydrocarbon, 3634–3635

Bacterial oils, 2996, 2997

– for nutritional purposes, 2999

Bacterial response, hydrocarbon-water interface, 4377

Bacterial secretion systems

– cell staining, 4597–4598

– cell surface exposition, 4594

– electroporation, 4595–4596

– equipment, 4593

– esterases, 4598

– HRP, 4597

– hydrolases screening, 4596

– library, 4592, 4594–4596

– materials, 4592–4593

– type II machineries, 4590

Bacterial stress response, 1189–1190

Bacterial toxins, 426

Bacterial two-hybrid (B2H) system, 4408–4419

Bacterial vaginosis, 3227–3237

Bactericides, 302

Bacteriodetes, 1814–1817, 2364, 2365

Bacteriohopanepolyols, 135, 138

Bacteriophages, 699

Bacterioplankton, 1202, 1203, 1205–1207, 1209

Bacteroides, 3122, 3135–3138

Bacteroides thetaiotaomicron, 3153

Bacteroidetes, 1357, 1370, 1381, 1382, 1681, 1814–1817

BAK1, 2972

Band intensity, 3912

Bannock, 670, 671

Bannock basin, 671

B[a]P. See Benzo[a]pyrene

Barite, 197

Barkeri, 699

Base Oil, 2644

Basicity, 31, 32

Basic nitrogen compounds, 2144, 2154, 2773

Basidiomycota, 2070–2072, 2085

Basin, sedimentary, 102–105

Batch cultivation, 3530, 3532, 3535, 3539

BATH, 3632–3635

Bathymodiolus, 670

B-BRAT, 4452

Bead beating, 4185, 4187

Beggiatoa, 2195, 2206

Behavioral response, 3935

Benthic ecosystems, 311

Benthic filter, 197

Benthic microbial community, 311

Benthic microbial fuel cell (BMFC), 198

Benz[a]anthracene, 2080, 2088, 2095, 2100

Benzaldehyde dehydrogenase, 1916

Benzaldehyde lyases, 2922

Benzene, 16–26, 29, 34, 41, 42, 936–938, 942, 993, 994,

1003, 1005, 1012, 1013, 1019–1021, 1362, 1368, 1369,

1375–1377, 1459, 1536, 1540, 1716, 1719, 1940, 1943,

1947, 2035, 2042, 2044, 2294, 2296, 2299, 2300, 2307,

2308, 2610–2613

– interaction with the plasma membrane, 1455

– movement within the cell, 1458

Benzene carboxylation, 1021

Benzene mono-oxygenase, 942

Benzene specialists, 2612

Benzene, toluene, ethylbenzene, and xylenes (BTEX),

307, 2294–2303, 2305, 2308, 2610–2614, 3576, 3744

– inwater treatments, 3506

Benzene/toluene monooxygenase, 1368

Benzo[a]pyrene (B[a]P), 991, 1005, 1709–1713, 2080,

2082, 2088, 2089, 2096–2100, 3151, 3153, 3154

Benzoate, 1185, 1186, 1193, 1341

Benzoate-cis-dihydrodiol, 801

Benzoate degradation pathway, 2777

Benzoate dioxygenase, 1375, 1376

Benzo[b]fluoranthene, 2096

Benzo[e]pyrene, 2080, 2098

Benzofuran, 29, 30

Benzo[ghi]perylene, 2098

Benzo[k]fluoranthene, 2096

Benzopyrene hydrodiol, 1005

Benzoquinol 1,2-dioxygenase, 1357, 1368

Benzothiazole, 3211

Benzothiophene (BT), 29, 30, 2130, 2131, 2136,

2137, 2139

Benzothiophene degraders, 4163–4164

Benzoyl-CoA ligase(s), 949, 951

Benzoyl-CoA oxygenase, 1357, 1368, 1369

Benzoyl-CoA pathway, 1341

Benzoyl-coenzyme (CoA), 339, 346–348, 949–953, 1719,

2035, 2036, 2042, 2043

Benzyl alcohol dehydrogenase, 1916

Benzylsuccinate, 926, 1001, 1002, 1719, 2035, 2298,

2305, 2306

Subject Index 4645

Benzylsuccinate synthase (BSS), 915, 916, 926, 930, 1002,

1017, 1018, 1021, 2305, 2306

Berberine, 3264

Beta-galactosidase, 3646

Beta hairpin, 430, 431

Betaine, 3228–3231

Betaine lipid, 402–404

Betaproteobacteria, 1716–1721, 3831, 3832

Betaproteobacterium, 912, 917, 919, 921

Beta structure, 428–431

Bicarbonate, 3790

Biddulphia sinensis, 176

Bidentate, 1073

Bifidobacteriales, 1823

Bifidobacterium infantis, 3116

Big Soda Lake, 674

Bile acids, 960, 3134, 3137–3139

Bile salt hydrolases, 3137

1,1 Binapthyl, 3909

Binary protein interaction, 4409, 4419

Bioaccessibility, 1445–1449, 1470, 1475, 1556, 1558,

1560, 3642

Bioaccumulation, 302, 305, 311, 1442, 1443, 1481, 1484

Bioactive dental prosthetics, 3176

Bioactive lipids, 2382, 2383

Bioaffinity, 2700, 2702, 2704

Bioassays, 2496, 3482, 3492, 3500, 4466–4469, 4471

Bioaugmentation, 1665, 1666, 2495, 2522, 2532–2534,

2537–2540, 2585, 2587, 2589–2595, 2635, 3400, 4519,

4524, 4532–4541, 4545–4546, 4550

– design protocols, 3399

Bioavailability, 9, 41, 1440–1449, 1471–1476, 1480,

1485, 1486, 1502, 1505, 1509, 1532, 1540, 1558,

1560, 1616, 1617, 1620, 1777, 1942, 2295, 2488,

2495, 2496, 2516–2518, 2579, 3148, 3642, 3848,

3849, 3853

– bioemulsifiers, 2351

– biosurfactants, 2351

– surface active agents, 2351

Bioavailability, definition, 1442

Biocatalysis, 1050–1053, 1083, 1090, 1093, 1094, 1413,

1420, 1421, 1424, 1426, 1430, 1431, 2877–2888,

2905–2906, 2908

Biocatalysts, 1050, 2773, 2837, 2912, 2920

Biocatalytic potential, 1315

Biocenosis, 621

Biochemical reactions, 751–752

Biochemistry of methanotrophs, 769

Biocompetitive exclusion, 2755, 2757, 2758, 2760

Biocontrol, 3462

Bioconversions, 2920

Biodearomatizing (BDA), 2777

Biodegradable films, 2976

Biodegradable plastics, 2968, 2971, 2972

Biodegradable polymers, 2897, 2900, 2968, 2970, 2975,

2976, 3376, 3378

Biodegradation, 53, 55, 56, 59, 61, 100–102, 105–108,

959–961, 1179–1194, 1412, 1417–1419, 1421–1424,

1426, 1428–1430, 2273–2274, 2294–2305, 2537, 2539,

2576, 2580, 2581, 2912, 2919, 3098–3101, 3103–3108,

3376, 3378, 3604, 3610, 3771–3775, 4532, 4535–4538,

4540, 4546, 4549, 4550

– efficiency, 1910

– microbial ecology, 4292–4295

– prediction, 4181

– tools, 4181

Biodenitrogenation (BDN), 2773, 4554, 4558–4561

Biodenitrogenization, 2788, 2798

Biodesulfurization (BDS), 2131, 2136, 2137, 2770,

2795–2799, 4554–4559

Biodeterioration, MWF, 2643–2647, 2649

Biodiesel, 2272–2274, 2804, 2805, 2827–2838, 2892,

2897, 3336

Bioemulsifiers, 1502–1511, 2516–2518, 2731–2732

Bioenergetic, 339–341, 345, 348, 350, 636, 637, 639–650

Bioenergy, 3000

Bioethanol, 3336

Biofilm-mediated, 1502

Biofilms, 1291–1293, 1295, 2165, 2167, 2170, 2732,

2886–2887, 3171–3173, 3235, 3562–3563,

4074–4076, 4078

– activity measurement, 3549–3550

– biofilm on HOCs, 1495, 1496

– environmental samples, 3545

– formation, 1275–1277

– hydrophobic interface(s), 1492, 1494, 1495

– interfacial growth, 1492

– proteome, 4185

– structure and dynamic, 3550

Biofilters, 1925–1927

Bio filtration, 1924

Biofuel(s), 2443–2446, 2454, 2804–2807, 2818, 2825,

2828, 2829, 2837, 3022, 3025, 3358

Biogas, 2810–2814

Biogas formation, 969–975

Biogas plant, 2894

Biogenic anabolic processes, 4292

Biogenic hydrocarbons, 2714–2723

Biogenic methane, 193, 2730–2731, 3056, 3058–3063

Biogenic sources, 270, 276

Biogeography, 2413–2420

Biogeomacromolecules, 58

Biohydrogenation, 2247, 2252–2255, 2385, 2387, 2388

Bioinformatic tools, 4314

BIOLOG anomaly, 1766

BIOLOG assay, 4524–4525

Biological activity, 3148, 3152, 3155

Biological desulfurization, 3364

Biological systems, 2940–2941, 2947–2948

Biological energy quantum (BEQ), 640, 641, 643

– ATP synthase, 332

– ATP synthesis, 332

4646 Subject Index

– methane, 332

– protons, 332

– Thermacetogenium phaeum, 332

– Wood-Ljungdahl pathway, 332

Biological role, 1094

Bioluminescence, 3642–3643, 3646–3647,

3649, 3651

Bioluminescence full cell bioreporters, 4447–4456

Biomarker lipids, 2197

Biomarkers, 102, 103, 194, 195, 197, 198, 670, 672, 2522,

2523, 3174–3175, 3191, 3576, 3671–3680, 3907, 3914

– analysis, 3407–3417, 3743–3750

Biomass collection, 3672, 3673

Biomass-to-biogas-to-energy combination, 3336

Biomass yields

– acetate, 324, 325, 328, 330, 332

– activities of products and reactants, 327

– anaerobic decomposition, 328

– ATP formation, 327

– biochemical work, 326

– chemolithotrophic bacteria, 326

– Ds01/rx, 325

– environmental activities, 327

– glucose, 326

– hydrogen activities, 328

– hydrogenotrophic methanogenesis, 328–331

– hydrothermal systems, 328

– nitrifiers, 326

– propionate, 326

– reverse electron transport, 326

– standard free energy changes, 327–329

– sulfatereducing conditions, 326

– Syntrophobacter fumaroxidans, 326

– thiobacilli, 326

– toluene, 326, 327

Biomaterials, 2973, 2976

Biomedical and pharmaceutical applications, 2973–2975

Biomethanation, 2894

Biomethane, 2810–2814

Biomimetic, 2852

Biomonitoring, 2702–2703, 2705, 2708, 4063–4071

Bioplastics, 2969, 2976, 3376, 3377

BIOPLUME model, 2593, 2594

Biopol1, 2971

Biopolymer analysis, 3691

Biopolymers, 1509, 2732, 2968, 2969, 2972, 2974–2976,

3376–3378, 3726

Bio-Rad Dcode system, 4145, 4148, 4154

Biorefineries, 2893

Bioremediation, 1050–1053, 1083, 1094, 1558, 1560,

1629–1630, 1840, 1842, 1843, 1847, 1854, 1858, 1860,

1862, 1975, 2098–2101, 2341–2342, 2424, 2425, 2427,

2432, 2442, 2446–2447, 2452, 2461–2463, 2488, 2495,

2497, 2516–2518, 2577, 2579, 2580, 2705, 2708, 3008,

3046, 3351–3353, 3358, 3544, 3958, 4455, 4456, 4532,

4538–4541

– characterization and monitoring, 4521–4527

– chemical composition, 3400–3401

– efficacy, 3399

– fertilizers, 3400

– hydrocarbon spills, 3398

– oil composition, 3399

– planning, 3401–3402

– statistical techniques, 3402–3403

– systems biology approach, 4527–4528

– techniques, 3744

– technologies, 4518

Bioreporters

– applications, 4448–4449

– B-BRATmap, 4455

– calibration and characterization, 4450–4451

– groundwater samples, 4456

– pollutants distribution, 4443–4454

– response, Zn, 4452

– risk and hazard, 4449

– soils risk assessment, 4451–4455

Biosensing, 1083

Biosensors, 1094, 1236, 1237, 1239, 1317, 1318, 2497,

2653–2671, 2799, 4430, 4431

Bioslurping, 2606

Biostatic, 3107, 3108

Biostimulation, 2495, 2522, 2523, 2525–2528, 2585,

2587, 2589–2595, 4519, 4520, 4532, 4535, 4536,

4540, 4541

– biodegradation affecting factors, 4520–4521

– bioremediation technologies, 4518–4519

– characterization and monitoring, 4521–4527

– critical biogeochemistry, 4521, 4522

– systems biology approach, 4527–4528

Biosurfactant-producing microorganisms, 1503

Biosurfactants, 784, 912, 1462, 1502–1511, 1842, 1904,

1912, 2515–2518, 2525, 2731–2732, 2795, 2798, 3046,

3687–3703, 3706, 3710, 3714, 3721

– ecological implications, 1461

– interactions with hydrocarbons, 1461

Biosynthesis, 9, 17, 23, 26

Biosynthetic oils, 79–93

Biosynthetic pathways, 61

Biotechnological aspects, PHA, 2990–2991

Biotechnology, 2714, 2720, 2844, 2845, 2969

Biotic and abiotic transformation, 309, 310

Biotransformations, 1840, 2488, 2495, 2881, 2882, 2884,

2886, 3148, 3151, 3154, 3155

– crude oil, 2735

Bioventing, 2605

Biphasic nature of the process, 2772

Biphenyl catabolism, 1350

Biphenyl dioxygenase, 1376, 1377

Biphenyl 2,3-dioxygenase, 1183, 1184, 1192, 1193

Biphenyl metabolism, 1190–1193

Biphenylene, 2080, 2090

Biphenyls, 19, 20 , 24, 1179–1194, 1536–1538

Subject Index 4647

Birch reaction, 23

Bis-benzimide, 4021

Bischofite, 671

Bitumen, 144, 153, 2163, 2165, 2169, 2170

Black carbon, 285

Black Sea, 120, 195–196, 3090, 3092

Black-smoker, 219

Black water, 2394, 2395, 2397, 2398

Blank floating slide microcosm, 3545–3546

BLAST, 4319, 4321

– analysis, 4205

– atlas, 4314, 4315, 4322, 4324

– matrix, 4322

– searching, 3701

Bligh and Dyer procedure, 3747, 4207

Blocking, 4066, 4070

Blocking reagents, 2701, 2704

Block polymers, 2898

Boiling points, 41–43, 45

Bond lengths, 6

Bond strength, 25, 41

Bondyuzhshkoe oil deposit, 1946

Bonn agreement, 3473, 3478, 3480–3482

Bonn agreement oil appearance code, 3480–3481

BONN-OSINET (Oil spill identification network), 3482

Bordetella bronchiseptica, 414

Boron, 196

Botrytis cinerea, 1214, 3012, 3014, 3262

Bottle effect, 3524

Bottom simulating reflector (BSR), 3446

Boundary layers (BL), 1471, 1472

Box-corer, 3422

Box-core sampler, 3871, 3872

Box model, 2478–2480, 2482

Box-whisker plot, 4479

bph gene, 1187–1189, 1193

Brackish/freshwater environments, 4506

Bradford assay, 3695–3696, 3702, 3703

Bradyrhizobium, 1365, 1369, 1370, 1372, 1375, 1377, 1383

Bradyrhizobium-Agromonas-Nitrobacter-Afipia, 846

Bradyrhizobium sp., 844, 850

Branched alkanes, 9, 10, 12, 53, 3910

Branched-chain fatty acids (BCFA), 3123, 3124,

3129, 3198

Breakthrough curve, 3636, 3637

Breath analysis, 3093, 3168, 3169, 3174–3175

Brevibacteriaceae, 1827, 1828, 1854

Brevibacterium, 1854, 1855, 1860, 1861, 3172, 3173, 3204,

3207, 3208

Brine-pool methane seep, 674

Brine pools, 192, 196

Broad host range, 4246

Bromhidrosis, 3209–3210

Bromide, 4523

Bromomethane, 866, 869

Brumimicrobium sp. P99, 1817

BTEX. See Benzene, toluene, ethylbenzene, and xylenes

BTEX plume

– calculation, 4513

– redox shift, 4511–4512

Budding model, 477–479

Budding yeast, 538, 540, 543, 4224, 4227, 4228

Buffers, 4592–4595, 4597, 4598

Building blocks, 2943, 2944

Bunker oil, 3486

Buoyant density (BD), 4012–4018, 4021–4022

Buried reefs, 192

Burkholderia, 1361–1364, 1366–1370, 1372, 1373,

1375–1377, 1387, 1391, 1536, 1538, 1716, 1719, 1720,

2774, 2777

Burkholderia cenocepacia, 3296, 3297

Burkholderia cepacia, 803, 842, 844, 3295, 3296, 3300

Burkholderia xenovorans, 1061

Burkholderia xenovorans LB400, 1181, 1184, 1185, 1187,

1188, 1364, 1367, 1369, 1377, 1378, 1389–1391

Burkholderiacea, 1367–1370, 1377, 1387, 1391

Bushnell-Haas Broth, 4162, 4163

Butane, 120, 121, 152, 1720

Butane monooxygenase (BMO), 786, 1144–1145

2,3-Butanediol, 2898

Butanol, 2804–2807

1-Butene, 121

Butyl rubber, 3910

Butyrate, 3122–3124, 3129

Butyric acid, 2898

Butyrivibrio, 2248, 3125, 3126

Butyrivibrio fibrisolvens, 2249, 2250, 2252, 2253

Butyrivibrio fibrisolvens strain LM8/1B, 2249

Butyrivibrio fibrisolvens strain S2, 2249

Butyrovibrio proteoclasticus, 2253, 2255

γ-Butyrolactones, 390, 391

CCable-tool drilling, 3428–3430

Calcium carbonate, 193, 194

Caldarchaeol, 452

Caldariomyces fumago, 2769

Calibration, 3660, 3666

– curves, 2692, 2695, 4064, 4069

– H2S sensor, 3661–3662

– oxygen sensor, 3661

– pH sensor, 3662

– plot, 3588, 3589

Calvin cycle, 146–148, 153

Calyptogena, 2195

Cancer, 3123, 3124, 3128

Candida albicans, 3263–3266

Candida antarctica, 2850

Candida parapsilosis, 3265

Candida sp., 1913

Candidate phyla, 2213–2214

Candidatus methanoregula boonei, 584, 591, 592

4648 Subject Index

Candidiosis, 3264, 3265

Canonical correspondence analysis (CCA), 4115,

4120, 4121

Capillary array electrophoresis (CAE), 2866

Capillary chromatography, 3699–3703

Capillary electrophoresis, 4116, 4117, 4119–4120,

4123, 4266

Captain Arutyunov, 210

Capturing antibodies, 2703, 2704, 2706

car, 2793–2795, 2798

Carbazole, 1229, 2144, 2148–2155, 2788, 2793–2796,

2798, 2799, 4554–4555, 4558–4561

Carbazole 1,9a-dioxygenase (CARDO), 2148, 2151,

2152, 2155

Carbazole alkyl derivatives, 2154

Carbazole degradation, 2788, 2793, 2794, 2798

Carbazole dioxygenase (CARDO), 2793, 2799

CarB dioxygenase, 2793

Carbohydrate analysis, 3702

Carbohydrates, 162–163, 300, 301

Carbon, 161–162, 656–658, 661

Carbon assimilation in methanotrophs, 772–776

Carbonate minerals, 195

Carbonates, 190, 192–198

Carbon balance, 3536, 3537

Carbon cycle, 358, 636, 637, 1498

Carbon dioxide, 657, 658

Carbon isotope, 103–108, 2163

Carbon isotope analysis, 309

Carbon isotopic composition, 224

Carbon preference index, 287

Carbon sequestration, 3358

Carbon turnover times, 289

Carbonic anhydrase, 362, 365, 366

Carbonyl groups, 27, 41

Carboxy groups, 28

Carboxylation, 926–929, 931, 1019–1021

Carboxylesterase(s), 1100, 1102, 1110, 1115–1117

Carboxylic acids, 17, 28, 31, 35, 40–42, 300, 307

CarC hydrolase, 2793

Carcinogenesis, 2082

Cardiolipin, 397, 399, 419, 421, 422

Cardiovascular disease, 3136

Cariaco Trench, 3090

CAR-MM, 4558–4560

Carnitine, 3228–3231, 3236, 3283, 3285

Carotenoids, 14, 20, 129, 301, 310

Carrying capacity, 1444, 1446

Casein, 2972

Castellaniella, 958, 959

Catabolic enzymes, 1249

Catabolic functions, 4294–4302, 4304–4305

Catabolic genes, 1346, 1348–1350, 4016, 4022

– catabolic plasmids, 1221

– IncP-1, IncP-2, IncP-7, and IncP-9, 1221

Catabolic gene sequences, 4306

Catabolic island, 1173

Catabolic landscape, 1426, 1431

Catabolic operon(s), 1160, 1162, 1404

Catabolic pathways, 1840, 1916

– specific regulation, 1400–1402

Catabolic plasmids, 1157, 1348–1349, 1701

Catabolic strains, 1250–1251

Catabolism, 1298–1320, 1577–1581, 1855, 1861, 1862

Catabolite repression, 1142, 1148, 1151, 1581–1582

Catabolite repression control, 1148, 1151

Catagenesis, 144

Catalysts poisoning, 2788

Catalytic efficiency, 4200, 4201

Catalytic pentad, 1083

Catalytic residues, 1083–1084

Catalytic triad, 1084

Catalytic water, 1083, 1084

Catalyzed reporter deposition fluorescence in-situ

hybridization (CARD-FISH), 3449, 3883–3902,

4085–4091, 4094, 4097, 4098, 4100

Catechol 1,2-dioxygenase, 1359, 1360, 1390

Catechol 2,3-dioxygenase, 942, 1362, 1363, 1390

Catechol meta-cleavage pathway, 1791

Catechols, 800, 801, 803–806, 810, 812, 815–823, 829,

840–842, 854, 856, 1303–1304, 2082

Cation exchange capacity, 2466, 2468

Cationic antimicrobial peptides (CAMPs), 412, 414,

1103, 1104

Cavity, 1084, 1090, 1092

CBS scientific system, 4146–4148, 4155

CCD camera, 2703

C3/C4-plants, 283

CCS1, 1713, 1714

C1-C7 saturated hydrocarbons, alkenes, aromatics, 144

cDNA, 3671–3680, 4055, 4060, 4371–4372, 4502–4053

– labeling, 4355, 4357–4359, 4362

– sequencing, 4354, 4364

CDP-archaeol, 455, 457

CDP-diacylglycerol, 397, 399, 400

Cell dry mass, 747

Cell dry weight (CDW), 4606

Cell-environment continuum, 1454–1456

Cell imaging, 1083

Cell lysis, 4054

Cell membranes, 1566, 1568–1570, 1572

Cell pole tracking, 3570

Cell sorting, 4193

– bacteria, 4106, 4108, 4110

Cell surface, 1494, 1495

Cell surface display, 4587–4598

Cell surface hydrophobicity, 2404, 2407, 3632

Cell synthesis, 746–753

Cellular metabolism, 1283–1284

Cellulolytic, 199

Cellulomonadaceae, 1827, 1828

Cellulomonas, 1943

Subject Index 4649

Cellulose, 2804, 2968, 2970, 2972–2975

Cell wall hydrophobicity, 1874

Center, 990, 992, 995, 996

CEN/TR 15522-2, 3487–3488

CEN/TR 15522 oil spill identification, 3481–3482

Central metabolism, 1650, 1652, 1654, 1657

Ceramidase, 3219

Ceramide, 400–402, 3180–3182

Cetane number, 2776, 2777

CFU number, 2693, 2695

Chaotropic solutes, 1452, 1454, 1462

Chaperones, 676, 3958, 3962, 3963

C-H-bond, 984, 985, 990

– activation, 1011–1021

– cleavage, 1005

– dissociation energies, 1013, 1014

Chemical activity, 1443, 1445, 1446, 1471, 1472,

1474, 1476

Chemical analysis, 3575–3582

Chemical binding, 1236

Chemical cross-linker, 4423

Chemical gradient, 3935, 3947

Chemical ionization, 3736–3738

Chemical mechanisms, 2844

Chemical mutagenesis, 1238

Chemical oxygen demand (COD), 2645

Chemical-sensing, 1236

Chemoattractants, 1534, 1536, 3936–3949, 3951, 3952

Chemocline, 3081–3083, 3422

Chemoeffector, 1532

Chemo-enzymatic, 2850, 2854

Chemo herms, 195

Chemolithotroph, 2755, 2757, 2759

Chemoorganotroph, 2755, 2758, 2759

Chemostat, 3530–3539, 3925, 4343

Chemotactic assays, 3935, 3937

Chemotaxis, 1480, 1494, 1532–1540, 1558

Chemotaxonomy, 282

Chemotherapy, 3186, 3190, 3191

Chenodeoxycholic acids, 3134, 3137, 3138

Chimeric artifacts, 4256, 4258, 4261

ChIP-chip, 1260

Chiral, 2848, 2851

Chitin, 2968, 2970, 2972

Chlorate, 935–943

Chlorate reductase, 937, 942

Chlorinated biphenyls, 1194

Chlorinated methanes, 2059–2060

Chlorinated solvents

– nonreductive dechlorination, 4515

– reductive dechlorination, 4513–4514

Chlorine, 3235

Chlorite, 937, 938, 941, 942

Chlorite dismutase, 937, 941, 942

Chloroacetate, 875

3-Chloroacrylic acid dehalogenase, 876, 877

Chloroallylalcohols, 880

Chloroaniline, 1720

Chloroaromatics, 839–860

Chlorobenzene, 22, 1720

Chlorobenzoate, 1537, 1538

Chlorobiphenyls, 1536, 1537

Chlorocatechol(s), 844, 846, 850–858

2-Chloroethanol, 874, 878

Chloroflexi, 1357, 1381, 1382

Chlorofluorocarbons, 3342–3343, 3828

Chloromethane, 380, 866

Chloroperoxidase (CPO), 376, 377, 2769, 2770,

2781, 2905

Chlorophyll, 301, 310

Chloroplasts, 3160

Chloroprotocatechuate(s), 843, 850–858

Cholesterol, 958, 960, 961, 1016, 3134–3137, 3139

Cholesterol dependent cytolysins, 431, 432

Cholic, 3134, 3137, 3138

Choline, 700, 3228–3231, 3236

Chorobiphenyls, 1536, 1537

Chromatograms, 3578–3579

Chromobacterium violaceum, 1105

Chromosome

– GC skew, 4319

– lagging strand, 4319

– leading strand, 4319

– origin of replication, 4317, 4321

Chronic pollution, 2527

Chrysene, 1800, 2080, 2096

ChsA, 52314C-Hydrocarbon, 1460, 1462

Ciliate protozoa, 699

Circuit(s), 2654, 2659, 2662, 2669, 2670

Circular plasmids, 1346, 1348, 1349

CIR-TOF-MS, 3599

CIS and VC plumes

– anaerobic oxidation processes, 4510

– intrinsic remediation, 4515

Cis-2-butene, 121

Cis-1,2-dichloroethene (CIS), 4510

Cis-dihydrodiol(s), 996, 1059–1062

Cis-dihydrodiol dehydrogenase(s), 801, 1061–1062

Cis-9, trans–11 CLA, 2253

Cis-trans-isomerase (Cti), 390, 1601, 1602,

1606–1612

Cis-/trans-isomerism, 14

Cis-trans isomerization, 4203–4209

Citifluor mix, 4132, 4133

Citric acid cycle, 919–921

– Citrate synthase, 3283

– TCA cycle, 3281, 3282, 3284, 3285

CL-20, 153813C-labeled substrates, 4016

Claisen condensation, 370, 371

Classical microbiology, 3915, 3916

4650 Subject Index

Clay hutches

– bacterial growth, 3554–3555

– biofilms, 3555

– EELS, 3558

– element mapping, 3558

– experimental approach, 3555

– experimental setup, 3558–3559

– scanning micrographs, 3556

– soil colloids, 3554

– soil sample preparation, 3555–3557

– ultrastructural analysis, 3557–3558

Clay micelles

– interactions with hydrocarbons, 1461

Cleavage

– meta, 2082

– ortho, 2082

Climate, 3078

Climate change, 3340, 3341

Clinical diagnosis, 3169, 3172, 3174

Clone libraries, 2762, 3969–3970, 3973–3983, 3986, 3990

– community comparisons, 3987

– construction time, 3989

– ITS, 3984

– phylogenetic marker genes, 3971

– sequencing, 3985, 3987, 3988

– 16S rRNA, 3972

Cloning, 3814, 3816–3818, 3822, 3913, 3982, 4056–4059,

4348, 4350


– insert preparation, 3981

– screening clones, 3983

Clostridium, 420, 1662, 2248, 3125

Clostridium acetobutylicum, 421, 422

Clostridium beijerinckii, 421, 422

Clostridium bifermentans, 3116

Clostridium boltea, 2249

Clostridium butyricum, 420, 422

Clostridium ljungdahlii, 3364

Clostridium lundense, 2249, 2250

Clostridium perfringens, 3242, 3244, 3245, 3250–3251

Clostridium propionicum, 3280

Clostridium proteoclasticum, 2252

Cloud condensation, 3348

Cloud condensation nuclei, 3089, 3093, 3094

Clover, 3160, 3162, 3163

CLSM. See Confocal laser scanning microscopy

Cluster analysis, 4361–4362

Clusters of orthologous groups (COG), 4276, 4277

C metabolic flux analysis, 434414C-methane, 3810, 3811

C30 24-n-propylcholestanes, 174

CO2, 618–622, 3359

CoA ligases, 1356, 1357, 1359

CoA-transferase, 3285, 3286

Coal mining, 1924

Coal tar dyes, 234

Coarse-grained beaches, 2525, 2527

Coastal areas, 310, 311

Coastal sediments, 2340, 2343, 2346

Coal, 2080, 2082, 2101, 2277–2290, 3088,

3092, 3094

Coal-bed methane, 3059

Coal deposits, 115

Coal gasification plant, 2293–2308

Coal gasification sites, 2295–2308

Cockroaches, 709, 710, 712–714, 717–722

Cocktail fingerprinting, 2871

Cocoa butter equivalent fat (CBE), 3005

Co-digestion, 2634

Coding DNA sequences (CDS), 4298

Codon-optimization, 2944

Codon USAGE, wheel plot, 4322, 4323

Coefficient, 4341–4345

Coenzyme A (CoASH), 1653, 1657

Coenzyme F420, 3805

Coenzyme-M, 122

Coenzyme M (HS-CoM), 359, 360, 362–364

Cofactors, 2132, 2133

– and coenzymes, 359

Co/Fe-S component, 362, 363

Coimmunoprecipitation, 4419, 4420, 4424

Cold-adapted chaperonins, 1761–1762

Cold-adapted microorganisms, 1898, 1900, 1903,

1913, 1915

Cold-adapted yeast, 1913, 1914

