Sulfite oxidation in the purple sulfur bacterium Allochromatium vinosum: identification of SoeABC as a major player and relevance of SoxYZ in the process

Fe/S proteins in microbial sulfur oxidation

Iron-sulfur clusters serve as indispensable cofactors within proteins across all three domains of life. Fe/S clusters emerged early during the evolution of life on our planet and the biogeochemical cycle of sulfur is one of the most ancient and important element cycles. It is therefore no surprise that Fe/S proteins have crucial roles in the multiple steps of microbial sulfur metabolism. During dissimilatory sulfur oxidation in prokaryotes, Fe/S proteins not only serve as electron carriers in several steps, but also perform catalytic roles, including unprecedented reactions. Two cytoplasmic enzyme systems that oxidize sulfane sulfur to sulfite are of particular interest in this context: The rDsr pathway employs the reverse acting dissimilatory sulfite reductase rDsrAB as its key enzyme, while the sHdr pathway utilizes polypeptides resembling the HdrA, HdrB and HdrC subunits of heterodisulfide reductase from methanogenic archaea. Both pathways involve components predicted to bind unusual noncubane Fe/S clusters acting as catalysts for the formation of disulfide or sulfite. Mapping of Fe/S cluster machineries on the sulfur-oxidizing prokaryote tree reveals that ISC, SUF, MIS and SMS are all sufficient to meet the Fe/S cluster maturation requirements for operation of the sHdr or rDsr pathways. The sHdr pathway is dependent on lipoate-binding proteins that are assembled by a novel pathway, involving two Radical SAM proteins, namely LipS1 and LipS2. These proteins coordinate sulfur-donating auxiliary Fe/S clusters in atypical patterns by three cysteines and one histidine and act as lipoyl synthases by jointly inserting two sulfur atoms to an octanoyl residue. This article is part of a Special Issue entitled: Biogenesis and Function of Fe/S proteins.

Azotosporobacter soli gen. nov., sp. nov., a novel nitrogen-fixing bacterium isolated from paddy soil

A nitrogen-fixing strain designated SG130T was isolated from paddy soil in Fujian Province, China. Strain SG130T was Gram-staining-negative, rod-shaped, and strictly anaerobic. Strain SG130T showed the highest 16S rRNA gene sequence similarities with the type strains Dendrosporobacter quercicolus DSM 1736T (91.7%), Anaeroarcus burkinensis DSM 6283T (91.0%) and Anaerospora hongkongensis HKU 15T (90.9%). Furthermore, the phylogenetic and phylogenomic analysis also suggested strain SG130T clustered with members of the family Sporomusaceae and was distinguished from other genera within this family. Growth of strain SG130T was observed at 25-45 °C (optimum 30 °C), pH 6.0-9.5 (optimum 7.0) and 0-1% (w/v) NaCl (optimum 0.1%). The quinones were Q-8 and Q-9. The polar lipids were phosphatidylserine (PS), phosphatidylethanolamine (PE), glycolipid (GL), phospholipid (PL) and an unidentified lipid (UL). The major fatty acids (> 10%) were iso-C13:0 3OH (26.6%), iso-C17:1 (15.6%) and iso-C15:1 F (11.4%). The genomic DNA G + C content was 50.7%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain SG130T and the most closely related type strain D. quercicolus DSM 1736T (ANI 68.0% and dDDH 20.3%) were both below the cut-off level for species delineation. The average amino acid identity (AAI) between strain SG130T and the most closely related type strain D. quercicolus DSM 1736T was 63.2%, which was below the cut-off value for bacterial genus delineation (65%). Strain SG130T possessed core genes (nifHDK) involved in nitrogen fixation, and nitrogenase activity (106.38 μmol C2H4 g-1 protein h-1) was examined using the acetylene reduction assay. Based on the above results, strain SG130T is confirmed to represent a novel genus of the family Sporomusaceae, for which the name Azotosporobacter soli gen. nov., sp. nov. is proposed. The type strain is SG130T (= GDMCC 1.3312T = JCM 35641T).

Metabolic and phylogenetic diversity in the phylum Nitrospinota revealed by comparative genome analyses

The most abundant known nitrite-oxidizing bacteria in the marine water column belong to the phylum Nitrospinota. Despite their importance in marine nitrogen cycling and primary production, there are only few cultured representatives that all belong to the class Nitrospinia. Moreover, although Nitrospinota were traditionally thought to be restricted to marine environments, metagenome-assembled genomes have also been recovered from groundwater. Over the recent years, metagenomic sequencing has led to the discovery of several novel classes of Nitrospinota (UBA9942, UBA7883, 2-12-FULL-45-22, JACRGO01, JADGAW01), which remain uncultivated and have not been analyzed in detail. Here, we analyzed a nonredundant set of 98 Nitrospinota genomes with focus on these understudied Nitrospinota classes and compared their metabolic profiles to get insights into their potential role in biogeochemical element cycling. Based on phylogenomic analysis and average amino acid identities, the highly diverse phylum Nitrospinota could be divided into at least 33 different genera, partly with quite distinct metabolic capacities. Our analysis shows that not all Nitrospinota are nitrite oxidizers and that members of this phylum have the genomic potential to use sulfide and hydrogen for energy conservation. This study expands our knowledge of the phylogeny and potential ecophysiology of the phylum Nitrospinota and offers new avenues for the isolation and cultivation of these elusive bacteria.

