Isolation and characterisation of Thiobacillus halophilus sp. nov., a sulphur-oxidising autotrophic eubacterium from a Western Australian hypersaline lake

Thiobacillus spp. and Anaeromyxobacter spp. mediate arsenite oxidation-dependent biological nitrogen fixation in two contrasting types of arsenic-contaminated soils

As(III) oxidation-dependent biological nitrogen fixing (As-dependent BNF) bacteria use a novel biogeochemical process observed in tailings recently. However, our understanding of microorganisms responsible for As-dependent BNF is limited and whether such a process occurs in As-contaminated soils is still unknown. In this study, two contrasting types of soils (surface soils versus river sediments) heavily contaminated by As were selected to study the occurrence of As-dependent BNF. BNF was observed in sediments and soils amended with As(III), whereas no apparent BNF was found in the cultures without As(III). The increased abundances of the nitrogenase gene (nifH) and As(III) oxidation gene (aioA) suggest that an As-dependent BNF process was catalyzed by microorganisms harboring nifH and aioA. In addition, DNA-SIP demonstrated that Thiobacillus spp. and Anaeromyxobacter spp. were putative As-dependent BNF bacteria in As-contaminated soils and sediments, respectively. Metagenomic analysis further suggested that these taxa contained genes responsible for BNF, As(III) oxidation, and CO₂ fixation, demonstrating their capability for serving as As-dependent BNF. These results indicated the occurrence of As-dependent BNF in various As-contaminated habitats. The contrasting geochemical conditions in different types of soil suggested that these conditions may enrich different As-dependent BNF bacteria (Thiobacillus spp. for soils and Anaeromyxobacter spp. for sediments).

Metabolism of the Genus Guyparkeria Revealed by Pangenome Analysis

Halophilic sulfur-oxidizing bacteria belonging to the genus Guyparkeria occur at both marine and terrestrial habitats. Common physiological characteristics displayed by Guyparkeria isolates have not yet been linked to the metabolic potential encoded in their genetic inventory. To provide a genetic basis for understanding the metabolism of Guyparkeria, nine genomes were compared to reveal the metabolic capabilities and adaptations. A detailed account is given on Guyparkeria’s ability to assimilate carbon by fixation, to oxidize reduced sulfur, to oxidize thiocyanate, and to cope with salinity stress.

A combined approach of 16S rRNA and a functional marker gene, soxB to reveal the diversity of sulphur-oxidising bacteria in thermal springs

With the advent of new molecular tools, new taxa of sulphur-oxidising bacteria (SOB) in diverse environments are being discovered. However, there is a significant gap of knowledge about the ecology and diversity of SOB in thermal springs. Here, the species diversity and phylogenetic affiliations of SOB were investigated using 16S rRNA and functional gene marker, soxB in thermal springs of Thane district of Maharashtra, India. Most SOB detected by 16S rDNA sequences belong to different operational taxonomic units (OTU's): Firmicutes, α-, β-, γ-Proteobacteria and Actinobacteria with the dominance of first class. However, the soxB gene clone library sequences had shown affiliation with the β-, γ- and α-Proteobacteria. β-Proteobacteria-related sequences were dominant, with 53.3% clones belonging to genus Hydrogenophaga. The thiosulphate oxidation assay carried out for different isolates having distinct identity showed the mean sulphate-sulphur production from 117.86 ± 0.50 to 218.82 ± 2.56 mg SO₄-S l^-1 after 9 days of incubation. Also, sulphur oxidation by the genus Nitratireductor, Caldimonas, Geobacillus, Paenibacillus, Brevibacillus, Tristrella and Chelatococcus has been reported for the first time that reveals ecological widening over which thiotrophs are distributed.

