Role In Sulfur Cycling Research Articles

Genomic Analysis of Novel Sulfitobacter Bacterial Strains Isolated from Marine Biofilms.

Bacteria from the genus Sulfitobacter are distributed across various marine habitats and play a significant role in sulfur cycling. However, the metabolic features of Sulfitobacter inhabiting marine biofilms are still not well understood. Here, complete genomes and paired metatranscriptomes of eight Sulfitobacter strains, isolated from biofilms on subtidal stones, have been analyzed to explore their central energy metabolism and potential of secondary metabolite biosynthesis. Based on average nucleotide identity and phylogenetic analysis, the eight strains were classified into six novel species and two novel strains. The reconstruction of the metabolic pathways indicated that all strains had a complete Entner-Doudoroff pathway, pentose phosphate pathway, and diverse pathways for amino acid metabolism, suggesting the presence of an optimized central carbon metabolism. Pangenome analysis further revealed the differences between the gene cluster distribution patterns among the eight strains, suggesting significant functional variation. Moreover, a total of 47 biosynthetic gene clusters were discovered, which were further classified into 37 gene cluster families that showed low similarity with previously documented clusters. Furthermore, metatranscriptomic analysis revealed the expressions of key functional genes involved in the biosynthesis of ribosomal peptides in in situ marine biofilms. Overall, this study sheds new light on the metabolic features, adaptive strategies, and value of genome mining in this group of biofilm-associated Sulfitobacter bacteria.

Deep-sea in situ and laboratory multi-omics provide insights into the sulfur assimilation of a deep-sea Chloroflexota bacterium.

The cycling of sulfur is one of Earth's major biogeochemical processes and is closely related to the energy metabolism of microorganisms living in the deep-sea cold seep and hydrothermal vents. To date, some of the members of Chloroflexota are proposed to play a previously unrecognized role in sulfur cycling. However, the sulfur metabolic characteristics of deep-sea Chloroflexota bacteria have never been reported, and remain to be verified in cultured deep-sea representatives. Here, we show that the deep-sea Chloroflexota bacterium ZRK33 can perform sulfate assimilation in both laboratory and deep-sea conditions, which expands our knowledge of the sulfur metabolic potential of deep-sea Chloroflexota bacteria. We also show that the genes associated with assimilatory and dissimilatory sulfate reduction ubiquitously distribute in the deep-sea Chloroflexota members, providing hints to the roles of Chloroflexota bacteria in deep-sea sulfur biogeochemical cycling.

Evolutionary history and origins of Dsr-mediated sulfur oxidation.

Microorganisms play vital roles in sulfur cycling through the oxidation of elemental sulfur and reduction of sulfite. These metabolisms are catalyzed by dissimilatory sulfite reductases (Dsr) functioning in either the reductive or reverse, oxidative direction. Dsr-mediated sulfite reduction is an ancient metabolism proposed to have fueled energy metabolism in some of Earth's earliest microorganisms, whereas sulfur oxidation is believed to have evolved later in association with the widespread availability of oxygen on Earth. Organisms are generally believed to carry out either the reductive or oxidative pathway, yet organisms from diverse phyla have been discovered with gene combinations that implicate them in both pathways. A comprehensive investigation into the metabolisms of these phyla regarding Dsr is currently lacking. Here, we selected one of these phyla, the metabolically versatile candidate phylum SAR324, to study the ecology and evolution of Dsr-mediated metabolism. We confirmed that diverse SAR324 encode genes associated with reductive Dsr, oxidative Dsr, or both. Comparative analyses with other Dsr-encoding bacterial and archaeal phyla revealed that organisms encoding both reductive and oxidative Dsr proteins are constrained to a few phyla. Further, DsrAB sequences from genomes belonging to these phyla are phylogenetically positioned at the interface between well-defined oxidative and reductive bacterial clades. The phylogenetic context and dsr gene content in these organisms points to an evolutionary transition event that ultimately gave way to oxidative Dsr-mediated metabolism. Together, this research suggests that SAR324 and other phyla with mixed dsr gene content are associated with the evolution and origins of Dsr-mediated sulfur oxidation.

