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

Geological gas-storage shapes deep life

Around the world, several dozen deep sedimentary aquifers are being used for storage of natural gas. Ad hoc studies of the microbial ecology of some of them have suggested that sulfate reducing and methanogenic microorganisms play a key role in how these aquifers' communities function. Here, we investigate the influence of gas storage on these two metabolic groups by using high-throughput sequencing and show the importance of sulfate-reducing Desulfotomaculum and a new monophyletic methanogenic group. Aquifer microbial diversity was significantly related to the geological level. The distance to the stored natural gas affects the ratio of sulfate-reducing Firmicutes to deltaproteobacteria. In only one aquifer, the methanogenic archaea dominate the sulfate-reducers. This aquifer was used to store town gas (containing at least 50% H₂ ) around 50 years ago. The observed decrease of sulfates in this aquifer could be related to stimulation of subsurface sulfate-reducers. These results suggest that the composition of the microbial communities is impacted by decades old transient gas storage activity. The tremendous stability of these gas-impacted deep subsurface microbial ecosystems suggests that in situ biotic methanation projects in geological reservoirs may be sustainable over time.

Shotgun Metagenomics Reveals the Benthic Microbial Community Response to Plastic and Bioplastic in a Coastal Marine Environment

Plastic is incredibly abundant in marine environments but little is known about its effects on benthic microbiota and biogeochemical cycling. This study reports the shotgun metagenomic sequencing of biofilms fouling plastic and bioplastic microcosms staged at the sediment–water interface of a coastal lagoon. Community composition analysis revealed that plastic biofilms were indistinguishable in comparison to a ceramic biofilm control. By contrast, bioplastic biofilms were distinct and dominated by sulfate-reducing microorganisms (SRM). Analysis of bioplastic gene pools revealed the enrichment of esterases, depolymerases, adenylyl sulfate reductases (aprBA), and dissimilatory sulfite reductases (dsrAB). The nearly 20-fold enrichment of a phylogenetically diverse polyhydroxybutyrate (PHB) depolymerase suggests this gene was distributed across a mixed microbial assemblage. The metagenomic reconstruction of genomes identified novel species of Desulfovibrio, Desulfobacteraceae, and Desulfobulbaceae among the abundant SRM, and these genomes contained genes integral to both bioplastic degradation and sulfate reduction. Findings indicate that bioplastic promoted a rapid and significant shift in benthic microbial diversity and gene pools, selecting for microbes that participate in bioplastic degradation and sulfate reduction. If plastic pollution is traded for bioplastic pollution and sedimentary inputs are large, the microbial response could unintentionally affect benthic biogeochemical activities through the stimulation of sulfate reducers.

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.

Complete arsenic-based respiratory cycle in the marine microbial communities of pelagic oxygen-deficient zones

Microbial capacity to metabolize arsenic is ancient, arising in response to its pervasive presence in the environment, which was largely in the form of As(III) in the early anoxic ocean. Many biological arsenic transformations are aimed at mitigating toxicity; however, some microorganisms can respire compounds of this redox-sensitive element to reap energetic gains. In several modern anoxic marine systems concentrations of As(V) are higher relative to As(III) than what would be expected from the thermodynamic equilibrium, but the mechanism for this discrepancy has remained unknown. Here we present evidence of a complete respiratory arsenic cycle, consisting of dissimilatory As(V) reduction and chemoautotrophic As(III) oxidation, in the pelagic ocean. We identified the presence of genes encoding both subunits of the respiratory arsenite oxidase AioA and the dissimilatory arsenate reductase ArrA in the Eastern Tropical North Pacific (ETNP) oxygen-deficient zone (ODZ). The presence of the dissimilatory arsenate reductase gene arrA was enriched on large particles (>30 um), similar to the forward bacterial dsrA gene of sulfate-reducing bacteria, which is involved in the cryptic cycling of sulfur in ODZs. Arsenic respiratory genes were expressed in metatranscriptomic libraries from the ETNP and the Eastern Tropical South Pacific (ETSP) ODZ, indicating arsenotrophy is a metabolic pathway actively utilized in anoxic marine water columns. Together these results suggest arsenic-based metabolisms support organic matter production and impact nitrogen biogeochemical cycling in modern oceans. In early anoxic oceans, especially during periods of high marine arsenic concentrations, they may have played a much larger role.

Unraveling the diversity of sedimentary sulfate-reducing prokaryotes (SRP) across Tibetan saline lakes using epicPCR

Sulfate reduction is an important biogeochemical process in the ecosphere; however, the major taxa of sulfate reducers have not been fully identified. Here, we used epicPCR (Emulsion, Paired Isolation, and Concatenation PCR) technology to identify the phylogeny of sulfate-reducing prokaryotes (SRP) in sediments from Tibetan Plateau saline lakes. A total of 12,519 OTUs and 883 SRP-OTUs were detected in ten lakes by sequencing of 16S rRNA gene PCR amplicons and epicPCR products of fused 16S rRNA plus dsrB gene, respectively, with Proteobacteria, Firmicutes, and Bacteroidetes being the dominant phyla in both datasets. The 120 highly abundant SRP-OTUs (> 1% in at least one sample) were affiliated with 17 described phyla, only 7 of which are widely recognized as SRP phyla. The majority of OTUs from both the whole microbial communities and the SRPs were not detected in more than one specific lake, suggesting high levels of endemism. The α-diversity of the entire microbial community and SRP sub-community showed significant positive correlations. The pH value and mean water temperature of the month prior to sampling were the environmental determinants for the whole microbial community, while the mean water temperature and total nitrogen were the major environmental drivers for the SRP sub-community. This study revealed there are still many undocumented SRP in Tibetan saline lakes, many of which could be endemic and adapted to specific environmental conditions.

Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi

The methyl-coenzyme M reductase (MCR) complex is a key enzyme in archaeal methane generation and has recently been proposed to also be involved in the oxidation of short-chain hydrocarbons including methane, butane, and potentially propane. The number of archaeal clades encoding the MCR continues to grow, suggesting that this complex was inherited from an ancient ancestor, or has undergone extensive horizontal gene transfer. Expanding the representation of MCR-encoding lineages through metagenomic approaches will help resolve the evolutionary history of this complex. Here, a near-complete Archaeoglobi metagenome-assembled genome (MAG; Ca. Polytropus marinifundus gen. nov. sp. nov.) was recovered from the deep subseafloor along the Juan de Fuca Ridge flank that encodes two divergent McrABG operons similar to those found in Ca. Bathyarchaeota and Ca. Syntrophoarchaeum MAGs. Ca. P. marinifundus is basal to members of the class Archaeoglobi, and encodes the genes for β-oxidation, potentially allowing an alkanotrophic metabolism similar to that proposed for Ca. Syntrophoarchaeum. Ca. P. marinifundus also encodes a respiratory electron transport chain that can potentially utilize nitrate, iron, and sulfur compounds as electron acceptors. Phylogenetic analysis suggests that the Ca. P. marinifundus MCR operons were horizontally transferred, changing our understanding of the evolution and distribution of this complex in the Archaea.

Dietary Factors in Sulfur Metabolism and Pathogenesis of Ulcerative Colitis

The biogeography of inflammation in ulcerative colitis (UC) suggests a proximal to distal concentration gradient of a toxin. Hydrogen sulfide (H₂S) has long been considered one such toxin candidate, and dietary sulfur along with the abundance of sulfate reducing bacteria (SRB) were considered the primary determinants of H₂S production and clinical course of UC. The metabolic milieu in the lumen of the colon, however, is the result of a multitude of factors beyond dietary sulfur intake and SRB abundance. Here we present an updated formulation of the H₂S toxin hypothesis for UC pathogenesis, which strives to incorporate the interdependency of diet composition and the metabolic activity of the entire colon microbial community. Specifically, we suggest that the increasing severity of inflammation along the proximal-to-distal axis in UC is due to the dilution of beneficial factors, concentration of toxic factors, and changing detoxification capacity of the host, all of which are intimately linked to the nutrient flow from the diet.

