Sulfidogenesis under extremely haloalkaline conditions by Desulfonatronospira thiodismutans gen. nov., sp. nov., and Desulfonatronospira delicata sp. nov. - a novel lineage of Deltaproteobacteria from hypersaline soda lakes

Influence of environmental variables and anthropogenic activities on soda-saline lakes chemistry in northern Tanzania: A remote sensing and GIS approach

This study employed Remote Sensing and Geographical Information Systems to explore the influence of environmental factors and human-induced land use/land cover changes on the chemistry of soda-saline lakes in Northern Tanzania. Satellite-based rainfall data were sourced from the Climate Hazards Group Infrared Precipitation with Station (CHIRPS) datasets, and temperature data were obtained from MERRA-2. Monthly precipitation, temperature, and drought conditions in lake watersheds were analyzed from 1981 to 2022, while land use and land cover changes were assessed for 2000, 2014, and 2023. Soil types were acquired from the FAO Digital Soil Map of the World, while geological characteristics were sourced from the US Geological Survey database. The findings revealed that the region's climate is ideal for enhancing evapotranspiration, leading to mineral precipitation, and altering the chemistry of soda-saline lakes. The Standardized Precipitation Evapotranspiration Index revealed increased drought events in the lake basins since 1987, with prolonged drought occurrence between 2000 and 2017. The results also showed that the region is characterized by a variety of soil types, including ferric acrisols, chromic cambisols, calcic cambisols, entisols, inceptisols, eutric fluvisols, distric nitisols, humic nitisols, mollic andosols, ochric andosols, and pellic vertisols. Furthermore, the region is distinguished by diverse geological processes, from Precambrian-Cambrian to tertiary intrusive, triggered by volcanic and tectonic activity. Land use/land cover changes results indicated dynamics in the various classes with an overall decrease in areas under water bodies (-39.80 %), forests (-22.57 %) and bareland (-36.18) while agricultural land (111.01 %) built-up areas (434.72 %), shrubs and grasses (72.77 %) increased in area coverage over the 23 years study period (2000-2023). This study underscores the complex interplay between environmental variables and human activities in shaping the chemistry of soda-saline lakes.

Ecology and biogeochemistry of the microbial underworld in two sister soda lakes

BACKGROUND

Approximately 3.7 billion years ago, microbial life may have emerged in phosphate-rich salty ponds. Surprisingly, analogs of these environments are present in alkaline lake systems, recognized as highly productive biological ecosystems. In this study, we investigate the microbial ecology of two Canadian soda lake sediment systems characterized by naturally high phosphate levels.

RESULTS

Using a comprehensive approach involving geochemistry, metagenomics, and amplicon sequencing, we discovered that groundwater infiltration into Lake Goodenough sediments supported stratified layers of microbial metabolisms fueled by decaying mats. Effective degradation of microbial mats resulted in unexpectedly low net productivity. Evaporation of water from Last Chance Lake and its sediments led to saturation of brines and a habitat dominated by inorganic precipitation reactions, with low productivity, low organic matter turnover and little biological uptake of phosphorus, leading to high phosphate concentrations. Highly alkaline brines were found to be dominated by potentially dormant spore-forming bacteria. These saturated brines also hosted potential symbioses between Halobacteria and Nanoarchaeaota, as well as Lokiarchaea and bacterial sulfate reducers. Metagenome-assembled genomes of Nanoarchaeaota lacked strategies for coping with salty brines and were minimal for Lokiarchaea.

CONCLUSIONS

Our research highlights that modern analogs for origin-of-life conditions might be better represented by soda lakes with low phosphate concentrations. Thus, highly alkaline brine environments could be too extreme to support origin of life scenarios. These findings shed light on the complex interplay of microbial life in extreme environments and contribute to our understanding of early Earth environments.

Halonatronomonas betaini gen. nov., sp. nov., a haloalkaliphilic isolate from soda lake capable of betaine degradation and proposal of Halarsenatibacteraceae fam. nov. and Halothermotrichaceae fam. nov. within the order Halanaerobiales

A search for the organisms responsible for anaerobic betaine degradation in soda lakes resulted in isolation of a novel bacterial strain, designated Z-7014T. The cells were Gram-stain-negative, non-endospore-forming rods. Growth occurred at 8-52 °C (optimum 40-45 °C), pH 7.1-10.1 (optimum pH 8.1-8.8) and 1.0-3.5 M Na+ (optimum 1.8 M), i.e. it can be regarded as a haloalkaliphile. The strain utilized a limited range of substrates, mostly peptonaceous but not amino acids, and was able to degrade betaine. Growth on betaine occurred only in the presence of peptonaceous substances which could not be replaced by vitamins. The G + C content of the genomic DNA of strain Z-7014T was 36.1 mol%. The major cellular fatty acids (>5% of the total) were C16:0 DMA, C18: 0 DMA, C16:1ω8, C16:0, C18:1 DMA, C16:1 DMA, C18:1ω9, and C18:0. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain Z-7014T formed a distinct evolutionary lineage in the order Halanaerobiales with the highest similarity to Halarsenitibacter silvermanii SLAS-1T (83.6%), Halothermothrix orenii H168T (85.6%), and Halocella cellulosilytica DSM 7362T (85.6%). AAI and POCP values between strain Z-7014T and type strains of the order Halanaerobiales were 51.7-57.8%, and 33.8-58.3%, respectively. Based on polyphasic results including phylogenomic data, the novel strain could be distinguished from other genera, which suggests that strain Z-7014T represents a novel species of a new genus, for which the name Halonatronomonas betaini gen. nov., sp. nov. is proposed. The type strain is Z-7014T (=KCTC 25237T = VKM B-3506T). On the basis of phylogenomic data, it is also proposed to evolve two novel families Halarsenitibacteraceae fam. nov. and Halothermotrichaceae fam. nov. within the current order Halanaerobiales.

Biotechnological potentials of halophilic microorganisms and their impact on mankind

Background

Halophiles are extremophilic organisms represented by archaea, bacteria and eukaryotes that thrive in hypersaline environment. They apply different osmoadaptation strategies to survive in hostile conditions. Habitat diversity of halophilic microorganisms in hypersaline system provides information pertaining the evolution of life on Earth.

Main body

The microbiome-gut-brain axis interaction contributes greatly to the neurodegenerative diseases. Gut resident halophilic bacteria are used as alternative medication for chronic brain diseases. Halophiles can be used in pharmaceuticals, drug delivery, agriculture, saline waste water treatment, biodegradable plastic production, metal recovery, biofuel energy generation, concrete crack repair and other sectors. Furthermore, versatile biomolecules, mainly enzymes characterized by broad range of pH and thermostability, are suitable candidate for industrial purposes. Reflectance pattern of halophilic archaeal pigment rhodopsin is considered as potential biosignature for Earth-like planets.

Short conclusions

This review represents important osmoadaptation strategies acquired by halophilic archaea and bacteria and their potential biotechnological applications to resolve present day challenges.

