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

Biotic and Abiotic Regulations of Carbon Fixation into Lacustrine Sediments with Different Nutrient Levels

Lake sediments play a critical role in organic carbon (OC) conservation. However, the biogeochemical processes of the C cycle in lake ecosystems remain limitedly understood. In this study, Fe fractions and OC fractions, including total OC (TOC) and OC associated with iron oxides (TOCFeO), were measured for sediments from a eutrophic lake in China. The abundance and composition of bacterial communities encoding genes cbbL and cbbM were obtained by using high-throughput sequencing. We found that autochthonous algae with a low C/N ratio together with δ13C values predominantly contributed to the OC burial in sediments rather than terrigenous input. TOCFeO served as an important C sink deposited in the sediments. A significantly positive correlation (r = 0.92, p < 0.001) suggested the remarkable regulation of complexed FeO (Fep) on fixed TOC fractions, and the Fe redox shift triggered the loss of deposited OC. It should be noted that a significant correlation was not found between the absolute abundance of C-associating genera and TOC, as well as TOCFeO, and overlying water. Some rare genera, including Acidovora and Thiobacillus, served as keystone species and had a higher connected degree than the genera with high absolute abundance. These investigations synthetically concluded that the absolute abundance of functional genes did not dominate CO2 fixation into the sediments via photosynthesis catalyzed by the C-associating RuBisCO enzyme. That is, rare genera, together with high-abundance genera, control the C association and fixation in the sediments.

Microbial-driven carbon fixation in natural wetland

With the development of global industrialization, carbon neutrality has become an issue that we must be paid attention to. Microorganisms not only have an important impact on the carbon chemical cycle between the Earth's biosphere and biogeography but also play a key role in maintaining the global organic carbon balance. Wetlands are the main reservoir of organic carbon in the mainland of China, and wetland carbon sinks are indispensable for China to achieve the goal of "dual carbon," and China has taken the consolidation and improvement of wetland carbon sink capacity as an important part of the carbon peaking action plan. As a unique low-latitude, high-altitude seasonal plateau wetland in China, Napahai shows high research value. However, the role of microbes in maintaining dissolved organic carbon balance in this area has not been reported. In the study, six carbon fixation genes, accA, aclB, acsA, acsB, cbbL, and rbcL, were analyzed based on metagenomics to elucidate the rich genetic diversity, uniqueness and differences in the Napahai plateau wetland. It was found that the microbial diversity in the Napahai plateau wetland was different from other habitats. In addition, the aclB gene, a rare taxon with high genetic diversity and rich species in the Napahai plateau wetland, played a key role in the microbial metabolic pathway. Finally, the construction of a metabolic pathway through the Kyoto encyclopedia for genes and genomes revealed the contribution of microbes to carbon fixation and the role of microbes in maintaining the organic carbon balance of the Napahai plateau wetland.

The effect of biochar prepared at different pyrolysis temperatures on microbially driven conversion and retention of nitrogen during composting

Aerobic composting is one of the most economical ways to produce organic fertilizer from agricultural wastes. In this research, we independently developed a simple composting simulation reactor. The effects of biochar pyrolysised at different pyrolysis temperatures (B1-450 °C; B2-550 °C; and B3-650 °C) on nitrogen conversion (Total nitrogen (TN), ammonium nitrogen (NH₄ ⁺-N), nitrate nitrogen (NO₃ ^--N), cumulative amount of ammonia (CEA) and nitrous oxide (CEN) emission, nitrogen loss rate (NLR), etc.) and functional microbial community (cbbL, cbbM and nifH) structure in the composting system were studied. Results showed that the addition of biochar significantly improved the efficiency of composting, increased the NO₃ ^--N concentration and reduced the NLR (%) in the composting system (B3 (31.4 ± 2.73)<B2=B1 (41.7 ± 3.29)<B0 (54.5 ± 3.34), p ≤ 0.05), while the loss rate of nitrogen positively correlated with compost pH. Denitrifying bacterial genera such as Pseudomonas, Alcaligenes, Paracoccus, Bacillus, Citrobacter, Mesorhizobium, Thiobacillus and Rhodococcus in this study was an important reason for nitrogen loss during composting, and the abundance of autotrophic microorganisms (such as Sulfuritalea, Hydrogenophaga, Thiobacillus, Thiomonas and Candidatus_Thioglobus) in treatments with biochar (B1, B2 and B3) were higher than that in B0. Besides, the community structure in the treatments B2 and B3 was similar at the end of composting and clearly distinguished from that in B1. Moreover, the five functions predicted by OTUs in this study with the highest proportions were chemoheterotrophy, nitrate reduction, fermentation, aerobic chemoheterotrophy and nitrogen respiration. The study provided a theoretical basis for the application of biochar to improve the compost-related processes.

