Light and polyphosphate kinase 2 cooperatively regulate the production of zero-valent sulfur in a deep-sea bacterium

It is well established that different wavelengths of light exist in various deep-sea environments, and many deep-sea microorganisms have evolved specialized mechanisms for sensing and utilizing light energy. Our previous research found that blue light promotes zero-valent sulfur (ZVS) production in Erythrobacter flavus 21-3, a bacterium isolated from a deep-sea cold seep. Given that long-wavelength light is more prevalent in deep-sea environments, the present study investigates the mechanism by which E. flavus 21-3 senses infrared light (wavelength 940 nm) and regulates ZVS production. We found that the bacteriophytochrome BPHP-15570 is responsible for sensing infrared light, which induces autophosphorylation of BPHP-15570, activating the diguanylate cyclase DGC-0450 for c-di-GMP biosynthesis. Subsequently, the PilZ domain-containing protein mPilZ-1753 binds to c-di-GMP, triggering a well-established ZVS production pathway involving thiosulfate dehydrogenase (TsdA) and two homologs of thiosulfohydrolases (SoxB). Notably, polyphosphate kinase 2 (PPK2) is recruited to compete for GTP, the direct precursor of c-di-GMP biosynthesis. This competition downregulates ZVS production as well as other important metabolic processes. This negative regulatory pathway helps the bacterium avoid excessive ZVS accumulation, which could be toxic to bacterial growth. Overall, E. flavus 21-3 has evolved a sophisticated regulatory pathway to sense both blue and infrared light, triggering ZVS production. Our study provides a valuable model for understanding light utilization and its coupling with sulfur cycling in deep-sea environments.IMPORTANCEIt is widely believed that deep-sea ecosystems operate independently of light, relying primarily on chemical energy. However, the discovery of non-photosynthetic bacteria in various deep-sea environments that can sense and utilize light has challenged this assumption. In a recent study, we found that blue light significantly promotes the production of zero-valent sulfur (ZVS) in the deep-sea bacterium Erythrobacter flavus 21-3. Given that long-wavelength light is more prevalent in deep-sea environments, we investigated whether infrared light also plays a role in regulating ZVS production in E. flavus 21-3. Our results indicate that infrared light does promote ZVS formation in this bacterium. We identified PPK2 as a negative regulator, maintaining intracellular ZVS at safe levels to prevent toxicity due to excessive accumulation. Overall, our study offers a valuable model for exploring how light is utilized and its interaction with microbial sulfur cycling in the extreme conditions of the deep sea.

Mercury Immobilization without Methylation in Sulfidogenic Systems Dominated by Sulfur Disproportionating Bacteria

The sulfidogenic process mediated by sulfate-reducing bacteria (SRB) is not ideal for treating mercury (Hg)-bearing wastewater due to the risk of methylmercury (MeHg) production. Addressing this challenge, our study demonstrated that, under S0-rich conditions and without organic additives, sulfidogenic communities dominated by sulfur-disproportionating bacteria (SDB) can effectively remove Hg(II) and prevent MeHg production. Using various inocula, we successfully established biological sulfidogenic systems driven separately by SDB and SRB. Batch experiments revealed that SDB cultures completely removed Hg(II) from the solution as HgS. Remarkably, no MeHg production was observed in the SDB cultures, while an average concentration of 0.32 μg/L of MeHg was detected in the SRB cultures. The absence of MeHg production in the SDB cultures could be mainly attributed to the cultivation conditions that reshaped the microbial community, resulting in a rapid decline of SRB-dominated Hg-methylating microorganisms. Consequently, the average abundance of the hgcA gene was 28 times lower than the levels before cultivation. Additionally, we found that the enriched Dissulfurimicrobium sp. bin121 can produce biogenic sulfide through sulfur disproportionation but lacks the hgcA gene, rendering it incapable of methylating Hg. Overall, we propose a novel biotechnology driven by SDB that can safely and sustainably treat Hg-bearing wastewater.

Abiotic and biotic-controlled nanomaterial formation pathways within the Earth's nanomaterial cycle

Nanomaterials have unique properties and play critical roles in the budget, cycling, and chemical processing of elements on Earth. An understanding of the cycling of nanomaterials can be greatly improved if the pathways of their formation are clearly recognized and understood. Here, we show that nanomaterial formation pathways mediated by aqueous fluids can be grouped into four major categories, abiotic and biotic processes coupled and decoupled from weathering processes. These can be subdivided in 18 subcategories relevant to the critical zone, and environments such as ocean hydrothermal vents and the upper mantle. Similarly, pathways in the gas phase such as volcanic fumaroles, wildfires and particle formation in the stratosphere and troposphere can be grouped into two major groups and five subcategories. In the most fundamental sense, both aqueous-fluid and gaseous pathways provide an understanding of the formation of all minerals which are inherently based on nanoscale precursors and reactions.

Influence of oxidation-reduction potential and pH on polysulfide concentrations and chain lengths in the biological desulfurization process under haloalkaline conditions

Biological desulfurization under haloalkaline conditions has been applied worldwide to remove hydrogen sulfide (H2S) from sour gas steams. The process relies on sulfide-oxidizing bacteria (SOB) to oxidize H2S to elemental sulfur (S8), which can then be recovered and reused. Recently, a dual-reactor biological desulfurization system was implemented where an anaerobic (sulfidic) bioreactor was incorporated as an addition to a micro-oxic bioreactor, allowing for higher S8 selectivity by limiting by-product formation. The highly sulfidic bioreactor environment enabled the SOB to remove (poly)sulfides (Sx2-) in the absence of oxygen, with Sx2- speculated as a main substrate in the removal pathway, thus making it vital to understand its role in the process. The SOB are influenced by the oxidation-reduction potential (ORP) set-point of the micro-oxic bioreactor as it is used to control the product of oxidation (S8 vs. SO42-), while the uptake of Sx2- by SOB has been qualitatively linked to pH. Therefore, to quantify these effects, this work determined the concentration and speciation of Sx2- in the biological desulfurization process under various pH values and ORP set-points. The total Sx2- concentrations in the sulfidic zone increased at elevated pH (8.9) compared to low pH (< 8.0), with on average 3.3 ± 1.0 mM-S more Sx2-. Chain lengths varied, with S72- only doubling in concentration while S52- increased 9 fold, which is in contrast with observations from abiotic systems. Changes to the ORP set-point of the micro-oxic reactor did not produce substantial changes in Sx2- concentration in the sulfidic zone. This illustrates that the reduction degree of the SOB in the micro-oxic bioreactor does not enhance their ability to interact with Sx2- in the sulfidic bioreactor. This increased understanding of how both pH and ORP affect changes in Sx2- concentration and chain length can lead to improved efficiency and design of the dual-reactor biological desulfurization process.

Inorganic Polysulfides in Solution: Structural Properties and Conformational Isomerism

We present a comprehensive theoretical examination of the structural properties of dianionic polysulfides [Sn]2- (n = 2-6), their conjugated monoacids [HSn]- (n = 2-6), and a selection of 1e--oxidized radical anions [Sn]•- (n = 2-4), in aqueous and dimethyl sulfoxide (DMSO) solutions. We investigated the structures and stabilities of various conformational isomers within these families of compounds by employing Quantum Mechanics-Molecular Mechanics (QM-MM) Molecular Dynamics (MD) simulations. The explicit inclusion of solvent molecules in the calculations revealed stable conformational structures that were previously unreported and might have appreciable concentrations in real systems. The interconversions between the isomeric structures proceed on the order of hundreds of picoseconds and are energetically similar to the isomerization processes in substituted cyclohexanes. We also conducted a detailed analysis of the stability of different isomers of the radical anion [S4]•- in solution. Our findings highlight the significant influence of the solvent on the isomerizations, a result that could be particularly relevant for enhancing the performance of metal-sulfur batteries.

