Disproportionation of elemental sulfur by haloalkaliphilic bacteria from soda lakes

Feedback inhibition derived from hydrogen sulfide in microbial sulfidogenic process via elemental sulfur disproportionation

Elemental sulfur disproportionation (S0Disp), a key sulfidogenic process, has not only been known to play significant roles in biogeochemical sulfur cycles but has also received increasing attention in various wastewater treatment systems. For a sulfidogenic process, understanding the feedback inhibition (FBI) derived from the sulfide it produces is essential and fundamental, while this issue has yet to be systematically studied within the context of S0Disp. In this study, the FBI for S0Disp was investigated in Desulfocapsa-enriched mixed cultures. H2S was identified as the form of sulfide to bring about the FBI directly, which has a half-maximal inhibitory concentration (IC50-H2S) and an almost complete inhibitory concentration (ICthreshold-H2S) at 22 mg-S/L and 40 mg-S/L, respectively. The ICthreshold-H2S was also found to be a critical concentration in governing the FBI from reversible to irreversible. Furthermore, based on the metatranscriptomic analysis, the possible metabolic pathways of S0Disp were proposed, implying the mechanism of H2S-derived FBI may be involved in the deactivation of heme-functional enzymes (e.g., dsrAB, qmoABC, and sox) and the substrate (persulfide) deficiency of the hdrABC-catalyzed reaction. The findings of this study will not only help to better understand the S0Disp-involved natural water systems but can also guide the optimization of the S0Disp-related wastewater treatment systems.

Ecology and biogeochemistry of the microbial underworld in two sister soda lakes

BACKGROUND

Approximately 3.7 billion years ago, microbial life may have emerged in phosphate-rich salty ponds. Surprisingly, analogs of these environments are present in alkaline lake systems, recognized as highly productive biological ecosystems. In this study, we investigate the microbial ecology of two Canadian soda lake sediment systems characterized by naturally high phosphate levels.

RESULTS

Using a comprehensive approach involving geochemistry, metagenomics, and amplicon sequencing, we discovered that groundwater infiltration into Lake Goodenough sediments supported stratified layers of microbial metabolisms fueled by decaying mats. Effective degradation of microbial mats resulted in unexpectedly low net productivity. Evaporation of water from Last Chance Lake and its sediments led to saturation of brines and a habitat dominated by inorganic precipitation reactions, with low productivity, low organic matter turnover and little biological uptake of phosphorus, leading to high phosphate concentrations. Highly alkaline brines were found to be dominated by potentially dormant spore-forming bacteria. These saturated brines also hosted potential symbioses between Halobacteria and Nanoarchaeaota, as well as Lokiarchaea and bacterial sulfate reducers. Metagenome-assembled genomes of Nanoarchaeaota lacked strategies for coping with salty brines and were minimal for Lokiarchaea.

CONCLUSIONS

Our research highlights that modern analogs for origin-of-life conditions might be better represented by soda lakes with low phosphate concentrations. Thus, highly alkaline brine environments could be too extreme to support origin of life scenarios. These findings shed light on the complex interplay of microbial life in extreme environments and contribute to our understanding of early Earth environments.

Anaerobic microbial metabolism in soil columns affected by highly alkaline pH: Implication for biogeochemistry near construction and demolition waste disposal sites

Construction and demolition wastes (CDWs) have become a significant environmental concern due to urbanization. CDWs in landfill sites can generate high-pH leachate and various constituents (e.g., acetate and sulfate) following the dissolution of cement material, which may affect subsurface biogeochemical properties. However, the impact of CDW leachate on microbial reactions and community compositions in subsurface environments remains unclear. Therefore, we created columns composed of layers of concrete debris containing-soil (CDS) and underlying CDW-free soil, and fed them artificial groundwater with or without acetate and/or sulfate. In all columns, the initial pH 5.6 of the underlying soil layer rapidly increased to 10.8 (without acetate and sulfate), 10.1 (with sulfate), 10.1 (with acetate), and 8.3 (with acetate and sulfate) within 35 days. Alkaliphilic or alkaline-resistant microbes including Hydrogenophaga, Silanimonas, Algoriphagus, and/or Dethiobacter were dominant throughout the incubation in all columns, and their relative abundance was highest in the column without acetate and sulfate (50.7-86.6%). Fe(III) and sulfate reduction did not occur in the underlying soil layer without acetate. However, in the column with acetate alone, pH was decreased to 9.9 after day 85 and Fe(II) was produced with an increase in the relative abundance of Fe(III)-reducing bacteria up to 9.1%, followed by an increase in the methanogenic archaea Methanosarcina, suggestive of methanogenesis. In the column with both acetate and sulfate, Fe(III) and sulfate reduction occurred along with an increase in both Fe(III)- and sulfate-reducing bacteria (19.1 and 17.7%, respectively), while Methanosarcina appeared later. The results demonstrate that microbial Fe(III)- and sulfate-reduction and acetoclastic methanogenesis can occur even in soils with highly alkaline pH resulting from the dissolution of concrete debris.

Biogenic sulfur recovery from sulfate-laden antibiotic production wastewater using a single-chamber up-flow bioelectrochemical reactor

The high-concentration sulfate (SO42-) in the antibiotic production wastewater hinders the anerobic methanogenic process and also proposes possible environmental risk. In this study, a novel single-chamber up-flow anaerobic bioelectrochemical reactor (UBER) was designed to realize simultaneous SO42- removal and elemental sulfur (S0) recovery. With the carbon felt, the cathode was installed underneath and the anode above to meet the different biological niches for sulfate reducing bacteria (SRB) and sulfur oxidizing bacteria (SOB). The bio-anode UBER (B-UBER) demonstrated a much higher average SO42- removal rate (SRR) of 113.2 ± 5.7 mg SO42--S L-1 d-1 coupled with a S0 production rate (SPR) of 54.4 ± 5.8 mg S0-S L-1 d-1 at the optimal voltage of 0.8 V than that in the abio-anode UBER (control reactor) (SRR = 86.6 ± 13.4 mg SO42--S L-1 d-1; SPR = 25.5 ± 9.7 mg S0-S L-1 d-1) under long-term operation. A large amount of biogenic S0 (about 72.2 mg g-1 VSS) was recovered in the B-UBER. The bio-anode, dominated by Thiovirga (SOB genus) and Acinetobacter (electrochemically active bacteria genus), exhibited a higher current density, lower overpotential, and lower internal resistance. C-type cytochromes mainly served as the crucial electron transfer mediator for both direct and indirect electron transfer, so that significantly increasing electron transfer capacity and biogenic S0 recovery. The reaction pathways of the sulfur transformation in the B-UBER were hypothesized that SRB utilized acetate as the main electron donor for SO42- reduction in the cathode zone and SOB transferred electrons to the anode or oxygen to produce biogenic S0 in the anode zone. This study proved a new pathway for biogenic S0 recovery and sulfate removal from sulfate-laden antibiotic production wastewater using a well-designed single-chamber bioelectrochemical reactor.

Microorganisms uptake zero-valent sulfur via membrane lipid dissolution of octasulfur and intracellular solubilization as persulfide

Zero-valent sulfur, commonly utilized as a fertilizer or fungicide, is prevalent in various environmental contexts. Its most stable and predominant form, octasulfur (S8), plays a crucial role in microbial sulfur metabolism, either through oxidation or reduction. However, the mechanism underlying its cellular uptake remains elusive. We presented evidence that zero-valent sulfur was adsorbed to the cell surface and then dissolved into the membrane lipid layer as lipid-soluble S8 molecules, which reacted with cellular low-molecular thiols to form persulfide, e.g., glutathione persulfide (GSSH), in the cytoplasm. The process brought extracellular zero-valent sulfur into the cells. When persulfide dioxygenase is present in the cells, GSSH will be oxidized. Otherwise, GSSH will react with another glutathione (GSH) to produce glutathione disulfide (GSSG) and hydrogen sulfide (H2S). The mechanism is different from simple diffusion, as insoluble S8 becomes soluble GSSH after crossing the cytoplasmic membrane. The uptake process is limited by physical contact of insoluble zero-valent sulfur with microbial cells and the regeneration of cellular thiols. Our findings elucidate the cellular uptake mechanism of zero-valent sulfur, which provides critical information for its application in agricultural practices and the bioremediation of sulfur contaminants and heavy metals.

