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Microbial dissimilatory sulfate reduction is a key process in the global sulfur and carbon cycles in anoxic ecosystems. In this anaerobic respiration, sulfate is phosphorylated and reduced to sulfite, which is further reduced to a DsrC‐trisulfide by the dissimilatory sulfite reductase DsrAB. DsrD is a small protein that acts as an allosteric activator of DsrAB, increasing the efficiency of sulfite reduction. Here, we report a detailed study of DsrD and its interaction with DsrAB. Sequence similarity analyses show that there are three groups of DsrD in organisms with a reductive‐type DsrAB. The protein regions involved in the DsrD–DsrAB interaction and activity‐promoting effect were investigated through in vitro and in silico studies, including mutations of conserved DsrD residues. The results reveal that the conserved β‐loop of DsrD is involved in the interaction, contributing to a better understanding of its mechanism of action. [ABSTRACT FROM AUTHOR]

Sulfate/sulfite-reducing microorganisms (SRM) are ubiquitous in nature, driving the global sulfur cycle. A hallmark of SRM is the dissimilatory sulfite reductase encoded by the genes dsrAB. Based on analysis of 950 mainly metagenome-derived dsrAB -carrying genomes, we redefine the global diversity of microorganisms with the potential for dissimilatory sulfate/sulfite reduction and uncover genetic repertoires that challenge earlier generalizations regarding their mode of energy metabolism. We show: (i) 19 out of 23 bacterial and 2 out of 4 archaeal phyla harbor uncharacterized SRM, (ii) four phyla including the Desulfobacterota harbor microorganisms with the genetic potential to switch between sulfate/sulfite reduction and sulfur oxidation, and (iii) the combination as well as presence/absence of different dsrAB- types , dsrL -types and dsrD provides guidance on the inferred direction of dissimilatory sulfur metabolism. We further provide an updated dsrAB database including > 60% taxonomically resolved, uncultured family-level lineages and recommendations on existing dsrAB -targeted primers for environmental surveys. Our work summarizes insights into the inferred ecophysiology of newly discovered SRM, puts SRM diversity into context of the major recent changes in bacterial and archaeal taxonomy, and provides an up-to-date framework to study SRM in a global context. [ABSTRACT FROM AUTHOR]

[Display omitted] • A global view on necessary genes profiled the complex evolution of Dsr pathway. • Phylum-specific analyses showed great diversity in dsrAB genes across lineages. • Interdisciplinary alignment shed light on the Earth-microorganism interaction. • Geological events have shaped the divergence and metabolism of SRM and SOM. Sulfate is the second most common nonmetallic ion in modern oceans, as its concentration dramatically increased alongside tectonic activity and atmospheric oxidation in the Proterozoic. Microbial sulfate/sulfite metabolism, involving organic carbon or hydrogen oxidation, is linked to sulfur and carbon biogeochemical cycles. However, the coevolution of microbial sulfate/sulfite metabolism and Earth's history remains unclear. Here, we conducted a comprehensive phylogenetic analysis to explore the evolutionary history of the dissimilatory sulfite reduction (Dsr) pathway. The phylogenies of the Dsr-related genes presented similar branching patterns but also some incongruencies, indicating the complex origin and evolution of Dsr. Among these genes, dsrAB is the hallmark of sulfur-metabolizing prokaryotes. Our detailed analyses suggested that the evolution of dsrAB was shaped by vertical inheritance and multiple horizontal gene transfer events and that selection pressure varied across distinct lineages. Dated phylogenetic trees indicated that key evolutionary events of dissimilatory sulfur-metabolizing prokaryotes were related to the Great Oxygenation Event (2.4–2.0 Ga) and several geological events in the "Boring Billion" (1.8–0.8 Ga), including the fragmentation of the Columbia supercontinent (approximately 1.6 Ga), the rapid increase in marine sulfate (1.3–1.2 Ga), and the Neoproterozoic glaciation event (approximately 1.0 Ga). We also proposed that the voluminous iron formations (approximately 1.88 Ga) might have induced the metabolic innovation of iron reduction. In summary, our study provides new insights into Dsr evolution and a systematic view of the coevolution of dissimilatory sulfur-metabolizing prokaryotes and the Earth's environment. [ABSTRACT FROM AUTHOR]