Optimizing Autotrophic Sulfide Oxidation in the Oxygen-Based Membrane Biofilm Reactor to Recover Elemental Sulfur

Biological sulfide oxidation is an efficient means to recover elemental sulfur (S0) as a valuable resource from sulfide-bearing wastewater. This work evaluated the autotrophic sulfide oxidation to S0 in the O2-based membrane biofilm reactor (O2-MBfR). High recovery of S0 (80-90% of influent S) and high sulfide oxidation (∼100%) were simultaneously achieved when the ratio of O2-delivery capacity to sulfide-to S0 surface loading (SL) (O2/S2- → S0 ratio) was around 1.5 (g O2/m2-day/g O2/m2-day). On average, most of the produced S0 was recovered in the MBfR effluent, although the biofilm could be a source or sink for S0. Shallow metagenomic analysis of the biofilm showed that the top sulfide-oxidizing genera present in all stages were Thauera, Thiomonas, Thauera_A, and Pseudomonas. Thiomonas or Pseudomonas was the most important genus in stages that produced almost only S0 (i.e., the O2/S2- → S0 ratio around 1.5 g of the O2/m2-day/g O2/m2-day). With a lower sulfide SL, the S0-producing genes were sqr and fccAB in Thiomonas. With a higher sulfide SL, the S0-producing genes were in the soxABDXYZ system in Pseudomonas. Thus, the biofilm community of the O2-MBfR adapted to different sulfide-to-S0 SLs and corresponding O2-delivery capacities. The results illustrate the potential for S0 recovery using the O2-MBfR.

Multi-omics study of sulfur metabolism affecting functional microbial community succession during aerobic solid-state fermentation

Microbial-mediated sulfur metabolism is closely related to carbon and nitrogen metabolism in natural biological systems. In this study, the effects of sulfur metabolism on microbial communities and functional enzyme succession were investigated based on integrated multi-omics by adding sulfur-containing compounds to aerobic fermentation systems. Sulfur powder was oxidized to S2O32- and subsequently to SO42- by the microbial sulfur-oxidizing system, which lowered the pH to 7.5 on day 7. The decrease in pH resulted in Planifilum (secreted S8, M17 and M32 proteases) losing its competitive advantage, whereas Novibacillus (secreted M14 and M19 metalloproteases) became dominant. Structural proteomics indicated that the surface of Novibacillus proteases has more negatively charged amino acid residues that help maintain protein stability at low pH. These findings aid understanding of the effects of sulfur metabolism on fermentation and the mechanism of microbial adaptation after pH reduction, providing new perspectives on the optimization of fermentation processes.

Thiorhodovibrio frisius and Trv. litoralis spp. nov., Two Novel Members from a Clade of Fastidious Purple Sulfur Bacteria That Exhibit Unique Red-Shifted Light-Harvesting Capabilities

In the pursuit of cultivating anaerobic anoxygenic phototrophs with unusual absorbance spectra, a purple sulfur bacterium was isolated from the shoreline of Baltrum, a North Sea island of Germany. It was designated strain 970, due to a predominant light harvesting complex (LH) absorption maximum at 963-966 nm, which represents the furthest infrared-shift documented for such complexes containing bacteriochlorophyll a. A polyphasic approach to bacterial systematics was performed, comparing genomic, biochemical, and physiological properties. Strain 970 is related to Thiorhodovibrio winogradskyi DSM 6702T by 26.5, 81.9, and 98.0% similarity via dDDH, ANI, and 16S rRNA gene comparisons, respectively. The photosynthetic properties of strain 970 were unlike other Thiorhodovibrio spp., which contained typical LH absorbing characteristics of 800-870 nm, as well as a newly discovered absorption band at 908 nm. Strain 970 also had a different photosynthetic operon composition. Upon genomic comparisons with the original Thiorhodovibrio strains DSM 6702T and strain 06511, the latter was found to be divergent, with 25.3, 79.1, and 97.5% similarity via dDDH, ANI, and 16S rRNA gene homology to Trv. winogradskyi, respectively. Strain 06511 (=DSM 116345T) is thereby described as Thiorhodovibrio litoralis sp. nov., and the unique strain 970 (=DSM 111777T) as Thiorhodovibrio frisius sp. nov.

Microbial communities related to the sulfur cycle in the Sansha Yongle Blue Hole

The Sansha Yongle Blue Hole (SYBH), the deepest blue hole in the world, is an excellent habitat for revealing biogeochemical cycles in the anaerobic environment. However, how sulfur cycling is mediated by microorganisms in the SYBH hasn't been fully understood. In this study, the water layers of the SYBH were divided into oxic zone, hypoxic zone, anoxic zone I and II, and microbial-mediated sulfur cycling in the SYBH was comprehensively interpreted. The 16S rRNA genes/transcripts analyses showed that the microbial community structures associated with the sulfur cycling in each zone had distinctive features. Sulfur-oxidizing bacteria were mostly constituted by Gammaproteobacteria, Alphaproteobacteria, Campylobacterota, and Chlorobia above the anoxic zone I and sulfate-reducing bacteria were dominated by Desulfobacterota in anoxic zones. Metagenomic analyses showed that the sulfide-oxidation-related gene sqr and genes encoding the Sox system were mainly distributed in the anoxic zone I, while genes related to dissimilatory sulfate reduction and sulfur intermediate metabolite reduction were mainly distributed in the anoxic zone II, indicating different sulfur metabolic processes between these two zones. Moreover, sulfur-metabolism-related genes were identified in 81 metagenome-assembled genomes (MAGs), indicating a high diversity of microbial communities involved in sulfur cycling. Among them, three MAGs from the candidate phyla JdFR-76 and AABM5-125-24 with genes related to dissimilatory sulfate reduction exhibited distinctive metabolic features. Our results showed unique and novel microbial populations in the SYBH sulfur cycle correlated to the sharp redox gradients, revealing complex biogeochemical processes in this extreme environment. IMPORTANCE Oxygen-deficient regions in the global ocean are expanding rapidly and affect the growth, reproduction and ecological processes of marine organisms. The anaerobic water body of about 150 m in the Sansha Yongle Blue Hole (SYBH) provided a suitable environment to study the specific microbial metabolism in anaerobic seawater. Here, we found that the vertical distributions of the total and active communities of sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) were different in each water layer of the SYBH according to the dissolved oxygen content. Genes related to sulfur metabolism also showed distinct stratification characteristics. Furthermore, we have obtained diverse metagenome-assembled genomes, some of which exhibit special sulfur metabolic characteristics, especially candidate phyla JdFR-76 and AABM5-125-24 were identified as potential novel SRB. The results of this study will promote further understanding of the sulfur cycle in extreme environments, as well as the environmental adaptability of microorganisms in blue holes.

