Application of ribulose-1,5-bisphosphate carboxylase/oxygenase genes as molecular markers for assessment of the diversity of autotrophic microbial communities inhabiting the upper sediment horizons of the saline and soda lakes of the Kulunda Steppe

The genes encoding the key metabolic reactions are often used as functional markers for phylogenetic analysis and microbial ecology studies. The composition and structure of the genes encoding ribulose-1,5-bisphosphate carboxylase (RuBisCO) of various photoautotrophic bacteria, representatives of the order Chromatiales, including collection strains and the strains isolated from saline and soda lakes, were studied in detail. The green-like form I RuBisCO was detected in the majority of the studied strains. In some strains, the genes encoding both form I and form II RuBisCO were present, which has not been previously known for the representatives of this group of bacteria. Moreover, RuBisCO genes were used as functional markers to investigate the autotrophic microbial community inhabiting the upper horizons of bottom sediments of two saline soda lakes and two hypersaline neutral lakes of the Kulunda Steppe. In general, the diversity of autotrophic bacteria in the studied sediment horizons was low. In soda lakes, haloalkaliphilic cyanobacteria and sulfuroxidizing bacteria (SOB) of the genus Halorhodospira were predominant. In saline lakes, halophilic chemoautotrophic SOB Halothiobacillus and Thioalkalivibrio were found, as well as photoautotrophic bacteria of the genus Ectothiorhodosinus and cyanobacteria. Many phylotypes remained unidentified, which indicates the presence of groups of microorganisms with an unknown type of metabolism.     

Bacteria--chlorophyll relationships in Ethiopian lakes of varying salinity: are soda lakes different?

Some soda lakes in East Africa are extreme with respect to theirhigh abundance of bac teria and phytoplankton. We used regressionanalysis of 52 samples from 18 lakes in Ethiopia to demonstratethat soda lakes conform to a different relationship betweenbacterial abundance and phytoplankton biomass. The exponentof the power function relating bacteria and chlorophyll is muchsteeper for saline lakes, although still less than one. Thismay reflect that bacteria in eutrophic soda lakes are more substratelimited, and less controlled by graxers.     

Carboanhydrase activity in halophilic anaerobes from soda lakes

The activity and cellular localization of carboanhydrase (CA) in two alkaliphilic anaerobes growing in soda lakes at pH 9-10 was studied. CA activity in the cell extracts of the acetogenic bacterium Natroniella acetigena was comparable to that of the neutrophilic acetogens. Hydrogenotrophically grown cells of Desulfonatronum lacustre exhibited higher CA activity compared to the cells grown on media with formate. High CA activity in the cytoplasmic fraction and the absence of high activity in the extracellular fraction were demonstrated. We propose that the cytoplasmic CA in alkaliphilic sulfate-reducers participates in conversion of bicarbonate to CO2, which is reduced in the cell to acetate via the acetyl-CoA pathway.     

The structure of phototrophic communities of soda lakes of the southeastern Transbaikal region

The structure of benthic phototrophic communities of 24 soda lakes of the southeastern Transbaikal Region was studied. The physicochemical properties of the lakes were determined. The results of the cell count of anoxygenic phototrophic bacteria (APB) belonging to various groups are presented. The influence of salinity on the structure of APB communities was investigated. The APB reaction to environmental conditions was determined. Massive development of phototrophic microorganisms in the form of mats and films was observed in the majority of the investigated lakes. The APB communities were characterized by a wide diversity of species and evenness of species composition. Purple sulfur bacteria of the families Ectothiorhodospiraceae and Chromatiaceae were predominant. Purple nonsulfur bacteria of the family Rhodobacteraceae, green filamentous bacteria Oscillochloris sp., and heliobacteria were also detected. According to preliminary data, no less than 15 species of APB occur in the studied lakes. Among them, three novel genera and four species have already been described. Identification of other isolates is still in progress. The lakes make an almost continuous series of fresh, brackish, and saline water bodies, varying in their degree of mineralization. It was demonstrated that the structure of APB communities was unaffected by salinity ranging from 5 to 40 g/l. At salt concentrations of lower than 5 g/l, the level of water mineralization became a limiting factor. Experiments with the isolated cultures showed that the APB were obligately dependent on the presence of carbonate ions in the medium. They were haloalkalitolerant or haloalkaliphilic. Thus, they are well adapted to the conditions of soda lakes with a high mineralization. It was demonstrated that soda lakes of the southeastern Transbaikal Region represent a special type of habitat which harbors a peculiar autochthonous microflora and differs from both highly mineralized soda lakes and shallow saline water bodies of the sea origin.     