Reclassification of Halothiobacillus hydrothermalis and Halothiobacillus halophilus to Guyparkeria gen. nov. in the Thioalkalibacteraceae fam. nov., with emended descriptions of the genus Halothiobacillus and family Halothiobacillaceae

The genus Halothiobacillus contains four species of obligate autotrophs with validly published names, of which Halothiobacillus halophilus and Halothiobacillus hydrothermalis are very distant from the type species - on the basis of the 16S rRNA gene, they have 90.7 % and 90.9 % identity to that of the type species, Halothiobacillus neapolitanus. As these values fall below the Yarza cut-off for the rank of genus, and these two species also show no clear affiliation to the closely related genus Thioalkalibacter, a polyphasic study was undertaken to determine if they represent a separate genus. Unlike Halothiobacillus spp. sensu stricto, H. halophilus and H. hydrothermalis are halophilic (rather than halotolerant) and moderately alkaliphilic (rather than neutrophilic) and additionally do not produce tetrathionate as a detectable intermediate of thiosulfate metabolism, indicating some significant metabolic differences. On the basis of these data and of functional gene examination, it is proposed that they be circumscribed as a new genus Guyparkeria gen.nov, for which the type species is Guyparkeria halophila gen. nov., comb. nov. Additionally, Thioalkalibacter and Guyparkeria gen. nov. fall distant from the Halothiobacillaceae so the Thioalkalibacteraceae fam. nov. is proposed, for which Thioalkalibacter is the type genus. Emended descriptions of Halothiobacillus, Halothiobacillus neapolitanus and the Halothiobacillaceae are provided.

Large perturbations in CO2 flux and subsequent chemosynthesis are induced in agricultural soil by the addition of elemental sulfur

The microbial contribution to soil organic matter has been shown to be much larger than previously thought and thus it plays a major role in carbon cycling. Among soil microorganisms, chemoautotrophs can fix CO₂ without sunlight and can glean energy through the oxidation of reduced elements such as sulfur. Here we show that the addition of sulfur to soil results in an initial surge in production of CO₂ through microbial respiration, followed by an order of magnitude increase in the capture of carbon from the atmosphere as elemental sulfur is oxidised to sulfate. Thiobacillus spp., take advantage of specific conditions to become the dominant chemoautotrophic group that consumes CO₂. We discern the direct incorporation of atmospheric carbon into soil carbohydrate, protein and aliphatic compounds and differentiate these from existing biomass. These results suggest that chemoautotrophs can play a large role in carbon cycling and that this carbon is heavily influenced by land management practises.

An overview of siderophores for iron acquisition in microorganisms living in the extreme

Siderophores are iron-chelating molecules produced by microbes when intracellular iron concentrations are low. Low iron triggers a cascade of gene activation, allowing the cell to survive due to the synthesis of important proteins involved in siderophore synthesis and transport. Generally, siderophores are classified by their functional groups as catecholates, hydroxamates and hydroxycarboxylates. Although other chemical structural modifications and functional groups can be found. The functional groups participate in the iron-chelating process when the ferri-siderophore complex is formed. Classified as acidophiles, alkaliphiles, halophiles, thermophiles, psychrophiles, piezophiles, extremophiles have particular iron requirements depending on the environmental conditions in where they grow. Most of the work done in siderophore production by extremophiles is based in siderophore concentration and/or genomic studies determining the presence of siderophore synthesis and transport genes. Siderophores produced by extremophiles are not well known and more work needs to be done to elucidate chemical structures and their role in microorganism survival and metal cycling in extreme environments.

Thiohalobacter thiocyanaticus gen. nov., sp. nov., a moderately halophilic, sulfur-oxidizing gammaproteobacterium from hypersaline lakes, that utilizes thiocyanate