Adaptability of sulfur-disproportionating bacteria for mine water remediation under the pressures of heavy metal ions and high sulfate content

Biological sulfide production processes mediated by sulfate/sulfur reduction have gained attention for metal removal from industrial wastewater (e.g., mine water (MW) and metallurgical wastewater) via forming insoluble metal sulfides. However, these processes often necessitate the addition of external organic compounds as electron donors, which poses a constraint on the broad application of this technology. A recent proof of concept study reported that microbial sulfur disproportionation (SD) produced sulfide with no demand for organics, which could achieve more cost-benefit MW treatment against the above-mentioned processes. However, the resistance of SD bioprocess to different metals and high sulfate content in MW remains mysterious, which may substantially affect the practical applicability of such process. In this study, the sulfur-disproportionating bacteria (SDB)-dominated consortium was enriched from a previously established SD-driven bioreactor, in which Dissulfurimicrobium sp. with a relative abundance of 39.9 % was the predominated SDB. When exposed to the real pretreated acidic MW after the pretreatment process of pH amelioration, the sulfur-disproportionating activity remained active, and metals were effectively removed from the MW. Metal tolerance assays further demonstrated that the consortium had a good tolerance to different metal ions (i.e., Pb2+, Cu2+, Ni2+, Mn2+, Zn2+), especially for Mn2+ with a concentration of approximately 20 mg/L. It suggested the robustness of Dissulfurimicrobium sp. likely due to the presence of genes encoding for the enzymes associated with metal(loid) resistance/uptake. Additionally, although high sulfate content resulted in a slight inhibition on the sulfur-disproportionating activity, the consortium still achieved sulfide production rates of 27.3 mg S/g VSS-d on average under an environmentally relevant sulfate level (i.e., 1100 mg S/L), which is comparable to those reported in sulfate reduction. Taken together, these findings imply that SDB could ensure sustainable MW treatment in a more cost-effective and organic-free way.

Influence of sulfate reducing bacteria cultured from the paddy soil on the solubility and redox behavior of Cd in a polymetallic system

As a toxic heavy metal, cadmium (Cd) easily enters into rice while rice grains greatly contribute to the dietary Cd intake in the populations consuming rice as a staple food. The availability of Cd in paddy soil determines the accumulation of grain Cd. Soil drainage leads to the remobilization of Cd, increasing bioavailability of Cd. In contrast, soil flooding results in little contribution of soil Cd to grain Cd, which is generally attributed to sulfate reduction induced by sulfate-reducing bacteria (SRB) in paddy soils. However, effects of SRB cultured from the paddy soil on the solubility and redox behavior of Cd have been seldom investigated before. Here, we used SRB enrichment cultures to investigate the temporal dynamics of Cd2+. The results showed that SRB enrichment cultures efficiently reduced solution redox potential (Eh) to less than -100 mV and gradually increased pH to neutral, demonstrating their ability to create a good anaerobic environment. The solubility of Cd obviously decreased in the anaerobic phase and Cd2+ was transformed into poorly dissolved CdS near the SRB cell wall edge. The addition of Zn2+ and/or Fe2+ further improved the decrease in Cd solubility and facilitated the formation of polymetallic sulfides as a consequence of promoting the production of S0 and dissolved sulfides (S2-/HS-) and the transformation of S0 into S2-/HS-. Little of Cd was detected in the media upon reoxidation, which was probably due to the high pH and the interaction between CdS and ZnS/FeS. Conclusively, these results demonstrate the detailed dynamic processes that explain the essential role of SRB in regulating the redox dynamics of chalcophile heavy metals and their bioavailability in paddy soils.

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.

Impact of redox fluctuations on microbe-mediated elemental sulfur disproportionation and coupled redox cycling of iron

Elemental sulfur (S0) plays a vital role in the coupled cycling of sulfur and iron, which in turn affects the transformation of carbon and various pollutants. These processes have been well characterized under static anoxic or oxic conditions, however, how the natural redox fluctuations affect the bio-mediated sulfur cycling and coupled iron cycling remain enigmatic. The present work examined S0 disproportionation as driven by natural microbial communities under fluctuating redox conditions and the contribution of S0 disproportionation to ferrihydrite transformation. Samples were incubated at either neutral or alkaline pH values, applying sequential anaerobic, aerobic and anaerobic conditions over 60 days. Under anaerobic conditions, S0 was found to undergo disproportionation to sulfate and sulfide, which subsequently reduced ferrihydrite at both pH 7.4 and 9.5. Ferrihydrite promoted S0 disproportionation by scavenging biogenic sulfide and maintaining a suitable degree of sulfate formation. After an oxic period, during the subsequent anoxic incubation, bioreduction of sulfate occurred and the biogenic sulfide reduced iron (hydr)oxides at a rate approximately 25 % lower than that observed during the former anoxic period. A 16S rDNA-based microbial community analysis revealed changes in the microbial community in response to the redox fluctuations, implying an intimate association with the coupled cycling of sulfur and iron. Microscopic and spectroscopic analyses confirmed the S0-mediated transformation of ferrihydrite to crystalline iron (hydr)oxide minerals such as lepidocrocite and magnetite and the formation of iron sulfides precipitated under fluctuating redox conditions. Finally, a reaction mechanism based on mass balance was proposed, demonstrating that bio-mediated sulfur transformation maintained a sustainable redox reaction with iron (hydr)oxides under fluctuating anaerobic-aerobic-anaerobic conditions tested in this study. Altogether, the finding of our study is critical for obtaining a more complete understanding of the dynamics of iron redox reactions and pollutant transformation in sulfur-rich aquatic environments.

Thiovibrio frasassiensis gen. nov., sp. nov., an autotrophic, elemental sulphur disproportionating bacterium isolated from sulphidic karst sediment, and proposal of Thiovibrionaceae fam. nov

A novel, autotrophic, mesophilic bacterium, strain RS19-109T, was isolated from sulphidic stream sediments in the Frasassi Caves, Italy. The cells of this strain grew chemolithoautotrophically under anaerobic conditions while disproportionating elemental sulphur (S0) and thiosulphate, but not sulphite with bicarbonate/CO2 as a carbon source. Autotrophic growth was also observed with molecular hydrogen as an electron donor, and S0, sulphate, thiosulphate, nitrate and ferric iron as electron acceptors. Oxygen was not used as an electron acceptor and sulphide was not used as an electron donor. Weak growth was observed with sulphate as an electron acceptor and organic carbon as an electron donor and carbon source. The strain also showed weak growth by fermentation of tryptone. It grew at pH 5.5–7.5 (optimum, pH 7.0), 4–35 °C (optimum, 30 °C) and between 0–1.7 % NaCl. Strain RS19-109T was found to be phylogenetically distinct based on 16S rRNA gene sequence similarity (89.2 %) to its closest relative, Desulfurivibrio alkaliphilus AHT2T. The draft genome sequence for strain RS19-109T had average nucleotide identity, average amino acid identity and in silico DNA–DNA hybridization values of 72.2, 63.0 and 18.3 %, respectively, compared with the genome sequence of D. alkaliphilus AHT2T. On the basis of its physiological and genomic properties, strain RS19-109T is proposed as the type strain of a novel species of a novel genus, Thiovibrio frasassiensis gen. nov., sp. nov. A novel family, Thiovibrionaceae fam. nov., is proposed to accommodate Thiovibrio within the order Desulfobulbales . Strain RS19-109T has been deposited at the DSMZ-German Collection of Microorganisms and Cell Cultures (=DSM 115074T) and the American Type Culture Collection (=ATCC TSD-325T).