Graphical Abstract

Desulfovulcanus ferrireducens gen. nov., sp. nov., a thermophilic autotrophic iron and sulfate-reducing bacterium from subseafloor basalt that grows on akaganéite and lepidocrocite minerals

A deep-sea thermophilic bacterium, strain Ax17T, was isolated from 25 °C hydrothermal fluid at Axial Seamount. It was obligately anaerobic and autotrophic, oxidized molecular hydrogen and formate, and reduced synthetic nanophase Fe(III) (oxyhydr)oxide minerals, sulfate, sulfite, thiosulfate, and elemental sulfur for growth. It produced up to 20 mM Fe2+ when grown on ferrihydrite but < 5 mM Fe2+ when grown on akaganéite, lepidocrocite, hematite, and goethite. It was a straight to curved rod that grew at temperatures ranging from 35 to 70 °C (optimum 65 °C) and a minimum doubling time of 7.1 h, in the presence of 1.5-6% NaCl (optimum 3%) and pH 5-9 (optimum 8.0). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was 90-92% identical to other genera of the family Desulfonauticaceae in the phylum Pseudomonadota. The genome of Ax17T was sequenced, which yielded 2,585,834 bp and contained 2407 protein-coding sequences. Based on overall genome relatedness index analyses and its unique phenotypic characteristics, strain Ax17T is suggested to represent a novel genus and species, for which the name Desulfovulcanus ferrireducens is proposed. The type strain is Ax17T (= DSM 111878T = ATCC TSD-233T).

Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups

Deltaproteobacteria, now proposed to be the phyla Desulfobacterota, Myxococcota, and SAR324, are ubiquitous in marine environments and play essential roles in global carbon, sulfur, and nutrient cycling. Despite their importance, our understanding of these bacteria is biased towards cultured organisms. Here we address this gap by compiling a genomic catalog of 1 792 genomes, including 402 newly reconstructed and characterized metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments. Phylogenomic analyses reveal that many of these novel MAGs are uncultured representatives of Myxococcota and Desulfobacterota that are understudied. To better characterize Deltaproteobacteria diversity, metabolism, and ecology, we clustered ~1 500 genomes based on the presence/absence patterns of their protein families. Protein content analysis coupled with large-scale metabolic reconstructions separates eight genomic clusters of Deltaproteobacteria with unique metabolic profiles. While these eight clusters largely correspond to phylogeny, there are exceptions where more distantly related organisms appear to have similar ecological roles and closely related organisms have distinct protein content. Our analyses have identified previously unrecognized roles in the cycling of methylamines and denitrification among uncultured Deltaproteobacteria. This new view of Deltaproteobacteria diversity expands our understanding of these dominant bacteria and highlights metabolic abilities across diverse taxa.

Genetic Potential of Dissulfurimicrobium hydrothermale, an Obligate Sulfur-Disproportionating Thermophilic Microorganism

The biochemical pathways of anaerobic sulfur disproportionation are only partially deciphered, and the mechanisms involved in the first step of S⁰-disproportionation remain unknown. Here, we present the results of sequencing and analysis of the complete genome of Dissulfurimicrobium hydrothermale strain Sh68^T, one of two strains isolated to date known to grow exclusively by anaerobic disproportionation of inorganic sulfur compounds. Dissulfurimicrobium hydrothermale Sh68^T is a motile, thermophilic, anaerobic, chemolithoautotrophic microorganism isolated from a hydrothermal pond at Uzon caldera, Kamchatka, Russia. It is able to produce energy and grow by disproportionation of elemental sulfur, sulfite and thiosulfate. Its genome consists of a circular chromosome of 2,025,450 base pairs, has a G + C content of 49.66% and a completion of 97.6%. Genomic data suggest that CO₂ assimilation is carried out by the Wood–Ljungdhal pathway and that central anabolism involves the gluconeogenesis pathway. The genome of strain Sh68^T encodes the complete gene set of the dissimilatory sulfate reduction pathway, some of which are likely to be involved in sulfur disproportionation. A short sequence protein of unknown function present in the genome of strain Sh68^T is conserved in the genomes of a large panel of other S⁰-disproportionating bacteria and was absent from the genomes of microorganisms incapable of elemental sulfur disproportionation. We propose that this protein may be involved in the first step of elemental sulfur disproportionation, as S⁰ is poorly soluble and unable to cross the cytoplasmic membrane in this form.

Highly integrated adaptive mechanisms in Spiribacter halalkaliphilus, a bacterium abundant in Chinese soda-saline lakes

Soda-saline lakes are polyextreme environments inhabited by many haloalkaliphiles, including one of the most abundant Spiribacter species. However, its mechanisms of adaptation are not ecophysiologically characterized. Based on a large-scale cultivation strategy, we obtained a representative isolate of this Spiribacter species whose relative abundance was the highest (up to 15.63%) in a wide range of salinities in the soda-saline lakes in Inner Mongolia, China. This species is a chemoorganoheterotrophic haloalkaliphile. It has a small and streamlined genome and utilizes a wide variety of compatible solutes to resist osmotic pressure and multiple monovalent cation/proton antiporters for pH homeostasis. In addition to growth enhancement by light under microaerobic conditions, cell growth, organic substrate consumption and polyhydroxybutyrate biosynthesis were also improved by inorganic sulfide. Both quantitative RT-PCR and enzymatic assays verified that sulfide:quinone oxidoreductase was upregulated during this process. Metatranscriptomic analysis indicated that all genes related to environmental adaptation were transcribed in natural environments. Overall, this study has identified a novel abundant haloalkaliphile with multiple and highly integrated adaptive strategies and found that inorganic sulfide was able to improve the adaptation of a heterotroph to polyextreme environments.

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.

Recent advances in dissimilatory sulfate reduction: From metabolic study to application

Sulfate-reducing bacteria (SRB) are a group of diverse anaerobic microorganisms omnipresent in natural habitats and engineered environments that use sulfur compounds as the electron acceptor for energy metabolism. Dissimilatory sulfate reduction (DSR)-based techniques mediated by SRB have been utilized in many sulfate-containing wastewater treatment systems worldwide, particularly for acid mine drainage, groundwater, sewage and industrial wastewater remediation. However, DSR processes are often operated suboptimally and disturbances are common in practical application. To improve the efficiency and robustness of SRB-based processes, it is necessary to study SRB metabolism and operational conditions. In this review, the mechanisms of DSR processes are reviewed and discussed focusing on intracellular and extracellular electron transfer with different electron donors (hydrogen, organics, methane and electrodes). Based on the understanding of the metabolism of SRB, responses of SRB to environmental stress (pH-, temperature-, and salinity-related stress) are summarized at the species and community levels. Application in these stressed conditions is discussed and future research is proposed. The feasibility of recovering energy and resources such as biohydrogen, hydrocarbons, polyhydroxyalkanoates, magnetite and metal sulfides through the use of SRB were investigated but some long-standing questions remain unanswered. Linking the existing scientific understanding and observations to practical application is the challenge as always for promotion of SRB-based techniques.