Cold environments, 1899–1901, 1903, 1904, 1908, 1913,

1915, 1918

Cold seep(s), 1978, 1979, 1982, 1983, 1987, 1989, 1990,

2194–2198

Cold seep ecosystems

– biogeochemical diversity, 3450

– chemosynthetic organisms, 3444

– detection, 3445–3446

– exploration, 3445

– geochemical analysis, 3447–3448

– geophysical indicators, 3445–3446

– measurements, 3448

– microbial processes, 3444

– microbiological sampling, 3449

– in situ microsensor, 3448

– visual indicators, 3446–3447

Cold temperature, 1855, 1858

Colitis, 701

Collagen, 2972

Colloidal coomassie brilliant blue (cCBB), 4391, 4399,

4401, 4402

Colloidal interactions, 1483

Colloidal organic matter, 299

Colon, 3148, 3149, 3151, 3153, 3154

Colonization of hydrocarbons, 4075

Colony forming units (CFU), 3748

Colored metabolites, 4162

Subject Index 4651

Colorimetric assay, phenol-sulphuric acid assay, 3697

Colorimetric detection, 3710–3712

Colorless sulfur bacteria, 2341

Color Peak spring, 673

Column chromatography, 3712–3715, 3720, 3721

Comamonadaceae, 1365, 1368–1370, 1372, 1387, 1391

Comamonas, 1716, 2775

Comamonas testosteroni, 843

Combustion, 12, 13, 17, 19

– of biomass, 280

– residues, 285

Cometabolic, 2298

Cometabolic bioremediation, 2505–2513

Cometabolic conversion, 2881

Co-metabolism, 1664, 1666, 3352–3353

CommOligo, 2680

Common ancestor, 456, 457

Communities, 618–623

– composition, 2353–2354

– fingerprinting, 3885, 3886

– genome arrays, 4040

– harbor sediment, 2353

– structure, 2353–2354, 3906, 3907, 3911–3914

Community DNA, 2680, 2681

Community genome arrays (CGA), 2678

Comparative genomics, 1229, 4277

Compatible solutes, 666–668, 672, 674, 676, 677, 1942,

1944, 1946, 1948, 3849

Competition, 3525, 3530, 3534, 3539

Competitive exclusion, 643, 644

Competitive interactions, 642–645, 650

Competitive microarray immunoassays, 2701,

2703–2705

Competitive substrates, 666, 667, 671

Complex antigenic mixtures, 4067

Complex artificial systems, 2944

Complex environmental samples, 2705, 2706

Composition of oils, 3576

Composting, 2394, 2396–2397

Compound-specific isotope analysis (CSIA), 308,

2299, 3604

Comprehensive two-dimensional gas

chromatography, 57

Computational methods, 3962

Condensation reactions, 27, 35

Conditional gene expression, 4249, 4253–4254

Conductivity, temperature and depth (CTD) sensors,

3871

Confocal laser scanning microscopy (CLSM), 2341, 4074

– analysis, 3547, 3548

– biofilm communities monitoring, 3545

Conformers, 9, 11

Congeners, 24, 29

Conjugated double bond, 14, 16, 18

Conjugated linoleic acids (CLA), 2253–2255, 2385–2386,

3126–3129, 3162, 3163

Conjugative, 3150

Connate water, 2166

Consed software package, 4270

Consortia, 2194

Consortium, 1229

Constraint-based analysis

– elementary flux modes (EFMS), 4331, 4333

– extreme pathways, 4331, 4334

– flux variability analysis (FVA), 4331, 4333, 4334

– minimization of metabolic adjustment (MoMA),

4331, 4333

– optimization-based-methods, 4331–43333

– OptKnock, 4331, 4333

– regulatory on-off minimization (ROOM),

4331, 4333

– unbiased-methods, 4331, 4333–4335

Contact angles measurements, 3632, 3634, 3637–3638

Containing strata, 188, 192

Contaminant aging, 1475–1476

Contaminant flux, 2476, 2477

Contaminant plume(s), 2475, 2478

Contaminants, 2294–2296, 2298–2302, 3148, 3149,

3153, 3155

Contaminated environment, 1855, 1860

Contaminated groundwater, 1843

Contaminated sites, 1840, 1841

Contamination plumes, 2295, 2300

Continuous culture, 3529–3539

Control engineering, 2943, 2948

Controlled evaporation, 3752

Control spots, 4069

Conventional oil reservoirs, 2162, 2165–2169

Conversion, 1606–1608

Coprostanol, 290, 3134–3136

Coptotermes lacteus, 723

CO2-reduction, 116–119

Corer, 3422–3423

Cores, 3428–3438

Core sections, 3909

Coring, 3427–3439

Coriobacteriales, 1823

Coronary heart disease, 3171

Coronene, 2098

Correspondence analysis (CA), 4115, 4120

Corrosion, 3091, 3092

Corynebacteriaceae, 1824

Corynebacterineae, 1823–1827, 1841

Corynebacterium, 3204, 3205, 3209

Corynebacterium glutamicum, 1657

Corynebacterium sp., 1506

CO2 sequestration, 289

COSI, 3488

Cosmeceutical(s), 3390, 3391

Cosmetics, 3047

Cosmetics industry, 3209–3210

Cosmeto-textiles, 3389, 3390

4652 Subject Index

Cost of microbial lipid production, 3001

Cost of plant-derived PHA, 2977

Cotransformation, 4418

Coumestans, 3151

Counteracting stress-induced ethylene, 2556–2557

Counter-rotation, 245

Coupling chemistry, 4066

Covalent bonds, 6, 7

C20 phytanyl chain, 454

Crabtree effect, 1653–1654

Crc, 1147

Crenarchaeota, 150, 659

Crenothrix, 3829

p-Cresol methyl hydroxylase, 1013

m and p-Cresol, 926

Cresols, 1076

Criegee intermediate, 275, 276

Critical micelle concentration (CMC), 1505

cRNA, 4355, 4357–4359, 4362, 4363

Crohns disease, 701

Crops, 2977

Cross-feeding, 3122, 3123, 4015

Cross-reactivities, 2701, 2704, 2705

CRP-dependent regulation, 1135

CRP regulator, 4417

Crude oils, 752–753, 1509, 1510, 1941–1943, 1945–1948,

2366, 3088, 3092, 3098–3103, 3105, 3107, 3400, 3480,

3486, 3488, 3493, 3494, 3496, 3501, 3502, 3793, 3797,

3906, 3909–3911

Crude oil washing (COW), 261, 262

Cryopreservation, 3423

Cryptic plasmids, 1915

Cryptococcus curvatus, 2227

Cryptocercus punctulatus, 709

Cryptococcus spp., 1913

Cryptococcus terreus, 1914

CsCl, 4013, 4015, 4017–4019, 4021–4023

d13C signature, 1989, 1991

CspA, 3958, 3963–3965

CsTFA, 4014, 4018, 4019, 4021, 4023

CTD, 3421, 3422

Cubitermes fungifaber, 717, 718

Cubitermes orthognathus, 717

Cu-inducible bioreporters, 4449

Cultivating microbes, 3851

Cultivation, 2296, 2297, 2300, 2305, 2306,

2719–2721, 2760–2763, 3422, 3423, 3787–3797,

3919–39267

Cultivation independent analysis, 1928

Cultivation independent characterization, 1929

Cultivation of methanotrophs, 1962–1963

Cultural enrichment, 2913

Culture, 2115, 2117

Culture medium, 4501

Cunninghamella elegans, 994

Cupin dioxygenases, 1367–1368

Cupriavidus, 1362, 1365, 1369, 1370, 1372, 1375,

1378, 1387

Cupriavidus necator, 3570

Cupriavidus necator H-850, 1249, 1251, 1252

Cupriavidus necator JMP134, 1365

Cutan, 282

Cuticular waxes, 281, 282

Cutinase, 3260–3263

Cutin(s), 39, 40, 281, 282, 3260–3263

Cyanobacteria, 173–174, 512, 672, 1664–1665,

1681–1682, 2341–2346, 2502, 3655–3667

Cyanobacterial mats, 3655–3667

Cyclase, 136–139

Cyclic lipopeptide, 3218

Cycloalkanes, 10–12, 23, 45, 53

Cycloalkenes, 13, 14, 17, 45

Cycloalkines, 14

Cyclobutane, 11

Cycloclasticus, 2625, 2626

– abundance, 4085–4091

– growth, 4090

– oligonucleotide probe, 4087

Cycloclasticus oligotrophicus, 1782

Cycloclasticus pugetii, 1782

Cycloclasticus spirillensis, 1782

Cyclodextrins, 38

Cyclohexane, 8–11, 42

Cyclohexanone monooxygenase, 2885, 2886

Cycloolefins, 13

Cyclooxygenases, 2846, 2848–2849

Cyclopentane, 8, 11

Cyclopropane, 10, 11, 372

Cyclopropane fatty acids (CFAs), 390, 1598,

1601, 1602

Cymene, 959

Cyo terminal oxidase, 1147

CYP153, 1293

CYP153 enzymes, 2689, 2690

CYP101 monooxygenase, 1249

Cysteine, 3169, 3170, 3172

Cyst membrane, 521, 523

Cytochrome, 364, 365

Cytochrome C, 2781

Cytochrome o ubiquinol oxidase (Cyo), 1147

Cytochrome P450, 785, 1149, 1150, 1844, 1846, 2082,

2084, 2089, 2091, 2095, 2096, 2098, 2100, 2101, 2688,

2689, 2691, 2692, 2695

Cytochrome P450a, 2692, 2695

Cytochrome P450 alkane hydroxylases, 789

Cytochrome P450 family, 787

Cytochrome P450 monooxygenases, 1166, 1875

Cytochrome-P450 systems, 4474

Cytogenetic assays, 4475

Cytokine, 3217

Cytophaga–Flexibacter–Bacteroides group, 1814

Cytoplasmatic proteins, 4188, 4190

Subject Index 4653

Cytoplasmic membrane, 1596–1603

Cytoskeleton, 1559

Cytosolic proteins, 4189–4190

Cytotoxicity, 3245, 3252–3254

DDalapon, 875

Dalibration chamber, 3659, 3661, 3666

Daqing oil field, 1947

Darcy’s law, 3764, 3765

Data acquisition, 4046

– box, 3659–3660, 3666

– card, 3660, 3666

– device, 3660, 3667

Data analysis, 2679, 2680, 4500, 4503

Databases for oil spill identification, 3488

Databasing, 4350

Data management, 1094

DBT biodesulfurization, 2788

DBT degradation, 2789, 2790

DBT desulfurization genes, 2135

DBT-Gly-MSM medium, 4555–4557

DBTmonooxygenase, 2771

DBTO2 monooxygenase (DszA), 2771

DBT sulfones, 2131, 2132, 2771, 2772, 2789, 2790,

2795, 4557

DBT sulfoxide, 2771, 2789, 4557

DCE. See Dichloroethylene

DddD, 1205, 1206

DddL, 1205, 1206

D-9 desaturase, 2253

Dead Sea, 671, 1940

Deaminases, 2799

Decarbonylation, 371

Decarboxylases, 2922

Decarboxylation, 286

Decarboxylative, 371

Dechloromonas, 2037, 2042

Dechloromonas aromatica, 938–940, 942

Decomposition, 637, 642, 646

Deconjugation, 3134, 3137, 3138, 3151

Decontamination, 1083, 1094

DeCyder™ 2D software, 4402

DEEPBATH, 3874–3877

Deep biosphere, 188, 197, 3098

Deep crustal subsurface, 636

Deep hydrosphere, 188

Deep-sea, 1978, 1979, 1984, 1988, 1992, 3870, 3872,

3874, 3875, 3877, 3880

– environments, 1911–1912

– fans, 192, 196

– grab sampler, 3871, 3873

– habitats, 1911

– hydrothermal vent, 3879

– hydrothermal vents, 685, 687–690

– sampling, 3780

– sediments, 1903, 1911, 2922

– technology, 3446

Deep-Sea Hypersaline Anoxic Brine Lakes, 670–671

Deep subsurface, 1694, 1699, 1700, 2195, 2197–2199

Defined consortia, 3916

Defluvibacter lusatiensis, 844

2DE gels, 4391–4393

Degradation, 538, 541–544, 619–621, 935–943, 1514,

1515, 1517, 1522–1525, 1889–1891


– processes, 301, 306, 308

– rates, 3525

Degradative mechanism, 1861

Degradative potential, 1616

Degrader diversity, 4012

Degrading short-chain-length alkanes, 784

Degrapol1, 2974

Dehalobacterium formicoaceticum, 2060

Dehalobacter restrictus, 2051

Dehalococcoides, 3672–3674, 3677–3680, 3683, 4514

Dehalococcoides biomarkers, 3408–3410, 3414–3416

Dehalococcoides ethenogenes, 2055–2058

Dehalogenases, 866, 870, 874–876, 880, 881, 1081–1094

Dehalogenation, 1085, 1845

Dehalorespiration, 2589, 2592

Dehalorespiring bacteria, 3923

Dehalospirillum multivorans, 2052

Dehydroxylation, 3138, 3150

Deinococcus-Thermus, 1682

Deleterious Environmental Effects, 3092–3093

Deletions, 1092, 1093

Delftia, 1716, 1720

Deliberate pollution, 3473, 3486

Deltaproteobacteria, 2027, 3090

Deltas, 191, 192

Denaturation, 1090

Denaturing gradient gel electrophoresis (DGGE), 2762,

3784, 3911–3912, 3971, 4301, 4306

– advantages, 4140

– apparatus cleaning and assembly, 4146–4147

– bacterial communities, 4144

– band excision and re-amplification, 4150–4151

– Bio-Rad Dcode system, 4154

– dsDNA, 4139

– electrophoresis [3–17 h], 4149

– equipment and reagents, 4155

– fluorophore-labeled primers, 4143

– gel analysis, 4151

– gel casting, 4147–4148

– gel sandwiches transfer, 4148–4149

– limitations, 4151

– PCR products, 4144–4145

– post-electrophoresis staining and gel imaging, 4150

– running buffer, 4145–4146

– sequencing, 4152

– 16S rRNA genes, 4141

4654 Subject Index

– SSU rRNA genes, 4142

– supplies, 4156

– wells cleaning and sample loading, 4149

DenGerNeth, 3474

Denitrification, 2036, 2758, 2759, 3080–3082, 3838

De novo DNA synthesis, 2946, 2947

De novo sequencing, 3689, 3694, 3700–3703, 4272–4273

Dense nonaqueous phase liquids (DNAPL), 240

Density, 16, 21, 22, 32, 35, 41–44

Density gradient, 4186

Deodorant products, 3209

Deodorants, 3388–3399

Deoxycholic, 3134, 3137, 3139

3-Deoxy-D-manno-2-octulosonic acid, 411

1-Deoxy-D-xylulose 5-phosphate pathway, 128

DEPC, 4055, 4058

Dermabacteraceae, 1827, 1828

Desaturases, 512–514, 516, 2846–2847, 2851,

2854, 2855

Desiccation, 666, 677, 1942

DesK, 513, 516

Desolvation, 1085, 1093

Desorption, 298, 309

DesR, 513, 516

DesT, 512

Desulfacinum, 2207

Desulfatation, 3134, 3137, 3139

Desulfatibacillum, 2208

Desulfatiferula, 2208

Desulfinase, 2771, 2772

Desulfitobacterium hafniense, 2052, 2057, 4322, 4323

Desulfobacterium, 2210

Desulfobacula, 2210

Desulfobulbaceae, 891, 948

Desulfobulbus, 2207, 2213, 3173

Desulfococcus, 2207, 2208, 2210

Desulfococcus oleovorans, 913, 919

Desulfoglaeba, 2208

Desulfomicrobium, 3173

Desulfonema, 2208, 2210

Desulfosarcina, 2207, 2208, 2210

Desulfothermus, 2208

Desulfotignum, 2210

Desulfotomaculum, 2207, 2208, 2216

Desulfovibrio, 2009, 2207, 2208, 2213, 3088, 3090, 3093,

3094, 3173

Desulfovibrio desulfuricans, 2791

Desulfovibrio oxyclinae, 1731

Desulfurization, 676, 2131–2138

Desulfurization pathway, 2772

Desulfurization rates, 2795

Desulfurizing plasmid, 2139

Desulfuromonas chloroethenica, 2052

Desulfuromonas spp., 3861

Detection and monitoring of pollution, 3474–3481

Detergent, 1777

Detergent related products, 302

Determination of flux, 4344–4345

Detoxification, 1168, 3150–3152, 3248, 3285–3286,

3288, 3289

Detoxification pathways, 1170

Deuterium, 105

Deuteromycota, 2086

Dewatering of sediments, 189

Dga1p, 539, 540, 544

DGGE, 4023

2,4-Diacetylphloroglucinol (DAPG), 3462, 3463

Diacylglycerol acyltransferases, 3187

Diacylglycerols (DAGs), 528, 533, 534

Diacylglyceryl-N,N,N-trimethylhomoserine (DGTS),

403, 404

Diagenesis, 144

Diagnostics, 2497

Diamantane, 8, 11

Di-and tetraphytanyl ethers, steroids, 310

Diastereomers, 10

Diazotrophic bacteria, 2553

Diazotrophy, 1662, 1663, 1666

Dibenz[a,h]anthracene, 2080, 2082, 2098

Dibenzofurans, 19, 24, 1698, 1699, 1800, 2788, 2793,

2795, 2799

Dibenzo-p-dioxins, 24, 26, 1698

Dibenzothiophenes (DBT), 19, 29, 30, 2130–2133,

2135–2139, 2769, 2788–2791, 2795–2799, 3092, 3094,

4554–4557, 4561

Dibiphytanyl diglycerol tetraether, 591

1,2-Dibromoethane, 874, 875, 878

2,3-Dibromo-l-propanol, 878

Dicarboxylic acids, 2896–2898

Dichlorobenzene, 3924

1,2-Dichloroethane (DCE), 873, 1087, 1090

Dichloroethene, 1720

Dichloroethylene (DCE), 1538, 1539

2,4-Dichlorophenol (2,4-D), 1567, 1571

2,4-Dichlorophenol hydroxylase, 1372

2,4-Dichlorophenoxacetic Acid, 1228

1,3-Dichloro-2-propanol, 878

1,3-Dichloropropene, 876, 877

2,2-Dichloropropionate, 875

Diesel, 2768, 2769, 2771, 2776, 2777, 4554, 4557–4558

Diesel oil-utilizing bacteria, 1910

Dietary fibers, 3152, 3155

Dietary supplements, 3231

Diethylpyrocarbonate (DEPC), 3673, 3675, 3676,

3680, 3681

Dietzia, 1933, 1934, 1943, 2405

Dietzia psychralcaliphila, 1933

Dietziaceae, 1824, 1825

Differential description, 4052, 4056

Differential display (DD), 2919, 4051–4060

Differential expression, 1142, 1147

Differential global positioning systems (dGPS), 3445

Subject Index 4655

Differentially expressed genes, 4052–4054

Differentially genes, 4055

Differential optical absorption spectroscopy, 3598

Diffuse emissions, 305

Diffusion, 206, 209–211, 2166, 3625–3629

– banding, 4014

– coefficient, 3665, 3667

Diffusion barriers, agar, 3930

Diffusive boundary layer (DBL), 3657, 3665

Diffusive mass transfer, 1481

Diffusive seabed systems, 2198

Diffusive transport, 3650

Digestability, 2633

Digital image analysis, 4074, 4081, 4082, 4162, 4166

Digital light units, 4169

Diglucosyldiacylglycerol (DGlcDAG), 420, 421

cis-2,3-Dihydro-2,3-dihydroxybiphenyl

dehydrogenase, 1183

Dihydrodiols, 2080, 2082, 2084, 2089–2091, 2093, 2095,

2096, 2101

Dihydroxyacetone phosphate (DHAP), 452, 453, 473, 474

2,3-Dihydroxybiphenyl, 1362, 1364

2,3-Dihydroxybiphenyl 1,2-dioxygenase,

1183–1185, 1189

Dihydroxylation, 996

2,3-Dihydroxy-p-cumate, 1362–1364

2,3-Dihydroxyphenylpropionate 1,2-dioxygenase,

1365–1367

Diiron monooxygenases, 841, 843–844

Diiron oxygenases, 1357, 1359, 1368–1369, 1378

Dilution factors, 4169–4171

Dilution ratio, 4171

Dilution-to-extinction, 4160

– method, 3873, 3877

Dimension of bioavailability, 1442, 1443

Dimethylamine, 3233, 3234

Dimethylaminuria, 3228

4,6-Dimethyl DBT, 2136, 2772

Dimethyldisulfide, 3233

Dimethyl ether, 2805

Dimethylglycine, 3229–3231, 3832

Dimethylglycinuria, 3228–3231

Dimethylsulfide, 667, 675, 676

Dimethylsulfide (DMS), 1201–1209, 3088, 3089, 3093,

3169, 3206, 3228, 3340, 3347–3348, 3389, 3828

Dimethylsulfone, 3173, 3176, 3207, 3211, 3228, 3828,

3830–3833, 3837

Dimethylsulfoniopropionate, 1201–1209, 3089, 3093

Dimethylsulfoxide (DMSO), 2136

Dimethylthallium, 310

Dinoflagellates, 174–177, 1290

Dinoroseobacter shibae, 1206

Diol, 1073

Diooxygenase, 989

Dioxin dioxygenase, 1698

Dioxins, bioassay, 4461, 4462

Dioxygen, 985–988, 990, 991, 996, 997, 1026–1028,

1030–1033, 1037, 1038

Dioxygenase(s), 1349, 1784, 1785, 1791–1794, 2082, 2848

Dioxygenation, 985, 997

Dipalmitoyl-phosphatidylcholine (DPPC), 1103, 1104

1,3-Diphenylurea, 1730

Diploptene, 134–136, 138, 139

Diplopterol, 138

Dipole-dipole interactions, 41

Dipole moments, 41, 42

Direct contact, 1506, 1507

Direct counts, 2163, 2167, 2168

Directed evolution, 1088, 1090, 1092, 2846, 2847, 2851,

2853, 2854, 2930–2932, 2935, 2936, 4431–4435

Direct fluorescent antibody staining (DFA), 4524

Direct interfacial transport, 1515

Directly bioavailable, 1485, 1486

Direct push sampling, 3760, 3761

Direct shotgun sequencing, 4267

Discovery brine, 671

Disintegrations per minute (DPM), 4216, 4218, 4219

Dispersal, 1556–1558

Dispersants, 1801, 2326, 2619–2621, 2623

Disposal, 3797–3798

Disruption buffer, 4186

Dissimilatory nitrate reduction to ammonia (DNRA),

2758, 2759

Dissimilatory sulfite reductase (Dsr), 2758, 2760,

2762, 2763

Dissolved inorganic carbon (DIC), 3448

Dissolved organic carbon (DOC), 299–301, 307, 309, 310

Dissolved organic matter, 299, 300, 1487

Dissolved oxygen, 2526

Distal gut, 695, 698

Distillation, 81–83

Diterpenes, 129

Diterpenoid, 1362–1364, 1376–1377

Diversity, 936, 943, 2176, 2362–2366, 2636, 2844, 2846,

2847, 2853–2855

Diverticulosis, 701

DLVO theories, 1494, 3633

DmdA, 1204–1206

DmpR, 1131, 1135, 4433, 4434

DMS monooxygenase, 1206, 1208

DMSO, 1207, 1208

DMSP transporter, 1206

DNA, 3672–3674, 3676–3680

– bending, 1132, 1134

– extraction, 2919, 3812–3814, 3816, 3820,

3823, 4041

– family shuffling, 4432, 4433

– polymerases, 4042

– quality, 4048

– sequencing, 3985

– shuffling, 1086, 1238, 1240, 1242

– template, 4295–4297

4656 Subject Index

DNase, 3676, 3680–3682

DNA-SIP gradients, 4017–4018

DOC. See Dissolved organic carbon

Docking platform, 1517

Docosahexaenoic Acid, 3023, 3024, 3027

Doctrine of Infallibility, 4518

Dogs, 3206, 3207, 3210

Dokdonia sp. P79, 1815, 1817

Domain, 1083–1086, 1092, 1093

Domain repression, 1132, 1134

DON gene, 1278

Donghaeana sp. P100, 1817

Don Juan Pond, 666

Dormant state, 3187

dosR hypoxia-responsive regulon, 3189

Dot-blot, 4054, 4057–4059

Dot blotter, 4057

Double-phase systems, 3958

Double-stranded DNA (dsDNA), 4139, 4486, 4487

Doubling times, 3788

Downstream processes, 2976–2977

DOXP pathway, 454

DpgA, 520

Dredger, 3871

Dreissena polymorpha, 4476, 4493

Drill cuttings, 1941

Drilling, 2165, 3427–3439

Drilling fluid, 3429–3431, 3433–3436

Drilling muds, 1941

Drugs, 3153, 3155

DSC, 3726, 3738

DsRed, 3462–3464, 3466–3469

dszABC, 2132, 2135, 2138, 2789, 2791, 2795–2798

DszA monooxygenase, 2789, 2790, 2797

DszB, 2789, 2790, 2796–2798

DszB desulfinase, 2789

DszC enzymes, 2789, 2797

DszC monooxygenase, 2772, 2789, 2790, 2797

DszD oxidoreductase, 2789, 2791

Dual tagging, 4422

Dvurechenski, 210

Dye-terminator, 4266, 4272

Dynamics, 1084, 1085, 1090, 1091, 2413–2420

Dynamic Wilhelmy method, 3637

EEagle Harbor, 1774, 1778

Early evolution, 2216

Earthquake precursors, 191

Earthworm survival, 2497

Earwax, 3206

Ebelactone B, 3261, 3262, 3265

EbN1, 4390–4391

EBP structures, 1131

EC50, 1568, 1572

Eccrine glands, 3204, 3205, 3207

Ech hydrogenase, 364, 365

Echo-sounder, 2715

Ecoflexl1, 2972, 2976

E. coli, 410, 412–414, 421–423, 1597, 1598, 1600, 1602,

1650, 1652–1654, 1656, 1657, 2884–2886, 2955–2961,

3033–3034, 3368, 3370, 3371, 3373, 4589, 4590, 4592,

4594–4598

E. coli B, 1654, 1656

E. coli K

– anapleurotic reactions, 1654

– Mycobacterium tuberculosis, 1654

E. coli lpir strain, 4251Ecolocality, 1855

Ecological archives, 305

Ecological principles, 1560

Ecological risk assessment, 4465–4471

Ecology of aerobic methanotrophs, 3068–3074

Ecology of methanotrophs, 1960–1962

Economically feasible at industrial scale, 3002

Ecosystem, 694, 695, 697–703

Ecosystem impact, 3493

Ecotoxicity tests, 4450

Ecotoxicology, 3493, 4482, 4483

Ectoine, 1944

Ectopic metabolism, 1426–1429

Edman degradation, 3689–3691, 3694, 3698–3700,

3702, 3703

Effector, 4430, 4442, 4443

– recognition, 4431, 4433, 4434, 4441

– specificity, 4432

Effector-binding, 1238, 1240–1243

Effector-binding affinity, 1241, 1243

Effector response profiles, 1238, 1239, 1242

Effector responses, 1239–1243

Efflux pumps, 1550

Egfp, 4441, 4442

Eicosapentaenoic acid, 3023–3024, 3027

Eilat, 672

Eilat salterns, 674

Einstein’s relativity theories, 162

Electrical conductivity, 3761, 3764

Electrical conductivity logging, 3762, 3764

Electrical potential (ΔΨ), 1569Electrochemical tool, 3421

Electron acceptors, 840, 2294, 2295, 2300–2302, 2305

– anoxic, 2356

– mud flats, 2356

– oxygen, 2356

– oxygen limited, 2356

Electron balance, 2478, 2479, 2482

Electron carrier, 341, 348

Electron conductive pili, 341

Electron donors, 325, 326, 2754–2758, 2760

Electronegativity, 6, 7, 12, 25

Electron energy loss spectroscopy (EELS), 3558

Electron flux balance(s), 2477–2481

Subject Index 4657

Electron micrographs of methanotrophs, 1958

Electron microscopy, 3838

Electron spectroscopic imaging (ESI), 3558

Electron transfer, 198, 1034

Electron transfer flavoprotein, 346

Electron transport chain, 1147

Electrophile(s), 16, 22, 31

Electrophilic aromatic substitution, 21, 22

Electrophilic substitution, 22, 23, 32

Electrophoresis, 4055, 4057, 4059, 4060, 4149, 4153

Electroporation, 3963–3964, 4595–4596

Electrospray (ES), 85

Electrospray ionization (ESI), 58, 59

Electrospray ionization mass spectrometry

(ESI-MS), 4582

Electrostatic interactions, 3633, 3634

Elemental recycling, 188

Embryo-toxicity test, 4495

Emergency ballast water, 262

Emiliana, 3093

Emissions, 2176

Emission sources, 298, 302, 304, 305, 307

Emulsan, 1509, 1801

Emulsification, 1503, 1506, 1507, 1510, 1946

Emulsifiers, 1293, 1496, 1800–1802, 2644–2645, 3298

Emulsifying glycolipid, 1910

Emulsion, 3321–3324

Emuslan, 3690

Enantiomers, 10, 452, 454, 456, 1092, 1093

Enantioselective enzymes, 2859–2873

Enantioselective lipases

– mass spectrometric assay, 4583–4585

– photometric assay, 4582–4583

Enantioselectivity, 1092–1094

Enantiospecific epoxidation, 2886

Enchira, 2770, 2772

Endodontic disease, 701

Endonuclease digestions, 4057

Endophyte, 1077

Endophytic bacteria, 2547–2554, 2556–2558,

2562, 2564

Endospore, 1888, 1892

Endosymbionts, 701

Endothelial cell-luekocyte adherence molecule-1

(ELAM-1), 3245, 3251

End-sequencing, 4349

Energetically limited, 338

Energetics, microbial utilization, 736–739

Energy, 636, 637, 639–651

Energy BioSystems Corporation (EBC), 2770

Energy carriers, 754

Energy conservation, 340, 342, 350

Energy feedstock, 2894

Energy taxis, 1532, 1533, 1538–1540

Engineered microorganisms, 2847

Engineered strain(s), 2884, 2887

Enrichment, 1925, 1926, 1928, 1929, 3788, 3792,

3796–3797, 3923–3925

– alkane-degrading bacteria, 3779

– culture, 3772–3773

– initiation, 3780

– and isolation

– metal respirers and hydrocarbon oxidizers,

3855–3868


Enteric fermentation, 3343

Enterobacter, 2548–2551, 2553–2558, 2664