Cold Sulfur Springs-Neglected Niche for Autotrophic Sulfur-Oxidizing Bacteria

Since the beginning of unicellular life, dissimilation reactions of autotrophic sulfur bacteria have been a crucial part of the biogeochemical sulfur cycle on Earth. A wide range of sulfur oxidation states is reflected in the diversity of metabolic pathways used by sulfur-oxidizing bacteria. This metabolically and phylogenetically diverse group of microorganisms inhabits a variety of environments, including extreme environments. Although they have been of interest to microbiologists for more than 150 years, meso- and psychrophilic chemolithoautotrophic sulfur-oxidizing microbiota are less studied compared to the microbiota of hot springs. Several recent studies suggested that cold sulfur waters harbor unique, yet not described, bacterial taxa.

O2 partitioning of sulfur oxidizing bacteria drives acidity and thiosulfate distributions in mining waters

The acidification of water in mining areas is a global environmental issue primarily catalyzed by sulfur-oxidizing bacteria (SOB). Little is known about microbial sulfur cycling in circumneutral pH mine tailing impoundment waters. Here we investigate biological sulfur oxidation over four years in a mine tailings impoundment water cap, integrating aqueous sulfur geochemistry, genome-resolved metagenomics and metatranscriptomics. The microbial community is consistently dominated by neutrophilic, chemolithoautotrophic SOB (relative abundances of ~76% in 2015, ~55% in 2016/2017 and ~60% in 2018). Results reveal two SOB strategies alternately dominate across the four years, influencing acid generation and sulfur speciation. Under oxic conditions, novel Halothiobacillus drive lower pH conditions (as low as 4.3) and lower [S₂O₃^2-] via the complete Sox pathway coupled to O₂. Under anoxic conditions, Thiobacillus spp. dominate in activity, via the incomplete Sox and rDSR pathways coupled to NO₃^-, resulting in higher [S₂O₃^2-] and no net significant acidity generation. This study provides genomic evidence explaining acidity generation and thiosulfate accumulation patterns in a circumneutral mine tailing impoundment and has significant environmental applications in preventing the discharge of sulfur compounds that can impact downstream environments. These insights illuminate opportunities for in situ biotreatment of reduced sulfur compounds and prediction of acidification events using gene-based monitoring and in situ RNA detection.

Sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) in oil reservoir and biological control of SRB: a review

Sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) inhabit oilfield production systems. Sulfur oxidation driven by SOB and dissimilatory sulfate reduction driven by SRB play important roles in sulfur cycle of oil reservoirs. More importantly, hydrogen sulfide produced by SRB is an acidic, flammable, and smelly toxic gas associated with reservoir souring, corrosion of oil-production facilities, and personnel safety. Effective control of SRB is urgently needed for the oil industry. This depends on an in-depth understanding of the microbial species that drive sulfur cycle and other related microorganisms in oil reservoir environments. Here, we identified SOB and SRB in produced brines of Qizhong block (Xinjiang Oilfield, China) from metagenome sequencing data based on reported SOB and SRB, reviewed metabolic pathways of sulfur oxidation and dissimilatory sulfate reduction, and ways for SRB control. The existing issues and future research of microbial sulfur cycle and SRB control are also discussed. Knowledge of the distribution of the microbial populations, their metabolic characteristics and interactions can help to develop an effective process to harness these microorganisms for oilfield production.

Replicated life-history patterns and subsurface origins of the bacterial sister phyla Nitrospirota and Nitrospinota

The phyla Nitrospirota and Nitrospinota have received significant research attention due to their unique nitrogen metabolisms important to biogeochemical and industrial processes. These phyla are common inhabitants of marine and terrestrial subsurface environments and contain members capable of diverse physiologies in addition to nitrite oxidation and complete ammonia oxidation. Here, we use phylogenomics and gene-based analysis with ancestral state reconstruction and gene-tree-species-tree reconciliation methods to investigate the life histories of these two phyla. We find that basal clades of both phyla primarily inhabit marine and terrestrial subsurface environments. The genomes of basal clades in both phyla appear smaller and more densely coded than the later-branching clades. The extant basal clades of both phyla share many traits inferred to be present in their respective common ancestors, including hydrogen, one-carbon, and sulfur-based metabolisms. Later-branching groups, namely the more frequently studied classes Nitrospiria and Nitrospinia, are both characterized by genome expansions driven by either de novo origination or laterally transferred genes that encode functions expanding their metabolic repertoire. These expansions include gene clusters that perform the unique nitrogen metabolisms that both phyla are most well known for. Our analyses support replicated evolutionary histories of these two bacterial phyla, with modern subsurface environments representing a genomic repository for the coding potential of ancestral metabolic traits.