PH and thiosulfate dependent microbial sulfur oxidation strategies across diverse environments.

Sulfur oxidizing bacteria (SOB) play a key role in sulfur cycling in mine tailings impoundment (TI) waters, where sulfur concentrations are typically high. However, our understanding of SOB sulfur cycling via potential S oxidation pathways (sox, rdsr, and S4I) in these globally ubiquitous contexts, remains limited. Here, we identified TI water column SOB community composition, metagenomics derived metabolic repertoires, physicochemistry, and aqueous sulfur concentration and speciation in four Canadian base metal mine, circumneutral-alkaline TIs over four years (2016 - 2019). Identification and examination of genomes from nine SOB genera occurring in these TI waters revealed two pH partitioned, metabolically distinct groups, which differentially influenced acid generation and sulfur speciation. Complete sox (csox) dominant SOB (e.g., Halothiobacillus spp., Thiomonas spp.) drove acidity generation and S2O3 2- consumption via the csox pathway at lower pH (pH ~5 to ~6.5). At circumneutral pH conditions (pH ~6.5 to ~8.5), the presence of non-csox dominant SOB (hosting the incomplete sox, rdsr, and/or other S oxidation reactions; e.g. Thiobacillus spp., Sulfuriferula spp.) were associated with higher [S2O3 2-] and limited acidity generation. The S4I pathway part 1 (tsdA; S2O3 2- to S4O6 2-), was not constrained by pH, while S4I pathway part 2 (S4O6 2- disproportionation via tetH) was limited to Thiobacillus spp. and thus circumneutral pH values. Comparative analysis of low, natural (e.g., hydrothermal vents and sulfur hot springs) and high (e.g., Zn, Cu, Pb/Zn, and Ni tailings) sulfur systems literature data with these TI results, reveals a distinct TI SOB mining microbiome, characterized by elevated abundances of csox dominant SOB, likely sustained by continuous replenishment of sulfur species through tailings or mining impacted water additions. Our results indicate that under the primarily oxic conditions in these systems, S2O3 2- availability plays a key role in determining the dominant sulfur oxidation pathways and associated geochemical and physicochemical outcomes, highlighting the potential for biological management of mining impacted waters via pH and [S2O3 2-] manipulation.

Gephyrocapsa huxleyi (Emiliania huxleyi) as a model system for coccolithophore biology.

Coccolithophores are the most abundant calcifying organisms in modern oceans and are important primary producers in many marine ecosystems. Their ability to generate a cellular covering of calcium carbonate plates (coccoliths) plays a major role in marine biogeochemistry and the global carbon cycle. Coccolithophores also play an important role in sulfur cycling through the production of the climate-active gas dimethyl sulfide. The primary model organism for coccolithophore research is Emiliania huxleyi, now named Gephyrocapsa huxleyi. G. huxleyi has a cosmopolitan distribution, occupying coastal and oceanic environments across the globe, and is the most abundant coccolithophore in modern oceans. Research in G. huxleyi has identified many aspects of coccolithophore biology, from cell biology to ecological interactions. In this perspective, we summarize the key advances made using G. huxleyi and examine the emerging tools for research in this model organism. We discuss the key steps that need to be taken by the research community to advance G. huxleyi as a model organism and the suitability of other species as models for specific aspects of coccolithophore biology.