Metabolism and Occurrence of Methanogenic and Sulfate-Reducing Syntrophic Acetate Oxidizing Communities in Haloalkaline Environments

Anaerobic syntrophic acetate oxidation (SAO) is a thermodynamically unfavorable process involving a syntrophic acetate oxidizing bacterium (SAOB) that forms interspecies electron carriers (IECs). These IECs are consumed by syntrophic partners, typically hydrogenotrophic methanogenic archaea or sulfate reducing bacteria. In this work, the metabolism and occurrence of SAOB at extremely haloalkaline conditions were investigated, using highly enriched methanogenic (M-SAO) and sulfate-reducing (S-SAO) cultures from south-western Siberian hypersaline soda lakes. Activity tests with the M-SAO and S-SAO cultures and thermodynamic calculations indicated that H₂ and formate are important IECs in both SAO cultures. Metagenomic analysis of the M-SAO cultures showed that the dominant SAOB was ‘Candidatus Syntrophonatronum acetioxidans,’ and a near-complete draft genome of this SAOB was reconstructed. ‘Ca. S. acetioxidans’ has all genes necessary for operating the Wood–Ljungdahl pathway, which is likely employed for acetate oxidation. It also encodes several genes essential to thrive at haloalkaline conditions; including a Na⁺-dependent ATP synthase and marker genes for ‘salt-out‘ strategies for osmotic homeostasis at high soda conditions. Membrane lipid analysis of the M-SAO culture showed the presence of unusual bacterial diether membrane lipids which are presumably beneficial at extreme haloalkaline conditions. To determine the importance of SAO in haloalkaline environments, previously obtained 16S rRNA gene sequencing data and metagenomic data of five different hypersaline soda lake sediment samples were investigated, including the soda lakes where the enrichment cultures originated from. The draft genome of ‘Ca. S. acetioxidans’ showed highest identity with two metagenome-assembled genomes (MAGs) of putative SAOBs that belonged to the highly abundant and diverse Syntrophomonadaceae family present in the soda lake sediments. The 16S rRNA gene amplicon datasets of the soda lake sediments showed a high similarity of reads to ‘Ca. S. acetioxidans’ with abundance as high as 1.3% of all reads, whereas aceticlastic methanogens and acetate oxidizing sulfate-reducers were not abundant (≤0.1%) or could not be detected. These combined results indicate that SAO is the primary anaerobic acetate oxidizing pathway at extreme haloalkaline conditions performed by haloalkaliphilic syntrophic consortia.

Convergent evolution of unusual complex I homologs with increased proton pumping capacity: energetic and ecological implications

Respiratory complex I is part of a large family of homologous enzymes that carry out the transfer of electrons between soluble cytoplasmic electron carriers and membrane-bound electron carriers. These complexes are vital bioenergetic enzymes that serve as the entry points into electron transport chains for a wide variety of microbial metabolisms, and electron transfer is coupled to proton translocation. The core complex of this enzyme is made up of 11 protein subunits, with three major proton pumping subunits. Here, we document a large number of modified complex I gene cassettes found in genome sequences from diverse cultured bacteria, shotgun metagenomics, and environmentally derived archaeal fosmids all of which encode a fourth proton pumping subunit. The incorporation of this extra subunit into a functional protein complex is supported by large amino acid insertions in the amphipathic helix that runs the length of the protein complex. Phylogenetic analyses reveal that these modified complexes appear to have arisen independently multiple times in a remarkable case of convergent molecular evolution. From an energetic perspective, we hypothesize that this modification on the canonical complex I architecture allows for the translocation of a fifth proton per reaction cycle-the physiological utility of this modified complex is discussed.

The Impacts of Soil Fertility and Salinity on Soil Nitrogen Dynamics Mediated by the Soil Microbial Community Beneath the Halophytic Shrub Tamarisk

Nitrogen (N) is one of the most common limiting nutrients for primary production in terrestrial ecosystems. Soil microbes transform organic N into inorganic N, which is available to plants, but soil microbe activity in drylands is sometimes critically suppressed by environmental factors, such as low soil substrate availability or high salinity. Tamarisk (Tamarix spp.) is a halophytic shrub species that is widely distributed in the drylands of China; it produces litter enriched in nutrients and salts that are thought to increase soil fertility and salinity under its crown. To elucidate the effects of tamarisks on the soil microbial community, and thus N dynamics, by creating "islands of fertility" and "islands of salinity," we collected soil samples from under tamarisk crowns and adjacent barren areas at three habitats in the summer and fall. We analyzed soil physicochemical properties, inorganic N dynamics, and prokaryotic community abundance and composition. In soils sampled beneath tamarisks, the N mineralization rate was significantly higher, and the prokaryotic community structure was significantly different, from soils sampled in barren areas, irrespective of site and season. Tamarisks provided suitable nutrient conditions for one of the important decomposers in the area, Verrucomicrobia, by creating "islands of fertility," but provided unsuitable salinity conditions for other important decomposers, Flavobacteria, Gammaproteobacteria, and Deltaproteobacteria, by mitigating salt accumulation. However, the quantity of these decomposers tended to be higher beneath tamarisks, because they were relatively unaffected by the small salinity gradient created by the tamarisks, which may explain the higher N mineralization rate beneath tamarisks.

Microbial community structure with trends in methylation gene diversity and abundance in mercury-contaminated rice paddy soils in Guizhou, China

Paddy soils from mercury (Hg)-contaminated rice fields in Guizhou, China were studied with respect to total mercury (THg) and methylmercury (MeHg) concentrations as well as Bacterial and Archaeal community composition. Total Hg (0.25-990 μg g-1) and MeHg (1.3-30.5 ng g-1) varied between samples. Pyrosequencing (454 FLX) of the hypervariable v1-v3 regions of the 16S rRNA genes showed that Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, Euryarchaeota, and Crenarchaeota were dominant in all samples. The Bacterial α-diversity was higher in samples with relatively Low THg and MeHg and decreased with increasing THg and MeHg concentrations. In contrast, Archaeal α-diversity increased with increasing of MeHg concentrations but did not correlate with changes in THg concentrations. Overall, the methylation gene hgcAB copy number increased with both increasing THg and MeHg concentrations. The microbial communities at High THg and High MeHg appear to be adapted by species that are both Hg resistant and carry hgcAB genes for MeHg production. The relatively high abundance of both sulfate-reducing δ-Proteobacteria and methanogenic Archaea, as well as their positive correlations with increasing THg and MeHg concentrations, suggests that these microorganisms are the primary Hg-methylators in the rice paddy soils in Guizhou, China.

The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. II. Metabolic Functions of Abundant Community Members Predicted from Metagenomic Analyses

Microbial mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin of Yellowstone National Park have been extensively characterized. Previous studies have focused on the chlorophototrophic organisms of the phyla Cyanobacteria and Chloroflexi. However, the diversity and metabolic functions of the other portion of the community in the microoxic/anoxic region of the mat are poorly understood. We recently described the diverse but extremely uneven microbial assemblage in the undermat of Mushroom Spring based on 16S rRNA amplicon sequences, which was dominated by Roseiflexus members, filamentous anoxygenic chlorophototrophs. In this study, we analyzed the orange-colored undermat portion of the community of Mushroom Spring mats in a genome-centric approach and discuss the metabolic potentials of the major members. Metagenome binning recovered partial genomes of all abundant community members, ranging in completeness from ~28 to 96%, and allowed affiliation of function with taxonomic identity even for representatives of novel and Candidate phyla. Less complete metagenomic bins correlated with high microdiversity. The undermat portion of the community was found to be a mixture of phototrophic and chemotrophic organisms, which use bicarbonate as well as organic carbon sources derived from different cell components and fermentation products. The presence of rhodopsin genes in many taxa strengthens the hypothesis that light energy is of major importance. Evidence for the usage of all four bacterial carbon fixation pathways was found in the metagenome. Nitrogen fixation appears to be limited to Synechococcus spp. in the upper mat layer and Thermodesulfovibrio sp. in the undermat, and nitrate/nitrite metabolism was limited. A closed sulfur cycle is indicated by biological sulfate reduction combined with the presence of genes for sulfide oxidation mainly in phototrophs. Finally, a variety of undermat microorganisms have genes for hydrogen production and consumption, which leads to the observed diel hydrogen concentration patterns.

