Distribution of RuBisCO genotypes along a redox gradient in Mono Lake, California

Regime difference between macrophyte and Cyanophyta dominance regulate microbial carbon sequestration mode in lake sediments

Different nutrient load in the lake ecosystems trigger the regime difference and change of predominant biotype. The regulation of carbon (C) sequestration mode in the lacustrine sediments in response to this process need prudent clarification. Fluorescence measurements and high-throughput sequencing for functional genes cbbL and cbbM encoding C-fixing bacteria genus were executed for sediments from two representative regimes dominated by macrophyte and Cyanophyta, respectively. The results showed that humic-like and fulvic-acid like materials dominated the dissolved organic matter (DOM) from the algae and macrophyte-dominated lake regions, respectively. Microbial assimilation played critical influence on C fixation into the sediments in both of the two regimes. However, higher diversity was detected in macrophyte-dominated regime compared to that in Cyanophyta-dominated regime, suggesting that moderate nutrient levels facilitated the species richness of bacteria encoding functional genes concerning C fixation. Bacterial species and diversities varied between two regimes including predominant and rare taxa, suggesting that community structure alteration due to regime difference triggered the regulation the C sequestration mode and stability. Predominant genera manipulated the abundance of C-fixing bacteria genes in response to the regulation of nutrient levels. Noted that rare genera also responded to the regime difference and played key role in C sequestration into lacustrine sediments. Our results suggest that more abundant macrophyte-dominated regime facilitated the C sequestration in the lake ecosystems for atmospheric C reduction.

Spatial heterogeneity plays a vital role in shaping the structure and function of estuarine carbon-fixing bacterial communities

Carbon-fixing bacterial communities are essential drivers of carbon fixation in estuarine ecosystems that critically affect the global carbon cycle. This study compared the abundances of the Calvin cycle functional genes cbbL and cbbM and Reductive tricarboxylic acid cycle gene aclB, as well as compared carbon-fixing bacterial community features in the two estuaries, predicted potential ecological functions of carbon-fixation bacteria, and analyzed their symbiosis strategies in two estuaries having different geographical distributions. Gammaproteobacteria was the dominant carbon-fixing bacterial community in the two estuaries. However, a higher number of Alphaproteobacteria were noted in the Liaohe Estuary, and a higher number of Betaproteobacteria were found in the Yalujiang Estuary. The carbon-fixing functional gene levels exhibited the order of aclB > cbbL > cbbM, and significant effects of Cu, Pb, and petroleum were observed (p < 0.05). Nitrogen-associated nutrient levels are major environmental factors that affect carbon-fixing bacterial community distribution patterns. Spatial factors significantly affected cbbL carbon-fixing functional bacterial community structure more than environmental factors. With the increase in offshore distance, the microbial-led processes of methylotrophy and nitrogen fixation gradually weakened, but a gradual strengthening of methanotrophy and nitrification was observed. Symbiotic network analysis of the microorganisms mediating these ecological processes revealed that the carbon-fixing bacterial community in these two estuaries had a non-random symbiotic pattern, and microbial communities from the same module were strongly linked among the carbon, nitrogen, and sulfur cycle. These findings could advance the understanding of carbon fixation in estuarine ecosystems.

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.

Metagenome-based analysis of carbon-fixing microorganisms and their carbon-fixing pathways in deep-sea sediments of the southwestern Indian Ocean

Carbon fixation by chemoautotrophic microorganisms in the dark ocean makes a large contribution to oceanic primary production and the global carbon cycle. In contrast to the Calvin cycle-dominated carbon-fixing pathway in the marine euphotic zone, carbon-fixing pathways and their hosts in deep-sea areas are diverse. In this study, four deep-sea sediment samples close to hydrothermal vents in the southwestern Indian Ocean were collected and processed using metagenomic analysis to investigate carbon fixation potential. Functional annotations revealed that all six carbon-fixing pathways had genes to varied degrees present in the samples. The reductive tricarboxylic acid cycle and Calvin cycle genes occurred in all samples, in contrast to the Wood-Ljungdahl pathway, which previous studies found mainly in the hydrothermal area. The annotations also elucidated the chemoautotrophic microbial members associated with the six carbon-fixing pathways, and the majority of them containing key carbon fixation genes belonged to the phyla Pseudomonadota and Desulfobacterota. The binned metagenome-assembled genomes revealed that key genes for the Calvin cycle and the 3-hydroxypropionate/4-hydroxybutyrate cycle were also found in the order Rhodothermales and the family Hyphomicrobiaceae. By identifying the carbon metabolic pathways and microbial populations in the hydrothermal fields of the southwest Indian Ocean, our study sheds light on complex biogeochemical processes in deep-sea environments and lays the foundation for further in-depth investigations of carbon fixation processes in deep-sea ecosystems.