Iron or sulfur respiration-an adaptive choice determining the fitness of a natronophilic bacterium Dethiobacter alkaliphilus in geochemically contrasting environments

Haloalkaliphilic microorganisms are double extremophiles functioning optimally at high salinity and pH. Their typical habitats are soda lakes, geologically ancient yet widespread ecosystems supposed to harbor relict microbial communities. We compared metabolic features and their determinants in two strains of the natronophilic species Dethiobacter alkaliphilus, the only cultured representative of the class "Dethiobacteria" (Bacillota). The strains of D. alkaliphilus were previously isolated from geographically remote Mongolian and Kenyan soda lakes. The type strain AHT1^T was described as a facultative chemolithoautotrophic sulfidogen reducing or disproportionating sulfur or thiosulfate, while strain Z-1002 was isolated as a chemolithoautotrophic iron reducer. Here, we uncovered the iron reducing ability of strain AHT1^T and the ability of strain Z-1002 for thiosulfate reduction and anaerobic Fe(II) oxidation. Key catabolic processes sustaining the growth of both D. alkaliphilus strains appeared to fit the geochemical settings of two contrasting natural alkaline environments, sulfur-enriched soda lakes and iron-enriched serpentinites. This hypothesis was supported by a meta-analysis of Dethiobacterial genomes and by the enrichment of a novel phylotype from a subsurface alkaline aquifer under Fe(III)-reducing conditions. Genome analysis revealed multiheme c-type cytochromes to be the most probable determinants of iron and sulfur redox transformations in D. alkaliphilus. Phylogeny reconstruction showed that all the respiratory processes in this organism are likely provided by evolutionarily related early forms of unconventional octaheme tetrathionate and sulfite reductases and their structural analogs, OmhA/OcwA Fe(III)-reductases. Several phylogenetically related determinants of anaerobic Fe(II) oxidation were identified in the Z-1002 genome, and the oxidation process was experimentally demonstrated. Proteomic profiling revealed two distinct sets of multiheme cytochromes upregulated in iron(III)- or thiosulfate-respiring cells and the cytochromes peculiar for Fe(II) oxidizing cells. We suggest that maintaining high variation in multiheme cytochromes is an effective adaptive strategy to occupy geochemically contrasting alkaline environments. We propose that sulfur-enriched soda lakes could be secondary habitats for D. alkaliphilus compared to Fe-rich serpentinites, and that the ongoing evolution of Dethiobacterales could retrace the evolutionary path that may have occurred in prokaryotes at a turning point in the biosphere's history, when the intensification of the sulfur cycle outweighed the global significance of the iron cycle.

Petroleum pollution changes microbial diversity and network complexity of soil profile in an oil refinery

Introduction

Petroleum pollution resulting from spills and leakages in oil refinery areas has been a significant environmental concern for decades. Despite this, the effects of petroleum pollutants on soil microbial communities and their potential for pollutant biodegradation still required further investigation.

Methods

In this study, we collected 75 soil samples from 0 to 5 m depths of 15 soil profiles in an abandoned refinery to analyze the effect of petroleum pollution on soil microbial diversity, community structure, and network co-occurrence patterns.

Results

Our results suggested soil microbial a-diversity decreased under high C10-C40 levels, coupled with significant changes in the community structure of soil profiles. However, soil microbial network complexity increased with petroleum pollution levels, suggesting more complex microbial potential interactions. A module specific for methane and methyl oxidation was also found under high C10-C40 levels of the soil profile, indicating stronger methanotrophic and methylotrophic metabolic activities at the heavily polluted soil profile.

Discussion

The increased network complexity observed may be due to more metabolic pathways and processes, as well as increased microbial interactions during these processes. These findings highlight the importance of considering both microbial diversity and network complexity in assessing the effects of petroleum pollution on soil ecosystems.

Sulfur disproportionation realizes an organic-free sulfidogenic process for sustainable treatment of acid mine drainage

Biological sulfidogenic processes (BSPs) have been considered effective biotechnologies for the treatment of organic-deficit acid mine drainage (AMD) and heavy metal recovery. However, high-rate sulfide production relies on the continuous addition of exogenous organic substrates as electron donors to facilitate dissimilatory sulfate reduction, which substantially increases the operational cost and CO₂ emission and also limits the wide application of BSPs in AMD treatment. In this study, we proposed a novel chemoautotrophic elemental sulfur disproportionation (SD) process as an alternative to conventional BSPs for treating AMD, in which sulfur-disproportionating bacteria (SDB) disproportionates sulfur to sulfide and sulfate without organic substrate supplementation. During the 393-day lab-scale test, we observed that the sulfur-disproportionating reactor (SDR) achieved a stable high-rate sulfide production, with a maximal rate of 21.10 mg S/L-h at an organic-substrate-free condition. This high rate of sulfide production suggested that the SD process could provide sufficient sulfide to precipitate metal ions from AMD. Thermodynamics analysis and batch tests further revealed that alkalinity rather than sulfate was the critical factor influencing the SD process, suggesting that the abundant sulfate present in AMD would not inhibit the SD process. The critical condition of SD in the SDR was therefore determined. Microbial community analysis showed that Dissulfurimicrobium sp. was the dominant SDB during the long-term operation regardless of dynamic sulfate and/or alkalinity concentrations, which provides evidence that SDB can be employed for sustainable and high-rate sulfide production for engineering purposes. A multi-stage AMD treatment system equipped with a SDR removed over 99% of the influent metals (i.e., Fe, Al, Zn, Cu, Pb) from AMD except for Mn. This study demonstrated that the novel SD process is a green and promising biotechnology for the sustainable treatment of organic-deficient metal-laden wastewater, such as AMD.

Quantifying sulfidization and non-sulfidization in long-term in-situ microbial colonized As(V)-ferrihydrite coated sand columns: Insights into As mobility

Sulfide-induced reduction (sulfidization) of arsenic (As)-bearing Fe(III) (oxyhydro)oxides may lead to As mobilization in aquifer systems. However, little is known about the relative contributions of sulfidization and non-sulfidization of Fe(III) (oxyhydro)oxides reduction to As mobilization. To address this issue, high As groundwater with low sulfide (LS) and high sulfide (HS) concentrations were pumped through As(V)-bearing ferrihydrite-coated sand columns (LS-column and HS-column, respectively) being settled within wells in the western Hetao Basin, China. Sulfidization of As(V)-bearing ferrihydrite was evidenced by the increase in dissolved Fe(II) and the presence of solid Fe(II) and elemental sulfur (S⁰) in both the columns. A conceptual model was built using accumulated S⁰ and Fe(II) produced in the columns to calculate the proportions of sulfidization-induced Fe(III) (oxyhydro)oxide reduction and non-sulfidization-induced Fe(III) (oxyhydro)oxide reduction. Fe(III) reduction via sulfidization occurred preferentially in the inlet ends (LS-column, 31 %; HS-column, 86 %), while Fe(III) reduction via non-sulfidization processes predominated in the outlet ends (LS-column, 96 %; HS-column, 86 %), and was attributed to the metabolism of genera associated with Fe(III) reduction (including Shewanella, Ferribacterium, and Desulfuromonas). Arsenic was mobilized in the columns via sulfidization and non-sulfidization processes. More As was released from the solid of the HS-column than that of the LS-column due to the higher intensity of sulfidization in the presence of higher concentrations of dissolved S(-II). Overall, this study highlights the sulfidization of As-bearing Fe(III) (oxyhydro)oxides as an important As-mobilizing pathway in complex As-Fe-S bio-hydrogeochemical networks.