Different Types of Dietary Fibers Trigger Specific Alterations in Composition and Predicted Functions of Colonic Bacterial Communities in BALB/c Mice

Soluble dietary fibers (SDF) are fermented more than insoluble dietary fibers (IDF), but their effect on colonic bacterial community structure and function remains unclear. Thus, bacterial community composition and function in the colon of BALB/c mice (n = 7) fed with a high level (approximately 20%) of typical SDF, oat-derived β-glucan (G), microcrystalline cellulose (M) as IDF, or their mixture (GM), were compared. Mice in group G showed a lowest average feed intake (p < 0.05) but no change on the average body weight gain (p > 0.05) compared to other groups, which may be associated with the highest concentration of colonic propionate (p < 0.05) in these mice. The bacterial α-diversity of group G was significantly lower than other groups (p < 0.01). In group G, the relative abundance of bacteria belonging to the phylum Bacteroidetes was significantly increased, whereas bacteria from the phylum Firmicutes were significantly decreased (p < 0.01). The core bacteria for different treatments showed distinct differences. Bacteroides, Dehalobacterium, and Prevotella, including known acetogens and carbohydrate fermenting organisms, were significantly increased in relative abundance in group G. In contrast, Adlercreutzia, Odoribacter, and Coprococcus were significantly more abundant in group M, whereas Oscillospira, Desulfovibrio, and Ruminoccaceae, typical hydrogenotrophs equipped with multiple carbohydrate active enzymes, were remarkably enriched in group GM (p < 0.05). The relative abundance of bacteria from the three classes of Proteobacteria, Betaproteobacteria, Gammaproteobacteria (including Enterobacteriaceae) and Deltaproteobacteria, were significantly more abundant in group G, indicating a higher ratio of conditional pathogenic bacteria in mice fed dietary β-glucan in current study. The predicted colonic microbial function showed an enrichment of “Energy metabolism” and “Carbohydrate metabolism” pathways in mice from group G and M, suggesting that the altered bacterial community in the colon of mice with the two dietary fibers probably resulted in a more efficient degradation of dietary polysaccharides. Our result suggests that the influence of dietary β-glucan (SDF) on colonic bacterial community of mice was more extensively than MCC (IDF). Co-supplementation of the two fibers may help to increase the bacterial diversity and reduce the conditional pathogens in the colon of mice.

Metabolomic and Metagenomic Analysis of Two Crude Oil Production Pipelines Experiencing Differential Rates of Corrosion

Corrosion processes in two North Sea oil production pipelines were studied by analyzing pig envelope samples via metagenomic and metabolomic techniques. Both production systems have similar physico-chemical properties and injection waters are treated with nitrate, but one pipeline experiences severe corrosion and the other does not. Early and late pigging material was collected to gain insight into the potential causes for differential corrosion rates. Metabolites were extracted and analyzed via ultra-high performance liquid chromatography/high-resolution mass spectrometry with electrospray ionization (ESI) in both positive and negative ion modes. Metabolites were analyzed by comparison with standards indicative of aerobic and anaerobic hydrocarbon metabolism and by comparison to predicted masses for KEGG metabolites. Microbial community structure was analyzed via 16S rRNA gene qPCR, sequencing of 16S PCR products, and MySeq Illumina shotgun sequencing of community DNA. Metagenomic data were used to reconstruct the full length 16S rRNA genes and genomes of dominant microorganisms. Sequence data were also interrogated via KEGG annotation and for the presence of genes related to terminal electron accepting (TEA) processes as well as aerobic and anaerobic hydrocarbon degradation. Significant and distinct differences were observed when comparing the ‘high corrosion’ (HC) and the ‘low corrosion’ (LC) pipeline systems, especially with respect to the TEA utilization potential. The HC samples were dominated by sulfate-reducing bacteria (SRB) and archaea known for their ability to utilize simple carbon substrates, whereas LC samples were dominated by pseudomonads with the genetic potential for denitrification and aerobic hydrocarbon degradation. The frequency of aerobic hydrocarbon degradation genes was low in the HC system, and anaerobic hydrocarbon degradation genes were not detected in either pipeline. This is in contrast with metabolite analysis, which demonstrated the presence of several succinic acids in HC samples that are diagnostic of anaerobic hydrocarbon metabolism. Identifiable aerobic metabolites were confined to the LC samples, consistent with the metagenomic data. Overall, these data suggest that corrosion management might benefit from a more refined understanding of microbial community resilience in the face of disturbances such as nitrate treatment or pigging, which frequently prove insufficient to alter community structure toward a stable, less-corrosive assemblage.

Thiosulfate Conversion to Sulfide by a Haloalkaliphilic Microbial Community in a Bioreactor Fed with H2 Gas

In industrial gas biodesulfurization systems, where haloalkaline conditions prevail, a thiosulfate containing bleed stream is produced. This bleed stream can be treated in a separate bioreactor by reducing thiosulfate to sulfide and recycling it. By performing treatment and recycling of the bleed stream, its disposal decreases and less caustics are required to maintain the high pH. In this study, anaerobic microbial thiosulfate conversion to sulfide in a H₂/CO₂ fed bioreactor operated at haloalkaline conditions was investigated. Thiosulfate was converted by reduction to sulfide as well as disproportionation to sulfide and sulfate. Formate production from H₂/CO₂ was observed as an important reaction in the bioreactor. Formate, rather than H₂, might have been used as the main electron donor by thiosulfate/sulfate-reducing bacteria. The microbial community was dominated by bacteria belonging to the family Clostridiaceae most closely related to Tindallia texcoconensis. Bacteria phylogenetically related to known haloalkaline sulfate and thiosulfate reducers, thiosulfate-disproportionating bacteria, and remarkably sulfur-oxidizing bacteria were also detected. On the basis of the results, two approaches to treat the biodesulfurization waste stream are proposed: (i) addition of electron donor to reduce thiosulfate to sulfide and (ii) thiosulfate disproportionation without the need for an electron donor. The concept of application of solely thiosulfate disproportionation is discussed.

Dissulfurirhabdus thermomarina gen. nov., sp. nov., a thermophilic, autotrophic, sulfite-reducing and disproportionating deltaproteobacterium isolated from a shallow-sea hydrothermal vent

A thermophilic, anaerobic, chemolithoautotrophic bacterium, strain SH388^T, was isolated from a shallow, submarine hydrothermal vent (Kuril Islands, Russia). Cells of strain SH388^T were Gram-stain-negative short rods, 0.2-0.4 µm in diameter and 1.0-2.5 µm in length, and motile with flagella. The temperature range for growth was 25-58 °C (optimum 50 °C), and the pH range for growth was pH 5.0-7.0 (optimum pH 6.0-6.5). Growth of strain SH388^T was observed in the presence of NaCl concentrations ranging from 0.5 to 4.0 % (w/v) (optimum 2.0-2.5 %). The strain grew chemolithoautotrophically with molecular hydrogen as electron donor, sodium sulfite as electron acceptor and bicarbonate/CO2 as a carbon source. It was also able to grow by disproportionation of sulfite and elemental sulfur but not thiosulfate. Sulfate, Fe(III) and nitrate were not used as electron acceptors either with H2 or organic electron donors. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belonged to the class Deltaproteobacteria and was most closely related to Dissulfuribacter thermophilus and Dissulfurimicrobium hydrothermale (91.6 % and 90.4 % sequence similarity). On the basis of its physiological properties and results of phylogenetic analyses, strain SH388^T is considered to represent a novel species of a new genus, for which the name Dissulfurirhabdus thermomarina gen. nov., sp. nov. is proposed. The type strain of the species is SH388^T (=DSM 100025^T=VKM B-2960^T). It is the first thermophilic disproportionator of sulfur compounds isolated from a shallow-sea environment.