Application of seawater for secondary oil recovery stimulates the development of sulfidogenic bacteria in the oil field leading to microbially influenced corrosion of steel equipment, oil souring, and environmental issues. The aim of this work was to investigate potential sulfide producers in the high-temperature Uzen oil field (Republic of Kazakhstan) exploited with seawater flooding and the possibility of suppressing growth of sulfidogens in both planktonic and biofilm forms. Approaches used in the study included 16S rRNA and dsrAB gene sequencing, scanning electron microscopy, and culture-based techniques. Thermophilic hydrogenotrophic methanogens of the genus Methanothermococcus (phylum Euryarchaeota) predominated in water from the zone not affected by seawater flooding. Methanogens were accompanied by fermentative bacteria of the genera Thermovirga, Defliviitoga, Geotoga, and Thermosipho (phylum Thermotogae), which are potential thiosulfate- or/and sulfur-reducers. In the sulfate- and sulfide-rich formation water, the share of Desulfonauticus sulfate-reducing bacteria (SRB) increased. Thermodesulforhabdus, Thermodesulfobacterium, Desulfotomaculum, Desulfovibrio, and Desulfoglaeba were also detected. Mesophilic denitrifying bacteria of the genera Marinobacter, Halomonas, and Pelobacter inhabited the near-bottom zone of injection wells. Nitrate did not suppress sulfidogenesis in mesophilic enrichments because denitrifiers reduced nitrate to dinitrogen; however, thermophilic denitrifiers produced nitrite, an inhibitor of SRB. Enrichments and a pure culture Desulfovibrio alaskensis Kaz19 formed biofilms highly resistant to biocides. Our results suggest that seawater injection and temperature of the environment determine the composition and functional activity of prokaryotes in the Uzen oil field. [ABSTRACT FROM AUTHOR]

DsrAB-type dissimilatory sulfite reductase is a key enzyme of microbial sulfur-dependent energy metabolism. Sulfur oxidizers also contain DsrL, which is essential for sulfur oxidation in Allochromatium vinosum. This NAD(P)H oxidoreductase acts as physiological partner of oxidative-type rDsrAB. Recent analyses uncovered that DsrL is not confined to sulfur oxidizers but also occurs in (probable) sulfate/sulfur-reducing bacteria. Here, phylogenetic analysis revealed a separation into two major branches, DsrL-1, with two subgroups, and DsrL-2. When present in organisms with reductive-type DsrAB, DsrL is of type 2. In the majority of cases oxidative-type rDsrAB occurs with DsrL-1 but combination with DsrL-2-type enzymes is also observed. Three model DsrL proteins, DsrL-1A and DsrL-1B from the sulfur oxidizers A. vinosum and Chlorobaculum tepidum, respectively, as well as DsrL-2 from thiosulfate- and sulfur-reducing Desulfurella amilsii were kinetically characterized. DaDsrL-2 is active with NADP(H) but not with NAD(H) which we relate to a conserved YRR-motif in the substrate-binding domains of all DsrL-2 enzymes. In contrast, AvDsrL-1A has a strong preference for NAD(H) and the CtDsrL-1B enzyme is completely inactive with NADP(H). Thus, NAD+ as well as NADP+ are suitable in vivo electron acceptors for rDsrABL-1-catalyzed sulfur oxidation, while NADPH is required as electron donor for sulfite reduction. This observation can be related to the lower redox potential of the NADPH/NADP+ than the NADH/NAD+ couple under physiological conditions. Organisms with a rdsrAB and dsrL-1 gene combination can be confidently identified as sulfur oxidizers while predictions for organisms with other combinations require much more caution and additional information sources.