Insights into carbon-fixation pathways through metagonomics in the sediments of deep-sea cold seeps

Carbon fixation by chemoautotrophic microorganisms in the dark ocean has a major impact on global carbon cycling and ecological relationships in the ocean's interior. At present, six pathways of autotrophic carbon fixation have been found: the Calvin cycle, the reductive Acetyl-CoA or Wood-Ljungdahl pathway (rAcCoA), the reductive tricarboxylic acid cycle (rTCA), the 3-hydroxypropionate bicycle (3HP), the 3-hydroxypropionate/4-hydroxybutyrate cycle (3HP/4HB), and the dicarboxylate/4-hydroxybutyrate cycle (DC/4HB). Although our knowledge about carbon fixation pathways in the ocean has increased significantly, carbon fixation pathways in the cold seeps are still unknown. In this study, we collected sediment samples from two cold seeps and one trough in the south China sea (SCS), and investigated with metagenomic and metagenome assembled genomes (MAGs). We found that six autotrophic carbon fixation pathways present in the cold seeps and trough with rTCA cycle was the most common pathway, whose genes were particularly high in the cold seeps and increased with sediment depths; the rAcCoA cycle mainly occurred in the cold seep regions, and the abundance of module genes increased with sediment depths. We also elucidated members of chemoautotrophic microorganisms involved in these six carbon-fixation pathways. The rAcCoA, rTCA and DC/4-HB cycles required significantly less energy probably play an important role in the deep-sea environments, especially in the cold seeps. This study provided metabolic insights into the carbon fixation pathways in the cold seeps, and laid the foundation for future detailed study on processes and rates of carbon fixation in the deep-sea ecosystems.

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.

Spatiotemporal dynamics of different CO2 fixation strategies used by prokaryotes in a dimictic lake

The Calvin-Benson-Bassham (CBB) cycle and the 3-hydroxypropionate/4-hydroxybutyrate (HP/HB) cycle are two inorganic carbon assimilation pathways widely used by prokaryotic autotrophs in lakes. We investigated the effect of mixing periods and stable water stratification patterns on the trajectories of both CO₂ fixation strategies in a dimictic lake (Piburger See), because information on the spatiotemporal dynamics of prokaryotes using these pathways in freshwater ecosystems is far from complete. Based on a quantitative approach (droplet digital PCR) of genes coding for key enzymes in different CO₂ assimilation pathways, nine depths covering the entire water column were investigated on a monthly basis for one year. Our data show that the abundance of photoautotrophs and obligate chemolithoautotrophs preferentially using form IA RubisCO was determined by seasonal variations. Highest numbers were observed in summer, while a strong decline of prokrayotes using RubisCO form IA was measured between December and May, the period where the lake was mostly covered by ice. The spatiotemporal distribution patterns of genes coding for RubisCO form IC genes, an enzyme usually used by facultative autotrophs for CO₂ assimilation, were less pronounced. Bacteria harboring RubisCO form II were dominating the oxygen limited hypolimnion, while nitrifying Thaumarchaeota using the HP/HB cycle were of minor importance in the lake. Our data reveal that the seasonal heterogeneity, which is determined by the dimictic thermal regime of the lake, results in pronounced spatiotemporal changes of different CO₂ assimilation pathways with depth-dependent environmental parameters as key factors for their distribution.

Autotrophic microbial arsenotrophy in arsenic-rich soda lakes

A number of prokaryotes are capable of employing arsenic oxy-anions as either electron acceptors [arsenate; As(V)] or electron donors [arsenite; As(III)] to sustain arsenic-dependent growth ('arsenotrophy'). A subset of these microorganisms function as either chemoautotrophs or photoautotrophs, whereby they gain sufficient energy from their redox metabolism of arsenic to completely satisfy their carbon needs for growth by autotrophy, that is the fixation of inorganic carbon (e.g. HCO3-) into their biomass. Here we review what has been learned of these processes by investigations we have undertaken in three soda lakes of the western USA and from the physiological characterizations of the relevant bacteria, which include the critical genes involved, such as respiratory arsenate reductase (arrA) and the discovery of its arsenite-oxidizing counterpart (arxA). When possible, we refer to instances of similar process occurring in other, less extreme ecosystems and by microbes other than haloalkaliphiles.

Composition and Activity of Microbial Communities along the Redox Gradient of an Alkaline, Hypersaline, Lake

We compared the composition of microbial communities obtained by sequencing 16S rRNA gene amplicons with taxonomy derived from metatranscriptomes from the same samples. Samples were collected from alkaline, hypersaline Mono Lake, California, USA at five depths that captured the major redox zones of the lake during the onset of meromixis. The prokaryotic community was dominated by bacteria from the phyla Proteobacteria, Firmicutes, and Bacteroidetes, while the picoeukaryotic chlorophyte Picocystis dominated the eukaryotes. Most (80%) of the abundant (>1% relative abundance) OTUs recovered as amplicons of 16S rRNA genes have been reported in previous surveys, indicating that Mono Lake's microbial community has remained stable over 12 years that have included periods of regular, annual overturn interspersed by episodes of prolonged meromixis that result in extremely reducing conditions in bottom water. Metatranscriptomic sequences binned predominately to the Gammaproteobacteria genera Thioalkalivibrio (4–13%) and Thioalkalimicrobium (0–14%); and to the Firmicutes genera Dethiobacter (0–5%) and Clostridium (1–4%), which were also abundant in the 16S rRNA gene amplicon libraries. This study provides insight into the taxonomic affiliations of transcriptionally active communities of the lake's water column under different redox conditions.