Impact of the Dimethyl Sulfoxide Reductase Superfamily on the Evolution of Biogeochemical Cycles

The dimethyl sulfoxide reductase (or MopB) family is a diverse assemblage of enzymes found throughout Bacteria and Archaea. Many of these enzymes are believed to have been present in the last universal common ancestor (LUCA) of all cellular lineages. However, gaps in knowledge remain about how MopB enzymes evolved and how this diversification of functions impacted global biogeochemical cycles through geologic time. In this study, we perform maximum likelihood phylogenetic analyses on manually curated comparative genomic and metagenomic data sets containing over 47,000 distinct MopB homologs. We demonstrate that these enzymes constitute a catalytically and mechanistically diverse superfamily defined not by the molybdopterin- or tungstopterin-containing [molybdopterin or tungstopterin bis(pyranopterin guanine dinucleotide) (Mo/W-bisPGD)] cofactor but rather by the structural fold that binds it in the protein. Our results suggest that major metabolic innovations were the result of the loss of the metal cofactor or the gain or loss of protein domains. Phylogenetic analyses also demonstrated that formate oxidation and CO2 reduction were the ancestral functions of the superfamily, traits that have been vertically inherited from the LUCA. Nearly all of the other families, which drive all other biogeochemical cycles mediated by this superfamily, originated in the bacterial domain. Thus, organisms from Bacteria have been the key drivers of catalytic and biogeochemical innovations within the superfamily. The relative ordination of MopB families and their associated catalytic activities emphasize fundamental mechanisms of evolution in this superfamily. Furthermore, it underscores the importance of prokaryotic adaptability in response to the transition from an anoxic to an oxidized atmosphere. IMPORTANCE The MopB superfamily constitutes a repertoire of metalloenzymes that are central to enduring mysteries in microbiology, from the origin of life and how microorganisms and biogeochemical cycles have coevolved over deep time to how anaerobic life adapted to increasing concentrations of O2 during the transition from an anoxic to an oxic world. Our work emphasizes that phylogenetic analyses can reveal how domain gain or loss events, the acquisition of novel partner subunits, and the loss of metal cofactors can stimulate novel radiations of enzymes that dramatically increase the catalytic versatility of superfamilies. We also contend that the superfamily concept in protein evolution can uncover surprising kinships between enzymes that have remarkably different catalytic and physiological functions.

Oxidative Stress Regulates a Pivotal Metabolic Switch in Dimethylsulfoniopropionate Degradation by the Marine Bacterium Ruegeria pomeroyi

Dimethylsulfoniopropionate (DMSP) is an abundant organic compound in marine surface water and source of dimethyl sulfide (DMS), the largest natural sulfur source to the upper atmosphere. Marine bacteria either mineralize DMSP through the demethylation pathway or transform it to DMS through the cleavage pathway. Factors that regulate which pathway is utilized are not fully understood. In chemostat experiments, the marine Roseobacter Ruegeria pomeroyi DSS-3 was exposed to oxidative stress either during growth with H2O2 or by mutation of the gene encoding catalase. Oxidative stress reduced expression of the genes in the demethylation pathway and increased expression of those encoding the cleavage pathway. These results are contrary to the sulfur demand hypothesis, which theorizes that DMSP metabolism is driven by sulfur requirements of bacterial cells. Instead, we find strong evidence consistent with oxidative stress control over the switch in DMSP metabolism from demethylation to DMS production in an ecologically relevant marine bacterium. IMPORTANCE Dimethylsulfoniopropionate (DMSP) is the most abundant low-molecular-weight organic compound in marine surface water and source of dimethyl sulfide (DMS), a climatically active gas that connects the marine and terrestrial sulfur cycles. Marine bacteria are the major DMSP consumers, either generating DMS or consuming DMSP as a source of reduced carbon and sulfur. However, the factors regulating the DMSP catabolism in bacteria are not well understood. Marine bacteria are also exposed to oxidative stress. RNA sequencing (RNA-seq) experiments showed that oxidative stress induced in the laboratory reduced expression of the genes encoding the consumption of DMSP via the demethylation pathway and increased the expression of genes encoding DMS production via the cleavage pathway in the marine bacterium Ruegeria pomeroyi. These results support a model where DMS production in the ocean is regulated in part by oxidative stress.

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.

Roles, mechanism of action, and potential applications of sulfur-oxidizing bacteria for environmental bioremediation

Sulfur (S) is a crucial component in the environment and living organisms. This work is the first attempt to provide an overview and critical discussion on the roles, mechanisms, and environmental applications of sulfur-oxidizing bacteria (SOB). The findings reveal that key enzymes of SOB embarked on oxidation of sulfide, sulfite, thiosulfate, and elemental S. Conversion of reduced S compounds was oxidatively catalyzed by various enzymes (e.g. sulfide: quinone oxidoreductase, flavocytochrome c-sulfide dehydrogenase, dissimilatory sulfite reductase, heterodisulfide reductase-like proteins). Environmental applications of SOB discussed include detoxifying hydrogen sulfide, soil bioremediation, and wastewater treatment. SOB producing S⁰ engaged in biological S soil amendments (e.g. saline-alkali soil remediation, the oxidation of sulfide-bearing minerals). Biotreatment of H₂S using SOB occurred under both aerobic and anaerobic conditions. Sulfide, nitrate, and sulfamethoxazole were removed through SOB suspension cultures and S⁰-based carriers. Finally, this work presented future perspectives on SOB development, including S⁰ recovery, SOB enrichment, field measurement and identification of sulfur compounds, and the development of mathematical simulation.