Sulfate-Reducing Bacteria That Produce Exopolymers Thrive in the Calcifying Zone of a Hypersaline Cyanobacterial Mat

Calcifying microbial mats in hypersaline environments are important model systems for the study of the earliest ecosystems on Earth that started to appear more than three billion years ago and have been preserved in the fossil record as laminated lithified structures known as stromatolites. It is believed that sulfate-reducing bacteria play a pivotal role in the lithification process by increasing the saturation index of calcium minerals within the mat. Strain L21-Syr-AB^T was isolated from anoxic samples of a several centimeters-thick microbialite-forming cyanobacterial mat of a hypersaline lake on the Kiritimati Atoll (Kiribati, Central Pacific). The novel isolate was assigned to the family Desulfovibrionaceae within the Deltaproteobacteria. Available 16S rRNA-based population surveys obtained from discrete layers of the mat indicate that the occurrence of a species-level clade represented by strain L21-Syr-AB^T is restricted to a specific layer of the suboxic zone, which is characterized by the presence of aragonitic spherulites. To elucidate a possible function of this sulfate-reducing bacterium in the mineral formation within the mat a comprehensive phenotypic characterization was combined with the results of a comparative genome analysis. Among the determined traits of strain L21-Syr-AB^T, several features were identified that could play a role in the precipitation of calcium carbonate: (i) the potential deacetylation of polysaccharides and consumption of substrates such as lactate and sulfate could mobilize free calcium; (ii) under conditions that favor the utilization of formate and hydrogen, the alkalinity engine within the mat is stimulated, thereby increasing the availability of carbonate; (iii) the production of extracellular polysaccharides could provide nucleation sites for calcium mineralization. In addition, our data suggest the proposal of the novel species and genus Desulfohalovibrio reitneri represented by the type strain L21-Syr-AB^T (=DSM 26903^T = JCM 18662^T).

The Biogeochemical Sulfur Cycle of Marine Sediments

Microbial dissimilatory sulfate reduction to sulfide is a predominant terminal pathway of organic matter mineralization in the anoxic seabed. Chemical or microbial oxidation of the produced sulfide establishes a complex network of pathways in the sulfur cycle, leading to intermediate sulfur species and partly back to sulfate. The intermediates include elemental sulfur, polysulfides, thiosulfate, and sulfite, which are all substrates for further microbial oxidation, reduction or disproportionation. New microbiological discoveries, such as long-distance electron transfer through sulfide oxidizing cable bacteria, add to the complexity. Isotope exchange reactions play an important role for the stable isotope geochemistry and for the experimental study of sulfur transformations using radiotracers. Microbially catalyzed processes are partly reversible whereby the back-reaction affects our interpretation of radiotracer experiments and provides a mechanism for isotope fractionation. We here review the progress and current status in our understanding of the sulfur cycle in the seabed with respect to its microbial ecology, biogeochemistry, and isotope geochemistry.

Marine Deep Biosphere Microbial Communities Assemble in Near-Surface Sediments in Aarhus Bay

Analyses of microbial diversity in marine sediments have identified a core set of taxa unique to the marine deep biosphere. Previous studies have suggested that these specialized communities are shaped by processes in the surface seabed, in particular that their assembly is associated with the transition from the bioturbated upper zone to the nonbioturbated zone below. To test this hypothesis, we performed a fine-scale analysis of the distribution and activity of microbial populations within the upper 50 cm of sediment from Aarhus Bay (Denmark). Sequencing and qPCR were combined to determine the depth distributions of bacterial and archaeal taxa (16S rRNA genes) and sulfate-reducing microorganisms (SRM) (dsrB gene). Mapping of radionuclides throughout the sediment revealed a region of intense bioturbation at 0-6 cm depth. The transition from bioturbated sediment to the subsurface below (7 cm depth) was marked by a shift from dominant surface populations to common deep biosphere taxa (e.g., Chloroflexi and Atribacteria). Changes in community composition occurred in parallel to drops in microbial activity and abundance caused by reduced energy availability below the mixed sediment surface. These results offer direct evidence for the hypothesis that deep subsurface microbial communities present in Aarhus Bay mainly assemble already centimeters below the sediment surface, below the bioturbation zone.

Environmental filtering determines family-level structure of sulfate-reducing microbial communities in subsurface marine sediments

Recent work has shown that subsurface microbial communities assemble by selective survival of surface community members during sediment burial, but it remains unclear to what extent the compositions of the subsurface communities are a product of their founding population at the sediment surface or of the changing geochemical conditions during burial. Here we investigate this question for communities of sulfate-reducing microorganisms (SRMs). We collected marine sediment samples from the upper 3-5 m at four geochemically contrasting sites in the Skagerrak and Baltic Sea and measured SRM abundance (quantitative PCR of dsrB), metabolic activity (radiotracer rate measurements), and community composition (Illumina sequencing of dsrB amplicons). These data showed that SRM abundance, richness, and phylogenetic clustering as determined by the nearest taxon index peaked below the bioturbation zone and above the depth of sulfate depletion. Minimum cell-specific rates of sulfate reduction did not vary substantially between sites. SRM communities at different sites were best distinguished based on their composition of amplicon sequence variants (ASVs), while communities in different geochemical zones were best distinguished based on their composition of SRM families. This demonstrates environmental filtering of SRM communities in sediment while a site-specific fingerprint of the founding community is retained.

Co-occurring genomic capacity for anaerobic methane and dissimilatory sulfur metabolisms discovered in the Korarchaeota

Phylogenetic and geological evidence supports the hypothesis that life on Earth originated in thermal environments and conserved energy through methanogenesis or sulfur reduction. Here we describe two populations of the deeply rooted archaeal phylum Korarchaeota, which were retrieved from the metagenome of a circumneutral, suboxic hot spring that contains high levels of sulfate, sulfide, methane, hydrogen and carbon dioxide. One population is closely related to 'Candidatus Korarchaeum cryptofilum OPF8', while the more abundant korarchaeote, 'Candidatus Methanodesulfokores washburnensis', contains genes that are necessary for anaerobic methane and dissimilatory sulfur metabolisms. Phylogenetic and ancestral reconstruction analyses suggest that methane metabolism originated in the Korarchaeota, whereas genes for dissimilatory sulfite reduction were horizontally transferred to the Korarchaeota from the Firmicutes. Interactions among enzymes involved in both metabolisms could facilitate exergonic, sulfite-dependent, anaerobic oxidation of methane to methanol; alternatively, 'Ca. M. washburnensis' could conduct methanogenesis and sulfur reduction independently. Metabolic reconstruction suggests that 'Ca. M. washburnensis' is a mixotroph, capable of amino acid uptake, assimilation of methane-derived carbon and/or CO₂ fixation by archaeal type III-b RuBisCO for scavenging ribose carbon. Our findings link anaerobic methane metabolism and dissimilatory sulfur reduction within a single deeply rooted archaeal population and have implications for the evolution of these traits throughout the Archaea.

Expanding anaerobic alkane metabolism in the domain of Archaea

Methanogenesis and anaerobic methane oxidation through methyl-coenzyme M reductase (MCR) as a key enzyme have been suggested to be basal pathways of archaea¹. How widespread MCR-based alkane metabolism is among archaea, where it occurs and how it evolved remain elusive. Here, we performed a global survey of MCR-encoding genomes based on metagenomic data from various environments. Eleven high-quality mcr-containing metagenomic-assembled genomes were obtained belonging to the Archaeoglobi in the Euryarchaeota, Hadesarchaeota and different TACK superphylum archaea, including the Nezhaarchaeota, Korarchaeota and Verstraetearchaeota. Archaeoglobi WYZ-LMO1 and WYZ-LMO3 and Korarchaeota WYZ-LMO9 encode both the (reverse) methanogenesis and the dissimilatory sulfate reduction pathway, suggesting that they have the genomic potential to couple both pathways in individual organisms. The Hadesarchaeota WYZ-LMO4-6 and Archaeoglobi JdFR-42 encode highly divergent MCRs, enzymes that may enable them to thrive on non-methane alkanes. The occurrence of mcr genes in different archaeal phyla indicates that MCR-based alkane metabolism is common in the domain of Archaea.