DsrAB-type dissimilatory sulfite reductase is a key enzyme of microbial sulfur-dependent energy metabolism. Sulfur oxidizers also contain DsrL, which is essential for sulfur oxidation in Allochromatium vinosum. This NAD(P)H oxidoreductase acts as physiological partner of oxidative-type rDsrAB. Recent analyses uncovered that DsrL is not confined to sulfur oxidizers but also occurs in (probable) sulfate/sulfur-reducing bacteria. Here, phylogenetic analysis revealed a separation into two major branches, DsrL-1, with two subgroups, and DsrL-2. When present in organisms with reductive-type DsrAB, DsrL is of type 2. In the majority of cases oxidative-type rDsrAB occurs with DsrL-1 but combination with DsrL-2-type enzymes is also observed. Three model DsrL proteins, DsrL-1A and DsrL-1B from the sulfur oxidizers A. vinosum and Chlorobaculum tepidum , respectively, as well as DsrL-2 from thiosulfate- and sulfur-reducing Desulfurella amilsii were kinetically characterized. Da DsrL-2 is active with NADP(H) but not with NAD(H) which we relate to a conserved YRR-motif in the substrate-binding domains of all DsrL-2 enzymes. In contrast, Av DsrL-1A has a strong preference for NAD(H) and the Ct DsrL-1B enzyme is completely inactive with NADP(H). Thus, NAD+ as well as NADP+ are suitable in vivo electron acceptors for rDsrABL-1-catalyzed sulfur oxidation, while NADPH is required as electron donor for sulfite reduction. This observation can be related to the lower redox potential of the NADPH/NADP+ than the NADH/NAD+ couple under physiological conditions. Organisms with a rdsrAB and dsrL-1 gene combination can be confidently identified as sulfur oxidizers while predictions for organisms with other combinations require much more caution and additional information sources. [ABSTRACT FROM AUTHOR]

Application of seawater for secondary oil recovery stimulates the development of sulfidogenic bacteria in the oil field leading to microbially influenced corrosion of steel equipment, oil souring, and environmental issues. The aim of this work was to investigate potential sulfide producers in the high-temperature Uzen oil field (Republic of Kazakhstan) exploited with seawater flooding and the possibility of suppressing growth of sulfidogens in both planktonic and biofilm forms. Approaches used in the study included 16S rRNA and dsrAB gene sequencing, scanning electron microscopy, and culture-based techniques. Thermophilic hydrogenotrophic methanogens of the genus Methanothermococcus (phylum Euryarchaeota) predominated in water from the zone not affected by seawater flooding. Methanogens were accompanied by fermentative bacteria of the genera Thermovirga, Defliviitoga, Geotoga, and Thermosipho (phylum Thermotogae), which are potential thiosulfate- or/and sulfur-reducers. In the sulfate- and sulfide-rich formation water, the share of Desulfonauticus sulfate-reducing bacteria (SRB) increased. Thermodesulforhabdus, Thermodesulfobacterium, Desulfotomaculum, Desulfovibrio, and Desulfoglaeba were also detected. Mesophilic denitrifying bacteria of the genera Marinobacter, Halomonas, and Pelobacter inhabited the near-bottom zone of injection wells. Nitrate did not suppress sulfidogenesis in mesophilic enrichments because denitrifiers reduced nitrate to dinitrogen; however, thermophilic denitrifiers produced nitrite, an inhibitor of SRB. Enrichments and a pure culture Desulfovibrio alaskensis Kaz19 formed biofilms highly resistant to biocides. Our results suggest that seawater injection and temperature of the environment determine the composition and functional activity of prokaryotes in the Uzen oil field.

