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EXTREMOPHILIES (LIFE UNDER EXTREME ENVIRONMENTAL CONDITION) - Alkaline Environments and Biodiversity - Grant W.D.

ALKALINE ENVIRONMENTS AND BIODIVERSITY Grant W.D. University of Leicester, Leicester, UK Keywords: Alkaliphile, haloalkaliphile, soda lake, biodiversity, bacteria, archaea, productivity, phototroph, halomonad, bacillus, haloanaerobe, methanogen, element cycles Contents 1. Introduction 2. Genesis of Soda Lakes 3. Microbial Diversity 4. Conclusion Glossary Bibliography Biographical Sketch To cite this chapter Summary Stable alkaline conditions are caused by an unusual combination of climatic, geological, and topological conditions. Soda lakes represent the most stable high-pH environments on Earth and commonly have pH values above 11.5. These environments are characteristically associated with a low Mg2+, Ca2+ geology together with rates of evaporation that exceed any inflow. Such environments are found in arid and semi-arid areas of tropical or subtropical rain-shadow deserts such as in North America or in the continental interiors of Asia. Other examples are found in areas of tectonic rifting such as the East African Rift Valley. Despite apparently hostile conditions, these caustic lakes are the most productive aquatic environments in the world, with productivity rates an order of magnitude greater than the mean rate for all aquatic environments on Earth. Alkaliphilic cyanobacteria drive these systems, providing fixed carbon that is utilized by a vast range of alkaliphilic aerobic and anaerobic chemo-organotrophs, notably halomonads, bacilli and clostridia methanogens. There is also active cycling of nitrogen and sulfur in the lakes, brought about by novel alkaliphilic groups. 1. Introduction Transient alkalinity in microhabitats arising through biological activity such as ammonification or sulfate reduction is a widespread feature of heterogeneous environments such as soils. This is presumably the reason for the widespread presence of alkaliphiles in such environments that would be considered neutral or even acid on the basis of bulk pH measurements. Commercial processes such as cement manufacture, and paper and hide processes also generate alkaline conditions because of the chemistry of the components used as part of the process. However, such environments have a relatively restricted range of alkaliphilic inhabitants, usually Bacillus or related species that survive from one alkaline episode until the next by producing endospores. A far

©Encyclopedia of Life Support Systems (EOLSS)

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more diverse population of alkaliphiles is to be found where stable, naturally occurring alkaline conditions are maintained. ,There are two kinds of such environments caused by a combination of geological, geographical and climatic conditions. Highly alkaline Ca2+-dominated groundwaters are present in various geological locations around the world. This type of alkaline groundwater has been of interest because the hydrochemical characteristics mimic the conditions in cement pore water. Concrete is a major structural component and there is a need to assess any microbial or chemical activity that might compromise long-term integrity. The chemistry of such groundwater is determined by CO2-mediated weathering of the calcium and magnesium minerals olivine and pyroxene, which decompose as depicted in Figure 1, resulting in the release of OH-, which generates alkaline conditions. Mg2+ is removed by precipitation as serpentine, leaving a Ca(OH)2-dominated environment which is, in addition, highly reducing because of the release of Fe2+ and H2. There are records of pH values of >11 in these low-ionic content environments and preliminary microbiological analyses have been recorded in a few instances, although culture procedures have not been attempted under the conditions pertaining at the site. As such, the low bacterial populations are reported as being similar to that in much less extreme soil and water environments.

Figure 1. Scheme for the hydrogeological generation of alkalinity in Ca2+-dominated groundwaters

Soda lakes and soda deserts represent the other and major type of naturally occurring highly alkaline environment, often exhibiting pH values >11.5. Such environments are widely distributed, but the more extreme examples are often relatively inaccessible. Examples are known in North America, Central America, South America, Europe, Asia (notably in Siberia, Outer Mongolia, and Tibet), throughout Africa, and in Australia (Table 1). Although highly alkaline lakes are confined to specific geographic regions, more than 80% of all inland waters, by volume, are on the alkaline side of neutrality,


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exhibiting a less intense form of the chemistry seen in the more concentrated and alkaline types. Soda lakes exist throughout the geological record. One of the largest fossil soda lakes is the Green River formation in Wyoming and Utah, which is between 36 and 55 million years old. Fossil soda lakes of even greater age are implied from geological formations such as the 2.3 billion-year-old Ventersdorf formation in South Africa.