Contrasting Pathways for Anaerobic Methane Oxidation in Gulf of Mexico Cold Seep Sediments

Cold seep sediments are complex and widespread marine ecosystems emitting large amounts of methane, a potent greenhouse gas, and other hydrocarbons. Within these sediments, microbial communities play crucial roles in production and degradation of hydrocarbons, modulating oil and gas emissions to seawater. Despite this ecological importance, our understanding of microbial functions and methane oxidation pathways in cold seep ecosystems is poor. Based on gene expression profiling of environmental seep sediment samples, the present work showed that (i) the composition of the emitted fluids shapes the microbial community in general and the anaerobic methanotroph community specifically and (ii) AOM by ANME-2 in this seep may be coupled to sulfate reduction by Deltaproteobacteria by electron transfer through multiheme cytochromes, whereas AOM by ANME-1 lineages in this seep may involve a different, bacterium-independent pathway, coupling methane oxidation to elemental sulfur/polysulfide reduction.

Gulf of Mexico sediments harbor numerous hydrocarbon seeps associated with high sedimentation rates and thermal maturation of organic matter. These ecosystems host abundant and diverse microbial communities that directly or indirectly metabolize components of the emitted fluid. To investigate microbial function and activities in these ecosystems, metabolic potential (metagenomic) and gene expression (metatranscriptomic) analyses of two cold seep areas of the Gulf of Mexico were carried out. Seeps emitting biogenic methane harbored microbial communities dominated by archaeal anaerobic methane oxidizers of phylogenetic group 1 (ANME-1), whereas seeps producing fluids containing a complex mixture of thermogenic hydrocarbons were dominated by ANME-2 lineages. Metatranscriptome measurements in both communities indicated high levels of expression of genes for methane metabolism despite their distinct microbial communities and hydrocarbon composition. In contrast, the transcription level of sulfur cycle genes was quite different. In the thermogenic seep community, high levels of transcripts indicative of syntrophic anaerobic oxidation of methane (AOM) coupled to sulfate reduction were detected. This syntrophic partnership between the dominant ANME-2 and sulfate reducers potentially involves direct electron transfer through multiheme cytochromes. In the biogenic methane seep, genes from an ANME-1 lineage that are potentially involved in polysulfide reduction were highly expressed, suggesting a novel bacterium-independent anaerobic methane oxidation pathway coupled to polysulfide reduction. The observed divergence in AOM activities provides a new model for bacterium-independent AOM and emphasizes the variation that exists in AOM pathways between different ANME lineages.

IMPORTANCE Cold seep sediments are complex and widespread marine ecosystems emitting large amounts of methane, a potent greenhouse gas, and other hydrocarbons. Within these sediments, microbial communities play crucial roles in production and degradation of hydrocarbons, modulating oil and gas emissions to seawater. Despite this ecological importance, our understanding of microbial functions and methane oxidation pathways in cold seep ecosystems is poor. Based on gene expression profiling of environmental seep sediment samples, the present work showed that (i) the composition of the emitted fluids shapes the microbial community in general and the anaerobic methanotroph community specifically and (ii) AOM by ANME-2 in this seep may be coupled to sulfate reduction by Deltaproteobacteria by electron transfer through multiheme cytochromes, whereas AOM by ANME-1 lineages in this seep may involve a different, bacterium-independent pathway, coupling methane oxidation to elemental sulfur/polysulfide reduction.

Quantifying population-specific growth in benthic bacterial communities under low oxygen using H218O

The benthos in estuarine environments often experiences periods of regularly occurring hypoxic and anoxic conditions, dramatically impacting biogeochemical cycles. How oxygen depletion affects the growth of specific uncultivated microbial populations within these diverse benthic communities, however, remains poorly understood. Here, we applied H₂¹⁸O quantitative stable isotope probing (qSIP) in order to quantify the growth of diverse, uncultured bacterial populations in response to low oxygen concentrations in estuarine sediments. Over the course of 7- and 28-day incubations with redox conditions spanning from hypoxia to euxinia (sulfidic), ¹⁸O labeling of bacterial populations exhibited different patterns consistent with micro-aerophilic, anaerobic, facultative anaerobic, and aerotolerant anaerobic growth. ¹⁸O-labeled populations displaying anaerobic growth had a significantly non-random phylogenetic distribution, exhibited by numerous clades currently lacking cultured representatives within the Planctomycetes, Actinobacteria, Latescibacteria, Verrucomicrobia, and Acidobacteria. Genes encoding the beta-subunit of the dissimilatory sulfate reductase (dsrB) became ¹⁸O labeled only during euxinic conditions. Sequencing of these ¹⁸O-labeled dsrB genes showed that Acidobacteria were the dominant group of growing sulfate-reducing bacteria, highlighting their importance for sulfur cycling in estuarine sediments. Our findings provide the first experimental constraints on the redox conditions underlying increased growth in several groups of "microbial dark matter", validating hypotheses put forth by earlier metagenomic studies.

The Active Sulfate-Reducing Microbial Community in Littoral Sediment of Oligotrophic Lake Constance

Active sulfate-reducing microorganisms (SRM) in freshwater sediments are under-examined, despite the well-documented cryptic sulfur cycle occurring in these low-sulfate habitats. In Lake Constance sediment, sulfate reduction rates of up to 1,800 nmol cm^-3 day^-1 were previously measured. To characterize its SRM community, we used a tripartite amplicon sequencing approach based on 16S rRNA genes, 16S rRNA, and dsrB transcripts (encoding the beta subunit of dissimilatory sulfite reductase). We followed the respective amplicon dynamics in four anoxic microcosm setups supplemented either with (i) chitin and sulfate, (ii) sulfate only, (iii) chitin only, or (iv) no amendment. Chitin was used as a general substrate for the whole carbon degradation chain. Sulfate turnover in sulfate-supplemented microcosms ranged from 38 to 955 nmol day^-1 (g sediment f. wt.)^-1 and was paralleled by a decrease of 90–100% in methanogenesis as compared to the respective methanogenic controls. In the initial sediment, relative abundances of recognized SRM lineages accounted for 3.1 and 4.4% of all bacterial 16S rRNA gene and 16S rRNA sequences, respectively. When normalized against the 1.4 × 10⁸ total prokaryotic 16S rRNA gene copies as determined by qPCR and taking multiple rrn operons per genome into account, this resulted in approximately 10⁵–10⁶ SRM cells (g sediment f. wt.)^-1. The three amplicon approaches jointly identified Desulfobacteraceae and Syntrophobacteraceae as the numerically dominant and transcriptionally most active SRM in the initial sediment. This was corroborated in the time course analyses of sulfate-consuming sediment microcosms irrespective of chitin amendment. Uncultured dsrAB family-level lineages constituted in sum only 1.9% of all dsrB transcripts, with uncultured lineage 5 and 6 being transcriptionally most active. Our study is the first holistic molecular approach to quantify and characterize active SRM including uncultured dsrAB lineages not only in Lake Constance but for lake sediments in general.

Impacts of Human Activities on the Composition and Abundance of Sulfate-Reducing and Sulfur-Oxidizing Microorganisms in Polluted River Sediments

Water system degradation has a severe impact on daily life, especially in developing countries. However, microbial changes associated with this degradation, especially changes in microbes related to sulfur (S) cycling, are poorly understood. In this study, the abundance, structure, and diversity of sulfate-reducing microorganisms (SRM) and sulfur-oxidizing microorganisms (SOM) in the sediments from the Ziya River Basin, which is polluted by various human interventions (urban and agricultural activities), were investigated. Quantitative real-time PCR showed that the S cycling-related (SCR) genes (dsrB and soxB) were significantly elevated, reaching 2.60 × 10⁷ and 1.81 × 10⁸ copies per gram of dry sediment, respectively, in the region polluted by human urban activities (RU), and the ratio of dsrB to soxB abundance was significantly elevated in the region polluted by human agricultural activities (RA) compared with those in the protected wildlife reserve (RP), indicating that the mechanisms underlying water system degradation differ between RU and RA. Based on a 16S rRNA gene analysis, human interventions had substantial effects on microbial communities, particularly for microbes involved in S cycling. Some SCR genera (i.e., Desulfatiglans and Geothermobacter) were enriched in the sediments from both RA and RU, while others (i.e., Desulfofustis and Desulfonatronobacter) were only enriched in the sediments from RA. A redundancy analysis indicated that NH₄⁺-N and total organic carbon significantly influenced the abundance of SRM and SOM, and sulfate significantly influenced only the abundance of SRM. A network analysis showed high correlation between SCR microorganisms and other microbial groups for both RU and RA, including those involved in carbon and metal cycling. These findings indicated the different effects of different human interventions on the microbial community composition and water quality degradation.