Enterobacteria, 3282

Enterobacteriaceae, 1367–1371, 1373, 1377, 1387, 1388

Enterohepatic, 3151

Enterohepatic circulation, 3137

Enthalpy, 4232, 4233, 4236, 4240, 4241

Entner–Doudoroff pathway, 135

Environment, 1503, 1507–1508

– changes, 621

– contamination, 3575–3582

– diagnostics, 4447–4456

– limited access, 3524

– probes, 3839

– responsive reporter, 349

– samples, 4064, 4067, 4071

Environmental acid precipitation, 2788

Environmental DNA (eDNA), 4302, 4304

Environmental factors affecting microbial

metabolism, 1166

Environmental fate, 2494, 2497

Environmental microbiology, 3369, 3372

Environmental microorganisms identification

– counterstaining and microscopy, 4132

– hybridization and washing buffer, 4130–4131

– probe binding, 4129

– probes quality check, 4130

– solutions and materials, 4133

– troubleshooting, 4133–4134

Environmental mining, 1213–1217

Environmental monitoring, 2700–2708

Environmental release, 2654, 2663, 2669

Environmental RNAomics, 3369–3370

Environmental stress, 282

Enzymatic cracking, 2782

Enzymatic depolymerization, 282

Enzyme activities measurement

– enzyme assays, 4196–4198

– kinetic parameters, 4199–4201

– solutions and materials, 4201

– substrate specificities, 4198–4199

– trouble shooting, 4201–4202

Enzyme assays, 1987

– detection method, 4197

– measurement units, 4196–4197

– types, 4198

Enzyme-coupled assays, 2862

4658 Subject Index

Enzyme kinetics, 1083, 2882

Enzymes, 2772, 2773, 2777, 2778, 2781, 2782

– activity assays, 4344

– extraction, 4343, 4345

– rate, 4342

Epichlorohydrin, 878

Epifluorescence microscope, 3565, 3569

Epimerization, 3134, 3137, 3138

Epi-metabolome, 1424, 1426

Epoxidation, 2881, 2883, 2886, 2887

Epoxide hydrolase(s), 992, 1168, 2080, 2082, 2084, 2089,

2100, 2101

Epoxides, 878, 991–994, 998, 1005, 2848, 2850, 2851

Epoxy, 4065, 4066, 4069

epPCR, 2932–2935

Epsilonproteobacteria, 3103, 3104

EptA, 414

Equations, 4341, 4342

Equinatoxin, 429–431

Equivalent carbon, 2489

Equol, 3152

Ergosterol, 284

Erosive margins, 189, 191, 197

Error-prone PCR, 1086, 1238, 4431, 4432, 4434,

4440, 4441

Erwinia, 414

ESCAPED-technology, 4596

Escherichia coli. See E. coli

Escherichia coli HB101 pUCD607, 4448

Esterases, 1101, 1102, 1110–1117, 4590–4592,

4596, 4598

Esterification, 2805, 3134, 3137, 3139

Esters, 28, 31, 35, 42

Estradiol, 3151, 3233

Estrogenic, 3149–3151, 3153, 3154

Estuaries, 2330–2337

Estuarine sediment, 3914

Ethane, 6, 9, 44, 114, 120–122, 610

Ethanethiol, 122

Ethanogenic, 114–119, 122

Ethanol, 2804–2807, 2898–2900, 3363–3364

Ethers, 24, 26, 28, 33, 35

Ethidium bromide, 4014

Ethylbenzene, 19, 20, 985, 994, 996, 1002–1004, 1376,

1377, 1388, 1536, 1716, 1719

Ethylbenzene dehydrogenase, 1014, 1016, 2035, 2036

Ethylbenzene hydroxylating, 1012

Ethylene, 120, 121, 3016–3018

Ethylene dichloride. See 1,2-Dichloroethane

Ethylene forming enzyme, 3015

Ethylene glycol, 3017

Eubacterium, 2252, 2254, 3135, 3139

Eukaryotes, 1928, 1929

European Maritime Safety Agency, 3473

European Monitoring and Evaluation Programme

(EMEP), 3595–3596

Euryarchaea, 3801

Euryarchaeota, 622, 659, 666, 668, 673, 676, 694,

2024, 2025

E-value, 1093

Evaporation, 1941, 1948

Evaporative weathering, 3751–3756

Evaporite deposits, 673, 1946

Evolution, 1088, 1090–1093, 4325

– of antibiotic resistance, 1631

Evolutionary adaptation, 1090–1091

Evolutionary steps, 1220, 1229

Exopolysaccharides (EPS), 1550, 2732

Expansion of C4 grasses, 290

Experimental spill, 3493, 3496–3497, 3501

Experimental studies, 3752

Exponential growth, 3533

Exponential silencing, 1135

Exposure assessment, 2493–2495

Expoxide, 992, 997

Expression, 4347–4351

– experiments, 2692

Extended 4S pathway, 2791

Extracellular polymeric substances (EPS), 1454, 1461,

1497, 3849

– clay negative charges, 3558

– network, 3556

– ultrastructural analysis, 3557

Extracellular polysaccharide, 1841

Extracellular vesicles, 1293

Extract, 3729, 3731–3733

Extractability, 1475

Extraction, 51, 52, 54, 81–83

– hydrocarbons, 4496

– yields, 4186

Extradiol, 1071–1078

Extradiol dioxygenases, 1357, 1359, 1361, 1363–1365,

1367, 1368, 1381, 1382

Extreme environments, 685, 687–689, 1291,

1503, 1508

Extreme halophiles, 666

Extreme thermophiles, 2798

Extremophiles, 2283, 2284, 3870, 3958

Extremophilic microbes, 661

Extrusion pumps, 1586–1592

FFabF, 510, 512, 513, 516, 517

FabH, 511, 514

FabI, 514

FabT, 515

FACE, 289

FACScalibur, 3465, 3466

Factor III, 359, 363

Facultative endophytic bacteria, 2550

Facultative methanotrophs, 1968, 1970, 1973–1975, 2185

Facultative methylotrophy, 3235

Subject Index 4659

FADH2-dependent halogenases, 377–379, 381, 382, 2905,

2907, 2908

FadL, 1547, 1548, 1551

FadR, 512

False discovery rate (FDR), 4361, 4362

Family wise error rate (FWER), 4361

FapR, 511, 515, 516

FAS II, 388–390, 392

Fast atom bombardment (FAB), 85

Fast-DNA-Spin kit, 3548

Fat metabolism, 3113–3117

Fats, 87–89

Fatty acid methyl esters (FAME), 2272, 3506, 3696,

4206, 4207

– analysis, 3745

– external calibration techniques, 3507

– isotopic composition, 3507

– methylation, 3746–3747

– reference compounds, 3746

– sediment samples, 3747

Fatty acids (FA), 370–372, 386–392, 460, 462, 464, 782,

784, 791, 792, 2828–2831, 2834, 2836–2838,

2896–2898, 2900, 3114–3116

– biosynthesis, 388–389, 510, 511, 514, 515

– desaturases, 995

– hydration, 2254

– hydroxylase, 1005

– long chain alkanones, 310

– synthesis, 1655

Fatty acid synthases (FASs), 387, 389, 390, 392, 446–449

Fatty alcohols, 528, 533, 534, 784, 791

Fatty aldehyde reductase, 533, 534

F430 cofactor, 359, 360, 363, 364, 898, 902

Feces, 3134–3140

Feed particle phase, 699

Fe(III)-NTA stock (1 M), 3866

Fe-oxidizing, 1293

Fermentation, 116–119, 152–153, 1653, 1654, 3122–3124

Fermentative archaea, 2212–2213

Fermentative bacteria, 338, 2213

Fermentative decomposition, 194

Fermentative microorganisms, 2266, 2267

Fermentative production of tag, 2999

Fermenters, 2167, 2168

Ferredoxin, 362, 364, 365, 787, 789, 1071–1078

Ferredoxin reductase, 787, 789

Ferric citrate stock, 3866

Ferric hydroxide, 2634

Ferryl, 988, 991

Fertility, 3160, 3163

Fertilization, 3082

Fertilizers, 305, 307, 2501–2503, 2523–2327, 2976

Fe2S2, 990

Fiaf, 3143, 3144

Fick’s first law, 3664

Field data, 3914, 3915

Filamentous fungi, 1902, 1913–1915

Filter, 3851–3853

Filtration, 3423

Fine chemicals, 2891–2901

Fine chemicals industry, 1092

Fingerprinting, 4015, 4016, 4022, 4023

Fingerprinting oils, 3575

Firmicutes, 1357, 1381, 1382, 1682, 2051, 2053, 2060,

3142, 3143

First-order kinetics, 3627

Fischer–Tropsch reaction, 2214, 2215

Fischer–Tropsch type, 217, 221, 222

Fish

– petroleum toxicity assays, 4492, 4496

– toxicological assays, 4493

Fish odor syndrome, 3174, 3228

Fishy breath, 3174

Fission yeast, 478

Fjord ice, 1902

Flagellar motility, 3935, 3951

FLAG-tag system, 4424

Flame ionization detector (FID), 4557, 4558, 4560

Flame retardants, 302

Flavin-4a-hydroperoxide, 996, 998

Flavin-containing hydroxylases, 996

Flavin-containing monooxygenases, 996–998

Flavin-containing monooxygenase gene, 3230

Flavin mononucleotide, 997

Flavin reductase, 2797

Flavobacterium DS-711, 1816

Flavoprotein monooxygenases, 844–845, 850, 1357,

1359, 1369–1375

Flavor, 3163

Flexibility, 1085

Flotation, 2403, 2407

Flow cytometry, 3461–3469, 4193, 4430, 4433, 4434,

4441–4443, 4500–4502, 4505

Flow model, 2613

Fluid emission, 197

Fluid expulsion, 189, 191, 192

Fluid flow velocity, 210, 211

Fluid inclusions, 222, 223, 227

Fluidity, 513, 515–516

– membrane, 387

Fluoranthene, 1167, 1168, 1170, 1173–1175, 1695, 1699,

2080, 2089, 2093, 2096, 2100

Fluoranthene degraders, 4164

Fluorene, 1550, 1800, 1948, 2080, 2089, 2090, 2100

Fluorene degraders, 4162, 4164

Fluorescein diacetate (FDA), 4500–4506

Fluorescence, 3462–3464, 3466–3468, 3643, 3646,

3649, 3651

– lectin-binding analysis, 4074, 4079

– microscope, 3726–3727

– microscopy, 3805

– staining, 4074, 4075, 4079–4080

4660 Subject Index

Fluorescence-activated cell sorting (FACS), 3462–3468,

4592, 4593, 4596, 4598

Fluorescence microscopy, 1261

Fluorescent

– dyes, 4043, 4046

– intensity, 4069

– microspheres, 3466–3468

– reporters, 3461–3469

– sandwich microarray immunoassay, 4064,

4065, 4068

Fluorescent in situ hybridization (FISH), 891, 2163,

2169, 2233, 3449, 3885, 3886, 3892–3899,

4027–4036, 4307

– background fluorescence, 4134

– planktonic, soil and sediment samples,

4129–4130

– procedure, 4129

– too low/no signal, 4133–4134

Fluorescent lipid probes, 3186

Fluorescent pseudomonads, 1508

Fluorescien isothiocyanate (FITC), 4524

Fluorimetric quantification, 4017, 4022, 4023

Fluorinase, 2905, 2906, 2908

Fluoroacetate, 2853

Fluorophore, 2920

Flux, 206, 209–211, 2176, 3656, 3664, 3665

Flux balance analysis (FBA), 4340, 4341

Flux-space, 4331–4333, 4335

Foam, 2401–2408

Foaming thresholds, 2406

Food process engineering, 3047

Foot, 3204, 3207–3209

– odor, 3206–3209

Footwear, 3389, 3393

Forest soils, 3347

Formaldehyde, 273, 276, 3228, 3233, 3234, 3237

– metabolism, 769, 771–772

Formate, 115, 116, 118, 696, 697, 700, 3173, 3175, 3176

– dehydrogenase, 697

– metabolism, 771–772

– transporter (FdhC6), 697

Formation, 68–76

– kinetics, 74–75

– pathways, 460–465

– threshold, 2406

Forward engineering, 2945, 2946, 2948

Fosmids, 2233, 2235, 2239, 2240, 2242, 3823,

4348–4351

– library, 2233

Fossil fuels, 5, 10–14, 16, 19, 36

Fossilized microbes, 197

Fouling, 3586, 3588

Fourier transform ion cyclotron resonance

(FTICR), 4389

Fourier transform ion cyclotron resonance mass

spectrometry (FT-ICR-MS), 50, 58, 62, 85

Fractionation, 144–153, 1989–1991, 4015, 4016, 4018,

4020–4021, 4023, 4024

– cold trap, 3929

– MSGC, 3929

– recoveries, 3929

Frankineae, 1823, 1827

Free disposal service, 264

Free energies activation, 744

Free energy, 117, 119

– changes, 339, 340, 343, 346, 348, 350

Freeze-thaw cycles, 1900, 1901, 1907, 1908, 3454,

3457–3459

– microcosm, 3455, 3456

Fresh crude oil, 3752, 3754, 3756

Freshwater, 359, 360, 362, 364, 365

Freshwater Fe(III)

– citrate medium, 3864, 3867

– oxide basal medium, 3862–3863

– pyrophosphate, 3861, 3862, 3864

Freshwater samples, 4185, 4193

Freund adjuvant, 3321–3323

Frimbriae, 1495

Frozen soils, 1901, 1904

Fugacity, 2494

Fulvic acids, 40, 300

Fumarate, 984, 1001–1003, 1005

Functional analysis, 2690

Functional annotation(s), 1173, 4266, 4274–4277

Functional bacterial groups, 2340, 2346

Functional expression, 2689

Functional foods, 3154

Functional gene arrays (FGA), 2678–2683, 4040,

4041, 4048

Functional gene diversity, 2413–2420

Functional gene probes, 3072

Functional gene(s), 2176, 2678, 2679, 2682, 2683,

3839, 3840

– copies, 4299–4300

– hybridization-based detection, 4303

Functional groups, 11, 12, 17, 23, 28, 29, 32, 33, 35, 36,

39–41, 44

Functional guild, 2306

Functionalization, 2843–2855

Functionalized materials, 2855

Functional marker gene assays, 4289–4308

Functional marker genes, 2306

Functional potential, 2678, 2682, 2683

Functional proteins, 4303–4306

Functional selections, 2920

Function-driven analysis, 4566–4570

Fundibacter, 1738, 1740

Fungal biomass, 283

Fungal communities, 2226–2229

Fungal highways, 1556, 1558

Fungal lipids, 284

Fungal mycelium, 1559

Subject Index 4661

Fungi, 1948, 2080–2101, 2163, 3270, 3274, 3275,

3282–3287, 3289

– ligninolytic, 2084, 2088, 2089,

2099–2101

– mycorrhizal, 2095, 2100

– non-ligninolytic, 2084, 2089, 2099–2101

– white-rot, 2084, 2088, 2090, 2091, 2093, 2095,

2096, 2098

– wood-decaying, 2084, 2088, 2091, 2095, 2101

Fungus-bacteria interaction, 1556–1558

Fusarium, 3261–3263

Fusarium solani pisi, 3261

Fusion proteins, 4409, 4414–4416, 4418,

4419, 4421

Fusocillus, 2252

GGain-of-function mutations, 2797

Galactolipid, 699

Galactose, 2248, 2249, 2252

β-Galactosidase, 1406, 2899β-Galactosidase activity, 4409, 4418–4419α-Galactosylceramide, 3318–3321

Galacturonic acid, 601

Gallate dioxygenase, 1365–1367

Gammacerane, 135

Gammaproteobacteria, 1751, 2342, 2364, 3829,

3831, 3832

Gardnerella, 3232

Gas

– biogenic gas, 104

– natural gas, 100, 102, 104, 105

– thermogenic gas, 104

Gas chromatograph-flame ionization detector

(GC-FID), 3486, 3747, 4207

Gas chromatography (GC), 50, 52–57, 60, 62, 83–84,

3401, 3549–3550, 3805, 4556–4561

– analysis, 3578, 3736

– clamp, 4301

– content, 4015

– skew, 4276, 4277

Gas chromatography-mass spectrometry (GC-MS),

2599, 2600, 2604, 3373, 3726, 3732, 3733,

3736–3738, 3747

– analysis, 3486–3487, 3505, 4495, 4496

– carbohydrates, 3691, 3697–3698, 3702

– fatty acids, 3696, 3702


Gaseous hydrocarbons, 3793

Gas exploration, 2714–2723

Gas hydrates, 68–76, 193–195, 2195, 2197–2198, 2226,

2228, 3342, 3347, 3801, 3816, 3823

Gasification, 3364

Gas Institute of Technology, 2131

Gas oil, 2771, 2774, 2778

Gasoline, 2776

Gasoline and diesel, 2600–2605

Gasoline substitute, 2893

Gas phase cultivation, 3923–3925

GasQuant, 197

Gastrointestinal, 3148, 3149

Gastrointestinal microbiota

– lipase, 3115–3116

– phospholipase, 3116–3117

Gastrointestinal (GI) tract, 324, 3113–3117, 3148,

3149, 3155, 4193

Gas wetness, 104

Gating, 3466, 3467

GC-assay, 2865

G + C content analysis, 2242

GC-FID, 2489, 2492

GC-MS, 2489, 2492

GDGT. See Glyceroldialkylglyceroltetraethers

Gel

– analysis, 4151

– bands migration, 4153

– casting, 4147–4148, 4154, 4155

– imaging, 4145, 4150

– purification, 3976, 3981, 3989

– rips, 4152

– sandwiches transfer, 4148–4149

– smiling/frowning, 4154

Gel permeation chromatography (GPC), 3726, 3738

GenDB, 4273–4275

Gene

– fishing, 4054

– functions, 4040, 4041

– libraries, 3814

– prediction, 4266, 4273, 4275

– shuffling, 4431

– synteny, 4325

Gene discovery, 3370–3371

Gene expression, 2678, 2682, 3461–3469, 3672, 3674,

4052, 4053

Gene family, 3263–3266

Gene fingerprinting, 3369

Gene mining, 2440–2441, 2449, 2456

– in methanotrophs, 1331

Gene redundancy, 1378, 1389–1390

Gene regulators, 1576

Genes clusters, 2690–2692

Genetically engineered microorganisms (GEMs), 2463

Genetically engineered plants, 3377

Genetically modified organisms (GMOs),

1249, 1251

Genetic and metabolic manipulation, 3001

Genetic circuitry, 1236

Genetic determinants, 2691

Genetic engineering, 2502, 3018

Genetic fingerprinting methods, 4300–4302

Genetics, 941, 1859–1862, 2117–2119

Genetic selections, 1239, 1243

4662 Subject Index

Genetic traps, 2799, 4305, 4563–4576

Genome analyses, 1187–1189

Genome annotation

– automatic, 4282–4284

– manual editing, 4284–4285

– tools, 4283–4284

– wet-lab experiments, 4285–4286

Genome atlas, 4314, 4315, 4317–4320, 4322

Genomes, 1346–1349, 1351, 1861, 1862, 3218, 3219,

3221–3224, 3260, 3262, 3263, 3266

– annotation, 4273, 4274

– atlas, 4314, 4315, 4317–4320, 4322

– coding fraction, 4321

– GC content, 4315, 4322

– OnLine Database, 4266

– prey library, 4415

– reduction, 2942

– sequences, 4267, 4277

– sequencing, 1267–1268, 1336, 1339–1342,

4265–4277

– size, 4314, 4315

Genomic, 2846, 2853, 2913, 2919, 2923, 2924

Genomic revolution, 4387

Genomics, 1346–1351, 4265–4277

– catabolic gene, 1860

– methanotrophs, 1332, 1963

– Methylococcus capsulatus, 1328–1332

– plasmid, 1860

Genotoxic carcinogens, 2493

Genotoxicity, 3151, 3152, 3154, 4473–4479

Gentisate 1,2-dioxygenase, 1367, 1368, 1381

Gentisates, 800, 803, 806, 823–826, 828, 1305, 1339,

1341, 1719

Genus Methylocella, 1968, 1969

Geo and bioaccumulation, 302, 305

Geobacilli, 1888–1895

– distribution, 1892–1894

– ecology, 1894–1895

– exploitation, 1894–1895

– genome, 1891, 1892

– growth, 1892–1893

– survival, 1892–1893

Geobacillus, 1887–1895, 1947

– kaustophilus, 4317

– species, 1889, 1895

– thermodenitrificans NG80-2, 790

– thermoleovorance, 1893

Geobacter metallireducens, 948, 951

Geobacter spp., 1683, 2035, 2036, 2043, 3857, 3860,

3861, 3867

Geochemical cycling, 2679

Geochemical forcing, 209–211

Geochemical prospecting, 2718,

2721, 2722

Geochemical surveys, 2721, 2722

Geochemistry, 3907, 3909

GeoChip, 2678–2684, 4039–4049, 4303

Geo-engineering, 3348

Geophysical indicators

– echosounders, 3445

– sediment depth, 3446

Geophysical measurements, 2485

Geophysical method, 3762

Geothermal environments, 2182, 2187–2188

Geothrix spp., 3861, 3862

Geotoga, 2165, 2719

Geranic acid, 959

Giant panda, 698

Gibberella zeae, 3262

Gibbs free energy

– fatty and aromatic acids, 322

– hydrogen, 329

– temperature, 327

Gibbs free energy yields, 642, 649, 892

Gibbs reagent, 4555, 4556

Gingivitis, 3171, 3237

Ginkgo biloba, 446

Glacial drifts, 115

Glacier cryoconite, 1908, 1913, 1914

Gland, 3216, 3218, 3219, 3224

Glassware, 3589

Global atmosphere watch, 3596, 3597

Global carbon cycle, 144

Global control, 1146, 1147

Global control networks, 1142

Global sulfur cycle, 3093

Global warming, 2176, 2182, 3340–3342, 3344–3345,

3347, 3348

Gluconeogenesis, 1282–1283

Glucose, 38

Glucose lipid, 2516

Glucose-lipid surfactant, 1744

α-Glucosylglycerate, 676Glucuronidase, 3151, 3152

β-Glutamine, 676

Glutaraldehyde, 3728

Glutaraldehyde solution, 3728, 3729

Glutathione-S-transferase (GST), 1185–1186

Glutathione-S-transferase-system, 4421, 4422, 4424

Glycerol, 26, 30, 33, 2247–2252, 2892,

2896–2898, 2900

Glyceroldialkylglyceroltetraethers (GDGT), 284

Glycerol-3-phosphate, 397, 399

– pathway, 473

Glycerophospholipids, 396–400

Glycine betaine, 666, 667, 672, 674, 676

Glycine cleavage T-family, 1204

Glycolipids, 402–403, 418, 422, 1506–1509, 2246, 3475

– extraction, 3708–3710

Glycomycineae, 1823, 1827

Glycosidic linkage, 39

Glycosphingolipid, 1694

Subject Index 4663

Glycosyl diacylglycerols, 402

Glycyl radical, 1001–1003, 1017, 1021

Glycyl radical enzyme(s), 915–917, 921, 1001–1003,

1019, 1021

Glyoxylate bypass, 1282–1283

Glyoxylate shunt, 1649–1657

– α-ketoglutarate, 1653, 1654Gnotobiotic animals, 3139

Goose, 698

Gordonia amarae, 2405

Gordonia sp., 1507, 2132, 2135–2137, 2403, 2405, 2406,

2415, 3173

Gordonia sp. F.5.25.8, 2795

Gordonia sp. TY-5, 786, 792

G-1-P dehydrogenase, 452–456

GPo1, 1794, 1795

Gradient

– fractionation, 4014–4018, 4020–4024

– plates, 3851

Gram-negative, 122

Gram-negative bacteria, 4096, 4204

Gram-positive, 122

Gram-positive bacteria, 2163, 2296, 3832, 4096

Grass, 3160, 3161, 3163

Gravity-corer, 3422

Grazing, 2425, 2426, 3885, 3886, 3889, 3892–3899

Great oxidation event, 173–174

Great Salt Lake, 666, 1940, 1942

Great Salt Plains, 1943

Green fluorescent protein (GFP), 1261, 3462–3464,

3466–3469

Greenhouse gas (GHG), 636, 2174, 2176, 2177,

3340–3343, 3348, 3349

Green liver, 2577

Gross photosynthesis (GP), 3656, 3657,

3663–3665

Grounded oil tanker, 244

Ground water, 298, 305–308, 1086, 2294, 2295,

2298–2303, 2306, 2610–2614, 3524, 3526, 3744

– aquifers, 188

– biomass collection, 3408, 3410–3413, 3417

– microbial monitoring, 3408, 3416, 3417

– remediation, 4541

– sampling, 3407–3417

Groundwater systems, 306, 307

Growth-inhibiting toxicity, 4205

Growth phases, 2693, 2694

Growth pouch assay, 3463–3465, 3468

Growth rate (m), 1638, 1641Guaymas Basin, 2204–2206, 2208, 2210, 2211, 2213,

2214, 2216

Guerrero Negro, 667, 671–672

Guilt by association, 4408

Gulf of Mexico, 666, 670, 674, 2205, 2206,

2208, 2715

Gullfaks, 107

Gut, microbiology, 1626, 1628–1633

Gut microbiota, 3148, 3149, 3151, 3153, 3155

Gut microorganisms, 3155

Gypsum, 162–163

HH2, 619–622, 641–644, 646, 649, 650

H2 production, 220

H2S, 2130, 2131, 2167

HS droplets, 1514–1516

H2S microsensor, 3657–3659

H2/CO2, 696, 700, 701

Haakon Mosby, 207, 208, 212

Habitat, 2114–2115

Hair odor, 3205

Halanaerobiales, 674

Half life, 1086, 1090

Halite, 636, 648, 666, 673

Halitosis, 3168–3176

Haloacid dehalogenase, 874, 876, 881

Haloalkane, 1081–1094

Haloalkane dehalogenase, 874–877, 880

Haloanaerobium, 2719

Haloarcula, 1947

Halobacteriaceae, 673, 677, 1941, 1945–1948

Halobacteriales, 1945–1947

Halobacterium, 1946, 3850

Halocline, 670, 671

Haloferax, 1946, 1947

Halogenases, 2852, 2853

Halogenated aliphatics, 865–881

Halogenated alkanes, 1090

Halogenated compounds, 310

Halogenated hydrocarbons (HHCs), 1843, 2050–2060

Halogenated organic compounds, 5, 23–25, 46

Halogenating enzymes, 2904, 2905

Halogenations, 13, 21, 24, 42, 2852

Halohydrin dehalogenases, 878, 880, 881

Halohydrin hydrogen-halide lyases, 878

Halohydrolases, 1845, 1847

Halomethanes, 3340, 3344, 3828, 3831, 3833, 3837

Halomethanococcus doii, 676

Halomonadaceae, 1943–1946

Halomonas, 1933, 1943, 1945, 2167, 2168

Halomonas campisalis, 1945

Halomonas eurihalina, 1510

Halomonas shengliensis, 1945

Haloperoxidases, 376–377, 2852

Halophiles, 666, 668, 1940, 1942, 1946, 1948,

3847–3853

Halophilic, 668, 673–676, 1290, 1291

Halophilic and halotolerant methanogens, 674

Halophilic archaea, 3850

Halophilic hydrocarbon degraders, 1939–1948,

3847–3853

Halophilic hydrocarbon-degrading consortia, 1944

4664 Subject Index

Halophilic hydrocarbon-degrading microbes, 3848, 3850

Halophilic methanogens, 674–676

Halophilic methylotrophs, 3837

Halophilic oil degraders, 1941, 1942

Halophilic oil-degrading microbes, 1946

Haloterant, 1940, 1943

Halotolerant, 1943–1948

Halotolerant bacillus strains, 2742

HandleBar, 4350

Harbor(s), 2362–2366

Haslea, 177

2HBP production, 2797

HbpR, 4433, 4434

HBP sulfinate, 2132

hcuABC, 2797

Head blight, 3262

Health, 3388, 3391–3393

Health care industry, 3391

Health risks, 3148

Heat inactivation, 3676–3677

Heavy fuel oil (HFO), 3486

Heavy metals, 1924, 1926, 1929

Heavy oil, 2130, 3098, 3100, 3105

Heavy Oil Reservoirs, 2162–2170

HELCOM treaty, 263

Helicobacter pylori, 3174, 3242, 3251–3252

HeliScope, 4261

Helix-turn-helix (HTH), 1132

Helper plasmid, 3959

HELSINKI convention, 3473

Heme-iron monooxygenases, 990–993

Hemiacetals, 27, 28, 35, 38

Hemi-micelles, 1505

Hemolysin, 3219

Henry coefficient, 1441

Henry’s Law, 46

Henry’s Law constant, 2603, 2604

Heptamethylnonane, 2037, 3794

Heptane, 1720

Herbicides, 305

Heteroaromatic compounds, 2788, 2799, 2800

Heteroatom, 2130

Heterocycle, 1855

Heterocyclic compounds, 1846, 2294, 2296, 2298

Heterocyclic thiophenic compounds, 2130

Heterodisulfide, 362–365

Heterodisulfide reductase, 362–365, 697

Heterogeneity, 2295, 2296, 2300, 2301, 3468–3469

Heterologous DNA, 4251

Heteropolysaccharide, 596, 601

Heterotrophic Methanococcus voltae, 579

γ-Hexachlorocyclohexane, 880

γ-Hexachlorocyclohexane (γ−HCH), 1406

Hexadecane, 1537, 1732

Hexagonal II phase, 420

Hexahydro-2-naphthoic acid, 929

Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), 1538

Hidden heat, 735

Hierarchical regulation

– analysis, 4340–4343, 4345

– coefficients, 4342, 4344, 4345

High-affinity methane oxidizers, 2189

High cell density cultivation, 2999, 3002

High density microarray analysis, 4526

High energy grasses, 3163

High latitudes, 656

High-molecular-mass (HMM)

– bacteria mineralizing, 3778

– enrichment, 3780

High performance liquid chromatography (HPLC),

3585, 3588, 3708, 3716–3721, 4184, 4555–4559

– lipopeptides, 3693–3694, 3703

– peptides, 3693–3694, 3700, 3703

High pH, 1843, 1932–1935

High-pressure

– bioscience, 3880

– vessel, 3872

High pressure serial samplers (HPSS)

