soil microorganisms lecture 3 sep 13th today: 1.discussion questions 2.reading assignments from last...
TRANSCRIPT
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Soil Microorganisms Lecture 3 Sep 13th
TODAY:
1. Discussion Questions2. Reading Assignments from last week
1. Smith et al. (Eutrophication) – will discuss beginning of N lecture (9-26)2. Condron et al. 98-108 – will discuss beginning of metabolism lecture (9-19)
3. Lecture
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OutlineA. Bacterial Morphology
1. Cell Structure2. Cell Motility3. Cell Wall Structures
a. Odd Soil and Water Bacteria
B. Intro to Bacterial Growth
C. Intro to Bacterial Genetics1. Central Dogma2. Gene Exchange
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New Course Schedule
9/12 Intro to Bacteria and Viruses – Structure and Genetics9/19 Bacterial Diversity, Metabolism, and Viruses9/26 Bacterial-mediated Nitrogen Cycling10/03 Exam 110/10 Bacterial-mediated Sulfur and Phosphorus Cycling Plant-Bacteria Interactions10/17 Methods of Assessment of Soil Bacteria10/24 Soil Fungi – Diversity, Function, and Competition10/31 Mycorrhizae and N Fixation11/7 Exam 211/14 Soil Microfauna11/21 Soil Mesofauna11/28 Soil Macrofauna12/5 Frontiers of Research in Soil Biology12/14 Final Exam
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I. Bacteria & Archaea
• Prokaryotic• Lack organelles• No true nucleus
• Unicellular
• Range in size from 0.1 um to > um• Why would it be disadvantageous for bacteria to be large?
• Most abundant “living” organisms in soil
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Prokaryotes: The unseen majority
~108 – 1010 bacteria g-1 soil
1019 grains of sand in the world1023 stars in the observable universe1027 bacteria in tropical rain forest soils1030 bacteria on earth
biomass exceeds that of all plants and animals
1013 cells in human body1014 bacterial cells on and in the human body
Can persist for eons8 million yr old bacteria revived from Antarctic ice
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Bacterial Morphology
spirilla bacilli (rods)
filamentous
cocci(spheres)
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Pili “Walking”
Polar flagella motility
Bacterial Morphology
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Gliding
• Slime layer capsule• Polysaccharide layer• Antibiotics, dessication, chemical attack
• Endospore• Long-term survival• Dormant state• Nutrient deficiency
Slime Layer Capsule
Bacterial Morphology
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Gram + and Gram -
• Two main sub-groups of bacteria• Based on differences in the structure of the ________
Bacterial Morphology
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Bacteria vs. Archaea
Archaea
EukaryotaBacteria
Bacterial Morphology
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Beggiatoa (genus)
2H2S + O2 → 2S + 2H2O
• Oxidize Hydrogen Sulfide to S• Store S intracellular (golden granules)
• Visible with naked eye• Marine sediments
• Move up and down for optimum balance• Single cells or in filaments
Strange Bacteria
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Pseudomonas fluorescens
• 1 um short rods
• Siderophore producing
Strange Bacteria
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Strange Bacteria
• Actinobacteria (phylum)• Used to be classified as a fungus, Actinomycetes• Some form branching filaments• Geosmin
• Petrichor -
Oldest living thing on Earth? 500,000 yo Nocardia – Lignin and Gingival Pockets
Frankia – N2 Fixing Bacteria
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Strange Bacteria
• Burkholderia (genus)• ~35 species• Cystic Fibrosis • Chloroorganic pesticides
• PCB
• Agricultural• Biocontrol Agents• PGP
• Biowarfare Agents
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Strange Bacteria
• Deinococcus radiodurans• Soil bacteria• Toughest bacteria on Earth• Radiation, acid, dehydration, vacuum
• 5 gy kills human, 800 gy kill E. coli, 5000 kills radiodurans• Conan the bacterium
Tetrads, 4 cells sticking together
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II. Bacterial Growth
"The mathematics of uncontrolled growth are frightening. A single cell of the bacterium E. coli would, under ideal circumstances, divide every twenty minutes. That is not particularly disturbing until you think about it, but the fact is that bacteria multiply geometrically: one becomes two, two become four, four become eight, and so on. In this way it can be shown that in a single day, one cell of E. coli could produce a super-colony equal in size and weight to the entire planet Earth."