Distribution of bacterial polycyclic aromatic hydrocarbon (PAH) ring-hydroxylating dioxygenases genes in oilfield soils and mangrove sediments explored by gene-targeted metagenomics

PAH ring-hydroxylating dioxygenases (PAH-RHDα) gene, a useful biomarker for PAH-degrading bacteria, has been widely used to examine PAH-degrading bacterial community in different contaminated sites. However, the distribution of PAH-RHDα genes in oilfield soils and mangrove sediments and their relationship with environmental factors still remain largely unclear. In this study, gene-targeted metagenomics was first used to investigate the diversity of PAH-degrading bacterial communities in oilfield soils and mangrove sediments. The results showed that higher diversity of PAH-degrading bacteria in the studied samples was revealed by gene-targeted metagenomics than traditional clone library analysis. Pseudomonas, Burkholderia, Ralstonia, Polymorphum gilvum, Mycobacterium, Sciscionella marina, Rhodococcus, and potential new degraders were prevailed in the oilfield area. For mangrove sediments, novel PAH degraders and Mycobacterium were predominated. The spatial distribution of PAH-RHDα gene was dependent on geographical location and regulated by local environmental variables. PAH content played a key role in shaping PAH-degrading bacterial communities in the studied samples, which would enrich PAH-degrading bacterial population and decrease PAH-degrading bacterial diversity. This work brings a more comprehensive and some new insights into the distribution and biodegradation potential of PAH-degrading bacteria in soil and sediments ecosystems.

"Candidatus Thermonerobacter thiotrophicus," A Non-phototrophic Member of the Bacteroidetes/Chlorobi With Dissimilatory Sulfur Metabolism in Hot Spring Mat Communities

In this study we present evidence for a novel, thermophilic bacterium with dissimilatory sulfur metabolism, tentatively named “Candidatus Thermonerobacter thiotrophicus,” which is affiliated with the Bacteroides/Ignavibacteria/Chlorobi and which we predict to be a sulfate reducer. Dissimilatory sulfate reduction (DSR) is an important and ancient metabolic process for energy conservation with global importance for geochemical sulfur and carbon cycling. Characterized sulfate-reducing microorganisms (SRM) are found in a limited number of bacterial and archaeal phyla. However, based on highly diverse environmental dsrAB sequences, a variety of uncultivated and unidentified SRM must exist. The recent development of high-throughput sequencing methods allows the phylogenetic identification of some of these uncultured SRM. In this study, we identified a novel putative SRM inhabiting hot spring microbial mats that is a member of the OPB56 clade (“Ca. Kapabacteria”) within the Bacteroidetes/Chlorobi superphylum. Partial genomes for this new organism were retrieved from metagenomes from three different hot springs in Yellowstone National Park, United States, and Japan. Supporting the prediction of a sulfate-reducing metabolism for this organism during period of anoxia, diel metatranscriptomic analyses indicate highest relative transcript levels in situ for all DSR-related genes at night. The presence of terminal oxidases, which are transcribed during the day, further suggests that these organisms might also perform aerobic respiration. The relative phylogenetic proximity to the sulfur-oxidizing, chlorophototrophic Chlorobi further raises new questions about the evolution of dissimilatory sulfur metabolism.

Elucidating functional microorganisms and metabolic mechanisms in a novel engineered ecosystem integrating C, N, P and S biotransformation by metagenomics

Denitrifying sulfur conversion-associated enhanced biological phosphorous removal (DS-EBPR) system is not only a novel wastewater treatment process, but also an ideal model for microbial ecology in a community context. However, it exists the knowledge gap on the roles and interactions of functional microorganisms in the DS-EBPR system for carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) bioconversions. We use genome-resolved metagenomics to build up an ecological model of microbial communities in a lab-scale DS-EBPR system with stable operation for more than 400 days. Our results yield 11 near-complete draft genomes that represent a substantial portion of the microbial community (39.4%). Sulfate-reducing bacteria (SRB) and sulfide-oxidizing bacteria (SOB) promote complex metabolic processes and interactions for C, N, P and S conversions. Bins 1-4 and 10 are considered as new potential polyphosphate-accumulating organisms (PAOs), in which Bins 1-4 can be considered as S-related PAOs (S-PAOs) with no previously cultivated or reported members. Our findings give an insight into a new ecological system with C, N, P and S simultaneous bioconversions and improve the understanding of interactions among SRB, SOB, denitrifiers and PAOs within a community context.

Metabolic potential of microbial communities from ferruginous sediments

Ferruginous (Fe-rich, SO₄ -poor) conditions are generally restricted to freshwater sediments on Earth today, but were likely widespread during the Archean and Proterozoic Eons. Lake Towuti, Indonesia, is a large ferruginous lake that likely hosts geochemical processes analogous to those that operated in the ferruginous Archean ocean. The metabolic potential of microbial communities and related biogeochemical cycling under such conditions remain largely unknown. We combined geochemical measurements (pore water chemistry, sulfate reduction rates) with metagenomics to link metabolic potential with geochemical processes in the upper 50 cm of sediment. Microbial diversity and quantities of genes for dissimilatory sulfate reduction (dsrAB) and methanogenesis (mcrA) decrease with increasing depth, as do rates of potential sulfate reduction. The presence of taxa affiliated with known iron- and sulfate-reducers implies potential use of ferric iron and sulfate as electron acceptors. Pore-water concentrations of acetate imply active production through fermentation. Fermentation likely provides substrates for respiration with iron and sulfate as electron donors and for methanogens that were detected throughout the core. The presence of ANME-1 16S and mcrA genes suggests potential for anaerobic methane oxidation. Overall our data suggest that microbial community metabolism in anoxic ferruginous sediments support coupled Fe, S and C biogeochemical cycling.

Pathogenic functions of host microbiota

BACKGROUND

It is becoming evident that certain features of human microbiota, encoded by distinct autochthonous taxa, promote disease. As a result, borders between the so-called opportunistic pathogens, pathobionts, and commensals are increasingly blurred, and specific targets for manipulating microbiota to improve host health are becoming elusive.

RESULTS

In this study, we focus on the functions of host bacterial communities that have the potential to cause disease, proposing the term "pathogenic function (pathofunction)". The concept is presented via three distinct examples, namely, the formation of (i) trimethylamine, (ii) secondary bile acids, and (iii) hydrogen sulfide, which represent metabolites of the gut microbiota linked to the development of non-communicable diseases. Using publicly available metagenomic and metatranscriptomic data (n = 2975), we quantified those pathofunctions in health and disease and exposed the key players. Pathofunctions were ubiquitously present with increased abundances in patient groups. Overall, the three pathofunctions were detected at low mean concentrations (< 1% of total bacteria carried respective genes) and encompassed various taxa, including uncultured members.

CONCLUSIONS

We outline how this function-centric approach, where all members of a community exhibiting a particular pathofunction are redundant, can contribute to risk assessment and the development of precision treatment directing gut microbiota to increase host health.