Adaptive strategies in the double-extremophilic prokaryotes inhabiting soda lakes

Haloalkaliphiles are double extremophilic organisms thriving both at high salinity and alkaline pH. Although numerous haloalkaliphilic representatives have been identified among Archaea and Bacteria over the past 15 years, the adaptations underlying their prosperity at haloalkaline conditions are scarcely known. A multi-level adaptive strategy was proposed to occur in haloalkaliphilic organisms isolated from saline alkaline and soda environments including adjustments in the cell wall structure, plasma membrane lipid composition, membrane transport systems, bioenergetics, and osmoregulation. Isolation of chemolithoautotrophic sulfur-oxidizing γ-Proteobacteria from soda lakes allowed the elucidation of the structural and physiological differences between haloalkaliphilic (prefer NaCl) and natronophilic (prefer NaHCO3/Na2CO3, i.e. soda) microbes.

Sulfate reduction in a hydrogen fed bioreactor operated at haloalkaline conditions

Biological sulfate reduction is used as a biotechnological process to treat sulfate rich streams. However, application of biological sulfate reduction at high pH and high salinity using H₂ was not thoroughly investigated before. In this work the sulfate reduction activity, biomass growth, microbial community and biomass aggregation were investigated in a H₂-fed gas lift bioreactor at haloalkaline conditions. The process was characterized by low sulfate reduction volumetric rates due to slow growth and lack of biomass aggregation. Apparently, the extreme conditions and absence of organic compounds prevented the formation of stable aggregates. The microbial community analysis revealed a low abundance of known haloalkaliphilic sulfate reducers and presence of a Tindallia sp. The identified archaea were related to Methanobacterium alcaliphilum and Methanocalculus sp. The biomass did not attach to metal sulfides, calcite and magnesite crystals. However, biofilm formation on the glass bioreactor walls showed that attachment to glass occurs.

Desulfosporosinus acididurans sp. nov.: an acidophilic sulfate-reducing bacterium isolated from acidic sediments

Three strains of sulfate-reducing bacteria (M1(T), D, and E) were isolated from acidic sediments (White river and Tinto river) and characterized phylogenetically and physiologically. All three strains were obligately anaerobic, mesophilic, spore-forming straight rods, stained Gram-negative and displayed variable motility during active growth. The pH range for growth was 3.8-7.0, with an optimum at pH 5.5. The temperature range for growth was 15-40 °C, with an optimum at 30 °C. Strains M1(T), D, and E used a wide range of electron donors and acceptors, with certain variability within the different strains. The nominated type strain (M1(T)) used ferric iron, nitrate, sulfate, elemental sulfur, and thiosulfate (but not arsenate, sulfite, or fumarate) as electron acceptors, and organic acids (formate, lactate, butyrate, fumarate, malate, and pyruvate), alcohols (glycerol, methanol, and ethanol), yeast extract, and sugars (xylose, glucose, and fructose) as electron donors. It also fermented some substrates such as pyruvate and formate. Strain M1(T) tolerated up to 50 mM ferrous iron and 10 mM aluminum, but was inhibited by 1 mM copper. On the basis of phenotypic, phylogenetic, and genetic characteristics, strains M1(T), D, and E represent a novel species within the genus Desulfosporosinus, for which the name Desulfosporosinus acididurans sp. nov. is proposed. The type strain is M1(T) (=DSM 27692(T) = JCM 19471(T)). Strain M1(T) was the first acidophilic SRB isolated, and it is the third described species of acidophilic SRB besides Desulfosporosinus acidiphilus and Thermodesulfobium narugense.

How could haloalkaliphilic microorganisms contribute to biotechnology?

Haloalkaliphiles are microorganisms requiring Na+concentrations of at least 0.5 mol·L–1and an alkaline pH of 9 for optimal growth. Their unique features enable them to make significant contributions to a wide array of biotechnological applications. Organic compatible solutes produced by haloalkaliphiles, such as ectoine and glycine betaine, are correlated with osmoadaptation and may serve as stabilizers of intracellular proteins, salt antagonists, osmoprotectants, and dermatological moisturizers. Haloalkaliphiles are an important source of secondary metabolites like rhodopsin, polyhydroxyalkanoates, and exopolysaccharides that play essential roles in biogeocycling organic compounds. These microorganisms also can secrete unique exoenzymes, including proteases, amylases, and cellulases, that are highly active and stable in extreme haloalkaline conditions and can be used for the production of laundry detergent. Furthermore, the unique metabolic pathways of haloalkaliphiles can be applied in the biodegradation and (or) biotransformation of a broad range of toxic industrial pollutants and heavy metals, in wastewater treatment, and in the biofuel industry.

Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases

The energy metabolism of essential microbial guilds in the biogeochemical sulfur cycle is based on a DsrAB-type dissimilatory (bi)sulfite reductase that either catalyzes the reduction of sulfite to sulfide during anaerobic respiration of sulfate, sulfite and organosulfonates, or acts in reverse during sulfur oxidation. Common use of dsrAB as a functional marker showed that dsrAB richness in many environments is dominated by novel sequence variants and collectively represents an extensive, largely uncharted sequence assemblage. Here, we established a comprehensive, manually curated dsrAB/DsrAB database and used it to categorize the known dsrAB diversity, reanalyze the evolutionary history of dsrAB and evaluate the coverage of published dsrAB-targeted primers. Based on a DsrAB consensus phylogeny, we introduce an operational classification system for environmental dsrAB sequences that integrates established taxonomic groups with operational taxonomic units (OTUs) at multiple phylogenetic levels, ranging from DsrAB enzyme families that reflect reductive or oxidative DsrAB types of bacterial or archaeal origin, superclusters, uncultured family-level lineages to species-level OTUs. Environmental dsrAB sequences constituted at least 13 stable family-level lineages without any cultivated representatives, suggesting that major taxa of sulfite/sulfate-reducing microorganisms have not yet been identified. Three of these uncultured lineages occur mainly in marine environments, while specific habitat preferences are not evident for members of the other 10 uncultured lineages. In summary, our publically available dsrAB/DsrAB database, the phylogenetic framework, the multilevel classification system and a set of recommended primers provide a necessary foundation for large-scale dsrAB ecology studies with next-generation sequencing methods.

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.

Phylogenetic diversity of microorganisms in subseafloor crustal fluids from Holes 1025C and 1026B along the Juan de Fuca Ridge flank

To expand investigations into the phylogenetic diversity of microorganisms inhabiting the subseafloor biosphere, basalt-hosted crustal fluids were sampled from Circulation Obviation Retrofit Kits (CORKs) affixed to Holes 1025C and 1026B along the Juan de Fuca Ridge (JdFR) flank using a clean fluid pumping system. These boreholes penetrate the crustal aquifer of young ocean crust (1.24 and 3.51 million years old, respectively), but differ with respect to borehole depth and temperature at the sediment-basement interface (147 m and 39°C vs. 295 m and 64°C, respectively). Cloning and sequencing of PCR-amplified small subunit ribosomal RNA genes revealed that fluids retrieved from Hole 1025C were dominated by relatives of the genus Desulfobulbus of the Deltaproteobacteria (56% of clones) and Candidatus Desulforudis of the Firmicutes (17%). Fluids sampled from Hole 1026B also contained plausible deep subseafloor inhabitants amongst the most abundant clone lineages; however, both geochemical analysis and microbial community structure reveal the borehole to be compromised by bottom seawater intrusion. Regardless, this study provides independent support for previous observations seeking to identify phylogenetic groups of microorganisms common to the deep ocean crustal biosphere, and extends previous observations by identifying additional lineages that may be prevalent in this unique environment.