Sulfur and methane oxidation by a single microorganism

Wetlands are the major natural source of methane, an important greenhouse gas. The sulfur and methane cycles in wetlands are linked—e.g., a strong sulfur cycle can inhibit methanogenesis. Although there has historically been a clear distinction drawn between methane and sulfur oxidizers, here, we isolated a methanotroph that also performed respiratory oxidization of sulfur compounds. We experimentally demonstrated that thiotrophy and methanotrophy are metabolically compatible, and both metabolisms could be expressed simultaneously in a single microorganism. These findings suggest that mixotrophic methane/sulfur-oxidizing bacteria are a previously overlooked component of environmental methane and sulfur cycles. This creates a framework for a better understanding of these redox cycles in natural and engineered wetlands.

Natural and anthropogenic wetlands are major sources of the atmospheric greenhouse gas methane. Methane emissions from wetlands are mitigated by methanotrophic bacteria at the oxic–anoxic interface, a zone of intense redox cycling of carbon, sulfur, and nitrogen compounds. Here, we report on the isolation of an aerobic methanotrophic bacterium, ‘Methylovirgula thiovorans' strain HY1, which possesses metabolic capabilities never before found in any methanotroph. Most notably, strain HY1 is the first bacterium shown to aerobically oxidize both methane and reduced sulfur compounds for growth. Genomic and proteomic analyses showed that soluble methane monooxygenase and XoxF-type alcohol dehydrogenases are responsible for methane and methanol oxidation, respectively. Various pathways for respiratory sulfur oxidation were present, including the Sox–rDsr pathway and the S₄I system. Strain HY1 employed the Calvin–Benson–Bassham cycle for CO₂ fixation during chemolithoautotrophic growth on reduced sulfur compounds. Proteomic and microrespirometry analyses showed that the metabolic pathways for methane and thiosulfate oxidation were induced in the presence of the respective substrates. Methane and thiosulfate could therefore be independently or simultaneously oxidized. The discovery of this versatile bacterium demonstrates that methanotrophy and thiotrophy are compatible in a single microorganism and underpins the intimate interactions of methane and sulfur cycles in oxic–anoxic interface environments.

Into the darkness: The ecologies of novel 'microbial dark matter' phyla in an Antarctic lake

Uncultivated microbial clades ("microbial dark matter") are inferred to play important, but uncharacterized roles in nutrient cycling. Using Antarctic lake (Ace Lake, Vestfold Hills) metagenomes, 12 metagenome-assembled genomes (MAGs; 88-100% complete) were generated for four "dark matter" phyla: six MAGs from Candidatus Auribacterota (= Aureabacteria, SURF-CP-2), inferred to be hydrogen- and sulfide-producing fermentative heterotrophs, with individual MAGs encoding bacterial microcompartments (BMCs), gas vesicles, and type IV pili; one MAG (100% complete) from Candidatus Hinthialibacterota (= OLB16), inferred to be a facultative anaerobe capable of dissimilatory nitrate reduction to ammonia, specialized for mineralization of complex organic matter (e.g., sulfated polysaccharides), and encoding BMCs, flagella, and Tad pili; three MAGs from Candidatus Electryoneota (= AABM5-125-24), previously reported to include facultative anaerobes capable of dissimilatory sulfate reduction, and here inferred to perform sulfite oxidation, reverse tricarboxylic acid cycle for autotrophy, and possess numerous proteolytic enzymes; two MAGs from Candidatus Lernaellota (= FEN-1099), inferred to be capable of formate oxidation, amino acid fermentation, and possess numerous enzymes for protein and polysaccharide degradation. The presence of 16S rRNA gene sequences in public metagenome datasets (88-100% identity) suggests these "dark matter" phyla contribute to sulfur cycling, degradation of complex organic matter, ammonification and/or chemolithoautrophic CO₂ fixation in diverse global environments. This article is protected by copyright. All rights reserved.

Horizontal transmission enables flexible associations with locally adapted symbiont strains in deep-sea hydrothermal vent symbioses

SignificanceIn marine ecosystems, transmission of microbial symbionts between host generations occurs predominantly through the environment. Yet, it remains largely unknown how host genetics, symbiont competition, environmental conditions, and geography shape the composition of symbionts acquired by individual hosts. To address this question, we applied population genomic approaches to four species of deep-sea hydrothermal vent snails that live in association with chemosynthetic bacteria. Our analyses show that environment is more important to strain-level symbiont composition than host genetics and that symbiont strains show genetic variation indicative of adaptation to the distinct geochemical conditions at each vent site. This corroborates a long-standing hypothesis that hydrothermal vent invertebrates affiliate with locally adapted symbiont strains to cope with the variable conditions characterizing their habitats.