Semi-passive in-situ pilot scale bioreactor successfully removed sulfate and metals from mine impacted water under subarctic climatic conditions

Mine drainage contaminated with metals is a major environmental threat since it is a source of water pollution with devastating effects on aquatic ecosystems. Conventional active treatment technologies are prohibitively expensive and so there is increasing demand to develop reliable, cost-effective and sustainable passive or semi-passive treatment. These are promising alternatives since they leverage the metabolism of microorganisms native to the disturbed site at in situ or close to in situ conditions. Since this is a biological approach, it is not clear if semi-passive treatment would be effective in remote locations with extremely cold weather such as at mines in the subarctic. In this study we tested the hypothesis that sulfate-reducing bacteria, which are microorganisms that promote metal precipitation, exist in subarctic mine environments and their activity can be stimulated by adding a readily available carbon source. An experiment was setup at a closed mine in the Yukon Territory, Canada, where leaching of Zn and Cd occurs. To test if semi-passive treatment could precipitate these metals and prevent further leaching from waste rock, molasses as a carbon source was added to anaerobic bioreactors mimicking the belowground in-situ conditions. Microbial community analysis confirmed that sulfate-reducing bacteria became enriched in the bioreactors upon addition of molasses. The population composition remained fairly stable over the 14 month operating period despite temperature shifts from 17 to 5 °C. Sulfate reduction functionality was confirmed by quantification of the gene for dissimilatory sulfite reductase. Metals were removed from underground mine drainage fed into the bioreactors with Zn removal efficiency varying between 20.9% in winter and 89.3% in summer, and Cd removal efficiency between 39% in winter and 90.5% in summer. This study demonstrated that stimulation of native SRB in MIW was possible and that in situ semi-passive treatment can be effective in removing metals despite the cold climate.

In situ development of a methanotrophic microbiome in deep-sea sediments

Emission of the greenhouse gas methane from the seabed is globally controlled by marine aerobic and anaerobic methanotrophs gaining energy via methane oxidation. However, the processes involved in the assembly and dynamics of methanotrophic populations in complex natural microbial communities remain unclear. Here we investigated the development of a methanotrophic microbiome following subsurface mud eruptions at Håkon Mosby mud volcano (1250 m water depth). Freshly erupted muds hosted deep-subsurface communities that were dominated by Bathyarchaeota, Atribacteria and Chloroflexi. Methanotrophy was initially limited to a thin surface layer of Methylococcales populations consuming methane aerobically. With increasing distance to the eruptive center, anaerobic methanotrophic archaea, sulfate-reducing Desulfobacterales and thiotrophic Beggiatoaceae developed, and their respective metabolic capabilities dominated the biogeochemical functions of the community. Microbial richness, evenness, and cell numbers of the entire microbial community increased up to tenfold within a few years downstream of the mud flow from the eruptive center. The increasing diversity was accompanied by an up to fourfold increase in sequence abundance of relevant metabolic genes of the anaerobic methanotrophic and thiotrophic guilds. The communities fundamentally changed in their structure and functions as reflected in the metagenome turnover with distance from the eruptive center, and this was reflected in the biogeochemical zonation across the mud volcano caldera. The observed functional succession provides a framework for the response time and recovery of complex methanotrophic communities after disturbances of the deep-sea bed.

Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle

A critical step in the biogeochemical cycle of sulfur on Earth is microbial sulfate reduction, yet organisms from relatively few lineages have been implicated in this process. Previous studies using functional marker genes have detected abundant, novel dissimilatory sulfite reductases (DsrAB) that could confer the capacity for microbial sulfite/sulfate reduction but were not affiliated with known organisms. Thus, the identity of a significant fraction of sulfate/sulfite-reducing microbes has remained elusive. Here we report the discovery of the capacity for sulfate/sulfite reduction in the genomes of organisms from 13 bacterial and archaeal phyla, thereby more than doubling the number of microbial phyla associated with this process. Eight of the 13 newly identified groups are candidate phyla that lack isolated representatives, a finding only possible given genomes from metagenomes. Organisms from Verrucomicrobia and two candidate phyla, Candidatus Rokubacteria and Candidatus Hydrothermarchaeota, contain some of the earliest evolved dsrAB genes. The capacity for sulfite reduction has been laterally transferred in multiple events within some phyla, and a key gene potentially capable of modulating sulfur metabolism in associated cells has been acquired by putatively symbiotic bacteria. We conclude that current functional predictions based on phylogeny significantly underestimate the extent of sulfate/sulfite reduction across Earth's ecosystems. Understanding the prevalence of this capacity is integral to interpreting the carbon cycle because sulfate reduction is often coupled to turnover of buried organic carbon. Our findings expand the diversity of microbial groups associated with sulfur transformations in the environment and motivate revision of biogeochemical process models based on microbial community composition.

Peatland Acidobacteria with a dissimilatory sulfur metabolism

Sulfur-cycling microorganisms impact organic matter decomposition in wetlands and consequently greenhouse gas emissions from these globally relevant environments. However, their identities and physiological properties are largely unknown. By applying a functional metagenomics approach to an acidic peatland, we recovered draft genomes of seven novel Acidobacteria species with the potential for dissimilatory sulfite (dsrAB, dsrC, dsrD, dsrN, dsrT, dsrMKJOP) or sulfate respiration (sat, aprBA, qmoABC plus dsr genes). Surprisingly, the genomes also encoded DsrL, which so far was only found in sulfur-oxidizing microorganisms. Metatranscriptome analysis demonstrated expression of acidobacterial sulfur-metabolism genes in native peat soil and their upregulation in diverse anoxic microcosms. This indicated an active sulfate respiration pathway, which, however, might also operate in reverse for dissimilatory sulfur oxidation or disproportionation as proposed for the sulfur-oxidizing Desulfurivibrio alkaliphilus. Acidobacteria that only harbored genes for sulfite reduction additionally encoded enzymes that liberate sulfite from organosulfonates, which suggested organic sulfur compounds as complementary energy sources. Further metabolic potentials included polysaccharide hydrolysis and sugar utilization, aerobic respiration, several fermentative capabilities, and hydrogen oxidation. Our findings extend both, the known physiological and genetic properties of Acidobacteria and the known taxonomic diversity of microorganisms with a DsrAB-based sulfur metabolism, and highlight new fundamental niches for facultative anaerobic Acidobacteria in wetlands based on exploitation of inorganic and organic sulfur molecules for energy conservation.

Beyond the tip of the iceberg; a new view of the diversity of sulfite- and sulfate-reducing microorganisms

Sulfite-reducing and sulfate-reducing microorganisms (SRM) play important roles in anoxic environments, linking the sulfur and carbon cycles. With climate warming, the distribution of anoxic habitats conductive to dissimilatory SRM is expanding. Consequently, we hypothesize that novel SRM are likely to emerge from the rare biosphere triggered by environmental changes. Using the dsrB gene as a  molecular marker of sulfite-reducers and sulfate-reducers, we analyzed the diversity, community composition, and abundance of SRM in 200 samples representing 14 different ecosystems, including marine and freshwater environments, oil reservoirs, and engineered infrastructure. Up to 167,397 species-level OTUs affiliated with 47 different families were identified. Up to 96% of these can be considered as "rare biosphere SRM". One  third of the dsrB genes identified belonged to uncharacterized lineages. The dsrB sequences exhibited a  strong pattern of selection in different ecosystems. These results expand our knowledge of the biodiversity and distribution of SRM, with implications for carbon and sulfur cycling in anoxic ecosystems.

Sulfate Transporters in Dissimilatory Sulfate Reducing Microorganisms: A Comparative Genomics Analysis

The first step in the sulfate reduction pathway is the transport of sulfate across the cell membrane. This uptake has a major effect on sulfate reduction rates. Much of the information available on sulfate transport was obtained by studies on assimilatory sulfate reduction, where sulfate transporters were identified among several types of protein families. Despite our growing knowledge on the physiology of dissimilatory sulfate-reducing microorganisms (SRM) there are no studies identifying the proteins involved in sulfate uptake in members of this ecologically important group of anaerobes. We surveyed the complete genomes of 44 sulfate-reducing bacteria and archaea across six phyla and identified putative sulfate transporter encoding genes from four out of the five surveyed protein families based on homology. We did not find evidence that ABC-type transporters (SulT) are involved in the uptake of sulfate in SRM. We speculate that members of the CysP sulfate transporters could play a key role in the uptake of sulfate in thermophilic SRM. Putative CysZ-type sulfate transporters were present in all genomes examined suggesting that this overlooked group of sulfate transporters might play a role in sulfate transport in dissimilatory sulfate reducers alongside SulP. Our in silico analysis highlights several targets for further molecular studies in order to understand this key step in the metabolism of SRMs.