Versatile Medium for the Isolation of Sulfur-Reducing Bacteria from Natural Ecotypes

Sulfate-reducing bacteria (SRB) are a diverse group of microorganisms that are commonly isolated from anoxygenic environments (lake depths, soil, or swamps) and are also found in the intestines of humans and animals. They are well known for outcompeting methanogens for common substrates thereby helping in the decrease of methane emissions and also playing a major role in sulfur cycling. Therefore, determining the cultivable methods for their isolation is important. Various media has been used for the cultivation and purification of SRB from natural wetlands. The luxuriant growth of SRB was observed in all the media tested, out of which the best suitable media to recover a maximum of colonies from the natural soil/sediment samples was discovered as a modified postage medium. The enumeration of the isolated SRB was done by the most probable number (MPN) technique. A total of twenty pure isolates of SRB were isolated from different ecotypes.

Bioelectrocatalytic sulfide oxidation by a haloalkaliphilic electroactive microbial community dominated by Desulfobulbaceae

Sulfide-oxidizing microorganisms (SOMs) play a vital role in biogeochemical sulfur cycling and are useful for the bioremediation of sulfide-rich wastewaters and environments. The electroactive SOMs remain poorly explored from extreme environments. This study presents the autotrophic electroactive microbial biofilm capable of sulfide oxidation under haloalkaline conditions (pH – 9.5; salinity – 20 g/L). It was obtained through electrochemical microbial enrichment from sub-surface sediments of the haloalkaline Lonar lake at an applied anode potential of -330 mV vs. Ag/AgCl in microbial electrolysis cells (MECs). The sulfide-oxidizing electroactive biofilm achieved a maximum average current density of 315±23 µA/cm2 with 87±10% coulombic efficiency and 34±8% sulfide oxidation to sulfate. The bioelectrocatalytic sulfide oxidation at the anode facilitated 0.16±0.02 mM/day hydrogen production at the cathode of MECs. Low current densities and neither sulfate nor hydrogen production were observed in abiotic electrochemical controls suggesting the bioelectrocatalytic role of anodic microbial biofilm in the sulfide to sulfate oxidation process. The sulfide oxidation process was faster in bioelectrochemical (0.94±0.2 mM/day) than the abiotic reactors (0.49±0.01 mM/day), confirming the microbial role in the enhanced sulfide oxidation bioelectrocatalysis. Sulfur was detected at the anode surface in both abiotic and biotic electrochemical experiments, suggesting the occurrence of electrochemical sulfide oxidation to sulfur process under here-tested conditions. The bio-anode analysis through scanning electron microscopic imaging confirmed the microbial growth at the anode surface, and 16S-rRNA based amplicon sequencing revealed the dominance of unclassified Desulfobulbaceace at a relative sequence abundance of 61.8 ± 9.9% in anodic biofilm. This work on electroactive SOMs from a natural haloalkaline habitat contributes to the limited understanding of extreme electroactive microorganisms and their role in sulfur cycling in such environments.

Diversity and Distribution of Microbial Communities Associated with Reef Corals of the Malay Peninsula.

Coral-associated bacteria play critical roles in the regulation of coral health and function. Environmental perturbations that alter the bacterial community structure can render the coral holobiont more susceptible and less resilient to disease. Understanding the natural variation of the coral microbiome across space and host species provides a baseline that can be used to distinguish shifts in community structure. Using a 16S rRNA gene metabarcoding approach, this study examines bacterial community structure across three scleractinian coral hosts. Our results show that corals of three regions-eastern and western Peninsular Malaysia and Singapore-host distinct bacterial communities; despite these differences, we were able to identify a core microbiome shared across all three species. This core microbiome was also present in samples previously collected in Thailand, suggesting that these core microbes play an important role in promoting and maintaining host health. For example, several have been identified as dimethylsulfoniopropionate (DMSP) metabolizers that have roles in sulfur cycling and the suppression of bacterial pathogens. Pachyseris speciosa has the most variable microbiome, followed by Porites lutea, with the composition of the Diploastrea heliopora microbiome the least variable throughout all locations. Microbial taxa associated with each region or site are likely shaped by local environmental conditions. Taken together, host identity is a major driver of differences in microbial community structure, while environmental heterogeneity shapes communities at finer scales.