– Niskin bottles, 3422

– in situ pump, 3422

High salinity, 1942–1944, 1948

High-temperature gas chromatography, 50

High-throughput analytical genomic technologies, 1175

High-throughput screening, 1090, 2920

High throughput sequence technologies,

3368–3369, 3371

Higher termites, 708, 712, 715–718, 720

Hippopotamus, 698

His-tag, 4421–4422

Hitchhiker cells, 2716–2723

HMMER, 2679

HMX. See octahydro-1,3,5,7-tetranitro-1,3,5,7-

tetrazocine

Hollow-stem auger, 3428–3431, 3760, 3761

Holo-ACP synthase (AcpS), 388

Homeostasis, 509–517, 3341–3343

Homeostatic, 4345

Homoacetogenesis, 150–151, 199

Homoacetogens, 621, 645, 674

Homogentisate, 1305

Homogentisate 1,2-dioxygenase, 1367, 1368, 1381

Homologous recombination, 1349

Homology screening, 2913, 2919

Homolytic bond dissociation energy, 12

Homolytic C-H bond cleavage, 985

Homolytic cleavage, 12, 13, 22, 32

Homoprotocatechuate, 1306, 1339, 1341

Homoprotocatechuate 2,3-dioxygenase, 1362, 1363,

1365–1367, 1382, 1389

Hopanes, 134, 135, 137, 139, 303, 311, 2523,

3099, 3100

Hopanoids, 11, 134–139, 286, 401, 402

Subject Index 4665

Horizontal gene transfer, 1778, 1847

Horizontal transfer, 790, 791

Hormoconis resinae, 1902, 1904

Horse, 698

Horseradish peroxidase (HRP), 4596–4597

– labeled probe, 4088

Hotdog fold, 848

Hot ecosystems, 682–690

Hot spot, 1090

Hot spot tubes, 2537, 4545–4550

Hot springs and hydrothermal vents, 636

Howell-Jolly bodies, 4475

hpaC, 2797

HPLC, 2865–2866

HSA, 3125, 3127

HTH domains, 1134

Huckel rule, 18

Human, 5

Human body odor, 3204, 3206–3207, 3209

Human breath, 3175

Human colon, 694–698, 701–703

Human disease, 3235–3236

Human gut, 3134, 3135, 3137, 3139

Human health, 3148, 3155

Human health risk assessments, 2489

Human-like surface glycans, 698

Human Microbiome Project, 3155

Human odors, 3207

Human pathogens, 392

Human pathology, 3236

Human pheromones, 3209, 3211

Humic acids, 40, 4185, 4188

Humic compounds, 4187

Humic precursors, 307

Humic substances, 26, 40, 301, 307, 310

Hungate-syringe, 3789

Hyaluronan, 3220, 3221

Hyaluronate, 3220, 3221

Hybridization, 2680, 2681, 2683, 4040, 4042, 4043, 4045,

4052, 4053, 4057–4060, 4127–4129, 4132–414

– buffer, 4130–4131

– chamber, 4067

– quality, 4046

– signal, 4046

– temperature, 4044, 4048

Hydration, 3124, 3125

Hydraulic conductivity, 2587, 2592

Hydraulic pressure, 3794

Hydrocarbon activation, 739–746

Hydrocarbon analysis, 50–62, 2489–2490

Hydrocarbon biodegradation, 1942–1943

Hydrocarbon-cell interaction, 4378

Hydrocarbon degradation, 1336–1339, 1342, 1855–1860,

1945, 1946, 1948, 2424–2428, 2432

Hydrocarbon degradation-enhancing, 2425

Hydrocarbon degradation-inhibiting, 2425

Hydrocarbon degradation potential, 1823–1831

Hydrocarbon degraders, 325, 1935, 1939–1948

– bacterial energy sources, 3779

– bacterial growth, 3778

– isolate characterization and preservation, 3782

– marine enrichment, 3779–3781

Hydrocarbon degrading algae, 2073–2074

Hydrocarbon-degrading bacteria (HDB), 2365, 2366,

2981–2991

– enrichment cultures and isolation, 3782–3783

– isolation, plate purification, 3781–3782

– marine enrichment, 3779–3781

– types, 3778

Hydrocarbon-degrading enzymes, 1214

Hydrocarbon degrading fungi, 2066–2073

Hydrocarbon-degrading microbial communities,

2206, 2211

Hydrocarbon-degrading microorganisms, 1510

Hydrocarbon-degrading species

– distribution, 2351–2352

– habitat, 2351–2352

– OHCB, 2351, 2352

Hydrocarbon-degrading strains, 1859

Hydrocarbon emission, 208–209

Hydrocarbon exposure, 2424, 2427–2432

Hydrocarboniphaga, 1806

Hydrocarboniphaga effusa, 1806

Hydrocarbon metabolism, 1861, 3368, 3372–3373

Hydrocarbonoclastic, 1800

Hydrocarbonoclastic alkane degrading bacteria, 783

Hydrocarbonoclastic bacteria, 1290, 2696

Hydrocarbon-oxidizing bacteria, 3858–3859

Hydrocarbon production

– energy flux, 333

– isoprenoid lipids, 324, 332

Hydrocarbon removal, 2576–2581

Hydrocarbons, 144–123, 460–464, 935–943, 1502,

1505–1510, 1887–1895, 1940, 1941, 1943–1948, 2314,

2321–2325, 2330–2333, 2335–2337, 2804–2807,

3098–3108, 3906–3910, 3912–3916

– acetogenic bacteria, 324

– acetotrophic methanogens, 324

– analysis, 3575–3582

– archaea, 324, 333

– Bacillus subtilis, 324

– bioaccumulation assays, 4495

– bioavailability, 1461

– Botryococcanes, 2818

– boundaries, 3450

– C-17-cyclopropylalkane, 322

– compounds, 3449

– decarbonylated octadencanal, 322

– decarbonylation, 323

– decarboxylation, 323

– degradation, 3448, 3506

– degrading bacteria, 4277

4666 Subject Index

– degrading microbial communities, 4294, 4296

– dimethylallyl-diphosphate, 324

– ethane and propane, 322

– ethylene, 322

– in the extracellular environment, 1454, 1456,

1460, 1461

– fermentative bacteria, 324

– head-to-head condensation, 323

– heptadecane, 322

– hexadecanal, 323

– hexadecane, 323

– hexadecanol, 323

– hydrogenotrophic methanogens, 324, 328–331

– hydrophobicity, 1453, 1457, 1461

– interactions with macromolecules, 1458,

1460, 1461

– interactions with the cell, 1456, 1457

– interactions with the plasma membrane,

1455, 1458

– interactions with water, 1453, 1456

– isopentenyl-phosphate rather than

diphosphomevalonic acid, 324

– isopentyldiphosphate, 324

– isoprene (2-methyl-1,3-butadiene), 324

– isoprenoid lipids, 324, 332

– Kocuria, 323

– location in cellular macromolecules, 1455

– metabolic oxidation, 4176

– metabolic pathways, 4180–4181

– metabolism, 4303–4306

– metabolizing microorganisms, 4179–4180

– methylerythritol phosphate pathway, 324

– 6-methylhexadecane, 322

– 4-methyl-octadecane, 322

– mevalonic acid pathway, 324

– Micrococcus, 323

– movement within the cellular system,

1458, 1460

– n-heptadecane, 322

– n-pentadecane, 322

– oxidizers, 3855–3868

– partitioning in the membrane, 1456–1458

– pentadecane, 323

– pollutants, 3463

– redistribution within the membrane, 1459, 1460

– terpenes, 324

– toxicity, 1461

– turnover rates, 3445

– Vibrio furnissi, 323–324

Hydrocarbons degraders, 1291

Hydrocarbon seeps, 1928, 2716–2718

Hydrocarbons length, 2688, 2689

Hydrocarbons/oils substrates, 1514

Hydrocarbons, polycyclic aromatic. See Polycyclic

aromatic hydrocarbons

Hydrocarbon tolerance, 2427–2428

Hydrocarbon transport measurement

– calculations, 4219–4220

– cell growth and preparation, 4216–4218

– cytoplasmic membrane, 4221

– energy requirement, 4220

– materials, 4221

– transport assay, 4215–4216, 4218–4219

Hydrocarbon utilization, 1887–1895

Hydrocarbon-utilizing microorganisms, 2716–2718

Hydrochlorofluorocarbons, 3340, 3342–3343

Hydrodesulfurization (HDS), 2131, 2769

Hydrogen, 711–715, 719, 720, 2632, 2633, 2636

Hydrogenation, 16, 17, 23

Hydrogen atrophy, 1348

Hydrogen autotrophy, 1843

Hydrogen bonding, 41

Hydrogen bonds, 23, 25, 31, 36, 38, 41, 42, 44

Hydrogen exchange, 108

Hydrogen isotopes, 102, 105, 108, 308

Hydrogenophaga, 1719

Hydrogenosomes, 701

Hydrogenotrophic, 116, 117, 120, 659, 660, 668, 670, 673,

676, 2211, 2212, 2216

Hydrogenotrophic methanogen(s), 666, 670, 672

Hydrogenotrophic methanogenesis, 485–487, 490–492,

2166, 3913, 3915

Hydrogenotrophic pathway, 2236, 2239

Hydrogenotrophs, 622

Hydrogen scavenger, 3915

Hydrogen sulfide (H2S), 2757, 3088–3091, 3169–3171,

3206, 3364, 3389

α/β-Hydrolase(s), 1083, 1084, 1101, 1108–1110, 1116Hydrolases screening, 4596

Hydrolysis, 119, 305, 2632–2635, 3731–3733

Hydrolytic, 119

Hydrolytic enzymes

– chitinases and gluconases, 2558

Hydroperoxide, 986–988, 991, 996–998

Hydrophile-lipophile balance (HLB), 1507, 1508

Hydrophobic, 2502, 2503, 2772, 2781

Hydrophobic and electrostatic interactions, 1483

Hydrophobic cell surfaces, 1841

Hydrophobic compounds, 1502, 1505, 1507–1510

Hydrophobic contaminant, 1560

Hydrophobic effect, 1440–1441, 1453

– in proteins, 1458

Hydrophobic interaction, 1093

Hydrophobic interaction chromatography, 3632,

3634–3637

Hydrophobicity (logP), 1440–1449, 1566–1572, 1948

Hydrophobic particles, 2403, 2404

Hydrophobic substrate-carrying floating dish

microcosm, 3546–3548

Hydrophobic substrate (HS) degrading microorganisms,

2112–2114

Hydrophobic substrates, 1513–1526

Subject Index 4667

Hydroponic, 3462–3464

Hydroquinone (1,4-dihydroxybenzene), 1308

Hydrosphere, 298–312

Hydrostatic pressure pumps, 3870

Hydrothermal circulation, 2204

Hydrothermal sediments, 2205, 2207, 2208, 2214

Hydrothermal vents, 149, 150, 1979, 1982, 1983, 1989,

1991, 1992, 2198, 2199

3-Hydroxyacyl-ACP dehydratase, 389

3-Hydroxyanthranilate 3,4-dioxygenase, 1367, 1368, 1381

3-Hydroxybenzoate 4-hydroxylase, 1369, 1372, 1383

3-Hydroxybenzoate 6-hydroxylase, 1370, 1371

4-Hydroxybenzoate 3-hydroxylase, 1369, 1370, 1383

Hydroxybenzoquinol(s), 840, 848–850, 858–859

Hydroxybenzoquinol 1,2-dioxygenase, 1359

Hydroxy benzoquinols, 800

2-Hydroxybiphenyl (2-HBP), 2132, 2136, 2789, 3651

α-Hydroxyketone, 3196, 3200–3201Hydroxylase, 785–793, 1927

β-Hydroxyl-β-methylglutaryl CoA lyase, 959

Hydroxyl fatty acids, 2845, 2846, 2850, 2851, 2854

Hydroxyl functions, 986, 996

Hydroxyl radical, 988, 992

27-Hydroxyocatacosanoic acid, 390, 3198, 3199

3-Hydroxypentadecan-4-one, 3200, 3201

2-Hydroxypenta-2,4-dienoate, 1185–1187

2-Hydroxypentadienoate (HPD), 1307–1308

3-Hydroxyphenylacetate 6-hydroxylase, 1372

4-Hydroxyphenylacetate 3-hydroxylase, 1373, 1374

2-Hydroxy-6-phenyl-6-oxohexa-2,4-dieneoate

(HOPDA) hydrolase, 1185

3-Hydroxyphenylpropionate monooxygenase,

1371, 1372

3-Hydroxypropionate, 150

Hydroxypropyl-β-cyclodextrin, 364710-Hydroxystearic acid, 2254

Hydroxystearic acids (HSA), 3125, 3127

– affinity chromatography, 4421

– tag, 4421

Hydroxysteroid dehydrogenases, 3138

Hygiene, 3388

Hymenaea oblongifolia, 179

Hymenomonas carterae, 176

Hymenomycetes, 1914

Hyperosmotic shock, 676

Hypersaline, 666–677, 1940–1948, 3338

– environments, 3848

– microbial mat, 3657

Hypersaline brines, 666, 670, 671, 1940–1942, 1946, 1947

Hypersaline environments, 666–677, 1940–1946, 1948

Hypersalinity, 666

Hypersensitivity pneumonitis (HP), 3306–3309

Hyperthermophilic, 116

Hyperthermophilic archaeon, 3879, 3880

Hyphomicrobium, 3173, 3830, 3831, 3834, 3835

Hyphosphere, 1556

IIbogaine, 3264

Ice cave(s), 1908, 1913, 1914

Ice cave sediment(s), 1914

Ideonella dechloratans, 942

Idiomarina, 1943

IHF, 1132, 1133

IL-8, 3245, 3251, 3253

Illegal discharge, 3479

Illegitimate recombination, 1346, 1349

Illumina, 4261

Illumina/Solexa genome analyzer, 4270

Image analysis, 4069

Imaging, 4046

Imaging program, 3568

Immiscibility, 1446, 1448

Immobilization, 2837

Immobilization strategies, 2772

Immobilized affinity media, 4419, 4420

Immunocomplexes, 4192

Immunogenicity, 3384

Immunoprecipitation, 2916, 4191–4192

Immunoprofile, 2705–2707

Immunosensors, 2700, 2706

Include rotary drilling, 3760, 3761

Incomplete tricarboxylic acid cycle, 697

Incorporation efficiency, 4043

Incubation

– buffer, 4066–4068

– times, 3808, 3809, 3812

Indeno[1,2,3-cd]pyrene, 2098

Independent of acyl-CoA, 539

Indicative ratios, 304

Indicator compounds, 2493, 2494

Indigenous microbiota, 2163, 2165, 2167, 2170

Indigenous reservoir microorganisms, 2716, 2718–2719

Indigo, 1932

Indigo production, 1778

Indole-3-acetic acid (IAA), 2555

Induced systemic resistance (ISR), 2559

Induction, 1175

Inductive effects, 16, 25, 26

Industrial effluents, 302

Industrial scale, 2882

Inelastic scattering, 4028

Inexpensive organic residues, 2999, 3002

Inflammation, 3216, 3218, 3219, 3221, 3223, 3224

Inflammatory bowel disease, 3124, 3128

Inflammatory response, 3245, 3251, 3253

Information service, 3483

Infrared (IR) line scanner/camera, 3477, 3478

Infra-red spectrophotometry, 3578

Infrastructure, 1556, 1558

INGENYphorU system, 4146, 4154

Inhibition, 2632–2635

Inhibitors, 3675–3676, 3681–3682, 4042, 4043, 4048

4668 Subject Index

Inipol, 2502, 2503, 2525, 2622

Inoculation, 2532–2534, 2537, 2538, 4545–4550

Inorganic peroxide, 988

Insecticides, 305, 866, 880, 2976

Insertion, 1092

Insertion sequences, 1220, 1346, 1347

In situ, 3655–3667, 3883–3902

In situ biodegradation, 3607, 3608

In situ bioremediation, 2614

In situ microcosms

– applications, 3504

– GC-MS techniques, 3507

– isotope label, 3504–3505

– isotope tracer techniques, 3505

In situ product removal (ISPR), 2886

Institute for Coastal Marine Environment (IAMC), 2517

Instruments capacity, 3476

Intact archaeal lipids, 2199

Integrated ocean drilling program (IODP), 3429, 3438

Integration host factor (IHF), 1405

Intensity and position of the bands, 3911–3912

Intercellular leukocyte adherence molecule-1 (ICAM-1),

3245, 3251

Interesterification, 2849

Interface(s), 1491–1498

Interfacial access, 1292

Interfacial area, 1448, 3921, 3922

Interfacial scale, 431

Interfacial tension, 1508

Intergenic spacer (ITS), 3972, 3973, 3975–3980,

3984–3988

Interindividual variability, 3152, 3153, 3155

Interleukin, 3223

Intermolecular forces, 25, 38, 41

Internal standards, 3673–3674, 3679, 3682

– cometabolism, 3931

– deuterium oxide, 3930

Internal transcribed spacer (ITS), 2227

International oil pollution compensation funds,

3482, 3483

Interpretox, 4455–4456

Interspecies, 619

Interspecies electron carrier, 341

Interspecies electron transfer, 892, 895, 905, 3915

Interspecies hydrogen transfer, 642, 700

Interspecies oxygen transfer, 938, 941

Inter-well tracer test, 3765–3767

Intestinal microbiota, 3134

Intestine, 3122, 3123, 3125, 3127, 3128

Intradiol dioxygenase(s), 1062–1063, 1357,

1359–1361, 1381

Intramolecular repression, 1131, 1134

Intrasporangiaceae, 1827, 1828, 1854

Intravacuolar transport, 1559

Intrinsic bioremediation, 2474, 2584, 2592–2594,

4511–4515

Inventories of PAH in soils, 288

Invertrons, 1348

In vitro compartmentalization, 4193, 4433

In vivo expression technology (IVET), 1261,

2578, 2579

Iodonitrotetrazolium violet (INT), 4160, 4161,

4163, 4164

Ion gradient, 340, 350

Ionic strength, 4068

Ions, 666, 668, 675, 676

Iron, 161–162, 3343, 3348

Iron reduction, 3101

Iron-seeding, 3343, 3348

Iron-sulfur redox center, 1060

ISCOM, 3323, 3324

Island

– genome, 4325

– magnetosome, 4325

Isoalkanes, 994

Isobutene, 120, 121, 611

Isocitrate lyase, 3288, 3289

Isoflavones, 3151, 3152

Isolation, 3796–3797

– characterization and preservation, 3782

– HDB, plate purification, 3781–3782

– organisms, 3915–3916

Isoleucine, 3282, 3286, 3288

Isomerase, 389, 390

Isopentenyl diphosphate, 128, 129

Isoprene, 114, 115, 120–122, 128–130, 610, 611, 3168,

3169, 3174, 3176

Isoprenoid compounds, 1291

Isoprenoid hydrocarbons, 2690, 2694

Isoprenoids, 121, 122, 128–130, 370, 460, 462–465, 469,

470, 610, 611, 959–961, 2163, 2165, 2951–2962,

3576, 3579

Isopropylbenzene, 1376, 1377, 1536

Isopycnic ultracentrifugation, 4013

Isothermal titration calorimetry (ITC), 4232–4241

Isotope analysis, 60–62

– compound-specific isotope analysis, 108

– 2-dimensional isotope analysis, 108

Isotope-coded affinity tags (ICAT), 4389

Isotope-coded protein label (ICPL), 4389

Isotope effect

– equilibrium isotope effect, 100

– kinetic isotope effect, 101, 103, 104, 108

Isotope fractionation, 102, 106–108

Isotope ratio mass spectrometry (IRMS), 60, 61

Isotopes, 144–148, 150–152, 194, 195, 3101, 3103, 3107

– BTEX compounds, 3508

– carbon isotope, 103–108

– fractionation, 3603–3610

– hydrogen isotope, 102, 105, 108

– incorporation, 4015

– label, 3504–3505

Subject Index 4669

– stable isotope, 99–108

– tracer compounds, 3506

– tracer techniques, 3505

Isotopically heavy CO2, 3915

Isotopically labeled hydrocarbon, 3589

Isotopic ratio, 85–86

Isovaleric acid, 3208

Itaconic acid, 2897

Iturin, 1508

JJanibacter, 1854, 1855, 1859, 1861

Jannaschia sp., 1713, 1714

Janthinobacterium sp. J3, 2793, 2794

Jonesiaceae, 1827, 1829

KKaempferol, 3264

Kazan, 210

Kebrit and Shaban Basins, 670

Keratinocyte, 3217, 3220, 3222

Kerogen, 1, 13, 26, 40, 44, 103, 144, 151, 153, 309,

2162–2165, 2167, 2170

Kervalet saltern, 672

β-Ketoadipate, 1302β-Ketoadipate pathway, 1170, 1173, 1339Keto-enol tautomerism, 27, 28

α-Ketoglutarate dependent halogenases, 379–381α-Keto-γ-methylthiobutyric, 3014, 3015

2-Keto-4-methylthiobutyric acid pathway, 121

Ketones, 17, 27, 41

Killing curve, 3960

Kineosporiineae, 1827

Kinetic isotope effect, 146, 147, 150, 151

Kinetic mechanism, 1085

Kinetic models, 4340, 4341

Kinetic parameters, 3916

– inhibition degrees, 4200

– Michaelis–Menten kinetics, 4200–4201

– substrate concentration, 4199

Kinetic selection, 2407

Kluyveromyces marxianus, 2899

Kodama pathway, 2131, 2132, 2789,

2790, 2795

Kordiimonadales, 1708

Kordiimonas gwangyangensis, 1708–1710

Kosmotropic solutes, 1452, 1460

Kow, 1440, 1441

Kow-values, 299

Krebs cycle, 815, 816, 823, 824, 826

Kyoto, 2828

LLabeling, 4040, 4042–4044, 4047, 4048

– strategies, 2701

“Lab on a chip”-system, 2947

La Brea tar composition, 1629–1630

La Brea tar pits, 1626, 1627, 1632

Laccase, 2080, 2084, 2088–2091, 2093, 2095, 2096,

2098–2100

Lactams, 28

Lactate, 3122–3124

Lactic acid, 2899, 2900

Lactobacilli, 3232

Lactococcus lactis, 1110

Lactones, 28, 1073, 2851

Lacustrine organic matter, 300

LadA, 790

Lake Chaka, 670

Landfill, 2810, 2812, 2814, 3342, 3347

– leachates, 308

Large linear plasmids, 1346–1349, 1351, 1840, 1847

Laser fluorosensor (LFS), 3478

Laser scanning microscopy (LSM), 4073–4083

Lateral dioxygenation, 1792

Lateral gene transfer (LGT), 1220

LC-ESI-MS(/MS), 4388–4389

LCFA-degrading anaerobes, 964–969, 975, 977

LC-IRMS, 4024

LC-MS, 4424

Leg 201, 120

Legionaminic acid, 3198

Legionella pneumophila, 414, 3196–3197, 3199, 3201,

3242, 3244, 3248–3249

Legionaires’ disease, 3196, 3200

Leguminous plants, 3347

Leifsonia, 3173

Lena Delta, 2176

Leptin, 3123

Leptospirillum, 2278, 2285–2288

Leucine, 959

Levoglucosan, 285

Lewis acids, 33

Libraries, 2912, 2913, 2916, 2919, 2920, 2923, 2924,

4347–4351, 4409, 4412, 4415–4419

– screening, 4349, 4350

Lichenysin, 1508

Ligand-induced, 1084, 1085

Ligation, 4595, 4596

LigB family, 1363, 1365, 1389

Light-dark shift method, 3657, 3663–3665

Light energy, 2340

Light hydrocarbons, 105, 107, 108

Light nonaqueous phase liquids (LNAPL), 240,

4521, 4670

Lignans, 3151, 3152

Lignins, 26, 37, 40, 281, 283, 285, 289, 2080, 2084, 2088,

3151, 3152

– peroxidase, 2080, 2084

– peroxidise, 1927

Lignocellulosic biofuels, 1652

Limestone, 162–163

4670 Subject Index

Lindane, 880, 1694, 1695, 1698, 2579

Linear alkanes, branched aliphatics, 311

Linear growth, 3920, 3922

Lines of evidence, 2475–2477

Linoleic acid (LA), 2252–2255, 3125, 3126

Linolenic acid (LNA), 3125

LIP1, 2249, 2250

LIP4, 2249, 2250

LIP5, 2249, 2250

Lipases, 1515, 1518, 1519, 2247, 2250,

2254–2255, 2837, 2838, 2845, 2846, 2849–2851,

2853–2855, 3205, 3218–3220, 3259–3267,

3269–3276

Lipid A, 386, 389–391, 397, 404, 410–415,

3197–3200

Lipid analysis, 3714–3716, 3720, 3721

– chemicals, 3747

– soils and sediments sampling, 3744, 3746

Lipid I

– biosynthesis, 437–439

– membrane topology, 438

– structure, 438, 440

– transferase MraY, 437–439

Lipidic inclusions, 3726

Lipid II

– antibiotic complexes, 442


– glycosyltransferases (GT), 441

– membrane topology, 438

– reaction mechanism, 442

– structure, 438

– transferase MurG, 439–440

– transglycosylation, 441–442

– translocase MurJ, 441

– translocation, 440, 441, 443

Lipid-lipid interactions, 1456, 1459

Lipids, 2246–2255, 2845–2847, 2849–2851, 2854,

3022–3024, 3026–3028, 3114, 3115, 3117

– bilayer, 418–422

– biomarkers, 2026–2027, 3372, 3373

– biosynthesis, 2997, 3001

– body, 3186–3191

– domains, 396, 422–423


– hydrolysis, 2246, 2248–2253, 2255

– membrane, 456–457

– particle, 475–479

– particle biogenesis, 477, 479, 4227, 4228

– particles, 538–542, 544, 4223–4228

– rafts, 396, 400

– spirals, 396

Lipid X, 411

Lipitor, 2935, 2936

Lipoglycan, 3222

Lipolysis, 2247–2249, 2254, 2255, 2387–2389

Lipolytic enzyme(s), 1099–1117

Lipooxygenases, 2846, 2848–2849, 2854, 2855

Lipopeptides, 1508, 1509, 3687–3703

– purification, 3693–3694, 3701

Lipophilic, 3186

Lipophilicity, 299, 305, 309

Lipopolysaccharides (LPS), 410, 412, 414, 1494, 1617,

1619, 1620, 3144, 3196–3201

Lipoproteins, 3689, 3690, 3692, 3701–3703

Liposan, 1515, 1516, 1525

Liposomes, 3313–3314, 3318

Liquid chromatography (LC), 52–53, 57, 60, 84, 4388

Liquid hydrocarbons, 3788, 3793–3796

Liquid pentane, 735–736

Liquid petroleum gas (LPG), 262

Lisbon conventions, 3473

Lithium, 196

Lithocholic acids, 3138

Live/dead, 4500, 4502, 4506

Live/dead reagent, 3564

Liver disease, 3169, 3174

Log Poctanol-water, 1453, 1461, 1462

Long chain fatty acids, 2632–2636, 3186

Long-chain fatty acids-degrading bacteria,

2633, 2636

Long-chain-length alkanes, 784

Long chain n-aldehydes, 300

Long-chain n-alkanes, 783–789–790

Long range transport, 311

Long-ranging hydrophobic interactions, 3638

Long term environmental protection, 3483

Loop, 1083, 1093

Loss of function, 3958

Loss rate, 272

Lost City, 2204, 2214–2216

Low energy conditions, 340

Lower termites, 708, 709, 712–718, 720, 722

Low-temperature

– bioremediation, 1913

– environments, 1898

– reservoirs, 2162

LpxA, 410, 411

LpxB, 411

LpxC, 410, 411

LpxD, 411

LpxL, 411, 412

LpxM, 411, 412

LpxP, 412

Lro1p, 539, 540

Lubricating oil, 3486, 3487

Luciferase, 3674, 3676, 3678–3679, 3681, 3682

– family, 997

LukF, 426

Luminescence, 3646

Lux genes, 4449

Lyophilization of the sample, 3729–3731

Lysine, 3832

Subject Index 4671

Lysis, 426

– methods, 4186

Lysophospholipase, 3200, 3243, 3244, 3247

LysR, 1239, 1240

LysR type transcriptional regulators, 1240–1241

Lysyl-phosphatidylglycerol, 399

Lytic peptides, 427–429

MMACiE, 1026, 1028, 1030, 1039

Macromolecules

– hydrophilic & hydrophobic interactions, 1456

– interactions with hydrocarbons, 1456, 1459

– interactions with water, 1453

– non-covalent interactions, 1453

– stability, 1453, 1454

Macrotermes

– jeanneli, 723

– subhyalinus, 717

Magentospirillum magnetotacticum, 948

Magnaporthe grisea, 3262

Magnetic activated cell sorting (MACS), 4592, 4593,

4596, 4598

Magnetic bead capturing, 4024

Magnetite, 219, 220

MAH. See Monocyclic aromatic hydrocarbon

Maillard reaction, 31

Maintenance, 1444, 1445, 3923

Maintenance energy (ME), 640, 641, 647, 648, 650

Major histocompatibility complex (MHC), 3209

Malassezia, 3260, 3265, 3266

MALDI-TOF, 3691, 3699, 3702, 3703

MALDI-TOF-MS(/MS), 4388

Malodor, 3388

Malonyl CoA, 389, 510, 514–516

MALP-2, 3314–3318

Mammalian gastrointestionl ecosystems, 694, 695,

701, 702

Mammalian P450, 991, 1004

Manganese, 1927, 3081

– peroxidase, 2080, 2084

Mannosylerythritol lipids (MELs)