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Continent Country Location

Africa Libya Lake Fezzan Egypt Wadi Natrun Ethiopia

Lake Aranguadi, Lake Kilotes, Lake Abiata, Lake Shala, Lake Chilu, Lake Hertale, Lake Metahara

Sudan Dariba Lakes

Kenya

Lake Bogoria, Lake Nakuru, Lake Elmenteita, Lake Magadi, Lake Simbi, Crater Lake (Lake Sonachi), Lake Oloidien

Tanzania

Lake Natron, Lake Eyasi, Lake Magad, Lake Manyara, Lake Balangida, Bosotu Crater Lake, Lake Kusare, Lake Tulusia, El Kekhooito, Momela Lakes, Lake Lekandiro, Lake Reshitani, Lake Lgarya, Lake Ndutu,

Uganda

Lake Rukwa North Lake Katwe, Lake Mahenga, Lake Kikorongo, Lake Nyamunuka,

Chad

Lake Munyanyange, Lake Murumuli, Lake Nunyampaka Lake Bodu, Lake Rombou, Lake Dijikare, Lake Monboio, Lake Yoan,

Asia Siberia

Kulunda Steppe, Tanatar Lakes, Karakul, Chita, Barnaul, Slavgerod, Lake Baikal region, Lake Khatyn

Armenia Araxes Plain Lakes Turkey Lake Van, Lake Salda India Lake Looner, Lake Sambhar

China Outer Mongolia, various “nors”; Sui-Yuan, Cha-Han-Nor and Na-Lin-Nor; Heilungkiang, Hailar and Tsitsihar; Kirin, Fu-U-Hsein and Taboos-Nor; Liao-Ning, Tao-Nan Hsein; Jehol, various soda lakes; Tibet, alkaline deserts; Chahar, Lang-Chai; Shansi, U-Tsu-Hsein; Shensi, Shen-Hsia-Hsein; Kansu, Ning-Hsia-Hsein, Qinhgai Hu

Australia Lake Corangamite, Red Rock Lake, Lake Werowrap, Lake Chidnup Central America Mexico Lake Texcoco Europe Hungary

Former Yugoslavia Lake Feher Pecena Slatina


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North America Canada Manito USA Alkali Valley, Albert Lake Lenore, Soap Lake, Big Soda Lake,

Owens Lake, Borax Lake, Mono Lake, Searles Lake, Deep Springs, Rhodes Marsh, Harney Lake, Summer Lake, Surprise Valley, Pyramid Lake, Walker Lake, Union Pacific Lakes (Green River), Ragtown Soda Lakes

South America Venezuela Chile

Langunilla Valley Antofagasta

Table 1. Worldwide distribution of soda lakes and soda deserts


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2. Genesis of Soda Lakes As the name implies, these environments are characterized by the presence of large amounts of sodium carbonate (or complexes of this salt) formed by evaporative concentration under particular conditions of geology, geography, and climate. In surface and near-surface zones, weathering and biological activity produces CO2-charged surface water and thus a bicarbonate/carbonate solution is produced that leaches surrounding minerals that reflect the geology of the area. The formation of soda lakes has much in common with athalassahaline (not derived from seawater) salt lakes. The chemistry of all brine development is complex and influenced by local factors. It is clear that the absence of significant amounts of Ca2+ and Mg2+ in the surrounding topography is a key feature in the generation of alkalinity. In most environments, groundwater rapidly becomes saturated with respect to Ca2+, resulting in the precipitation of calcite (CaCO3), often in association with magnesite (MgCO3) and dolomite (MgCa(CO3)2). In situations where the concentration of Mg2+ and Ca2+ exceed that of CO3

2–, carbonate is removed from solution and the genesis of alkalinity is prevented. Thus hypersaline lakes like the Great Salt Lake are essentially neutral in pH (Figure 2). The Dead Sea is another example of an athalassohaline lake that is also Mg2+ rich, because of the dissolution of an earlier Mg2+ evaporite. Additionally, because of the precipitation of minerals such as sepiolite that generate H+ during the evaporative process, this particular hypersaline lake is on the acid side of neutrality. If the CO3

2– concentration exceeds that of Mg2+ and Ca2+, alkalinity develops as evaporative concentration progresses, as a consequence of a shift in the CO2/HCO3

–/CO3-/OH-

equilibrium.

Figure 2. Schematic representation of the genesis of saline and alkaline lakes


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Since the surrounding geology is often dominated by Na+, this ion, together with Cl–, which is ubiquitous, also concentrates, producing an alkaline soda/salt brine with pH values up to 12, a well-studied example being that of Lake Magadi in Kenya. It also follows that these brines are essentially devoid of soluble Ca2+ and Mg2+, an unusual situation for the aquatic environment. In certain soda lakes, calcium-rich groundwater seeps into the alkaline lake water, producing localized Ca2+ precipitation in the form of columns that may rise well above the surface of the lake. Mono Lake in California (Figure 3) and Lake Van in Turkey exhibit formations of these so-called “tufa” columns.