Kinetics and mechanism of polysulfides and elemental sulfur formation by a reaction between hydrogen sulfide and δ-MnO2

Formation rates for various products of hydrogen sulfide oxidation by δ-MnO2 were studied as a function of pH, temperature, concentration of the reactants, and ionic strength at the environmentally-relevant conditions. The main goals of this work were studying the effects of these parameters on speciation of zero-valent sulfur, including individual polysulfides and revealing the mechanism of its formation. A reaction between hydrogen sulfide and manganese dioxide is the fastest environmentally-relevant abiotic process of polysulfides formation, reactive sulfur species, which participate in complexation of metals, pyrite formation, sulfurization of organic matter and may serve as a substrate for microorganisms. In the pH range of 7.0 to 10.5, zero-valent sulfur accounted for > 55% of the sulfur in the products of hydrogen sulfide oxidation, while at pH ≥ 7.5, the formation rates of polysulfide zero-valent sulfur were higher than those of particulate zero-valent sulfur formation. Speciation of polysulfides on the initial stage of the reaction shows significant shift toward the higher polysulfides compared to their speciation calculated under assumption of thermodynamic equilibrium in both H2S - Sn2− - S8(aq) - α-S8 and H2S - Sn2− - S8(aq) - S8(coll) systems. We suggest that the shift in the speciation of polysulfide system results from the presence of a short-living highly reactive sulfur atoms, which are formed on the first stage of the reaction: two-electron transfer from hydrogen sulfide to manganese dioxide. Results of this study provide constraints on the rates of polysulfide formation at the redox interfaces of the stratified aquatic systems, and allows quantitative assessment of their role in sulfur cycling.

Ice Melting Can Change DMSP Production and Photosynthetic Activity of the Haptophyte Phaeocystis antarctica1.

Phaeocystis antarctica is an important primary producer in the Southern Ocean and plays roles in sulfur cycles through intracellular production of dimethylsulfoniopropionate (DMSP), a principal precursor of dimethyl sulfide (DMS). Haptophytes, including P. antarctica, are known to produce more DMSP than other phytoplankton groups such as diatoms and green algae, suggesting their important contribution to DMS concentrations in the Southern Ocean. We assessed how sea ice formation and melting affect photosynthesis and DMSP accumulation in P. antarctica both in seawater and in sea ice. Incubations were undertaken in an ice tank, which simulated sea ice formation and melting dynamics. The maximum quantum yield of photochemistry (Fv /Fm ) in photosystem II, as estimated from pulse-amplitude-modulated (PAM) fluorometry, was generally higher under low-light conditions than high-light conditions. Values of Fv /Fm , the relative maximum electron rate (rETRmax ), and photosynthetic efficiency (α) were lower in sea ice than in seawater, implying reduced photosynthetic function inside the sea ice. The reduction in photosynthetic function was probably due to the hypersaline environment in the brine channels. Total DMSP (DMSPt) concentration normalized by chlorophyll-a concentration was significantly higher in the sea ice than in the other environments, suggesting high accumulation of DMSP, probably due to its osmotic properties. Fv /Fm , specific growth rate, and DMSPt concentrations decreased with decreasing salinity with the lowest values found at a salinity of 22, that is, the lowest salinity tested. These results suggest that sea ice melting is responsible for a reduction in growth rate and DMSP production of P. antarctica.

Methanethiol and Dimethylsulfide Cycling in Stiffkey Saltmarsh.

