Complete genome sequence of Desulfarculus baarsii type strain (2st14)

Nitrate and oxygen significantly changed the abundance rather than structure of sulphate-reducing and sulphur-oxidising bacteria in water retrieved from petroleum reservoirs

Sulphate-reducing bacteria (SRB) are the main culprits of microbiologically influenced corrosion in water-flooding petroleum reservoirs, but some sulphur-oxidising bacteria (SOB) are stimulated when nitrate and oxygen are injected, which control the growth of SRB. This study aimed to determine the distributions of SRB and SOB communities in injection-production systems and to analyse the responses of these bacteria to different treatments involving nitrate and oxygen. Desulfovibrio, Desulfobacca, Desulfobulbus, Sulfuricurvum and Dechloromonas were commonly detected via 16S rRNA gene sequencing. Still, no significant differences were observed for either the SRB or SOB communities between injection and production wells. Three groups of water samples collected from different sampling sites were incubated. Statistical analysis of functional gene (dsrB and soxB) clone libraries and quantitative polymerase chain reaction showed that the SOB community structures were more strongly affected by the nitrate and oxygen levels than SRB clustered according to the sampling site; moreover, both the SRB and SOB community abundances significantly changed. Additionally, the highest SRB inhibitory effect and the lowest dsrB/soxB ratio were obtained under high concentrations of nitrate and oxygen in the three groups, suggesting that the synergistic effect of nitrate and oxygen level was strong on the inhibition of SRB by potential SOB.

Biogeochemical characterization of four depleted gas reservoirs for conversion into underground hydrogen storage

Depleted gas reservoirs are a valuable option for underground hydrogen storage (UHS). However, different classes of microorganisms, which are capable of using free H2 as a reducing agent for their metabolism, inhabit deep underground formations and can potentially affect the storage. This study integrates metagenomics based on Illumina-NGS sequencing of bacterial and archaeal 16S rRNA and dsrB and mcrA functional genes to unveil the composition and the variability of indigenous microbial populations of four Italian depleted reservoirs. The obtained mcrA sequences allow us to implement the existing taxonomic database for mcrA gene sequences with newly classified sequences obtained from the Italian gas reservoirs. Moreover, the KEGG and COG predictive functional annotation was used to highlight the metabolic pathways potentially associated with hydrogenotrophic metabolisms. The analyses revealed the specificity of each reservoir microbial community, and taxonomic and functional data highlighted the presence of an enriched number of taxa, whose activity depends on both reservoir hydrochemical composition and nutrient availability, of potential relevance in the context of UHS. This study is the very first to address the profiling of the microbial population and allowed us to perform a preliminary assessment of UHS feasibility in Italy.

Desulfoferula mesophilus gen. nov. sp. nov., a mesophilic sulfate-reducing bacterium isolated from a brackish lake sediment

A novel sulfate-reducing bacterium (strain 12FAKT) was isolated from sediment sampled from a brackish lake in Japan. Respiratory growth was observed with formate and pyruvate as an electron donor. Sulfate, thiosulfate, elemental sulfur and dimethyl sulfoxide were utilized as an electron acceptor. The isolate grew over a temperature range of 18-42 °C (optimum 35-37 °C), a NaCl concentration range of 50-450 mM (optimum 150-300 mM) and a pH range of 6.6-7.5. The 12FAKT genome consists of a circular chromosome with a length of 4.5 Mbp and G + C content of 63.6%. Based on 16S rRNA gene sequence similarity, the closest cultured relative was Desulfarculus baarsii 2st14T (92.2%). Genome-based phylogenetic analysis placed strain 12FAKT within the family Desulfarculaceae but did not affiliate the strain with any existing genus. Taken together, we propose a novel species of a novel genus, Desulfoferula mesophilus gen. nov. sp. nov. with the type strain 12FAKT (= DSM 115219T = JCM 39399T).