A moderately halophilic, obligately chemolithoautotrophic, sulfur-oxidizing bacterium, designated strain HRh1T, was obtained from mixed sediment samples from hypersaline chloride–sulfate lakes in the Kulunda Steppe, in south-western Siberia (Russia), using aerobic enrichment culture at 1 M NaCl with thiocyanate as substrate. Cells of the isolate were short, non-motile rods with a Gram-negative type of cell wall. The bacterium was an obligate aerobe capable of chemolithoautotrophic growth with thiocyanate and thiosulfate. With thiosulfate, it grew at NaCl concentrations of 0.2–3.0 M (optimum 0.5 M) and at pH 6.3–8.0 (optimum pH 7.3–7.5). During growth on thiocyanate, cyanate was identified as an intermediate. The dominant cellular fatty acids were C16 : 0 and C18 : 1 ω7. Phylogenetic analysis based on 16S rRNA gene sequencing placed the isolate in the class Gammaproteobacteria as an independent lineage, with an unclassified marine sulfur-oxidizing bacterium as the closest culturable relative (93 % sequence similarity). A single cbbL gene (coding for the key enzyme of the Calvin–Benson cycle of autotrophic CO2 assimilation) with relatively low similarity to any homologous genes found in chemolithoautotrophs was detected in strain HRh1T. On the basis of our phenotypic and phylogenetic analysis, the halophilic isolate is proposed to represent a new genus and novel species, Thiohalobacter thiocyanaticus gen. nov., sp. nov. The type strain of Thiohalobacter thiocyanaticus is HRh1T (=DSM 21152T =UNIQEM U249T).

Molecular analysis of the microbial communities of Mars analog lakes in Western Australia

Unique, shallow interdune lakes and groundwaters with extremely low pH and high salinity exist in Australia, along with nearby lakes that possess higher pH values. These acidic hypersaline environments are possibly the best modern terrestrial analogues for past martian environments. However, no previous microbiological analyses of these lakes have been conducted. During the Australian winter of 2005, water samples were taken from several hypersaline lakes located in southern Western Australia that possessed acidic to slightly alkaline pH. These samples were subjected to molecular analysis to identify bacterial communities. DNA extraction and polymerase chain reaction (PCR) amplification of the 16S rRNA gene sequences, by using universal bacterial primers, were also performed on the samples. Extracted DNA was amplified with 1070 forward and 1392 GC-clamped reverse primers and analyzed by using denaturant gradient gel electrophoresis (DGGE). In addition, libraries were developed from DNA retrieved from four lakes, including a marginal marine neutral lake, an inland neutral lake, and two inland acid lakes, and selected clones with distinct operational taxonomic units were sequenced. The DGGE profiles and clone sequence data indicate that there are distinct, abundant, and diverse microbial populations in these Australian hypersaline environments, especially the acidic ones. These results are significant for two reasons: (1) they provide the first microbiological survey of natural acid saline lakes and (2) they hint at the possibility that there could have been a diverse microbial population in acidic hypersaline environments on Mars.

Biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse bacteria and archaea

Lithotrophic sulfur oxidation is an ancient metabolic process. Ecologically and taxonomically diverged prokaryotes have differential abilities to utilize different reduced sulfur compounds as lithotrophic substrates. Different phototrophic or chemotrophic species use different enzymes, pathways and mechanisms of electron transport and energy conservation for the oxidation of any given substrate. While the mechanisms of sulfur oxidation in obligately chemolithotrophic bacteria, predominantly belonging to Beta- (e.g. Thiobacillus) and Gammaproteobacteria (e.g. Thiomicrospira), are not well established, the Sox system is the central pathway in the facultative bacteria from Alphaproteobacteria (e.g. Paracoccus). Interestingly, photolithotrophs such as Rhodovulum belonging to Alphaproteobacteria also use the Sox system, whereas those from Chromatiaceae and Chlorobi use a truncated Sox complex alongside reverse-acting sulfate-reducing systems. Certain chemotrophic magnetotactic Alphaproteobacteria allegedly utilize such a combined mechanism. Sulfur-chemolithotrophic metabolism in Archaea, largely restricted to Sulfolobales, is distinct from those in Bacteria. Phylogenetic and biomolecular fossil data suggest that the ubiquity of sox genes could be due to horizontal transfer, and coupled sulfate reduction/sulfide oxidation pathways, originating in planktonic ancestors of Chromatiaceae or Chlorobi, could be ancestral to all sulfur-lithotrophic processes. However, the possibility that chemolithotrophy, originating in deep sea, is the actual ancestral form of sulfur oxidation cannot be ruled out.