The Impact of Fertilizer Amendments on Soil Autotrophic Bacteria and Carbon Emissions in Maize Field on the Semiarid Loess Plateau

Soil autotrophic bacteria play a crucial role in regulating CO₂ fixation and crop productivity. However, the information is limited to how fertilization amendments alter soil autotrophic bacterial community, crop yield, and carbon emission efficiency (CEE). Here, we estimated the impact of the structure and co-occurrence network of soil autotrophic bacterial community on maize yield and CEE. A long-term field experiment was conducted with five fertilization treatments in semiarid Loess Plateau, including no amendment (NA), chemical fertilizer (CF), chemical fertilizer plus commercial organic fertilizer (SC), commercial organic fertilizer (SM), and maize straw (MS). The results showed that fertilization amendments impacted the structure and network of soil Calvin-Benson-Bassham (CBB) (cbbL) gene-carrying bacterial community via changing soil pH and NO₃-N. Compared with no amendment, the cbbL-carrying bacterial diversity was increased under the SC, SM, and MS treatments but decreased under the CF treatment. Soil autotrophic bacterial network contained distinct microbial modules that consisted of closely associated microbial species. We detected the higher abundances of soil cbbL-carrying bacterial genus Xanthobacter, Bradyrhizobium, and Nitrosospira. Structural equation modeling further suggested that the diversity, composition, and network of autotrophic bacterial community had strongly positive relationships with CEE and maize yield. Taken together, our results suggest that soil autotrophic bacterial community may drive crop productivity and CEE, and mitigate the atmospheric greenhouse effect.

Bicarbonate uptake rates and diversity of RuBisCO genes in saline lake sediments

There is limited knowledge of microbial carbon fixation rate, and carbon-fixing microbial abundance and diversity in saline lakes. In this study, the inorganic carbon uptake rates and carbon-fixing microbial populations were investigated in the surface sediments of lakes with a full range of salinity from freshwater to salt saturation. The results showed that in the studied lakes light-dependent bicarbonate uptake contributed substantially (>70%) to total bicarbonate uptake, while the contribution of dark bicarbonate uptake (1.35-25.17%) cannot be ignored. The light-dependent bicarbonate uptake rates were significantly correlated with pH and turbidity, while dark bicarbonate uptake rates were significantly influenced by dissolved inorganic carbon, pH, temperature and salinity. Carbon-fixing microbial populations using the Calvin-Benson-Bassham pathway were widespread in the studied lakes, and they were dominated by the cbbL and cbbM gene types affiliated with Cyanobacteria and Proteobacteria, respectively. The cbbL and cbbM gene abundance and population structures were significantly affected by different environmental variables, with the cbbL and cbbM genes being negatively correlated with salinity and organic carbon concentration, respectively. In summary, this study improves our knowledge of the abundance, diversity and function of carbon-fixing microbial populations in the lakes with a full range of salinity.

Abundant Taxa and Favorable Pathways in the Microbiome of Soda-Saline Lakes in Inner Mongolia

Soda-saline lakes are a special type of alkaline lake in which the chloride concentration is greater than the carbonate/bicarbonate concentration. Due to the high pH and a usually higher osmotic pressure than that of a normal soda lake, the microbes may need more energy to thrive in such a double-extreme environment. In this study, we systematically investigated the microbiome of the brine and sediment samples of nine artificially separated ponds (salinities from 5.5% to saturation) within two soda-saline lakes in Inner Mongolia of China, assisted by deep metagenomic sequencing. The main inorganic ions shaped the microbial community in both the brines and sediments, and the chloride concentration exhibited the most significant effect. A total of 385 metagenome-assembled genomes (MAGs) were generated, in which 38 MAGs were revealed as the abundant species in at least one of the eighteen different samples. Interestingly, these abundant species also represented the most branches of the microbiome of the soda-saline lakes at the phylum level. These abundant taxa were close relatives of microorganisms from classic soda lakes and neutral saline environments, but forming a combination of both habitats. Notably, approximately half of the abundant MAGs had the potential to drive dissimilatory sulfur cycling. These MAGs included four autotrophic Ectothiorhodospiraceae MAGs, one Cyanobacteria MAG and nine heterotrophic MAGs with the potential to oxidize sulfur, as well as four abundant MAGs containing genes for elemental sulfur respiration. The possible reason is that reductive sulfur compounds could provide additional energy for the related species, and reductions of oxidative sulfur compounds are more prone to occur under alkaline conditions which support the sulfur cycling. In addition, a unique 1,4-alpha-glucan phosphorylation pathway, but not a normal hydrolysis one, was found in the abundant Candidatus Nanohaloarchaeota MAG NHA-1, which would produce more energy in polysaccharide degradation. In summary, this work has revealed the abundant taxa and favorable pathways in the soda-saline lakes, indicating that efficient energy regeneration pathway may increase the capacity for environmental adaptation in such saline-alkaline environments. These findings may help to elucidate the relationship between microbial metabolism and adaptation to extreme environments.