Michael Crichton (1969) The Andromeda Strain, Dell, N.Y. p247
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Is he correct?
272 = 4.7*1021
10-12 g/cell= 4.72* 106 kg
Mass of Earth = 5.98*1024 kg
Would actually take about 40 hours
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• Factors affecting growth are:•1. •2.•3.
• Limiting nutrient:
CLASSIC GROWTH CURVE
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Killham and Prosser, 2007
Copiotrophy (r-strategists) vs. oligotrophy (K-strategists)
umax A
umax B
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umax A
½ umax A
Ks
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umax B
½ umax B
Ks AKs B
Higher Ks:
Lower KS:
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Bacterial Evolution – NichingEveryone Competes
• 12 identical populations of E. Coli over 23 years• 50,000 generations• After 20,000 grew 70% faster than parent strain• 120 mutations were fixed in the populations• Some could not repair DNA any more• Some could use citrate under aerobic conditions
• Never seen in the wild
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• Bacterial Crosstalk• “Please pass the sugar”• Rhizobia inoculation
• Quorom Sensing• Is everyone ready?
• Putting relatives first• Bacterial “suicide
bombers”
Everyone Competes……But Will Also Cooperate
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C. Intro to Bacterial Genetics
1. Central Dogma2. Gene Exchange3. Examples in Soil
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The ability to extract DNA (deoxyribonucleic acids (DNA) and ribonucleic acids (RNA) from cells within soils have given us great new insights into soil microbial communities
TA
G C
CENTRAL DOGMA
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CENTRAL DOGMA
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Ribonucleic Acid – Secondary Structure
CENTRAL DOGMA
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The Ribosome
CENTRAL DOGMA
• Translates mRNA (gene transcript)• mRNA Protein
• Consists of protein and RNA• Active sites are conserved
• Genes encoding protein and RNA are conserved
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Replication
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Transcription
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Translation
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16S rRNA gene
16S rRNA
• Acts as scaffold for ribosomal proteins
• Conserved and hypervariable regions
• Basis of bacterial taxonomy
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2. Gene Exchange
• Plasmid
• Extrachromosomal circular genetic structure that can reproduce autonomously but is not essential
• Generally 1-10% the size of the chromosome• Provides genetic diversity and enables bacteria to rapidly adapt to a wide range of ecological niches
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• Some plasmid – encoded functions
• Antibiotic and toxin resistance• Enzymes for xenobiotic degradation• N2 fixation genes
• Transfer Method #1: Conjugation• Requires cell to cell contact, usually plasmid mediated• Most important mechanism• Uses pili• Does not have to be closely related• Does not involve the chromosome
2. Gene Exchange
SOUND
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2. Gene Exchange
• Transfer Method #2: Transduction• Bacteriophage infection• Transfer by delivery of viral DNA• Sometimes species or strain specific due to attachment sites
• Phage attached to pili• Bacteria change their pili
• May become adsorbed to soil
SOUND
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• Transfer Method #2: Transduction
• Lytic Phage: Inserted phage DNA is copied by cell machinery• Many copies are made• Phage components assemble themselves• Cell wall bursts and phage replicates are released
• Lysogenic Phage: Integration of phage DNA into host chromosome
• Replicated as part of chromosome• ~10% of human genome is ancient viruses• May enter lytic cycle
• Sometimes mistakes are made in copying viral DNA• Portion of host DNA integrated into viral DNA• Transfer of genes among hosts via viral infection
2. Gene Exchange
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• Transfer Method #3: Transformation
• Uptake of naked extracellular DNA – closely related species• Incorporation into the genome• Originated as a way to obtain nutrients• Extracellular DNA can be stabilized onto soil• Least important of three genetic exchange mechanisms
2. Gene Exchange