Modes of carbon fixation in an arsenic and CO2-rich shallow hydrothermal ecosystem

The seafloor sediments of Spathi Bay, Milos Island, Greece, are part of the largest arsenic-CO₂-rich shallow submarine hydrothermal ecosystem on Earth. Here, white and brown deposits cap chemically distinct sediments with varying hydrothermal influence. All sediments contain abundant genes for autotrophic carbon fixation used in the Calvin-Benson-Bassham (CBB) and reverse tricaboxylic acid (rTCA) cycles. Both forms of RuBisCO, together with ATP citrate lyase genes in the rTCA cycle, increase with distance from the active hydrothermal centres and decrease with sediment depth. Clustering of RuBisCO Form II with a highly prevalent Zetaproteobacteria 16S rRNA gene density infers that iron-oxidizing bacteria contribute significantly to the sediment CBB cycle gene content. Three clusters form from different microbial guilds, each one encompassing one gene involved in CO₂ fixation, aside from sulfate reduction. Our study suggests that the microbially mediated CBB cycle drives carbon fixation in the Spathi Bay sediments that are characterized by diffuse hydrothermal activity, high CO₂, As emissions and chemically reduced fluids. This study highlights the breadth of conditions influencing the biogeochemistry in shallow CO₂-rich hydrothermal systems and the importance of coupling highly specific process indicators to elucidate the complexity of carbon cycling in these ecosystems.

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.

Salinity and nutrient contents of tidal water affects soil respiration and carbon sequestration of high and low tidal flats of Jiuduansha wetlands in different ways

Soils were collected from low tidal flats and high tidal flats of Shang shoal located upstream and Xia shoal located downstream with different tidal water qualities, in the Jiuduansha wetland of the Yangtze River estuary. Soil respiration (SR) in situ and soil abiotic and microbial characteristics were studied to clarify the respective differences in the effects of tidal water salinity and nutrient levels on SR and soil carbon sequestration in low and high tidal flats. In low tidal flats, higher total nitrogen (TN) and lower salinity in the tidal water of Shang shoal resulted in higher TN and lower salinity in its soils compared with Xia shoal. These would benefit β-Proteobacteria and Anaerolineae in Shang shoal soil, which might have higher heterotrophic microbial activities and thus soil microbial respiration and SR. In low tidal flats, where soil moisture was high and the major carbon input was active organic carbon from tidal water, increasing TN was a more important factor than salinity and obviously enhanced soil microbial heterotrophic activities, soil microbial respiration and SR. While, in high tidal flats, higher salinity in Xia shoal due to higher salinity in tidal water compared with Shang shoal benefited γ-Proteobacteria which might enhance autotrophic microbial activity, and was detrimental to β-Proteobacteria in Xia shoal soil. These might have led to lower soil microbial respiration and thus SR in Xia shoal compared with Shang shoal. In high tidal flats, where soil moisture was relatively lower and the major carbon input was plant biomass that was difficult to degrade, soil salinity was the major factor restraining microbial activities, soil microbial respiration and SR.

Carbon-Fixation Rates and Associated Microbial Communities Residing in Arid and Ephemerally Wet Antarctic Dry Valley Soils

Carbon-fixation is a critical process in severely oligotrophic Antarctic Dry Valley (DV) soils and may represent the major source of carbon in these arid environments. However, rates of C-fixation in DVs are currently unknown and the microorganisms responsible for these activities unidentified. In this study, C-fixation rates measured in the bulk arid soils (<5% moisture) ranged from below detection limits to ∼12 nmol C/cc/h. Rates in ephemerally wet soils ranged from ∼20 to 750 nmol C/cc/h, equating to turnover rates of ∼7-140 days, with lower rates in stream-associated soils as compared to lake-associated soils. Sequencing of the large subunit of RuBisCO (cbbL) in these soils identified green-type sequences dominated by the 1B cyanobacterial phylotype in both arid and wet soils including the RNA fraction of the wet soil. Red-type cbbL genes were dominated by 1C actinobacterial phylotypes in arid soils, with wetted soils containing nearly equal proportions of 1C (actinobacterial and proteobacterial signatures) and 1D (algal) phylotypes. Complementary 16S rRNA and 18S rRNA gene sequencing also revealed distinct differences in community structure between biotopes. This study is the first of its kind to examine C-fixation rates in DV soils and the microorganisms potentially responsible for these activities.