Thiofaba tepidiphila gen. nov., sp. nov., a novel obligately chemolithoautotrophic, sulfur-oxidizing bacterium of the Gammaproteobacteria isolated from a hot spring

A novel obligately chemolithoautotrophic, sulfur-oxidizing bacterium designated strain BDA453T was isolated from a hot spring in Fukushima prefecture, Japan. The cells were short-rod-shaped and possessed an inclusion, a Gram-negative type cell wall and a single polar flagellum. Strain BDA453T grew by sulfur-oxidizing respiration with thiosulfate, elemental sulfur, sulfide and tetrathionate as electron donors and used only carbon dioxide as a carbon source. The optimum growth conditions were 45 degrees C, pH 6.5 and the absence of NaCl. Analysis of the 16S rRNA gene revealed that the isolate was a member of the Gammaproteobacteria and related to the genera Halothiobacillus and Thiovirga in the family Halothiobacillaceae. However, the phylogenetic tree constructed using 16S rRNA gene sequences showed that strain BDA453T was distant from any other known bacteria with sequence similarities of less than 90 %. On the basis of phenotypic features and phylogenetic analysis, strain BDA453T is considered to represent a novel species of a new genus within the family Halothiobacillaceae, for which the name Thiofaba tepidiphila gen. nov., sp. nov. is proposed. The type strain of Thiofaba tepidiphila is BDA453T (=NBRC 103218T=DSM 19618T).

Thiohalomonas denitrificans gen. nov., sp. nov. and Thiohalomonas nitratireducens sp. nov., novel obligately chemolithoautotrophic, moderately halophilic, thiodenitrifying Gammaproteobacteria from hypersaline habitats

A novel group of moderately halophilic, obligately chemolithoautotrophic, sulfur-oxidizing Gammaproteobacteria was found in sediments of various inland hypersaline lakes and a solar saltern. These bacteria were enriched and isolated with thiosulfate as electron donor and nitrate as electron acceptor at 2 M NaCl. Ten isolates (HLD strains) were long non-motile rods. They grew anaerobically as complete denitrifiers, and aerobically under micro-oxic conditions. Sulfate was the final product of thiosulfate and sulfide oxidation, and nitrite and N2O were intermediates of nitrate reduction to N2. The HLD strains grew optimally at pH 7.3–7.8, and at NaCl concentrations of 1.5–2.0 M. On the basis of phenotypic and genetic analysis, the moderately halophilic, thiodenitrifying isolates are proposed to be assigned to a new genus and species, Thiohalomonas denitrificans gen. nov., sp. nov. The type strain is HLD 2T (=DSM 15841T=UNIQEM U222T ). A single strain, HRhD 3spT, with vibrio-shaped cells, was obtained from a co-culture capable of complete denitrification of nitrate in the presence of either thiocyanate or thiosulfate as electron donor. It grew anaerobically with thiosulfate, reducing nitrate to nitrite, or under micro-oxic conditions at 1.0–2.5 M NaCl with an optimum at 1.0 M. Strain HRhD 3spT was genetically related to the HLD strains at the level of a separate species and is described as Thiohalomonas nitratireducens sp. nov. The type strain is HRhD 3spT (=DSM 16925T=UNIQEM U248T).

Denitrification in a binary culture and thiocyanate metabolism in Thiohalophilus thiocyanoxidans gen. nov. sp. nov. – a moderately halophilic chemolithoautotrophic sulfur-oxidizing Gammaproteobacterium from hypersaline lakes

Anaerobic enrichment culture with thiocyanate as electron donor and nitrate as electron acceptor at 2 M NaCl inoculated with a mixture of sediments from hypersaline lakes in Kulunda Steppe (Altai, Russia) resulted in a selection of a binary consortium of moderately halophilic, obligately chemolithoautotrophic sulfur-oxidizing bacteria (SOB) capable of complete denitrification of nitrate with thiosulfate as the electron donor. One consortium member, strain HRhD 3sp, was isolated into pure culture with nitrate and thiosulfate using a density gradient. This strain was responsible for the reduction of nitrate to nitrite in the consortium, while a second strain, HRhD 2, isolated under microoxic conditions with thiosulfate as substrate, was capable of anaerobic growth with nitrite and thiosulfate. Nitrite, either as substrate or as product, was already toxic at very low concentrations for both strains. As a result, optimal growth under anaerobic conditions could only be achieved within the consortium. On the basis of phylogenetic analysis, both organisms were identified as new lineages within the Gammaproteobacteria. As well as thiosulfate, strain HRhD 2 can also use thiocyanate as electron donor, representing a first halophilic SOB capable of growth with thiocyanate at 2-4 M NaCl. Product and enzymatic analysis identified the "carbonyl sulfide (COS) pathway" of primary thiocyanate degradation in this new species. On the basis of phenotypic and genetic analysis, strain HRhD 2 is proposed to be assigned to a new genus and species Thiohalophilus thiocyanoxidans.