Generation and Physiology of Hydrogen Sulfide and Reactive Sulfur Species in Bacteria

Sulfur is not only one of the most abundant elements on the Earth, but it is also essential to all living organisms. As life likely began and evolved in a hydrogen sulfide (H₂S)-rich environment, sulfur metabolism represents an early form of energy generation via various reactions in prokaryotes and has driven the sulfur biogeochemical cycle since. It has long been known that H₂S is toxic to cells at high concentrations, but now this gaseous molecule, at the physiological level, is recognized as a signaling molecule and a regulator of critical biological processes. Recently, many metabolites of H₂S, collectively called reactive sulfur species (RSS), have been gradually appreciated as having similar or divergent regulatory roles compared with H₂S in living organisms, especially mammals. In prokaryotes, even in bacteria, investigations into generation and physiology of RSS remain preliminary and an understanding of the relevant biological processes is still in its infancy. Despite this, recent and exciting advances in the fields are many. Here, we discuss abiotic and biotic generation of H₂S/RSS, sulfur-transforming enzymes and their functioning mechanisms, and their physiological roles as well as the sensing and regulation of H₂S/RSS.

Composition and key-influencing factors of bacterial communities active in sulfur cycling of soda lake sediments

Bacteria are important participants in sulfur cycle of the extremely haloalkaline environment, e.g. soda lake. The effects of physicochemical factors on the composition of sulfide-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) in soda lake have remained elusive. Here, we surveyed the community structure of total bacteria, SOB and SRB based on 16S rRNA, soxB and dsrB gene sequencing, respectively, in five soda lakes with different physicochemical factors. The results showed that the dominant bacteria belonged to the phyla Proteobacteria, Bacteroidetes, Halanaerobiaeota, Firmicutes and Actinobacteria. SOB and SRB were widely distributed in lakes with different physicochemical characteristics, and the community composition were different. In general, salinity and inorganic nitrogen sources (NH₄⁺-N, NO₃^--N) were the most significant factors. Specifically, the communities of SOB, mainly including Thioalkalivibrio, Burkholderia, Paracoccus, Bradyrhizobium, and Hydrogenophaga genera, were remarkably influenced by the levels of NH₄⁺-N and salinity. Yet, for SRB communities, including Desulfurivibrio, Candidatus Electrothrix, Desulfonatronospira, Desulfonatronum, Desulfonatronovibrio, Desulfonatronobacter and so on, the most significant determinants were salinity and NO₃^--N. Besides, Rhodoplanes played a significant role in the interaction between SOB and SRB. From our results, the knowledge regarding the community structures of SOB and SRB in extremely haloalkaline environment was extended.

Continuous electron shuttling by sulfide oxidizing bacteria as a novel strategy to produce electric current

Sulfide oxidizing bacteria (SOB) are widely applied in industry to convert toxic H₂S into elemental sulfur. Haloalkaliphilic planktonic SOB can remove sulfide from solution under anaerobic conditions (SOB are 'charged'), and release electrons at an electrode (discharge of SOB). The effect of this electron shuttling on product formation and biomass growth is not known. Here, we study and demonstrate a continuous process in which SOB remove sulfide from solution in an anaerobic 'uptake chamber', and shuttle these electrons to the anode of an electrochemical cell, in the absence of dissolved sulfide. Two experiments over 31 and 41 days were performed. At a sulfide loading rate of 1.1 mmolS/day, electricity was produced continuously (3 A/m²) without dissolved sulfide in the anolyte. The main end product was sulfate (56% in experiment 1% and 78% in experiment 2), and 87% and 77% of the electrons in sulfide were recovered as electricity. It was found that the current density was dependent on the sulfide loading rate and not on the anode potential. Biological growth occurred, mainly at the anode as biofilm, in which the deltaproteobacterial genus Desulfurivibrio was dominating. Our results demonstrate a novel strategy to produce electricity from sulfide in an electrochemical system.

Hydrogen sulphide management in anaerobic digestion: A critical review on input control, process regulation, and post-treatment

Hydrogen sulphide (H₂S) in biogas is a problematic impurity that can inhibit methanogenesis and cause equipment corrosion. This review discusses technologies to remove H₂S during anaerobic digestion (AD) via: input control, process regulation, and post-treatment. Post-treatment technologies (e.g. biotrickling filters and scrubbers) are mature with >95% removal efficiency but they do not mitigate H₂S toxicity to methanogens within the AD. Input control (i.e. substrate pretreatment via chemical addition) reduces sulphur input into AD via sulphur precipitation. However, available results showed <75% of H₂S removal efficiency. Microaeration to regulate AD condition is a promising alternative for controlling H₂S formation. Microaeration, or the use of oxygen to regulate the redox potential at around -250 mV, has been demonstrated at pilot and full scale with >95% H₂S reduction, stable methane production, and low operational cost. Further adaptation of microaeration relies on a comprehensive design framework and exchange operational experience for eliminating the risk of over-aeration.

Elemental sulfur as electron donor and/or acceptor: Mechanisms, applications and perspectives for biological water and wastewater treatment

Biochemical oxidation and reduction are the principle of biological water and wastewater treatment, in which electron donor and/or acceptor shall be provided. Elemental sulfur (S⁰) as a non-toxic and easily available material with low price, possesses both reductive and oxidative characteristics, suggesting that it is a suitable material for water and wastewater treatment. Recent advanced understanding of S⁰-respiring microorganisms and their metabolism further stimulated the development of S⁰-based technologies. As such, S⁰-based biotechnologies have emerged as cost-effective and attractive alternatives to conventional biological methods for water and wastewater treatment. For instance, S⁰-driven autotrophic denitrification substantially lower the operational cost for nitrogen removal from water and wastewater, compared to the conventional process with exogenous carbon source supplementation. The introduction of S⁰ can also avoid secondary pollution commonly caused by overdose of organic carbon. S⁰ reduction processes cost-effectively mineralize organic matter with low sludge production. Biological sulfide production using S⁰ as electron acceptor is also an attractive technology for metal-laden wastewater treatment, e.g. acid mine drainage. This paper outlines an overview of the fundamentals, characteristics and advances of the S⁰-based biotechnologies and highlights the functional S⁰-related microorganisms. In particular, the mechanisms of microorganisms accessing insoluble S⁰ and feasibility to improve S⁰ bio-utilization efficiency are critically discussed. Additionally, the research knowledge gaps, current process limitations, and required further developments are identified and discussed.

Microbial sulfur metabolism and environmental implications

Sulfur as a macroelement plays an important role in biochemistry in both natural environments and engineering biosystems, which can be further linked to other important element cycles, e.g. carbon, nitrogen and iron. Consequently, the sulfur cycling primarily mediated by sulfur compounds oxidizing microorganisms and sulfur compounds reducing microorganisms has enormous environmental implications, particularly in wastewater treatment and pollution bioremediation. In this review, to connect the knowledge in microbial sulfur metabolism to environmental applications, we first comprehensively review recent advances in understanding microbial sulfur metabolisms at molecular-, cellular- and ecosystem-levels, together with their energetics. We then discuss the environmental implications to fight against soil and water pollution, with four foci: (1) acid mine drainage, (2) water blackening and odorization in urban rivers, (3) SANI® and DS-EBPR processes for sewage treatment, and (4) bioremediation of persistent organic pollutants. In addition, major challenges and further developments toward elucidation of microbial sulfur metabolisms and their environmental applications are identified and discussed.

Expanded Genomic Sampling Refines Current Understanding of the Distribution and Evolution of Sulfur Metabolisms in the Desulfobulbales

The reconstruction of modern and paleo-sulfur cycling relies on understanding the long-term relative contribution of its main actors; these include microbial sulfate reduction (MSR) and microbial sulfur disproportionation (MSD). However, a unifying theory is lacking for how MSR and MSD, with the same enzyme machinery and intimately linked evolutionary histories, perform two drastically different metabolisms. Here, we aim at shedding some light on the distribution, diversity, and evolutionary histories of MSR and MSD, with a focus on the Desulfobulbales as a test case. The Desulfobulbales is a diverse and widespread order of bacteria in the Desulfobacterota (formerly Deltaproteobacteria) phylum primarily composed of sulfate reducing bacteria. Recent culture- and sequence-based approaches have revealed an expanded diversity of organisms and metabolisms within this clade, including the presence of obligate and facultative sulfur disproportionators. Here, we present draft genomes of previously unsequenced species of Desulfobulbales, substantially expanding the available genomic diversity of this clade. We leverage this expanded genomic sampling to perform phylogenetic analyses, revealing an evolutionary history defined by vertical inheritance of sulfur metabolism genes with numerous convergent instances of transition from sulfate reduction to sulfur disproportionation.