Microbiology of Lonar Lake and other soda lakes

Soda lakes are saline and alkaline ecosystems that are believed to have existed throughout the geological record of Earth. They are widely distributed across the globe, but are highly abundant in terrestrial biomes such as deserts and steppes and in geologically interesting regions such as the East African Rift valley. The unusual geochemistry of these lakes supports the growth of an impressive array of microorganisms that are of ecological and economic importance. Haloalkaliphilic Bacteria and Archaea belonging to all major trophic groups have been described from many soda lakes, including lakes with exceptionally high levels of heavy metals. Lonar Lake is a soda lake that is centered at an unusual meteorite impact structure in the Deccan basalts in India and its key physicochemical and microbiological characteristics are highlighted in this article. The occurrence of diverse functional groups of microbes, such as methanogens, methanotrophs, phototrophs, denitrifiers, sulfur oxidizers, sulfate reducers and syntrophs in soda lakes, suggests that these habitats harbor complex microbial food webs that (a) interconnect various biological cycles via redox coupling and (b) impact on the production and consumption of greenhouse gases. Soda lake microorganisms harbor several biotechnologically relevant enzymes and biomolecules (for example, cellulases, amylases, ectoine) and there is the need to augment bioprospecting efforts in soda lake environments with new integrated approaches. Importantly, some saline and alkaline lake ecosystems around the world need to be protected from anthropogenic pressures that threaten their long-term existence.     

Carbonic anhydrase activity in halophilic anaerobes from soda lakes

The activity and cellular localization of carbonic anhydrase (CA) in two alkaliphilic anaerobes growing in soda lakes at pH 9–10 were studied. CA activity in the cell extracts of the acetogenic bacterium Natroniella acetigena was comparable to that of neutrophilic acetogens. Hydrogenotrophically grown cells of Desulfonatronum lacustre exhibited higher CA activity compared to the cells grown on medium with formate. High CA activity in the cytoplasmic fraction and the absence of high activity in the extracellular fraction were demonstrated. We propose that the cytoplasmic CA in alkaliphilic sulfate-reducers participates in conversion of bicarbonate to CO₂, which is reduced in the cell to acetate via the acetyl-CoA pathway.     

Growth physiology and competitive interaction of obligately chemolithoautotrophic,haloalkaliphilic, sulfur-oxidizing bacteria from soda lakes

Two different groups of haloalkaliphilic, obligately autotrophic, sulfur-oxidizing bacteria belonging to the genera Thioalkalimicrobium and Thioalkalivibrio have recently been discovered in highly alkaline and saline soda lakes. To understand response to their extreme environment and different occurrence in soda lakes, the growth kinetics and competitive behavior of several representatives have been characterized in detail using batch and pH-controlled continuous cultivation. The bacteria belong to the true alkaliphiles, growing within the pH range 7.5-10.6 with maximum growth rate and maximum growth yield at pH 9.5-10. On the basis of their response to salt content, three groups can be identified. All the Thioalkalimicrobium strains and some of the Thioalkalivibrio strains belonged to the moderate halophiles. Some of the Thioalkalivibrio strains from hypersaline soda lakes were extremely salt-tolerant and capable of growth in saturated soda brines. The Thioalkalimicrobium strains demonstrated relatively high specific growth rates, low growth yield, high maintenance, and extremely high rates of thiosulfate and sulfide oxidation. In contrast, the Thioalkalivibrio strains, in general, were slow-growing, high-yield organisms with lower maintenance and much lower rates of oxidation of sulfide and thiosulfate. Moreover, the latter survived starvation much better than Thioalkalimicrobium. Different growth characteristics and salt resistance appear to determine the outcome of the enrichment cultures from different soda lakes: Thioalkalimicrobium dominated in the enrichments with freshly obtained samples from diluted soda lakes at low-medium salinity, while Thioalkalivibrio was the predominant organism in enrichments from aged samples and at hypersaline conditions. In mixed thiosulfate-limited chemostat cultures at low salinity, Thioalkalimicrobium strains (mu(max)=0.33 h(-1)) out-competed Thioalkalivibrio strains (mu(max)=0.15 h(-1)) at D>0.02 h(-1). The overall results suggest that Thioalkalimicrobium and Thioalkalivibrio represent two different ecological strategies.     