Cropping systems modulate the rate and magnitude of soil microbial autotrophic CO2 fixation in soil

The effect of different cropping systems on CO₂ fixation by soil microorganisms was studied by comparing soils from three exemplary cropping systems after 10 years of agricultural practice. Studied cropping systems included: continuous cropping of paddy rice (rice-rice), rotation of paddy rice and rapeseed (rice-rapeseed), and rotated cropping of rapeseed and corn (rapeseed-corn). Soils from different cropping systems were incubated with continuous ¹⁴C-CO₂ labeling for 110 days. The CO₂-fixing bacterial communities were investigated by analyzing the cbbL gene encoding ribulose-1,5-bisphosphate carboxylase oxygenase (RubisCO). Abundance, diversity and activity of cbbL-carrying bacteria were analyzed by quantitative PCR, cbbL clone libraries and enzyme assays. After 110 days incubation, substantial amounts of ¹⁴C-CO₂ were incorporated into soil organic carbon (¹⁴C-SOC) and microbial biomass carbon (¹⁴C-MBC). Rice-rice rotated soil showed stronger incorporation rates when looking at ¹⁴C-SOC and ¹⁴C-MBC contents. These differences in incorporation rates were also reflected by determined RubisCO activities. ¹⁴C-MBC, cbbL gene abundances and RubisCO activity were found to correlate significantly with ¹⁴C-SOC, indicating cbbL-carrying bacteria to be key players for CO₂ fixation in these soils. The analysis of clone libraries revealed distinct cbbL-carrying bacterial communities for the individual soils analyzed. Most of the identified operational taxonomic units (OTU) were related to Nitrobacter hamburgensis, Methylibium petroleiphilum, Rhodoblastus acidophilus, Bradyrhizobium, Cupriavidus metallidurans, Rubrivivax, Burkholderia, Stappia, and Thiobacillus thiophilus. OTUs related to Rubrivivax gelatinosus were specific for rice-rice soil. OTUs linked to Methylibium petroleiphilum were exclusively found in rice-rapeseed soil. Observed differences could be linked to differences in soil parameters such as SOC. We conclude that the long-term application of cropping systems alters underlying soil parameters, which in turn selects for distinct autotrophic communities.

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.

Chemoautotrophic carbon fixation rates and active bacterial communities in intertidal marine sediments

Chemoautotrophy has been little studied in typical coastal marine sediments, but may be an important component of carbon recycling as intense anaerobic mineralization processes in these sediments lead to accumulation of high amounts of reduced compounds, such as sulfides and ammonium. We studied chemoautotrophy by measuring dark-fixation of ¹³C-bicarbonate into phospholipid derived fatty acid (PLFA) biomarkers at two coastal sediment sites with contrasting sulfur chemistry in the Eastern Scheldt estuary, the Netherlands. At one site where free sulfide accumulated in the pore water right to the top of the sediment, PLFA labeling was restricted to compounds typically found in sulfur and ammonium oxidizing bacteria. At the other site, with no detectable free sulfide in the pore water, a very different PLFA labeling pattern was found with high amounts of label in branched i- and a-PLFA besides the typical compounds for sulfur and ammonium oxidizing bacteria. This suggests that other types of chemoautotrophic bacteria were also active, most likely Deltaproteobacteria related to sulfate reducers. Maximum rates of chemoautotrophy were detected in first 1 to 2 centimeters of both sediments and chemosynthetic biomass production was high ranging from 3 to 36 mmol C m⁻² d⁻¹. Average dark carbon fixation to sediment oxygen uptake ratios were 0.22±0.07 mol C (mol O₂)⁻¹, which is in the range of the maximum growth yields reported for sulfur oxidizing bacteria indicating highly efficient growth. Chemoautotrophic biomass production was similar to carbon mineralization rates in the top of the free sulfide site, suggesting that chemoautotrophic bacteria could play a crucial role in the microbial food web and labeling in eukaryotic poly-unsaturated PLFA was indeed detectable. Our study shows that dark carbon fixation by chemoautotrophic bacteria is a major process in the carbon cycle of coastal sediments, and should therefore receive more attention in future studies on sediment biogeochemistry and microbial ecology.

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.

The origin of cyanobacteria in Antarctic sea ice: marine or freshwater?

Cyanobacteria play an important role in the primary productivity of many ecosystems and are dominant in non-marine polar environments. Apart from detecting low levels of cyanobacteria-like pigments in the Southern Ocean, little effort has been spent in trying to elucidate Cyanobacteria in Antarctic sea ice. Here, we report the first use of culture, microscope, microarray and molecular techniques to show that marine Cyanobacteria are rare or absent in sea ice. Our infrequent positive signals were most closely related to freshwater Cyanobacteria from neighbouring terrestrial sources, which illustrates our techniques were sensitive enough to find sea-ice cyanobacteria if they were present. It is still possible that minute quantity of marine cyanobacteria may exist in sea ice and do not contribute significantly to the polar marine ecosystems.