Thiomicrospira halophila sp. nov., a moderately halophilic, obligately chemolithoautotrophic, sulfur-oxidizing bacterium from hypersaline lakes

Enrichments at 2 M NaCl and pH 7.5–8, with thiosulfate or sulfide as electron donor, inoculated with sediments from hypersaline chloride–sulfate lakes of the Kulunda Steppe (Altai, Russia) resulted in the domination of two different groups of moderately halophilic, chemolithoautotrophic, sulfur-oxidizing bacteria. Under fully aerobic conditions with thiosulfate, bacteria belonging to the genus Halothiobacillus dominated while, under microaerophilic conditions, a highly motile, short vibrio-shaped phenotype outcompeted the halothiobacilli. Three genetically and phenotypically highly similar vibrio-shaped isolates were obtained in pure culture and one of them, strain HL 5T, was identified as a member of the Thiomicrospira crunogena cluster by 16S rRNA gene sequencing. The new isolates were able to grow with thiosulfate as electron donor within a broad salinity range from 0.5 to 3.5 M NaCl with an optimum at 1.5 M and within a pH range from 6.5 to 8.5 with an optimum at pH 7.5–7.8. Comparative analysis of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) gene sequences demonstrated that strain HL 5T possessed two genes, cbbL-1 and cbbL-2, of the form I RuBisCO and a cbbM gene of the form II RuBisCO, similar to the other members of the Thiomicrospira crunogena cluster. On the basis of phenotypic and genetic comparison, the new halophilic isolates are proposed to be placed into a novel species, Thiomicrospira halophila sp. nov. (type strain HL 5T=DSM 15072T=UNIQEM U 221T).

Halothiobacillus neapolitanus strain OSWA isolated from "The Old Sulphur Well" at Harrogate (Yorkshire, England)

The "Old Sulphur Well" has a subterranean input of water containing 5.5mM total sulfide, which would be inhibitory to the growth of most bacteria. The obligately chemolithoautotrophic Halothiobacillus neapolitanus is a sulfur bacterium known to tolerate and metabolize high sulfide concentrations, and we report the isolation of H. neapolitanus strain OSWA from this source. Strain OSWA grows well on thiosulfate and tetrathionate as energy sources, and tolerates at least 5mM sulfide. Its specific growth rates and yields in batch culture were 0.22h(-1) and 5.3 gmol(-1) (thiosulfate), and 0.23 h(-1) and 9.5 gmol(-1) (tetrathionate). Its 16S rRNA gene sequence shows >99% identity to reference sequences of H. neapolitanus, and it shares morphological and physiological characteristics typical of the species. It is one of a very small number of strains of H. neapolitanus described to date, and the first to be isolated from an ancient sulfide-rich natural spa.

Isolation, characterization, and in situ detection of a novel chemolithoautotrophic sulfur-oxidizing bacterium in wastewater biofilms growing under microaerophilic conditions