Sulfate-dependent acetate oxidation under extremely natron-alkaline conditions by syntrophic associations from hypersaline soda lakes

So far, anaerobic sulfate-dependent acetate oxidation at high pH has only been demonstrated for a low-salt-tolerant syntrophic association of a clostridium 'Candidatus Contubernalis alkalaceticum' and its hydrogenotrophic sulfate-reducing partner Desulfonatronum cooperativum. Anaerobic enrichments at pH 10 inoculated with sediments from hypersaline soda lakes of the Kulunda Steppe (Altai, Russia) demonstrated the possibility of sulfate-dependent acetate oxidation at much higher salt concentrations (up to 3.5 M total Na(+)). The most salt-tolerant purified cultures contained two major components apparently working in syntrophy. The primary acetate-fermenting component was identified as a member of the order Clostridiales forming, together with 'Ca. Contubernalis alkalaceticum', an independent branch within the family Syntrophomonadaceae. A provisional name, 'Ca. Syntrophonatronum acetioxidans', is suggested for the novel haloalkaliphilic clostridium. Two phylotypes of extremely haloalkaliphilic sulfate-reducing bacteria of the genus Desulfonatronospira were identified as sulfate-reducing partners in the acetate-oxidizing cultures under extreme salinity. The dominant phylotype differed from the two species of Desulfonatronospira described so far, whilst a minor component belonged to Desulfonatronum thiodismutans. The results proved that, contrary to previous beliefs, sulfate-dependent acetate oxidation is possible, albeit very slowly, in nearly saturated soda brines.

Mercury methylation by novel microorganisms from new environments

Microbial mercury (Hg) methylation transforms a toxic trace metal into the highly bioaccumulated neurotoxin methylmercury (MeHg). The lack of a genetic marker for microbial MeHg production has prevented a clear understanding of Hg-methylating organism distribution in nature. Recently, a specific gene cluster (hgcAB) was linked to Hg methylation in two bacteria.1 Here we test if the presence of hgcAB orthologues is a reliable predictor of Hg methylation capability in microorganisms, a necessary confirmation for the development of molecular probes for Hg-methylation in nature. Although hgcAB orthologues are rare among all available microbial genomes, organisms are much more phylogenetically and environmentally diverse than previously thought. By directly measuring MeHg production in several bacterial and archaeal strains encoding hgcAB, we confirmed that possessing hgcAB predicts Hg methylation capability. For the first time, we demonstrated Hg methylation in a number of species other than sulfate- (SRB) and iron- (FeRB) reducing bacteria, including methanogens, and syntrophic, acetogenic, and fermentative Firmicutes. Several of these species occupy novel environmental niches for Hg methylation, including methanogenic habitats such as rice paddies, the animal gut, and extremes of pH and salinity. Identification of these organisms as Hg methylators now links methylation to discrete gene markers in microbial communities.

Enrichment and isolation of acidophilic sulfate-reducing bacteria from Tinto River sediments

Although some acidophilic and alkaliphilic species have been described recently, most of the known sulfate-reducing bacteria (SRB) grow optimally at neutral pH. In this study, sulfate reduction was studied with sediment samples from the extremely acidic Tinto River basin. Stable enrichments of SRB were obtained at pH 4 with glycerol, methanol and hydrogen; at pH 4.5 with lactate and at pH 5.5 with succinate as substrates. Inhibition of sulfate reduction by organic acids below their pKa was observed. Cloning and sequencing of 16S rRNA gene showed that fermentative bacteria (Paludibacter spp., Oscillibacter spp.) and SRB (Thermodesulfobium spp., Desulfosporosinus spp., Desulfitobacterium spp., Desulfotomaculum spp.) were co-enriched. By repeated serial dilutions and streaking on agar plates, four strains of SRB belonging to the Firmicutes phylum were obtained. Two of them show 96% 16S rRNA gene sequence similarity with Desulfosporosinus acidophilus, and a third one with Desulfosporosinus orientis. Another isolate has just 93% rRNA gene sequence similarity with the Desulfosporosinus/Desulfitobacterium cluster and might represent a novel species within a novel genus. One of the Desulfosporosinus strains was further investigated showing maximum growth at pH 5.5, and a pH-dependent inhibitory effect of organic acids and sulfide.

Disproportionation of elemental sulfur by haloalkaliphilic bacteria from soda lakes

Microbial disproportionation of elemental sulfur to sulfide and sulfate is a poorly characterized part of the anoxic sulfur cycle. So far, only a few bacterial strains have been described that can couple this reaction to cell growth. Continuous removal of the produced sulfide, for instance by oxidation and/or precipitation with metal ions such as iron, is essential to keep the reaction exergonic. Hitherto, the process has exclusively been reported for neutrophilic anaerobic bacteria. Here, we report for the first time disproportionation of elemental sulfur by three pure cultures of haloalkaliphilic bacteria isolated from soda lakes: the Deltaproteobacteria Desulfurivibrio alkaliphilus and Desulfurivibrio sp. AMeS2, and a member of the Clostridia, Dethiobacter alkaliphilus. All cultures grew in saline media at pH 10 by sulfur disproportionation in the absence of metals as sulfide scavengers. Our data indicate that polysulfides are the dominant sulfur species under highly alkaline conditions and that they might be disproportionated. Furthermore, we report the first organism (Dt. alkaliphilus) from the class Clostridia that is able to grow by sulfur disproportionation.

Fuchsiella alkaliacetigena gen. nov., sp. nov., an alkaliphilic, lithoautotrophic homoacetogen from a soda lake

The first alkaliphilic obligately anaerobic hydrogenotrophic homoacetogenic bacterium, strain Z-7100T, was isolated from sediments of the soda-depositing soda lake Tanatar III (Altay, Russia). Cells were thin, flexible rods, motile, Gram-negative and spore-forming. The organism was an obligate alkaliphile, growing at pH 8.5 to 10.5, with optimum growth at pH 8.8–9.3, and it grew in soda brines containing 1.9–4.7 M total Na+ (optimum at 2.8–3.3 M). It exhibited an obligate dependence upon sodium carbonate but not upon chloride ions with an NaCl range for growth of 0–14 % (w/v) and an optimum at 7.0–8.5 % (w/v). The isolate was mesophilic and grew at temperatures from 25 to 45 °C, with an optimum at 40 °C. An H2+CO2 mixture, ethanol, pyruvate and lactate were utilized with the formation of acetate as the sole metabolic product. Carbohydrates and amino acids did not support growth. The isolate had a respiratory type of metabolism, reducing NO 3 – , SeO4 2− or anthraquinone-2,6-disulfonate (as electron acceptors with ethanol as an electron donor). It was able to grow chemolithotrophically on H2+CO2 in medium supplemented with a vitamin solution only. The major cellular fatty acids were the saturated fatty acids anteiso-C15, C14 : 0 and C16 : 0 and the aldehydes C16, C14 and anteiso-C15. The DNA G+C content of the isolate was 32.0 mol%. 16S rRNA gene sequence analysis showed that strain Z-7100T is a member of the order Halanaerobiales and represents a new branch within the family Halobacteroidaceae , clustering with the type strain of Selenihalanaerobacter shriftii (92.9 % gene sequence similarity). On the basis of its physiological characteristics and phylogenetic position, the isolate is considered to represent a novel species in a new genus within the family Halobacteroidaceae . The name Fuchsiella alkaliacetigena gen. nov., sp. nov. is proposed. The type strain of the type species is Z-7100T ( = DSM 24880T = VKM B-2667T).