Comparative molecular analysis of chemolithoautotrophic bacterial diversity and community structure from coastal saline soils, Gujarat, India

Background

Soils harbour high diversity of obligate as well as facultative chemolithoautotrophic bacteria that contribute significantly to CO₂ dynamics in soil. In this study, we used culture dependent and independent methods to assess the community structure and diversity of chemolithoautotrophs in agricultural and coastal barren saline soils (low and high salinity). We studied the composition and distribution of chemolithoautotrophs by means of functional marker gene cbbL encoding large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase and a phylogenetic marker 16S rRNA gene. The cbbL form IA and IC genes associated with carbon fixation were analyzed to gain insight into metabolic potential of chemolithoautotrophs in three soil types of coastal ecosystems which had a very different salt load and sulphur content.

Results

In cbbL libraries, the cbbL form IA was retrieved only from high saline soil whereas form IC was found in all three soil types. The form IC cbbL was also amplified from bacterial isolates obtained from all soil types. A number of novel monophyletic lineages affiliated with form IA and IC phylogenetic trees were found. These were distantly related to the known cbbL sequences from agroecosystem, volcanic ashes and marine environments. In 16S rRNA clone libraries, the agricultural soil was dominated by chemolithoautotrophs (Betaproteobacteria) whereas photoautotrophic Chloroflexi and sulphide oxidizers dominated saline ecosystems. Environmental specificity was apparently visible at both higher taxonomic levels (phylum) and lower taxonomic levels (genus and species). The differentiation in community structure and diversity in three soil ecosystems was supported by LIBSHUFF (P = 0.001) and UniFrac.

Conclusion

This study may provide fundamentally new insights into the role of chemolithoautotrophic and photoautotrophic bacterial diversity in biochemical carbon cycling in barren saline soils. The bacterial communities varied greatly among the three sites, probably because of differences in salinity, carbon and sulphur contents. The cbbL form IA-containing sulphide-oxidizing chemolithotrophs were found only in high saline soil clone library, thus giving the indication of sulphide availability in this soil ecosystem. This is the first comparative study of the community structure and diversity of chemolithoautotrophic bacteria in coastal agricultural and saline barren soils using functional (cbbL) and phylogenetic (16S rDNA) marker genes.

Diversity and expression of RubisCO genes in a perennially ice-covered Antarctic lake during the polar night transition

The autotrophic communities in the lakes of the McMurdo Dry Valleys, Antarctica, have generated interest since the early 1960s owing to low light transmission through the permanent ice covers, a strongly bimodal seasonal light cycle, constant cold water temperatures, and geographical isolation. Previous work has shown that autotrophic carbon fixation in these lakes provides an important source of organic matter to this polar desert. Lake Bonney has two lobes separated by a shallow sill and is one of several chemically stratified lakes in the dry valleys that support year-round biological activity. As part of an International Polar Year initiative, we monitored the diversity and abundance of major isoforms of RubisCO in Lake Bonney by using a combined sequencing and quantitative PCR approach during the transition from summer to polar winter. Form ID RubisCO genes related to a stramenopile, a haptophyte, and a cryptophyte were identified, while primers specific for form IA/B RubisCO detected a diverse autotrophic community of chlorophytes, cyanobacteria, and chemoautotrophic proteobacteria. Form ID RubisCO dominated phytoplankton communities in both lobes of the lake and closely matched depth profiles for photosynthesis and chlorophyll. Our results indicate a coupling between light availability, photosynthesis, and rbcL mRNA levels in deep phytoplankton populations. Regulatory control of rbcL in phytoplankton living in nutrient-deprived shallow depths does not appear to be solely light dependent. The distinct water chemistries of the east and west lobes have resulted in depth- and lobe-dependent variability in RubisCO diversity, which plays a role in transcriptional activity of the key gene responsible for carbon fixation.

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 CO2-concentrating mechanism of Synechococcus WH5701 is composed of native and horizontally-acquired components

The cyanobacterial CO(2)-concentrating mechanism (CCM) is an effective adaptation that increases the carbon dioxide (CO(2)) concentration around the primary photosynthetic enzyme Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (RuBisCO). α-Cyanobacteria (those containing Form1-A RuBisCO within cso-type α-carboxysomes) have a limited CCM composed of a small number of Ci-transporters whereas β-cyanobacteria (those species containing Form-1B RuBisCO within ccm-type β-carboxysomes) exhibit a more diverse CCM with a greater variety in Ci-transporter complement and regulation. In the coastal species Synechococcus sp. WH5701 (α-cyanobacteria), the minimal α-cyanobacterial CCM has been supplemented with β-cyanobacterial Ci transporters through the process of horizontal gene transfer (HGT). These transporters are transcriptionally regulated in response to external Ci-depletion however this change in transcript abundance is not correlated with a physiological induction. WH5701 exhibits identical physiological responses grown at 4% CO(2) (K (1/2) ≈ 31 μM Ci) and after induction with 0.04% CO(2) (K (1/2) ≈ 29 μM Ci). Insensitivity to external Ci concentration is an unusual characteristic of the WH5701 CCM which is a result of evolution by HGT. Our bioinformatic and physiological data support the hypothesis that WH5701 represents a clade of α-cyanobacterial species in transition from the marine/oligotrophic environment to a coastal/freshwater environment.

