Microbial diversity surveys and species richness

In general, the microbial biodiversity of soda lakes is relatively poorly studied. Many studies have focused on the primary producers, namely the photosynthesizing cyanobacteria or eukaryotic algae (see Carbon cycle). As studies have traditionally relied on microscopy, identification has been hindered by the fact that many soda lakes harbour poorly studied species, unique to these relatively unusual habitats and in many cases thought to be endemic, i.e. existing only in one lake.^[5] The morphology (appearance) of algae and other organisms may also vary from lake to lake, depending on local conditions, making their identification more difficult, which has probably led to several instances of taxonomic confusions in the scientific literature.

Recently, a number of studies have used molecular methods such as DNA fingerprinting or sequencing to study the diversity of organisms in soda lakes.^{[5][6][7][8][9]} These methods are based on DNA extracted directly from the environment and thus do not require microorganisms to be cultured. This is a major advantage, as culturing of novel microorganisms is a laborious technique known to seriously bias the outcome of diversity studies, since only about one in a hundred organisms can be cultured using standard techniques.^[10] For microorganisms, the phylogenetic marker gene small subunit (SSU) ribosomal RNA is typically targeted, due to its good properties such as existence in all cellular organisms and ability to be used as a "molecular clock" to trace the evolutionary history of an organism.^[11] For instance, 16S ribosomal RNA gene clone libraries revealed that the bacterial community of the lake with the highest salinity was characterized by a higher recent accelerated diversification than the community of a freshwater lake, whereas the phylogenetic diversity in the hypersaline lake was lower than that in a freshwater lake.^[12] Culture-independent surveys have revealed that the diversity of microorganisms in soda lakes is very high, with species richness (number of species present) of individual lakes often rivaling that of freshwater ecosystems.^[12]

Biogeography and uniqueness

In addition to their rich biodiversity, soda lakes often harbour many unique species, adapted to alkalic conditions and unable to live in environments with neutral pH. These are called alkaliphiles. Organisms also adapted to high salinity are called haloalkaliphiles. Culture-independent genetic surveys have shown that soda lakes contain an unusually high amount of alkaliphilic microorganisms with low genetic similarity to known species.^[6][7][8][9] This indicates a long evolutionary history of adaptation to these habitats with few new species from other environments becoming adapted over time.

In-depth genetic surveys also show an unusually low overlap in the microbial community present, between soda lakes with slightly different conditions such as pH and salinity.^[3][8] This trend is especially strong in the bottom layer (hypolimnion) of stratified lakes,^[5] probably because of the isolated character of such environments. Diversity data from soda lakes suggest the existence of many endemic microbial species, unique to individual lakes.^[3][8] This is a controversial finding, since conventional wisdom in microbial ecology dictates that most microbial species are cosmopolitan and dispersed globally, thanks to their enormous population sizes, a famous hypothesis first formulated by Lourens Baas Becking in 1934 ("Everything is everywhere, but the environment selects").^[13]

Carbon cycle

Photosynthesis provides the primary energy source for life in soda lakes and this process dominates the activity at the surface. The most important photosynthesizers are typically cyanobacteria, but in many less "extreme" soda lakes, eukaryotes such as green algae (Chlorophyta) can also dominate. Major genera of cyanobacteria typically found in soda lakes include Arhtrospira (formerly Spirulina) (notably A. platensis), Anabaenopsis,^[14] Cyanospira, Synechococcus or Chroococcus.^[15] In more saline soda lakes, haloalkaliphilic archaea such as Halobacteria and bacteria such as Halorhodospira dominate photosynthesis. However, it is not clear whether this is an autotrophic process or if these require organic carbon from cyanobacterial blooms, occurring during periods of heavy rainfall that dilute the surface waters.^[1]

Below the surface, anoxygenic photosynthesizers using other substances than carbon dioxide for photosynthesis also contribute to primary production in many soda lakes. These include purple sulfur bacteria such as Ectothiorhodospiraceae and purple non-sulfur bacteria such as Rhodobacteraceae (for example the species Rhodobaca bogoriensis isolated from Lake Bogoria^[16]).

The photosynthesizing bacteria provide a food source for a vast diversity of aerobic and anaerobic organotrophic microorganisms from phyla including Pseudomonadota, Bacteroidota, Spirochaetota, Bacillota, Thermotogota, Deinococcota, Planctomycetota, Actinomycetota, Gemmatimonadota, and more.^[1][3] The stepwise anaerobic fermentation of organic compounds originating from the primary producers, results in one-carbon (C1) compounds such as methanol and methylamine.

At the bottom of lakes (in the sediment or hypolimnion, methanogens use these compounds to derive energy, by producing methane, a procedure known as methanogenesis. A diversity of methanogens including the archaeal genera Methanocalculus, Methanolobus, Methanosaeta, Methanosalsus and Methanoculleus have been found in soda lake sediments.^[1][17] When the resulting methane reaches the aerobic water of a soda lake, it can be consumed by methane-oxidizing bacteria such as Methylobacter or Methylomicrobium.^[1]

Sulfur cycle

Sulfur-reducing bacteria are common in anoxic layers of soda lakes. These reduce sulfate and organic sulfur from dead cells into sulfide (S²⁻). Anoxic layers of soda lakes are therefore often rich in sulfide. As opposed to neutral lakes, the high pH prohibits the release of hydrogen sulfide (H₂S) in gas form. Genera of alkaliphilic sulfur-reducers found in soda lakes include Desulfonatronovibrio and Desulfonatronum.^[1] These also play important an ecological role besides in the cycling of sulfur, as they also consume hydrogen, resulting from the fermentation of organic matter.

Sulfur-oxidating bacteria instead derive their energy from oxidation of the sulfide reaching the oxygenated layers of soda lakes. Some of these are photosynthetic sulfur phototrophs, which means that they also require light to derive energy. Examples of alkaliphilic sulfur-oxidizing bacteria are the genera Thioalkalivibrio, Thiorhodospira, Thioalkalimicrobium and Natronhydrogenobacter.^[1]

Nitrogen and other nutrients

Nitrogen is a limiting nutrient for growth in many soda lakes, making the internal nitrogen cycle very important for their ecological functioning.^[18] One possible source of bio-available nitrogen is diazotrophic cyanobacteria, which can fix nitrogen from the atmosphere during photosynthesis. However, many of the dominant cyanobacteria found in soda lakes such as Arthrospira are probably not able to fix nitrogen.^[1] Ammonia, a nitrogen-containing waste product from degradation of dead cells, can be lost from soda lakes through volatilization because of the high pH. This can hinder nitrification, in which ammonia is "recycled" to the bio-available form nitrate. However, ammonia oxidation seems to be efficiently carried out in soda lakes in either case, probably by ammonia-oxidizing bacteria as well as Thaumarchaea.^[18]