Alkaline soda Lake Velika Rusanda (Serbia): the first insight into diatom diversity of this extreme saline lake

Alkaline soda lakes are unique habitats found in specific geographic regions, usually with dry climate. The Carpathian Basin is one of those regions very important for habitat and biodiversity conservation in Europe, with natural soda lakes found in Austria, Hungary and Serbia. In comparison to other two countries from Central Europe, algal biodiversity studies of saline soda lakes in Serbia are scarce. Lake Velika Rusanda has the highest measured salinity of all saline lakes in the Carpathian Basin and there were no reports of its diatom species richness and diversity till now. We conducted 2-year investigation programme to study biodiversity and seasonal dynamics of diatoms in this lake. A total of 27 diatom taxa were found, almost all of them attached to reed and much less in benthos and plankton. Five new diatom species for Serbia were recorded, Craticula halopannonica, Navicymbula pusilla, Hantzschia weyprechtii, Nitzschia thermaloides and Navicula staffordiae. The last mentioned is new for Europe as well. Lake Velika Rusanda is inhabited mostly by alkaliphilous and halophilic diatoms. Since diatoms are used as bioindicators in soda lakes, our results will improve their further application in ecological status assessment of these fragile habitats in the Carpathian Basin.

     

Succession of planktonic rotifer populations in some lakes of the Eastern Rift Valley,Kenya

The quantitative succession of the spring and summer rotifer plankton and its biomass in six lakes of the Eastern Rift Valley of Kenya is discussed. The lakes can be divided into two groups: the low conductivity slightly alkaline lakes Naivasha, Oloidien and the Winam Gulf of Lake Victoria; and the high conductivity, highly alkaline-saline lakes Nakuru, Elmenteita and Bogoria. The former three show a qualitatively rich, typical warmwater rotifer association dominated by Brachionids and Filinia. The saline soda lakes are dominated by several populations of Brachionus dimidiatus, which can reach enormous numbers. The taxonomy and biometry of this species was subjected to statistical analysis. Some interesting and rare species are described: Anuraeopsis coelata, Lepadella triptera f. deconincki, Trichocerca gracilis and T. mus.The chemical limnology of the lakes is discussed and compared with other soda lakes in Central Africa, Europe and North America.     

Ecology and habitats of extremophiles

This review describes the main natural extreme environments, characterized by high temperature, high and low pH and high salinity, that can be colonized by microorganisms. The environments covered are: freshwater alkaline hot springs; acidic solfatara fields; anaerobic geothermal mud and soils; acidic sulphur and pyrite areas; carbonate springs and alkaline soil; and soda and highly saline lakes. The community structure, in terms of available energy sources and representative autotrophic and heterotrophic microorganisms, is discussed for each type of habitat.The authors are with the Department of Biotechnology. Technological Institute of Iceland, Keldnaholt, 112 Reykjavik, Iceland and with the Institute of Biology, University of Iceland, Reykjavik, Iceland     