Figure 3: Tufa columns in Lake Mono, California, USA

The Great Rift Valley running through East Africa is an arid tropical zone where tectonic activity has created a series of shallow depressions. These are often closed basins with no significant outflow, where groundwater and seasonal streams flowing from the surrounding highlands form permanent standing bodies of water. Surface evaporation rates allow the dissolved minerals to concentrate into alkali basins with Na+, CO3

2–, and Cl– as the major ions, creating pH values ranging from 8.5, in the most dilute lakes, to around 12 in the most concentrated. Measurement of such high pH in the presence of large amounts of Na+ presents technical problems, so there is some doubt about exactly how alkaline the most concentrated lakes actually are. Calculation of pH based on ionic composition suggest pH 12 is probably the upper pH limit, making these lakes the most alkaline naturally occurring sites on Earth. Lake Magadi, at the lowest point in the Rift Valley, represents the final stage of maximum evaporative concentration, where there is active deposition of carbonate minerals, notably trona (NaHCO3.Na2CO3.12 H2O) which is mined on site as a source of soda ash for glass manufacture. The brines in this particular lake are saturated with respect to Na2CO3 and NaCl at pH 11.5–12.0. Although the complex geochemical and hydrological processes leading to the selective removal of ions and crystallization appear well understood, microbiological processes undoubtedly play a role that has yet


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to be fully assessed. At Lake Magadi, if it were simply a matter of precipitation, then thermonatrite (Na2CO3.H2O) or natron (Na2CO3 10 H2O), not trona, would crystallize preferentially. The microbial population presumably influences the kinetics of CO2 addition or depletion in the system, contributing to trona formation. In the East African Rift Valley, detailed limnological comparisons of soda lakes with other African lakes have been carried out over the years. Total salts vary from about 5% (mass per volume) in the northern lakes (Bogoria, Nakuru, Elmenteita, Sonachi) to saturation in parts of the Magadi/Natron basin in the south. The more dilute lakes represent earlier evolutionary stages in the genesis of a saturated soda lake. Chemical compositions of some East African soda lakes are shown in Table 2. The lakes are situated in a I line in the rift valley floor that stretches from some 200 Km north of Nairobi (the most northerly soda lake is Lake Bogoria) to Lake Magadi some 200 Km south of Nairobi, with Lakes Natron, Eyasi, and Manyara considerably further south and much less accessible in Tanzania.


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Lake Na+ K+ Ca2+ Mg2+ SiO2 PO4

3- Cl- SO42- CO3

2- pH

Elmenteita 195.7 3.6 0.07 <0.004 2.9 0.03 65.1 2.0 68.0 10.5

Nakuru 326.1 5.6 0.15 <0.004 3.3 0.15 57.5 0.5 198.3 10,5

Bogoria (north) 734.8 5.5 0.21 0.008 2.2 0.09 100.9 1.0 476.7 11.0

Bogoria (south) 795.7 6.8 0.19 0.008 2.0 0.17 115.5 1.1 516.7 11.0

Sonachi 140.4 9.0 0.05 0.008 2.1 0.04 12.4 0.8 90.0 10.0

Oloidien 8.7 1.8 0.28 0.65 1.0 0.003 4.8 0.5 <10.0 9.0

Magadi (lake

brines)

7000.0 57.0 <0.01 <0.01 14.9 1.82 3154.9 17.5 3900.0 >11.5

(lagoon

brines)

2826.1 26.1 0.03 <0.01 7.1 0.23 1123.9 12.8 1816.7 >11.5

Little Magadi 4626.1 61.1 0.02 0.03 7.5 0.31 1856.3 13.1 2433.3 >11.5

Natron 4521.7 43.7 0.04 0.03 3.1 4.21 1464.8 1.7 2666.7 >11.5

All concentrations given in mM.

Table 2. Ionic compositions of some East African soda lakes. All concentrations given in mM.


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The African Rift Valley is probably unusual in having lakes with significant, largely permanent bodies of brine, although the total salinities may vary considerably according to the seasonal weather conditions. The pH, however, remains more or less constant, regardless of season, at around 10–10.5 for the dilute lakes, rising to pH 12 at saturation point for Na2CO3 and NaCl in concentrated lakes. Detailed analyses of the soda lakes of North America are also available from a number of sources, and the lakes of the Wadi Natrun depression in Egypt have also been examined. Rather less information is available about the enormous range of soda lakes throughout Siberia, Mongolia, and Tibet. 3. Microbial Diversity

3.1. Primary Production in Soda Lakes

One of the striking facts about soda lakes is that, despite apparently inhospitable caustic conditions, these environments are extremely productive because of high ambient temperatures, high light intensities, and effectively unlimited supplies of CO2 via the HCO3

–/CO32–/CO2 equilibrium. Primary production rates in excess of 10 g cm–2 day–1,

have been recorded (the mean primary productivity of streams and lakes of the world is about 0.6 g cm–2 day–1), making these the most productive aquatic environments anywhere in the world. A characteristic feature of the majority of soda lakes is the presence of permanent or seasonal colored blooms of phototropic microorganisms. Thus, dependent on the water chemistry, the lakes are likely to be green (Figure 4) due to cyanobacteria, but may also have areas that are orange or red due to other organisms (Figure 5). Unlike other types of lakes, the microbial biomass is dominated by prokaryotes, with only rare instances where eukaryotic algae and protozoans make up a significant fraction of the population (usually in the more dilute and less alkaline examples of soda lakes).