Dark carbon fixation and chemolithotrophic microbial community in surface sediments of the cascade reservoirs, Southwest China

Dark carbon fixation (DCF) by chemolithotrophic microbes can make considerable contribution to inorganic carbon fixation in aquatic ecosystems. However, little is known about the importance and diversity of chemolithotrophic microbes in cascade reservoir sediments. In this study, we determined the potential DCF rates of sediments of three cascade reservoirs in Wujiang River basin by carbon isotopic labeling. The results showed that the DCF rates of the surface sediments ranged from 1.5 to 14.7 mmol C m^-2 d^-1. The ratio of DCF to mineralization rate of sediment organic matter of surface sediment was between 11.6%~60.9%. High-throughput sequencing analysis of cbbL and cbbM genes involved in Calvin Benson Cycle indicated that cbbL-carrying CO₂-assimilating bacteria included diverse functional groups, while cbbM type was mostly involved in sulfur oxidation. The sediments of Hongfeng (HF) reservoir, which has much longer hydraulic residence time (HRT) and locates in most upstream of a major tributary of Wujiang River, have substantially higher DCF rates. The cbbL and cbbM communities in HF were dominated by sulfur oxidizing bacteria, and were largely different from that in the other two reservoirs. Our results suggested that chemolithotrophy plays an important role in carbon cycling of sediments in cascade reservoir. Meanwhile, HRT and relative location of cascade reservoirs are the key control factors of both DCF and composition of autotrophic microbial communities in cascade reservoir sediments.

Community response of microbial primary producers to salinity is primarily driven by nutrients in lakes

Higher microbial diversity was frequently observed in saline than fresh waters, but the underlying mechanisms remains unknown, particularly in microbial primary producers (MPP). MPP abundance and activity are notably constrained by high salinity, but facilitated by high nutrients. It remains to be ascertained whether and how nutrients regulate the salinity constraints on MPP abundance and community structure. Here we investigated the impact of nutrients on salinity constraints on MPP abundance and diversity in undisturbed lakes with a wide salinity range on the Tibetan Plateau. MPP community was explored using quantitative PCR, terminal restriction fragment length polymorphism and sequencing of cloning libraries targeting form IC cbbL gene. The MPP community structure was sorted by salinity into freshwater (salinity<1‰), saline (1‰ < salinity<29‰) and hypersaline (salinity>29‰) lakes. Furthermore, while MPP abundance, diversity and richness were significantly constrained with increasing salinity, these constraints were mitigated by enhancing total organic carbon (TOC) and total nitrogen (TN) contents in freshwater and saline lakes. In contrast, the MPP diversity increased significantly with the salinity in hypersaline lakes, due to the mitigation of enhancing TOC and TN contents and salt-tolerant MPP taxa. The mitigating effect of nutrients was more pronounced in saline than in freshwater and hypersaline lakes. The MPP compositions varied along salinity, with Betaproteobacteria dominating both the freshwater and saline lakes and Gammaproteobacteria dominating the hypersaline lakes. We concluded that high nutrients could mitigate the salinity constraining effects on MPP abundance, community richness and diversity. Our findings offer a novel insight into the salinity effects on primary producers and highlight the interactive effects of salinity and nutrients on MPP in lakes. These findings can be used as a baseline to illuminate the effects of increased anthropogenic activities altering nutrient dynamics on the global hydrological cycle and the subsequent responses thereof by MPP communities.

Autotrophic carbon fixation strategies used by nitrifying prokaryotes in freshwater lakes

Niche specialization of nitrifying prokaryotes is usually studied with tools targeting molecules involved in the oxidation of ammonia and nitrite. The ecological significance of diverse CO₂ fixation strategies used by nitrifiers is, however, mostly unexplored. By analyzing autotrophy-related genes in combination with amoA marker genes based on droplet digitial PCR and CARD-FISH counts targeting rRNA, we quantified the distribution of nitrifiers in eight stratified lakes. Ammonia oxidizing (AO) Thaumarchaeota using the 3-hydroxypropionate/4-hydroxybutyrate pathway dominated deep and oligotrophic lakes, whereas Nitrosomonas-related taxa employing the Calvin cycle were important AO bacteria in smaller lakes. The occurrence of nitrite oxidizing Nitrospira, assimilating CO₂ with the reductive TCA cycle, was strongly correlated with the distribution of Thaumarchaeota. Recently discovered complete ammonia-oxidizing bacteria (comammox) belonging to Nitrospira accounted only for a very small fraction of ammonia oxidizers (AOs) present at the study sites. Altogether, this study gives a first insight on how physicochemical characteristics in lakes are associated to the distribution of nitrifying prokaryotes with different CO₂ fixation strategies. Our investigations also evaluate the suitability of functional genes associated with individual CO₂ assimilation pathways to study niche preferences of different guilds of nitrifying microorganisms based on an autotrophic perspective.