Chemolithotrophic haloalkaliphiles from soda lakes

This paper summarizes recent data on the occurrence and properties of lithotrophic prokaryotes found in extremely alkaline, saline (soda) lakes. Among the chemolithotrophs found in these lakes the obligately autotrophic sulfur-oxidizing bacteria were the dominant, most diverse group, best adapted to haloalkaline conditions. The culturable forms are represented by three new genera, Thioalkalimicrobium, Thioalkalivibrio and Thioalkalispira in the Gammaproteobacteria. Among them, the genus Thioalkalivibrio was most metabolically diverse, including denitrifying, thiocyanate-oxidizing and facultatively alkaliphilic species. Culturable methane-oxidizing populations in the soda lakes belong to the type I methanotroph group in the Gammaproteobacteria, mostly in the genus Methylomicrobium. The nitrifying bacteria in hyposaline soda lakes were represented by a new species Nitrobacter alkalicus (Alphaproteobacteria), and by an alkaliphilic subspecies of Nitrosomonas halophila (Betaproteobacteria). Both belonged to the low salt-tolerant alkaliphiles. The facultatively autotrophic haloalkaliphilic isolates able to grow with hydrogen as electron donor were identified as representatives of the alpha-3 subclass of the Proteobacteria (aerobic) and of the Natronolimnicola - Alkalispirillum group in the gammaproteobacteria (nitrate-reducing). While all chemolithotrophic isolates from soda lakes belong to the alkaliphiles with a pH optimum for growth around 10, only the sulfur-oxidizing group included species able to grow under hypersaline conditions. This indicates that carbon and nitrogen cycles in the hypersaline alkaline lakes might not be closed.     

The structure of phototrophic communities of soda lakes of the southeastern Transbaikal Region

The structure of benthic phototrophic communities of 24 soda lakes of the southeastern Transbaikal Region was studied. The physicochemical properties of the lakes were determined. The results of enumeration of anoxygenic phototrophic bacteria (APB) belonging to various groups are presented. The influence of salinity on the structure of APB communities was investigated. The APB reaction to environmental conditions was determined. Massive development of phototrophic microorganisms in the form of mats and films was observed in the majority of the investigated lakes. The APB communities were characterized by a wide diversity and evenness of species composition. Purple sulfur bacteria of the families Ectothiorhodospiraceae and Chromatiaceae were predominant. Purple nonsulfur bacteria of the family Rhodobacteraceae, green filamentous bacteria Oscillochloris sp., and heliobacteria were also detected. According to preliminary data, no less than 15 species of APB occur in the studied lakes. Among them, three novel genera and four species have already been described. Identification of other isolates is still in progress. The lakes make an almost continuous series of fresh, brackish, and saline water bodies, varying in their degree of mineralization. It was demonstrated that the structure of APB communities was unaffected by changes in salinity from 5 to 40 g/l. At salt concentrations of lower than 5 g/l, the level of water mineralization became a limiting factor. Experiments with the isolated cultures showed that the APB were obligately dependent on the presence of carbonate ions in the medium. They were haloalkalitolerant or haloalkaliphilic. Thus, they are well adapted to the conditions of soda lakes with a low of moderate mineralization. It was demonstrated that soda lakes of the southeastern Transbaikal Region represent a special type of habitat which harbors a peculiar autochthonous microflora and differs from both highly mineralized soda lakes and shallow saline water bodies of the sea origin.     

Diversity of RuBisCO and ATP citrate lyase genes in soda lake sediments

Sediments from six soda lakes of the Kulunda Steppe (Altai, Russia) and from hypersaline alkaline lakes of Wadi Natrun (Egypt) were analyzed for the presence of cbb and aclB genes encoding key enzymes Ci assimilation (RuBisCO in Calvin-Benson and ATP citrate lyase in rTCA cycles, respectively). The cbbL gene (RuBisCO form I) was found in all samples and was most diverse, while the cbbM (RuBisCO form II) and aclB were detected only in few samples and with a much lower diversity. The cbbL libraries from hypersaline lakes were dominated by members of the extremely haloalkaliphilic sulfur-oxidizing Ectothiorhodospiraceae, i.e. the chemolithotrophic Thioalkalivibrio and the phototrophic Halorhodospira. In the less saline soda lakes from the Kulunda Steppe, the cbbL gene comprised up to ten phylotypes with a domination of members of a novel phototrophic Chromatiales lineage. The cbbM clone libraries consisted of two major unidentified lineages probably belonging to chemotrophic sulfur-oxidizing Gammaproteobacteria. One of them, dominating in the haloalkaline lakes from Wadi Natrun, was related to a cbbM phylotype detected previously in a hypersaline lake with a neutral pH, and another, dominating in lakes from the Kulunda Steppe, was only distantly related to the Thiomicrospira cluster. The aclB sequences detected in two samples from the Kulunda Steppe formed a single, deep branch in the Epsilonproteobacteria, distantly related to Arcobacter sulfidicus.     