Isethionate is an intermediate in the degradation of sulfoacetate by the human gut pathobiont Bilophila wadsworthia

The obligately anaerobic sulfite-reducing bacterium Bilophila wadsworthia is a common human pathobiont inhabiting the distal intestinal tract. It has a unique ability to utilize a diverse range of food- and host-derived sulfonates to generate sulfite as a terminal electron acceptor (TEA) for anaerobic respiration, converting the sulfonate sulfur to H2S, implicated in inflammatory conditions and colon cancer. The biochemical pathways involved in the metabolism of the C2 sulfonates isethionate and taurine by B. wadsworthia were recently reported. However, its mechanism for metabolizing sulfoacetate, another prevalent C2 sulfonate, remained unknown. Here, we report bioinformatics investigations and in vitro biochemical assays that uncover the molecular basis for the utilization of sulfoacetate as a source of TEA (STEA) for B. wadsworthia, involving conversion to sulfoacetyl-CoA by an ADP-forming sulfoacetate-CoA ligase (SauCD), and stepwise reduction to isethionate by NAD(P)H-dependent enzymes sulfoacetaldehyde dehydrogenase (SauS) and sulfoacetaldehyde reductase (TauF). Isethionate is then cleaved by the O2-sensitive isethionate sulfolyase (IseG), releasing sulfite for dissimilatory reduction to H2S. Sulfoacetate in different environments originates from anthropogenic sources such as detergents, and natural sources such as bacterial metabolism of the highly abundant organosulfonates sulfoquinovose and taurine. Identification of enzymes for anaerobic degradation of this relatively inert and electron-deficient C2 sulfonate provides further insights into sulfur recycling in the anaerobic biosphere, including the human gut microbiome.

Iron and sulfate reduction structure microbial communities in (sub-)Antarctic sediments

Permanently cold marine sediments are heavily influenced by increased input of iron as a result of accelerated glacial melt, weathering, and erosion. The impact of such environmental changes on microbial communities in coastal sediments is poorly understood. We investigated geochemical parameters that shape microbial community compositions in anoxic surface sediments of four geochemically differing sites (Annenkov Trough, Church Trough, Cumberland Bay, Drygalski Trough) around South Georgia, Southern Ocean. Sulfate reduction prevails in Church Trough and iron reduction at the other sites, correlating with differing local microbial communities. Within the order Desulfuromonadales, the family Sva1033, not previously recognized for being capable of dissimilatory iron reduction, was detected at rather high relative abundances (up to 5%) while other members of Desulfuromonadales were less abundant (<0.6%). We propose that Sva1033 is capable of performing dissimilatory iron reduction in sediment incubations based on RNA stable isotope probing. Sulfate reducers, who maintain a high relative abundance of up to 30% of bacterial 16S rRNA genes at the iron reduction sites, were also active during iron reduction in the incubations. Thus, concurrent sulfate reduction is possibly masked by cryptic sulfur cycling, i.e., reoxidation or precipitation of produced sulfide at a small or undetectable pool size. Our results show the importance of iron and sulfate reduction, indicated by ferrous iron and sulfide, as processes that shape microbial communities and provide evidence for one of Sva1033's metabolic capabilities in permanently cold marine sediments.

Microbial ecology of sulfur cycling near the sulfate-methane transition of deep-sea cold seep sediments

Microbial sulfate reduction is largely associated with anaerobic methane oxidation and alkane degradation in sulfate-methane transition zone (SMTZ) of deep-sea cold seeps. How the sulfur cycling is mediated by microbes near SMTZ has not been fully understood. In this study, we detected a shallow SMTZ in three of eight sediment cores sampled from two cold seep areas in the South China Sea. One hundred ten genomes representing sulfur-oxidizing bacteria (SOB) and sulfur-reducing bacteria (SRB) strains were identified from three SMTZ-bearing cores. In the layers above SMTZ, SOB were mostly constituted by Campylobacterota, Gammaproteobacteria and Alphaproteobacteria that probably depended on nitrogen oxides and/or oxygen for oxidation of sulfide and thiosulfate in near-surface sediment layers. In the layers below the SMTZ, the deltaproteobacterial SRB genomes and metatranscriptomes revealed CO₂ fixation by Wood-Ljungdahl pathway, sulfate reduction and nitrogen fixation for syntrophic or fermentative lifestyle. A total of 68% of the metagenome assembled genomes were not adjacent to known species in a phylogenomic tree, indicating a high diversity of bacteria involved in sulfur cycling. With the large number of genomes for SOB and SRB, our study uncovers the microbial populations that potentially mediate sulfur metabolism and associated carbon and nitrogen cycles, which sheds light on complex biogeochemical processes in deep-sea environments.