Most sulfate-reducing microorganisms (SRMs) present in subsurface marine sediments belong to uncultured groups only distantly related to known SRMs, and it remains unclear how changing geochemical zones and sediment depth influence their community structure. We mapped the community composition and abundance of SRMs by amplicon sequencing and quantifying the dsrB gene, which encodes dissimilatory sulfite reductase subunit beta, in sediment samples covering different vertical geochemical zones ranging from the surface sediment to the deep sulfate-depleted subsurface at four locations in Aarhus Bay, Denmark. SRMs were present in all geochemical zones, including sulfate-depleted methanogenic sediment. The biggest shift in SRM community composition and abundance occurred across the transition from bioturbated surface sediments to nonbioturbated sediments below, where redox fluctuations and the input of fresh organic matter due to macrofaunal activity are absent. SRM abundance correlated with sulfate reduction rates determined for the same sediments. Sulfate availability showed a weaker correlation with SRM abundances and no significant correlation with the composition of the SRM community. The overall SRM species diversity decreased with depth, yet we identified a subset of highly abundant community members that persists across all vertical geochemical zones of all stations. We conclude that subsurface SRM communities assemble by the persistence of members of the surface community and that the transition from the bioturbated surface sediment to the unmixed sediment below is a main site of assembly of the subsurface SRM community. [ABSTRACT FROM AUTHOR]

Biogas produced from the anaerobic digestion of animal slurry consists mainly of methane (CH) and carbon dioxide (CO), but also includes other minor gases, such as hydrogen sulfide (HS). Since it can act as a potent corrosive agent and presents a health hazard even at low concentrations, HS is considered an undesirable by-product of anaerobic digestion. Sulfate-reducing bacteria (SRBs) have been identified as the main biological source of HS in a number of natural, biological, and human-made habitats, and thus represent likely candidate microorganisms responsible for the production of HS in anaerobic manure digesters. Phylogenetically, SRBs form a divergent group of bacteria that share a common anaerobic respiration pathway that allows them to use sulfate as a terminal electron acceptor. While the composition and activity of SRBs have been well documented in other environments, their metabolic potential remains largely uncharacterized and their populations poorly defined in anaerobic manure digesters. In this context, a combination of in vitro culture-based studies and DNA-based approaches, respectively, were used to gain further insight. Unexpectedly, only low to nondetectable levels of HS were produced by digestate collected from a manure biogas plant documented to have persistently high concentrations of HS in its biogas (2000-3000 ppm). In contrast, combining digestate with untreated manure (a substrate with comparatively lower sulfate and SRB cell densities than digestate) was found to produce elevated HS levels in culture. While a 16S rRNA gene-based community composition approach did not reveal likely candidate SRBs in digestate or untreated manure, the use of the dsrAB gene as a phylogenetic marker provided more insight. In digestate, the predominant SRBs were found to be uncharacterized species likely belonging to the genus Desulfosporosinus ( Peptococcaceae, Clostridiales, Firmicutes), while Desulfovibrio-related SRBs ( Desulfovibrionaceae, Desulfovibrionales, Proteobacteria) were the most highly represented in untreated manure. Intriguingly, the same species-level OTUs with a similar pattern of opposite relative abundance were also found in two other digesters with lower HS levels in their biogas. Together, our results suggest that elevated HS production in anaerobic digesters requires the combination of biological and nutritional factors from both untreated manure and digestate. [ABSTRACT FROM AUTHOR]

Pitting corrosion due to microbial activity is the most severe type of corrosion that occurs in ship hull. Since biogenic sulfide produced by sulfate-reducing bacteria (SRB) is involved in the acceleration of pitting corrosion of marine vessels, so it is important to collect information about SRB community involved in maritime vessel failure. We investigated the SRB community on corroded hull portion of the ship. With the use of common cultural method and 16S rDNA sequencing, ten bacteria with sulfate reduction ability were isolated and identified. They belonged to both traditional ( Desulfovibrio, Desulfotomaculum) and non-traditional ( Citrobacter) sulfate-reducing bacteria. All the isolates were able to produce a high amount of sulfide. However, only traditional isolates were showing the amplification for the SRB-specific gene, dsrAB. Further studies on corrosion potential of these two groups of bacteria showed that in spite of high sulfide and biofilm production by non-traditional SRB, they are less aggressive towards the mild steel compare to the traditional group. [ABSTRACT FROM AUTHOR]