Specific detection of form IA RubisCO genes in chemoautotrophic bacteria

The analysis of RubisCO genes is a highly useful instrument to explore the diversity of chemoautotrophic bacteria using the Calvin–Benson–Bassham cycle for CO₂ fixation. However, because of the wide taxonomic distribution of phylogenetically related RubisCO forms, environmental studies targeting chemoautotrophs are hampered in habitats dominated by phototrophs. Here, we report the development of a gene marker that specifically detects form IA RubisCO genes in bacteria, excluding photoautotrophic representatives. The high specificity of the PCR assay was confirmed by sequence analysis of DNA obtained from the photic zone of six lakes, were chemoautotrophs are outnumbered by Cyanobacteria also using form IA RubisCO for CO₂ assimilation.

CO2 assimilation strategies in stratified lakes: Diversity and distribution patterns of chemolithoautotrophs

While mechanisms of different carbon dioxide (CO₂) assimilation pathways in chemolithoautotrohic prokaryotes are well understood for many isolates under laboratory conditions, the ecological significance of diverse CO₂ fixation strategies in the environment is mostly unexplored. Six stratified freshwater lakes were chosen to study the distribution and diversity of the Calvin-Benson-Bassham (CBB) cycle, the reductive tricarboxylic acid (rTCA) cycle, and the recently discovered archaeal 3-hydroxypropionate/4-hydroxybutyrate (HP/HB) pathway. Eleven primer sets were used to amplify and sequence genes coding for selected key enzymes in the three pathways. Whereas the CBB pathway with different forms of RubisCO (IA, IC and II) was ubiquitous and related to diverse bacterial taxa, encompassing a wide range of potential physiologies, the rTCA cycle in Epsilonproteobacteria and Chloribi was exclusively detected in anoxic water layers. Nitrifiying Nitrosospira and Thaumarchaeota, using the rTCA and HP/HB cycle respectively, are important residents in the aphotic and (micro-)oxic zone of deep lakes. Both taxa were of minor importance in surface waters and in smaller lakes characterized by an anoxic hypolimnion. Overall, this study provides a first insight on how different CO₂ fixation strategies and chemical gradients in lakes are associated to the distribution of chemoautotrophic prokaryotes with different functional traits.

Comparative Genome Analysis of Three Thiocyanate Oxidizing Thioalkalivibrio Species Isolated from Soda Lakes

Thiocyanate is a C1 compound containing carbon, nitrogen, and sulfur. It is a (by)product in a number of natural and industrial processes. Because thiocyanate is toxic to many organisms, including humans, its removal from industrial waste streams is an important problem. Although a number of bacteria can use thiocyanate as a nitrogen source, only a few can use it as an electron donor. There are two distinct pathways to use thiocyanate: (i) the “carbonyl sulfide pathway,” which has been extensively studied, and (ii) the “cyanate pathway,” whose key enzyme, thiocyanate dehydrogenase, was recently purified and studied. Three species of Thioalkalivibrio, a group of haloalkaliphilic sulfur-oxidizing bacteria isolated from soda lakes, have been described as thiocyanate oxidizers: (i) Thioalkalivibrio paradoxus (“cyanate pathway”), (ii) Thioalkalivibrio thiocyanoxidans (“cyanate pathway”) and (iii) Thioalkalivibrio thiocyanodenitrificans (“carbonyl sulfide pathway”). In this study we provide a comparative genome analysis of these described thiocyanate oxidizers, with genomes ranging in size from 2.5 to 3.8 million base pairs. While focusing on thiocyanate degradation, we also analyzed the differences in sulfur, carbon, and nitrogen metabolism. We found that the thiocyanate dehydrogenase gene is present in 10 different Thioalkalivibrio strains, in two distinct genomic contexts/genotypes. The first genotype is defined by having genes for flavocytochrome c sulfide dehydrogenase upstream from the thiocyanate dehydrogenase operon (present in two strains including the type strain of Tv. paradoxus), whereas in the second genotype these genes are located downstream, together with two additional genes of unknown function (present in eight strains, including the type strains of Tv. thiocyanoxidans). Additionally, we found differences in the presence/absence of genes for various sulfur oxidation pathways, such as sulfide:quinone oxidoreductase, dissimilatory sulfite reductase, and sulfite dehydrogenase. One strain (Tv. thiocyanodenitrificans) lacks genes encoding a carbon concentrating mechanism and none of the investigated genomes were shown to contain known bicarbonate transporters. This study gives insight into the genomic variation of thiocyanate oxidizing bacteria and may lead to improvements in the application of these organisms in the bioremediation of industrial waste streams.