Competition of Cd(II) and Pb(II) on the bacterial cells: a new insight from bioaccumulation based on NanoSIMS imaging

Polymetallic exposure causes complex toxicity to microorganisms. In this study, we investigated the responses of Escherichia coli under co-existence of cadmium (Cd) and lead (Pb), primarily based on biochemical analysis and RNA sequencing. Cd completely inhibited bacterial growth at a concentration of 2.41 mmol/L, with its removal rate as low as <10%. In contrast, the Pb removal rate was >95% under equimolar sole Pb stress. In addition, the Raman analysis confirmed the loss of proteins for the bacterial cells. Under the co-existence of Cd and Pb, the Cd toxicity to E. coli was alleviated. Meanwhile, the biosorption of Pb cations was more intense during the competitive sorption with Cd. Transmission electron microscopy images showed that a few cells were elongated during incubation, i.e., the average cellular length increased from 1.535 ± 0.407 to 1.845 ± 0.620 µm. Moreover, NanoSIMS imaging showed that the intracellular distribution of Cd and Pb was coupled with sulfur. Genes regulating sulfate transporter were also upregulated to promote sulfate assimilation. Then, the subsequent production of biogenic sulfide and sulfur-containing amino acids was enhanced. Although this strategy based on S enrichment could resist the polymetallic stress, not all related genes were induced to upregulate under sole Cd stress. Therefore, the S metabolism might remodel the microbial resistance to variable occurrence of heavy metals. Furthermore, the competitive sorption (in contrast to sole Cd stress) could prevent microbial cells from strong Cd toxicity.IMPORTANCEMicrobial tolerance and resistance to heavy metals have been widely studied under stress of single metals. However, the polymetallic exposure seems to prevail in the environment. Though microbial resistance can alleviate the effects of exogenous stress, the taxonomic or functional response to polymetallic exposure is still not fully understood. We determined the strong cytotoxicity of cadmium (Cd) on growth, and cell elongation would be driven by Cd stress. The addition of appropriate lead (Pb) showed a stimulating effect on microbial bioactivity. Meanwhile, the biosorption of Pb was more intense during co-existence of Pb and Cd. Our work also revealed the spatial coupling of intracellular S and Cd/Pb. In particular, the S assimilation was promoted by Pb stress. This work elucidated the microbial responses to polymetallic exposure and may provide new insights into the antagonistic function during metal stresses.

Metabolic features that select for Bathyarchaeia in modern ferruginous lacustrine subsurface sediments

Ferruginous conditions prevailed through Earth's early oceans history, yet our understanding of biogeochemical cycles in anoxic iron-rich, sulfate-poor sediments remains elusive in terms of redox processes and organic matter remineralization. Using comprehensive geochemistry, cell counts, and metagenomic data, we investigated the taxonomic and functional distribution of the microbial subsurface biosphere in Lake Towuti, a stratified ferruginous analogue. Below the zone in which pore water becomes depleted in electron acceptors, cell densities exponentially decreased while microbial assemblages shifted from iron- and sulfate-reducing bacterial populations to fermentative anaerobes and methanogens, mostly selecting Bathyarchaeia below the sulfate reduction zone. Bathyarchaeia encode metabolic machinery to cycle and assimilate polysulfides via sulfhydrogenase, sulfide dehydrogenase, and heterodisulfide reductase, using dissimilatory sulfite reductase subunit E and rubredoxin as carriers. Their metagenome-assembled genomes showed that carbon fixation could proceed through the complete methyl-branch Wood-Ljungdahl pathway, conducting (homo)acetogenesis in the absence of methyl coenzyme M reductase. Further, their partial carbonyl-branch, assumed to act in tetrahydrofolate interconversions of C1 and C2 compounds, could support close interactions with methylotrophic methanogens in the fermentation zone. Thus, Bathyarchaeia appeared capable of coupling sulfur-redox reactions with fermentative processes, using electron bifurcation in a redox-conserving (homo)acetogenic Wood-Ljungdahl pathway, and revealing geochemical ferruginous conditions at the transition between the sulfate reduction and fermentation zone as their preferential niche.

Enhanced Biogenic Sulfidation of Zero-Valent Iron in Columns: Implications for Promoting Dechlorination in Permeable Reactive Barriers

Biogenic sulfidation of zero-valent iron (ZVI) using sulfate reducing bacteria (SRB) has shown enhanced dechlorination rates comparable to those produced by chemical sulfidation. However, controlling and sustaining biogenic sulfidation to enhance in situ dechlorination are poorly understood. Detailed interactions between SRB and ZVI were examined for 4 months in column experiments under enhanced biogenic sulfidation conditions. SRB proliferation and changes in ZVI surface properties were characterized along the flow paths. The results show that ZVI can stimulate SRB activity by removing excessive free sulfide (S2-), in addition to lowering reduction potential. ZVI also hinders downgradient movement of SRB via electrostatic repulsion, restricting SRB presence near the upgradient interface. Dissolved organic carbon (e.g., >2.2 mM) was essential for intense biogenic sulfidation in ZVI columns. The presence of SRB in the upgradient zone appeared to promote the formation of iron polysulfides. Biogenic FeSx deposition increased the S content on ZVI surfaces ∼3-fold, corresponding to 3-fold and 2-fold improvements in the trichloroethylene degradation rate and electron efficiency in batch tests. Elucidation of SRB and ZVI interactions enhances sustained sulfidation in ZVI permeable reactive barrier.

Sulfur disproportionating microbial communities in a dynamic, microoxic-sulfidic karst system

Biogeochemical sulfur cycling in sulfidic karst systems is largely driven by abiotic and biological sulfide oxidation, but the fate of elemental sulfur (S0 ) that accumulates in these systems is not well understood. The Frasassi Cave system (Italy) is intersected by a sulfidic aquifer that mixes with small quantities of oxygen-rich meteoric water, creating Proterozoic-like conditions and supporting a prolific ecosystem driven by sulfur-based chemolithoautotrophy. To better understand the cycling of S0 in this environment, we examined the geochemistry and microbiology of sediments underlying widespread sulfide-oxidizing mats dominated by Beggiatoa. Sediment populations were dominated by uncultivated relatives of sulfur cycling chemolithoautotrophs related to Sulfurovum, Halothiobacillus, Thiofaba, Thiovirga, Thiobacillus, and Desulfocapsa, as well as diverse uncultivated anaerobic heterotrophs affiliated with Bacteroidota, Anaerolineaceae, Lentimicrobiaceae, and Prolixibacteraceae. Desulfocapsa and Sulfurovum populations accounted for 12%-26% of sediment 16S rRNA amplicon sequences and were closely related to isolates which carry out autotrophic S0 disproportionation in pure culture. Gibbs energy (∆Gr ) calculations revealed that S0 disproportionation under in situ conditions is energy yielding. Microsensor profiles through the mat-sediment interface showed that Beggiatoa mats consume dissolved sulfide and oxygen, but a net increase in acidity was only observed in the sediments below. Together, these findings suggest that disproportionation is an important sink for S0 generated by microbial sulfide oxidation in this oxygen-limited system and may contribute to the weathering of carbonate rocks and sediments in sulfur-rich environments.