– column chromatography, 3714

– extraction, 3710

– GC-MS, 3716

– HPLC-ELSD, 3717

– structure, 3706

– TLC, 3712, 3714

M2 antibody, 4421

Manufactured gas plants (MGPs), 235, 240

Margins-accretionary and erosive, 189

Marine, 298, 310, 359, 360, 362, 365, 1336, 1341,

1342, 1774, 1775, 1777, 1778, 3492, 3493, 3496,

3500, 3501

– ecosystems, 310, 311

– environments, 298–312, 1507–1508

– fungi, 2226–2228

– hydrocarbon-degrading bacteria, 2365

– hydrocarbonoclastic Gammaproteobacteria, 1903

– medium, 3791, 3792

– oil spills, 2617–2626

– organism, 309, 311

– phyto-and zooplankton, 310

– Roseobacter clade, 1713

– sediment(s), 115–117, 120, 121, 1290–1292,

2226–2228

– systems, 304, 309, 312

Marine ammonium mineral salts (MAMS) medium, 3834

Marine Benthic Group B (MBGB), 2199

Marine seeps, cyanobacteria, 2354

Marinobacter, 1725–1733, 1934, 1943, 1944, 2345

– alkaliphilus, 1934

– aquaeolei, 1726, 1732

– hydrocarbonoclasticus, 1726, 1730, 1731, 1733, 1944

– hydrocarbonoclasticus SP17

– biofilm, 4378

Maritime transport, 2362, 2366

Marker compounds, 305, 309

MARPOL

– convention, 3473

– regulations, 3478, 3480, 3481

Mars, 3439

MARTE project, 2708

Mascot database, 4425

Mass and volume loss, 3752, 3756

Mass balance, 2477–2479, 3910

Mass extinction, 3347

Mass spectrometric assay

– procedures, 4583–4584

– solutions and materials, 4584–4585

– time considerations and troubleshooting, 4585

Mass spectrometry (MS), 53, 57, 58, 60, 62, 3576, 3578,

3580, 3581, 4184, 4190, 4409, 4415, 4419, 4420, 4424,

4425, 4557, 4560

– glycolipids, 3706, 3708, 3716–3718

Mass transfer, 1443, 1445, 1446, 2772, 2781, 2782,

3920–3923, 3926

– barrier, 3921

– rhamnolipids, 1496

Mass transport, 206, 209

MATH, 3632–3635

Matrix assisted laser desorption ionization (MALDI),

3717, 3719, 3720

Maturity

– thermal maturity, 105

Maximum membrane concentration (MMC),

1571, 1572

mCherry, 3468

MCL-PHA synthase, 4604

– collocation statergies, 4603

– Pseudomonas oleovorans, 4605–4606

MCP, 1532, 1536, 1537, 1539

4672 Subject Index

mcrA gene, 668, 2025–2026, 2029

MDA amplification, 4257, 4259–4260

Measurement

– online, 3421

– in situ, 3420, 3421

Media, 3788–3797, 3828–3830, 3832–3835, 3837, 3838,

3848, 3850, 3851, 3853, 4593

– recipes, 3862–3865

Median esterase activity, 4503, 4506

Mediterranean ridge, 196

Mediterranean Sea, 666, 670, 671

Medium, 3788–3792, 3794–3796, 3798

Medium-chain-length (MCL), 4602–4605

Medium-chain-length alkanes, 784

Medium for gram-positive methylotrophs, 3836

Megasphaera elsdenii, 2252, 2254

Melittin, 427–431

Melting points, 42

Membrane, 137–138, 3829, 3834, 3837, 3838

– AlkB alkane hydroxylase, 788

– damaging proteins, 426, 427, 430–432

– fluidity, 389, 513, 515–516

– fraction, 4190

– functions, 1600

– interaction with hydrocarbons, 1456, 1457

– interaction with water, 1457

– lipid, 509–517

– proteins, 4189–4190

– solubilization, 4190

Membrane lipids

– interaction with hydrocarbons, 1458

Membrane-protein stability, 1458

MEOR

– field trials, 2742

– oilfields, 2742–2745

MEP. See Methylerythritol phosphate

Mercaptopropionate, 1205

Merodiploids, 3963, 3964

Merox (mercaptan oxidation) process, 258, 262

Mesocosms, 3524, 3526

– advantages, 3515

– applications and parameters, 3514

– ecosystems, 3514

– structure, 3517–3520

– water aspiration and treatment, 3517–3518

Mesophilic, 116

Messenger RNA, 1991

Metabolically active microorganism identification,

4093–4101

Metabolic control analysis (MCA), 4341, 4342

Metabolic disease, 3210

Metabolic diversity, 1840

Metabolic flux analysis, 4341, 4344

Metabolic intermediates, 2878, 2884

Metabolic networks, 1414, 1416, 1421, 1424, 4339–4345

Metabolic pathways, 145–153

Metabolic pool, 3188

Metabolic processes, 3655–3667

Metabolic reconstruction, 4330–4332, 4334, 4335

Metabolic regulation, 4340–4343, 4345

Metabolic selection, 2407

Metabolism, 3149, 3151–3153, 3155

Metabolite fingerprinting, 2297

Metabolome, 1862

Metabolomics, 1260, 1262, 3155

Meta-cleavage, 1299, 1302, 1306–1308

– pathway, 1130, 1133–1134

Metagenomes, 1258, 2853–2855, 4564–4567, 4570, 4571,

4575, 4576

Metagenomics, 900, 902, 905, 1633, 2233–2243, 2438,

2440, 2441, 2449, 2450, 2799, 2912, 2913, 2919, 2920,

2923, 2924, 3370–3371, 4256, 4258, 4262, 4304–4305,

4348–4351

Metal

– respirers, 3855–3868

– toxicity, 3092

Metalloenzyme, 1026, 1040

Metal-reducers, 3857, 3865–3867

Metal-reducing bacteria, 3859

Metal working fluids (MWF), 2370–2375, 2641–2649

Meta-Methanoxgenome, 2232–2243

Metaproteomes, 4186, 4189

Metatranscriptome, 4259

Metatranscriptomics, 4256, 4257, 4351

Methane, 6, 9, 25, 30, 41, 42, 114–123, 188, 189, 192–198,

484, 486, 491, 493, 495, 610, 611, 618–623, 626–631,

656–659, 666, 668, 670–674, 676, 677, 709–715,

719–724, 985, 994–996, 999–1002, 1004, 2000–2009,

2164–2166, 2169, 2174–2177, 2182, 2185–2189,

2226–2229, 2632–2636, 2810–2813, 3077–3083, 3168,

3169, 3173, 3176, 3337–3338, 3340, 3342, 3344–3347,

3438, 3439, 3788, 3793, 3794, 3828–3834, 3837–3841

– activation, 745–746

– clathrate breakdown, 3345–3347

– consumption rates, 1983, 1987

– cycle, 2216

– cycling, 666, 668, 674–675

– cycling in the environment, 1973

– dehydrogenase, 743–745

– flux, 668, 672, 674, 1979

– hydrate, 3058–3062, 3438

– monooxygenase, 151, 3829, 3833, 3839, 3840

– oxidation, 672, 674, 769–772, 778, 1053, 2197,

2205, 2207

– oxidizers, 358

– production, 656, 658, 660, 2024, 4319, 4322

– snowball Earth, 637

Methane monooxygenase gene probes, 3072

Methane monooxygenases (MMO), 768, 769, 784, 786,

1663, 2895

– biochemistry, 1045–1054

– molecular biology, 1045–1054

Subject Index 4673

– mutagenesis, 1048–1050, 1053, 1054

– particulate (pMMO), 2508–2512

– soluble (sMMO), 2508–2512

Methane-oxidizing archaea, 2207, 2216, 2217

Methane-oxidizing bacteria, 674, 1046

Methanesulfonic acid (MSA), 1202, 3089, 3093, 3094,

3348, 3831

Methanethiol, 676, 3168–3171, 3206, 3207, 3228,

3229, 3389

Methanimicrococcus, 699

– blatticola, 602

Methanoarchaea, 682–690, 2262–2269

Methanobacteriaceae, 560, 569, 659

Methanobacteriales, 551, 559–569

Methanobacterium, 116, 560, 561, 569, 656, 658, 701,

2167, 2168

– ruminantium, 695, 699, 700

Methanobacterium formicium, 699

Methanobacterium (Mb.) bryantii, 699

Methanobrevibacter, 560, 563, 656, 658, 669, 694, 695,

697–701, 703, 3173

– arboriphilus, 719

– oralis, 695, 697

– smithii, 695

Methanobrevibacter (Mbb.) millerae, 699

Methanobrevibacter (Mbb.) olleyae, 699

Methanocalculus, 591, 592

– haloterans, 670

– halotolerans, 676

Methanocaldococcaceae, 574

Methanocaldococcus, 574–576, 579, 580, 2211

– jannaschii, 507

Methanocellales, 551

Methanocella paludicola, 551

Methanococcaceae, 579, 580

Methanococcales, 551, 573–580

Methanococcoides, 596, 601, 602, 656, 659, 672, 673, 675

Methanococcoides burtonii, 503, 507

Methanococcus, 116, 577–580, 2211

– aeolicus, 579, 580

– maripaludis, 487, 490, 492, 503, 505, 579

– voltae, 574, 579, 580

Methanocorpusculaceae, 584, 591

Methanocorpusculum, 660, 670

Methanoculleus, 699, 2211, 2212, 3915

Methanoculleus olentangyi, 700

Methanofuran, 116

Methanogenesis, 150–151, 153, 618–622, 636–651,

656–661, 666–677, 707–724, 984, 1000, 2205, 2211,

2212, 2215, 2894, 3101–3103, 3105, 3107, 3108, 3162,

3338, 3799–3824

– consortium, 326, 327

Methanogenesis from methylamine, 3805, 3809,

3812, 3818

Methanogen functional genes (mcrA), 3816–3818,

3821–3823

Methanogen functional genomics, 501–507

Methanogenic, 637, 640–645, 647–650

Methanogenic archaea, 172–173, 502–505, 507, 656,

658–661, 891, 896–898, 902, 1000, 1001, 2025, 2027,

2029, 3173, 3342

Methanogenic degradation, 3906, 3907, 3910

Methanogenic environments, 3813

Methanogenic habitats, 556

Methanogenic hydrocarbon biodegradation mechanism,

3915

Methanogenic microcosms, 3914

Methanogenic oil degradation, 3906–3910, 3913,

3915, 3916

Methanogens, 115–116, 118–122, 338–342, 346,

549–557, 618–623, 666–677, 2167, 2168, 2206, 2211,

2212, 2216, 2227, 2610, 2612, 3059–3061, 3063,

3168–3176, 3799–3807, 3809–3811, 3824

Methanogens alkali lakes, 648

Methanogens dead seas, 647

Methanogens diversity, 3812–3823

Methanogens halite crystallizing, 648

Methanogens ponds, 648

Methanogens solar salterns, 648

Methanogens substrates, 3808

Methanohalobium, 596, 601, 602

Methanohalobium evestigatum, 675

– halobacteria, 648

– salt in, 648

– salt out, 648

Methanohalophilus, 596, 601, 602, 666, 670–676

– halophilus, 648

– mahii, 648, 671

– portucalensis, 675

– Zhilinae, 647

Methanol, 26, 46, 696, 700, 3228, 3233, 3236, 3237,

3828–3833, 3835–3841

– coenzyme M methyltransferase, 697

– dehydrogenase, 2895, 3233, 3236, 3237, 3829, 3832,

3839, 3840

– oxidation, 771

Methanolacinia, 590, 591

Methanolinea, 592

– tarda, 591

Methanol medium for Hyphomicrobium, 3835

Methanolobus, 506, 601, 602, 672, 676

– oregonensis, 676

Methanolysis, 3731–3732

Methanolysis with BF3/MeOH, 3732

Methanomethylovorans, 660

Methanomicrobiaceae, 584

Methanomicrobiales, 551, 583–592, 659, 675, 2025, 3815,

3819–3822

Methanomicrobium, 590, 591, 699

Methanomicrobium mobile, 699

Methanomicrococcus blatticola, 718, 719

Methanophenazine, 360, 362, 364, 365

4674 Subject Index

Methanoplanus, 2212

– petrolearius, 670

Methanopyrales, 551, 606–607

Methanopyrus kandleri, 606, 607, 646

Methanosacrinales, 672, 673

Methanosaeta, 116, 359, 360, 362, 365, 366, 2211, 2212

Methanosaetaceae, 596, 602, 659

Methanosalsum, 596, 601, 602

Methanosalsum (Methanohalophilus) zhilinae, 675

Methanosarcina, 116, 596, 601, 602, 656, 658–660,

697, 699

– acetivorans, 359, 362, 364, 365, 503, 506,

4319, 4320

– barkeri, 487

– mazei, 487, 506

– thermophila, 495

Methanosarcinacea, 659

Methanosarcinaceae, 596, 601

Methanosarcinales, 551, 557, 595–603, 618, 622, 672, 673,

2025, 2027, 3815, 3819–3822

Methanosphaera, 560, 565, 569

Methanosphaera stadtmanae, 695, 4322, 4323

Methanospirillaceae, 584, 590

Methanospirillum, 116, 3915

Methanothermaceae, 560

Methanothermobacter, 560, 566, 569

– marburgensis, 364, 487, 490

– thermautotrophicus, 453, 457

Methanothermococcus, 577–580, 2211

Methanothermococcus okinawensis, 579, 580

Methanothermus, 560, 567–569

– fervidus, 646

Methanotorris, 575, 576, 579, 580

Methanotrophic, 2174–2177

Methanotrophic archaea, 898, 2229

Methanotrophic bacteria, 3342

Methanotrophic microbes, 308

Methanotrophs, 786, 1046, 1047, 1049–1053, 1662, 1663,

1666, 1953–1964, 2182, 2185–2190, 2507–2512, 2895,

3827–3841

– membranes, 1955

– type I and type II, 3079

Methanotrophs classification, 770

Methanotrophy, 151–152, 674, 2174–2177, 2229

Methermicoccaceae, 602

Methermicoccus shengliensis, 596, 602

L-Methionine, 3013–3016, 3018

Methionine, 3014–3015, 3018, 3169, 3172, 3282,

3286, 3288

2-Methlnaphthalene, 926, 928, 929

Methoxy radical, 272, 273

Methyl-accepting chemotaxis proteins (MCPs), 1532

(1-Methylalkyl)succinate, 916, 918

Methylamines, 666–668, 671, 672, 674–677, 700, 3172,

3173, 3175, 3176, 3228, 3229, 3233, 3237, 3828, 3832,

3833, 3841

Methylated amines, 115

Methylated sulfur, 3828

Methylated sulfur compounds, 3235

Methylation, 1019–1021, 4206, 4207

3-Methylbenzoate (3MB), 1133

Methylcatechol, 1074–1077

Methylcitrate cycle, 3281–3283, 3286–3289

Methylcitrate synthase, 3281, 3283–3289

Methylcitrate synthase mutant (mcsA mutant), 3283–3287

Methyl-coenzyme M reductases (MCR), 116, 668, 671,

697, 891, 894, 1001, 2025–2026, 2239, 2240

Methyl-coenzyme-M reductase subunit-A, 668

Methyl-CoM reductase (MCR), 1018, 1019

Methylerythritol phosphate, 121–122

Methyl group hydroxylation, 1013

Methylisocitrate lyase, 3281, 3282, 3287, 3288

Methylmalonic acidemia, 3282

Methylmalonyl-CoA

– mutase, 3280–3282, 3289

– pathway, 340, 343, 344, 3280–3283, 3285, 3287, 3289

Methylmercaptopropionate (MMPA), 1204

Methyl mercury, 3091

Methylnaphthalene, 1775, 1777, 1778

2-Methylnaphthalene, 926, 928, 929, 1019, 1020, 2298

Methylobacter, 2187

Methylobacterium, 3173, 3176, 3235, 3236, 3830,

3831, 3834

– podarium, 3208

Methylocapsa, 2182, 2185, 2187, 2189, 2190

Methylocella, 2182, 2185, 2187, 2190, 3829, 3837, 3839

Methylococcus, 134, 2187, 2190, 3829, 3837, 3839

Methylocystis, 2182, 2185–2187, 3829

Methylophaga, 1207, 1208

Methylosinus, 2186, 2187, 3829, 3839

– trichosporium, 2509–2511

– trichosporium OB3b, 2983, 2990

Methylotrophic, 666–668, 670, 672, 673, 676

Methylotrophic autotrophs, 3828, 3830–3832, 3837

Methylotrophic bacteria, 3168–3176, 3204–3212,

3227–3237

Methylotrophic methanogenesis, 492–494, 666, 668, 670

Methylotrophic methanogens, 146, 151, 152

Methylotrophic pathway, 2236, 2239

Methylotrophic yeasts, 2229

Methylotrophs, 622, 3827–3841

Methyl peroxy radical, 272

Methyl redutase, 363–365

Methyl substrates, 116

Methylsulfonylmethane (MSM), 3389

Methyl tertiary butylether (MTBE), 27, 30, 1683, 1684,

1844, 2599, 2603–2606, 3398

Mevalonate, 121, 1655

– pathway, 128, 453, 454

MgCl2, 671

Micelles, 1505, 1507, 1508

Michaelis constant (Km), 1639

Subject Index 4675

Michaelis Menten, 4342

Michaelis-Menten relationship, 1444

Microaerophilic, 1292

Microalgae, 2827–2838

Microalgal oil, 2830–2832, 2834

Microarrays, 1846, 2678, 2680–2682, 3839, 3840,

4040, 4045

– analysis, 4047, 4048, 4256, 4373

– assembly, 4044

– immunoassays, 2701, 2703–2706, 2708

– preprocessing methods, 4360

– printers, 4066

– sensitivities, 2701, 2704, 2705, 2708

– technology, 2680, 4354, 4364

Microarrays, bacterial responses, 4368–4370, 4374

– cDNA synthesis and labeling, 4371–4372

– culture conditions, 4369

– hybridization, 4372

– RNA extraction, 4369–4371

– scanning and data analysis, 4373

– slide array washing, 4372–4373

Microautoradiography (MAR), 1205

– MAR-CARD-FISH, 4097

– MAR-FISH, 4094, 4095, 4097, 4099, 4101

– signals, 4100

Microautoradiography and fluorescence in situ

hybridization (MAR-FISH)

– autoradiographic procedure, 4098–4099

– development and microscopic evaluation, 4099

– FISH procedure, 4097–4098

– fixation and staining, 4096–4097

– microbial ecology, 4094

– procedure, 4095

– sampling and incubation planning, 4095–4096

– solutions and materials, 4099–4100

– time, 4100

– trouble shooting, 4100–4101

Microbacteriaceae, 1827, 1829, 1854

Microbacterium, 1854, 1855, 1861, 2345

Microbial, 2893, 2896, 2897, 2899

Microbial activity, 2205, 2779, 2781, 2782, 3468–3469

Microbial adhesion to hydrocarbon (MATH) test,

1616, 1618

Microbial biofilms, 4075

Microbial cell, 3423

Microbial cellulose, 2968, 2975

Microbial community, 1230, 2226, 2229, 2313–2325,

2334–2336, 2362–2364, 2366, 4184–4193, 4340

– analysis, 3101, 3103–3105, 3107, 4137–4156

– clone libraries, 3986

– composition and diversity, 3971

– DNA/RNA extract, 3973–3974

– fungal, 3987

– profiling, 3818

– shifts, 284

– studies, 2682

Microbial consortium, 1910, 2027, 2811, 2812, 2814

Microbial decomposition, 310

Microbial degradation, 305, 307, 308

Microbial ecology, 1556, 2263

– function-based screens, 4294

– molecular, 4292

– OHCB, 2355

– polluted Coasts, 2355–2357

– sequence and activity based approaches,

4293–4294

Microbial ecosystem, 3149

Microbial flow cytometry, 4104–4112

Microbial food web, 2482

Microbial habitats, 2205, 2216

Microbial inoculants, 3468–3469

Microbial key-players, 4012, 4016

Microbial lipid metabolism, 3372–3373

Microbially enhanced oil recovery (MEOR), 2729–2737

– economics, 2747–2750

Microbial mats, 193, 194, 667, 671–672, 674, 2195,

2339–2347, 3525, 4054

Microbial mat structure, 2340

Microbial metabolic functions, 4306–4308

Microbial oil survey technique (MOST), 2716, 2718

Microbial oxygenases, 1844

Microbial phylogeny, 2325

Microbial releases, 1251–1253

Microbiome, 3149, 3151, 3155

Microcalorimetry, 4231–4241

Micrococcaceae, 1827, 1854

Micrococcineae, 1824, 1827–1829, 1854–1862

Micrococcus, 1854, 1855, 1860, 1861

Microcoleus, 2341, 2344

Microcoleus chthonoplastes, 2341, 2344

Microcosms, 1901–1903, 3624–3629

– experiments, 3453–3459

– processes, 3914

– types, 3545–3548

Microdiesel, 3000

Microencapsulation, 3391

Microflora, 3388, 3391

Microfluidics, 2947, 3564

Microfossils, 173, 174, 2340

Micrographies, 3729, 3730

Micromanipulator, 3659, 3662, 3666, 3667

Micromonas pusilla, 4500, 4501, 4504, 4506

Micromonosporineae, 1824, 1829

Micronucleus assay

– advantages, 4475–4476

– cell counting and division, 4474–4475

– equipment list and suppliers, 4479

– Mytilus edulis, 4477

– non micronuclei structure analysis, 4478

– protocol, 4476–4478

– tissue concentration vs. micronuclei number,

4478–4479

4676 Subject Index

Microorganisms, 2997, 2999–3002, 3389–3391

Microscopy, 3726–3729, 3838

Microsensor, 3655

– measurements, 3656–3659, 3662–3663

– polarization and calibration, 3660–3662

– setup, 3656, 3658–3660, 3666, 3667

Microspheres, 3433–3435

Microthrix parvicella, 1104, 2405

Microtiter plate assays, 2870–2871

Microwave radiometer (MWR), 3476, 3478

Middle distillates, 2136, 2771, 2773

Mid-ocean ridge, 217, 220

MIL-1, 1766, 1767

Mild extraction, 1476

Milk fatty acid profiles, 3163

Milk fatty acids, 2383, 2384, 2387

Millisia, 2405

Millivoltmeter, 3659–3660, 3662

Mineralization, 326

Mineral medium, 3774–3775

Mineral oil, 4460, 4511–4513

Mineral oil/BTEX spills, 4515

Minerals, 752, 753

Miniaturization, 2947, 2948

Mini-dish microcosm, 3548

Minimal bacterial genome, 2943

Minimal medium, 3848, 3851, 3852

Mini-Tn5, 3958–3959, 3961–3962, 4245–4254

Mini-transposon, 4246, 4247

Miscellaneous Crenarchaeotal Group (MCG), 2199

Mitigation, 2346, 2347

Mixed pollution, 3358

Mixed substrate growth, 3533

mmoX, 2182, 2185–2187

Mobile genetic elements, 1219–1230, 1268–1269

Mobile sorbents, 1473–1476

Mobilome, 1673

Mobiluncus, 3232, 3236

Moisturizers, 3388–3391

MolDarT, 4482–4484

Molecular, 2719, 2720, 2760–2763

Molecular approaches, 2405–2406

Molecular archaeology, 290

Molecular biology, 2969, 2977

Molecular ecology, 2700

Molecular ecology of methanotrophs, 3072–3073

Molecular ecology techniques, 3069, 3072–3073

Molecular fingerprinting techniques, 4301

Molecular interaction, 4232, 4234, 4236, 4239, 4240

Molecular-mechanistic test system, 4483

Molecular microbial ecology, 2305

Molecular modeling, 1083

Molecular operational taxonomic units (MOTUs), 4115

Molecular profiling, bacterial communities

– T-RFLP experimental procedure, 4115–4123

– T-RFs, 4123–4124

Molecular techniques, 3839

Molecular tracers of land use, 289

Molecular weight distribution (MWD), 3738

Molecular weight distribution gel permeation

chromatography, 3738–3739

Molecule orbitals, 6

Molybdenum cofactor (MoCo), 1016

Molybdoenzymes, 1003

Monitored natural attenuation, 2475, 2610, 2614

Monitoring networks, 3596

Monitoring programs, 3473, 3474

Monkey, 698

Monocyclic aromatic hydrocarbon (MAH), 2042

Monod

– kinetics, 3626, 3629

– relationship, 1444

Monoglucosyldiacylglycerol (MGlcDAG), 420

Mono-iron dioxygenase, 997

Mono Lake, 374, 673

Monomeric, 3468

Monomeric composition, 3729

Mononitrotoluenes, 1538

Monooxygenase (CYP), 1167

Monooxygenase DszA, 2772

Monooxgenase subunit A (SmoA), 1216

Monooxygenases, 152, 988, 990–998, 1004, 1844, 1845,

2082, 2084, 2089, 2132, 2133, 2846, 2849–2852, 2854,

2855, 3079, 3080, 3082

(P450-type) Monooxygenases, 992

Monooxygenation, 992, 994

Monoterpenes, 129, 958, 959

Moorella thermoacetica, 362, 363

Mosaicity, 1221, 1229

Mosquitoes, 3207

Most probable number (MPN), 2760–2763, 3867,

4159–4171

– extinction dilution techniques, 4523

Mound 12, 210

Mouth odor, 3168, 3169

MPN calculator, 4169

MPN-Enumeration, 4159–4171

M reductase (Mcr) reaction, 745–746

mRNA, 2680, 2683, 3672–3674, 3677–3679, 3682–3683

– copies, 2692, 2693, 2695

– purification, 4053–4055, 4057, 4059

MSA monooxygenase, 1208

MSBL-1, 670, 671

MSBL-1 group, 671, 673

MSM, 3173, 3176

– toothpaste, 3176

MTBE, 307

Mud mounds, 189, 191, 192, 195–197

Mud volcanoes, 206–212, 1979, 1989, 2194–2197, 2199

Multianalyte, 4064, 4065, 4067

– biosensors, 2706

– extracts, 4064, 4067

Subject Index 4677

Multi array analysis module (MAAM), 2701–2702

Multi-bottle rosette sampler, 3871

Multi-component systems, 990

Multi-corer, 3422

Multidisciplinary approach, 3914–3915

Multidrug resistance (MDR) efflux pumps,

3297, 3298

Multienzymes, 387

Multi-level sampler (MLS), 2481, 2482

Multi-partner protein complexes, 4419

Multiple displacement amplification, 4255–4262

Multiplexing, 2701, 2708

Multispecies associations establishment and

maintenance, 350

Multivariate data analysis, 1086

Municipal solid waste (MSW), 2812

Municipal waste water, 302

Mur1, 1768

Mussels, 1979, 1982–1983, 1985–1992

– hydrocarbon bioaccumulation assays, 4495

– vs. micronuclei incidence, 4479

– Mytilus edulis, 4477

– species, 4493

– WAF, 4478

Mutant, 3261–3263, 3265, 3266

Mutations, 1082, 1088, 1090, 1092, 1093

Mutator strain, 2935

Mutualistic, 338

MVA. See Mevalonate

MWF types, 2370

Mycelial networks, 1558

Mycobacteria, 1360, 1361, 1364, 1375, 1377, 1382, 1383,

3186–3191

Mycobacteriaceae, 1824, 1825, 1841

Mycobacterial lipid bodies, 3186–3191

Mycobacterial transcriptome, 3189–3190

Mycobacterium, 1167, 1168, 1549, 1550, 1865–1875,

1934, 2132, 2136, 2137, 2405, 2415, 2416, 2517,

2770, 2777

– montefiorense, 1924

– tuberculensis, 3047

– tuberculosis, 523, 528, 530, 3186, 3242, 3244,

3247–3248, 3288–3289, 3296, 3297

– vanbaalenii, 1868, 1874, 1875

Mycobacterium frederiksbergense LB501T, 1617

Mycobacterium in metal working fluids (MWF),

3306–3309

Mycobacterium sp., 1506, 1507

Mycobacterium sp. HXN-1500, 789

Mycobacterium sp. TY-6, 789, 790

Mycobacterium vaccae JOB5, 786, 792

Mycolata, 2405, 2406

Mycolic acids, 1494, 1866, 1874, 2404

Mycorrhizal symbiosis, 1559

Mycorrhizosphere, 1560

Myroides pelagius SM1, 1815, 1817

Mytilus

– eduli, 4493

– galloprovincialis, 4476, 4493

– trossulus, 4493

NNε-acetyl-β-lysine, 676NaCl, 1944–1948, 3848, 3849, 3851, 3852

N-acylated homoserine lactones (acyl-HSL), 3042

NADH, 990, 998, 1059, 1061, 1065

NADH:FMN flavin reductase, 2132

NADPH, 990

NAH7, 1536, 1537

nahAc gene, 1778

nahY. See Naphthalene transducer protein

Nakhodka oil spill, 1814, 1817

Nanocompounds, 3390

Nanoparticle-materials, 3391

Nanoparticles, 3390, 3392

Nanosorbents, 2772

Nanotechnology, 3392

Nanowires, 341

Naphthalene, 15, 18–20, 23, 926, 928–931, 938, 996,

1003, 1016, 1019–1021, 1155–1163, 1347, 1349, 1362,

1375–1377, 1382, 1536, 1537, 1548, 1549, 1716, 1719,

1720, 1774, 1775, 1777, 1778, 1842, 1845–1847,

1902–1904, 1906, 1907, 1910–1912, 2080, 2082,

2089–2091, 2095, 2298–2300, 2302, 2307, 2308, 2366,

2777, 2778, 3796

Naphthalene, anaerobic degradation, 926, 928–931

Naphthalene degraders, 4163–4164

Naphthalene dioxygenase, 1376, 1778,

1916, 2307, 2916

Naphthalene 1,2-dioxygenase, 2777, 2778

Naphthalene transducer protein (nahY), 1536, 1537

Naphthoic acid, 928, 929

2-Naphthoic acid, 1019, 1020

NAPL water interface, 1471

Na2S stock solution, 3661, 3666

Nasutitermes takasagoensis, 717, 718

Native metaproteomes, 4189

Natural attenuation, 308, 2295, 2296, 2299, 2307,

2473–2485

Natural gas, 2164

Natural oil-seep sediments, 1911

Natural organic matter, 300–302, 312

Natural polymers, 2972

Natural strain variants, 3370

Navicula, 177

NbaY, 1537

Ndo gene, 1916

Neptunomonas, 1774–1778

– naphthalene-spiked microcosms, 1770

Net photosynthesis (NP), 3656, 3664–3665

– photosynthetic zone, 3665

Neurospora crassa, 523

4678 Subject Index

Neutral lipids, 3186, 3188, 3191, 3745

– degradation, 3382

– storage, 3382

– synthesis, 538–541, 544, 3382

Newbler assembler, 4271, 4272

New lipid-accumulating bacteria, 3001

Newton’s Laws, 162

Next generation Roche/454 sequencing technique,

4270–4272

Next generation sequencing techniques, 1261, 1262,

4270–4273

N2 fixation, 1662, 1665–1667

N-Hexadecane, 1549, 1550

Nickel, 984, 985, 1000

nidAB-like oxygenase, 1167, 1174

nidA3B3-like oxygenase, 1167, 1174

Ni/Fe-S component, 362, 363

nif gene, 2502

nifH gene, 1663, 1665

NIH shift4, 992

Nile red, 3726–3727

Nitrate, 937, 938, 941, 942, 1387, 2034–2038, 2042–2044,

2754–2763

Nitrate mineral salts (NMS) medium, 3833, 3834

Nitrate-reducing bacteria, 3789

Nitrate reduction, 2034, 2036, 2042–2044, 2756–2760,

2762, 2763, 3101, 3175

Nitration, 21

Nitriles, 2774

Nitrilotriacetic acid (NTA), 3859–3861, 3863, 3864,

3866, 3867

Nitrite, 1538, 2755–2760

Nitrite inhibition, 2758, 2760

Nitrite production, 2755, 2758, 2759

Nitrobenzene, 22, 1222–1227, 1720

4-Nitrobenzoate, 1537, 1538

4-Nitrocatechol, 1537

Nitrogen, 2144, 2145, 2154, 2155, 2502, 2503,

2523–2525, 4554–4555, 4560, 4561

Nitrogen and phosphorus fertilizer, 1741

Nitrogenase, 1662–1667

Nitrogen fixation, 402, 2502

Nitrogen heterocycles, 2144, 2773

Nitrogen heterocyclic compounds, 2127

Nitrogen phosphorous detector (NPD), 4561

4-Nitrophenol, 1537

4-Nitrophenol hydroxylase, 1373

p-Nitrophenyl esters, 4582–4583

Nitrosomonas europaea, 2512

Nitrotoluene, 1720

Nitrous oxide, 3340, 3342

NMR spectroscopy, 57, 60

N5,N10-methenyl-H4MPT cyclohydrolase (MCH),

485, 490

N5,N10-methylene-H4MPT dehydrogenase

(MTD), 490

N,N,N’,N’-Tetramethylethylenediamine (TEMED), 4145,

4147, 4148, 4153, 4155

Nocardia, 1841, 2402–2405, 2407

– amarae, 2404, 2405

Nocardiaceae, 1360, 1364, 1368, 1369, 1383, 1824–1826

Nocardia sp., 1506

Nocardioidaceae, 1829–1830

Nocardioides, 2777

Nocardioides sp. CF8, 786, 790

NodF, 390

Nod factors, 390, 391

Nonantibiotic selection markers, 4252

Nonaqueous phase liquids (NAPL), 44, 1536, 2494, 2600,

2601, 2604–2606

Nonbasic compounds, 2773

Nonbasic nitrogen compounds, 2144

Non-canonical amino acids, 2941, 2942

Non-competitive substrates, 666, 667, 671

2-Nonenal, 3211

Nonexhaustive extractants, 3647

Non food grade microbial oils, 3000

Non-F420 reducing hydrogenase, 697

Non-functionalized hydrocarbons, 299

Non-heme di-iron monooxygenases, 993–995

Non-heme Fe (II) dependent halogenases, 379–381

Non-methane hydrocarbons, 114–115, 121–123

Non-methane volatile hydrocarbons, 114, 120–122

Non-methanogenic archaea, 717, 718

Non-radioactive stable isotopes, 4029

Nonreplicating cells, 3190

Nonreplicating persistence, 3189

Non ribosomal peptide synthetase (NRPS), 1508

Non-thermal enhanced oil recovery (EOR)