The biological deep sea hydrothermal vent as a model to study carbon dioxide capturing enzymes

Deep sea hydrothermal vents are located along the mid-ocean ridge system, near volcanically active areas, where tectonic plates are moving away from each other. Sea water penetrates the fissures of the volcanic bed and is heated by magma. This heated sea water rises to the surface dissolving large amounts of minerals which provide a source of energy and nutrients to chemoautotrophic organisms. Although this environment is characterized by extreme conditions (high temperature, high pressure, chemical toxicity, acidic pH and absence of photosynthesis) a diversity of microorganisms and many animal species are specially adapted to this hostile environment. These organisms have developed a very efficient metabolism for the assimilation of inorganic CO₂ from the external environment. In order to develop technology for the capture of carbon dioxide to reduce greenhouse gases in the atmosphere, enzymes involved in CO₂ fixation and assimilation might be very useful. This review describes some current research concerning CO₂ fixation and assimilation in the deep sea environment and possible biotechnological application of enzymes for carbon dioxide capture.

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.

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.

Ribulose-1,5-bisphosphate carboxylase/oxygenase genes as a functional marker for chemolithoautotrophic halophilic sulfur-oxidizing bacteria in hypersaline habitats

The presence and diversity of the cbb genes encoding the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) (a key enzyme of the Calvin–Benson cycle of autotrophic CO2 assimilation) were investigated in pure cultures of seven genera of halophilic chemolithoautotrophic sulfur-oxidizing bacteria (SOB) and in sediments from a hypersaline lake in which such bacteria have been recently discovered. All of the halophilic SOB strains (with the exception of Thiohalomonas nitratireducens) possessed the cbbL gene encoding RuBisCO form I, while the cbbM gene encoding RuBisCO form II was detected only in some of the pure cultures. The general topologies of the CbbL/CbbM trees and the 16S rRNA gene tree were different, but both markers showed that the halophilic SOB genera formed independent lineages in the Gammaproteobacteria. In some cases, such as with several strains of the genus Thiohalospira and with Thioalkalibacter halophilus, the cbbL clustering was incongruent with the positions of these strains on the ribosomal tree. In the cbbM tree, the clustering of Thiohalospira and Thiohalorhabdus strains was incongruent with their branching in both cbbL and 16S rRNA gene trees. cbbL and cbbM genes related to those found in the analysed halophilic SOB were also detected in a sediment from a hypersaline lake in Kulunda Steppe (Russia). Most of the cbbL and cbbM genes belonged to members of the genus Thiohalorhabdus. In the cbbL clone library, sequences related to those of Halothiobacillus and Thiohalospira were detected as minor components. Some of the environmental cbbM sequences belonged to as yet unknown phylotypes, representing deep lineages of halophilic autotrophs.

Life without light: microbial diversity and evidence of sulfur- and ammonium-based chemolithotrophy in Movile Cave

Microbial diversity in Movile Cave (Romania) was studied using bacterial and archaeal 16S rRNA gene sequence and functional gene analyses, including ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), soxB (sulfate thioesterase/thiohydrolase) and amoA (ammonia monooxygenase). Sulfur oxidizers from both Gammaproteobacteria and Betaproteobacteria were detected in 16S rRNA, soxB and RuBisCO gene libraries. DNA-based stable-isotope probing analyses using 13C-bicarbonate showed that Thiobacillus spp. were most active in assimilating CO2 and also implied that ammonia and nitrite oxidizers were active during incubations. Nitrosomonas spp. were detected in both 16S rRNA and amoA gene libraries from the 'heavy' DNA and sequences related to nitrite-oxidizing bacteria Nitrospira and Candidatus 'Nitrotoga' were also detected in the 'heavy' DNA, which suggests that ammonia/nitrite oxidation may be another major primary production process in this unique ecosystem. A significant number of sequences associated with known methylotrophs from the Betaproteobacteria were obtained, including Methylotenera, Methylophilus and Methylovorus, supporting the view that cycling of one-carbon compounds may be an important process within Movile Cave. Other sequences detected in the bacterial 16S rRNA clone library included Verrucomicrobia, Firmicutes, Bacteroidetes, alphaproteobacterial Rhodobacterales and gammaproteobacterial Xanthomonadales. Archaeal 16S rRNA sequences retrieved were restricted within two groups, namely the Deep-sea Hydrothermal Vent Euryarchaeota group and the Miscellaneous Crenarchaeotic group. No sequences related to known sulfur-oxidizing archaea, ammonia-oxidizing archaea, methanogens or anaerobic methane-oxidizing archaea were detected in this clone library. The results provided molecular biological evidence to support the hypothesis that Movile Cave is driven by chemolithoautotrophy, mainly through sulfur oxidation by sulfur-oxidizing bacteria and reveal that ammonia- and nitrite-oxidizing bacteria may also be major primary producers in Movile Cave.