Figure 4. Green cyanobacterial bloom in Lake Sonachi, Kenya


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In the moderately saline lakes, cyanobacteria (usually Arthrospira platensis, formerly known as Spirulina platensis) are the key primary producers, although a range of other types, particularly Cyanospira spp., have been described. Identification has almost always been on the basis of morphology, although Arthrospira platensis has been isolated from Lake Magadi. A variety of other types have been reported, based on microscopic observation, notably unicellular types which may be Chroococcus spp., which may contribute major blooms in some of the less saline soda lakes. There is also a report of a small unicellular eukaryotic alga that may be a Chlorella sp., which can be microscopically confused with cyanobacteria. However, there is no doubt that Arthrospira platensis dominates the primary production in most of the East African lakes (although probably not in other geographical locations where the lake chemistry is different). A. platensis not only supports large numbers of chemo-organotrophic bacteria (at least 106 cfu mL–1 can be recovered from most of the lakes) but is also the food source for the vast flocks (> 106 individuals) of the Lesser Flamingo (Phoeniconaias minor) that graze on these lakes. The sieve-feeding mechanism employed by these birds is perfectly suited to the harvesting of these large cyanobacteria. There is probably also a significant contribution to primary productivity by anaerobic anoxygenic phototropic bacteria, since the East African lakes are often low in oxygen content due to the activity of the large numbers of aerobic chemo-organotrophic bacteria. Anoxygenic phototrophs that have been isolated include Ectothiorhodospira, Halorhodospira, Rhodobacter a, Roseinatronobacter, Alkalispirillum, and Heliorestis spp.

3.2. Chemo-Organotrophs in Soda Lakes

Early studies on the cultivable population of soda lakes concentrated on aerobic chemo-organotrophic bacteria (a commonly used medium contains ing glucose, peptone and yeast extract as nutrient sources, made alkaline with Na2CO3 and with varying amounts of NaCl dependent on the salinity of the source material), and many isolates have been obtained on a variety of similar media. An examination of the many strains brought into laboratory culture reveals a remarkable diversity of prokaryotes, where alkaliphiles are represented in most of the major taxonomic groups. Since the early attempts at cultivation that concentrated almost exclusively on aerobic chemo-organotrophs, there have been increasing numbers of attempts to look at other groups, including phototrophs, lithotrophs, spirochetes, and a range of different anaerobes. This has permitted the identification of most of the major tropic groups responsible for the cycling of carbon, sulfur, and nitrogen in the lakes, using the obvious parallels with better characterized aquatic systems. Many of the strains isolated in pure culture can be assigned to existing groups as new species or genera, but some isolates have no particularly close relationship with known microbes and appear to be separate lines of evolutionary descent perhaps peculiar to the soda lake environment. However, to date, there is no distinct and exclusive soda lake taxon at the hierarchical level of the major prokaryote lines of descent (e.g., comparable to the proteobacteria or the cyanobacteria), rather, the existing soda lake isolates are clearly assignable to existing groups, albeit often within new generic groupings. In common with other environments, direct DNA extraction of soda lake samples, followed by amplification and sequence analysis of prokaryote 16s rRNA genes, reveals novel taxa yet to be brought into culture. Table 3 lists examples of taxonomic groups containing prokaryotes isolated from highly alkaline environments, with soda lake isolates (the majority) highlighted in bold.


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Table 3. Prokaryotes growing under alkaline conditions Groups known to be present Strains and species (EU)BACTERIA

Arthrospira platensis,a Cyanospira rippkae,a Synechocystis sp.,a Synechococcus sp.,a Phormidium sp.a

Cyanobacteria

Gram-positive (high G+C) Corynebacteria Bogoriella caseilyticus,a

Dietzia natronolimnaeaa

Micrococci/Nesterenkonia Lake Bogoria isolate 69B4a

Lake Nakuru isolate 11AG8aStreptomyces/Nocardiopsis Gram-positive (low G+C) Bacillus agaradhaerens,a Bacillus clarkii,a Bacillus cohnii,a Bacillus alcalophilus, Bacillus halmapalus, Bacillus halodurans, Bacillus pseudalcalophilus,a Bacillus horikoshii,a Bacillus gibbonsii,a Bacillus haloalkaliphilusa Bacillus hortii,a Bacillus vedderi,a Bacillus haloalkaliphilus Alkalibacterium olivoapovliticus, Anoxybacillus pushchinensis, Clostridium paradoxum, Clostridium thermoalcaliphilum, Anaerobranca gottschalkii,a Tindallia magadiensis,a Natronincola histidinovoransa

Bacillus/Clostridium

Natroniella acetigena,a Halonatronum saccharophilum,a Thermosyntropha lypolyticum, Anaerobranca horikoshiia

Haloanaerobes

Exiguobacterium aurantiacum Others

Heliorestis durensis,a Heliorestis baculata,a Heliospira dauricaa

Heliobacteria

Proteobacteria Thioakalimicrobium sibericum,a Thioalkalimicrobium aerophilum,a Thioalcalivibrio versutus,aThioalcalivibrio nitratus,a Thioalcalivibrio denitrificans,a Thioalkalimicrobium cyclum,a Thioalkalivibrio jannaschiia