Desulfohalophilus alkaliarsenatis gen. nov., sp. nov., an extremely halophilic sulfate- and arsenate-respiring bacterium from Searles Lake, California

A haloalkaliphilic sulfate-respiring bacterium, strain SLSR-1, was isolated from a lactate-fed stable enrichment culture originally obtained from the extreme environment of Searles Lake, California. The isolate proved capable of growth via sulfate-reduction over a broad range of salinities (125–330 g/L), although growth was slowest at salt-saturation. Strain SLSR-1 was also capable of growth via dissimilatory arsenate-reduction and displayed an even broader range of salinity tolerance (50–330 g/L) when grown under these conditions. Strain SLSR-1 could also grow via dissimilatory nitrate reduction to ammonia. Growth experiments in the presence of high borate concentrations indicated a greater sensitivity of sulfate-reduction than arsenate-respiration to this naturally abundant anion in Searles Lake. Strain SLSR-1 contained genes involved in both sulfate-reduction (dsrAB) and arsenate respiration (arrA). Amplicons of 16S rRNA gene sequences obtained from DNA extracted from Searles Lake sediment revealed the presence of close relatives of strain SLSR-1 as part of the flora of this ecosystem despite the fact that sulfate-reduction activity could not be detected in situ. We conclude that strain SLSR-1 can only achieve growth via arsenate-reduction under the current chemical conditions prevalent at Searles Lake. Strain SLSR-1 is a deltaproteobacterium in the family Desulfohalobiacea of anaerobic, haloalkaliphilic bacteria, for which we propose the name Desulfohalophilus alkaliarsenatis gen. nov., sp. nov.

Thermosulfurimonas dismutans gen. nov., sp. nov., an extremely thermophilic sulfur-disproportionating bacterium from a deep-sea hydrothermal vent

An extremely thermophilic, anaerobic, chemolithoautotrophic bacterium (strain S95(T)) was isolated from a deep-sea hydrothermal vent chimney located on the Eastern Lau Spreading Center, Pacific Ocean, at a depth of 1910 m. Cells of strain S95(T) were oval to short Gram-negative rods, 0.5-0.6 µm in diameter and 1.0-1.5 µm in length, growing singly or in pairs. Cells were motile with a single polar flagellum. The temperature range for growth was 50-92 °C, with an optimum at 74 °C. The pH range for growth was 5.5-8.0, with an optimum at pH 7.0. Growth of strain S95(T) was observed at NaCl concentrations ranging from 1.5 to 3.5% (w/v). Strain S95(T) grew anaerobically with elemental sulfur as an energy source and bicarbonate/CO(2) as a carbon source. Elemental sulfur was disproportionated to sulfide and sulfate. Growth was enhanced in the presence of poorly crystalline iron(III) oxide (ferrihydrite) as a sulfide-scavenging agent. Strain S95(T) was also able to grow by disproportionation of thiosulfate and sulfite. Sulfate was not used as an electron acceptor. Analysis of the 16S rRNA gene sequence revealed that the isolate belongs to the phylum Thermodesulfobacteria. On the basis of its physiological properties and results of phylogenetic analyses, it is proposed that the isolate represents the sole species of a new genus, Thermosulfurimonas dismutans gen. nov., sp. nov.; S95(T) (=DSM 24515(T)=VKM B-2683(T)) is the type strain of the type species. This is the first description of a thermophilic micro-organism that disproportionates elemental sulfur.

Desulfonatronobacter acidivorans gen. nov., sp. nov. and Desulfobulbus alkaliphilus sp. nov., haloalkaliphilic heterotrophic sulfate-reducing bacteria from soda lakes

Two types of heterotrophic sulfate-reducing bacteria (SRB) were isolated from anoxic sediments of hypersaline soda lakes in Kulunda Steppe (Altai, Russia). The isolates used propionate as an energy and carbon source. Strain APT2(T) was enriched and isolated with thiosulfate as the electron acceptor. Strains APS1(T) and ASS1 were isolated with sulfate. Strain APT2(T) was a short rod and motile with a single subpolar flagellum, while strains APS1(T) and ASS1 were lemon-shaped oval rods and motile with a single polar flagellum and thin flagella-like filaments. Strain APT2(T) grew by complete oxidation of C(3)-C(8) fatty acids with thiosulfate or sulfate as the electron acceptor, while strains APS1(T) and ASS1 were much less versatile and utilized only propionate and pyruvate as the electron donor and carbon source with sulfate or sulfite as the electron acceptor. Furthermore, strains APS1(T) and ASS1 oxidized propionate incompletely to form acetate. All of the isolates were moderately halophilic and obligately alkaliphilic. Phylogenetic analysis based on 16S rRNA gene sequences placed the isolates in the order Desulfobacterales of the class Deltaproteobacteria. Strain APT2(T) belonged to the family Desulfobacteraceae and clustered with a halophilic SRB, Desulfosalsimonas propionicica PropA(T). Strains APS1(T) and ASS1 were closely related to each other and clustered with the genus Desulfobulbus of the family Desulfobulbaceae. On the basis of phenotypic and phylogenetic analysis, the isolates are proposed to represent two novel taxa, Desulfonatronobacter acidivorans gen. nov., sp. nov. (type strain of the type species APT2(T) = DSM 24257(T) = UNIQEM U853(T)) and Desulfobulbus alkaliphilus sp. nov. (type strain APS1(T) = DSM 24258(T) = UNIQEM U900(T)).

Culturable diversity of lithotrophic haloalkaliphilic sulfate-reducing bacteria in soda lakes and the description of Desulfonatronum thioautotrophicum sp. nov., Desulfonatronum thiosulfatophilum sp. nov., Desulfonatronovibrio thiodismutans sp. nov., and Desulfonatronovibrio magnus sp. nov

Soda lake sediments usually contain high concentrations of sulfide indicating active sulfate reduction. Monitoring of sulfate-reducing bacteria (SRB) in soda lakes demonstrated a dominance of two groups of culturable SRB belonging to the order Desulfovibrionales specialized in utilization of inorganic electron donors, such as formate, H₂ and thiosulfate. The most interesting physiological trait of the novel haloalkaliphilic SRB isolates was their ability to grow lithotrophically by dismutation of thiosulfate and sulfite. All isolates were obligately alkaliphilic with a pH optimum at 9.5–10 and moderately salt tolerant. Among the fifteen newly isolated strains, four belonged to the genus Desulfonatronum and the others to the genus Desulfonatronovibrio. None of the isolates were closely related to previously described species of these genera. On the basis of phylogenetic, genotypic and phenotypic characterization of the novel soda lake SRB isolates, two novel species each in the genera Desulfonatronum and Desulfonatronovibrio are proposed.