Rice Paddy Nitrospirae Carry and Express Genes Related to Sulfate Respiration: Proposal of the New Genus "Candidatus Sulfobium"

Nitrospirae spp. distantly related to thermophilic, sulfate-reducing Thermodesulfovibrio species are regularly observed in environmental surveys of anoxic marine and freshwater habitats. Here we present a metaproteogenomic analysis of Nitrospirae bacterium Nbg-4 as a representative of this clade. Its genome was assembled from replicated metagenomes of rice paddy soil that was used to grow rice in the presence and absence of gypsum (CaSO₄·2H₂O). Nbg-4 encoded the full pathway of dissimilatory sulfate reduction and showed expression of this pathway in gypsum-amended anoxic bulk soil as revealed by parallel metaproteomics. In addition, Nbg-4 encoded the full pathway of dissimilatory nitrate reduction to ammonia (DNRA), with expression of its first step being detected in bulk soil without gypsum amendment. The relative abundances of Nbg-4 were similar under both treatments, indicating that Nbg-4 maintained stable populations while shifting its energy metabolism. Whether Nbg-4 is a strict sulfate reducer or can couple sulfur oxidation to DNRA by operating the pathway of dissimilatory sulfate reduction in reverse could not be resolved. Further genome reconstruction revealed the potential to utilize butyrate, formate, H₂, or acetate as an electron donor; the Wood-Ljungdahl pathway was expressed under both treatments. Comparison to publicly available Nitrospirae genome bins revealed the pathway for dissimilatory sulfate reduction also in related Nitrospirae recovered from groundwater. Subsequent phylogenomics showed that such microorganisms form a novel genus within the Nitrospirae, with Nbg-4 as a representative species. Based on the widespread occurrence of this novel genus, we propose for Nbg-4 the name “Candidatus Sulfobium mesophilum,” gen. nov., sp. nov.

IMPORTANCE Rice paddies are indispensable for the food supply but are a major source of the greenhouse gas methane. If it were not counterbalanced by cryptic sulfur cycling, methane emission from rice paddy fields would be even higher. However, the microorganisms involved in this sulfur cycling are little understood. By using an environmental systems biology approach with Italian rice paddy soil, we could retrieve the population genome of a novel member of the phylum Nitrospirae. This microorganism encoded the full pathway of dissimilatory sulfate reduction and expressed it in anoxic paddy soil under sulfate-enriched conditions. Phylogenomics and comparison to the results of environmental surveys showed that such microorganisms are actually widespread in freshwater and marine environments. At the same time, they represent an undiscovered genus within the little-explored phylum Nitrospirae. Our results will be important for the design of enrichment strategies and postgenomic studies to further understanding of the contribution of these novel Nitrospirae spp. to the global sulfur cycle.

A novel Chromatiales bacterium is a potential sulfide oxidizer in multiple orders of marine sponges

Sponges are benthic filter feeders that play pivotal roles in coupling benthic-pelagic processes in the oceans that involve transformation of dissolved and particulate organic carbon and nitrogen into biomass. While the contribution of sponge holobionts to the nitrogen cycle has been recognized in past years, their importance in the sulfur cycle, both oceanic and physiological, has only recently gained attention. Sponges in general, and Theonella swinhoei in particular, harbour a multitude of associated microorganisms that could affect sulfur cycling within the holobiont. We reconstructed the genome of a Chromatiales (class Gammaproteobacteria) bacterium from a metagenomic sequence dataset of a T. swinhoei-associated microbial community. This relatively abundant bacterium has the metabolic capability to oxidize sulfide yet displays reduced metabolic potential suggestive of its lifestyle as an obligatory symbiont. This bacterium was detected in multiple sponge orders, according to similarities in key genes such as 16S rRNA and polyketide synthase genes. Due to its sulfide oxidation metabolism and occurrence in many members of the Porifera phylum, we suggest naming the newly described taxon Candidatus Porisulfidus.

Comparative metagenomics of hydrocarbon and methane seeps of the Gulf of Mexico

Oil and gas percolate profusely through the sediments of the Gulf of Mexico, leading to numerous seeps at the seafloor, where complex microbial, and sometimes animal communities flourish. Sediments from three areas (two cold seeps with contrasting hydrocarbon composition and a site outside any area of active seepage) of the Gulf of Mexico were investigated and compared. Consistent with the existence of a seep microbiome, a distinct microbial community was observed in seep areas compared to sediment from outside areas of active seepage. The microbial community from sediments without any influence from hydrocarbon seepage was characterized by Planctomycetes and the metabolic potential was consistent with detrital marine snow degradation. By contrast, in seep samples with methane as the principal hydrocarbon, methane oxidation by abundant members of ANME-1 was likely the predominant process. Seep samples characterized by fluids containing both methane and complex hydrocarbons, were characterized by abundant Chloroflexi (Anaerolinaceae) and deltaproteobacterial lineages and exhibited potential for complex hydrocarbon degradation. These different metabolic capacities suggested that microorganisms in cold seeps can potentially rely on other processes beyond methane oxidation and that the hydrocarbon composition of the seep fluids may be a critical factor structuring the seafloor microbial community composition and function.

Depth Distribution and Assembly of Sulfate-Reducing Microbial Communities in Marine Sediments of Aarhus Bay

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.IMPORTANCE Sulfate-reducing microorganisms (SRMs) are key players in the marine carbon and sulfur cycles, especially in coastal sediments, yet little is understood about the environmental factors controlling their depth distribution. Our results suggest that macrofaunal activity is a key driver of SRM abundance and community structure in marine sediments and that a small subset of SRM species of high relative abundance in the subsurface SRM community persists from the sulfate-rich surface sediment to sulfate-depleted methanogenic subsurface sediment. More generally, we conclude that SRM communities inhabiting the subsurface seabed assemble by the selective survival of members of the surface community.

Microbial Diversity and Community Structure of Sulfate-Reducing and Sulfur-Oxidizing Bacteria in Sediment Cores from the East China Sea

Sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) have been studied extensively in marine sediments because of their vital roles in both sulfur and carbon cycles, but the available information regarding the highly diverse SRB and SOB communities is not comprehensive. High-throughput sequencing of functional gene amplicons provides tremendous insight into the structure and functional potential of complex microbial communities. Here, we explored the community structure, diversity, and abundance of SRB and SOB simultaneously through 16S rRNA, dsrB and soxB gene high-throughput sequencing and quantitative PCR analyses of core samples from the East China Sea. Overall, high-throughput sequencing of the dsrB and soxB genes achieved almost complete coverage (>99%) and revealed the high diversity, richness, and operational taxonomic unit (OTU) numbers of the SRB and SOB communities, which suggest the existence of an active sulfur cycle in the study area. Further analysis demonstrated that rare species make vital contributions to the high richness, diversity, and OTU numbers obtained. Depth-based distributions of the dsrB, soxB, and 16S rRNA gene abundances indicated that the SRB abundance might be more sensitive to the sedimentary dynamic environment than those of total bacteria and SOB. In addition, the results of unweighted pair group method with arithmetic mean (UPGMA) clustering analysis and redundancy analysis revealed that environmental parameters, such as depth and dissolved inorganic nitrogen concentrations, and the sedimentary dynamic environment, which differed between the two sampling stations, can significantly influence the community structures of total bacteria, SRB, and SOB. This study provided further comprehensive information regarding the characteristics of SRB and SOB communities.