Sulfur oxidizers

Nitrobacter alkalicusaNitrifiers Sulfate-reducing bacteria Desulfonatronovibrio


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hydrogenovorans,a Desulfonatronum lacustrea

Ectothiorhodospira mobilis,a Halorhodospira halophila,a Thiorhodospira siberica,a Roseinatronobacter thiooxidans,a Rhodobacter bogoriensis,a Alkalispirillum mobile,a Ectothiorhodospira vacuolata,a Ectothiorhodospira halochloris,a Ectothiorhodospira haloalkaliphilusa

Anoxygenic phototrophs

Halomonas magadii,a Halomonas campisalis,a Halomonas desiderata, Halomonas pantelleriense, Lake Bogoria isolatesa 25B1, WB2, etc, Lake Elmeteita isolatesa 44E3, WE5, etc., Lake Magadii isolate 27M1,a Lake Sonachi isolatesa 12C1, 75C4, etc.

Halomonads

Methylobacter alcaliphilus,a Methylomicrobium sp. AMO1a

Methylotrophs

Enterics/Vibrios/Aeromonads Lake Nakuru isolate 20N1,a etc.,a

Lake Elmenteita isolates 1E1,a etc.a

Lake Elmenteita isolates 45E3,a 97NT4a

Pseudomonads/Stentrophomonas

Spirochaeta alkalica,a Spirochaeta asiatica,a Spirochaeta africanaa

Spirochaetes

“Thermopallium natronophilum”aThermotogales ARCHAEA Halorubrum vacuolatum,a Natrialba magadii,a Natronobacterium gregoryi,a Natronomonas pharaonis,a Natronococcus occultus,a Natronococcus amylolyticus,a Natronorubrum bangensea

Halobacteria

Thermococcus alcaliphilus, Thermococcus fumicolans

Thermophiles

Methanolobus oregonensis,a Methanosalsus zhilinaeae,a Methanobacterium subterraneum, Methanobacteriun alcaliphiluma

Methanogens

aindicates a soda lake isolate It is possible to make some predictions as to the roles played by different organisms in the utilization and recycling of products of photosynthesis. Especially abundant in Kenya soda lakes are aerobic Gram-negative bacteria of the Proteobacteria lineage,


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including large numbers of types affiliated to the Halomonadaceae family (the halomonads) of moderately halophilic bacteria found in a range of terrestrial and marine saline environments. Other halomonads growing under alkaline conditions have been found in environments such as olive processing wastewater and alkaline soils. These organisms constitute probably the single most important Gram-negative group in the soda lake environment, although other proteobacteria related to pseudomonads and enterics can also be isolated. Aerobic Gram-positive isolates are found in both the high G+C and low G+C division of the Gram-positive lineage. Especially abundant are low G+C bacteria associated with the diverse Bacillus spectrum. Some of these are related to known Bacillus groups, but others form a distinct group of alkaliphilic bacilli. The dominance of Bacillus types may be due to those having dormant stages that survive drying in marginal areas around the lakes. There are, however, novel streptomycetes, species of Dietzia, Bogoriella and uncharacterized relatives of Nesterenkonia amongst the high G+C isolates. A quite different population of aerobic prokaryotes is present in the concentrated extremely hypersaline lakes such as Lake Magadi. Here, the basis of the primary production is unclear. It is possible that during rare periods of heavy rain, Arthrospira spp. are able to grow, although these are not usually a feature of hypersaline sites where the total dissolved salts exceed 20% (mass per volume). Extremely halophilic anoxygenic phototrophic bacteria of the Halorhodospira group may have a significant part to play under certain circumstances. What is not in doubt, is that hypersaline alkaline brines are dominated by bright red blooms of haloalkaliphilic archaea (Figure 5).

Figure 5. Red pigmentation due to haloalkaliphilic archaea natronobacteria on Trona crusts at Lake Magadi, Kenya

These brines provide the most extreme environment with pH values of around 12 and are relatively high in organic content, presumably due to evaporative concentration. Originally assigned to two genera, Natronobacterium and Natronococcus, these organisms turn out to have just as much diversity as their counterparts in pH-neutral