Methanethiol (MeSH) and dimethylsulfide (DMS) are volatile organic sulfur compounds (VOSCs) with important roles in sulfur cycling, signaling and atmospheric chemistry. DMS can be produced from MeSH through a reaction mediated by the methyltransferase MddA. The mddA gene is present in terrestrial and marine metagenomes, being most abundant in soil environments. The substrate for MddA, MeSH, can also be oxidized by bacteria with the MeSH oxidase (MTO) enzyme, encoded by the mtoX gene, found in marine, freshwater and soil metagenomes. Methanethiol-dependent DMS production (Mdd) pathways have been shown to function in soil and marine sediments, but have not been characterized in detail in the latter environments. In addition, few molecular studies have been conducted on MeSH consumption in the environment. Here, we performed process measurements to confirm that Mdd-dependent and Mdd-independent MeSH consumption pathways are active in tested surface saltmarsh sediment when MeSH is available. We noted that appreciable natural Mdd-independent MeSH and DMS consumption processes masked Mdd activity. 16S rRNA gene amplicon sequencing and metagenomics data showed that Methylophaga, a bacterial genus known to catabolise DMS and MeSH, was enriched by the presence of MeSH. Moreover, some MeSH and/or DMS-degrading bacteria isolated from this marine environment lacked known DMS and/or MeSH cycling genes and can be used as model organisms to potentially identify novel genes in these pathways. Thus, we are likely vastly underestimating the abundance of MeSH and DMS degraders in these marine sediment environments. The future discovery and characterization of novel enzymes involved in MeSH and/or DMS cycling is essential to better assess the role and contribution of microbes to global organosulfur cycling.

Self-Referenced Ratiometric Detection of Sulfatase Activity with Dual-Emissive Urease-Encapsulated Gold Nanoclusters.

In this study, on the basis of the biomineralization capability of urease, a facile, one-step, and green synthetic method has been proposed for the fabrication of gold nanoclusters (AuNCs). The prepared urease-encapsulated AuNCs (U-AuNCs) exhibited strong red fluorescence emission (λem = 630 nm) with a quantum yield as high as 17%. Interestingly, at a low concentration, the U-AuNC solution was found to be a dual-emissive system with the blue emission of the dityrosine (diTyr) residues of urease and the red emission of the embedded AuNCs. Further experiments demonstrated that p-nitrophenol (PNP) can selectively suppress the 410 nm emission of the diTyr residues of U-AuNCs without affecting the red emission of the U-AuNCs. The fluorescence quenching mechanism between U-AuNCs and PNP was systematically studied, and the leading role of the inner filter effect (IFE) was identified. Additionally, based on the sulfatase-catalyzed hydrolysis of p-nitrophenyl sulfate (PNPS) to release PNP, a self-referenced ratiometric detection method for sulfatase, which plays a crucial role in sulfur cycling, degradation of sulfated glycosaminoglycans and glycolipids, and extracellular remodeling of sulfated glycosaminoglycans, was developed by using dual-emissive U-AuNCs as the signal readout, in which the diTyr residues served as the probe and the AuNCs functioned as the internal reference. This IFE-based ratiometric sensing strategy showed a good linear relationship over the range of 0.01-1 U/mL ( R2 = 0.997). The detection limit for sulfatase activity was 0.01 U/mL. The developed protocol was successfully used to detect sulfatase activity in human serum samples. The simplicity, rapidity, low cost, high credibility, good reproducibility, and excellent selectivity of the detection platform serve as an inspiration for further applications of fluorescent AuNCs in chemo/biosensing.

Asgard archaea: Diversity, function, and evolutionary implications in a range of microbiomes.