Haloalkaliphilic sulfur-oxidizing bacteria in soda lakes

The existence of chemolithoautotrophic sulfur-oxidizing bacteria (SOB) capable of growth in an extremely alkaline and saline environment has not been recognized until recently. Extensive studies of saline, alkaline (soda) lakes located in Central Asia, Africa and North America have now revealed the presence, at relatively high numbers, of a new branch of obligately autotrophic SOB in these doubly extreme environments. Overall more than 100 strains were isolated in pure culture. All of them have the potential to grow optimally at around pH 10 in media strongly buffered with sodium carbonate/bicarbonate and cannot grow at pH<7.5 and Na(+) concentration <0.2 M. The majority of the isolates fell into two distinct groups with differing phylogeny and physiology, that have been described as two new genera in the Gammaproteobacteria; Thioalkalimicrobium and Thioalkalivibrio. The third genus, Thioalkalispira, contains a single obligate microaerophilic species T. microaerophila. The Thioalkalimicrobium group represents a typical opportunistic strategy, including highly specialized, relatively fast-growing and low salt-tolerant bacteria, dominating in hyposaline steppe soda lakes of Central Asia. The genus Thioalkalivibrio includes mostly slowly growing species better adapted to life in hypersaline conditions and with a more versatile metabolism. It includes denitrifying, thiocyanate-utilizing and facultatively alkaliphilic species.     

Structuring forces and β-diversity of benthic diatom metacommunities in soda pans of the Carpathian Basin

Small soda lakes represent one of the most vulnerable ecosystem types due to their high hydrological sensitivity to climate change and anthropogenic interventions. Since diatoms are excellent bioindicators, determining the β-diversity and the structuring dynamics of diatom metacommunities can provide valuable information for conservation planning for soda pans. In this study, two diatom metacommunities were surveyed monthly during a one-year period from distinct regions of the Carpathian basin: the Fert?-Hanság National Park (FH) between 2013 and 2014, and the Danube-Tisza Interfluve (DT) between 2014 and 2015. We explored whether β-diversity of diatom assemblages in the two regions is enhanced by species turnover or nestedness (related to richness differences) and investigated the role of deterministic and stochastic processes in shaping β-diversity patterns. Furthermore, we evaluated the contribution of environmental variables, geographic distance and temporal variation to community structure. High β-diversity (>90%) was revealed for both metacommunities, and was maintained primarily by species turnover. Within the metacommunity of the DT where the natural hydrological cycle of soda pans is not disturbed, diatom communities assembled mainly due to the selection force of environment at a spatiotemporal scale. In the soda pans located in the habitat reconstruction area of the FH, besides species-sorting, significant temporal variation in community structure appeared as a result of water management and periodic water supply. Our results point to the need for a conservation management strategy which maintains the natural hydrological regime of small saline lakes, and therefore their habitat heterogeneity which is of high conservation value.     

A test of traditional diversity measures and taxonomic distinctness indices on benthic diatoms of soda pans in the Carpathian basin

Saline lakes are threatened all over the world and their conservation has been a key issue. Various diversity indices are available for ecological status assessments, however, with poorly explored relevance and applicability in saline, alkaline pans. Therefore, traditional diversity measures (species richness and Shannon diversity) and taxonomic distinctness indices (Average [AvTD] and Variance of Taxonomic Distinctness [VarTD]) were tested in more than 100 sampling sites of 39 soda pans in Central-Europe to find sufficient indicators of the ecological condition and simultaneously to facilitate their preservation according to the modern conservation practices. Results of the analyses showed that healthy soda pan ecosystems with high level of natural stress and reduced habitat heterogeneity are characterized by low diversity diatom assemblages. In soda pans where the stress can be extremely high from natural reasons, oligopoly of closely related species can develop: the average taxonomic distinctness appeared between genus and family level. The non-DNA-sequence based phylogenetic diversity measures (AvTD and VarTD), were generally sensitive to the trophic state of the lakes, in contrast to traditional diversity metrics, which were unequivocally indicative for the special physical and chemical parameters (e.g. conductivity, pH) of the soda pans. In some cases, when the response of the diversity measures for a given environmental variable (pH, temperature) overlapped, the AvTD was found to be a more precise indicator of the environmental changes (pH) than traditional ones. The decreasing tendency of the AvTD along the intensified natural impact may be explained by the long available time for the species to adapt to these special environments.     