Thriving or surviving? Evaluating active microbial guilds in Baltic Sea sediment

Microbial life in the deep subsurface biosphere is taxonomically and metabolically diverse, but it is vigorously debated whether the resident organisms are thriving (metabolizing, maintaining cellular integrity and expressing division genes) or just surviving. As part of Integrated Ocean Drilling Program Expedition 347: Baltic Sea Paleoenvironment, we extracted and sequenced RNA from organic carbon-rich, nutrient-replete and permanently anoxic sediment. In stark contrast to the oligotrophic subsurface biosphere, Baltic Sea Basin samples provided a unique opportunity to understand the balance between metabolism and other cellular processes. Targeted sequencing of 16S rRNA transcripts showed Atribacteria (an uncultured phylum) and Chloroflexi to be among the dominant and the active members of the community. Metatranscriptomic analysis identified methane cycling, sulfur cycling and halogenated compound utilization as active in situ respiratory metabolisms. Genes for cellular maintenance, cellular division, motility and antimicrobial production were also transcribed. This indicates that microbial life in deep subsurface Baltic Sea Basin sediments was not only alive, but thriving.

Sulfur Cycling and the Intestinal Microbiome

In this review, we focus on the activities transpiring in the anaerobic segment of the sulfur cycle occurring in the gut environment where hydrogen sulfide is produced. While sulfate-reducing bacteria are considered as the principal agents for hydrogen sulfide production, the enzymatic desulfhydration of cysteine by heterotrophic bacteria also contributes to production of hydrogen sulfide. For sulfate-reducing bacteria respiration, molecular hydrogen and lactate are suitable as electron donors while sulfate functions as the terminal electron acceptor. Dietary components provide fiber and macromolecules that are degraded by bacterial enzymes to monomers, and these are fermented by intestinal bacteria with the production to molecular hydrogen which promotes the metabolic dominance by sulfate-reducing bacteria. Sulfate is also required by the sulfate-reducing bacteria, and this can be supplied by sulfate- and sulfonate-containing compounds that are hydrolyzed by intestinal bacterial with the release of sulfate. While hydrogen sulfide in the intestinal biosystem may be beneficial to bacteria by increasing resistance to antibiotics, and protecting them from reactive oxygen species, hydrogen sulfide at elevated concentrations may become toxic to the host.

The life sulfuric: microbial ecology of sulfur cycling in marine sediments

Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes. Sulfur-transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate-rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep-subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle.

Phylogenetic and Structural Comparisons of the Three Types of Methyl Coenzyme M Reductase from Methanococcales and Methanobacteriales

The phylogenetically diverse family of methanogenic archaea universally use methyl coenzyme M reductase (MCR) for catalyzing the final methane-forming reaction step of the methanogenic energy metabolism. Some methanogens of the orders Methanobacteriales and Methanococcales contain two isoenzymes. Comprehensive phylogenetic analyses on the basis of all three subunits grouped MCRs from Methanobacteriales and Methanococcales into three distinct types: (i) MCRs from Methanobacteriales, (ii) MCRs from Methanobacteriales and Methanococcales, and (iii) MCRs from Methanococcales The first and second types contain MCR isoenzymes I and II from Methanothermobacter marburgensis, respectively; therefore, they were designated MCR type I and type II and accordingly; the third one was designated MCR type III. For comparison with the known MCR type I and type II structures, we determined the structure of MCR type III from Methanotorris formicicus and Methanothermococcus thermolithotrophicus As predicted, the three MCR types revealed highly similar overall structures and virtually identical active site architectures reflecting the chemically challenging mechanism of methane formation. Pronounced differences were found at the protein surface with respect to loop geometries and electrostatic properties, which also involve the entrance of the active-site funnel. In addition, the C-terminal end of the γ-subunit is prolonged by an extra helix after helix γ8 in MCR type II and type III, which is, however, differently arranged in the two MCR types. MCR types I, II, and III share most of the posttranslational modifications which appear to fine-tune the enzymatic catalysis. Interestingly, MCR type III lacks the methyl-cysteine but possesses in subunit α of M. formicicus a 6-hydroxy-tryptophan, which thus far has been found only in the α-amanitin toxin peptide but not in proteins.IMPORTANCE Methyl coenzyme M reductase (MCR) represents a prime target for the mitigation of methane releases. Phylogenetic analyses of MCRs suggested several distinct sequence clusters; those from Methanobacteriales and Methanococcales were subdivided into three types: MCR type I from Methanobacteriales, MCR type II from Methanobacteriales and Methanococcales, and the newly designated MCR type III exclusively from Methanococcales We determined the first X-ray structures for an MCR type III. Detailed analyses revealed substantial differences between the three types only in the peripheral region. The subtle modifications identified and electrostatic profiles suggested enhanced substrate binding for MCR type III. In addition, MCR type III from Methanotorris formicicus contains 6-hydroxy-tryptophan, a new posttranslational modification that thus far has been found only in the α-amanitin toxin.

Disguised as a Sulfate Reducer: Growth of the Deltaproteobacterium Desulfurivibrio alkaliphilus by Sulfide Oxidation with Nitrate

This study demonstrates that the deltaproteobacterium Desulfurivibrio alkaliphilus can grow chemolithotrophically by coupling sulfide oxidation to the dissimilatory reduction of nitrate and nitrite to ammonium. Key genes of known sulfide oxidation pathways are absent from the genome of D. alkaliphilus. Instead, the genome contains all of the genes necessary for sulfate reduction, including a gene for a reductive-type dissimilatory bisulfite reductase (DSR). Despite this, growth by sulfate reduction was not observed. Transcriptomic analysis revealed a very high expression level of sulfate-reduction genes during growth by sulfide oxidation, while inhibition experiments with molybdate pointed to elemental sulfur/polysulfides as intermediates. Consequently, we propose that D. alkaliphilus initially oxidizes sulfide to elemental sulfur, which is then either disproportionated, or oxidized by a reversal of the sulfate reduction pathway. This is the first study providing evidence that a reductive-type DSR is involved in a sulfide oxidation pathway. Transcriptome sequencing further suggests that nitrate reduction to ammonium is performed by a novel type of periplasmic nitrate reductase and an unusual membrane-anchored nitrite reductase.

Sulfide oxidation and sulfate reduction, the two major branches of the sulfur cycle, are usually ascribed to distinct sets of microbes with distinct diagnostic genes. Here we show a more complex picture, as D. alkaliphilus, with the genomic setup of a sulfate reducer, grows by sulfide oxidation. The high expression of genes typically involved in the sulfate reduction pathway suggests that these genes, including the reductive-type dissimilatory bisulfite reductases, are also involved in as-yet-unresolved sulfide oxidation pathways. Finally, D. alkaliphilus is closely related to cable bacteria, which grow by electrogenic sulfide oxidation. Since there are no pure cultures of cable bacteria, D. alkaliphilus may represent an exciting model organism in which to study the physiology of this process.

Organismal and spatial partitioning of energy and macronutrient transformations within a hypersaline mat

Phototrophic mat communities are model ecosystems for studying energy cycling and elemental transformations because complete biogeochemical cycles occur over millimeter-to-centimeter scales. Characterization of energy and nutrient capture within hypersaline phototrophic mats has focused on specific processes and organisms; however, little is known about community-wide distribution of and linkages between these processes. To investigate energy and macronutrient capture and flow through a structured community, the spatial and organismal distribution of metabolic functions within a compact hypersaline mat community from Hot Lake have been broadly elucidated through species-resolved metagenomics and geochemical, microbial diversity and metabolic gradient measurements. Draft reconstructed genomes of 34 abundant organisms revealed three dominant cyanobacterial populations differentially distributed across the top layers of the mat suggesting niche separation along light and oxygen gradients. Many organisms contained diverse functional profiles, allowing for metabolic response to changing conditions within the mat. Organisms with partial nitrogen and sulfur metabolisms were widespread indicating dependence on metabolite exchange. In addition, changes in community spatial structure were observed over the diel. These results indicate that organisms within the mat community have adapted to the temporally dynamic environmental gradients in this hypersaline mat through metabolic flexibility and fluid syntrophic interactions, including shifts in spatial arrangements.