Diversity and succession of autotrophic microbial community in high-elevation soils along deglaciation chronosequence

Global warming has resulted in substantial glacier retreats in high-elevation areas, exposing deglaciated soils to harsh environmental conditions. Autotrophic microbes are pioneering colonizers in the deglaciated soils and provide nutrients to the extreme ecosystem devoid of vegetation. However, autotrophic communities remain less studied in deglaciated soils. We explored the diversity and succession of the cbbL gene encoding the large subunit of form I RubisCO, a key CO2-fixing enzyme, using molecular methods in deglaciated soils along a 10-year deglaciation chronosequence on the Tibetan Plateau. Our results demonstrated that the abundance of all types of form I cbbL (IA/B, IC and ID) rapidly increased in young soils (0-2.5 years old) and kept stable in old soils. Soil total organic carbon (TOC) and total nitrogen (TN) gradually increased along the chronosequence and both demonstrated positive correlations with the abundance of bacteria and autotrophs, indicating that soil TOC and TN originated from autotrophs. Form IA/B autotrophs, affiliated with cyanobacteria, exhibited a substantially higher abundance than IC and ID. Cyanobacterial diversity and evenness increased in young soils (<6 years old) and then remained stable. Our findings suggest that cyabobacteria play an important role in accumulating TOC and TN in the deglaciated soils.

Analysis of cbbL, nifH, and pufLM in Soils from the Sør Rondane Mountains, Antarctica, Reveals a Large Diversity of Autotrophic and Phototrophic Bacteria

Cyanobacteria are generally thought to be responsible for primary production and nitrogen fixation in the microbial communities that dominate Antarctic ecosystems. Recent studies of bacterial communities in terrestrial Antarctica, however, have shown that Cyanobacteria are sometimes only scarcely present, suggesting that other bacteria presumably take over their role as primary producers and diazotrophs. The diversity of key genes in these processes was studied in surface samples from the Sør Rondane Mountains, Dronning Maud Land, using clone libraries of the large subunit of ribulose-1,5-biphosphate carboxylase/oxygenase (RuBisCO) genes (cbbL, cbbM) and dinitrogenase-reductase (nifH) genes. We recovered a large diversity of non-cyanobacterial cbbL type IC in addition to cyanobacterial type IB, suggesting that non-cyanobacterial autotrophs may contribute to primary production. The nifH diversity recovered was predominantly related to Cyanobacteria, particularly members of the Nostocales. We also investigated the occurrence of proteorhodopsin and anoxygenic phototrophy as mechanisms for non-Cyanobacteria to exploit solar energy. While proteorhodopsin genes were not detected, a large diversity of genes coding for the light and medium subunits of the type 2 phototrophic reaction center (pufLM) was observed, suggesting for the first time, that the aerobic photoheterotrophic lifestyle may be important in oligotrophic high-altitude ice-free terrestrial Antarctic habitats.

Functional microbiology of soda lakes

Soda lakes represent unique permanently haloalkaline system. Despite the harsh conditions, they are inhabited by abundant, mostly prokaryotic, microbial communities. This review summarizes results of studies of main functional groups of the soda lake prokaryotes responsible for carbon, nitrogen and sulfur cycling, including oxygenic and anoxygenic phototrophs, aerobic chemolithotrophs, fermenting and respiring anaerobes. The main conclusion from this work is that the soda lakes are very different from other high-salt systems in respect to microbial richness and activity. The reason for this difference is determined by the major physico-chemical features of two dominant salts - NaCl in neutral saline systems and sodium carbonates in soda lakes, that are influencing the amount of energy required for osmotic adaptation.