Elucidating the diversity of the Archaea has many important ecological and evolutionary implications. The Asgard superphylum of the archaea, described recently from metagenomic data, has reignited the decades-old debate surrounding the topology of the tree of life. This review synthesizes recent findings through publicly available genomes and literature to describe the current ecological and evolutionary significance of the Asgard superphylum. Asgard archaea have been found in a diverse range of microbiomes across the globe, primarily from sedimentary environments. Within these environments, positive correlations between specific members of the Asgard archaea and Candidate Division TA06 bacteria have been observed, opening up the possibility of symbiotic interactions between the groupings. Asgard archaeal genomes encode functionally diverse metabolic pathways, including the Wood-Ljungdahl pathway as a carbon-fixation strategy, putative nucleotide salvaging pathways, and novel mechanisms of phototrophy including new rhodopsins. Asgard archaea also appear to be active in nitrogen cycling. Asgard archaea encode genes involved in both dissimilatory nitrate reduction and denitrification, and for the potential to use atmospheric nitrogen or nitrite as nitrogen sources. Asgard archaea also may be involved in the transformation of sulfur compounds, indicating a putative role in sulfur cycling. To date, all Asgard archaeal genomes identified were described as obligately anaerobic. The Asgard archaea also appear to have important evolutionary implications. The presence of eukaryotic signature proteins and the affiliation of Asgard archaea in phylogenetic analyses appears to support two-domain topologies of the tree of life with eukaryotes emerging from within the domain of archaea, as opposed to the eukaryotes being a separate domain of life. Thus far, Heimdallarchaeota appears as the closest archaeal relative of eukaryotes.

Stratification of Sulfur Species and Microbial Community in Launched Marine Sediment by an Improved Sulfur-Fractionation Method and 16S rRNA Gene Sequencing

With a focus on marine sediment launched by the tsunami accompanying the Great East Japan Earthquake, we examined the vertical (i.e., depths of 0–2, 2–10, and 10–20 mm) profiles of reduced inorganic sulfur species and microbial community using a newly improved sulfur-fractionation method and 16S rRNA gene sequencing. S0 accumulated at the largest quantities at a depth of 2–10 mm, while the reduced forms of sulfur, such as iron(II) sulfide and pyrite, were abundant below 2 mm of the sediment. Operational taxonomic units (OTUs) related to chemolithotrophically sulfur-oxidizing Sulfurimonas denitrificans and Sulfurimonas autotrophica were only predominant at 2–10 mm, suggesting the involvement of these OTUs in the oxidation of sulfide to S0. In addition, Desulfocapsa sulfexigens, which is capable of chemolithotrophically disproportionating S0, prevailed at the same depth, indicating that accumulated S0 was converted to sulfate and sulfide. Although no significant differences were observed in sulfate concentrations across the depths examined, specific species of chemoorganotrophic sulfate reducers, i.e., Desulfotignum toluenicum and Desulfosalsimonas propionicica, showed significantly higher abundance at a depth of 2–10 mm than at the other depths examined. Organic matter potentially generated from sulfur oxidation and disproportionation may have served as the carbon source for the growth of these sulfate reducers. The present results demonstrated that sulfur oxidizers, a sulfur disproportionator, and sulfate reducers played vital roles in sulfur cycling with S0 as the key inorganic sulfur species in the oxic-anoxic boundary layer of the launched marine sediment.

Microbiomes of the Enteropneust, Saccoglossus bromophenolosus, and Associated Marine Intertidal Sediments of Cod Cove, Maine.

Enteropneusts are widely distributed marine invertebrates that accumulate high concentrations of halogenated aromatics. Some of these compounds affect benthic biogeochemistery (e.g., denitrification and ammonia oxidation), but little is known about interactions between enteropneusts and their associated microbial communities. Even less is known about enteropneust host-microbe relationships in the digestive tract. More generally, microbial community composition and diversity in intertidal sediments have received little attention. In this study, high throughput sequence analyses of 16S rRNA genes extracted from microbial communities associated with sediment-free whole individuals of Saccoglossus bromophenolosus and freshly excreted S. bromophenolosus gut sediments revealed a potential Spirochaete symbiont that was abundant, present in gut sediment, but absent in other sediments. Relative to surface sediments, gut communities also revealed evidence for selective losses of some groups and blooms of others, especially Colwellia, Photobacterium, Pseudoalteromonas, and Vibrio. After deposition, gut sediment communities rapidly resembled those of surface sediments. Although hierarchical cluster analysis and Linear Discriminant Analysis Effect Size (LEfSe) differentiated among burrow walls of S. bromophenolosus and a polychaete, Alitta virens, as well as between surface and sub-surface sediments, most operational taxonomic units (OTUs) were shared, with differences largely occurring in relative abundances. This suggests that sediment mixing through bioturbation might act to homogenize community composition, while species-specific impacts by infauna might alter local population abundances. Although Cod Cove is a relatively isolated intertidal system, microbial community members included groups with cosmopolitan distributions and roles in sulfur cycling, e.g., Gammaproteobacteria BD7 and Sva0071, as well as novel OTUs representing a large number of phyla.