Polysulfide Concentration and Chain Length in the Biological Desulfurization Process: Effect of Biomass Concentration and the Sulfide Loading Rate

Removal of hydrogen sulfide (H2S) can be achieved using the sustainable biological desulfurization process, where H2S is converted to elemental sulfur using sulfide-oxidizing bacteria (SOB). A dual-bioreactor process was recently developed where an anaerobic (sulfidic) bioreactor was used between the absorber column and micro-oxic bioreactor. In the absorber column and sulfidic bioreactor, polysulfides (Sx2-) are formed due to the chemical equilibrium between H2S and sulfur (S8). Sx2- is thought to be the intermediate for SOB to produce sulfur via H2S oxidation. In this study, we quantify Sx2-, determine their chain-length distribution under high H2S loading rates, and elucidate the relationship between biomass and the observed biological removal of sulfides under anaerobic conditions. A linear relationship was observed between Sx2- concentration and H2S loading rates at a constant biomass concentration. Increasing biomass concentrations resulted in a lower measured Sx2- concentration at similar H2S loading rates in the sulfidic bioreactor. Sx2- of chain length 6 (S62-) showed a substantial decrease at higher biomass concentrations. Identifying Sx2- concentrations and their chain lengths as a function of biomass concentration and the sulfide loading rate is key in understanding and controlling sulfide uptake by the SOB. This knowledge will contribute to a better understanding of how to reach and maintain a high selectivity for S8 formation in the dual-reactor biological desulfurization process.

Dynamically Quantifying Intracellular Elemental Sulfur and Predicting Pertinent Gene Transcription by Raman Spectroscopy in Living Cells

The ability to monitor changes in metabolites and corresponding gene transcription within living cells is highly desirable. However, most current assays for quantification of metabolites or for gene transcription are destructive, precluding tracking the real-time dynamics of living cells. Here, we used the intracellular elemental sulfur in a Thiophaeococcus mangrovi cell as a proof-of-concept to link the quantity of metabolites and relevant gene transcription in living cells by a nondestructive Raman approach. Raman spectroscopy was utilized to quantify intracellular elemental sulfur noninvasively, and a computational mRR (mRNA and Raman) model was developed to infer the transcription of genes relevant to elemental sulfur. The results showed a significant linear correlation between the exponentially transformed Raman spectral intensity of intracellular elemental sulfur and the mRNA levels of genes encoding sulfur globule proteins in T. mangrovi. The mRR model was verified independently in two genera of Thiocapsa and Thiorhodococcus, and the mRNA levels predicted by mRR showed high consistency with actual gene expression detected by real-time polymerase chain reaction (PCR). This approach could enable noninvasive assessment of the quantity of metabolites and link the pertinent gene expression profiles in living cells, providing useful baseline data to spectroscopically map various omics in real time.

Determining resident microbial community members and their correlations with geochemistry in a serpentinizing spring

Terrestrial serpentinizing systems allow us insight into the realm of alkaliphilic microbial communities driven by geology in a way that is frequently more accessible than their deep subsurface or marine counterparts. However, these systems are also marked by geochemical and microbial community variation due to the interactions of serpentinized fluids with host geology and the surface environment. To separate the transient from the endemic microbes in a hyperalkaline environment, we assessed the Ney Springs terrestrial serpentinizing system microbial community and geochemistry at six time points over the span of a year. Using 16S rRNA gene surveys we observed 93 amplicon sequence variants (ASVs) that were found at every sampling event. This is compared to ~17,000 transient ASVs that were detected only once across the six sampling events. Of the resident community members, 16 of these ASVs were regularly greater than 1% of the community during every sampling period. Additionally, many of these core taxa experienced statistically significant changes in relative abundance with time. Variation in the abundance of some core populations correlated with geochemical variation. For example, members of the Tindallia group, showed a positive correlation with variation in levels of ammonia at the spring. Investigating the metagenome assembled genomes of these microbes revealed evidence of the potential for ammonia generation via Stickland reactions within Tindallia. This observation offers new insight into the origin of high ammonia concentrations (>70 mg/L) seen at this site. Similarly, the abundance of putative sulfur-oxidizing microbes like Thiomicrospira, Halomonas, and a Rhodobacteraceae species could be linked to changes observed in sulfur-oxidation intermediates like tetrathionate and thiosulfate. While these data supports the influence of core microbial community members on a hyperalkaline spring's geochemistry, there is also evidence that subsurface processes affect geochemistry and may impact community dynamics as well. Though the physiology and ecology of these astrobiologically relevant ecosystems are still being uncovered, this work helps identify a stable microbial community that impacts spring geochemistry in ways not previously observed in serpentinizing ecosystems.

Effect of exogenous and endogenous sulfide on the production and the export of methylmercury by sulfate-reducing bacteria

Mercury (Hg) is a global pollutant of environmental and health concern; its methylated form, methylmercury (MeHg), is a potent neurotoxin. Sulfur-containing molecules play a role in MeHg production by microorganisms. While sulfides are considered to limit Hg methylation, sulfate and cysteine were shown to favor this process. However, these two forms can be endogenously converted by microorganisms into sulfide. Here, we explore the effect of sulfide (produced by the cell or supplied exogenously) on Hg methylation. For this purpose, Pseudodesulfovibrio hydrargyri BerOc1 was cultivated in non-sulfidogenic conditions with addition of cysteine and sulfide as well as in sulfidogenic conditions. We report that Hg methylation depends on sulfide concentration in the culture and the sulfides produced by cysteine degradation or sulfate reduction could affect the Hg methylation pattern. Hg methylation was independent of hgcA expression. Interestingly, MeHg production was maximal at 0.1-0.5 mM of sulfides. Besides, a strong positive correlation between MeHg in the extracellular medium and the increase of sulfide concentrations was observed, suggesting a facilitated MeHg export with sulfide and/or higher desorption from the cell. We suggest that sulfides (exogenous or endogenous) play a key role in controlling mercury methylation and should be considered when investigating the impact of Hg in natural environments.

New globally distributed bacterial phyla within the FCB superphylum

Microbes in marine sediments play crucial roles in global carbon and nutrient cycling. However, our understanding of microbial diversity and physiology on the ocean floor is limited. Here, we use phylogenomic analyses of thousands of metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments to identify 55 MAGs that are phylogenetically distinct from previously described bacterial phyla. We propose that these MAGs belong to 4 novel bacterial phyla (Blakebacterota, Orphanbacterota, Arandabacterota, and Joyebacterota) and a previously proposed phylum (AABM5-125-24), all of them within the FCB superphylum. Comparison of their rRNA genes with public databases reveals that these phyla are globally distributed in different habitats, including marine, freshwater, and terrestrial environments. Genomic analyses suggest these organisms are capable of mediating key steps in sedimentary biogeochemistry, including anaerobic degradation of polysaccharides and proteins, and respiration of sulfur and nitrogen. Interestingly, these genomes code for an unusually high proportion (~9% on average, up to 20% per genome) of protein families lacking representatives in public databases. Genes encoding hundreds of these protein families colocalize with genes predicted to be involved in sulfur reduction, nitrogen cycling, energy conservation, and degradation of organic compounds. Our findings advance our understanding of bacterial diversity, the ecological roles of these bacteria, and potential links between novel gene families and metabolic processes in the oceans.