Microbial chemolithotrophic oxidation of pyrite in a subsurface shale weathering environment: Geologic considerations and potential mechanisms

Oxidative weathering of pyrite plays an important role in the biogeochemical cycling of Fe and S in terrestrial environments. While the mechanism and occurrence of biologically accelerated pyrite oxidation under acidic conditions are well established, much less is known about microbially mediated pyrite oxidation at circumneutral pH. Recent work (Percak-Dennett et al., 2017, Geobiology, 15, 690) has demonstrated the ability of aerobic chemolithotrophic microorganisms to accelerate pyrite oxidation at circumneutral pH and proposed two mechanistic models by which this phenomenon might occur. Here, we assess the potential relevance of aerobic microbially catalyzed circumneutral pH pyrite oxidation in relation to subsurface shale weathering at Susquehanna Shale Hills Critical Zone Observatory (SSHCZO) in Pennsylvania, USA. Specimen pyrite mixed with native shale was incubated in groundwater for 3 months at the inferred depth of in situ pyrite oxidation. The colonized materials were used as an inoculum for pyrite-oxidizing enrichment cultures. Microbial activity accelerated the release of sulfate across all conditions. 16S rRNA gene sequencing and metagenomic analysis revealed the dominance of a putative chemolithoautotrophic sulfur-oxidizing bacterium from the genus Thiobacillus in the enrichment cultures. Previously proposed models for aerobic microbial pyrite oxidation were assessed in terms of physical constraints, enrichment culture geochemistry, and metagenomic analysis. Although we conclude that subsurface pyrite oxidation at SSCHZO is largely abiotic, this work nonetheless yields new insight into the potential pathways by which aerobic microorganisms may accelerate pyrite oxidation at circumneutral pH. We propose a new "direct sulfur oxidation" pathway, whereby sulfhydryl-bearing outer membrane proteins mediate oxidation of pyrite surfaces through a persulfide intermediate, analogous to previously proposed mechanisms for direct microbial oxidation of elemental sulfur. The action of this and other direct microbial pyrite oxidation pathways have major implications for controls on pyrite weathering rates in circumneutral pH sedimentary environments where pore throat sizes permit widespread access of microorganisms to pyrite surfaces.

Genomic Comparison, Phylogeny and Taxonomic Reevaluation of the Ectothiorhodospiraceae and Description of Halorhodospiraceae fam. nov. and Halochlorospira gen. nov

The Ectothiorhodospiraceae family represents purple sulfur bacteria of the Gammaproteobacteria found primarily in alkaline soda lakes of moderate to extremely high salinity. The main microscopically visible characteristic separating them from the Chromatiaceae is the excretion of the intermediate elemental sulfur formed during oxidation of sulfide prior to complete oxidation to sulfate rather than storing it in the periplasm. We present a comparative study of 38 genomes of all species of phototrophic Ectothiorhodospiraceae. We also include a comparison with those chemotrophic bacteria that have been assigned to the family previously and critically reevaluate this assignment. The data demonstrate the separation of Halorhodospira species in a major phylogenetic branch distant from other Ectothiorhodospiraceae and support their separation into a new family, for which the name Halorhodospiraceae fam. nov. is proposed. In addition, the green-colored, bacteriochlorophyll-containing species Halorhodospira halochloris and Halorhodospira abdelmalekii were transferred to the new genus Halochlorospira gen. nov. of this family. The data also enable classification of several so far unclassified isolates and support the separation of Ectothiorhodospira shaposhnikovii and Ect. vacuolata as well as Ect. mobilis and Ect. marismortui as distinct species.

Allochromatium tepidum, sp. nov., a hot spring species of purple sulfur bacteria

We describe a new species of purple sulfur bacteria (Chromatiaceae, anoxygenic phototrophic bacteria) isolated from a microbial mat in the sulfidic geothermal outflow of a hot spring in Rotorua, New Zealand. This phototroph, designated as strain NZ, grew optimally near 45 °C but did not show an absorption maximum at 915 nm for the light-harvesting-reaction center core complex (LH1-RC) characteristic of other thermophilic purple sulfur bacteria. Strain NZ had a similar carotenoid composition as Thermochromatium tepidum, but unlike Tch. tepidum, grew photoheterotrophically on acetate in the absence of sulfide and metabolized thiosulfate. The genome of strain NZ was significantly larger than that of Tch. tepidum but slightly smaller than that of Allochromatium vinosum. Strain NZ was phylogenetically more closely related to mesophilic purple sulfur bacteria of the genus Allochromatium than to Tch. tepidum. This conclusion was reached from phylogenetic analyses of strain NZ genes encoding 16S rRNA and the photosynthetic functional gene pufM, from phylogenetic analyses of entire genomes, and from a phylogenetic tree constructed from the concatenated sequence of 1090 orthologous proteins. Moreover, average nucleotide identities and digital DNA:DNA hybridizations of the strain NZ genome against those of related species of Chromatiaceae supported the phylogenetic analyses. From this collection of properties, we describe strain NZ here as the first thermophilic species of the genus Allochromatium, Allochromatium tepidum NZ^T, sp. nov.

Complete genome of the thermophilic purple sulfur Bacterium Thermochromatium tepidum compared to Allochromatium vinosum and other Chromatiaceae

The complete genome sequence of the thermophilic purple sulfur bacterium Thermochromatium tepidum strain MC^T (DSM 3771^T) is described and contrasted with that of its mesophilic relative Allochromatium vinosum strain D (DSM 180^T) and other Chromatiaceae. The Tch. tepidum genome is a single circular chromosome of 2,958,290 base pairs with no plasmids and is substantially smaller than the genome of Alc. vinosum. The Tch. tepidum genome encodes two forms of RuBisCO and contains nifHDK and several other genes encoding a molybdenum nitrogenase but lacks a gene encoding a protein that assembles the Fe-S cluster required to form a functional nitrogenase molybdenum-iron cofactor, leaving the phototroph phenotypically Nif^-. Tch. tepidum contains genes necessary for oxidizing sulfide to sulfate as photosynthetic electron donor but is genetically unequipped to either oxidize thiosulfate as an electron donor or carry out assimilative sulfate reduction, both of which are physiological hallmarks of Alc. vinosum. Also unlike Alc. vinosum, Tch. tepidum is obligately phototrophic and unable to grow chemotrophically in darkness by respiration. Several genes present in the Alc. vinosum genome that are absent from the genome of Tch. tepidum likely contribute to the major physiological differences observed between these related purple sulfur bacteria that inhabit distinct ecological niches.