Crystalline iron oxides stimulate methanogenic benzoate degradation in marine sediment-derived enrichment cultures

Elevated dissolved iron concentrations in the methanic zone are typical geochemical signatures of rapidly accumulating marine sediments. These sediments are often characterized by co-burial of iron oxides with recalcitrant aromatic organic matter of terrigenous origin. Thus far, iron oxides are predicted to either impede organic matter degradation, aiding its preservation, or identified to enhance organic carbon oxidation via direct electron transfer. Here, we investigated the effect of various iron oxide phases with differing crystallinity (magnetite, hematite, and lepidocrocite) during microbial degradation of the aromatic model compound benzoate in methanic sediments. In slurry incubations with magnetite or hematite, concurrent iron reduction, and methanogenesis were stimulated during accelerated benzoate degradation with methanogenesis as the dominant electron sink. In contrast, with lepidocrocite, benzoate degradation, and methanogenesis were inhibited. These observations were reproducible in sediment-free enrichments, even after five successive transfers. Genes involved in the complete degradation of benzoate were identified in multiple metagenome assembled genomes. Four previously unknown benzoate degraders of the genera Thermincola (Peptococcaceae, Firmicutes), Dethiobacter (Syntrophomonadaceae, Firmicutes), Deltaproteobacteria bacteria SG8_13 (Desulfosarcinaceae, Deltaproteobacteria), and Melioribacter (Melioribacteraceae, Chlorobi) were identified from the marine sediment-derived enrichments. Scanning electron microscopy (SEM) and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) images showed the ability of microorganisms to colonize and concurrently reduce magnetite likely stimulated by the observed methanogenic benzoate degradation. These findings explain the possible contribution of organoclastic reduction of iron oxides to the elevated dissolved Fe²⁺ pool typically observed in methanic zones of rapidly accumulating coastal and continental margin sediments.

Prospecting bacterial consortia from a geothermal site for metals biotransformation

Biomats that flourished in a fumarole located on the geothermal site Los Azufres (Mexico) were used as inocula to select aerobic and sulfate-reducing bacteria consortia for studying their capacity to reduce hexavalent chromium [Cr(VI)], aiming to use these consortia in biotransformation technologies. The sample site is characterized by slightly warm (nearly 27 [Formula: see text]C), acid (pH 3) and about hypoxic (1.8 mg L[Formula: see text] of dissolved oxygen) conditions. Four culture systems (2 aerobic and 2 anaerobic) were investigated, including their enzymatic activity, capacity to produce biofilms, and an analysis of the total bacterial populations. For the anaerobic condition (using sulfate and sulfur as electron acceptors), four pH values (from 2 to 8) and four carbon sources (pyruvate, glycerol, Na-lactate and Na-acetate) were probed. Significant biological Cr(VI) removal was observed for all the pH values probed, particularly during the first 12 h, being more effective at the most acid conditions. At a pH value of 4 and using pyruvate as carbon source, 100 mg L[Formula: see text] of Cr(VI) were completely depleted in less than 12 h, while the use of Na-lactate was less effective but still reasonable. These results indicate that sulfate-reducing bacteria consortia from geothermal sites like the one studied here are capable of biotransforming Cr(VI) and have the potential to provide metal bioremediation technologies.

A dynamic microbial sulfur cycle in a serpentinizing continental ophiolite

Serpentinization is the hydration and oxidation of ultramafic rock, which occurs as oceanic lithosphere is emplaced onto continental margins (ophiolites), and along the seafloor as faulting exposes this mantle-derived material to circulating hydrothermal fluids. This process leads to distinctive fluid chemistries as molecular hydrogen (H₂ ) and hydroxyl ions (OH^- ) are produced and reduced carbon compounds are mobilized. Serpentinizing ophiolites also serve as a vector to transport sulfur compounds from the seafloor onto the continents. We investigated hyperalkaline, sulfur-rich, brackish groundwater in a serpentinizing continental ophiolite to elucidate the role of sulfur compounds in fuelling in situ microbial activities. Here we illustrate that key sulfur-cycling taxa, including Dethiobacter, Desulfitispora and 'Desulforudis', persist throughout this extreme environment. Biologically catalysed redox reactions involving sulfate, sulfide and intermediate sulfur compounds are thermodynamically favourable in the groundwater, which indicates they may be vital to sustaining life in these characteristically oxidant- and energy-limited systems. Furthermore, metagenomic and metatranscriptomic analyses reveal a complex network involving sulfate reduction, sulfide oxidation and thiosulfate reactions. Our findings highlight the importance of the complete inorganic sulfur cycle in serpentinizing fluids and suggest sulfur biogeochemistry provides a key link between terrestrial serpentinizing ecosystems and their submarine heritage.

Active sulfur cycling in the terrestrial deep subsurface

The deep terrestrial subsurface remains an environment where there is limited understanding of the extant microbial metabolisms. At Olkiluoto, Finland, a deep geological repository is under construction for the final storage of spent nuclear fuel. It is therefore critical to evaluate the potential impact microbial metabolism, including sulfide generation, could have upon the safety of the repository. We investigated a deep groundwater where sulfate is present, but groundwater geochemistry suggests limited microbial sulfate-reducing activity. Examination of the microbial community at the genome-level revealed microorganisms with the metabolic capacity for both oxidative and reductive sulfur transformations. Deltaproteobacteria are shown to have the genetic capacity for sulfate reduction and possibly sulfur disproportionation, while Rhizobiaceae, Rhodocyclaceae, Sideroxydans, and Sulfurimonas oxidize reduced sulfur compounds. Further examination of the proteome confirmed an active sulfur cycle, serving for microbial energy generation and growth. Our results reveal that this sulfide-poor groundwater harbors an active microbial community of sulfate-reducing and sulfide-oxidizing bacteria, together mediating a sulfur cycle that remained undetected by geochemical monitoring alone. The ability of sulfide-oxidizing bacteria to limit the accumulation of sulfide was further demonstrated in groundwater incubations and highlights a potential sink for sulfide that could be beneficial for geological repository safety.

Effects of Habitat Partitioning on the Distribution of Bacterioplankton in Deep Lakes

In deep lakes, many investigations highlighted the existence of exclusive groups of bacteria adapted to deep oxygenated and hypoxic and anoxic hypolimnia. Nevertheless, the extent of bacterial strain diversity has been much less scrutinized. This aspect is essential for an unbiased estimation of genetic variation, biodiversity, and population structure, which are essential for studying important research questions such as biogeographical patterns, temporal and spatial variability and the environmental factors affecting this variability. This study investigated the bacterioplankton community in the epilimnetic layers and in the oxygenated and hypoxic/anoxic hypolimnia of five large and deep lakes located at the southern border of the Alps using high throughput sequencing (HTS) analyses (16S rDNA) and identification of amplicon sequence variants (ASVs) resolving reads differing by as little as one nucleotide. The study sites, which included two oligomictic (Garda and Como) and three meromictic lakes (Iseo, Lugano, and Idro) with maximum depths spanning from 124 to 410 m, were chosen among large lakes to represent an oxic-hypoxic gradient. The analyses showed the existence of several unique ASVs in the three layers of the five lakes. In the case of cyanobacteria, this confirmed previous analyses made at the level of strains or based on oligotyping methods. As expected, the communities in the hypoxic/anoxic monimolimnia showed a strong differentiation from the oxygenated layer, with the exclusive presence in single lakes of several unique ASVs. In the meromictic lakes, results supported the hypothesis that the formation of isolated monimolimnia sustained the development of highly diversified bacterial communities through ecological selection, leading to the establishment of distinctive biodiversity zones. The genera identified in these layers are well-known to activate a wide range of redox reactions at low O₂ conditions. As inferred from 16S rDNA data, the highly diversified and coupled processes sustained by the monimolimnetic microbiota are essential ecosystem services that enhance mineralization of organic matter and formation of reduced compounds, and also abatement of undesirable greenhouse gasses.

Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake

BACKGROUND

The planetary sulfur cycle is a complex web of chemical reactions that can be microbial-mediated or can occur spontaneously in the environment, depending on the temperature and pH. Inorganic sulfur compounds can serve as energy sources for specialized prokaryotes and are important substrates for microbial growth in general. Here, we investigate dissimilatory sulfur cycling in the brine and sediments of a southwestern Siberian soda lake characterized by an extremely high pH and salinity, combining meta-omics analyses of its uniquely adapted highly diverse prokaryote communities with biogeochemical profiling to identify key microbial players and expand our understanding of sulfur cycling under haloalkaline conditions.

RESULTS

Peak microbial activity was found in the top 4 cm of the sediments, a layer with a steep drop in oxygen concentration and redox potential. The majority of sulfur was present as sulfate or iron sulfide. Thiosulfate was readily oxidized by microbes in the presence of oxygen, but oxidation was partially inhibited by light. We obtained 1032 metagenome-assembled genomes, including novel population genomes of characterized colorless sulfur-oxidizing bacteria (SOB), anoxygenic purple sulfur bacteria, heterotrophic SOB, and highly active lithoautotrophic sulfate reducers. Surprisingly, we discovered the potential for nitrogen fixation in a new genus of colorless SOB, carbon fixation in a new species of phototrophic Gemmatimonadetes, and elemental sulfur/sulfite reduction in the "Candidatus Woesearchaeota." Polysulfide/thiosulfate and tetrathionate reductases were actively transcribed by various (facultative) anaerobes.

CONCLUSIONS

The recovery of over 200 genomes that encoded enzymes capable of catalyzing key reactions in the inorganic sulfur cycle indicates complete cycling between sulfate and sulfide at moderately hypersaline and extreme alkaline conditions. Our results suggest that more taxonomic groups are involved in sulfur dissimilation than previously assumed.

Physiology and Distribution of Archaeal Methanotrophs That Couple Anaerobic Oxidation of Methane with Sulfate Reduction

In marine anaerobic environments, methane is oxidized where sulfate-rich seawater meets biogenic or thermogenic methane. In those niches, a few phylogenetically distinct microbial types, i.e., anaerobic methanotrophs (ANME), are able to grow through anaerobic oxidation of methane (AOM). Due to the relevance of methane in the global carbon cycle, ANME have drawn the attention of a broad scientific community for 4 decades. This review presents and discusses the microbiology and physiology of ANME up to the recent discoveries, revealing novel physiological types of anaerobic methane oxidizers which challenge the view of obligate syntrophy for AOM. An overview of the drivers shaping the distribution of ANME in different marine habitats, from cold seep sediments to hydrothermal vents, is given. Multivariate analyses of the abundance of ANME in various habitats identify a distribution of distinct ANME types driven by the mode of methane transport. Intriguingly, ANME have not yet been cultivated in pure culture, despite intense attempts. Further advances in understanding this microbial process are hampered by insufficient amounts of enriched cultures. This review discusses the advantages, limitations, and potential improvements for ANME laboratory-based cultivation systems.

Synchronous response in methanogenesis and anaerobic degradation of pentachlorophenol in flooded soil

Methanogenesis is commonly mass-produced under anaerobic conditions and serves as a major terminal electron accepting process driving the degradation of organic biomass. In this study, a cofactor of methanogenesis (coenzyme M, CoM) and a classic methanogensis inhibitor (2-bromoethanesulfonate, BES) were added at different concentrations to investigate how methanogenesis would affect PCP degradation in flooded soil. Strikingly, the processes of methanogenesis and PCP degradation were simultaneously promoted with CoM, or inhibited with BES, significantly (p <  0.05). High-throughput sequencing for soil bacterial and archaeal community structures revealed that members of Desulfitobacterium, Dethiobacter, Sedimentibacter, Bacillus and Methanosarcina might act as the core functional groups jointly perform PCP degradation in flooded soil, possibly through assisting microbial mediated dechlorination in direct organohalide-respiration, and/or indirect co-metabolization in complex anaerobic soil conditions. This study implied an underlying synergistic coupling between methanogenesis and dechlorination, and provided insights into a novel consideration with respect to coordinating methanogenesis while promoting anaerobic degradation of PCP for complex polluted soil environment, which is necessary for the improved all-win remediation.

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.

Haloalkaliphilic microorganisms assist sulfide removal in a microbial electrolysis cell

Several industrial processes produce toxic sulfide containing streams that are often scrubbed using caustic solutions. An alternative, cost effective sulfide treatment method is bioelectrochemical sulfide removal. For the first time, a haloalkaliphilic sulfide-oxidizing microbial consortium was introduced to the anodic chamber of a microbial electrolysis cell operated at alkaline pH and with 1.0 M sodium ions. Under anode potential control, the highest sulfide removal rate was 2.16 mM/day and chemical analysis supported that the electrical current generation was from the sulfide oxidation. Biotic operation produced a maximum current density of 3625 mA/m² compared to 210 mA/m² while under abiotic operation. Furthermore, biotic electrical production was maintained for a longer period than for abiotic operation, potentially due to the passivation of the electrode by elemental sulfur during abiotic operation. The use of microorganisms reduced the energy input in this study compared to published electrochemical sulfide removal technologies. Sulfide-oxidizing populations dominated both the planktonic and electrode-attached communities with 16S rRNA gene sequences aligning within the genera Thioalkalivibrio, Thioalkalimicrobium, and Desulfurivibrio. The dominance of the Desulfurivibrio-like population on the anode surface offered evidence for the first haloalkaliphilic bacterium able to couple electrons from sulfide oxidation to extracellular electron transfer to the anode.

Nitrate supply and sulfate-reducing suppression facilitate the removal of pentachlorophenol in a flooded mangrove soil

An anaerobic incubation was launched with varying nitrate (1, 5, 10 and 20 mM exogenous NaNO₃) and molybdate (20 mM Na₂MoO₄, a sulfate-reducing inhibitor) additions to investigate the characteristics of PCP dechlorination, as well as the reduction of natural co-occurring electron acceptors, including NO₃^-, Fe(III) and SO₄^2-, and the responses of microbial community structures under a unique reductive mangrove soil. Regardless of exogenous addition, nitrate was rapidly eliminated in the first 12 days. The reduction process of Fe(III) was inhibited, while that of SO₄^2- reduction depended on addition concentration as compared to the control. PCP was mainly degraded from orth-position, forming the only intermediate 2,3,4,5-TeCP by anaerobic microbes, with the highest PCP removal rate of average 21.9% achieved in 1 and 5 mM NaNO₃ as well as 20 mM Na₂MoO₄ treatments and the lowest of 7.5% in 20 mM NaNO₃ treatment. The effects of nitrate on PCP dechlorination depended on addition concentration, while molybdate promoted PCP attenuation significantly. Analyses of the Illumina sequencing data and the relative abundance of dominant microorganisms indicated that the core functional groups regulated PCP removal at genera level likely included Bacillus, Pesudomonas, Dethiobacter, Desulfoporosinus and Desulfovbrio in the nitrate treatments; while that was likely Sedimentibacter and Geosporobacter_Thermotalea in the molybdate treatment. Nitrate supplement but not over supplement, or addition of molybdate are suggested as alternative strategies for better remediation in the nitrate-deficient and sulfur-accumulated soil ecosystem contaminated by PCP, through regulating the growth of core functional groups and thereby coordinating the interaction between dechlorination and its coupled soil redox processes due to shifts of more available electrons to dechlorination. Our results broadened the knowledge regarding microbial PCP degradation and their interactions with natural soil redox processes under anaerobic soil ecosystems.