Hydrobiogechemical interactions in the hyporheic zone of a sulfate-impacted, freshwater stream and riparian wetland ecosystem

Coupled abiotic and biotic processes in the hyporheic zone, where surface water and groundwater mix, play a critical role in the biogeochemical cycling of carbon, nutrients, and trace elements in streams and wetlands. Dynamic hydrologic conditions and anthropogenic pollution can impact redox gradients and biogeochemical response, although few studies examine the resulting hydrobiogeochemical interactions generated within the hyporheic zone. This study examines the effect of hyporheic flux dynamics and anthropogenic sulfate loading on the biogeochemistry of a riparian wetland and stream system. The hydrologic gradient as well as sediment, surface water, and porewater geochemistry chemistry was characterized at multiple points throughout the 2017 spring-summer-fall season at a sulfate-impacted stream flanked by wetlands in northern Minnesota. Results show that organic-rich sediments largely buffer the geochemical responses to brief or low magnitude changes in hydrologic gradient, but sustained or higher magnitude fluxes may variably alter the redox regime and, ultimately, the environmental geochemistry. This has implications for a changing climate that is expected to dramatically alter the hydrological cycle. Further, increased sulfate loading and dissolved or adsorbed ferric iron complexes in the hyporheic zone may induce a cryptic sulfur cycle linked to iron and carbon cycling, as indicated by the abundance of intermediate valence sulfur compounds (e.g., polysulfide, elemental sulfur, thiosulfate) throughout the anoxic wetland and stream-channel sediment column. The observed deviation from a classical redox tower coupled with potential changes in hydraulic gradient in these organic-rich wetland and stream hyporheic zones has implications for nutrient, trace element, and greenhouse gas fluxes into surface water and groundwater, ultimately influencing water quality and global climate.

Applying the concept of liquid biopsy to monitor the microbial biodiversity of marine coastal ecosystems

Liquid biopsy (LB) is a concept that is rapidly gaining ground in the biomedical field. Its concept is largely based on the detection of circulating cell-free DNA (ccfDNA) fragments that are mostly released as small fragments following cell death in various tissues. A small percentage of these fragments are from foreign (nonself) tissues or organisms. In the present work, we applied this concept to mussels, a sentinel species known for its high filtration capacity of seawater. We exploited the capacity of mussels to be used as natural filters to capture environmental DNA fragments of different origins to provide information on the biodiversity of marine coastal ecosystems. Our results showed that hemolymph of mussels contains DNA fragments that varied considerably in size, ranging from 1 to 5 kb. Shotgun sequencing revealed that a significant amount of DNA fragments had a nonself microbial origin. Among these, we found DNA fragments derived from bacteria, archaea, and viruses, including viruses known to infect a variety of hosts that commonly populate coastal marine ecosystems. Taken together, our study shows that the concept of LB applied to mussels provides a rich and yet unexplored source of knowledge regarding the microbial biodiversity of a marine coastal ecosystem.

Metagenomic and Metatranscriptomic Characterization of a Microbial Community That Catalyzes Both Energy-Generating and Energy-Storing Electrode Reactions

Electroactive bacteria are living catalysts, mediating energy-generating reactions at anodes or energy storage reactions at cathodes via extracellular electron transfer (EET). The Cathode-ANode (CANode) biofilm community was recently shown to facilitate both reactions; however, the identities of the primary constituents and underlying molecular mechanisms remain unknown. Here, we used metagenomics and metatranscriptomics to characterize the CANode biofilm. We show that a previously uncharacterized member of the family Desulfobulbaceae, Desulfobulbaceae-2, which had <1% relative abundance, had the highest relative gene expression and accounted for over 60% of all differentially expressed genes. At the anode potential, differential expression of genes for a conserved flavin oxidoreductase (Flx) and heterodisulfide reductase (Hdr) known to be involved in ethanol oxidation suggests a source of electrons for the energy-generating reaction. Genes for sulfate and carbon dioxide reduction pathways were expressed by Desulfobulbaceae-2 at both potentials and are the proposed energy storage reactions. Reduction reactions may be mediated by direct electron uptake from the electrode or from hydrogen generated at the cathode potential. The Desulfobulbaceae-2 genome is predicted to encode at least 85 multiheme (≥3 hemes) c-type cytochromes, some with as many as 26 heme-binding domains, that could facilitate reversible electron transfer with the electrode. Gene expression in other CANode biofilm species was also affected by the electrode potential, although to a lesser extent, and we cannot rule out their contribution to observed current. Results provide evidence of gene expression linked to energy storage and energy-generating reactions and will enable development of the CANode biofilm as a microbially driven rechargeable battery. IMPORTANCE Microbial electrochemical technologies (METs) rely on electroactive bacteria to catalyze energy-generating and energy storage reactions at electrodes. Known electroactive bacteria are not equally capable of both reactions, and METs are typically configured to be unidirectional. Here, we report on genomic and transcriptomic characterization of a recently described microbial electrode community called the Cathode-ANode (CANode). The CANode community is able to generate or store electrical current based on the electrode potential. During periods where energy is not needed, electrons generated from a renewable source, such as solar power, could be converted into energy storage compounds to later be reversibly oxidized by the same microbial catalyst. Thus, the CANode system can be thought of as a living "rechargeable battery." Results show that a single organism may be responsible for both reactions demonstrating a new paradigm for electroactive bacteria.

Rapid, concurrent formation of organic sulfur and iron sulfides during experimental sulfurization of sinking marine particles

Organic matter (OM) sulfurization can enhance the preservation and sequestration of carbon in anoxic sediments, and it has been observed in sinking marine particles from marine O₂-deficient zones. The magnitude of this effect on carbon burial remains unclear, however, because the transformations that occur when sinking particles encounter sulfidic conditions remain undescribed. Here, we briefly expose sinking marine particles from the eastern tropical North Pacific O₂-deficient zone to environmentally relevant sulfidic conditions (20°C, 0.5 mM [poly]sulfide, two days) and then characterize the resulting solid-phase organic and inorganic products in detail. During these experiments, the abundance of organic sulfur in both hydrolyzable and hydrolysis-resistant solids roughly triples, indicating extensive OM sulfurization. Lipids also sulfurize on this timescale, albeit less extensively. In all three pools, OM sulfurization produces organic monosulfides, thiols, and disulfides. Hydrolyzable sulfurization products appear within ≤ 200-μm regions of relatively homogenous composition that are suggestive of sulfurized extracellular polymeric substances (EPS). Concurrently, reactions with particulate iron oxyhydroxides generate low and fairly uniform concentrations of iron sulfide (FeS) within these same EPS-like materials. Iron oxyhydroxides were not fully consumed during the experiment, which demonstrates that organic materials can be competitive with reactive iron for sulfide. These experiments support the hypothesis that sinking, OM- and EPS-rich particles in a sulfidic water mass can sulfurize within days, potentially contributing to enhanced sedimentary carbon sequestration. Additionally, sulfur-isotope and chemical records of organic S and iron sulfides in sediments have the potential to incorporate signals from water column processes.