Assessing the Diversity of Benthic Sulfate-Reducing Microorganisms in Northwestern Gulf of Mexico by Illumina Sequencing of dsrB Gene

This study investigates the community composition, structure, and abundance of sulfate-reducing microorganisms (SRM) in surficial sediments of the Northwestern Gulf of Mexico (NWGoM) along a bathymetric gradient. For these purposes, Illumina sequencing and quantitative PCR (qPCR) of the dissimilatory sulfite reductase gene beta subunit (dsrB gene) were performed. Bioinformatic analyses indicated that SRM community was predominantly composed by members of Proteobacteria and Firmicutes across all the samples. However, Actinobacteria, Thermodesulfobacteria, and Chlorobi were also detected. Phylogenetic analysis indicated that unassigned dsrB sequences were related to Deltaproteobacteria and Nitrospirota superclusters, Euryarchaeota, and to environmental clusters. PCoA ordination revealed that samples clustered in three different groups. PERMANOVA indicated that water depth, temperature, redox, and nickel and cadmium content were the main environmental drivers for the SRM communities in the studied sites. Alpha diversity and abundance of SRM were lower for deeper sites, suggesting decreasing sulfate reduction activity with respect to water depth. This study contributes with the understanding of distribution and composition of dsrAB-containing microorganisms involved in sulfur transformations that may contribute to the resilience and stability of the benthic microbial communities facing metal and hydrocarbon pollution in the NWGoM, a region of recent development for oil and gas drilling.

High rate of biological removal of sulfate, organic matter, and metals in UASB reactor to treat synthetic acid mine drainage and cheese whey wastewater as carbon source

The anaerobic biological treatment of sulfate-rich effluents, such as acid mine drainage (AMD), is mediated by sulfate-reducing bacteria (SRB). This process involves the reduction of sulfates in the presence of an electron donor. Complex carbon compounds can be used as electron donors. In the present study, was used an upflow anaerobic sludge blanket (UASB) reactor to co-treat a low-pH synthetic AMD and cheese whey wastewater (CWW). Were observed higher sulfate and COD removal rates (1,114 ± 88 and 1,214 ± 128 mg L^-1  day^-1 , respectively) at higher sulfate and applied COD loading rates (1,500 mg L^-1  day^-1 ). The overall pH of the effluent remained above 6.4 without any bicarbonate supplementation. Almost 100% of the Fe, Zn, and Cu was removed and the presence of metals improved the process. The use of a single reactor to treat AMD and CWW is promising. PRACTITIONER POINTS: Wastewater cheese whey was electron donor for treating acid mine drainage in an UASB reactor. Metals additions in the system indicated an increased removal of COD. About 99% of the metals were removed with the treatment.

COD/sulfate ratio does not affect the methane yield and microbial diversity in anaerobic digesters

Anaerobic digestion of organic matter is the major route of biomethane production. However, in the presence of sulfate, sulfate-reducing bacteria (SRB) typically outcompete methanogens, which may reduce or even preclude methane production from sulfate-containing wastewaters. Although sulfate-reduction and methanogenesis can occur simultaneously, our limited understanding of the microbiology of anaerobic digesters treating sulfate-containing wastewaters constrains improvements in the production of methane from these systems. This study tested the effects of carbon sources and chemical oxygen demand-to-sulfate ratio (COD/SO₄^2-) on the diversity and interactions of SRB and methanogens in an anaerobic digester treating a high-sulfate waste stream. Overall, the data showed that sulfate removal and methane generation occurred in varying efficiencies and the carbon source had limited effect on the methane yield. Importantly, the results demonstrated that methanogenic and SRB diversities were only affected by the carbon source and not by the COD/SO₄^2- ratio.