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hypersaline environments and there are currently six genera, Natronococcus, Natronobacterium, Natrialba, Halorubrum, Natronorubrum, and Natronomonas that harbor haloalkaliphilic representatives living in these environments. The only other aerobes to have been cultivated from these environments are haloalkaliphile Bacillus spp., which are distinct in having a minimum requirement of at least 15% (mass per volume) NaCl for growth. As might be expected from the nutrient-rich environments that they inhabit, the majority of the soda lake isolates are biochemically reactive with an arsenal of extracellular hydrolytic enzymes including proteinases, cellulases, xylanases, and lipases. Two different cellulases from Gram-positive soda lake isolates are currently marketed for use in laundry and textile processes. Hydrolysis products of complex polymers form the substrates for not only the aerobic organotrophs, but also for chemo-organotrophic alkaliphilic anaerobes. Viable counts performed under anaerobic conditions on anoxic soda lake sediments indicate >106 cfu mL–1 (see glossary for definition of “cfu”). Members of the Haloanaerobiales are found in such sites, with organisms such as Natrionella, Tindallia, and Natronoincola spp. carrying out acetogenesis and ammonification at high pH. Thermophilic acetogens are also known, such as Thermosyntropha lipolytica found in the hot spring areas that commonly surround the soda lakes. Other alkaliphilic thermophiles that are probably thermotogas have also been described in these springs, which range in temperature from around 50 °C to boiling, depending on location. Saccharolytic types include spirochetes, which have been isolated from soda lakes on two continents and clostridial types that are probably similar to the organisms Clostridium paradoxum and C. thermoalcaliphilum isolated from alkaline, non-soda lake habitats, plus distinct taxa related to the Haloanaerobiales and other clostridial groups in the low G+C division of the Gram-positive bacteria. Enrichments of soda lake material with cellulose as substrate followed by analyses of the end products of some of these anaerobes indicate the production of isobutyric acid, acetic acid, and hydrogen, that, in turn, is consumed by anoxygenic phototrophs, acetogenic bacteria, and sulfate-reducing bacteria.

3.3. Methanogenesis in Soda Lakes

There is no doubt that methanogenesis occurs in soda lakes. Methanogenic archaea isolated to date are mainly methylotrophic, utilizing a variety of one carbon (C1) compounds including methanol and methylamine. C1 compounds are likely to be abundant in soda lakes, probably being derived from the anaerobic digestion of cyanobacterial mats. These particular methanogens have been assigned to the genus Methanosalsus m and Methanolobus. There are, in addition, hydrogen-utilizing methanogens currently described as Methanobacterium spp. which These, however, are probably alkalitolerant rather than alkaliphilic. Methane-oxidizing bacteria that require aerobic or microaerophilic conditions consume methane in soda lakes. These have been assigned to the genus Methylobacter and there are others that are probably Methylomicrobium spp. Thus methanotrophy provides for the return of methane carbon into the common pool of organic matter.


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3.4. Sulfur in Soda Lakes

A typical process in soda lakes is sulfidogenesis. Most soda lakes show black sediments, although the high pH prohibits the release of H2S, retaining sulfide as odor-free sulfide anion (S2–). Rates of sulfate reduction comparable to those in marine sediments have been measured. Isolation of alkaliphilic sulfate-reducing bacteria (aSRBs) has proven to be somewhat difficult in the past, but towards the end of the twentieth century, a number of successful isolations were made, the organisms being named Desulfonatronovibrio hydrogenovorans and Desulfonatronum lacustre. Both organisms utilize hydrogen as an electron donor and probably have a significant role to play as play as hydrogen sinks in the soda lake community. In this respect, H2 consumption by these bacteria is 3–4 orders of magnitude more significant than hydrogen-utilizing methanogens. Cocultures of these aSRBs with saccharolytic hydrogen-producing anaerobes demonstrate significantly improved rates of carbon utilization, indicating their important role in interspecies hydrogen transfer. Oxidation of reduced sulfur is brought about under anaerobic conditions by sulfur phototrophs such as Halorhodospira spp. and Thiorhodospira spp. Growing mainly under aerobic conditions, the newly isolated lithotrophic sulfide oxidizers in the genera Thioalkalimicrobium and Thioalkalivibrio have been discovered in the less saline and alkaline Lake Mono and in Kenyan and Siberian soda lakes. There is also a hydrogen and sulfide oxidizing isolate, Natronohydrogenobacter thiooxidans.

3.5. Nitrogen in Soda Lakes

There is undoubtedly an active nitrogen cycle in soda lakes. Whereas Arthrospira platensis appears to be unable to fix molecular nitrogen, there is no doubt that heterocystous cyanobacteria (heterocysts are specialized cells that are the sites of nitrogen fixation in many filamentous cyanobacteria), such as Cyanospira rippkae, are active in this respect. The phototrophic bacteria present in soda lakes also have nitrogen-fixing capacity and it is probable that some of the aerobic and anaerobic chemo-organotrophs also contribute fixed ing nitrogen to the ecosystem. Several strains of lithotrophic and alkaliphilic ammonia and nitrite oxidizers are known from Siberian and Kenyan soda lakes. Enrichments from Siberian soda lakes exhibit rapid ammonia oxidation despite the fact that at alkaline pH ammonia tends to be lost from the system by volatilization. As of this writing (2002), the only ammonia-oxidizing strains in culture are also methane oxidizers. Nitrate reduction and denitrification occur widely, carried out by both lithotrophic bacteria like Thioalkalivibrio denitrificans and the widely distibuted chemo-organotrophic halomonads. 4. Conclusion In summary, despite the apparently inhospitable conditions imposed by high alkalinity (and sometimes high salinity), soda lakes contain alkaliphilic representatives of most of the main evolutionary and trophic groups of bacteria and archaea, including cyanobacteria, haloanaerobes, spirochetes, high and low G+C Gram positives, proteobacteria, thermotogas, halophilic, and methanogenic archaea, with concomitant


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active carbon, nitrogen, and sulfur cycling under aerobic and anaerobic conditions. Trophic relations in the alkaliphilic community are depicted in Figure 6. The full extent of soda lake microbial diversity and structure and the roles played by individual organisms has yet to be wholly revealed; doubtless as yet unrepresented phylogenetic groups will eventually prove to have soda lake members and perhaps the elusive, exclusively soda lake group will emerge in the future.