Diversity and Composition of Sulfate-Reducing Microbial Communities Based on Genomic DNA and RNA Transcription in Production Water of High Temperature and Corrosive Oil Reservoir

Deep subsurface petroleum reservoir ecosystems harbor a high diversity of microorganisms, and microbial influenced corrosion is a major problem for the petroleum industry. Here, we used high-throughput sequencing to explore the microbial communities based on genomic 16S rDNA and metabolically active 16S rRNA analyses of production water samples with different extents of corrosion from a high-temperature oil reservoir. Results showed that Desulfotignum and Roseovarius were the most abundant genera in both genomic and active bacterial communities of all the samples. Both genomic and active archaeal communities were mainly composed of Archaeoglobus and Methanolobus. Within both bacteria and archaea, the active and genomic communities were compositionally distinct from one another across the different oil wells (bacteria p = 0.002; archaea p = 0.01). In addition, the sulfate-reducing microorganisms (SRMs) were specifically assessed by Sanger sequencing of functional genes aprA and dsrA encoding the enzymes adenosine-5'-phosphosulfate reductase and dissimilatory sulfite reductase, respectively. Functional gene analysis indicated that potentially active Archaeoglobus, Desulfotignum, Desulfovibrio, and Thermodesulforhabdus were frequently detected, with Archaeoglobus as the most abundant and active sulfate-reducing group. Canonical correspondence analysis revealed that the SRM communities in petroleum reservoir system were closely related to pH of the production water and sulfate concentration. This study highlights the importance of distinguishing the metabolically active microorganisms from the genomic community and extends our knowledge on the active SRM communities in corrosive petroleum reservoirs.

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

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

Draft genome sequence of Desulfoplanes formicivorans Pf12BT, a sulfate-reducing bacterium of the family Desulfomicrobiaceae

Desulfoplanes formicivorans strain Pf12B^T is the type strain of the type species in the genus Desulfoplanes, which is the one of the genera in the family Desulfomicrobiaceae within the order Desulfovibrionales. This deltaproteobacterium was isolated from a blackish meromictic lake sediment. D. formicivorans strain Pf12B^T is a Gram-negative, motile and sulfate-reducing bacterium. Cells of strain Pf12B^T are characterized by possession of vibroid morphology and red fluorescent pigment. Here we describe the features, draft genome sequence and annotation of this organism, the sole species of the genus Desulfoplanes. The genome comprised 3,000,979 bp, 2,657 protein-coding genes and 58 RNA genes.

Metatranscriptomic analysis of prokaryotic communities active in sulfur and arsenic cycling in Mono Lake, California, USA

This study evaluates the transcriptionally active, dissimilatory sulfur- and arsenic-cycling components of the microbial community in alkaline, hypersaline Mono Lake, CA, USA. We sampled five depths spanning the redox gradient (10, 15, 18, 25 and 31 m) during maximum thermal stratification. We used custom databases to identify transcripts of genes encoding complex iron-sulfur molybdoenzyme (CISM) proteins, with a focus on arsenic (arrA, aioA and arxA) and sulfur cycling (dsrA, aprA and soxB), and assigned them to taxonomic bins. We also report on the distribution of transcripts related to the ars arsenic detoxification pathway. Transcripts from detoxification pathways were not abundant in oxic surface waters (10 m). Arsenic cycling in the suboxic and microaerophilic zones of the water column (15 and 18 m) was dominated by arsenite-oxidizing members of the Gammaproteobacteria most closely affiliated with Thioalkalivibrio and Halomonas, transcribing arxA. We observed a transition to arsenate-reducing bacteria belonging to the Deltaproteobacteria and Firmicutes transcribing arsenate reductase (arrA) in anoxic bottom waters of the lake (25 and 31 m). Sulfur cycling at 15 and 18 m was dominated by Gammaproteobacteria (Thioalkalivibrio and Thioalkalimicrobium) oxidizing reduced S species, with a transition to sulfate-reducing Deltaproteobacteria at 25 and 31 m. Genes related to arsenic and sulfur oxidation from Thioalkalivibrio were more highly transcribed at 15 m relative to other depths. Our data highlight the importance of Thioalkalivibrio to arsenic and sulfur biogeochemistry in Mono Lake and identify new taxa that appear capable of transforming arsenic.

Diversity of aromatic hydroxylating dioxygenase genes in mangrove microbiome and their biogeographic patterns across global sites

Aromatic hydrocarbons (AH), such as polycyclic aromatic hydrocarbons, are compounds largely found in nature. Aromatic‐ring‐hydroxylating dioxygenases (ARHD) are proteins involved in AH degradation pathways. We used ARHD functional genes from an oil‐impacted mangrove area and compared their diversity with other sites around the world to understand the ARHD biogeographic distribution patterns. For this, a comprehensive database was established with 166 operational protein families (OPFs) from 1,758 gene sequences obtained from 15 different sites worldwide, of which twelve are already published studies and three are unpublished. Based on a deduced ARHD peptide sequences consensus phylogeny, we examined trends and divergences in the sequence phylogenetic clustering from the different sites. The taxonomic affiliation of the OPF revealed that Pseudomonas, Streptomyces, Variovorax, Bordetella and Rhodococcus were the five most abundant genera, considering all sites. The functional diversity analysis showed the enzymatic prevalence of benzene 1,2‐dioxygenase, 3‐phenylpropionate dioxygenase and naphthalene 1,2‐dioxygenase, in addition to 10.98% of undefined category ARHDs. The ARHD gene correlation analysis among different sites was essentially important to gain insights on spatial distribution patterns, genetic congruence and ecological coherence of the bacterial groups found. This work revealed the genetic potential from the mangrove sediment for AH biodegradation and a considerable evolutionary proximity among the dioxygenase OPFs found in Antarctica and South America sites, in addition to high level of endemism in each continental region.

Succession in the petroleum reservoir microbiome through an oil field production lifecycle

Subsurface petroleum reservoirs are an important component of the deep biosphere where indigenous microorganisms live under extreme conditions and in isolation from the Earth’s surface for millions of years. However, unlike the bulk of the deep biosphere, the petroleum reservoir deep biosphere is subject to extreme anthropogenic perturbation, with the introduction of new electron acceptors, donors and exogenous microbes during oil exploration and production. Despite the fundamental and practical significance of this perturbation, there has never been a systematic evaluation of the ecological changes that occur over the production lifetime of an active offshore petroleum production system. Analysis of the entire Halfdan oil field in the North Sea (32 producing wells in production for 1–15 years) using quantitative PCR, multigenic sequencing, comparative metagenomic and genomic bins reconstruction revealed systematic shifts in microbial community composition and metabolic potential, as well as changing ecological strategies in response to anthropogenic perturbation of the oil field ecosystem, related to length of time in production. The microbial communities were initially dominated by slow growing anaerobes such as members of the Thermotogales and Clostridiales adapted to living on hydrocarbons and complex refractory organic matter. However, as seawater and nitrate injection (used for secondary oil production) delivered oxidants, the microbial community composition progressively changed to fast growing opportunists such as members of the Deferribacteres, Delta-, Epsilon- and Gammaproteobacteria, with energetically more favorable metabolism (for example, nitrate reduction, H₂S, sulfide and sulfur oxidation). This perturbation has profound consequences for understanding the microbial ecology of the system and is of considerable practical importance as it promotes detrimental processes such as reservoir souring and metal corrosion. These findings provide a new conceptual framework for understanding the petroleum reservoir biosphere and have consequences for developing strategies to manage microbiological problems in the oil industry.

Implications from distinct sulfate-reducing bacteria populations between cattle manure and digestate in the elucidation of H2S production during anaerobic digestion of animal slurry

Biogas produced from the anaerobic digestion of animal slurry consists mainly of methane (CH₄) and carbon dioxide (CO₂), but also includes other minor gases, such as hydrogen sulfide (H₂S). Since it can act as a potent corrosive agent and presents a health hazard even at low concentrations, H₂S is considered an undesirable by-product of anaerobic digestion. Sulfate-reducing bacteria (SRBs) have been identified as the main biological source of H₂S in a number of natural, biological, and human-made habitats, and thus represent likely candidate microorganisms responsible for the production of H₂S 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 H₂S were produced by digestate collected from a manure biogas plant documented to have persistently high concentrations of H₂S 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 H₂S 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 H₂S levels in their biogas. Together, our results suggest that elevated H₂S production in anaerobic digesters requires the combination of biological and nutritional factors from both untreated manure and digestate.