A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments

BACKGROUND

Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but the microbiome of soda lake sediments received much less attention of microbiologists. Here, we performed metagenomic sequencing on soda lake sediments to give the first extensive overview of the taxonomic diversity found in these complex, extreme environments and to gain novel physiological insights into the most abundant, uncultured prokaryote lineages.

RESULTS

We sequenced five metagenomes obtained from four surface sediments of Siberian soda lakes with a pH 10 and a salt content between 70 and 400 g L^-1. The recovered 16S rRNA gene sequences were mostly from Bacteria, even in the salt-saturated lakes. Most OTUs were assigned to uncultured families. We reconstructed 871 metagenome-assembled genomes (MAGs) spanning more than 45 phyla and discovered the first extremophilic members of the Candidate Phyla Radiation (CPR). Five new species of CPR were among the most dominant community members. Novel dominant lineages were found within previously well-characterized functional groups involved in carbon, sulfur, and nitrogen cycling. Moreover, key enzymes of the Wood-Ljungdahl pathway were encoded within at least four bacterial phyla never previously associated with this ancient anaerobic pathway for carbon fixation and dissimilation, including the Actinobacteria.

CONCLUSIONS

Our first sequencing effort of hypersaline soda lake sediment metagenomes led to two important advances. First, we showed the existence and obtained the first genomes of haloalkaliphilic members of the CPR and several hundred other novel prokaryote lineages. The soda lake CPR is a functionally diverse group, but the most abundant organisms in this study are likely fermenters with a possible role in primary carbon degradation. Second, we found evidence for the presence of the Wood-Ljungdahl pathway in many more taxonomic groups than those encompassing known homo-acetogens, sulfate-reducers, and methanogens. Since only few environmental metagenomics studies have targeted sediment microbial communities and never to this extent, we expect that our findings are relevant not only for the understanding of haloalkaline environments but can also be used to set targets for future studies on marine and freshwater sediments.

Realizing high-rate sulfur reduction under sulfate-rich conditions in a biological sulfide production system to treat metal-laden wastewater deficient in organic matter

Biological sulfur reduction can theoretically produce sufficient sulfide to effectively remove and recover heavy metals in the treatment of organics-deficient sulfate-rich metal-laden wastewater such as acid mine drainage and metallurgic wastewater, using 75% less organics than biological sulfate reduction. However, it is still unknown whether sulfur reduction can indeed compete with sulfate reduction, particularly under high-strength sulfate conditions. The aim of this study was to investigate the long-term feasibility of biological sulfur reduction under high sulfate conditions in a lab-scale sulfur-reducing biological sulfide production (BSP) system with sublimed sulfur added. In the 169-day trial, an average sulfide production rate (SPR) as high as 47 ± 9 mg S/L-h was achieved in the absence of sulfate, and the average SPR under sulfate-rich conditions was similar (53 ± 10 mg S/L-h) when 1300 mg S/L sulfate were fed with the influent. Interestingly, sulfate was barely reduced even at such a high strength and contributed to only 1.5% of total sulfide production. Desulfomicrobium was identified as the predominant sulfidogenic bacterium in the bioreactor. Batch tests further revealed that this sulfidogenic bacteria used elemental sulfur as the electron acceptor instead of the highly bioavailable sulfate, during which polysulfide acted as an intermediate, leading to an even higher bioavailability of sulfur than sulfate. The pathway of sulfur to sulfide conversion via polysulfide in the presence of both sulfur and sulfate was discussed. Collectively, when conditions favor polysulfide formation, sulfur reduction can be a promising and attractive technology to realize a high-rate and low-cost BSP process for treating sulfate-rich metal-laden wastewater.

Diversity of Rare and Abundant Prokaryotic Phylotypes in the Prony Hydrothermal Field and Comparison with Other Serpentinite-Hosted Ecosystems

The Bay of Prony, South of New Caledonia, represents a unique serpentinite-hosted hydrothermal field due to its coastal situation. It harbors both submarine and intertidal active sites, discharging hydrogen- and methane-rich alkaline fluids of low salinity and mild temperature through porous carbonate edifices. In this study, we have extensively investigated the bacterial and archaeal communities inhabiting the hydrothermal chimneys from one intertidal and three submarine sites by 16S rRNA gene amplicon sequencing. We show that the bacterial community of the intertidal site is clearly distinct from that of the submarine sites with species distribution patterns driven by only a few abundant populations, affiliated to the Chloroflexi and Proteobacteria phyla. In contrast, the distribution of archaeal taxa seems less site-dependent, as exemplified by the co-occurrence, in both submarine and intertidal sites, of two dominant phylotypes of Methanosarcinales previously thought to be restricted to serpentinizing systems, either marine (Lost City Hydrothermal Field) or terrestrial (The Cedars ultrabasic springs). Over 70% of the phylotypes were rare and included, among others, all those affiliated to candidate divisions. We finally compared the distribution of bacterial and archaeal phylotypes of Prony Hydrothermal Field with those of five previously studied serpentinizing systems of geographically distant sites. Although sensu stricto no core microbial community was identified, a few uncultivated lineages, notably within the archaeal order Methanosarcinales and the bacterial class Dehalococcoidia (the candidate division MSBL5) were exclusively found in a few serpentinizing systems while other operational taxonomic units belonging to the orders Clostridiales, Thermoanaerobacterales, or the genus Hydrogenophaga, were abundantly distributed in several sites. These lineages may represent taxonomic signatures of serpentinizing ecosystems. These findings extend our current knowledge of the microbial diversity inhabiting serpentinizing systems and their biogeography.

Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by waste water releases

Microbial mercury (Hg) methylation in sediments can result in bioaccumulation of the neurotoxin methylmercury (MMHg) in aquatic food webs. Recently, the discovery of the gene hgcA, required for Hg methylation, revealed that the diversity of Hg methylators is much broader than previously thought. However, little is known about the identity of Hg-methylating microbial organisms and the environmental factors controlling their activity and distribution in lakes. Here, we combined high-throughput sequencing of 16S rRNA and hgcA genes with the chemical characterization of sediments impacted by a waste water treatment plant that releases significant amounts of organic matter and iron. Our results highlight that the ferruginous geochemical conditions prevailing at 1–2 cm depth are conducive to MMHg formation and that the Hg-methylating guild is composed of iron and sulfur-transforming bacteria, syntrophs, and methanogens. Deltaproteobacteria, notably Geobacteraceae, dominated the hgcA carrying communities, while sulfate reducers constituted only a minor component, despite being considered the main Hg methylators in many anoxic aquatic environments. Because iron is widely applied in waste water treatment, the importance of Geobacteraceae for Hg methylation and the complexity of Hg-methylating communities reported here are likely to occur worldwide in sediments impacted by waste water treatment plant discharges and in iron-rich sediments in general.

Draft genome sequence of Dethiobacter alkaliphilus strain AHT1T, a gram-positive sulfidogenic polyextremophile

Dethiobacter alkaliphilus strain AHT1^T is an anaerobic, sulfidogenic, moderately salt-tolerant alkaliphilic chemolithotroph isolated from hypersaline soda lake sediments in northeastern Mongolia. It is a Gram-positive bacterium with low GC content, within the phylum Firmicutes. Here we report its draft genome sequence, which consists of 34 contigs with a total sequence length of 3.12 Mbp. D. alkaliphilus strain AHT1^T was sequenced by the Joint Genome Institute (JGI) as part of the Community Science Program due to its relevance to bioremediation and biotechnological applications.