Description of Pelomonas aquatica sp. nov. and Pelomonas puraquae sp. nov., isolated from industrial and haemodialysis water

Three Gram-negative, rod-shaped, non-spore-forming bacteria (strains CCUG 52769T, CCUG 52770 and CCUG 52771) isolated from haemodialysis water were characterized taxonomically, together with five strains isolated from industrial waters (CCUG 52428, CCUG 52507, CCUG 52575T, CCUG 52590 and CCUG 52631). Phylogenetic analysis based on 16S rRNA gene sequences indicated that these isolates belonged to the class Betaproteobacteria and were related to the genus Pelomonas, with 16S rRNA gene sequence similarities higher than 99% with the only species of the genus, Pelomonas saccharophila and to Pseudomonas sp. DSM 2583. The type strains of Mitsuaria chitosanitabida and Roseateles depolymerans were their closest neighbours (97.9 and 97.3% 16S rRNA gene sequence similarity, respectively). Phylogenetic analysis was also performed for the internally transcribed spacer region and for three genes [hoxG (hydrogenase), cbbL/cbbM (Rubisco) and nifH (nitrogenase)] relevant for the metabolism of the genus Pelomonas. DNA-DNA hybridization, major fatty acid composition and phenotypical analyses were carried out, which included the type strain of Pelomonas saccharophila obtained from different culture collections (ATCC 15946T, CCUG 32988T, DSM 654T, IAM 14368T and LMG 2256T), as well as M. chitosanitabida IAM 14711T and R. depolymerans CCUG 52219T. Results of DNA-DNA hybridization, physiological and biochemical tests supported the conclusion that strains CCUG 52769, CCUG 52770 and CCUG 52771 represent a homogeneous phylogenetic and genomic group, including strain DSM 2583, clearly differentiated from the industrial water isolates and from the Pelomonas saccharophila type strain. On the basis of phenotypic and genotypic characteristics, these strains belong to two novel species within the genus Pelomonas, for which the names Pelomonas puraquae sp. nov. and Pelomonas aquatica sp. nov. are proposed. The type strains of Pelomonas puraquae sp. nov. and Pelomonas aquatica sp. nov. are CCUG 52769T (=CECT 7234T) and CCUG 52575T (=CECT 7233T), respectively.

Disparate distributions of chemolithotrophs containing form IA or IC large subunit genes for ribulose-1,5-bisphosphate carboxylase/oxygenase in intertidal marine and littoral lake sediments

The distributions of bacterial form IA and form IC ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) were investigated using Lowes Cove intertidal mudflat and Damariscotta Lake littoral sediments by PCR amplification of 492-495 bp fragments of the large subunit RuBisCO gene, cbbL. Genomic extracts for amplification were obtained from lake surface (upper 2 mm), mudflat surface (upper 2 mm), subsurface (5-7 cm), and soft-shell clam (Mya arenaria) burrow-wall sediments, as well as from a sulfide-oxidizing mat. Phylogenetic analyses of cbbL clone libraries revealed that Lowes Cove sediments were dominated by form IA cbbL-containing sequences most closely related to cbbL genes of sulfur-oxidizing bacteria or sulfide-oxidizing mats. In contrast, Damariscotta Lake cbbL clones contained primarily form IC cbbL sequences, which typify aerobic CO- and hydrogen-oxidizing facultative chemolithotrophs. Statistical analyses supported clear differentiation of intertidal and lake chemolithotroph communities, and provided evidence for some differentiation among intertidal communities. amova and libshuff analyses of Lowes Cove libraries suggested that M. arenaria burrow-wall sediments did not harbour distinct communities compared with surface and subsurface sediments, but that surface and subsurface libraries displayed moderate differences. The results collectively support a conceptual model in which the relative distribution of form IA- and IC-containing bacterial chemolithotrophs depends on sulfide availability, which could reflect the role of sulfate reduction in sediment organic matter metabolism, or the presence of geothermal sulfide sources.