methods, 2746

Non-tiling arrays, 4355

Nordtest method, 3481, 3487

North Sea, 2715

No-template controls (NTCs), 3997, 3999, 4001,

4004–4006

Novosphingobium, 1694–1701, 1712

Novosphingobium pentaromativorans, 1712–1713

NOx, 2768, 2773, 2777

NSO-heterocyclic compounds, 236, 240, 241

N-tetradecane, 1549

Nuclear magnetic resonance (NMR), 3708, 3719–3721,

3726, 3733–3736

Nuclei, 3348

Nucleic acids, 28, 29, 32, 36, 38, 41

– biomarkers, 3407–3417

– extraction, 3974–3975, 4349

Nucleophile, 1083, 1084

– elbow, 1083

Nucleophiles, 16, 17, 22, 33

Nucleophilic attack, 1082, 1084

Nucleophilic substitution, 22, 32, 33, 35

Number average (Mn) and weight average (Mw), 3738

Subject Index 4679

Number of bands, 3911

Numerical analysis of banding patterns, 3912

Numerical models, 2481–2484

Nutraceuticals, 3391

Nutrient, 1558–1559

Nutrient partitioning, 3163

Nutrients, 2523–2525, 2528, 3524–3525

– bioemulsifier, 2352

– microcosms, 2352

– resource ratio theory, 2352

Nutrient transport and sodium dependency,

1277–1278

Nycodenz, 4185, 4186

Nylon, 1228

OOasis-type ecosystems, 188

Obesity, 3142–3145

Obligate hydrogenotrophs, 492

Obligately hydrocarbonoclastic bacteria (OHCB), 1266,

1267, 1282, 1283, 1507, 1756, 1757, 1761, 4086

Obligate methanotroph, 2185

Ocean-floor, 3347

Oceanic crust, 188, 189

Oceanic plates, 189–191

Oceanospirillaceae, 1775

Oceanospirillales, 2365

Oceanospirillum linum, 1727

OCT, 1145

Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine

(HMX), 1538

Octane, 1720, 2599

1-Octanol, 45

Octanolwater partition coefficient, 45

OCT plasmid of P. putida GPo1, 786

Odd chain fatty acids, 3282

O2-dependent halogenases, 379–381

Odontotermes formosanus, 717

Odorous compounds, 3204–3206, 3212

Odors, 3204–3212, 3389, 3390, 3393

– perception, 3230

OH radical, 270, 272, 274–277

Oil-derived plastics, 2977

Oil-field processes, 1942

Oil flies, 1631, 1632

Oil fly larvae, 1625–1633

Oil industry, 2997

Oil mill wastewater (OMW), 3008

Oil or petroleum hydrocarbon degradation, 1806

Oil-polluted ecosystems, 1900

Oil pollution, 244, 246–255, 1940, 1941

Oil reservoirs, 682, 685, 687, 688, 690, 2262–2269

Oil-response vessel “Arca,” 3479

Oils, 100, 102–108, 1940–1948, 2997–3001, 3098–3108

– biodegradation, 3297

– exploration, 2714–2723, 3105

– hydrocarbons, 3586–3589

– pathogenesis, 3297

– removal techniques, 3515

– sample preparation, 3486

– sampling purposes, 3482

– sands, 2169–2170

– seepages, 1924, 1927

– shales, 2162–2170

– souring, 3091

– spill evaluation, 2580

– weathering processes, 3515

– weathering protocol, 3753

Oil spills, 311, 1809, 2342, 2343, 2522, 2525, 2527

– bioremediation, 1738

– simulation

– ecological research, 3520

– removal techniques, 3515

– shore environment, 3516

Oil storage tanks, 2527

Oil tanker, 257–265, 2502

Oil-water contact, 105

Oil-water separation, 2782

Oil water transition zone, 3106, 3107

Oil wells, 3091

O-isotope, 195

Old people smell, 3211, 3212

Oleaginous bacteria, 2997, 2999

Oleaginous yeasts, 472, 476, 478, 479, 538, 1655,

3004–3005

Olefins, 13, 16, 3012, 3017

Oleiphilaceae, 1750, 1754

Oleiphilus, 783, 1749–1754

Oleiphilus messinensis, 1750–1754

Oleispira, 783, 1755–1762

– antarctica, 1756–1762

Oleochemicals, 2896, 2999, 3000

Oleo-chemistry, 2845

Oleomonas, 2415

Oleophilic, 2524–2528

Olfactory fingerprints, 3211

Oligo-based probes, 2681

Oligonucleotide

– arrays, 4354–4364

– microarray design, 4355–4356

– Signatures, 1258–1259

– usage, 1259

Oligotrophic environments, 1281–1282

Olive, 2394–2395, 2397–2398

Olivine, 217, 219, 220

Oman, 1941, 1947

Omega-3, 2851

Omega-hydroxylation, 988, 991

O-Methyltransferases, 1170

Omic approaches, 1309, 1320

O2 microsensors, 3656, 3657, 3659, 3666

Omics, 1167

4680 Subject Index

OmpA, 2517

Online monitoring, 2708

ONR 7a mineral medium, 1767

ONR 7a plates, 2694

Operational parameters, 2635

Operational taxonomic units (OTUs), 3973, 3986, 3988,

4115, 4116, 4119, 4121

Ophryoscolecidae, 701

Opportunistic pathogens, 784, 3236

Optical density, 4161

Optically-based oxygen sensors, 3620

Oral candidiosis, 3264

Oral care, 3388, 3391

Oral cavity, 695

Oral ecology, 3173

Oral malodor, 3169, 3172, 3173, 3175, 3176

Oral microbiology, 3168–3176

Oral uptake, 3148

Orbital hybridization, 6

Orcinol method, 3710–3711

Ordered-clone approach, 4266–4268

Ordered-clone/hierarchical approach, 4266–4268

Organic geochemistry, 3909

Organic matter, 115, 117–120, 657, 658

Organic pollutants, 302, 307

Organic solvents, 1094, 3958, 3962

Organofluorine, 2852, 2853

Organonitrogen compounds, 4559–4560

Organosulfur, 3204, 3206, 3208

Organosulfur compounds, 2131, 2135–2137, 2139, 3088,

3092, 4556–4558

oriT origin of conjugative transfer, 4247

Ornithine-containing lipids (OL), 389, 390, 402,

404–406

Orphan genes, 4351

Orpinomyces, 2253

Ortho-cleavage, 1299, 1302, 1303, 1307, 1308

Orthogonality, 2941, 2948

Orthogonal regulatory systems, 2669

Oscillatoria, 2341, 2344

Osedax symbionts, 1775, 1778

Osmium tetroxide solution, 3728, 3729

Osmoprotectant, 676

Osmoregulation, 1278–1280

Outer-membrane protein, 1546–1548

Outer-membrane protein A (OmpA) proteins,

3033, 3034

Outer membranes vesicles, 3200

Over-pressured formations, 191

Oxaloacetate, 3280–3283, 3285, 3288

Oxic conditions, 2345, 2346

Oxidant, 115, 119

Oxidation, 12, 13, 16, 17, 26–28, 31, 32, 35, 1027, 1028,

1032–1039

β-Oxidation, 1650, 1652

β-Oxidation pathway, 345, 959

Oxidative, 3150–3153

Oxidative mineralization, 2206

Oxidoreductase(s), 2878, 2887

3-Oxoacyl-ACP synthase I, 512

3-Oxoacyl-ACP synthase II, 512

3-Oxoadipate pathway, 1793

2’-Oxoalkylresorcinolic acid synthase (ORAS), 523, 524

2-Oxoglutarate, 3014–3016

2-Oxoglutarate dehydrogenase, 921

Oxtahydro-naphthoic acid

Oxyanion hole, 1083

Oxygen, 1841, 1844, 1847, 3614–3621

– microsensors, 3656, 3657

– profiles, 3663–3665

Oxygenase-dependent, 943

Oxygenases, 936, 938, 941, 942, 988–991, 993, 996, 1004,

1005, 1347, 1843–1845, 2846, 2848

Oxygenated volatile organic compounds, 277

Oxygen consumption rate during light (OCL), 3665

Oxygen consumption rate in the dark, 3665

Oxygen tolerance, 645

Ozone, 3340, 3342

Ozonolysis, 17

PP450, 990–994, 1004

Packaged products, 2973

Packaging applications, 2969–2973

Paenibacillus, 2770

Paenibacillus sp. A11-2, 2791

PagP, 412, 414

PAH. See Polycyclic aromatic hydrocarbons

Pair wise similarity coefficients, 3912

Palaeopasteurization, 3105

Paleoenvironment, 104

Paleosols, 281

Paleosterilization, 2166

Paleovegetation, 281

Paleovegetation change, 289

PAN. See Peroxyacetylnitrate

Pan-enzyme(s), 1424, 1426, 1427, 4572

Panesthia angustipennis, 717

Pantoea, 1943

Pantothenate, 1653, 1657

Panus tigrinus, 2781

Parabens, 3209

Paracentrotus lividus, 4493

Paracoccus, 3830, 3831, 3834, 3837

Paracoccus versutus medium, 3834

Paraffin, 12, 3486

Paraffin bacteria, 2779

Paraffin wax, 2768, 2779

Paraformaldehyde (PFA), 4095, 4096

Parallelization, 2947

Parsimony insertion tool, 3913

Particle associated pollution, 305

Subject Index 4681

Particulate associated matter, 309

Particulate matter, 298–300, 305, 306, 309, 310, 1474

Particulate methane monooxygenase (pMMO), 786, 995,

1047, 1052, 2182, 2185–2188

Particulate organic carbon (POC), 299, 309

Particulate organic matter (POM), 299

Partitioning, 298, 1448, 1470–1473, 1476

PAS domain, 1539

Passive flux meter, 3765, 3767

Patatin-like proteins, 3245, 3248, 3249, 3253, 3254

Pathogen detection in MWF, 3305–3309

Pathogenicity, 3241–3254

Pathway evolution, 1221, 1229

Pathway prediction system (PPS)