Anaerobic degradation of hexadecane and phenanthrene coupled to sulfate reduction by enriched consortia from northern Gulf of Mexico seafloor sediment

To advance understanding of the fate of hydrocarbons released from the Deepwater Horizon oil spill and deposited in marine sediments, this study characterized the microbial populations capable of anaerobic hydrocarbon degradation coupled with sulfate reduction in non-seep sediments of the northern Gulf of Mexico. Anaerobic, sediment-free enrichment cultures were obtained with either hexadecane or phenanthrene as sole carbon source and sulfate as a terminal electron acceptor. Phylogenetic analysis revealed that enriched microbial populations differed by hydrocarbon substrate, with abundant SSU rRNA gene amplicon sequences from hexadecane cultures showing high sequence identity (up to 98%) to Desulfatibacillum alkenivorans (family Desulfobacteraceae), while phenanthrene-enriched populations were most closely related to Desulfatiglans spp. (up to 95% sequence identity; family Desulfarculaceae). Assuming complete oxidation to CO2, observed stoichiometric ratios closely resembled the theoretical ratios of 12.25:1 for hexadecane and 8.25:1 for phenanthrene degradation coupled to sulfate reduction. Phenanthrene carboxylic acid was detected in the phenanthrene-degrading enrichment cultures, providing evidence to indicate carboxylation as an activation mechanism for phenanthrene degradation. Metagenome-assembled genomes (MAGs) revealed that phenanthrene degradation is likely mediated by novel genera or families of sulfate-reducing bacteria along with their fermentative syntrophic partners, and candidate genes linked to the degradation of aromatic hydrocarbons were detected for future study.

Acetate Activates Deep Subsurface Fracture Fluid Microbial Communities in Olkiluoto, Finland

Crystalline bedrock has been chosen for deep geologic long-term storage of used nuclear fuel in Finland. The risks generated by the deep subsurface microbial communities in these disposal sites need to be well characterised in advance to ensure safety. Deep subsurface microbial communities in a steady state are unlikely to contribute to known risk factors, such as corrosion or gas production. However, the construction of the geological final-disposal facility, bedrock disturbances, and hydraulic gradients cause changes that affect the microbial steady-state. To study the induced metabolism of deep microbial communities in changing environmental conditions, the activating effect of different electron donors and acceptors were measured with redox sensing fluorescent dyes (5-Cyano-2,3-ditolyl tetrazolium chloride, CTC and RedoxSensor™ Green, RSG). Fluids originating from two different fracture zones of the Finnish disposal site in Olkiluoto were studied. These fracture fluids were very dissimilar both chemically and in terms of bacterial and archaeal diversity. However, the microbial communities of both fracture fluids were activated, especially with acetate, which indicates the important role of acetate as a preferred electron donor for Olkiluoto deep subsurface communities.

Biogeochemical Cycling by a Low-Diversity Microbial Community in Deep Groundwater

Olkiluoto, an island on the south-west coast of Finland, will host a deep geological repository for the storage of spent nuclear fuel. Microbially induced corrosion from the generation of sulphide is therefore a concern as it could potentially compromise the longevity of the copper waste canisters. Groundwater at Olkiluoto is geochemically stratified with depth and elevated concentrations of sulphide are observed when sulphate-rich and methane-rich groundwaters mix. Particularly high sulphide is observed in methane-rich groundwater from a fracture at 530.6 mbsl, where mixing with sulphate-rich groundwater occurred as the result of an open drill hole connecting two different fractures at different depths. To determine the electron donors fuelling sulphidogenesis, we combined geochemical, isotopic, metagenomic and metaproteomic analyses. This revealed a low diversity microbial community fuelled by hydrogen and organic carbon. Sulphur and carbon isotopes of sulphate and dissolved inorganic carbon, respectively, confirmed that sulphate reduction was ongoing and that CO₂ came from the degradation of organic matter. The results demonstrate the impact of introducing sulphate to a methane-rich groundwater with limited electron acceptors and provide insight into extant metabolisms in the terrestrial subsurface.