Freshwater wetlands are a major source of the greenhouse gas methane but at the same time can function as carbon sink. Their response to global warming and environmental pollution is one of the largest unknowns in the upcoming decades to centuries. In this review, we highlight the role of sulfate-reducing microorganisms (SRM) in the intertwined element cycles of wetlands. Although regarded primarily as methanogenic environments, biogeochemical studies have revealed a previously hidden sulfur cycle in wetlands that can sustain rapid renewal of the small standing pools of sulfate. Thus, dissimilatory sulfate reduction, which frequently occurs at rates comparable to marine surface sediments, can contribute up to 36–50% to anaerobic carbon mineralization in these ecosystems. Since sulfate reduction is thermodynamically favored relative to fermentative processes and methanogenesis, it effectively decreases gross methane production thereby mitigating the flux of methane to the atmosphere. However, very little is known about wetland SRM. Molecular analyses using dsrAB [encoding subunit A and B of the dissimilatory (bi)sulfite reductase] as marker genes demonstrated that members of novel phylogenetic lineages, which are unrelated to recognized SRM, dominate dsrAB richness and, if tested, are also abundant among the dsrAB-containing wetland microbiota. These discoveries point towards the existence of so far unknown SRM that are an important part of the autochthonous wetland microbiota. In addition to these numerically dominant microorganisms, a recent stable isotope probing study of SRM in a German peatland indicated that rare biosphere members might be highly active in situ and have a considerable stake in wetland sulfate reduction. The hidden sulfur cycle in wetlands and the fact that wetland SRM are not well represented by described SRM species explains their so far neglected role as important actors in carbon cycling and climate change.

Abstract: Water-flooding is a common strategy to enhance oil recovery in reservoirs. Maintaining quality and standards of produced water avoids oil biodegradation, biogenic souring and biocorrosion during operations, which are influenced by sulfate-reducing (SRB) and Fe (III) reducing bacteria. The aim of this work was to increase our knowledge of corrosive bacterial communities inhabiting saline produced waters of offshore oil exploitation facilities through retrieving sequences of functional genes, for instance, dsrAB and nifD of Desulfovibrionales, Desulfobacterales and Desulfuromonadales taxonomical orders. Five clone libraries were generated with retrieved sequences acquired from different saline produced waters, with and without biocide dosing. The dsrAB phylogenetic analyses showed Desulfomicrobium, Desulfovibrio, and Desulfohalobium as well as Desulfococcus, Desulfosarcina, Desulfobacter, Desulfobacterium and Desulfobulbus. The retrieved nifD genes displayed the Fe (III) reducing bacteria (Desulfuromonadales) such as Desulfuromusa, Pelobacter, Malonomonas, and Desulfuromonas. The relative abundance in all waters was: the Desulfovibrionales were represented by 55.28% of analyzed clones; the Desulfobacterales by 26.83% and 17.89% for the Desulfuromonadales. Diversity measures were calculated by the Shannon index (H′), which showed that there was a high degree of diversity between all produced waters; however, dominance in produced water with biocide was detected by a Desulfovibrio taxon. [Copyright &y& Elsevier]

A 3-year survey on sulfate-reducing bacteria ( SRB) was conducted in the waters of the arsenic-rich acid mine drainage ( AMD) located at Carnoulès ( France) to determine the influence of environmental parameters on their community structure. The source ( S5 station) exhibited most extreme conditions with p H lowering to ~1.2; iron, sulfate, and arsenic concentrations reaching 6843, 29 593, and 638 mg L−1, respectively. The conditions were less extreme at the downstream stations S1 (p H ~3.7; iron, sulfate, and arsenic concentrations of 1114, 4207, and 167 mg L−1, respectively) and COWG (p H ~3.4; iron, sulfate, and arsenic concentrations of 854, 3134, and 110 mg L−1, respectively). SRB community structures were characterized by terminal restriction fragment length polymorphism and library analyses based on dsrAB genes. The predominant dsrAB sequences detected were most similar to the family Desulfobulbaceae. Additionally, certain phylotypes could be related to spatio-temporal fluctuations of p H, iron, and arsenic species. For example, Desulfohalobiaceae-related sequences were detected at the most acidic sample (p H 1.4) with high iron and arsenic concentrations (6379 and 524 mg L−1, respectively). New dsrAB sequences, with no isolated representatives, were found exclusively in COWG. This study gives new insights on SRB community dynamics in AMD systems. [ABSTRACT FROM AUTHOR]