The bacterial sulfur cycle in expanding dysoxic and euxinic marine waters

Dysoxic marine waters (DMW, < 1 μM oxygen) are currently expanding in volume in the oceans, which has biogeochemical, ecological and societal consequences on a global scale. In these environments, distinct bacteria drive an active sulfur cycle, which has only recently been recognized for open-ocean DMW. This review summarizes the current knowledge on these sulfur-cycling bacteria. Critical bottlenecks and questions for future research are specifically addressed. Sulfate-reducing bacteria (SRB) are core members of DMW. However, their roles are not entirely clear, and they remain largely uncultured. We found support for their remarkable diversity and taxonomic novelty by mining metagenome-assembled genomes from the Black Sea as model ecosystem. We highlight recent insights into the metabolism of key sulfur-oxidizing SUP05 and Sulfurimonas bacteria, and discuss the probable involvement of uncultivated SAR324 and BS-GSO2 bacteria in sulfur oxidation. Uncultivated Marinimicrobia bacteria with a presumed organoheterotrophic metabolism are abundant in DMW. Like SRB, they may use specific molybdoenzymes to conserve energy from the oxidation, reduction or disproportionation of sulfur cycle intermediates such as S0 and thiosulfate, produced from the oxidation of sulfide. We expect that tailored sampling methods and a renewed focus on cultivation will yield deeper insight into sulfur-cycling bacteria in DMW.

The physiology and evolution of microbial selenium metabolism

Selenium is an essential trace element whose compounds are widely metabolized by organisms from all three domains of life. Moreover, phylogenetic evidence indicates that selenium species, along with iron, molybdenum, tungsten, and nickel, were metabolized by the last universal common ancestor of all cellular lineages, primarily for the synthesis of the 21st amino acid selenocysteine. Thus, selenium metabolism is both environmentally ubiquitous and a physiological adaptation of primordial life. Selenium metabolic reactions comprise reductive transformations both for assimilation into macromolecules and dissimilatory reduction of selenium oxyanions and elemental selenium during anaerobic respiration. This review offers a comprehensive overview of the physiology and evolution of both assimilatory and dissimilatory selenium metabolism in bacteria and archaea, highlighting mechanisms of selenium respiration. This includes a thorough discussion of our current knowledge of the physiology of selenocysteine synthesis and incorporation into proteins in bacteria obtained from structural biology. Additionally, this is the first comprehensive discussion in a review of the incorporation of selenium into the tRNA nucleoside 5-methylaminomethyl-2-selenouridine and as an inorganic cofactor in certain molybdenum hydroxylase enzymes. Throughout, conserved mechanisms and derived features of selenium metabolism in both domains are emphasized and discussed within the context of the global selenium biogeochemical cycle.

Degradation of odorous sulfide compounds by different oxidation processes in drinking water: Performance, reaction kinetics and mechanism

Swampy/septic odor caused by various sulfides is one of the most frequently encountered odor problems in drinking water. However, even though it is much more offensive, few studies have specifically focused on swampy/septic odor compared to the extensively studied musty/earthy problems. In this work, four sulfide odorants, diamyl sulfide (DAS), dipropyl sulfide (DPS), dimethyl disulfide (DMDS) and diethyl disulfide (DEDS), were selected to evaluate the treatment performance of different oxidation processes in drinking water. The results demonstrated that DMDS, DEDS, DPS and DAS could be oxidized effectively by KMnO_4, NaClO and ClO₂. The oxidation processes could be well described by the second-order kinetic model, in which k values of selected sulfides followed the order DMDS≈DEDS ≪ DPS≈DAS. As for the three oxidants, the order of reactivity was KMnO₄ ≪ ClO₂ < NaClO, which was also verified in raw water. The results of oxidation treatability, reaction kinetics and mechanisms confirmed that the characteristics of the central sulfur atom rather than the side chain is the decisive factor in controlling the oxidation rate and transformation pathway of sulfides. The transformation products and pathways were significantly different for the three oxidants. Sulfones (DPSO, DASO) were always formed by cycloaddition reactions during KMnO₄ oxidation, yet recombination reactions proceeded during ClO₂ oxidation and formed more products, such as MADS, DADS and EADS. Density functional theory (DFT) calculations confirmed that the differences in transformation pathways were caused by the variations in the activity of the oxidants and sulfides. Finally, NaClO was certified as the most effective oxidant for controlling sulfide odorants in drinking water treatment.

Application of biochar prepared from ethanol refinery by-products for Hg stabilization in floodplain soil: Impacts of drying and rewetting

This study evaluated three biochars derived from bioenergy by-products - manure-based anaerobic digestate (DIG), distillers' grains (DIS), and a mixture thereof (75G25S) - as amendments to stabilize Hg in contaminated floodplain soil under long-term saturated (up to 200 d) and cyclic drying and rewetting conditions. Greater total Hg (THg) removal (72 to nearly 100%) and limited MeHg production (<65 ng L^-1) were observed in digestate-based biochar-amended systems under initial saturated conditions. Drying and rewetting resulted in limited THg release, increased aqueous MeHg, and decreased solid MeHg in digestate-based biochar-amended systems. Changes in Fe and S chemistry as well as microbial communities during drying and rewetting potentially affected MeHg production. Digestate-based biochars may be more effective as amendments to control Hg release and minimize MeHg production in floodplain soils under long-term saturated and drying and rewetting conditions compared to distillers' grains biochar.

Microbial selenium metabolism: a brief history, biogeochemistry and ecophysiology

Selenium is an essential trace element for organisms from all three domains of life. Microorganisms, in particular, mediate reductive transformations of selenium that govern the element's mobility and bioavailability in terrestrial and aquatic environments. Selenium metabolism is not just ubiquitous but an ancient feature of life likely extending back to the universal common ancestor of all cellular lineages. As with the sulfur biogeochemical cycle, reductive transformations of selenium serve two metabolic functions: assimilation into macromolecules and dissimilatory reduction during anaerobic respiration. This review begins with a historical overview of how research in both aspects of selenium metabolism has developed. We then provide an overview of the global selenium biogeochemical cycle, emphasizing the central role of microorganisms in the cycle. This serves as a basis for a robust discussion of current models for the evolution of the selenium biogeochemical cycle over geologic time, and how knowledge of the evolution and ecophysiology of selenium metabolism can enrich and refine these models. We conclude with a discussion of the ecophysiological function of selenium-respiring prokaryotes within the cycle, and the tantalizing possibility of oxidative selenium transformations during chemolithoautotrophic growth.

Single-step Replacement of an Unreactive C-H Bond by a C-S Bond Using Polysulfide as the Direct Sulfur Source in Anaerobic Ergothioneine Biosynthesis

Ergothioneine, a natural longevity vitamin and antioxidant, is a thiol-histidine derivative. Recently, two types of biosynthetic pathways were reported. In the aerobic ergothioneine biosynthesis, a non-heme iron enzyme incorporates a sulfoxide to an sp² C-H bond in trimethyl-histidine (hercynine) through oxidation reactions. In contrast, in the anaerobic ergothioneine biosynthetic pathway in a green sulfur bacterium, Chlorobium limicola, a rhodanese domain containing protein (EanB) directly replaces this unreactive hercynine C-H bond with a C-S bond. Herein, we demonstrate that polysulfide (HSS_nSR) is the direct sulfur-source in EanB-catalysis. After identifying EanB's substrates, X-ray crystallography of several intermediate states along with mass spectrometry results provide additional mechanistic details for this reaction. Further, quantum mechanics/molecular mechanics (QM/MM) calculations reveal that protonation of N_π of hercynine by Tyr353 with the assistance of Thr414 is a key activation step for the hercynine sp² C-H bond in this trans-sulfuration reaction.