Identification of Thiobacillus bacteria in agricultural soil in Iran using the 16S rRNA gene

Thiobacillus, as useful soil bacteria, plays an important role in sulfur cycling. The purpose of this study was to identify the species Thiobacillus thioparus, Thiobacillus novellas and Thiobacillus denitrificans in rainfed and irrigated lands soil in Ajabshir, Ilam, Qorveh, Rojintaak, Sonqor, Kermanshah and Research Farm of Razi University in Iran. Sampling was performed as randomized completely with three replications at depth of 0-30cm. The Thiobacillus species were determined via 16S rRNA characteristics. The results of agarose gel electrophoresis indicated that T. thioparus was the highest amount in the irrigated land in Research Farm and its lowest amount was in the Rojintaak rainfed land. These species not found in four locations and conditions including the Ajabshir irrigated, Qorveh rainfed, Research Farm rainfed and Rojintaak irrigated lands. The results of the T. novellas indicated that this was found in Ilam irrigated, Qorveh rainfed, Research Farm irrigated, Rojintaak irrigated and Rojintaak rainfed lands. The highest and lowest amount of T. novellas was indicated in the Rojintaak and Ilam irrigated lands respectively. The T. denitrificans gene showed that this bacterium was observed only in both samples of Ajabshir. Our study showed that Thiobacillus was not detected in all of the soils. If sulfur fertilizer is given to the soil without this bacterium, it is necessary to use sulfur fertilizer with Thiobacillus bacteria inoculation for better sulfur oxidation.

Methanethiol-dependent dimethylsulfide production in soil environments

Dimethylsulfide (DMS) is an environmentally important trace gas with roles in sulfur cycling, signalling to higher organisms and in atmospheric chemistry. DMS is believed to be predominantly produced in marine environments via microbial degradation of the osmolyte dimethylsulfoniopropionate (DMSP). However, significant amounts of DMS are also generated from terrestrial environments, for example, peat bogs can emit ~6 μmol DMS m−2 per day, likely via the methylation of methanethiol (MeSH). A methyltransferase enzyme termed ‘MddA’, which catalyses the methylation of MeSH, generating DMS, in a wide range of bacteria and some cyanobacteria, may mediate this process, as the mddA gene is abundant in terrestrial metagenomes. This is the first study investigating the functionality of MeSH-dependent DMS production (Mdd) in a wide range of aerobic environments. All soils and marine sediment samples tested produced DMS when incubated with MeSH. Cultivation-dependent and cultivation-independent methods were used to assess microbial community changes in response to MeSH addition in a grassland soil where 35.9% of the bacteria were predicted to contain mddA. Bacteria of the genus Methylotenera were enriched in the presence of MeSH. Furthermore, many novel Mdd+ bacterial strains were isolated. Despite the abundance of mddA in the grassland soil, the Mdd pathway may not be a significant source of DMS in this environment as MeSH addition was required to detect DMS at only very low conversion rates.

Sulfur Cycling-Related Biogeochemical Processes of Arsenic Mobilization in the Western Hetao Basin, China: Evidence from Multiple Isotope Approaches.