Short-sludge age EBPR process - Microbial and biochemical process characterisation during reactor start-up and operation

The new paradigm for used water treatment suggests the use of short solid retention times (SRT) to minimize organic substrate mineralization and to maximize resource recovery. However, little is known about the microbes and the underlying biogeochemical mechanisms driving these short-SRT systems. In this paper, we report the start-up and operation of a short-SRT enhanced biological phosphorus removal (EBPR) system operated as a sequencing batch reactor (SBR) fed with preclarified municipal wastewater, which is supplemented with propionate. The microbial community was analysed via 16S rRNA amplicon sequencing. During start-up (SRT = 8 d), the EBPR was removing up to 99% of the influent phosphate and completely oxidized the incoming ammonia. Furthermore, the sludge showed excellent settling properties. However, once the SRT was shifted to 3.5 days nitrification was inhibited and bacteria of the Thiothrix taxon proliferated in the reactor, thereby leading to filamentous bulking (sludge volume index up to SVI = 1100 mL/g). Phosphorus removal deteriorated during this period, likely due to the out-competition of polyphosphate accumulating organisms (PAO) by sulphate reducing bacteria (SRB). Subsequently, SRB activity was suppressed by reducing the anaerobic SRT from 1.2 day to 0.68 day, with a consequent rapid SVI decrease to ∼200 ml/g. The short-SRT EBPR effectively removed phosphate and nitrification was mitigated at SRT = 3 days and oxygen levels ranging from 2 to 3 mg/L.

Electricity Recovery from Municipal Sewage Wastewater Using a Hydrogel Complex Composed of Microbially Reduced Graphene Oxide and Sludge

Graphene oxide (GO) has recently been shown to be an excellent anode substrate for exoelectrogens. This study demonstrates the applicability of GO in recovering electricity from sewage wastewater. Anaerobic incubation of sludge with GO formed a hydrogel complex that embeds microbial cells via π-π stacking of microbially reduced GO. The rGO complex was electrically conductive (23 mS·cm⁻¹) and immediately produced electricity in sewage wastewater under polarization at +200 mV vs. Ag/AgCl. Higher and more stable production of electricity was observed with rGO complexes (179–310 μA·cm⁻³) than with graphite felt (GF; 79–95 μA·cm⁻³). Electrochemical analyses revealed that this finding was attributable to the greater capacitance and smaller internal resistance of the rGO complex. Microbial community analysis showed abundances of Geobacter species in both rGO and GF complexes, whereas more diverse candidate exoelectrogens in the Desulfarculaceae family and Geothrix genus were particularly prominent in the rGO complex.

Dethiosulfatarculus sandiegensis gen. nov., sp. nov., isolated from a methanogenic paraffin-degrading enrichment culture and emended description of the family Desulfarculaceae

A mesophilic deltaproteobacterium, designated strain SPR^T, was isolated from a methanogenic consortium capable of degrading long-chain paraffins. Cells were motile, vibrio-shaped, and occurred singly, in pairs or in clusters. Strain SPR^T did not metabolize hydrocarbons but grew fermentatively on pyruvate and oxaloacetate and autotrophically with H₂ and CO₂. Thiosulfate served as a terminal electron acceptor, but sulfate or sulfite did not. The organism required at least 10 g NaCl l^- 1 and a small amount of yeast extract (0.001%) for growth. Optimal growth was observed between 30 and 37 °C and a pH range from 6.0 to 7.2. The DNA G+C content of SPR^T's genome was 52.02 mol%. Based on 16S rRNA gene sequence analysis, strain SPR^T was distinct from previously described Deltaproteobacteria, exhibiting the closest affiliation to Desulfarculus baarsii DSM 2075^T and Desulfocarbo indianensis SCBM^T, with only 91% similarity between their respective 16S gene sequences. In silico genome comparison supported the distinctiveness between strain SPR^T and both Desulfocarbo indianensis SCBM^T and Desulfarculus baarsii DSM 2075^T. Based on physiological differences, as well as phylogenetic and genomic comparisons, we propose to classify SPR^T as the type strain ( = DSM 100305^T = JCM 30857^T) of a novel species of a new genus with the name Dethiosulfatarculus sandiegensis gen. nov., sp. nov.