A novel bacterial thiosulfate oxidation pathway provides a new clue about the formation of zero-valent sulfur in deep sea

Zero-valent sulfur (ZVS) has been shown to be a major sulfur intermediate in the deep-sea cold seep of the South China Sea based on our previous work, however, the microbial contribution to the formation of ZVS in cold seep has remained unclear. Here, we describe a novel thiosulfate oxidation pathway discovered in the deep-sea cold seep bacterium Erythrobacter flavus 21–3, which provides a new clue about the formation of ZVS. Electronic microscopy, energy-dispersive, and Raman spectra were used to confirm that E. flavus 21–3 effectively converts thiosulfate to ZVS. We next used a combined proteomic and genetic method to identify thiosulfate dehydrogenase (TsdA) and thiosulfohydrolase (SoxB) playing key roles in the conversion of thiosulfate to ZVS. Stoichiometric results of different sulfur intermediates further clarify the function of TsdA in converting thiosulfate to tetrathionate (⁻O₃S–S–S–SO₃⁻), SoxB in liberating sulfone from tetrathionate to form ZVS and sulfur dioxygenases (SdoA/SdoB) in oxidizing ZVS to sulfite under some conditions. Notably, homologs of TsdA, SoxB, and SdoA/SdoB widely exist across the bacteria including in Erythrobacter species derived from different environments. This strongly indicates that this novel thiosulfate oxidation pathway might be frequently used by microbes and plays an important role in the biogeochemical sulfur cycle in nature.

Use of hardwood and sulfurized-hardwood biochars as amendments to floodplain soil from South River, VA, USA: Impacts of drying-rewetting on Hg removal

Periodic flooding and drying conditions in floodplains affect the mobility and bioavailability of Hg in aquatic sediments and surrounding soils. Sulfurized materials have been recently proposed as Hg sorbents due to their high affinity to bind Hg, while sulfurizing organic matter may enhance methylmercury (MeHg) production, offsetting the beneficial aspects of these materials. This study evaluated hardwood biochar (OAK) and sulfurized-hardwood biochar (MOAK) as soil amendments for controlling Hg release in a contaminated floodplain soil under conditions representative of periodic flooding and drying in microcosm experiments in three stages: (1) wet biochar amended-systems with river water in an anoxic environment up to 200 d; (2) dry selected reaction vessels in an oxic environment for 90 d; (3) rewet such vessels with river water in an anoxic environment for 90 d. In Stage 1, greater Hg removal (17-98% for unfiltered total Hg (THg) and 47-99% for 0.45-μm THg) and lower MeHg concentrations (<20 ng L^-1) were observed in MOAK-amended systems (10%MOAKs). In Stage 3, release of Hg in 10%MOAKs was eight-fold lower than in soil controls (SedCTRs), while increases in aqueous (up to 21 ng L^-1) and solid (up to 88 ng g^-1) MeHg concentrations were observed. The increases in MeHg corresponded to elevated aqueous concentrations of Mn, Fe, SO₄^2-, and HS^- in Stage 3. Results of S K-edge X-ray absorption near edge structure (XANES) analysis suggest oxidation of S in Stage 2 and formation of polysulfur in Stage 3. Results of pyrosequencing analysis indicate sulfate-reducing bacteria (SRB) became abundant in Stage 3 in 10%MOAKs. The shifts in biogeochemical conditions in 10%MOAKs in Stage 3 may increase the bioavailability of Hg to methylating bacteria. The results suggest limited impacts on Hg removal during drying and rewetting, while changes in biogeochemical conditions may affect MeHg production in sulfurized biochar-amended systems.

Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom

BACKGROUND

Lagoons are common along coastlines worldwide and are important for biogeochemical element cycling, coastal biodiversity, coastal erosion protection and blue carbon sequestration. These ecosystems are frequently disturbed by weather, tides, and human activities. Here, we investigated a shallow lagoon in New England. The brackish ecosystem releases hydrogen sulfide particularly upon physical disturbance, causing blooms of anoxygenic sulfur-oxidizing phototrophs. To study the habitat, microbial community structure, assembly and function we carried out in situ experiments investigating the bloom dynamics over time.

RESULTS

Phototrophic microbial mats and permanently or seasonally stratified water columns commonly contain multiple phototrophic lineages that coexist based on their light, oxygen and nutrient preferences. We describe similar coexistence patterns and ecological niches in estuarine planktonic blooms of phototrophs. The water column showed steep gradients of oxygen, pH, sulfate, sulfide, and salinity. The upper part of the bloom was dominated by aerobic phototrophic Cyanobacteria, the middle and lower parts by anoxygenic purple sulfur bacteria (Chromatiales) and green sulfur bacteria (Chlorobiales), respectively. We show stable coexistence of phototrophic lineages from five bacterial phyla and present metagenome-assembled genomes (MAGs) of two uncultured Chlorobaculum and Prosthecochloris species. In addition to genes involved in sulfur oxidation and photopigment biosynthesis the MAGs contained complete operons encoding for terminal oxidases. The metagenomes also contained numerous contigs affiliating with Microviridae viruses, potentially affecting Chlorobi. Our data suggest a short sulfur cycle within the bloom in which elemental sulfur produced by sulfide-oxidizing phototrophs is most likely reduced back to sulfide by Desulfuromonas sp.

CONCLUSIONS

The release of sulfide creates a habitat selecting for anoxygenic sulfur-oxidizing phototrophs, which in turn create a niche for sulfur reducers. Strong syntrophism between these guilds apparently drives a short sulfur cycle that may explain the rapid development of the bloom. The fast growth and high biomass yield of Chlorobi-affiliated organisms implies that the studied lineages of green sulfur bacteria can thrive in hypoxic habitats. This oxygen tolerance is corroborated by oxidases found in MAGs of uncultured Chlorobi. The findings improve our understanding of the ecology and ecophysiology of anoxygenic phototrophs and their impact on the coupled biogeochemical cycles of sulfur and carbon.