Dynamic transition of chemolithotrophic sulfur-oxidizing bacteria in response to amendment with nitrate in deposited marine sediments

Although environmental stimuli are known to affect the structure and function of microbial communities, their impact on the metabolic network of microorganisms has not been well investigated. Here, geochemical analyses, high-throughput sequencing of 16S rRNA genes and transcripts, and isolation of potentially relevant bacteria were carried out to elucidate the anaerobic respiration processes stimulated by nitrate (20 mM) amendment of marine sediments. Marine sediments deposited by the Great East Japan Earthquake in 2011 were incubated anaerobically in the dark at 25∘C for 5 days. Nitrate in slurry water decreased gradually for 2 days, then more rapidly until its complete depletion at day 5; production of N₂O followed the same pattern. From day 2 to 5, the sulfate concentration significantly increased and the sulfur content in solid-phase sediments significantly decreased. These results indicated that denitrification and sulfur oxidation occurred simultaneously. Illumina sequencing revealed the proliferation of known sulfur oxidizers, i.e., Sulfurimonas sp. and Chromatiales bacteria, which accounted for approximately 43.5% and 14.8% of the total population at day 5, respectively. These oxidizers also expressed 16S rRNA to a considerable extent, whereas the other microorganisms, e.g., iron(III) reducers and methanogens, became metabolically active at the end of the incubation. Extinction dilution culture in a basal-salts medium supplemented with sulfur compounds and nitrate successfully isolated the predominant sulfur oxidizers: Sulfurimonas sp. strain HDS01 and Thioalkalispira sp. strain HDS22. Their 16S rRNA genes showed 95.2–96.7% sequence similarity to the closest cultured relatives and they grew chemolithotrophically on nitrate and sulfur. Novel sulfur-oxidizing bacteria were thus directly involved in carbon fixation under nitrate-reducing conditions, activating anaerobic respiration processes and the reorganization of microbial communities in the deposited marine sediments.

High phylogenetic diversity of glycosyl hydrolase family 10 and 11 xylanases in the sediment of Lake Dabusu in China

Soda lakes are one of the most stable naturally occurring alkaline and saline environments, which harbor abundant microorganisms with diverse functions. In this study, culture-independent molecular methods were used to explore the genetic diversity of glycoside hydrolase (GH) family 10 and GH11 xylanases in Lake Dabusu, a soda lake with a pH value of 10.2 and salinity of 10.1%. A total of 671 xylanase gene fragments were obtained, representing 78 distinct GH10 and 28 GH11 gene fragments respectively, with most of them having low homology with known sequences. Phylogenetic analysis revealed that the GH10 xylanase sequences mainly belonged to Bacteroidetes, Proteobacteria, Actinobacteria, Firmicutes and Verrucomicrobia, while the GH11 sequences mainly consisted of Actinobacteria, Firmicutes and Fungi. A full-length GH10 xylanase gene (xynAS10-66) was directly cloned and expressed in Escherichia coli, and the recombinant enzymes showed high activity at alkaline pH. These results suggest that xylanase gene diversity within Lake Dabusu is high and that most of the identified genes might be novel, indicating great potential for applications in industry and agriculture.

Unravelling the carbon and sulphur metabolism in coastal soil ecosystems using comparative cultivation-independent genome-level characterisation of microbial communities

Bacterial autotrophy contributes significantly to the overall carbon balance, which stabilises atmospheric CO₂ concentration and decelerates global warming. Little attention has been paid to different modes of carbon/sulphur metabolism mediated by autotrophic bacterial communities in terrestrial soil ecosystems. We studied these pathways by analysing the distribution and abundance of the diagnostic metabolic marker genes cbbM, apsA and soxB, which encode for ribulose-1,5-bisphosphate carboxylase/oxygenase, adenosine phosphosulphate reductase and sulphate thiohydrolase, respectively, among different contrasting soil types. Additionally, the abundance of community members was assessed by quantifying the gene copy numbers for 16S rRNA, cbbL, cbbM, apsA and soxB. Distinct compositional differences were observed among the clone libraries, which revealed a dominance of phylotypes associated with carbon and sulphur cycling, such as Gammaproteobacteria (Thiohalomonas, Allochromatium, Chromatium, Thiomicrospira) and Alphaproteobacteria (Rhodopseudomonas, Rhodovulum, Paracoccus). The rhizosphere soil was devoid of sulphur metabolism, as the soxB and apsA genes were not observed in the rhizosphere metagenome, which suggests the absence or inadequate representation of sulphur-oxidising bacteria. We hypothesise that the novel Gammaproteobacteria sulphur oxidisers might be actively involved in sulphur oxidation and inorganic carbon fixation, particularly in barren saline soil ecosystems, suggesting their significant putative ecological role and contribution to the soil carbon pool.