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.

Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics

Stratified sulfurous lakes are appropriate environments for studying the links between composition and functionality in microbial communities and are potentially modern analogs of anoxic conditions prevailing in the ancient ocean. We explored these aspects in the Lake Banyoles karstic area (NE Spain) through metagenomics and in silico reconstruction of carbon, nitrogen and sulfur metabolic pathways that were tightly coupled through a few bacterial groups. The potential for nitrogen fixation and denitrification was detected in both autotrophs and heterotrophs, with a major role for nitrogen and carbon fixations in Chlorobiaceae. Campylobacterales accounted for a large percentage of denitrification genes, while Gallionellales were putatively involved in denitrification, iron oxidation and carbon fixation and may have a major role in the biogeochemistry of the iron cycle. Bacteroidales were also abundant and showed potential for dissimilatory nitrate reduction to ammonium. The very low abundance of genes for nitrification, the minor presence of anammox genes, the high potential for nitrogen fixation and mineralization and the potential for chemotrophic CO2 fixation and CO oxidation all provide potential clues on the anoxic zones functioning. We observed higher gene abundance of ammonia-oxidizing bacteria than ammonia-oxidizing archaea that may have a geochemical and evolutionary link related to the dominance of Fe in these environments. Overall, these results offer a more detailed perspective on the microbial ecology of anoxic environments and may help to develop new geochemical proxies to infer biology and chemistry interactions in ancient ecosystems.

The class III ribonucleotide reductase from Neisseria bacilliformis can utilize thioredoxin as a reductant

The class III anaerobic ribonucleotide reductases (RNRs) studied to date couple the reduction of ribonucleotides to deoxynucleotides with the oxidation of formate to CO2. Here we report the cloning and heterologous expression of the Neisseria bacilliformis class III RNR and show that it can catalyze nucleotide reduction using the ubiquitous thioredoxin/thioredoxin reductase/NADPH system. We present a structural model based on a crystal structure of the homologous Thermotoga maritima class III RNR, showing its architecture and the position of conserved residues in the active site. Phylogenetic studies suggest that this form of class III RNR is present in bacteria and archaea that carry out diverse types of anaerobic metabolism.

Acetone utilization by sulfate-reducing bacteria: draft genome sequence of Desulfococcus biacutus and a proteomic survey of acetone-inducible proteins

Background

The sulfate-reducing bacterium Desulfococcus biacutus is able to utilize acetone for growth by an inducible degradation pathway that involves a novel activation reaction for acetone with CO as a co-substrate. The mechanism, enzyme(s) and gene(s) involved in this acetone activation reaction are of great interest because they represent a novel and yet undefined type of activation reaction under strictly anoxic conditions.

Results

In this study, a draft genome sequence of D. biacutus was established. Sequencing, assembly and annotation resulted in 159 contigs with 5,242,029 base pairs and 4773 predicted genes; 4708 were predicted protein-encoding genes, and 3520 of these had a functional prediction. Proteins and genes were identified that are specifically induced during growth with acetone. A thiamine diphosphate-requiring enzyme appeared to be highly induced during growth with acetone and is probably involved in the activation reaction. Moreover, a coenzyme B₁₂- dependent enzyme and proteins that are involved in redox reactions were also induced during growth with acetone.