Sulfide oxidation coupled to arsenate reduction by a diverse microbial community in a soda lake

We characterized the arsenate-reducing, sulfide-oxidizing population of Mono Lake, California, by analyzing the distribution and diversity of rrnA, cbbL, and dissimilatory arsenate reductase (arrA) genes in environmental DNA, arsenate-plus sulfide-amended lake water, mixed cultures, and isolates. The arsenate-reducing community was diverse. An organism represented by an rrnA sequence previously retrieved from Mono Lake and affiliated with the Desulfobulbaceae (Deltaproteobacteria) appears to be an important member of the arsenate-reducing, sulfide-oxidizing community. Sulfide oxidation coupled with arsenate reduction appears to proceed via a two-electron transfer, resulting in the production of arsenite and an intermediate S compound that is subsequently disproportionated. A realgar-like As/S mineral was formed in some experiments.

Metabolic versatility of haloalkaliphilic bacteria from soda lakes belonging to the Alkalispirillum-Alkalilimnicola group

Four new isolates were obtained from denitrifying enrichments with various electron donors using sediment samples from hypersaline soda lakes. Based on 16S rRNA gene analysis and DNA-DNA hybridization results, they were all identified as members of the Gammaproteobacteria closely associated with the Alkalispirillum-Alkalilimnicola group. Two isolates were obtained from samples enriched with nitrate as electron acceptor and H2 or polysulfide as electron donors, and another two strains were obtained with N2O as the electron acceptor and sulfide or acetate as electron donors. All four new isolates, together with the type strains of the genera Alkalispirillum and Alkalilimnicola originally described as obligate aerobes, were capable of anaerobic growth with acetate using either nitrate or N2O as electron acceptors. Their denitrification pathway, however, was disrupted at the level of nitrite. RuBisCO form I gene was detected and sequenced in the new isolates and in Alkalilimnicola halodurans but not in Alkalispirillum mobile. These data, together with the evidence of Oremland et al. (Appl Environ Microbiol 68:4795-4802, 2002) on the potential of Alkalilimnicola sp. MLHE-1 for autotrophic growth with arsenite as electron donor and nitrate as electron acceptor, demonstrate much higher metabolic diversity of this specific group of haloalkaliphilic Gammaproteobacteria than was originally anticipated.

Diversity and structure of bacterial chemolithotrophic communities in pine forest and agroecosystem soils

Obligate lithotrophs (e.g., ammonia oxidizers) and facultative lithotrophs (e.g., CO and hydrogen oxidizers) collectively comprise a phylogenetically diverse functional group that contributes significantly to carbon and nitrogen cycles in soils and plays important roles in trace gas dynamics (e.g., carbon monoxide and nitrous and nitric oxides) that affect tropospheric chemistry and radiative forcing. In spite of their diverse physiologies, facultative and obligate lithotrophs typically possess the Calvin-Benson-Bassham cycle enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisCO). In an effort designed to understand the structure of lithotrophic communities in soil, genomic DNA extracts from surface (0 to 2 cm) and subsurface (5 to 7 cm) soils have been obtained from two sites in a Georgia agroecosystem (peanut and cotton plots) and an unmanaged pine stand (>50 years old). The extracts have been used in PCR amplifications of the cbbL gene for the rubisCO large subunit protein. cbbL PCR products were cloned, sequenced, and subjected to phylogenetic and statistical analyses. Numerous novel lineages affiliated with the form IC clade (one of four form I rubisCO clades), which is typified by facultative lithotrophs, comprised lithotrophic communities from all soils. One of the form IC clone sequences clustered with a form IC clade of ammonia-oxidizing Nitrosospira. Distinct assemblages were obtained from each of the sites and from surface and subsurface soils. The results suggest that lithotrophic populations respond differentially to plant type and land use, perhaps forming characteristic associations. The paucity of clone sequences attributed to ammonia-oxidizing bacteria indicates that even though ammonia oxidation occurs in the various soils, the relevant populations are small compared to those of facultative lithotrophs.

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.

Quantitative analysis of nifH genes and transcripts from aquatic environments

The availability of fixed inorganic nitrogen often plays a fundamental role in regulating primary production in both aquatic and terrestrial ecosystems. Because biological nitrogen fixation is an important source of nitrogen in marine environments, the study of N2-fixing microorganisms is of fundamental importance to our understanding of global nitrogen and carbon cycles. Quantitative molecular tools have made it possible to examine uncultivated N2-fixing microorganisms directly in the environment. Currently, we are using quantitative polymerase chain reaction (PCR; Q-PCR) and quantitative reverse transcriptase PCR (Q-RT-PCR) to study the ecology and gene expression of N2-fixing bacteria in aquatic environments. Using these methods, we discovered that specific estuarine diazotrophs have distinct nonrandom distributions and that some diazotrophs in the open ocean have different diel patterns of nifH gene expression. This chapter describes briefly our 5' nuclease assay protocols for Q-PCR and Q-RT-PCR of nifH gene fragments in environmental samples and discusses some important methodological considerations for the quantitative molecular examination of microbes in aquatic environments.

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.