– catabolic pathway, 4182

– metabolism, 4176

– oxygenation rules, 4181

Pathways, 618, 620–623, 1515, 1516, 1522–1525, 3134,

3136, 3138

Patterns, 3907, 3911–3914

PcaK, 1538

pCAR1, 2793, 2794, 2798

pCAR3, 2794

PCBs. See Polychlorinated biphenyls

PCR. See Polymerase chain reaction

p-Cresol, 948

p-Cumate dioxygenase, 803, 804, 1376, 1377

Peat bogs, 115

Peatlands, 626–630, 2182–2187, 3347

Pedosphere, 280–290, 306

Pelagibacter ubique, 1204

Pelobacter acetylenicus, 2011

Pelotomaculum thermopropionicum, 341, 343, 344,

4322, 4324

Pentachlorophenol (PCP), 1222, 1695, 1698

Pentachlorophenol monooxygenase, 1373

Pentacyclic triterpenoids, 286

Peptide bonds, 36, 427, 428, 430, 432

Peptide fragment fingerprints (PFF), 4389

Peptide mass fingerprints (PMF), 3699, 4389

Peptides, 28, 31, 36, 301, 310

Peptidoglycan, 1596, 1597


– lipid I, 436–440

– lipid II, 436, 439–443

– monomer unit assembly, 437

Peptococcaceae, 948

PER, 307

Perchlorate, 2034–2044

Perchloroethylene (PCE), 1538–1540

Performance assessment, 2475, 2478, 2481–2484

Perfumes, 3390, 3392

Perfusion chamber system, 3565

Perhydrolysis, 2850

Pericapritermes nitobei, 717

Peridotite, 217, 219

Periodontal, 701

Periodontal disease, 3237

Periodontitis, 3168–3176

Periplaneta americana, 712, 714, 718, 721, 722

Periplasm, 1587–1591

Permafrost, 656–661, 3342, 3347

Permafrost microcosm

– applications, 3459

– installation, 3457

– measurements, 2457

– preparation, 3455–3457

– simulation experiments, 3458–3459

– undisturbed soil cores, 3455

Permafrost soils, 657–659, 661

– back freezing, 3454, 3455, 3459

– methane production, 3454

– microcosm, 3455

Permanent, 1084, 1085

Permeabilities, 192

Permeability barrier, 1546, 1547

Permian extinction, 3091

Permian–Triassic boundary (PTB), 175

Peroxidase, 2848

Peroxide, 984, 987, 988, 990, 991

Peroxidise, 1927

Peroxisomal targeting signal 1 (PTS1), 4603

Peroxyacetylnitrate (PAN), 275, 277

Persistence, 3189, 3190

Persistent organic pollutants (POPs), 1180, 1181

Personal care products, 302, 3388–3394

Perylene, 2080, 2089, 2096, 2098

Peters and Moldowan (PM) scale, 3099

Petrochemical plastics, 2968, 2969, 2977

Petrochemical production, 2878

Petrogenic contaminations, 303

Petroleum, 50–52, 54, 55, 58, 60–62, 99–108, 280,

287–288, 303, 304, 307, 309, 311, 2014–2015, 2080

– formation, 102–105

– reservoirs, 115, 118, 2715–2723, 3098–3108, 3906,

3907, 3915, 3916

– toxicity, 4492–4493, 4496

Petroleum hydrocarbons, 311

Petro-plastics, 2976

Petroporphyrin, 2781

Petrotoga, 2165, 2719

pH, 327, 331, 636, 637, 645–648

PHA. See Polyhydroxyalkanoates

Phage display, 2933

Pharmaceuticals, 302

Pharmaceuticals, agrochemicals, food additives, 1092

Pharmacokinetic, 3148

Pharmacological, 3155

Phase of kinetic limitation, 3533

Phaseolus lunatus, 91

Phase-partitioning, 4161

Phase variation, 3252

4682 Subject Index

PHB, 2972–2976

Phenanthrene, 928–930, 1003, 1377, 1536, 1549,

1550, 1558, 1559, 1774, 1775, 1777, 1778, 1800,

1902–1904, 1906–1908, 1911, 1913, 1942, 1943,

1948, 2080, 2081, 2084, 2088–2092, 2095, 2099,

2100, 2365, 2366

Phenanthrene degradation, 1783

Phenanthrene degraders, 4162, 4166, 4177

Phenanthrene dioxygenase, 1377

(Methyl)phenol (dmp), 1539

Phenol-degrading yeast, 1913, 1914

Phenol extraction, 4187, 4188

Phenol monooxygenase, 1368, 1373

Phenol red, 3835

Phenolic lipids, 404–405, 445–449, 519–524

Phenols, 17, 22, 25, 26, 31, 41, 46, 2080, 2084, 2088, 2091,

2093, 2101

– interaction with the plasma membrane, 1456

Phenotypic antibiotic resistance, 3190, 3191

Phenotypic differentiation, 3562

Phenotypic variation, 3563–3564, 3570

Phenylacetate, 1341

Phenylacetate-CoA, 1304

Phenylacetic acid pathway, 1341

Phenylacetyl-CoA oxygenase, 1368

Phenylphosphate carboxylase, 1021

Phenylpropenoids, 1302–1303

Pheromonal attraction, 3205, 3209

Pheromonic odor, 3205

pH homeostasis, 1927

pH-indicator assays, 2863

pH microsensors, 3657, 3658

pH-range, 1094

phi29

– amplification, 4259

– enzyme, 4256

Phialophora spp., 1902, 1904, 1915

PhlD, 520

Phoma, 2227, 2228

PhoP/PhoQ, 412–414

Phormidium, 2343, 2344

Phosphatase and dehydrogenase enzyme assays, 4525

Phosphate buffer, 3661, 3666, 3728, 3729

Phosphate ester, 2645

Phosphate mobilization, 2554

Phosphatidic acid (PtdOH), 397, 473, 474, 479,

533, 541

Phosphatidylcholine (PC), 400

Phosphatidylethanolamine (PE), 397, 399–400, 414, 419

Phosphatidylglycerol phosphate, 399

Phosphatidylinositol, 400, 406

Phosphoenolpiruvate:sugar phosphotransferase

system (PTS), 1135

Phosphoethanolamine (pEtN), 412–414

6-Phosphogluconate (Zwf-1), 1311, 1312

Phosphoglycolipids, 591

Phosphoinositide, 3196, 3201

Phospholipase(s), 3200, 3242–3254

Phospholipases A, 3243, 3244, 3248–3249

Phospholipases C, 3243, 3244, 3247–3248, 3251

Phospholipid, 418, 419, 423, 1598

Phospholipid:diacylglycerol acyltransferase, 534

Phospholipid fatty acids (PLFAs), 283, 1752, 1759–1761,

2163, 2189, 3505

– bioremediation sites, 4524

– environmental samples, 3747

– statistical analysis, 3748–3749

Phospholipids, 26, 29, 58, 699, 2246, 2249, 2250,

2252, 3475

4’-Phosphopantetheine, 388

Phosphorescent dyes, 3614

Phosphor screen(s), 4168, 4169

Phosphorus, 2502, 2503, 2523, 2524

Phosphorus-free membrane lipid, 402–404

Phosphotransacetylase, 360, 362

Photobioreactors, 2832, 2834–2836, 2838

Photobleached, 4046

Photographic camera (PHOTO), 3478

Photometric assays, 2860–2863, 4582–4583

Photooxidation, 305, 310, 311

Photorhabdus, 414

Photosynthesis, 2829, 2830, 3376, 3377, 3656–3657,

3659, 3663–3665

Phthalic acids, 2093, 2095

Phyla, 2213–2214

Phyllosphere, 2547–2549, 2551, 2552, 2557, 2560,

2561, 2565

Phylogenetic affiliation, 2691

Phylogenetic analysis, 1082, 3913

Phylogenetic anchor screening, 891, 2240

Phylogenetic arrays, 4040

Phylogenetic oligonucleotide arrays (POA), 2678

Phylogenomic analyses, 557

Phylogenomics, 1356–1392

Phylogeny of methanotrophs, 1955–1957

Phylogram, 1888, 1889

Phylotypes, 2208, 2210–2212, 2214

Physicochemical characteristics, 1480

Physiological adaptations, 1912

Physiological ecology, 636, 637, 650

Physiological status, 4501

Physiology of methanotrophs, 769

Phytane, 792, 2690, 2692, 2693, 3579

Phytenes, 300, 303

Phytoestrogens, 3149, 3151, 3152

Phytohormones, 3012

Phytol, 300, 958, 960, 961

Phytopathogen, 3270, 3271, 3273–3274

Phytoplankton, 3089, 3093, 3094, 4499–4507

Phytoplankton bloom, 3343

Phytoremediation, 1662, 1666, 1667, 2547, 2553,

2559–2564, 2576, 2577, 2579, 2581

Subject Index 4683

Pichia pastoris, 4602

Picoamperemeters, 3659–3662, 3666

Picric acid, 31

Piezophiles, 3870, 3872–3875, 3877–3880

Piezophilic, 3869–3880

Piezotolerant, 3870, 3873, 3877, 3878

Pigments, 4188

Pili, 1495

α-Pinene, 11, 15Pink-pigmented facultative methylotrophs, 3830

PLA. See Polylactic acids

Planctonic food web, 309

Plant, 694, 698–700, 3269–3276

Plant associated bacteria, 3358

Plant-beneficial, 3462, 3463

Plant endophytes, 1700

Plant-microbe-animal-system, 2177

Plant oils, 2273, 2896, 2898, 2900

Plant residue decomposition, 283

Plant roots, 3461–3469

Plant secondary compounds, 3162

Plaque, 3171, 3173

Plasmalogen, 419–422

Plasma membrane, 426

Plasmid DNA, 4003–4004

Plasmid-mediated horizontal transfer

– catabolic operon, 1860

Plasmids, 1220–1229, 1802, 1915, 1916,

2654–2667, 2669

Plasticizers, 302

Plastics, 302, 312, 2968–2973, 2977

Plate isolation method, 3873

Platelet-activating factor receptor, 3197, 3198

Pleurosigma, 177

Pleurotus ostreatus, 2396

PLFAs, 2189

PlsB, 391

PlsC, 391

Plume status, 2475–2477

pmoA gene, 1981, 1991, 2182, 2185–2187, 2189, 2190

Pm promoter, 1133, 1136

PmrA/PmrB, 412, 413

pmrHFIJKLM, 412

Pnematosis cystoids coli (PCC), 702

pNP-ester-based assays, 2860–2861

POC. See Particulate organic carbon

Pockets, 1084

Pockmarks, 191, 195, 196, 2715, 2722

Point dilution tracer test, 3765, 3766

Poisoning of refining and upgrading catalysts, 2768

Polar, 2163, 2169, 2324–2325

Polar and tropical regions, 4506

Polar areas, 1900, 1903

Polarity, 7, 25, 27, 32, 45, 298, 299, 309

Polarization, 3660–3662

Polaromonas, 1716, 1719, 1720, 2777

Pollutant, effects, 2314, 2325

Polluted sea ice, 1901

Polluter pays principle, 264

Pollution, 2339–2347, 2362, 2363, 2365

– air, 2080

– histories, 305

– soil, 2081

– surveillance, 3474–3475

– water, 2099

Polonator, 4261

Polychlorinated biphenyls (PCBs), 1179–1194,

1249–1252, 1388, 1538, 2576, 2579, 3398,

3401, 4462

– biofilms, 3546

– chemical analysis, 3548

– degrading organisms, 1193–1194

– microdroplets, 3546–3547

– polluted soil, 3554

– soil constituents, 3554

Polycyclic aromatic hydrocarbons (PAHs), 11, 19–20,

234, 236, 240, 285, 288, 303, 305, 311, 927–929,

1165–1175, 1248, 1505, 1549, 1550, 1558, 1559, 1694,

1695, 1774–1778, 1781–1785, 1800, 1844, 1847, 1854,

1855, 1861, 1865–1875, 1890, 2043, 2363, 2365, 2777,

3576, 3578, 3580, 4086, 4090, 4306, 4460, 4462, 4463,

4474, 4479

– accumulation histories, 288

– anaerobic degradation, 927–929

– coated plates, 3781

– degradation, 1156, 1160

– degradation genes, 1700

– degraders, 1902, 1912, 4162, 4164–4169

– degrading bacteria, 3778, 3783

– enrichment, 3781

– high molecular weight, 2080–2082, 2084, 2088,

2089, 2093–2098, 2100, 2101

– low molecular weight, 2080–2082, 2089–2093,

4089, 4091

– stock solutions, 3783

Polydimethylsiloxane (PDMS), 3584–3589

Polydispersity, 3738–3739

Polyethylene, 9, 13, 27, 3017

Polyethylene glycols, 27

Polyhydroxyalkanoates (PHAs), 386, 792, 1315, 1655,

1745, 2898–2899, 2968–2970, 2972, 2981–2991, 3376,

3377, 3726–3729, 3731–3736, 3738

– biosynthesis, 1284–1286, 2989–2990

– carbon source, 4603

– cellulose and chitin or chitosan, 2970

– characterization, 3733–3379

– composition analysis, 4606–4607

– production, 1284–1285

– S. cerevisiae, 4603–4605

– subclasses, 4602

Polyhydroxy butyric acid (PHB), 386, 792, 2898

Poly-β-hydroxyoctanoate, 792

4684 Subject Index

Polyketides, 1655, 3283, 3284

Polyketide synthase (PKS), 519–524, 2944

Polylactic acids (PLA), 2972, 2973, 2975

– polymers, 2973

Polymer(s), 2404, 2407, 2973–2977, 3376–3378

Polymerase chain reaction (PCR), 3813–3823, 4256,

4258, 4259, 4261, 4484–4486, 4526, 4555, 4558

– 3’ adenylation, 3981–3982

– archaeal 16S rRNA genes, 3976–3977

– bacterial community fingerprinting, 4118

– bacterial 16S rRNA genes, 3975–3976

– clone libraries, 4300

– ITS + partial 18S rRNA genes, 3977–3979

– phases, 3996–3997

– primers, 1214, 1215, 1217, 3813, 3815–3817

– products, 2681

– sequence-based methods, 4294–4302

Polymerase chain reaction, 2916

Polymeric biosurfactants, 3689–3691, 3701, 3702

Polymerization, 16, 31, 36, 40, 222, 223

Polymers

– derivatization, 3733


– purification, 3731

Polyomic approaches, 1170

Polyphasic approach, 1768

Polyphenols, 3151, 4188

Polyphenyls, 19

Polypropylene fibers, 1943, 3849

Polysaccharides, 28, 38, 118, 301, 310, 3220

Polysulfides, 29

Polyunsaturated fatty acids (PUFA), 2846–2848, 2853,

3004, 3006, 3160–3164

POM. See Particulate organic matter

Poor amplifications, 4048

Poorly water soluble substrate, 3922–3923

Population densities, 3525, 3526

Pore water concentrations, 3812

Pore water gradients, 209

Porins, 1546, 1548

Porous media, 1468

Porous nanocavity plates, 3563

Porphyrines, 301, 991, 992, 3222

Porphyromonas, 3172

Posphatidylcholine, 3196–3198, 3201

Posphatidylinositol-4-phosphate, 3201

Post-electrophoresis staining, 4150

Postgenomics of Methylococcus capsulatus, 1331

Posthybridization, 4045–4046

Posttreatment, 2494

Power, 640

POX genotype, 3005, 3007, 3008

(p)ppGpp, 1135

Prebiotic, 3211

Prebiotic supplements, 3176

Pre-cell, 456, 457

Preclinical validationm, 3385

Predation, 2425, 2426, 2432

Pregnancy, 3171, 3172, 3232, 3237

Prenylflavonoids, 3151, 3152

8-Prenylnaringenin, 3151, 3152

Preparation of media, 3791–3792

Preprocessing, 4046

Preservation, 309, 3647

Preservative, 3280, 3283, 3284

Pressure, 645, 649–650

– deep subsurface ecosystems, 331

– minimum free energy, 332

– ocean trench, 331

– solubility of gaseous substrates, 331

– thresholds for substrate metabolism, 331

Pressure bag method, 3873–3875

Prestige oil spill accident, 1814, 1817

Pre-treatment, 2633

Prey vector, 4415, 4416, 4418

Primary alcohols, 784, 790, 791

Primary production, 309, 4500

Primary recalcitrance, 287

Primers

– design, 4297–4299

– and probe design, 4003

– selection, 3985–3986

Primrose, 3913

Principal component analysis (PCA), 4115, 4120

Principal transport processes, 299

Printing, 4064–4066, 4069, 4070

Printing buffer, 4066, 4069, 4070

Pristane, 792, 3579

Probe coverage, 2680–2681

Probe criteria, 2680

Probe design, 2680, 2681

Probes, 3885, 3886, 3894–3896, 3899–3902

Probiotic, 3126, 3128, 3129, 3211

– supplements, 3175

Procarcinogens, 1005

Produced water, 1941, 1946, 2760, 2761

Production, 2968–2970, 2972, 2976, 2977,

3376–3378

– biofuels, 3000

Product repression, 1144, 1148

Profound database, 4425

Promicromonosporaceae, 1827, 1829

Propane, 114, 120–122, 152, 610

1,3-Propanediol, 2897, 2898

Propanethiol, 122

Propanogenic, 122

Propanolysis with HCl/PrOH, 3732–3733

Propeller(s), 245, 246, 249

Propene, 17, 120–121

Propionate, 3123, 3129, 3915

– Propionic acid, 3280, 3282, 3283

Propionate metabolism, 343–345, 349

Subject Index 4685

Propionibacteriaceae, 1829–1830

Propionibacterineae, 1824, 1829–1830

Propionibacterium, 2248, 2249, 2252, 2254

– acnes, 1104, 1109, 3215–3224

Propionic acid, 3207, 3208, 3216

Propionic aciduria, 3282, 3284, 3289

Propionobacterium, 3028, 3204, 3205, 3207

Propionyl-CoA, 3279–3289

Propylene, 121

Prospecting, 2714–2723

Protease, 3698–3700, 3702

Protein analysis, 1083

Protein BLAST-analysis, 1609, 1610, 1612

Protein crystallography, 1082

Protein emulsifiers, 2518, 3031–3035

Protein engineering, 1082, 2777, 2778, 2781,

2930, 2977

Protein families, 2920, 2923

Protein-ligand complexes, 1082

Protein microarrays, 2700, 2701

Protein–protein interactions (PPI), 4408, 4409, 4415,

4417–4420, 4425

Proteins, 28, 31, 35–38, 41, 310

– A/G purified immunoglobulin, 4065

– cell-free extract preparation, 4399

– detection, 2DE gels, 4391–4393

– determination, 3691, 3695–3696

– digestion, 3698–3699, 3702

– expression, 4351

– extraction, 4185–4191

– immunofluorescence staining, 4594

– LC-ESI-MS(/MS), 4388–4389

– MALDI-TOF-MS(/MS), 4388

– precipitation, 4189, 4191

– two-dimensional gel electrophoresis, 4388

Proteobacteria, 1682–1683, 2343, 3829–3833, 3841

Proteogenomics

– anaerobic degradation, 4390–4391

– Aromatoleum aromaticum, 4390–4391

– genomic revolution, 4387

Proteome, 1862

Proteomic analysis, 1348

Proteomics, 622–623, 1260, 1262, 4378, 4379, 4382

– databases, 1094

– gel-based, 4388

– LC-MS-based, 4389

– technologies, 4387

Protists, 2423–2432, 3885, 3887, 3893, 3894,

3899–3901

Protocatechuate(s), 800, 803, 804, 806, 810–812,

814–816, 818–822, 829, 840, 857, 858, 1339, 1341

Protocatechuate 3,4-dioxygenase, 1359, 1360

Protocatechuate 4,5-dioxygenase, 1357, 1365, 1366

Protocol for DNA sequencing, 3962

Protocol for PCR amplification, 3962

Proton, 7, 21, 23, 27, 28

Proton gradient (ΔpH), 1569

Proton transfer reaction-mass spectrometry (PTR-MS),

3598–3599

Proton-translocating ATPase, 697

Protrusion(s), 1515–1517

proU operon, 1948

Providencia rettgeri, 1626, 1629

Pseudobutyrivibrio, 2252, 2254

Pseudo-meso-1,4-diacetoxy-cyclopentene, 4583–4585

Pseudomonadaceae, 1367, 1369, 1370, 1387, 1388

Pseudomonas, 938, 941, 1298–1320, 1357, 1361, 1362,

1364, 1371–1373, 1375–1377, 1391, 1536–1539,

1662–1665, 1787–1796, 1902, 1904, 1906, 1908–1912,

1916, 1917, 2163, 2164, 2167–2170, 2345, 2548,

2549, 2551, 2553–2559, 2578, 2579, 2772, 2774,

2777, 2878, 2881, 2883–2887, 2982, 2983, 2991,

3180–3182, 3204, 3208, 3689–3690, 3692, 3701,

4572, 4574, 4576

– aducida IGTN9m, 2795

– aeruginosa, 410, 512, 784, 789, 790, 959, 1148, 1149,

1151, 1503–1506, 1508, 1549, 1788, 1793, 1794,

3038–3043, 3048, 3242, 3249, 3252–3254,

3295–3300, 4589–4591

– aeruginosa PAO1, 1619

– aeruginosa strains PAO1 and RR1, 790

– ayucida, 2774

– ayucida strain (IGTN9m), 2774

– butanovora, 786, 791, 1144–1145, 1148

– chloritidismutans AW–1T, 941

– citronellolis, 959

– fluorescens, 377, 378, 1549, 2777, 3462–3463

– fluorescens esterase, 2865

– fluorescens NRRL B-1244, 792

– lipopeptides, 3689–3690, 3692, 3701

– oleovorans, 4605–4606

– oleovorans GPo1, 786

– putida, 421, 994, 1130, 1249, 1250, 1403–1405,

1548, 1550, 1567, 1568, 1597, 1598, 1602, 1621,

1622, 2414, 2415, 2419, 3298

– putida cells, 3565, 3569, 4208, 4209, 4354,

4368–4370, 4374, 4451

– putida DOT-T1E, 1577, 1578, 1586, 1589

– putida GPo1, 786–792, 1145–1147

– putida GPo1 AlkB alkane, 784

– putida GPo1 OCT plasmid, 791

– putida Idaho, 2798

– putida KT2440, 1362, 1365, 1366, 1391, 2798,

3034, 4374

– resinovorans, 2774

– resinovorans CA10, 2148, 2150–2152, 2793

– rhamnolipids, 3038–3040

– stutzeri, 2059

Pseudomonas sp., 1503–1506, 1508

Pseudomurein, 560

Pseudonocardineae, 1824, 1830–1831

Pseudosolubilization, 1502, 1505

4686 Subject Index

Pseudoxanthomonas, 1806–1807

Psychrophiles, 3877

Psychrophilic, 658, 659, 661, 2175, 2176

Psychrophilic degraders, 4160

Psychrophilic microorganisms, 1898

Psychrophily

– antarctic, 645

– arctic, 645

– bogs, 637, 642, 645, 647

– boreal fens, 645

– Methanococciodes burtonii, 646

– Methanogenium frigidum, 646

– tundras, 645

Psychrotolerant, 673, 1800

Psychrotolerant microorganisms, 1898, 1899, 1901

Psychrotrophic, 2175

Psychrotrophic strains, 659

Psychrotrophs, 3837

PTA-1 (ATCC 29033) isolate, 1882

PtdOH. See Phosphatidic acid (PtdOH)