Anaerobic oxidation of methane coupled to thiosulfate reduction in a biotrickling filter

Microorganisms from an anaerobic methane oxidizing sediment were enriched with methane gas as the substrate in a biotrickling filter (BTF) using thiosulfate as electron acceptor for 213days. Thiosulfate disproportionation to sulfate and sulfide were the dominating sulfur conversion process in the BTF and the sulfide production rate was 0.5mmoll^-1day^-1. A specific group of sulfate reducing bacteria (SRB), belonging to the Desulforsarcina/Desulfococcus group, was enriched in the BTF. The BTF biomass showed maximum sulfate reduction rate (0.38mmoll^-1day^-1) with methane as sole electron donor, measured in the absence of thiosulfate in the BTF. Therefore, a BTF fed with thiosulfate as electron acceptor can be used to enrich SRB of the DSS group and activate the inoculum for anaerobic oxidation of methane coupled to sulfate reduction.

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

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

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

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

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

Complete genome sequence of Desulfurivibrio alkaliphilus strain AHT2(T), a haloalkaliphilic sulfidogen from Egyptian hypersaline alkaline lakes

Desulfurivibrio alkaliphilus strain AHT2^T is a strictly anaerobic sulfidogenic haloalkaliphile isolated from a composite sediment sample of eight hypersaline alkaline lakes in the Wadi al Natrun valley in the Egyptian Libyan Desert. D. alkaliphilus AHT2^T is Gram-negative and belongs to the family Desulfobulbaceae within the Deltaproteobacteria. Here we report its genome sequence, which contains a 3.10 Mbp chromosome. D. alkaliphilus AHT2^T is adapted to survive under highly alkaline and moderately saline conditions and therefore, is relevant to the biotechnology industry and life under extreme conditions. For these reasons, D. alkaliphilus AHT2^T was sequenced by the DOE Joint Genome Institute as part of the Community Science Program.

Indirect sulfur reduction via polysulfide contributes to serious odor problem in a sewer receiving nitrate dosage

Nitrate dosing is commonly used to control hydrogen sulfide production in sewer systems. However, quick rebound of the sulfide concentration after nitrate depletion has been observed and results in more serious odor and corrosion problem. To investigate the mechanism of sulfide regeneration in the nitrate-free period, a laboratory-scale sewer reactor was run for 30 days to simulate sulfide production and oxidation with intermittent nitrate addition. The results show that nitrate addition substantially reduced the sulfide concentration, but the produced elemental sulfur was then quickly reduced back to sulfide in nitrate-free periods. This induced more and more sulfide production in the sewer reactor. Elemental sulfur and polysulfide reductions were found in the sewage in nitrate-free periods, showing their contributions to the sulfide regeneration. Through batch tests, polysulfide was confirmed as the key intermediate for accelerating sulfur reduction during the nitrate-free period in the sewer. Sulfide production rates significantly increased by 65% and 59% in the presences of tetrasulfide and sulfur with sulfide, respectively, at the beginning of the test. While polysulfide formation was prevented by the ferrous chloride addition, the sulfur reduction rate remarkably decreased from 12.8 mgS/L-h to 1.8 mgS/L-h. This indicates that direct sulfur reduction was significantly slower than the indirect sulfur reduction via polysulfide; the latter process could be the cause for the quick rebound of the sulfide concentration in the sewer with intermittent nitrate dosing. Thus, the pathways of sulfur transformations in a sewer, both in the presence and absence of nitrate, were proposed. Microbial community analysis results reveal that some common sulfate-reducing bacteria (SRB) genera in sewer sediment were possible sulfur reducers. According to this finding, the effect and strategy of nitrate dosing for hydrogen sulfide control in sewers should be re-evaluated and re-considered.

Carbon and Sulfur Cycling below the Chemocline in a Meromictic Lake and the Identification of a Novel Taxonomic Lineage in the FCB Superphylum, Candidatus Aegiribacteria

Mahoney Lake in British Columbia is an extreme meromictic system with unusually high levels of sulfate and sulfide present in the water column. As is common in strongly stratified lakes, Mahoney Lake hosts a dense, sulfide-oxidizing phototrophic microbial community where light reaches the chemocline. Below this "plate," the euxinic hypolimnion is anoxic, eutrophic, saline, and rich in sulfide, polysulfides, elemental sulfur, and other sulfur intermediates. While much is known regarding microbial communities in sunlit portions of euxinic systems, the composition and genetic potential of organisms living at aphotic depths have rarely been studied. Metagenomic sequencing of samples from the hypolimnion and the underlying sediments of Mahoney Lake indicate that multiple taxa contribute to sulfate reduction below the chemocline and that the hypolimnion and sediments each support distinct populations of sulfate reducing bacteria (SRB) that differ from the SRB populations observed in the chemocline. After assembling and binning the metagenomic datasets, we recovered near-complete genomes of dominant populations including two Deltaproteobacteria. One of the deltaproteobacterial genomes encoded a 16S rRNA sequence that was most closely related to the sulfur-disproportionating genus Dissulfuribacter and the other encoded a 16S rRNA sequence that was most closely related to the fatty acid- and aromatic acid-degrading genus Syntrophus. We also recovered two near-complete genomes of Firmicutes species. Analysis of concatenated ribosomal protein trees suggests these genomes are most closely related to extremely alkaliphilic genera Alkaliphilus and Dethiobacter. Our metagenomic data indicate that these Firmicutes contribute to carbon cycling below the chemocline. Lastly, we recovered a nearly complete genome from the sediment metagenome which represents a new genus within the FCB (Fibrobacteres, Chlorobi, Bacteroidetes) superphylum. Consistent with the geochemical data, we found little or no evidence for organisms capable of sulfide oxidation in the aphotic zone below the chemocline. Instead, comparison of functional genes below the chemocline are consistent with recovery of multiple populations capable of reducing oxidized sulfur. Our data support previous observations that at least some of the sulfide necessary to support the dense population of phototrophs in the chemocline is supplied from sulfate reduction in the hypolimnion and sediments. These studies provide key insights regarding the taxonomic and functional diversity within a euxinic environment and highlight the complexity of biogeochemical carbon and sulfur cycling necessary to maintain euxinia.

Metabolic Capabilities of Microorganisms Involved in and Associated with the Anaerobic Oxidation of Methane

In marine sediments the anaerobic oxidation of methane with sulfate as electron acceptor (AOM) is responsible for the removal of a major part of the greenhouse gas methane. AOM is performed by consortia of anaerobic methane-oxidizing archaea (ANME) and their specific partner bacteria. The physiology of these organisms is poorly understood, which is due to their slow growth with doubling times in the order of months and the phylogenetic diversity in natural and in vitro AOM enrichments. Here we study sediment-free long-term AOM enrichments that were cultivated from seep sediments sampled off the Italian Island Elba (20°C; hereon called E20) and from hot vents of the Guaymas Basin, Gulf of California, cultivated at 37°C (G37) or at 50°C (G50). These enrichments were dominated by consortia of ANME-2 archaea and Seep-SRB2 partner bacteria (E20) or by ANME-1, forming consortia with Seep-SRB2 bacteria (G37) or with bacteria of the HotSeep-1 cluster (G50). We investigate lipid membrane compositions as possible factors for the different temperature affinities of the different ANME clades and show autotrophy as characteristic feature for both ANME clades and their partner bacteria. Although in the absence of additional substrates methane formation was not observed, methanogenesis from methylated substrates (methanol and methylamine) could be quickly stimulated in the E20 and the G37 enrichment. Responsible for methanogenesis are archaea from the genus Methanohalophilus and Methanococcoides, which are minor community members during AOM (1–7‰ of archaeal 16S rRNA gene amplicons). In the same two cultures also sulfur disproportionation could be quickly stimulated by addition of zero-valent colloidal sulfur. The isolated partner bacteria are likewise minor community members (1–9‰ of bacterial 16S rRNA gene amplicons), whereas the dominant partner bacteria (Seep-SRB1a, Seep-SRB2, or HotSeep-1) did not grow on elemental sulfur. Our results support a functioning of AOM as syntrophic interaction of obligate methanotrophic archaea that transfer non-molecular reducing equivalents (i.e., via direct interspecies electron transfer) to obligate sulfate-reducing partner bacteria. Additional katabolic processes in these enrichments but also in sulfate methane interfaces are likely performed by minor community members.