Conclusions

We present for the first time the genome of a sulfate reducer that is able to grow with acetone. The genome information of this organism represents an important tool for the elucidation of a novel reaction mechanism that is employed by a sulfate reducer in acetone activation.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-584) contains supplementary material, which is available to authorized users.

Desulfocarbo indianensis gen. nov., sp. nov., a benzoate-oxidizing, sulfate-reducing bacterium isolated from water extracted from a coal bed

A novel, strictly anaerobic, sulfate-reducing bacterium, designated strain SCBM(T), was isolated from water extracted from a coal bed in Indiana, USA. The isolate was characterized by a polyphasic taxonomic approach that included phenotypic and genotypic characterizations. Cells of strain SCBM(T) were vibrio-shaped, polarly flagellated, Gram-negative, motile, oxidase-negative and weakly catalase-positive. Growth of strain SCBM(T) was observed at NaCl concentrations ranging from 0 to 300 mM. However, no growth was observed when 1 M or more NaCl was present. Growth was observed at 16-37 °C, with optimal growth at 30 °C. The optimum pH for growth was 7, although growth was observed from pH 6.5 to 8. The doubling time under optimal growth conditions (30 °C, pH 7, 2.5 mM benzoate, 14 mM sulfate) was 2.7 days. Bicarbonate, HEPES, PIPES and MES were effective buffers for growth of strain SCBM(T), but citrate inhibited growth. When sulfate was provided as the electron acceptor, strain SCBM(T) grew autotrophically with hydrogen as the electron donor and heterotrophically on benzoate, formate, acetate, pyruvate, butyrate, fumarate, succinate and palmitate. None of the substrates tested supported fermentative growth. Thiosulfate and sulfate were used as electron acceptors coupled to benzoate oxidation, but sulfite, elemental sulfur, DMSO, anthraquinone 2,6-disulfonate, nitrate, nitrite, ferric citrate, hydrous iron oxide and oxygen were not. The G+C content of genomic DNA was 62.5 mol%. The major cellular fatty acids were anteiso-C(15 : 0) and C(18 : 1)ω7c. Phylogenetic analysis based on 16S rRNA gene sequencing placed strain SCBM(T) into a distinct lineage within the class Deltaproteobacteria. The closest, cultivated phylogenetic relative of strain SCBM(T) was Desulfarculus baarsii DSM 2075(T), with only 91.7% 16S rRNA gene sequence identity. On the basis of phenotypic and genotypic analyses, strain SCBM(T) represents a novel genus and species of sulfate-reducing bacteria, for which the name Desulfocarbo indianensis gen. nov., sp. nov. is proposed. The type strain of Desulfocarbo indianensis is SCBM(T) ( = DSM 28127(T) = JCM 19826(T)). Desulfocarbo is the second genus of the order Desulfarculales.

Phylogenetic analysis of a microbialite-forming microbial mat from a hypersaline lake of the Kiritimati atoll, Central Pacific

On the Kiritimati atoll, several lakes exhibit microbial mat-formation under different hydrochemical conditions. Some of these lakes trigger microbialite formation such as Lake 21, which is an evaporitic, hypersaline lake (salinity of approximately 170‰). Lake 21 is completely covered with a thick multilayered microbial mat. This mat is associated with the formation of decimeter-thick highly porous microbialites, which are composed of aragonite and gypsum crystals. We assessed the bacterial and archaeal community composition and its alteration along the vertical stratification by large-scale analysis of 16S rRNA gene sequences of the nine different mat layers. The surface layers are dominated by aerobic, phototrophic, and halotolerant microbes. The bacterial community of these layers harbored Cyanobacteria (Halothece cluster), which were accompanied with known phototrophic members of the Bacteroidetes and Alphaproteobacteria. In deeper anaerobic layers more diverse communities than in the upper layers were present. The deeper layers were dominated by Spirochaetes, sulfate-reducing bacteria (Deltaproteobacteria), Chloroflexi (Anaerolineae and Caldilineae), purple non-sulfur bacteria (Alphaproteobacteria), purple sulfur bacteria (Chromatiales), anaerobic Bacteroidetes (Marinilabiacae), Nitrospirae (OPB95), Planctomycetes and several candidate divisions. The archaeal community, including numerous uncultured taxonomic lineages, generally changed from Euryarchaeota (mainly Halobacteria and Thermoplasmata) to uncultured members of the Thaumarchaeota (mainly Marine Benthic Group B) with increasing depth.