Physiology, Metabolism, and Fossilization of Hot-Spring Filamentous Microbial Mats

The evolutionarily ancient Aquificales bacterium Sulfurihydrogenibium spp. dominates filamentous microbial mat communities in shallow, fast-flowing, and dysoxic hot-spring drainage systems around the world. In the present study, field observations of these fettuccini-like microbial mats at Mammoth Hot Springs in Yellowstone National Park are integrated with geology, geochemistry, hydrology, microscopy, and multi-omic molecular biology analyses. Strategic sampling of living filamentous mats along with the hot-spring CaCO3 (travertine) in which they are actively being entombed and fossilized has permitted the first direct linkage of Sulfurihydrogenibium spp. physiology and metabolism with the formation of distinct travertine streamer microbial biomarkers. Results indicate that, during chemoautotrophy and CO2 carbon fixation, the 87-98% Sulfurihydrogenibium-dominated mats utilize chaperons to facilitate enzyme stability and function. High-abundance transcripts and proteins for type IV pili and extracellular polymeric substances (EPSs) are consistent with their strong mucus-rich filaments tens of centimeters long that withstand hydrodynamic shear as they become encrusted by more than 5 mm of travertine per day. Their primary energy source is the oxidation of reduced sulfur (e.g., sulfide, sulfur, or thiosulfate) and the simultaneous uptake of extremely low concentrations of dissolved O2 facilitated by bd-type cytochromes. The formation of elevated travertine ridges permits the Sulfurihydrogenibium-dominated mats to create a shallow platform from which to access low levels of dissolved oxygen at the virtual exclusion of other microorganisms. These ridged travertine streamer microbial biomarkers are well preserved and create a robust fossil record of microbial physiological and metabolic activities in modern and ancient hot-spring ecosystems.

Insights into ecological role of a new deltaproteobacterial order Candidatus Acidulodesulfobacterales by metagenomics and metatranscriptomics

Several abundant but yet uncultivated bacterial groups exist in extreme iron- and sulfur-rich environments, and the physiology, biodiversity, and ecological roles of these bacteria remain a mystery. Here we retrieved four metagenome-assembled genomes (MAGs) from an artificial acid mine drainage (AMD) system, and propose they belong to a new deltaproteobacterial order, Candidatus Acidulodesulfobacterales. The distribution pattern of Ca. Acidulodesulfobacterales in AMDs across Southeast China correlated strongly with ferrous iron. Reconstructed metabolic pathways and gene expression profiles showed that they were likely facultatively anaerobic autotrophs capable of nitrogen fixation. In addition to dissimilatory sulfate reduction, encoded by dsrAB, dsrD, dsrL, and dsrEFH genes, these microorganisms might also oxidize sulfide, depending on oxygen concentration and/or oxidation reduction potential. Several genes with homology to those involved in iron metabolism were also identified, suggesting their potential role in iron cycling. In addition, the expression of abundant resistance genes revealed the mechanisms of adaptation and response to the extreme environmental stresses endured by these organisms in the AMD environment. These findings shed light on the distribution, diversity, and potential ecological role of the new order Ca. Acidulodesulfobacterales in nature.

DMSO Reductase Family: Phylogenetics and Applications of Extremophiles

Dimethyl sulfoxide reductases (DMSO) are molybdoenzymes widespread in all domains of life. They catalyse not only redox reactions, but also hydroxylation/hydration and oxygen transfer processes. Although literature on DMSO is abundant, the biological significance of these enzymes in anaerobic respiration and the molecular mechanisms beyond the expression of genes coding for them are still scarce. In this review, a deep revision of the literature reported on DMSO as well as the use of bioinformatics tools and free software has been developed in order to highlight the relevance of DMSO reductases on anaerobic processes connected to different biogeochemical cycles. Special emphasis has been addressed to DMSO from extremophilic organisms and their role in nitrogen cycle. Besides, an updated overview of phylogeny of DMSOs as well as potential applications of some DMSO reductases on bioremediation approaches are also described.

Mangrove Sediment Microbiome: Adaptive Microbial Assemblages and Their Routed Biogeochemical Processes in Yunxiao Mangrove National Nature Reserve, China

Microorganisms play important roles in mangrove ecosystems. However, we know little about the ecological implications of mangrove microbiomes for high productivity and the efficient circulation of elements in mangrove ecosystems. Here, we focused on mangrove sediments located at the Yunxiao National Mangrove Reserve in southeast China, uncovering the mangrove microbiome using the 16S rRNA gene and shotgun metagenome sequencing approaches. Physicochemical assays characterized the Yunxiao mangrove sediments as carbon (C)-rich, sulfur (S)-rich, and nitrogen (N)-limited environment. Then phylogenetic analysis profiling a distinctive microbiome with an unexpected high frequency of Chloroflexi and Nitrospirae appeared to be an adaptive characteristic of microbial structure in S-rich habitat. Metagenome sequencing analysis revealed that the metabolic pathways of N and S cycling at the community-level were routed through ammonification and dissimilatory nitrate reduction to ammonium for N conservation in this N-limited habitat, and dissimilatory sulfate reduction along with polysulfide formation for generating bioavailable S resource avoiding the biotoxicity of sulfide in mangrove sediments. In addition, methane metabolism acted as a bridge to connect C cycling to N and S cycling. Further identification of possible biogeochemical linkers suggested Syntrophobacter, Sulfurovum, Nitrospira, and Anaerolinea potentially drive the coupling of C, N, and S cycling. These results highlighting the adaptive routed metabolism flow, a previously undescribed property of mangrove sediment microbiome, appears to be a defining characteristic of this habitat and may significantly contribute to the high productivity of mangrove ecosystems, which could be used as indicators for the health and biodiversity of mangrove ecosystems.

From Elemental Sulfur to Hydrogen Sulfide in Agricultural Soils and Plants

Sulfur is an essential element in determining the productivity and quality of agricultural products. It is also an element associated with tolerance to biotic and abiotic stress in plants. In agricultural practice, sulfur has broad use in the form of sulfate fertilizers and, to a lesser extent, as sulfite biostimulants. When used in the form of bulk elemental sulfur, or micro- or nano-sulfur, applied both to the soil and to the canopy, the element undergoes a series of changes in its oxidation state, produced by various intermediaries that apparently act as biostimulants and promoters of stress tolerance. The final result is sulfate S⁺⁶, which is the source of sulfur that all soil organisms assimilate and that plants absorb by their root cells. The changes in the oxidation states of sulfur S⁰ to S⁺⁶ depend on the action of specific groups of edaphic bacteria. In plant cells, S⁺⁶ sulfate is reduced to S⁻² and incorporated into biological molecules. S⁻² is also absorbed by stomata from H₂S, COS, and other atmospheric sources. S⁻² is the precursor of inorganic polysulfides, organic polysulfanes, and H₂S, the action of which has been described in cell signaling and biostimulation in plants. S⁻² is also the basis of essential biological molecules in signaling, metabolism, and stress tolerance, such as reactive sulfur species (RSS), SAM, glutathione, and phytochelatins. The present review describes the dynamics of sulfur in soil and plants, considering elemental sulfur as the starting point, and, as a final point, the sulfur accumulated as S⁻² in biological structures. The factors that modify the behavior of the different components of the sulfur cycle in the soil–plant–atmosphere system, and how these influences the productivity, quality, and stress tolerance of crops, are described. The internal and external factors that influence the cellular production of S⁻² and polysulfides vs. other S species are also described. The impact of elemental sulfur is compared with that of sulfates, in the context of proper soil management. The conclusion is that the use of elemental sulfur is recommended over that of sulfates, since it is beneficial for the soil microbiome, for productivity and nutritional quality of crops, and also allows the increased tolerance of plants to environmental stresses.