Moderately haloalkaliphilic aerobic methylobacteria

Aerobic methylobacteria utilizing oxidized and substituted methane derivatives as carbon and energy sources are widespread in nature and involved in the global carbon cycle, being a unique biofilter on the path of these C₁ compounds from different ecosystems to the atmosphere. New data on the biological features of moderately halophilic, neutrophilic, and alkaliphilic methylobacteria isolated from biotopes with higher osmolarity (seas, saline and soda lakes, saline soils, and deteriorating marble) are reviewed. Particular attention is paid to the latest advances in the study of the mechanisms of osmoadaptation of aerobic moderately haloalkaliphilic methylobacteria: formation of osmolytes, in particular, molecular and genetic aspects of biosynthesis of the universal bioprotectant ectoine. The prospects for further studies of the physiological and biochemical principles of haloalkalophily and for the application of haloalkaliphilic aerobic methylobacteria in biosynthesis and biodegradation are discussed.     

Moderately haloalkaliphilic aerobic methylobacteria

Aerobic methylobacteria utilizing oxidized and substituted methane derivatives as carbon and energy sources are widespread in nature and involved in the global carbon cycle, being a unique biofilter on the path of these C1 compounds from different ecosystems to the atmosphere. New data on the biological features of moderately halophilic, neutrophilic, and alkaliphilic methylobacteria isolated from biotopes with higher osmolarity (seas, saline and soda lakes, saline soils, and deteriorating marble) are reviewed. Particular attention is paid to the latest advances in the study of the mechanisms of osmoadaptation of aerobic moderately haloalkaliphilic methylobacteria: formation of osmolytes, in particular, molecular and genetic aspects of biosynthesis of the universal bioprotectant ectoine. The prospects for further studies of the physiological and biochemical principles of haloalkalophily and for the application of haloalkaliphilic aerobic methylobacteria in biosynthesis and biodegradation are discussed.     

Growth Response of Soda Lake Bacterial Communities to Simulated Rainfall

Moderately saline soda lakes harbor extremely abundant and fast growing bacterial communities. An interesting phenomenon of an explosive bacterial growth in shallow soda lakes in Eastern Austria after dilution with rainwater, concomitantly with a significant decrease in temperature was observed in a former study. In the present study, we tried to identify the factors being responsible for this enhanced bacterial growth in laboratory batch cultures. Three experiments were performed with water taken from two different lakes at different seasons. Natural soda lake water was diluted with distilled water, artificial lake water, sterile filtered soda lake water, and grazer-free water to test (1) for the influence of compatible solutes released to the environment and reduced salt stress after osmotic down-shock, (2) for the influence of nutrients, which may be washed in from the dry areas of the lake bottom after rainfall and (3) for the decrease of grazing pressure due to dilution. The potential influence of (4) viruses was indirectly deduced. The response of the bacterial community to the manipulations was measured by changes in bacterial numbers, the incorporation of ³H-leucine and the concomitant determination of the amount of ³H-leucine uptaking bacteria by microautoradiography. The influence of the environmental factors enhancing bacterial growth after a simulated rainfall event showed variations between the lakes and over the seasons. The addition of nutrients was, in all experiments, the main factor triggering bacterial growth. The decrease in grazing pressure and viral lysis after dilution was of significant importance in two of three experiments. In the experiment with the highest salinity, we could show that either compatible solutes released after osmotic down-shock and used as a source of nutrients for the soda lake bacterial populations or reduced salt stress were most probably responsible for the observed marked enhancement of bacterial growth.