Sulfur-dependent respiration under extremely haloalkaline conditions in soda lake 'acetogens' and the description of Natroniella sulfidigena sp. nov

Microbial sulfidogenesis is the main dissimilatory anaerobic process in anoxic sediments of extremely haloalkaline soda lakes. In soda lakes with a salinity >2 M of the total Na(+) sulfate reduction is depressed, while thiosulfate- and sulfur-dependent sulfidogenesis may still be very active. Anaerobic enrichments at pH 10 and a salinity of 2-4 M total Na(+) from sediments of hypersaline soda lakes with thiosulfate and elemental sulfur as electron acceptors and simple nonfermentable electron donors resulted in the isolation of two groups of haloalkaliphilic bacteria capable of dissimilatory sulfidogenesis. Both were closely related to obligately heterotrophic fermentative homoacetogens from soda lakes. The salt-tolerant alkaliphilic thiosulfate-reducing isolates were identified as representatives of Tindallia magadiensis, while the extremely natronophilic obligate sulfur/polysulfide-respiring strains belonged to the genus Natroniella and are proposed here as a novel species Natroniella sulfidigena. Despite the close phylogenetic relation to Natroniella acetigena, it drastically differed from the type strain phenotypically (chemolithoautotrophic and acetate-dependent sulfur respiration, absence of acetate as the final metabolic product). Apparently, in the absence of specialized respiratory sulfidogens, primarily fermentative bacteria that are well adapted to extreme salinity may take over an uncharacteristic ecological function. This finding, once again, exemplifies the importance of isolation and phenotypic investigation of pure cultures.

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.

Thermodynamic limits to microbial life at high salt concentrations

Life at high salt concentrations is energetically expensive. The upper salt concentration limit at which different dissimilatory processes occur in nature appears to be determined to a large extent by bioenergetic constraints. The main factors that determine whether a certain type of microorganism can make a living at high salt are the amount of energy generated during its dissimilatory metabolism and the mode of osmotic adaptation used. I here review new data, both from field observations and from the characterization of cultures of new types of prokaryotes growing at high salt concentrations, to evaluate to what extent the theories formulated 12 years ago are still valid, need to be refined, or should be refuted on the basis of the novel information collected. Most data agree well with the earlier theories. Some new observations, however, are not easily explained: the properties of Natranaerobius and other haloalkaliphilic thermophilic fermentative anaerobes, growth of the sulfate-reducing Desulfosalsimonas propionicica with complete oxidation of propionate and Desulfovermiculus halophilus with complete oxidation of butyrate, growth of lactate-oxidizing sulfate reducers related to Desulfonatronovibrio at 346 g l(-1) salts at pH 9.8, and occurrence of methane oxidation in the anaerobic layers of Big Soda Lake and Mono Lake.

Sulfidogenesis under extremely haloalkaline conditions in soda lakes of Kulunda Steppe (Altai, Russia)

Sulfidogenic activity (SA) in anoxic sediments of several soda lakes with variable salinity in south Kulunda Steppe (Altai, Russia) has been investigated. The study included in situ measurements of sulfate reduction rates and laboratory experiments with sediment slurries in which sulfate, thiosulfate or elemental sulfur were used as electron acceptors. Despite the extreme conditions (high salt concentrations and high pH), the SA values were relatively high (ranging from 0.02 to 1.20 micromol HS(-) cm(-3) h(-1)), and only hampered under salt-saturated conditions. The highest SA was observed with elemental sulfur, followed by thiosulfate, while the lowest SA was determined in the presence of sulfate. Of all the electron donors tested, the addition of formate resulted in the highest SA with all three sulfur electron acceptors. Surprisingly, hydrogen as an electron donor had very little effect. Acetate was utilized as an electron donor only under sulfur-reducing conditions. Indigenous populations of sulfidogens in soda lake sediments showed an obligately alkaliphilic pH response of SA, showing a pattern that corresponded well to the in situ pH conditions. Sulfate reduction was much more susceptible to salt inhibition than thiosulfate and sulfur reduction. Microbiological investigations indicated that sulfate-reducing bacteria belonging to the orders Desulfovibrionales and Desulfobacterales could very likely be responsible for the SA with sulfate and thiosulfate as electron acceptors at moderate salt concentrations. Sulfur reduction at moderate salinity was carried out by a specialized group of haloalkaliphilic sulfur-reducing bacteria that utilize volatile fatty acids. In saturated soda brine, extremely natronophilic representatives of the order Halanaerobiales were responsible for the sulfur-dependent respiration.

Desulfurispira natronophila gen. nov. sp. nov.: an obligately anaerobic dissimilatory sulfur-reducing bacterium from soda lakes

Anaerobic enrichment cultures with elemental sulfur as electron acceptor and either acetate or propionate as electron donor and carbon source at pH 10 and moderate salinity inoculated with sediments from soda lakes in Kulunda Steppe (Altai, Russia) resulted in the isolation of two novel members of the bacterial phylum Chrysiogenetes. The isolates, AHT11 and AHT19, represent the first specialized obligate anaerobic dissimilatory sulfur respirers from soda lakes. They use either elemental sulfur/polysulfide or arsenate as electron acceptor and a few simple organic compounds as electron donor and carbon source. Elemental sulfur is reduced to sulfide through intermediate polysulfide, while arsenate is reduced to arsenite. The bacteria belong to the obligate haloalkaliphiles, with a pH growth optimum from 10 to 10.2 and a salt range from 0.2 to 3.0 M Na(+) (optimum 0.4-0.6 M). According to the phylogenetic analysis, the two strains were close to each other, but distinct from the nearest relative, the haloalkaliphilic sulfur-reducing bacterium Desulfurispirillum alkaliphilum, which was isolated from a bioreactor. On the basis of distinct phenotype and phylogeny, the soda lake isolates are proposed as a new genus and species, Desulfurispira natronophila (type strain AHT11(T) = DSM22071(T) = UNIQEM U758(T)).

Haloalkaliphilic spore-forming sulfidogens from soda lake sediments and description of Desulfitispora alkaliphila gen. nov., sp. nov

An anaerobic enrichment with pyruvate as electron donor and thiosulfate at pH 10 and 0.6 M Na(+) inoculated with pasteurized soda lake sediments resulted in a sulfidogenic coculture of two morphotypes of obligately anaerobic haloalkaliphilic endospore-forming clostridia, which were further isolated in pure culture. Strain AHT16 was a thin long rod able to ferment sugars and pyruvate and to respire H(2), formate and pyruvate using thiosulfate and fumarate as electron acceptors and growing optimally at pH 9.5. Thiosulfate was reduced incompletely to sulfide and sulfite. The strain was closely related (99% sequence similarity) to a peptolytic alkaliphilic clostridium Natronincola peptidovorans. Strain AHT17 was a short rod with a restricted respiratory metabolism, growing with pyruvate and lactate as electron donor and sulfite, thiosulfate and elemental sulfur as electron acceptors with a pH optimum 9.5. Thiosulfate was reduced completely via sulfite to sulfide. The ability of AHT17 to use sulfite explained the stability of the original coculture of the two clostridia-one member forming sulfite from thiosulfate and another consuming it. Strain AHT17 formed an independent deep phylogenetic lineage within the Clostridiales and is proposed as a new genus and species Desulfitisporum alkaliphilum gen. nov., sp. nov. (=DSM 22410(T) = UNIQEM U794(T)).