Microbial diversity and biogeochemical cycling in soda lakes

Soda lakes contain high concentrations of sodium carbonates resulting in a stable elevated pH, which provide a unique habitat to a rich diversity of haloalkaliphilic bacteria and archaea. Both cultivation-dependent and -independent methods have aided the identification of key processes and genes in the microbially mediated carbon, nitrogen, and sulfur biogeochemical cycles in soda lakes. In order to survive in this extreme environment, haloalkaliphiles have developed various bioenergetic and structural adaptations to maintain pH homeostasis and intracellular osmotic pressure. The cultivation of a handful of strains has led to the isolation of a number of extremozymes, which allow the cell to perform enzymatic reactions at these extreme conditions. These enzymes potentially contribute to biotechnological applications. In addition, microbial species active in the sulfur cycle can be used for sulfur remediation purposes. Future research should combine both innovative culture methods and state-of-the-art 'meta-omic' techniques to gain a comprehensive understanding of the microbes that flourish in these extreme environments and the processes they mediate. Coupling the biogeochemical C, N, and S cycles and identifying where each process takes place on a spatial and temporal scale could unravel the interspecies relationships and thereby reveal more about the ecosystem dynamics of these enigmatic extreme environments.

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.

Genetic evidence for bacterial chemolithoautotrophy based on the reductive tricarboxylic acid cycle in groundwater systems

Geologically and chemically distinct aquifers were screened for the presence of two genes coding for key enzymes of the reverse tricarboxylic acid (rTCA) cycle in autotrophic bacteria, 2-oxoglutarate : ferredoxin oxidoreductase (oorA) and the beta subunit of ATP citrate lyase enzymes (aclB). From 42 samples investigated, aclB genes were detected in two and oorA genes in six samples retrieved from polluted and sulfidic aquifers. aclB genes were represented by a single phylotype of almost identical sequences closely affiliated with chemolithoautotrophic Sulfurimonas species. In contrast, sequences analysis of oorA genes revealed diverse phylotypes mainly related to sequences from cultivation-independent studies.

Microbial population index and community structure in saline-alkaline soil using gene targeted metagenomics

Population indices of bacteria and archaea were investigated from saline-alkaline soil and a possible microbe-environment pattern was established using gene targeted metagenomics. Clone libraries were constructed using 16S rRNA and functional gene(s) involved in carbon fixation (cbbL), nitrogen fixation (nifH), ammonia oxidation (amoA) and sulfur metabolism (apsA). Molecular phylogeny revealed the dominance of Actinobacteria, Firmicutes and Proteobacteria along with archaeal members of Halobacteraceae. The library consisted of novel bacterial (20%) and archaeal (38%) genera showing ≤95% similarity to previously retrieved sequences. Phylogenetic analysis indicated ability of inhabitant to survive in stress condition. The 16S rRNA gene libraries contained novel gene sequences and were distantly homologous with cultured bacteria. Functional gene libraries were found unique and most of the clones were distantly related to Proteobacteria, while clones of nifH gene library also showed homology with Cyanobacteria and Firmicutes. Quantitative real-time PCR exhibited that bacterial abundance was two orders of magnitude higher than archaeal. The gene(s) quantification indicated the size of the functional guilds harboring relevant key genes. The study provides insights on microbial ecology and different metabolic interactions occurring in saline-alkaline soil, possessing phylogenetically diverse groups of bacteria and archaea, which may be explored further for gene cataloging and metabolic profiling.

Microbial communities at the borehole observatory on the Costa Rica Rift flank (Ocean Drilling Program Hole 896A)

The microbiology of subsurface, hydrothermally influenced basaltic crust flanking mid-ocean ridges has remained understudied, due to the difficulty in accessing the subsurface environment. The instrumented boreholes resulting from scientific ocean drilling offer access to samples of the formation fluids circulating through oceanic crust. We analyzed the phylogenetic diversity of bacterial communities of fluid and microbial mat samples collected in situ from the observatory at Ocean Drilling Program Hole 896A, drilled into ~6.5 million-year-old basaltic crust on the flank of the Costa Rica Rift in the equatorial Pacific Ocean. Bacterial 16S rRNA gene sequences recovered from borehole fluid and from a microbial mat coating the outer surface of the fluid port revealed both unique and shared phylotypes. The dominant bacterial clones from both samples were related to the autotrophic, sulfur-oxidizing genus Thiomicrospira. Both samples yielded diverse gamma- and alphaproteobacterial phylotypes, as well as members of the Bacteroidetes, Planctomycetes, and Verrucomicrobia. Analysis of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) genes (cbbL and cbbM) from the sampling port mat and from the borehole fluid demonstrated autotrophic carbon assimilation potential for in situ microbial communities; most cbbL genes were related to those of the sulfur-oxidizing genera Thioalkalivibrio and Thiomicrospira, and cbbM genes were affiliated with uncultured phylotypes from hydrothermal vent plumes and marine sediments. Several 16S rRNA gene phylotypes from the 896A observatory grouped with phylotypes recovered from seawater-exposed basalts and sulfide deposits at inactive hydrothermal vents, but there is little overlap with hydrothermally influenced basaltic boreholes 1026B and U1301A on the Juan de Fuca Ridge flank, suggesting that site-specific characteristics of Hole 896A (i.e., seawater mixing into borehole fluids) affect the microbial community composition.