The diversity of planktonic microorganisms in fluids from a group of flowing subterranean boreholes was monitored from the day they were drilled to as long as three and a half months after drilling as they drained into Evander Au mine. Geochemical analyses of the water, characterization of microbial communities by phospholipids fatty acid (PLFA) and DNA sequence analyses, and calculations of free energy flux indicated that mine-introduced microbial contaminants, dominated by β and γ Proteobacteria, Cenarchaeaceae and Candidatus Nitrososphaera, were flushed from the boreholes and replaced by fracture water derived microbial communities dominated by Firmicutes, Methanosarcinalesand Thermoproteaceaea. The fracture water was a mixture of paleometeoric water and 2.0 Ga old, diagenetically altered, hydrothermal fluid. The C and H isotopic data for C1-4 indicated that the CH4 was primarily abiogenic in origin although ∼35-50% of it might have originated from microbial methanogenesis. Noble gas analyses yielded estimated residence times of some 10 million years for the fracture water, which is estimated to represent a capture cross-section of 0.25-0.50 km2. The 16S rRNA and dsrAB gene sequences indicated that the indigenous bacterial communities were predominantly comprised of sulfate reducers belonging to the genera Desulfotomaculum, Candiditus Desulforudis and Desulfofustis. The sulfur isotopic analyses of sulfate and sulfide yielded fractionation Δ34S values ranging from 16 to 22% consistent with microbial sulfate reduction. Thermodynamic analyses indicate that methanogenic reactions are inhibited by the high partial pressure of abiogenic CH4 and that sulfate-reducing reactions are more favorable, which is consistent with the abundance of 16S rRNA genes belonging to known sulfate reducing bacteria. Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the free supplemental files. [ABSTRACT FROM AUTHOR]

This study intended to unravel the physiological interplay in an anaerobic microbial community that degrades toluene under sulfate-reducing conditions combining proteomic and genetic techniques. An enriched toluene-degrading community (Zz5-7) growing in batch cultures was investigated by DNA- and protein-based analyses. The affiliation and diversity of the community were analysed using 16S ribosomal RNA (rRNA) genes as a phylogenetic marker as well as bssA and dsrAB genes as functional markers. Metaproteome analysis was carried out by a global protein extraction and a subsequent protein separation by two-dimensional gel electrophoresis (2-DE). About 85% of the proteins in the spots were identified by nano-liquid chromatography coupled with electrospray mass spectrometry (nano-LC-ESI-MS/MS) analysis. DNA sequencing of bssA and the most abundant dsrAB amplicons revealed high similarities to a member of the Desulfobulbaceae, which was also predominant according to 16S rRNA gene amplicons. Metaproteome analysis provided 202 unambiguous protein identifications derived from 236 unique protein spots. The proteins involved in anaerobic toluene activation, dissimilatory sulfate reduction, hydrogen production/consumption and autotrophic carbon fixation were mainly affiliated to members of the Desulfobulbaceae and several other Deltaproteobacteria. Phylogenetic and metaproteomic analyses revealed a member of the Desulfobulbaceae as the key player of anaerobic toluene degradation in a sulfate-reducing consortium. This is the first study that combines genetic and proteomic analyses to indicate the interactions in an anaerobic toluene-degrading microbial consortium. [ABSTRACT FROM AUTHOR]