Figure 6. Trophic relationships in the soda lake ecosystem

Glossary Acetogenic bacteria: Prokaryotes that generate acetic acid as a result of carbon

metabolism. Alkaliphile: Organism with pH optima for growth greater than 8; usually

those with optima between pH 9 and 10 are defined as alkaliphiles. Obligate alkaliphiles are incapable of growth when pH values are near neutral, i.e., near 7.

Anaerobe: Organism that grows in the absence of oxygen. Anoxygenic phototroph:

Prokaryotes that carry out photosynthesis but do not produce oxygen.

Archaea (singular form, archaeon) :

A distinct line of prokaryotes which differ from the more common bacteria in genetic makeup; these prokaryotes are characteristically found in extreme environments (e.g., high temperature or high salinity sites).

Cfu (colony-forming units) :

Microorganisms that can be grown on solid media and thus counted.


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Chemo-organotroph: Prokaryotes that obtain energy and carbon from preformed carbon compounds.

Cyanobacteria: Prokaryotes that carry out oxygen-producing photosynthesis similar to that exhibited by higher plants.

Eukaryotic algae: Algae that have a cell structure similar to that in higher organisms, i.e., have a membrane-bounded nucleus.

Evaporite: Residue of salts left behind when brines evaporate to dryness.

G+C: Refers to the guanosine and cytosine content of microorganism’s DNA.

Haloalkaliphile: Organism that requires both alkaline conditions and high concentration of salt (NaCl) for growth.

Haloanaerobe: Particular bacterial lineage containing organisms that are anaerobes and that require high concentrations of salt (NaCl) for growth.

Lithotroph: Organism that obtains energy from inorganic compounds. Methanogens: Particular archaea that produce methane as a result of carbon

metabolism. Methanotrophy: The capacity to utilize methane as a carbon and energy

source. Natronobacterium: Haloalkaliphilic archaeon found in soda lakes saturated with

both Na2CO3 and NaCl. Prokaryotes: Unicellular organisms, typified by bacteria, which do not

have a membrane-bounded nucleus. Proteobacteria: Diverse bacterial lineage that includes many physiological

groups, all with a particular type of cell wall (Gram-negative).

Sulfidogenesis: Production of hydrogen sulfide (H2S). Soda: Sodium carbonate (Na2CO3). Tectonic activity: The movement of Earth’s crustal plates, which creates

volcanic activity. Bibliography Bryantseva I., Gorlenko V.M., Kompantseva E.I., Imhoff J.F., Suling J., and Mityushina L. (1999). Thiorhodospira sibirica gen. nov., sp. nov., a new alkaliphilic purple sulfur bacterium from a Siberian soda lake. International Journal of Systematic Microbiology 49, 697–703. [This item includes a good bibliography of anoxygenic phototrophs from soda lakes.] Dubinin A.V., Gerasimenko L.M., and Zavarzin G.A. (1995). Ecophysiology and species diversity of cyanobacteria from Lake Magadi. Microbiology 64, 717–721. [This is the only real ecology paper devoted to cyanobacteria in soda lakes.] Duckworth A.W., Grant W.D., Jones B.E., and Steenbergen van R. (1996). Phylogenetic diversity of soda lake alkaliphiles. Federation of European Microbiology Societies (FEMS) Microbiology Ecology 19, 181–191. [This is the most detailed paper to date on aerobic heterotrophs cultured from soda lakes.] Grant W.D., Mwatha W.E., and Jones B.E. (1990). Alkaliphiles: ecology, diversity and applications. FEMS Microbiology Reviews 75, 255–270. [This article provides a general review of alkaliphiles and their habitats, biotechnology, and biodiversity.]