Modularity of membrane-bound charge-translocating protein complexes

Energy transduction is the conversion of one form of energy into another; this makes life possible as we know it. Organisms have developed different systems for acquiring energy and storing it in useable forms: the so-called energy currencies. A universal energy currency is the transmembrane difference of electrochemical potential (Δμ~). This results from the translocation of charges across a membrane, powered by exergonic reactions. Different reactions may be coupled to charge-translocation and, in the majority of cases, these reactions are catalyzed by modular enzymes that always include a transmembrane subunit. The modular arrangement of these enzymes allows for different catalytic and charge-translocating modules to be combined. Thus, a transmembrane charge-translocating module can be associated with different catalytic subunits to form an energy-transducing complex. Likewise, the same catalytic subunit may be combined with a different membrane charge-translocating module. In this work, we analyze the modular arrangement of energy-transducing membrane complexes and discuss their different combinations, focusing on the charge-translocating module.

Metabolism of chiral sulfonate compound 2,3-dihydroxypropane-1-sulfonate (DHPS) by Roseobacter bacteria in marine environment

The sulfonate compound 2,3-dihydroxypropane-1-sulfonate (DHPS) is one of the most abundant organic sulfur compounds in the biosphere. DHPS derived from dietary intake could be transformed into sulfide by intestinal microbiota and thus impacts human health. However, little is known about its sulfur transformation and subsequent impacts in marine environment. In this study, laboratory-culturing was combined with targeted metabolomic, chemical fluorescence probing, and comparative proteomic methods to examine the bioavailability of chiral DHPS (R and S isomers) for bacteria belonging to the marine Roseobacter clade. The metabolic potential of DHPS in bacteria was further assessed based on genomic analysis. Roseobacter members Ruegeria pomeroyi DSS-3, Dinoroseobacter shibae DFL 12, and Roseobacter denitrificans OCh 114 could utilize chiral DHPS for growth, producing sulfite. They all contained a similar gene cluster for DHPS metabolism but differed in the genes encoding enzymes for desulfonation. There was no significant difference in the growth rate and DHPS consumption rate for R. pomeroyi DSS-3 between R- and S-DHPS cultures, with few proteins expressed differentially were found. Proteomic data suggested that a series of hydrogenases oxidized DHPS, after which desulfonation could proceed via three distinct enzymatic pathways. Strain R. pomeroyi DSS-3 completed the desulfonation via L-cysteate sulfo-lyase, while D. shibae DFL 12 and R. denitrificans OCh 114 primarily utilized sulfolactate sulfo-lyase, and sulfopyruvate decarboxylase followed by sulfoacetaldehyde acetyltransferase, respectively, to complete desulfonation releasing the sulfonate-moiety. The sulfite could be further oxidized or incorporated into sulfate assimilation, indicated by the proteomic data. Furthermore, DHPS metabolic pathways were found primarily in marine bacterial groups, including the majority of sequenced Roseobacter genomes. Our results suggest that chiral DHPS, as a vital reduced sulfur reservoir, could be metabolized by marine bacteria, providing a resource for bacterial growth, rather than acting as a source of toxic sulfide within the marine ecosystem.

Physiology, Taxonomy, and Sulfur Metabolism of the Sulfolobales, an Order of Thermoacidophilic Archaea

The order Sulfolobales (phylum Crenarchaeota) is a group of thermoacidophilic archaea. The first member of the Sulfolobales was discovered in 1972, and current 23 species are validly named under the International Code of Nomenclature of Prokaryotes. The majority of members of the Sulfolobales is obligately or facultatively chemolithoautotrophic. When they grow autotrophically, elemental sulfur or reduced inorganic sulfur compounds are their energy sources. Therefore, sulfur metabolism is the most important physiological characteristic of the Sulfolobales. The functions of some enzymes and proteins involved in sulfur reduction, sulfur oxidation, sulfide oxidation, thiosulfate oxidation, sulfite oxidation, tetrathionate hydrolysis, and sulfur trafficking have been determined. In this review, we describe current knowledge about the physiology, taxonomy, and sulfur metabolism of the Sulfolobales, and note future challenges in this field.

Identification and Genomic Characterization of Two Previously Unknown Magnetotactic Nitrospirae

Magnetotactic bacteria (MTB) are a group of microbes that biomineralize membrane-bound, nanosized magnetite (Fe3O4), and/or greigite (Fe3S4) crystals in intracellular magnetic organelle magnetosomes. MTB belonging to the Nitrospirae phylum can form up to several hundreds of Fe3O4 magnetosome crystals and dozens of sulfur globules in a single cell. These MTB are widespread in aquatic environments and sometimes account for a significant proportion of microbial biomass near the oxycline, linking these lineages to the key steps of global iron and sulfur cycling. Despite their ecological and biogeochemical importance, our understanding of the diversity and ecophysiology of magnetotactic Nitrospirae is still very limited because this group of MTB remains unculturable. Here, we identify and characterize two previously unknown MTB populations within the Nitrospirae phylum through a combination of 16S rRNA gene-based and genome-resolved metagenomic analyses. These two MTB populations represent distinct morphotypes (rod-shaped and coccoid, designated as XYR, and XYC, respectively), and both form more than 100 bullet-shaped magnetosomal crystals per cell. High-quality draft genomes of XYR and XYC have been reconstructed, and they represent a novel species and a novel genus, respectively, according to their average amino-acid identity values with respect to available genomes. Accordingly, the names Candidatus Magnetobacterium cryptolimnobacter and Candidatus Magnetomicrobium cryptolimnococcus for XYR and XYC, respectively, were proposed. Further comparative genomic analyses of XYR, XYC, and previously reported magnetotactic Nitrospirae reveal the general metabolic potential of this MTB group in distinct microenvironments, including CO2 fixation, dissimilatory sulfate reduction, sulfide oxidation, nitrogen fixation, or denitrification processes. A remarkably conserved magnetosome gene cluster has been identified across Nitrospirae MTB genomes, indicating its putative important adaptive roles in these bacteria. Taken together, the present study provides novel insights into the phylogenomic diversity and ecophysiology of this intriguing, yet poorly understood MTB group.