We successfully isolated a novel aerobic chemolithotrophic sulfur-oxidizing bacterium, designated strain SO07, from wastewater biofilms growing under microaerophilic conditions. For isolation, the use of elemental sulfur (S(0)), which is the most abundant sulfur pool in the wastewater biofilms, as the electron donor was an effective measure to establish an enrichment culture of strain SO07 and further isolation. 16S rRNA gene sequence analysis revealed that newly isolated strain SO07 was affiliated with members of the genus Halothiobacillus, but it was only distantly related to previously isolated species (89% identity). Strain SO07 oxidized elemental sulfur, thiosulfate, and sulfide to sulfate under oxic conditions. Strain SO07 could not grow on nitrate. Organic carbons, including acetate, propionate, and formate, could not serve as carbon and energy sources. Unlike other aerobic sulfur-oxidizing bacteria, this bacterium was sensitive to NaCl; growth in medium containing more than 150 mM was negligible. In situ hybridization combined with confocal laser scanning microscopy revealed that a number of rod-shaped cells hybridized with a probe specific for strain SO07 were mainly present in the oxic biofilm strata (ca. 0 to 100 micro m) and that they often coexisted with sulfate-reducing bacteria in this zone. These results demonstrated that strain SO07 was one of the important sulfur-oxidizing populations involved in the sulfur cycle occurring in the wastewater biofilm and was primarily responsible for the oxidation of H(2)S and S(0) to SO(4)(2-) under oxic conditions.

Bioenergetic aspects of halophilism

Examination of microbial diversity in environments of increasing salt concentrations indicates that certain types of dissimilatory metabolism do not occur at the highest salinities. Examples are methanogenesis for H2 + CO2 or from acetate, dissimilatory sulfate reduction with oxidation of acetate, and autotrophic nitrification. Occurrence of the different metabolic types is correlated with the free-energy change associated with the dissimilatory reactions. Life at high salt concentrations is energetically expensive. Most bacteria and also the methanogenic Archaea produce high intracellular concentrations of organic osmotic solutes at a high energetic cost. All halophilic microorganisms expend large amounts of energy to maintain steep gradients of NA+ and K+ concentrations across their cytoplasmic membrane. The energetic cost of salt adaptation probably dictates what types of metabolism can support life at the highest salt concentrations. Use of KCl as an intracellular solute, while requiring far-reaching adaptations of the intracellular machinery, is energetically more favorable than production of organic-compatible solutes. This may explain why the anaerobic halophilic fermentative bacteria (order Haloanaerobiales) use this strategy and also why halophilic homoacetogenic bacteria that produce acetate from H2 + CO2 exist whereas methanogens that use the same substrates in a reaction with a similar free-energy yield do not.

Biology of moderately halophilic aerobic bacteria

The moderately halophilic heterotrophic aerobic bacteria form a diverse group of microorganisms. The property of halophilism is widespread within the bacterial domain. Bacterial halophiles are abundant in environments such as salt lakes, saline soils, and salted food products. Most species keep their intracellular ionic concentrations at low levels while synthesizing or accumulating organic solutes to provide osmotic equilibrium of the cytoplasm with the surrounding medium. Complex mechanisms of adjustment of the intracellular environments and the properties of the cytoplasmic membrane enable rapid adaptation to changes in the salt concentration of the environment. Approaches to the study of genetic processes have recently been developed for several moderate halophiles, opening the way toward an understanding of haloadaptation at the molecular level. The new information obtained is also expected to contribute to the development of novel biotechnological uses for these organisms.

Taxonomic relationships of Thiobacillus halophilus, T. aquaesulis, and other species of Thiobacillus, as determined using 16S rDNA sequencing

Total base sequences of the 16S rRNA genes of Thiobacillus halophilus and Thiobacillus aquaesulis show that these bacteria fall into the gamma- and beta-subdivisions, respectively of the Proteobacteria. The closest relative of T. halophilus is Thiobacillus hydrothermalis (with 98.7% similarity), and the closest relative of T. aquaesulis is Thiobacillus thioparus (93.2% similarity). Physiological properties and mol% G+C content of their DNA serve to confirm that these four organisms are all distinct species. It is reiterated that the species currently assigned to the genus Thiobacillus are clearly so diverse that they need reclassification into several genera. The type species, T. thioparus, is unequivocally placed in the beta-subdivision of the Proteobacteria, thus requiring that the use of the genus name Thiobacillus be restricted to the chemolithoautotrophic species falling into that group. T. aquaesulis and T. thioparus may thus be regarded as true species of Thiobacillus. The relatively large number of obligately chemolithoautotrophic Thiobacillus species falling in the gamma-subdivision of the Proteobacteria need further study in order to assess the case for reclassification into one or more new or different genera.