Puget Sound, 1774, 1778

Pull down, 4419–4422, 4424

Purge and trap, 2491

Purification

– hydrocarbon, 3928, 3929

– storage, 3928

Purple anoxygenic bacteria (PAB), 4115,

4117, 4118

Purple sulfur bacteria, 2341

pUT delivery system, 4253

Pyrene, 1167, 1168, 1170, 1171, 1173–1175, 1536,

1695, 1699, 1800, 2080, 2082, 2088, 2089,

2093–2101

– degradation, 1784

– degraders, 4164

pyrF, 4434

Pyridines, 32, 2774

Pyrite, 3092

Pyrite Deposits, 162–163

Pyrococcus, 2213

Pyrogenic emissions, 303

Pyrolysis, 60

Pyrosequencing, 2228, 2235, 2240, 2913

454-Pyrosequenicng, 4349

Pyruvate, 1650, 1652, 1656

Pyruvate dehydrogenase complex (PDH), 3284, 3285

QQiagen Repli-g kit, 4261

Q-RT-PCR, 2688–2696

QSARs

– nonpolar narcotics, 4451

– nonpolar organic compounds, 4450

QTOF-MS/MS, 3699–3703

Quality of nucleic acids, 2680

Quantification, 4074, 4080–4083

Quantitative applications, 2681

Quantitative Polymerase chain reaction (qPCR),

3674, 3677–3683, 3821, 3913, 4015, 4022,

4023, 4299

Quantitative proteomics, 4422, 4425

Quantitative Reverse-transcription PCR

(qRT-PCR), 2690, 2692, 4022

Quantum theory, 162

Quik E test, 2861

Quinoline alkyl derivatives, 2148, 2149

Quinolines, 2144–2149, 2154, 2774, 2795

Quinolone, 1846

Quinone loop, 348

o-Quinone reductases, 1170

Quinones, 2080, 2084, 2088, 2089, 2093, 2095, 2096,

2098, 2100, 2101

o-Quinones, 1170

Quorum sensing (QS) systems, 3042, 3043, 3048, 3196,

3200, 3201

RRaceway ponds, 2832–2836, 2838

RACHITT, 2797

Radiative forcing, 3340–3344, 3347

Radical reactions, 13

Radicals, 7, 12, 13, 16, 23, 32, 985, 987, 988, 990, 992, 997,

1000–1003

Radioactive label, 1988

Radioactivity, 4166, 4168, 4169

Radiocarbon analysis, 62

Radiotracer activity measurements, 3807–3812

Radiotracer MPN, 4166

Raetz pathway, 410–412

Rahnella, 2777

Raleigh fractionation, 3915

Ralstonia, 1362, 1369, 1370, 1377, 1378, 1387, 1536,

1537, 1716, 1719, 1720, 2777

– eutropha, 3007

– pickettii, 1548

Raman FISH, 4027–4036

Raman spectroscopy, 4028

RAP-PCR, 4052–4055, 4059, 4060

Rare biosphere, 2721

Rare conversion, 2852, 2853

Rare organisms, 2919

Rarobacteraceae, 1827, 1829

Rate-limiting step, 1085

Rational design, 2940, 2941, 2943

Rational protein design, 2930, 2931, 2936

Raw materials, 2845–2846, 2855

Rayleigh equation, 101, 102, 106, 107

RBCA, 4451

RB-8Tand RB-9, 1756–1759, 1762

RDX, 1538

Reactive oxygen species (ROS), 1309, 1313

Reactive transport, 2482

Subject Index 4687

Reactivity, 5, 7, 16, 25, 26, 29, 32

Reactor technology, 2634

Reagents

– required for amplification, 4047

– required for hybridizations, 4047

– required for labeling, 4047

Real-time PCR (RT-PCR), 2694, 2695

– detection, 3998–3999

– hydrocarbon-degrading bacteria, 3998

– materials, 4002

– methods, 4003–4006

– quantification, 3999–4002

– SYBR green, 4006

– two-step, 4006–4008

Rearranged dszBCA, 2797

Recalcitrance, 1843

Recalcitrant, 1346

– contaminants, 2788

– organic chemicals, 2576

Recent environmental change, 288–289

Recognition specificity, 4431

Recombinant, 1315, 1318

Recombinant amino acid synthetase, 2942

Recombinant desulfurizers, 2795

Recombinant microbial strains, 3376

Recombination, 1346, 1349–1351

Reconnaissance flights, 262, 263

Recreational marinas, 2362, 2365

Redox-conditions, 306–307, 3909

Redox potential, 2611

Redox reaction, 1031, 2475

Red Sea, 666, 670

Red shift, 4028, 4033, 4034, 4036

Reducing agents, 3802

Reducing equivalents, aerobic catabolism, 752

Reduction, 16, 23, 32, 35, 1028, 1030, 1032–1035, 1038,

1039, 3153

Reductive dechlorination biomarkers, 3408, 3415

Reductive dehalogenase (RDase), 2057–2059, 3672, 3674,

3680, 3683

Reductive dehalogenation, 2051–2052, 2055,

2057–2059

Redundancy, 1173

Reference electrode, 3662, 3663, 3667

Reference test site zeitz for the implementation of the

natural attenuation approach (RETZINA),

2612–2614

Reference wavelength, 4165

Refractive index, 4018

Refractometer, 4018, 4019, 4021, 4023

Region that defines viable cells, 4503

Regression analysis, 3679

Regulated expression, 4249, 4254

Regulation, 509–517, 1166, 1173–1175, 1609

Regulation of methane oxidation, 1972–1973

Regulation of n-alkane metabolism, 1141–1151

Regulators, 1349

Regulatory cascades, 1236

Regulatory circuits, 2799

Regulatory protein Crc, 1147

Regulatory proteins, 4329–4443

Remediation, 2488–2490, 2493–2497, 3358

Remediation efficacy, 4455–4456

Remineralized nutrients, 193

Remote analysis, 2708

Remotely operating vehicles (ROVs), 3421, 3423,

3444, 3447

Remote sensing techniques, 3473

Removal efficiency, 2579

Removal of n-alkanes, 3914

R-Enantioselectivity, 4598

Renewable energy, 2438

Renewable resources, 3376, 3377

Repeats, 1092

– global, 4317, 4319

Reporter gene, 4433, 4441

Reporter gene fusion, 4253

Representational difference analysis (RDA),

4053, 4054

Reproducibility, 3912

Required clone number, 4416

Reservoir, 100, 103–108

Reservoir-degraded petroleum, 3914, 3915

Reservoir engineering, 2735–2736

Resin-acid degraders, 1906

Resins, 2768

Resistance-nodulation-cell, 1550

Resonance stabilization, 17, 18, 22, 25, 26

Resorufin assay, 2865

Resource-ratio theory, 3353

Respiration, Respirometry, 3613–3621

Response and cleanup, 3482

Restriction endonucleases, 4117–4119

Restriction fragment length polymorphism (RFLP),

3974, 4302

– unique clones, screening, 3984

Retardation, aquifers

– inorganic contaminants, 2468–2469

– organic contaminants, 2468

Reticulitermes flavipes, 712, 715, 718, 720

Revealing step, 4066, 4068

Reverse electron transport, 340, 341, 343, 346,

348–350

Reverse methanogenesis, 674, 1017–1019, 2232–2233,

2236, 2242, 2243, 3079–3081

Reverse transcriptase, 3677, 3678

Reverse transcription, 3677, 3679, 4052, 4055,

4058–4060

Reverse transcription-PCR (RT-PCR), 3972,

3974, 3989

– amplification, 3975

– archaeal 16S rRNA, 3980

4688 Subject Index

– bacterial 16S rRNA, 3979–3980

– fungal ITS, 3980

Rhamnolipids, 1503, 1505, 1506, 1550, 2525,

3037–3048, 3298, 3299

– acid precipitation, 3708



– GC-MS, 3715

– HPLC-ELSD, 3716

– HPLC-MS, 3718

– HPLC-UV, 3716, 3720

– structure, 3706

– surfactant, 784

– TLC, 3711

Rhinoceros, 698

Rhizobia, 390, 2502

Rhizodeposition, 280

Rhizomucor miehei, 1100

Rhizoremediation, 2577–2580, 3463

Rhizosolenia, 177

Rhizosphere, 1666, 1667, 1694, 1700, 2547–2550, 2552,

2554, 2555, 2557, 2558, 2560–2562, 2565, 2576–2581,

3462–3463, 3468–3469

Rhizospheric bacteria, 2578–2580

Rhlab operon, 1505

Rhodamine B, 2863

Rhodanobacter, 1806, 1807

– lindaniclasticus, 1807

Rhodobacterales, 1708

Rhodobacter capsulatus, 365

Rhodococci, 2135, 2773

Rhodococcus sp., 612, 1346–1351, 1406, 1506–1507,

1825, 1826, 1840–1847, 1902, 1904, 1907–1912,

1915–1917, 1933–1935, 2345, 2405, 2414–2416,

2517, 2777

– erythropolis, 1549, 1550, 2770

– erythropolis IGTS8, 2131, 2132, 2135

– erythropolis IGTS8 (ATCC 53968), 2789

– erythropolis 20S-E1-c, 1619

– jostii RHA1, 1187, 1188, 1191, 1347, 1351

– opacus, 854, 855

Rhodococcus rhodochrous PNKb1, 792

Rhodococcus strains Q15 and NRRL B–16531, 790

Rhodopseudomonas palustris, 173

Rhodospirillaceae, 1943

Rhodospirillales, 1708

Rhodospirillum, 523

Rhodotorula spp., 1913, 1948

– creatinivora, 1914

Ribosomal gene sequences, 4306

Ribosomal RNA genes, 3971, 3973, 3975–3978, 3987,

3989, 4319

Ribulose monophosphate cycles, 769

Rice Cluster I (RC-I), 551, 556, 557

Rice paddies, 3342, 3344

Rice paddy fields, 115

Richness, 3911

Rieske, 2151, 2153

Rieske non-heme iron oxygenase(s), 841–843, 1183,

1190–1192, 1359, 1375–1378, 1382, 1390

Rieske nonheme oxygenases, 1844

Rieske nonheme ring-hydroxylating, 1167

Rifampicin, 3683

Ring-cleavage, 801–808, 814–819, 821–826,

828, 2082

Ring-cleavage dioxygenases, 1058, 1059, 1061–1065,

1339, 1341, 2885

Ring-hydroxylating dioxygenases, 1058–1062, 1341,

1844–1845, 2343

Ring strain, 10, 26

RISC4, 4451

Risk assessment, 2488–2491, 2493, 2497, 4460, 4463

Riverine systems, 299

Rivers, 2330–2337

R6K γori replication origin, 4246

RNA

– cells cultivation and washing, 4370

– DNase I treatment, 4370–4372

– extraction, 3671–3683, 4054–4055, 4059, 4060

– hydrolysis and cDNA cleanup, 4372

– populations, 4052

– precipitation, 4369

– preservation, 3673, 3675

– stability, 3673, 3682

RNA-binding protein, 1147

16S RNA gene sequence analysis, 3829

RNAlater, 3423

RNase, 3673, 3675–3677, 3680–3682

RNase activity, 4058

RND pumps, 1587–1591

Rnf, 362, 365

Roche/454 FLX, 4270

Root colonization, 3462, 3463, 3465, 3466

Root exudate, 3462

Root-nodule, 3347

Root proliferation, 2577, 2579, 2580

Root washes, 3465

Roseburia, 3125, 3126

Roseobacter, 1204, 1206–1209, 1336–1342, 2364

Roseobacter genomes, 1714

Rotary drilling, 3428–3431, 3435

RppA, 520, 522

16S rRNA, 1888, 1889, 2720, 2762, 3104

16S rRNA gene, 2164, 2167, 2168, 2363, 3672,

3677–3680, 4297, 4300, 4301, 4305, 4306

– amplification, 4116–4117

– archaeal, 3976–3977, 3980

– bacterial, 3975–3976, 3979

16S rRNA gene probes for methanotrophs,

3072–3073

18S rRNA genes, 2227, 2228

16S rRNA gene sequencing, 1632, 1751, 1753, 1754

Subject Index 4689

16S rRNA phylogeny, 1984, 1985

rRNA-SIP gradients, 4018–4020

rRNA-SSCP, 4024

Rrumen cluster C (RCC) group, 702

rTCA, 146, 148–150, 152

RT-PCR, 4058, 4060

RuBisCO, 1989–1991

Rubredoxin (AlkG), 1145

Rubredoxin reductase (AlkT), 787–789, 1145

Rubrobacterales, 1823

Rubrobacter radiotolerans, 1884

Rumen, 2246–2255

– biohydrogenation, 3162, 3164

– ecosystem, 694, 699, 700, 702

– fluid phase, 699

Rumenic acid (RA), 2253, 3125, 3126

Rumen methanogenesis, 3343, 3345

Rumen micro-organisms, 3162

Ruminant(s), 2810–2812, 3094

Ruminant animals, 3342, 3344

Ruminantium, 2252, 2255

Sσ32 factors, 1133σ38 factors, 1133σ70 factors, 1133Sabatier process, 221

Sabkhas, 666

sacB gene, 3963

Saccharomyces cerevisiae, 538–540, 542, 543, 2959, 2961,

3382, 4224, 4227, 4228

– fatty acids, 4606

– PHAs synthesis, 4603

– strain identification and development, 4605

– variants, 4605

Sacrificial sampling, 3909, 3910

S-Adenosyl methionine (SAM), 916, 3014

S-Adenosyl methionine (SAM)-dependent halogenases,

380–381

Safah, 1941

Safah oil field, 1941, 1947

Salganea taiwanensis, 717

Salicylate, 1156–1162, 1719

Salicylate 1-hydroxylase, 1369–1371, 1376–1378

Salicylate 5-hydroxylase, 1375–1378

Saline, 2167, 3337–3338

Saline soil, 1943, 1945–1947

Salinities, 636, 637, 647–649

Salinity, 636, 640, 645–649, 667–669, 671–674, 676, 677,

1940–1944, 1946–1948, 3104, 3107, 3848–3851, 3853,

3906, 3907, 3909

Salmonella

– enterica, 3249

– typhimurim, 1597

Salt, 1940–1942, 1944, 1946, 1948

Salt bridge, 1092

Salt crystals, 5, 1946

Salt lakes, 666

Salt marshes, 115, 118

Salt mines, 673

Salt pans, 666

Saltern, 672

Saltwater fish, 3230

Saltwater land-farm, 1941

Sample

– collection, 3908–3909

– mounting, 4075, 4082

– preparation, 4041, 4044–4045

Sampler, high pressure, 3422

Sampling, 3419–3424

Sampling at sea, analysis and interpretation of the results,

3481–3488

Sandstone, 2610, 2611

Sandwich immunoassay, 2704–2706

Sanger sequencing, 3988, 4266, 4270–4272,

4274–4275

Sanger technique, 4266–4270

Sanguibacteraceae, 1827, 1829

Santa Barbara Basin, 120

Saponification, 3910

Sarcosine, 3229, 3230

Sargasso Sea, 2913

Satellite detection, 3473, 3474

Saturated hydrocarbons, 3576, 3578

Saturated hydrocarbons, aromatic hydrocarbons, 52

Saturation mutagenesis, 1090, 1091

Satyavati, 3228

Scaffold, 4268, 4269, 4272, 4274

Scanner, 4046, 4047

Scanning electron microscopy (SEM), 3727–3728

Scarab beetles, 708, 710, 712–715, 718, 720, 724

Schizzosaccharomyces pombe, 478

Scissor probing, 4024

Screening, 2853, 2854, 2912, 2913, 2919, 2920, 2923,

2924, 2930, 2931, 2933–2936

Scum layer, 2402

Sea ice, 1940, 1945

Sea-ice community, 1902

Sealing film(s), 4166–4168

Searles Lake, 673

Sea urchins

– pluteus normal and anomalous, 4494

– spermio-and embryotoxicity test, 4493–4496

– toxicological assays, 4493

Seawater, 3524

Sebaceous follicle, 3216, 3220

Sebaceous glands, 3204, 3205

Sebocyte, 3217, 3220, 3221

Sebum, 3205, 3207, 3219, 3220

Secondary structure, 427, 429, 432

Secreted enzyme, 3271

Sedimentary basins, 115

4690 Subject Index

Sediments, 102–105, 2330–2337, 2362, 2363, 2365, 2366,

2526–2528, 3421–3423, 3524–3526

– deposits, 305, 309

– lipid analysis, 3744

– porosity, 3812

Seed germination, 2497

Seedlings, 3463–3465, 3468

Seed sequences, 2679, 2680

Seep prospecting, 2715–2721

Segniliparaceae, 1824, 1827

Segregated ballast tank (SBT), 261–262

Selected ion monitoring mass spectrometry, 3581

Selection, 2930, 2931, 2933, 2934, 2936

Selective media, 3774

Selenite-tungstate solution, 3803

Semialdehyde, 1074

S-Enantioselectivity, 4598

Sensitivity, 2681, 4069, 4070

Sensor regulators, 1236–1241, 1243

Separate genome islands, 791

Sequence assembly and gap closure, 4269, 4275

Sequence data analyses, 3985–3986

Sequence similarity, 1083, 1094

Sequencing, 1092, 4056–4059

– library construction, 4274

– 16S rRNA gene, 4556, 4559

Sequencing libraries, 4259, 4261

Sequential reactions, 2844

Sequential ultrasonic solvent extraction, 2491

Serial analysis of ribosomal sequence tags (SARST),

3987, 4143

Serial dilution, 2695

Serine Pathway, 772, 775, 777

Serovar typhimurium, 3249

Serpentine, 189

Serpentinite mud mounds, 189

Serpentinization, 196, 197, 216–227, 647, 2204,

2214–2216

Serratia marcescens, 1108

Serum bottles, 3910

Serum cholesterol, 3136

Sewage digesters, 636, 637, 642

Shafts, 245, 246, 248

Shark Bay, 675

Sheen screen method, 4161

Shelf-life, 3163

SHERLOCK microbial identification system,

3749, 4207

S-Heterocycles, 2788–2792

Shewanella spp., 3861

Shikimic acid, 26, 30

Short-chain fatty acids (SCFA), 3122–3124

Short-chain-length (SCL), 4602

Short term environmental protection, 3482–3483

Shotgun proteomics, 902

Shotgun sequencing, 4266–4270, 4272, 4274

Shrinking core desorption, 1476

Shuffling, 2932–2935

Sialidase, 3221, 3224

Siberian, 2174–2176

Side looking airborne radar (SLAR), 3473–3477, 3480

Siderophores, 1731

Signal transduction, 1280–1281, 3935

Signature-Tagged Mutagenesis (STM), 1261

Signs of Life Detector, 2706

Silage, 2892, 2900

Silicibacter

– pomeroyi, 1203, 1204, 1206, 1713, 1714

Silicibacter sp.TM1040, 1713, 1714

Silicon cells, 4340, 4341

Silicone oil, 4161, 4163, 4164

Single cell

– analysis of the microbial cell, 4109

– cultivation, 4256

– tracking, 3564, 3566

Single cell genomics, 3371

Single cell oils (SCO), 2999, 3004–3006, 3008

Single nucleotide polymorphisms (SNPs), 4301

Single-point mutation, 1088, 1093

Single strand conformation polymorphism (SSCP),

3544, 4301

– fingerprint analysis, 3548

single stranded DNA (ssDNA), 4301

Singlet oxygen, 986, 988

Sink for acetate, 3915

Sinorhizobium, 2137

SINTEF, 3488

SIReN, 1932

Site-directed mutagenesis, 1083, 1094,

4329–4443

Site for innovative research in natural attenuation

(SIReN), 2610–2613

Site-specific conditions, 1901

Sivash Lake, 675

Size-selective filtration, 2913

Skagerrak sediments, 3811

Skermania, 2405

SK2 genome, 1267–1269

Skin, 3204–3212

Skin cancer, 3210

Skin microflora, 3204, 3211

S layer, 560, 574

Slide preparation, 4044

Slow release, 2537, 2538, 4545–4550

Slow-release fertilizer, 2524, 2525

Sludge wastewater, 4193

Slug test, 3762–3764

Small-insert libraries, 4267–4269

Small molecule binding, 1318

Small subunit (SSU) rRNA genes, 4140, 4142

Smoking, 3168, 3172

SMTZ, 2194, 2198

Subject Index 4691

Snail, 1979, 1983, 1987, 1988

S1 nuclease, 4257, 4261

Soap Lake, 1945

Sodium ascorbate solution, 3791, 3792

Sodium azide, 4167

Sodium dodecyl sulphate polyacrylamine gel

electrophoresis (SDS-PAGE), 3691, 3694–3695,

3701–3703, 4401, 4420, 4423–4425

Sodium-ion translocation, 348

Sodium nitrate, 1757

Sodium sulfide solution, 3791

Software-based image analysis, 4396–4398

Sohngen, 618

Soil, 1556–1560, 2313–2325, 3623–3629, 4466–4471

– borne bacteria, 3554

– contamination, 3744

– sample preparation, 3554–3557

– samples, 4193

Soil macroaggregates, 287

Soil macrobiota and microbiota, 280

Soil pollutant removal, 2576–2578

Soil Quality Index, 2496

Solar Lake, 670, 671, 673, 674

SOLID, 2706, 2708, 4261

– concept instrument, 2708

Solid-phase microextraction (SPME), 52, 3583

– calibration, 3587–3590

– fibres, 3587

– measurement, 3584–3590

Solubility, 1502, 1510

Solubility of n-alkanes, 783

Soluble diiron oxygenases, 804–805, 1359, 1368

Soluble methane monooxygenase (sMMO), 786, 994,

1046, 1048–1049, 1971, 2185, 2186

Solvation, 1085, 1090, 1094

Solvent


– free media, 2837

– stress, 2882, 2885

– tolerance, 1462, 1586, 1591, 2882, 3957–3966

– tolerant, 2798

– tolerant bacteria, 1633

Sonication of genomic DNA, 4415

Sophorolipids, 2516



– GC-MS, 3715

– HPLC-ELSD, 3717

– HPLC-MS, 3719

– structure, 3706

– TLC, 3711, 3712

Sorbents, 2634

Sorghum bicolor, 449, 523

Sorgoleone, 449

Sorption, 1448, 1469–1470, 1473–1476

Sour, 2167, 2168

Source area, 2475–2478, 2482

Source rock(s), 100, 102–104, 107

Souring, 2754–2763

Souring control, 2754–2763

Southeastern Transbaikal soda lakes, 673

Sox, 2130, 2768

Soxhlet extraction, 2490

Sox operon, 1209

SPA tag, 4421, 4422

4S pathway, 2131–2133, 2136, 2137, 2770, 2771,

2789–2791, 2797, 4557

Spatial distribution, 305, 308

Specialisation, 2176

Specific affinity (aos), 1639–1643, 1645

– biomass, 3928

Specific biomarkers, 2702, 2705

Specific gravity, 43

Specificity, 1083, 1084, 1086, 1088, 1090–1093, 2680, 2681

Specific regulators, 1142–1144, 1151

Spectrometric assays, 2866–2870

Spectrophotometry, 3576, 3578

Spermiotoxicity test, 4495

SPG tag, 4421, 4424

Sphagnum, 2182, 2185, 2187

Spheroplasting, 4225

Sphingans, 1510

Sphingobium, 1694–1701

Sphingobium yanoikuyae, 1060

Sphingolipids, 396, 400–401, 404, 406

Sphingomonadales, 1708

Sphingomonas, 1694–1701, 1902, 1904, 1906, 1907,

1910, 1916, 2345, 2517, 2579, 2770, 2774, 2777,

2778, 3173

Sphingomonas sp., 1249, 1251, 1713

Sphingomonas sp. KA1, 2794

Sphingomonas sp. XLDN2–5, 2795

Sphingomonas yanoikuyae, 2777, 2778

Sphingomyelinase, 432, 3244, 3251

Sphingopyxis, 1394–1701, 2415

Spitsbergen, 120

Spoil heaps, 2277–2290

Sponge, 1979, 1984, 1987

Spontaneous segregation, 456, 457

Spores, 1892, 1893

Sporopollenin, 40

Sporotomaculum syntrophicum, 346

Spotted arrays, 4354, 4355

Spurr resin, 3729

Sputum, 3186, 3187, 3189–3191

Squalene, 135–139, 300, 401, 402, 960, 3909

SRB populations, 2341

Srfa operon, 1508

SrsA, 522, 523

Stability threshold, 2406

Stabilization, 309, 1091

Stabilizing spotting solutions, 2704

4692 Subject Index

Stable carbon isotopes, 308, 2026, 2027, 2029

Stable isotope probing (SIP), 2916, 3073, 3504, 3823,

3831, 3839, 3840, 4011–4024, 4142, 4190–4191, 4259,

4305–4306

– alcanivorax, 3526

– in situ, 3526

Stable isotopes, 60, 62, 144, 145

– analyses, 1978, 1986, 3606–3607

– fractionation, 2294, 2296–2299

– labeling, 4425

– probing, 2307

– ratios, 2299

Staining of bacteria, 4104, 4109–4111

Standard curves

– construction, 4003–4004

– flow cytometry, 3930

– light scatter, 3930

– theory, 3930

Standard procedure for assessing the volume,

380–381

Staphylococcus, 3204, 3205, 3208

Starch, 2897, 2900

Stationary phase, 1146, 1149

Statistical analysis, 2680–2682

Steady state, 3530, 3532, 3534, 3536, 3538, 3539

Stearic acid, 2247, 2252–2254, 3125, 3128

Steatorrhoea (faecal fat excretion), 3125, 3127

Steel bottles, 3793

Stem protein, 4432

Stenotrophomonas, 1806–1808

– maltophilia, 611, 1807–1808

Steranes, 174–175, 612, 3099, 3576, 3580, 3581

Stereochemistry, 33

Stereoisomers, 9, 10

Sterile bag water sampler, 3871, 3872

Sterivex filter cartridges, 3410–3416

Steroids, 11, 14, 17, 26, 396, 401, 402, 3134

Sterol-esterase, 3264

Sterols, 79–93, 128–130, 137, 138, 310

– fatty acids, 300

Steryl esters (SE), 472, 475, 476, 478, 538, 540–543,

4224, 4225

– synthase, 540

Stimulated oil reservoirs, 2162

Stimulation, 2634

Stimulus sensing, 3935

Storage lipids, 792, 3186

Strain T80, 1893

Stratified lakes, 3091

Strep-tag, 4421, 4422, 4424

Streptococcus, 3172, 3173, 3204

Streptomyces, 87, 89, 138, 139

– albiaxialis, 1947

– cattleya, 380

– coelicolor, 512

– griseus, 448–449, 520, 522–523

Streptomycineae, 1824, 1831

Streptosporangineae, 1824, 1831

Stress, 4341, 4343

– asymmetrical, 1459, 1460

– cellular responses, 1460

– chaotrope-induced, 1452, 1454

– hydrocarbon-induced, 1457, 1459, 1460, 1462

– matric, 1452

– osmotic, 1452

– symmetrical, 1459, 1460

Stressors

– chaotropic solutes, 1452, 1456

– hydrocarbons, 1456

– modes-of-action, 1452

Stress response, 1133

Strict anaerobes (sulfatereducers), 2167

Stromatolites, 173, 2340

Strongylocentrotus nudus, 4493

Structural analysis, 3729, 3736

Structural genes, 3838

Structural techniques, 3733–3379

Structured lipids, 2849, 2850

Structure elucidation, 57

Structure-function relationships, 1081–1094

Structures, 68–75

StyE, 1547, 1548

Styrene, 996, 998, 1216, 1547, 1548

Styrene monooxygenase(s), 1373, 1374, 2886, 2887

Suberins, 35, 39, 40, 282

Subgingival, 3171, 3173

Sublittoral-marine sediments, 115

Submerged aquifers, 191

Submersed dishes microcosm, 3546

Submersible, 3871–3872, 3874

Sub-sea oil pipeline, 3479

Substituted aromatics, 1854, 1855

Substituted PAHs, 1695

Substitution reactions, 22, 32, 33, 35

Substrate, 1082–1086, 1089–1094

– specificities, 4198–4199

– uptake rates, 4344

Substrate, 2688–2696

Substrate binding, 1086

Substrate effect, 1502

Substrate feed and product removal, 2886

Substrate-Induced Gene Expression screening (SIGEX),

3370

Substrate microarrays, 2871

Substrate promiscuity, 1589

Substrate specificities, 1083, 1084, 1086, 1090–1092,

1519, 1523, 1525

Substrate structure, 2844

Sub-surface, 2162, 2165, 2166, 2170, 2306,

3906–3909

– characterization

– geology, 3760–3762

Subject Index 4693

– groundwater flow rate and direction,

3765–3767

– permeability, 3762–3765

– microbiology, 3880

Succinates, 2217, 3120, 3121

Succinic acid, 2897

Suicide delivery vector, 4246

Sulfate, 114, 116, 118–119, 636, 637, 642–644, 648,

666–668, 670–672, 674, 675, 2204–2217

Sulfate-methane transition zone (SMTZ), 890, 3061

Sulfate reducers, 618, 621, 643, 644

Sulfate-reducing, 2365

Sulfate-reducing archaea, 3088

Sulfate-reducing bacteria (SRB), 666, 667, 672, 674, 698,

890, 891, 3173, 3657, 3789, 4117, 4118

Sulfate-reducing conditions, 308

Sulfate-reducing microorganisms, 2264

Sulfate-reducing prokaryotes, 3088–3091, 3093

Sulfate reduction, 643, 644, 667, 672, 674, 2028–2030,

2205, 2214, 2755–2757, 2761, 3080, 3081, 3090, 3091,

3093, 3101, 3789, 3796, 3797

Sulfate reduction zone, 628

Sulfate repression, 2136, 2770

Sulfide oxidation, 2205, 2757–2758

Sulfides, 3088–3092

Sulfolipids, 402, 403, 699, 2246, 2249

Sulfonamides, 29, 31

Sulfonation, 21

Sulfonic acids, 29, 31

Sulfoquinovosyl diacylglycerol, 402, 403

Sulfur, 161–162, 2130–2139, 2768–2771, 2773, 2777,

2781, 4554, 4556–4559

Sulfur chemiluminescence detector (SCD), 4558

Sulfur compounds, 3087–3094

Sulfur content, 2130, 2136

Sulfur-content in diesel, 2769

Sulfur cycle, 2215, 2216, 2343

Sulfur dioxide, 3088, 3089, 3348

Sulfur heterocyclic compounds, 2126

Sulfur-in-oil

– analysis, 4557, 4558

– analyzer, 4558

Sulfur isotope mass independent fractionation, 3060

Sulfurospirillum, 2758, 2759

Sulfur-oxidizing bacteria, 2213

Sulfur reduction, 3088

Sulfur removal activity, 2773

Sulfur repression, 2795

Sulphate reducing bacteria (SRB), 2197,

2207–2211, 2213, 2216, 2217, 2232, 2233, 2242,

2341, 2343, 2375

Sulphate reduction

– thermochemical sulphate reduction (TSR), 108

Sunken wreck, 3479

Supercritical CO2, 2854

Superoxide, 987, 988, 998, 1072

Suppression subtractive hybridization, 4052

Surface-active agents, 3047

Surface active compounds (SACs), 1292, 1295, 1496

Surface activity, 1509

Surface loop, 1093

Surface-mediated transport, 1514

Surface sea, 1909, 1910

Surface skins, 1472

Surface water, 298–307, 310

Surfactants, 783, 784, 1469, 1474, 1475, 1481,

1485–1487, 1514–1516, 2345, 2346, 2404,

2407, 3248

Surfactants biosynthesis, 2796

Surfactin, 1508, 3689–3690

Survey

– geophysical, 3420, 3421, 3424

– video, 3420

Suspended particulate matter, 299, 300

Suspended solids (SS), 4096

Swamps, 115

Sweat glands, 3389

Sweaty odors, 3206

SYBR green assays, 3996, 3999, 4001–4004

SYBR green dye, 4487

SybrGreen I/PicoGreen I, 4259

Symbiosis, 1978, 1979, 1982, 1983, 1987–1989, 1991

Symbiotic methane oxidation, 3093

Symbiotic methane oxidizers, 1978–1992

Synergism, 2345, 3525

Syn-gas by biomass gasification, 2892

Synthase, 2035

Synthetic aperture radar (SAR), 3473–3477

Synthetic biology, 1657, 2940–2942, 2944, 2945, 2948

Synthetic intermediates, 1092

Synthetic operon, 2945

Synthetic polymers, 2968, 2969

Syntrophic, 119–120, 638, 642, 647, 650

Syntrophic acetate metabolism, 341, 342

Syntrophic acetate oxidation, 3102, 3103, 3105,

3107, 3915

Syntrophic and competitive LCFA-degrading microbial

communities, 964–967, 969, 975

Syntrophic interactions, 2028

– autotrophically, 641

Syntrophic lifestyle, 350

Syntrophic metabolism, 324, 325, 331–333

Syntrophobacter fumaroxidans, 341, 343, 349

Syntrophus aciditrophicus, 341, 346–348

Syntrophus spp., 3105, 3913

Syntrophy, 338–340, 350, 3906, 3913, 3915, 3916

Syringe pump, 4020–4024

System, 619–623

Systemic disease, 3168, 3169, 3171–3172, 3174–3176

Systems biology, 1175, 2887

Systems biotechnology, 2887

SYTOX green, 4500–4506

4694 Subject Index

TT-A cloning, 3972

Tagged multi-protein complexes, 4419, 4420

Tagged mutagenesis, 1510

Taking samples

– sampling of thin oil films (Sheens), 3484–3485

– thick waterborne layers, oil globules and tar balls,

3483–3484

– use of sampling buoy from airplane, 3485

– water samples for bioassays, 3485

Tanker slops, 257–265

Tanker sludges, 257–265

TAP tag, 4421, 4422

TaqMan probes, 3999, 4002, 4005–4006

Target preparation, 4041–4044

Tar pits, 2169–2170

Taxonomic binning, 2235, 2239, 2240

Taxonomy, 1821

– of methanotrophs, 1955–1957

Taxon-specific biomaker (TSBs), 173, 179

TbuX, 1547, 1548

TCA precipitation, 4425

TCE. See Trichloroethylene

tdsABC, 2791

Technology, 3388, 3390, 3392

Technology platforms, 2887

Tectonic environment, 188

TeflonTM pad, 3484, 3485

Temperate, 2321–2322

Temperature gradient gel electrophoresis (TGGE), 4301

Temperatures, 636, 637, 644–648, 2633, 2635, 3524, 3525

– cold regions, 2355

– entropic, 328

– entropy, 328

– moderate temperatures, 2355

– tropical habitats, 2355

– variations, 4044

Tergitol, 1777, 2517

Terminal and subterminal oxidation, 785

Terminal dioxygenase, 2885

Terminal electron acceptors (TEAs), 2475, 2588,

2589, 4521

Terminal oxidation, 919–921

Terminal restriction fragment length polymorphism

(T-RFLP), 3820–3821, 3887–3892, 4113–4114

– amplicons digestion, 4117–4119

– data set, 4122

– pattern analysis, 4120–4121

– solutions and materials, 4121, 4123

– 16S rRNA gene amplification, 4116–4117

– strategy, 4115–4116

– time and troubleshooting, 4123

– T-RFs, separation and detection, 4119–4120

Terminal restriction fragments (T-RFs)

– separation and detection, 4119–4120

Terminal-RFLP (T-RFLP), 4302

Terpanes, 3576, 3579–3581

Terpenes, 86–87, 1640, 1645, 2952–2960, 2962

Terpenoid lipid, 606

Terpenoids, 300, 307, 401, 402

Terrabacter, 1854, 1855, 1859–1861

Terra Nova Bay, 1945

Terrestrial aquatic systems, 310

Terrestrial ecosystems, 309

Terrestrial mud volcanoes, 2199

Terrestrial plant lipids, 281

Tertiary carbon atom, 959, 960

Tetrachloromethane (carbon tetrachloride), 873

n-Tetradecane, 1732, 1757

Tetradecane-spiked microcosms, 1770

Tetraesters, 1507

Tetraethers, 452

Tetrahydrofolate, 3229, 3233, 3234

Tetrahydromethanopterin, 3233, 3234

Tetrahydro-2-naphthoic acid, 929

Tetrahydrosarcinapterin, 360, 362

Tetrahymanol, 135

Tetranchys urticae, 91

Tetrazolium, 4161–4164

Tetryl, 31

Thalassobacillus devorans, 1947

Thalassolituus, 783, 1765–1771

– oleivorans, 1766–1770

Thalassospira, 1943

– profundimaris, 1710

– tepidiphila, 1710, 1711

– xiamenensis, 1710

Thauera sp., 958, 959, 1716, 1719

– aromatica, 949

– aromatica K172, 1567, 1568

Thermal desorption, 3585

Thermal properties, 3738

Thermal stability, 2782

Thermoanaerobacter, 2167, 2168

Thermococcus, 2167, 2168, 2212, 2213

Thermodesulfobacterium, 2207

Thermodynamic limits, 3907, 3914, 3915

Thermodynamics, 68, 74–75, 325–331, 618–621, 3907,

3914, 3915

– aspects, 732–736

– laws, 162

Thermogenic, 120, 216, 217, 224–226

– hydrocarbons, 2716, 2718, 2721

Thermogravimetric analysis (TGA), 3726, 3738

Thermoleophilum, 1882–1885

– album, 1882, 1883, 1885

– minutum, 1883–1885

Thermomonas, 1806

Thermophile Methanothermococcus, 579

Thermophiles, 2167, 2169

Thermophilic, 682–690, 2132–2135, 2137

Thermophilic bacteria, 2779

Subject Index 4695

Thermophilic strains, 2770

Thermophily, 646, 1891–1892

Thermostability, 1090, 1091

Thermo-stable orthologs, 2798

Thermotoga, 2167, 2168, 2719

Thermotogales, 2167, 2168

Thermus/Deinococcus, 1381, 1382

Thiamine, 3790, 3792

Thin layer chromatography (TLC), 3693, 3701–3703,

3711–3714, 3720, 3721

Thioethers, 26, 28, 29

Thiol-cleavable cross-linker, 4423

Thiols, 25, 28, 29

Thiomicrospira, 1207–1209, 2758, 2759

Thiophene, 2130, 3088, 3092

Thiyl radical, 1017

Three-mode scanning, 2D DIGE gels, 4401

Threshold, 2493, 3913

Threshold levels, 3206, 3208

Tidal rhythm, 3525

Tiling arrays, 4355

Time dependent phenomena, 4343

Time efficient, 3589

Time-lapse

– imaging, 3562, 3563, 3566, 3567

– microscopy, 3568

Time lapse two photon excitation microscopy (TPEM),

1559

Time-of-flight mass spectrometry, 3580

Tin organic compounds, 311

Tissue engineering, 2968, 2973, 2975, 2976

TLR, 3314–3318, 3322

TmoX, 1547

Tn7, 3463, 3464

TNT, 2579

Tocopherols, 301

TOD pathway, 1577–1580

TodX, 1547, 1548, 1551

Toll-like receptor, 3221, 3223

TOL plasmid, 1129–1137

TOL plasmid catabolic pathway, 1580–1582

Toluene, 19, 20, 22, 31, 42, 421, 1013–1017, 1019, 1021,

1362, 1368, 1369, 1375–1377, 1388, 1461, 1462, 1536,

1538–1540, 1547, 1548, 1550, 1716, 1719, 1791–1794,

2011, 2012

– anaerobic degradation, 926, 929

– degradation pathway, 2884, 2885

– degraders, 326, 327

Toothpastes, 3388, 3389, 3393

Torrey Canyon, 245, 246

Torsional strain, 11

Total hydrocarbons, 4558, 4560

Total lipid


– separation, 3745

Total nitrogen content, 4561

Total oil degraders, 4163–4164

Total petroleum hydrocarbons (TPH), 1808

Total sulfur content, 4558

Toxicants, modes-of-action, 1452

Toxic growth substrates, 3838

Toxicity, 1459, 1546, 1550, 1566–1572, 2037, 2488, 2489,

2493, 2494, 2496, 3155, 3920, 3921, 3924, 3926, 4204,

4205, 4208–4209, 4460–4462

Toxicity of PCBs and their metabolites, 1189–1190

Toxicological, 3153, 3155

Toxic pollutants, 1346

Toxic substrates, 1843, 1847, 3923–3924

TPH carbon banding, 2490

Trace element solution, 3789, 3803

Trace metal solution, 3833, 3835

Tracer injection and recovery, 2485

Tracers, 3428, 3431, 3433–3439

Tracker dogs, 3206

Tranquillimonas alkanivorans, 1713

Transacylase reaction, 475

trans-2-butene, 121

trans-10, cis-12 CLA, 2253, 2254

Transconjugants, 1076, 4246, 4251, 4252

Transcriptional activation, 1240–1242

Transcriptional regulation, 1400

Transcriptional regulators, 1175

Transcriptional response, 1242

Transcription profiling, 2692, 2695

Transcriptome analysis techniques

– cDNA/cRNA synthesis and labeling, 4357–4359

– cluster analysis, 4361–4362

– data preprocessing, 4359–4360

– differentially expressed genes, 4360–4361

– hybridization, washing and scanning, 4359

– oligonucleotide microarray design, 4355–4356

– problem, 4363

– RNA extraction and DNA removal, 4356–4357

– sample collection, 4356

– time, 4362–4363

Transcriptomes, 1258–1260

Transcriptomic, 1309, 1312, 1313, 1317, 1320

Transcriptomic analysis, 1348, 1350

Trans-dihydrodiols, 992

Trans fatty acids, 4204, 4208

Transferase MraY

– inhibitors, 439


– UDP-MurNAc-pentapeptide, 436, 437

– undecaprenyl phosphate, 436, 437, 439, 441

Transferase MurG

– cellular location, 441

– 3D structure, 440


– UDP-N-acetylglucosamine (UDP-GlcNAc), 436,

439, 440

Transformation processes, 298, 305, 306, 308, 309

4696 Subject Index

Transform boundaries, 191

Transgenic plants, 3376

Transient protein-protein interactions, 4408, 4425

Transition metals, 116

Transition state, 1083

Translation, 3385

Translocation, 1556–1559

Transmission, 3186–3191

Transmission electron microscopy (TEM), 1982, 1983,

3729–3730

trans-11 octadecanoic acid, 2252, 2253

Transport assay

– cells growth, 4216–4218

– mixture, 4215–4216

Transport constant ( Kt), 1642–1644

Transport/export mechanism, 1517

Transport of fatty acids (FA), 1519, 1520

Transport system, 1860

Transport vector, 1556–1560

Transposase, 1347

Transposase-like, 1173

Transposition, 1348, 1349

Transposition-mediated mutagenesis, 4246

Transposome, 2795

Transposons, 1220–1229, 2659–2661, 2663, 2664,

2669, 2670

Treatment effects, 3912

Trehalose lipids (TL), 1507, 2516



– GC-MS, 3715–3716

– structure, 3706

– TLC, 3712

Trehalose mycolates, 1507

T-RFLP, 4023

Triacylglycerol lipases, 1102, 1104–1110, 3264

Triacylglycerols (TAGs), 386, 472–478, 527–535,

538–544, 792, 1559, 2828, 2830, 2832, 2837, 2845,

2849, 2850, 3186, 3187, 4224, 4225

Triacylglycerols (TAGs) synthesis, 473–475, 478,

539–541, 544, 3187

Triad, 4465–4471

Triazines, 1843, 1845, 1846

1,2,3-Tribromopropane, 875

Tricarboxylic acid (TCA) cycle, 1299, 1302, 1304, 1306,

1309, 1313

– biodegradative, 1650

– biosynthetic, 1650, 1654, 1655

– carbon flux, 1650, 1654

Trichloroethylene (TCE), 1538–1540, 2506–2510, 2512

Trichloromethane (chloroform), 873

1,2,3-Trichloropropane (TCP), 875, 1086

Trichorderma viride, 3018

Trichosporon dulcitum, 1914

Trickling bed filter, 2878

Tri-copper methane monooxygenase, 994, 995

Triethanolamine (TEA), 2645, 2647

Triglycerides, 2246, 2252, 2849, 2852, 2853, 3219

Trimethylamine, 667, 674, 3228–3230, 3233, 3234, 3237

Trimethylamine N-oxide, 3228, 3233

Trimethylaminuria, 3227–3237

Trimethylglycine, 3229–3231

Trimethylsilyl derivatives, 3697

3-Trimethylsilyl methyl ester (TMSI), 3733, 3736, 3738

2,4,6-Trinitrophenol, 31

2,4,6-Trinitrotoluene, 31

Triplet oxygen, 986, 987

Triterpenes, 129, 134–138

Triterpenoids, 11, 14 , 17

Triton X–114, 4189, 4190

Troll, 107

Trophic, 618–621, 623

Trophic links, 4015

Tropical, 2322–2323

Truly dissolved state, 3586

Trypsin, 3698–3699, 3701, 3703

Tryptic soy broth (TSB), 3861

Tryptophan, 428, 430–432

Tryptophan degradation, 801, 814, 825

TSA-Toluenesulfonate, 1227

Tsukamurella, 2405

Tsukamurellaceae, 1824, 1827

Tubercle bacilli, 3186, 3187, 3189–3191

Tuberculous sputa, 3189, 3191

Tubeworms, 194, 195, 1979, 1983–1984, 1987, 1989

Tubular reactor, 2886

Tunable intergenic regions (TIGR), 2945

Tundra, 2174–2177

Tunnels, 1084–1086, 1089, 1090, 1093, 1094

Turbidostat, 3533

Turgor pressure, 1559

Turkey, 698

Tuva, 673

Tweenase activity, 1750

Two-component regulatory systems (TCSs), 516, 1349,

1401, 1577, 1582, 1583

Two-dimensional difference gel electrophoresis

(2D DIGE), 4184

– application development, 4396

– basic principles, 4395

– caveats, 4398–4399

– cell harvesting, 4399

– 2DE gel, 4396

– electrophoretic co-separation, 4393

– equilibration and SDS PAGE, 4401

– image acquisition and analysis, 4401–4402

– image analysis, 4396–4398

– isoelectric focusing, 4400

– labeling reaction, 4393, 4394, 4399–4400

– staining, cCBB, 4402

Two-hybrid systems, concept, 4408–4419

Two-liquid phase system, 3535

Subject Index 4697

Two-phase cultivation, 3919–3926

Two phase liquid concept, 2881, 2884

Two-photon laser scanning microscopy, 4077

Two-step reverse transcription real-time PCR

– standard curve, 4007–4008

– superscript III (invitrogen), 4006–4007

Type I FAS, 387, 392

Type II FAS, 387, 388

Type III polyketide synthases, 405

Type IV secretion system, 3196, 3197, 3200

Tyramide esters, 4596–4598

Tyrosine-phenol lyase gene (TPL), 1317

UUCM. See Unresolved complex mixture (UCM)

UDP–2,3-diacylglucosamine, 411

UDP-GlcNAc, 410, 411

UDP-glucose, 413

UDP-glucuronic acid, 413

UDP-L-Ara4-Formyl-N, 413

UDP-L-Ara4N, 413

UFA, 510–516

Ultracentrifugation, 4190, 4191

UltraGAPS, 4041, 4044, 4045

Ultra low interfacial tension (IFT), 1508

Ultralow sulfur diesel, 2769

Ultramafic, 217, 219, 220, 222, 224

Ultrasonication, 2490, 2706

Ultra violet line scanners/camera (UV), 3473, 3477, 3478

Umbelliferone assay, 2863–2865

Underwater

– instruments, 3420

– technology, 3420, 3421

– vehicles, 3421, 3423

Undisturbed environments, 1503

Unfunctionalized aliphatic hydrocarbons, 303

Universal biomarkers, 2702

Universal reference tree, 3913

University of Minnesota biocatalysis/biodegradation

database (UM-BBD)

– biodegradative pathways, 4176–4177

– compounds, 4177

– diversity and metabolism, 4177–4179

– hydrocarbon functional groups, 4179

– internet resources, 4176

– metabolic reaction types, 4180

– SMILES string representation, 4178

Unresolved complex mixture (UCM), 288, 3099, 3100,

3576, 3579

Unsaturated fatty acids, 14

Unusual lipids, 2999

Upflow anaerobic sludge blanket reactor (UASBR), 2812

Upgrading, 2162, 2165, 2170

Upper mantle, 188

Upper pathway, 1130–1133

Upstream activation sequences (UAS), 1132

Uptake modes, 1506

Uptake rate, 1639, 1640

Upward fluid flow, 2715, 2718–2719

Urania, 670

Urea breath test, 3174

Urediniomycetes, 1914

Uric acid, 2503, 2623, 2624

US Environmental Protection Agency, 3595

UV detector, 4557

UV-fluorescence, 2578

UV-induced DNA damage, 1279

UV irradiation, 1907

VVaccenic acid (VA), 3125, 3126

Vaccines, 3312–3314, 3316, 3318, 3320–3323,

3325, 3384

Vaccinology, 3383–3385

Vacuolar remodeling, 3249–3250

Vagina, 695, 701

Vaginal microflora, 3232, 3237

Vaginosis, 701

Valence bond model, 6

Validation of the assembly, 4267, 4270

Valine, 3282, 3286, 3288

Van der Waals, 3633

Van der Waals interactions, 41

Vapor, 3624, 3625, 3627, 3628

Vapor pressure, 41, 44, 3788, 3796

Vascular permeability, 3251, 3253

Vector DNA preparation, 4594

Vegetable oil(s), 2393–2399, 3486

Vegetable oil methyl esters (VOME), 2272

Verrucomicrobia, 2182, 2185, 2188, 2190, 3829,

3832, 3837

Verrucomicrobiales, 3079

Vertical growth reactor, 2832, 2835–2836

Very large crude carrier (VLCC), 245, 246, 251

Very-long-chain fatty acids, 3198–3200

Viability, 4499–4507

Viability probes, 4500, 4501, 4505

Vibrio, 4204–4205

– furnissii, 611

– harveyi, 1105

Vicinal oxygen chelate superfamily, 1357, 1361

Vienna Pee Dee Belemnite, 145

Vinyl chloride (chloroethene), 876

Vinyl chloride (VC), 4510

Virulence, 3242, 3245–3253, 3260–3266, 3286–3288

Virulence factor(s), 3260–3263, 3265, 3266,

3270, 3271

Viscosin, 3689

Viscosity, 41, 43–45, 1468, 1469, 1900

Visual indicators, 3446–3447

Visualization, 4074, 4075, 4080–4082

Visual observation, 3474–3475, 3478–3480

4698 Subject Index

Vitamins, 3391, 3789

– B12 solution, 3791

– mix, 3863

– mixture, 3790, 3792

– solution, 3802, 3804, 3834

Vitreoscilla haemoglobin, 2771

VOCs. See Volatile organic compounds

Volatile hydrocarbons, 114–123, 3626

Volatile oil compounds, 3752, 3753

Volatile organic compounds (VOCs), 270–277, 3207,

3594–3599, 4455

Volatile sulfur compounds, 3168, 3169

Volatilization, 1900, 3530, 3536, 3537

Volcanically-influenced settings, 636

Voltage, 640

Volumetric oxygen consumption rates in the

photosynthetic and non-photosynthetic zone, 3665

Volumetric rate, 3663

VOME. See Vegetable oil methyl esters

WWadi Natrun, 675

Warfare agents, 1083

Warming, 618

Washing buffer, 4130–4131

Washout, 2523, 2524

Waste, 3793, 3797, 3798

Waste deposit landfills, 307

Waste MWF treatment, 2375

Waste waters, 2394–2397, 2610

Wastewater treatment, 2401–2408

Water, 1082–1084, 1086, 1090, 1091, 1093, 2330–2332,

2334, 3420–3423

– activity as a chaperone, 1453–1454

– bilge mixtures, 3480

– in the hydrophobic membrane interior,

1456, 1457

– interaction with hydrocarbons, 1457

– interaction with macromolecules, 1453

– miscible solvent, 3586, 3588, 3589

– pressure, 3870

Water accommodated fractions (WAF), 4478, 4500,

4504, 4505

Water activity, 671, 677

Water column, 2194, 2199, 2363, 2365, 2366

Waterflooding, 2165

Water phase, 298–301, 306, 311

Water saturated zone, 306

Water solubility, 1899, 1900

Water-soluble fertilizers, 2525

Water soluble fraction (WSF), 4500

Water unsaturated zone, 306

Waxes, 89–91, 2768, 2779

Wax esters (WEs), 460–470, 528, 529, 792, 2996–2997,

3186, 3187

– aerobic, 1291

– denitrification, 1291

– microaerophilic, 1292

Wax ester synthase, 3186, 3187

Wax synthase/diacylglycerol acyltransferase, 3000

Weathered petroleum hydrocarbons, 2488, 2489,

2495, 2497

Weathering, 1472, 1475, 2522

Wetland ecosystems, 626, 627, 631

Wetlands, 636, 637, 642–646, 1979, 1984–1985,

2174–2177

Wettability, 1446, 1448

Whey, 2892, 2897–2900

Whole community genome amplification (WCGA),

2680, 2681

Whole community RNA amplification, 2683

Whole genome amplification (WGA), 2227, 2233, 2235,

4042, 4256

Whole-genome shotgun (WGS), 2233, 2239,

2240, 2242

Whole-organism fingerprints, 4028

Wildcat prospecting, 2721

Wild type, 1088, 1090–1093

Window of opportunity, 3915

Winogradskyella sp. P101, 1817

Wireline system, 3431

WMO Global Atmosphere Watch, 3596

Wood-Ljungdahl pathway, 920

Wound-dressing materials, 2975

WS/DGAT, 528–532, 534

WST–1, 4162, 4164–4166

XXanthomonadaceae, 1806

Xanthomonas, 1806, 1808–1809, 2345

Xanthomonas campestris, 1809

XenA, 3958, 3964

Xenobiotic(s), 2463, 3149, 3151–3153, 3155, 3772,

3773, 3775

– compound, 1090

– metabolism, 3154, 3155

Xylella, 1806, 1809

Xylella fastidiosa, 1809

Xylene, 19, 20, 31, 1539, 1719

m-Xylene, 1547, 1548

o-Xylene, 1539

Xylene degradation pathway, 2883

Xylene degraders, 4163–4164

Xylene monooxygenase (XylMA), 994, 2883

XylN, 1547, 1548

Xylose, 2898, 2900

XylR, 4433, 4434

XylR/DmpR, 4433

XylR regulator, 1130, 1580–1582

XylS, 1130, 1133, 1134, 1136

– dimerization, 1134

– regulator, 1580–1582

Subject Index 4699

YYeosuana aromativorans GW1–1T, 1814–1816

Yarrowia lipolytica, 538, 1513–1526, 1913, 2112–2119,

3003–3009

Yeast(s), 1513–1526, 1948, 2091, 2093, 2095, 2227–2229

– cultures, 4606

– MCL-PHA synthase cloning, 4605–4606

– PHB production, 4602

– two-hybrid system, 4409

Yellow fever mosquito, 3207

Yeosuana aromativorans, 1814, 1815

Yersinia, 414

Yield

– filter radioactivity, 3929

– products, 3928, 3929

ZZebrafish

– early stages, 4485

– maintenance and egg production, 4484

Zebrafish embryo toxicity assay

– aim/principles, 4482

– biological material, 4486

– ecotoxicological effect screening, 4483–4484

– maintenance and egg production, 4484

– mRNA levels, 4486–4488

– reverse transcription and quantitative real-time

PCR, 4485

– RNA extraction, 4484–4485

– subacute concentrations, 4487–4489

– technical materials and chemical solutions,

4485–4486

– toxicity testing, 4483

Zebra mussel, 4476

Zechstein, 666

Zero-order kinetics, 3626, 3627

ZoBell, 2131

Zonix™, 3047

Zoospores, 699

Zootermopsis nevadensis, 709, 720

Zotobacter vinelandii, 520, 521

Zygomycota, 2085

Zymomonas, 138

Zymomonas mobilis, 612

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