Distribution and phylogenetic diversity of cbbM genes encoding RubisCO form II in a deep-sea hydrothermal field revealed by newly designed PCR primers

To investigate the phylogenetic diversity of putative chemolithoautotrophs possessing the RubisCO form II gene (cbbM) in various environments, we designed a new PCR primer set targeting this gene. The primer set was designed to cover more diverse and longer sequences of cbbM genes than those reported previously. We analyzed various samples (i.e., benthic sands, basement rocks, sulfide chimneys, vent fluids and overlying bottom seawater) collected in a deep-sea hydrothermal field of the Suiyo Seamount, Izu-Bonin Arc, Western Pacific, by PCR-based analysis using the designed primer set. Most of the cbbM phylotypes recovered from the liquid samples were related to those of the SUP05 group that belongs to the Gammaproteobacteria and includes putative sulfide-oxidizing chemolithoautotrophs. In contrast, the cbbM phylotypes recovered from the solid samples were related to environmental clones with low similarity (74-90%) and not closely related to the SUP05 group (69-74%). The cbbM phylotypes recovered from the liquid samples were different from those of the solid samples. Furthermore, the cbbM phylotypes recovered from the solid samples were different from each other. Our results expand knowledge of the phylogenetic diversity and distribution of putative chemolithoautotrophs possessing RubisCO form II cbbM genes in deep-sea hydrothermal fields.

The microbial sulfur cycle at extremely haloalkaline conditions of soda lakes

Soda lakes represent a unique ecosystem with extremely high pH (up to 11) and salinity (up to saturation) due to the presence of high concentrations of sodium carbonate in brines. Despite these double extreme conditions, most of the lakes are highly productive and contain a fully functional microbial system. The microbial sulfur cycle is among the most active in soda lakes. One of the explanations for that is high-energy efficiency of dissimilatory conversions of inorganic sulfur compounds, both oxidative and reductive, sufficient to cope with costly life at double extreme conditions. The oxidative part of the sulfur cycle is driven by chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacteria (SOB), which are unique for soda lakes. The haloalkaliphilic SOB are present in the surface sediment layer of various soda lakes at high numbers of up to 10(6) viable cells/cm(3). The culturable forms are so far represented by four novel genera within the Gammaproteobacteria, including the genera Thioalkalivibrio, Thioalkalimicrobium, Thioalkalispira, and Thioalkalibacter. The latter two were only found occasionally and each includes a single species, while the former two are widely distributed in various soda lakes over the world. The genus Thioalkalivibrio is the most physiologically diverse and covers the whole spectrum of salt/pH conditions present in soda lakes. Most importantly, the dominant subgroup of this genus is able to grow in saturated soda brines containing 4 M total Na(+) - a so far unique property for any known aerobic chemolithoautotroph. Furthermore, some species can use thiocyanate as a sole energy source and three out of nine species can grow anaerobically with nitrogen oxides as electron acceptor. The reductive part of the sulfur cycle is active in the anoxic layers of the sediments of soda lakes. The in situ measurements of sulfate reduction rates and laboratory experiments with sediment slurries using sulfate, thiosulfate, or elemental sulfur as electron acceptors demonstrated relatively high sulfate reduction rates only hampered by salt-saturated conditions. However, the highest rates of sulfidogenesis were observed not with sulfate, but with elemental sulfur followed by thiosulfate. Formate, but not hydrogen, was the most efficient electron donor with all three sulfur electron acceptors, while acetate was only utilized as an electron donor under sulfur-reducing conditions. The native sulfidogenic populations of soda lakes showed a typical obligately alkaliphilic pH response, which corresponded well to the in situ pH conditions. Microbiological analysis indicated a domination of three groups of haloalkaliphilic autotrophic sulfate-reducing bacteria belonging to the order Desulfovibrionales (genera Desulfonatronovibrio, Desulfonatronum, and Desulfonatronospira) with a clear tendency to grow by thiosulfate disproportionation in the absence of external electron donor even at salt-saturating conditions. Few novel representatives of the order Desulfobacterales capable of heterotrophic growth with volatile fatty acids and alcohols at high pH and moderate salinity have also been found, while acetate oxidation was a function of a specialized group of haloalkaliphilic sulfur-reducing bacteria, which belong to the phylum Chrysiogenetes.