Occurrence of swampy/septic odor and possible odorants in source and finished drinking water of major cities across China

Swampy/septic odors are one of the most important odor types in drinking water. However, few studies have specifically focused on it compared to the extensive reported musty/earthy odor problems, even though the former is much more offensive. In this study, an investigation covering the odor characteristics, algal distribution and possible odorants contributing to swampy/septic odor, including dimethyl disulfide (DMDS), dimethyl trisulfide (DMTS), diisopropyl sulfide (DIPS), dipropyl sulfide (DPS), dibutyl sulfide (DBS), 2-methylisoborneol (2-MIB) and geosmin (GSM), was performed in source and finished water of 56 drinking water treatment plants (DWTPs) in 31 cities across China. While the musty/earthy and swampy/septic odors were dominant odor descriptors, the river source water exhibited a higher proportion of swampy/septic odor (38.5%) compared to much higher detection rate of musty/earthy odor (50.0%) in the lake/reservoir source water. The occurrence of swampy/septic odor, which was much easier to remove by conventional drinking water treatment processes compared to musty/earthy odors, was decreased by 62.9% and 46.3% in river and lake/reservoir source water respectively. Statistical analysis showed that thioethers might be responsible for the swampy/septic odor in source water (R² = 0.75, p < 0.05). Specifically, two thioethers, DMDS and DMTS were detected, and other thioethers were not found in all water samples. DMDS was predominant with a maximum odor activity value (OAV) of 2.0 in source water and 1.3 in finished water. The distribution of the thioethers exhibited a marked regional characteristics with higher concentrations being detected in the east and south parts of China. The high concentrations of thioethers in lake/reservoir source water samples could be partly interpreted as the bloom of the cyanobacteria. This study provides basic information for swampy/septic odor occurrence in drinking water and will be helpful for further water quality management in water industry in China.

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.

Respiratory Selenite Reductase from Bacillus selenitireducens Strain MLS10

The putative respiratory selenite [Se(IV)] reductase (Srr) from Bacillus selenitireducens MLS10 has been identified through a polyphasic approach involving genomics, proteomics, and enzymology. Nondenaturing gel assays were used to identify Srr in cell fractions, and the active band was shown to contain a single protein of 80 kDa. The protein was identified through liquid chromatography-tandem mass spectrometry (LC-MS/MS) as a homolog of the catalytic subunit of polysulfide reductase (PsrA). It was found to be encoded as part of an operon that contains six genes that we designated srrE, srrA, srrB, srrC, srrD, and srrF SrrA is the catalytic subunit (80 kDa), with a twin-arginine translocation (TAT) leader sequence indicative of a periplasmic protein and one putative 4Fe-4S binding site. SrrB is a small subunit (17 kDa) with four putative 4Fe-4S binding sites, SrrC (43 kDa) is an anchoring subunit, and SrrD (24 kDa) is a chaperon protein. Both SrrE (38 kDa) and SrrF (45 kDa) were annotated as rhodanese domain-containing proteins. Phylogenetic analysis revealed that SrrA belonged to the PsrA/PhsA clade but that it did not define a distinct subgroup, based on the putative homologs that were subsequently identified from other known selenite-respiring bacteria (e.g., Desulfurispirillum indicum and Pyrobaculum aerophilum). The enzyme appeared to be specific for Se(IV), showing no activity with selenate, arsenate, or thiosulfate, with a K_m of 145 ± 53 μM, a V _max of 23 ± 2.5 μM min^-1, and a k _cat of 23 ± 2.68 s^-1 These results further our understanding of the mechanisms of selenium biotransformation and its biogeochemical cycle.IMPORTANCE Selenium is an essential element for life, with Se(IV) reduction a key step in its biogeochemical cycle. This report identifies for the first time a dissimilatory Se(IV) reductase, Srr, from a known selenite-respiring bacterium, the haloalkalophilic Bacillus selenitireducens strain MLS10. The work extends the versatility of the complex iron-sulfur molybdoenzyme (CISM) superfamily in electron transfer involving chalcogen substrates with different redox potentials. Further, it underscores the importance of biochemical and enzymological approaches in establishing the functionality of these enzymes.

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.

A review of the mechanisms of mineral-based metabolism in early Earth analog rock-hosted hydrothermal ecosystems

Prior to the advent of oxygenic photosynthesis ~ 2.8-3.2 Ga, life was dependent on chemical energy captured from oxidation-reduction reactions involving minerals or substrates generated through interaction of water with minerals. Terrestrial hydrothermal environments host abundant and diverse non-photosynthetic communities and a variety of minerals that can sustain microbial metabolism. Minerals and substrates generated through interaction of minerals with water are differentially distributed in hot spring environments which, in turn, shapes the distribution of microbial life and the metabolic processes that support it. Emerging evidence suggests that terrestrial hydrothermal environments may have played a role in supporting the metabolism of the earliest forms of microbial life. It follows that these environments and their microbial inhabitants are increasingly being studied as analogs of early Earth ecosystems. Here we review current understanding of the processes that lead to variation in the availability of minerals or mineral-sourced substrates in terrestrial hydrothermal environments. In addition, we summarize proposed mechanisms of mineral substrate acquisition and metabolism in microbial cells inhabiting terrestrial hydrothermal environments, highlighting the importance of the dynamic interplay between biotic and abiotic reactions in influencing mineral substrate bioavailability. An emphasis is placed on mechanisms involved in the solubilization, acquisition, and metabolism of sulfur- and iron-bearing minerals, since these elements were likely integrated into the metabolism of the earliest anaerobic cells.

The role of polysulfide dianions and radical anions in the chemical, physical and biological sciences, including sulfur-based batteries

Polysulfide dianions and radical anions play a crucial role in biological chemistry, geochemical processes, alkali metal–sulfur batteries, organic syntheses, coordination chemistry, and materials sciences.

Turnover Rates of Intermediate Sulfur Species (Sx2-, S0, S2O32-, S4O62-, SO32-) in Anoxic Freshwater and Sediments

The microbial reduction of sulfate to sulfide coupled to organic matter oxidation followed by the transformation of sulfide back to sulfate drives a dynamic sulfur cycle in a variety of environments. The oxidative part of the sulfur cycle in particular is difficult to constrain because the eight electron oxidation of sulfide to sulfate occurs stepwise via a suite of biological and chemical pathways and produces a wide variety of intermediates (S x 2 - , S0, S2O 3 2 - , S4O 6 2 - , and SO 3 2 - ), which may in turn be oxidized, reduced or disproportionated. Although the potential processes affecting these intermediates are well-known from microbial culture and geochemical studies, their significance and rates in the environment are not well constrained. In the study presented here, time-course concentration measurements of intermediate sulfur species were made in amended freshwater water column and sediment incubation experiments in order to constrain consumption rates and processes. In sediment incubations, consumption rates were S colloidal 0 > S x 2 - > SO 3 2 - ≈ S4O 6 2 - > S2O 3 2 - , which is consistent with previous measurements of SO 3 2 - , S4O 6 2 - , and S2O 3 2 - consumption rates in marine sediments. In water column incubations, however, the relative reactivity was S colloidal 0 > SO 3 2 - > S x 2 - > S2O 3 2 - > S4O 6 2 - . Consumption of thiosulfate, tetrathionate and sulfite was primarily biological, whereas it was not possible to distinguish between abiotic and biological polysulfide consumption in either aqueous or sediment incubations. S colloidal 0 consumption in water column experiments was biologically mediated, however, rapid sedimentary consumption was likely due to reactions with iron minerals. These experiments provide important constraints on the biogeochemical reactivity of intermediate sulfur species and give further insight into the diversity of biological and geochemical processes that comprise (cryptic) environmental sulfur cycling.