An in situ culturing device was incubated within a flowing borehole in a mafic sill at 1.474 km depth in Evander Au mine, South Africa. The device was designed to enrich methanogenic, Fe3 +-reducing and SO42 --reducing microorganisms using acetate, formate, methanol, Fe3 +-citrate and SO42 - enriched agar and sand cartridges. At the end of the 33 day incubation geochemical analyses detected elevated H2, acetate, CH4 and Fe concentrations and depleted SO42 - concentrations. 16S rDNA sequences and PLFA analyses revealed that the microbial community composition of the substrate-bearing cartridges were distinct from that of the original borehole water and the non-substrate-bearing control cartridge. 16S rDNA and dissimilatory sulfite reductase, dsrAB, gene sequences indicated the device successfully targeted SO42 - reducing bacteria (SRB), which were not detected in the original borehole water. 16S rDNA sequences also revealed a shift in the microbial community from one relying on H2 based methanogenesis to one suggestive of H2 based acetogenesis supporting aceticlastic methanogenesis and SO42 - reduction compatible with the subsurface lithoautotrophic hypothesis. [ABSTRACT FROM AUTHOR]

The work is dedicated to searching for microorganisms of the domain Bacteria capable of dissimilatory sulfate reduction in the samples of microbial mats from a carbonate chimney in the Lost City hydro-thermal field. Cloning of 16S rRNA genes, the universal phylogenetic marker, and dsrAB, the functional marker for sulfate reduction, revealed phylotypes related to spore-forming Desulfotomaculum. No members of the Deltaproteobacteria, comprising the most numerous bacterial group with demonstrated capacity for dissimilatory sulfate reduction, were found. The phylogenetic position of 16S rRNA clones from the mats suggests that this microbial community is a unique consortium, where the energy flow is related to hydrogen of hydrothermal origin, while mass growth of primary produces results from utilization of sulfide formed by sulfate-and sulfur-reducing microorganisms. [ABSTRACT FROM AUTHOR]

Abstract: Microbial communities of methanogenic, sulfate-reducing and methanotrophic prokaryotes from deep-sea environments were investigated by molecular phylogenetic analysis of the deduced amino acid sequences of the genes encoding for the methyl coenzyme M reductase (mcrA), dissimilatory sulfite reductase (dsrAB) and particulate methane monoxygenase (pmoA), respectively. Clone libraries of PCR amplified genes were constructed using DNA extracted from deep-sea vent chimneys (Rainbow and Logatchev hydrothermal vent fields, Mid-Atlantic Ridge, Atlantic Ocean; 9°N East Pacific Rise, Pacific Ocean) and from vertically subsampled sediment cores from cold-seep areas (Blake Ridge, western Atlantic Ocean; Florida Escarpment, Gulf of Mexico). Recombinant clones were screened by RFLP and representative dsrAB, mcrA and pmoA genes were sequenced. The dsrAB sequences grouped primarily within the orders Desulfobacterales, Syntrophobacterales and the Gram-positive order Clostridales. Cold-seep mcrA sequences were distributed among the ANME-2c, -2d and -2e groups, which were previously shown to be associated with the anaerobic oxidation of methane. This study also reports the first mcrA sequences from a high-temperature, black smoker chimney (Logatchev) to group within the ANME-2e subgroup. The majority of the remaining hydrothermal vent mcrA sequences were primarily related to thermophilic members of the anaerobic, methanogenic order Methanococcales. A shift in the dominant ANME-2 group with depth in the sediment for both Florida Escarpment and Blake Ridge mcrA libraries was detected. ANME-2d related clones were detected in the top zones of both cores, with the frequency of ANME-2e related clones increasing with depth. All pmoA sequences retrieved from the cold-seep sites were found to be related to Type I methanotrophic members of the γ-proteobacteria, and were primarily distributed among three major clusters of sequences. No Type II pmoA sequences related to methanotrophic members of the α-proteobacteria were detected, suggesting that the methanotrophic communities in these cold-seep areas are dominated by Type I γ-proteobacteria. [Copyright &y& Elsevier]