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Grant S., Grant W.D., Jones B.E., Kato C., and Li L. (1999). Novel archaeal phylotypes from an East African alkaline saltern. Extremophiles 3, 139–145. [This is the first paper on non-cultivable populations in soda lakes detected by molecular methods.] Gorlenko V.M., Namsaraev B.B., Kulyrova A.V., Zavarzina D.G., and Zhilina T.N. (1999). The activity of sulfate-reducing bacteria in bottom sediments of soda lakes of the Southeastern Transbaikal region. Microbiology 68, 580–580. [This discussion of the sulfur cycle is useful.] Imhoff J.F., Sahl H.G., Soliman G.S.H., and Trűper H.G. (1979). The Wadi Natrun chemical composition and microbial mass developments in alkaline brines of eutrophic desert lakes. Geomicrobiology Journal 1, 219–234. [This is a good general description of the Wadi Natrun soda lake ecosystem.] Jones B.E., Grant W.D., Collins N.C., and Mwatha W.C. (1994). Alkaliphiles: diversity and identification. Bacterial Diversity and Systematics (eds. F.G. Priest, A. Ramos-Cormenzana, and B.J. Tindall), pp. 195–230. New York: Plenum Press. [This is a good general review of alkaliphiles and their habitats, biotechnology, and biodiversity, with concentration on soda lakes, including some data on populations in relation to physical/chemical measurements and seasons.] Jones B.E., Grant W.D., Duckworth A.W., and Owenson G.G. (1998). Microbial diversity of soda lakes. Extremophiles 2, 191–200. [A general review of soda lake microbial ecology with some detail of anaerobes.] Kalyuzhnaya M.G., Khmeleninaa V.N., Suzina N.E., Lysenko A.M., and Trotsenko Yu A. (1999). New methanotrophic isolates from soda lakes of the Southern Transbaikal region. Microbiology 68, 592–600. [This article provides details of methane oxidation in soda lakes.] Khmelenina V.N., Eshinimaev B.T., Kalyuzhnaya M.G., and Trotsenko Y.A. (2000). Potential activity of methane and ammonium oxidation by methanotrophic communities from the soda lakes of Southern Transbaikal. Microbiology 68, 460–465. [This article provides details on nitrification and the nitrogen cycle.] Namsaraev B.B., Zhilina T.N., Kulyrova A.V., and Gorlenko V.M. (1999). Bacterial methanogenesis in soda lakes of the Southeastern Transbaikal region. Microbiology 68, 586–591. [This article provides details of methanogenesis in soda lakes.] Sorokin D.Y., Jones B.E., and Kuenen, J.G. (2000). An obligate methylotrophic, methane-oxidizing Methylomicrobium species from a highly alkaline environment. Extremophiles 4, 145–155. [This article provides more details of methane oxidation and the organisms.] Sorokin D.Y., Kuenen J.G., and Jetten M.S.M. (2001). Denitrification at extremely high pH values by the alkaliphilic, obligately chemolithoautotrophic, sulfur-oxidising bacterium Thioalkalivibrio denitrificans strain ALJD. Archives of Microbiology 175, 94–101. [This article focuses on denitrification and the nitrogen cycle.] Sorokin D.Y., Lysenko A.M., Mityushina L.L., Tourova T.P., Jones B.E., Rainey F.A., Robertson L.A., and Kuenen G.J. (2001). Thioalkalimicrobium aerophilum gen. nov., sp nov and Thioalkalimicrobium sibericum sp nov., and Thioalkalivibrio versutus gen. nov., Thioalkalivibrio nitratis sp nov and Thioalkalivibrio denitrificans sp nov., novel obligately alkaliphilic and obligately chemolithoautotrophic sulfur-oxidizing bacteria from soda lakes. International Journal of Systematic and Evolutionary Microbiology 51, 565–580. [This is the first account of lithotrophic sulfur oxidation in soda lakes and the identification of the organisms.] Tourova T.P., Garnova E.S., and Zhilina T.N. (1999). Phylogenetic diversity of alkaliphilic saccharolytic bacteria isolated from soda lakes. Microbiology 68, 615–622. [This article is an analysis of the anaerobic heterotrophs in soda lakes.]


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Zavarzin G.A. (1993). Epicontinental soda lakes as probable relict biotopes of terrestrial biota formation. Microbiology 62, 473–479. [This is an interesting philosophical paper that proposes that abundant soda lakes in the past were significant sites for the evolution of microbes.] Zavarzin G.A., Zhilina T.N., and Kevbrin V.V. (1999). The alkaliphilic microbial community and its functional diversity. Microbiology 68, 503–521. [This is a good general account of microbial interrelationships in soda lakes.] Zhilina T.N. and Zavarzin G.A. (1994). Alkaliphilic anaerobic community at pH-10. Current Microbiology 29, 109–112. [This article is a specific account of anaerobes and their interactions in soda lakes.] Biographical Sketch Bill Grant is Professor of Environmental Microbiology at the University of Leicester, UK. He obtained his BSc and PhD in Microbiology from the University of Edinburgh, UK, and had a spell at the McArdle Laboratory for Cancer Research in Madison, Wisconsin, USA working on the cell cycle in slime molds. Since coming back to Leicester in the UK in the early 1970s he has developed a long-standing interest in microbial biodiversity in East African soda lakes and has repeatedly visited these sites since his first expedition in 1978. Other interests include the systematics of the haloarchaea (the halobacteria), originally driven by the discovery of a new group of these in an East African soda lake. He also has an interest in astrobiology, in particular, the detection of microbial signatures in ancient evaporite deposits as terrestrial analogues of extraterrestrial sites on Mars and other planets of the solar system. To cite this chapter Grant W.D., (2006), ALKALINE ENVIRONMENTS AND BIODIVERSITY, in Extremophilies, [Eds. Charles Gerday, and Nicolas Glansdorff], in Encyclopedia of Life Support Systems (EOLSS), Developed under the Auspices of the UNESCO, Eolss Publishers, Oxford ,UK, [http://www.eolss.net]


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