The role of sulfur cycling in arsenic behavior under reducing conditions is not well-understood in previous investigations. This study provides observations of sulfur and oxygen isotope fractionation in sulfate and evaluation of sulfur cycling-related biogeochemical processes controlling dissolved arsenic groundwater concentrations using multiple isotope approaches. As a typical basin hosting high arsenic groundwater, the western Hetao basin was selected as the study area. Results showed that, along the groundwater flow paths, groundwater δ34SSO4, δ18OSO4, and δ13CDOC increased with increases in arsenic, dissolved iron, hydrogen sulfide and ammonium concentrations, while δ13CDIC decreased with decreasing Eh and sulfate/chloride. Bacterial sulfate reduction (BSR) was responsible for many of these observed changes. The δ34SSO4 indicated that dissolved sulfate was mainly sourced from oxidative weathering of sulfides in upgradient alluvial fans. The high oxygen-sulfur isotope fractionation ratio (0.60) may result from both slow sulfate reduction rates and bacterial disproportionation of sulfur intermediates (BDSI). Data indicate that both the sulfide produced by BSR and the overall BDSI reduce arsenic-bearing iron(III) oxyhydroxides, leading to the release of arsenic into groundwater. These results suggest that sulfur-related biogeochemical processes are important in mobilizing arsenic in aquifer systems.

Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi) in Sulfur Cycling.

ABSTRACTThe marine subsurface sediment biosphere is widely inhabited by bacteria affiliated with the class Dehalococcoidia (DEH), phylum Chloroflexi, and yet little is known regarding their metabolisms. In this report, genomic content from a single DEH cell (DEH-C11) with a 16S rRNA gene that was affiliated with a diverse cluster of 16S rRNA gene sequences prevalent in marine sediments was obtained from sediments of Aarhus Bay, Denmark. The distinctive gene content of this cell suggests metabolic characteristics that differ from those of known DEH and Chloroflexi. The presence of genes encoding dissimilatory sulfite reductase (Dsr) suggests that DEH could respire oxidized sulfur compounds, although Chloroflexi have never been implicated in this mode of sulfur cycling. Using long-range PCR assays targeting DEH dsr loci, dsrAB genes were amplified and sequenced from various marine sediments. Many of the amplified dsrAB sequences were affiliated with the DEH Dsr clade, which we propose equates to a family-level clade. This provides supporting evidence for the potential for sulfite reduction by diverse DEH species. DEH-C11 also harbored genes encoding reductases for arsenate, dimethyl sulfoxide, and halogenated organics. The reductive dehalogenase homolog (RdhA) forms a monophyletic clade along with RdhA sequences from various DEH-derived contigs retrieved from available metagenomes. Multiple facts indicate that this RdhA may not be a terminal reductase. The presence of other genes indicated that nutrients and energy may be derived from the oxidation of substituted homocyclic and heterocyclic aromatic compounds. Together, these results suggest that marine DEH play a previously unrecognized role in sulfur cycling and reveal the potential for expanded catabolic and respiratory functions among subsurface DEH.

A novel large filamentous deltaproteobacterium on hydrothermally inactive sulfide chimneys of the Southern Mariana Trough

Unusual large filamentous bacteria (LFB) have been found on the deep seafloor environments. They play a significant role in geochemical cycling in the dark environments. However, our knowledge of the spatial distribution and phylogenetic diversity of the LFB on the deep seafloor are still limited due to the inaccessibility to these environments. Here, we report the discovery of a novel LFB on a hydrothermally inactive sulfide chimney in a deep-sea hydrothermal field of the Southern Mariana Trough. Light and electron microscopic observation showed that the width and total length of the LFB were >8µm and >100µm, respectively, of which morphology was similar to that of other known LFB such as “cable bacteria” of the Desulfobulbaceae. Analyses of a 16S rRNA gene clone library and fluorescence in situ hybridization revealed that this LFB belongs to the Desulfobulbaceae. The 16S rRNA gene of the LFB showed 94% similarity to those of the reported cable bacteria and cultured deltaproteobacterial species, suggesting that the LFB is a novel cable bacterium of the Desulfobulbaceae. The novel LFB potentially play a role in sulfur cycling on sulfide chimneys at the hydrothermally ceasing or even ceased deep-sea hydrothermal fields.