Abstract: Sulfate-reducing bacteria (SRB) are important regulators of a variety of processes in coastal marine sediments regarding organic matter turnover, biodegradation of pollutants, and sulfur and carbon cycles. Yet their community compositions have not been investigated in polluted harbor sediments. This study described the diversity and spatial variation of SRB communities in surface sediments in Victoria Harbor, Hong Kong. The spatial variation of SRB communities was described by terminal restriction fragment length polymorphism (T-RFLP). The results showed that the most diversified terminal restriction fragments were found at polluted sites. In addition, cluster analysis indicated that although the SRB communities were different at the two polluted sites, they were still more similar to each other than to the two more distant reference sites. Based on a dsrAB clone library constructed at a polluted site, diversified SRB were found, represented by 30 Operational Taxonomic Units (OTUs). Upon comparisons among the SRB sequences detected from this study and those in the GenBank, five clades of SRB were found. Three clades belonged to the known families Desulfobacteraceae, Desulfobulbaceae, and Syntrophobacteriaceae. The majority of sequenced clones, which distantly related to sequences in the GenBank, constituted the remaining two unclassified groups, suggesting unique SRB members related to the polluted harbor environment. Statistical analyses indicated that estimated SRB richness correlated with environment factors such as sulfur content, acid volatile sulfate, and redox potential. [Copyright &y& Elsevier]

The impact of legacy nuclear waste on the compositional diversity and distribution of sulfate-reducing bacteria in a heavily contaminated subsurface aquifer was examined. dsrAB clone libraries were constructed and restriction fragment length polymorphism (RFLP) analysis used to evaluate genetic variation between sampling wells. Principal component analysis identified nickel, nitrate, technetium, and organic carbon as the primary variables contributing to well-to-well geochemical variability, although comparative sequence analysis showed the sulfate-reducing bacteria community structure to be consistent throughout contaminated and uncontaminated regions of the aquifer. Only 3% of recovered dsrAB gene sequences showed apparent membership to the Deltaproteobacteria. The remainder of recovered sequences may represent novel, deep-branching lineages that, to our knowledge, do not presently contain any cultivated members; although corresponding phylotypes have recently been reported from several different marine ecosystems. These findings imply resiliency and adaptability of sulfate-reducing bacteria to extremes in environmental conditions, although the possibility for horizontal transfer of dsrAB is also discussed. [ABSTRACT FROM AUTHOR]

Abstract: A new mesophilic sulphate-reducing bacterium, designated strain DvO5T (T=type strain), was isolated from the outermost sulphate reduction-positive most-probable-number tube (10−6 dilution) of an activated sludge sample, which had been oxygenated at 100% air saturation for 120h. The motile, Gram-negative, curved 1 by 2–5μm and non-spore-forming cells of strain DvO5T existed singly or in chains. Strain DvO5T grew optimally at 29°C, pH 6.9 and 0.05% (w/v) NaCl in a medium containing lactate, sulphate and yeast extract. Sulphite, thiosulphate and elemental sulphur also served as electron acceptors whereas nitrate, nitrite or ferric iron were not reduced. Lactate, pyruvate, H2 (with acetate as carbon source), ethanol and glycerol efficiently supported growth as electron donors. Pyruvate and malate were fermented. Strain DvO5T reduced oxygen by oxidising endogenous polyglucose at rates ranging from 0.4 to 6.0nmol O2/mgprotein min depending on the oxygen concentration, the highest rates being observed at atmospheric oxygen saturation. The G+C content of the DNA was 57.2mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain DvO5T was a member of the genus Desulfovibrio with D. magneticus (98.2% 16S rRNA gene sequence similarity) and D. burkinensis (97.5% 16S rRNA gene sequence similarity) being its closest relatives among validly described species. A similar phylogenetic affiliation was obtained by sequence analyses of the genes encoding the alpha and the beta subunit of dissimilatory sulphite reductase (dsrAB) as well as the alpha subunit of adenosine-5′-phosphosulphate reductase (apsA) of strain DvO5T. On the basis of genotypic and phenotypic characteristics, strain DvO5T (DSM 16695T, JCM 12613T) is proposed as the type strain of a new species, Desulfovibrio aerotolerans sp. nov. [Copyright &y& Elsevier]