U(VI) reduction in sulfate-reducing subsurface sediments amended with ethanol or acetate

An experiment was conducted with subsurface sediments from Oak Ridge National Laboratory to determine the potential for reduction of U(VI) under sulfate-reducing conditions with either ethanol or acetate as the electron donor. The results showed extensive U(VI) reduction in sediments supplied with either electron donor, where geochemical and microbiological analyses demonstrated active sulfate reduction.

Multiple single-cell genomes provide insight into functions of uncultured Deltaproteobacteria in the human oral cavity

Despite a long history of investigation, many bacteria associated with the human oral cavity have yet to be cultured. Studies that correlate the presence or abundance of uncultured species with oral health or disease highlight the importance of these community members. Thus, we sequenced several single-cell genomic amplicons from Desulfobulbus and Desulfovibrio (class Deltaproteobacteria) to better understand their function within the human oral community and their association with periodontitis, as well as other systemic diseases. Genomic data from oral Desulfobulbus and Desulfovibrio species were compared to other available deltaproteobacterial genomes, including from a subset of host-associated species. While both groups share a large number of genes with other environmental Deltaproteobacteria genomes, they encode a wide array of unique genes that appear to function in survival in a host environment. Many of these genes are similar to virulence and host adaptation factors of known human pathogens, suggesting that the oral Deltaproteobacteria have the potential to play a role in the etiology of periodontal disease.

A genomic approach to the cryptic secondary metabolome of the anaerobic world

A total of 211 complete and published genomes from anaerobic bacteria are analysed for the presence of secondary metabolite biosynthesis gene clusters, in particular those tentatively coding for polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS). We investigate the distribution of these gene clusters according to bacterial phylogeny and, if known, correlate these to the type of metabolic pathways they encode. The potential of anaerobes as secondary metabolite producers is highlighted.

Novel B(12)-dependent acyl-CoA mutases and their biotechnological potential

The recent spate of discoveries of novel acyl-CoA mutases has engendered a growing appreciation for the diversity of 5'-deoxyadenosylcobalamin-dependent rearrangement reactions. The prototype of the reaction catalyzed by these enzymes is the 1,2 interchange of a hydrogen atom with a thioester group leading to a change in the degree of carbon skeleton branching. These enzymes are predicted to share common architectural elements: a Rossman fold and a triose phosphate isomerase (TIM)-barrel domain for binding cofactor and substrate, respectively. Within this family, methylmalonyl-CoA mutase (MCM) is the best studied and is the only member found in organisms ranging from bacteria to man. MCM interconverts (2R)-methylmalonyl-CoA and succinyl-CoA. The more recently discovered family members include isobutyryl-CoA mutase (ICM), which interconverts isobutyryl-CoA and n-butyryl-CoA; ethylmalonyl-CoA mutase, which interconverts (2R)-ethylmalonyl-CoA and (2S)-methylsuccinyl-CoA; and 2-hydroxyisobutyryl-CoA mutase, which interconverts 2-hydroxyisobutyryl-CoA and (3S)-hydroxybutyryl-CoA. A variant in which the two subunits of ICM are fused to a G-protein chaperone, IcmF, has been described recently. In addition to its ICM activity, IcmF also catalyzes the interconversion of isovaleryl-CoA and pivalyl-CoA. This review focuses on the involvement of acyl-CoA mutases in central carbon and secondary bacterial metabolism and on their biotechnological potential for applications ranging from bioremediation to stereospecific synthesis of C2-C5 carboxylic acids and alcohols, and for production of potential commodity and specialty chemicals.