DiSCo: a sequence-based type-specific predictor of Dsr-dependent dissimilatory sulphur metabolism in microbial data

Current methods in comparative genomic analyses for metabolic potential prediction of proteins involved in, or associated with the Dsr (dissimilatory sulphite reductase)-dependent dissimilatory sulphur metabolism are both time-intensive and computationally challenging, especially when considering metagenomic data. We developed DiSCo, a Dsr-dependent dissimilatory sulphur metabolism classification tool, which automatically identifies and classifies the protein type from sequence data. It takes user-supplied protein sequences and lists the identified proteins and their classification in terms of protein family and predicted type. It can also extract the sequence data from user-input to serve as basis for additional downstream analyses. DiSCo provides the metabolic functional prediction of proteins involved in Dsr-dependent dissimilatory sulphur metabolism with high levels of accuracy in a fast manner. We ran DiSCo against a dataset composed of over 190 thousand (meta)genomic records and efficiently mapped Dsr-dependent dissimilatory sulphur proteins in 1798 lineages across both prokaryotic domains. This allowed the identification of new micro-organisms belonging to Thaumarchaeota and Spirochaetes lineages with the metabolic potential to use the Dsr-pathway for energy conservation. DiSCo is implemented in Perl 5 and freely available under the GNU GPLv3 at https://github.com/Genome-Evolution-and-Ecology-Group-GEEG/DiSCo.

Molecular Physiology of Anaerobic Phototrophic Purple and Green Sulfur Bacteria

There are two main types of bacterial photosynthesis: oxygenic (cyanobacteria) and anoxygenic (sulfur and non-sulfur phototrophs). Molecular mechanisms of photosynthesis in the phototrophic microorganisms can differ and depend on their location and pigments in the cells. This paper describes bacteria capable of molecular oxidizing hydrogen sulfide, specifically the families Chromatiaceae and Chlorobiaceae, also known as purple and green sulfur bacteria in the process of anoxygenic photosynthesis. Further, it analyzes certain important physiological processes, especially those which are characteristic for these bacterial families. Primarily, the molecular metabolism of sulfur, which oxidizes hydrogen sulfide to elementary molecular sulfur, as well as photosynthetic processes taking place inside of cells are presented. Particular attention is paid to the description of the molecular structure of the photosynthetic apparatus in these two families of phototrophs. Moreover, some of their molecular biotechnological perspectives are discussed.

The Ion-Translocating NrfD-Like Subunit of Energy-Transducing Membrane Complexes

Several energy-transducing microbial enzymes have their peripheral subunits connected to the membrane through an integral membrane protein, that interacts with quinones but does not have redox cofactors, the so-called NrfD-like subunit. The periplasmic nitrite reductase (NrfABCD) was the first complex recognized to have a membrane subunit with these characteristics and consequently provided the family's name: NrfD. Sequence analyses indicate that NrfD homologs are present in many diverse enzymes, such as polysulfide reductase (PsrABC), respiratory alternative complex III (ACIII), dimethyl sulfoxide (DMSO) reductase (DmsABC), tetrathionate reductase (TtrABC), sulfur reductase complex (SreABC), sulfite dehydrogenase (SoeABC), quinone reductase complex (QrcABCD), nine-heme cytochrome complex (NhcABCD), group-2 [NiFe] hydrogenase (Hyd-2), dissimilatory sulfite-reductase complex (DsrMKJOP), arsenate reductase (ArrC) and multiheme cytochrome c sulfite reductase (MccACD). The molecular structure of ACIII subunit C (ActC) and Psr subunit C (PsrC), NrfD-like subunits, revealed the existence of ion-conducting pathways. We performed thorough primary structural analyses and built structural models of the NrfD-like subunits. We observed that all these subunits are constituted by two structural repeats composed of four-helix bundles, possibly harboring ion-conducting pathways and containing a quinone/quinol binding site. NrfD-like subunits may be the ion-pumping module of several enzymes. Our data impact on the discussion of functional implications of the NrfD-like subunit-containing complexes, namely in their ability to transduce energy.

Molecular and Physiological Adaptations to Low Temperature in Thioalkalivibrio Strains Isolated from Soda Lakes with Different Temperature Regimes

The genus Thioalkalivibrio comprises sulfur-oxidizing bacteria thriving in soda lakes at high pH and salinity. Depending on the geographical location and the season, these lakes can strongly vary in temperature. To obtain a comprehensive understanding of the molecular and physiological adaptations to low temperature, we compared the responses of two Thioalkalivibrio strains to low (10°C) and high (30°C) temperatures. For this, the strains were grown under controlled conditions in chemostats and analyzed for their gene expression (RNA sequencing [RNA-Seq]), membrane lipid composition, and glycine betaine content. The strain Thioalkalivibrio versutus AL2^T originated from a soda lake in southeast Siberia that is exposed to strong seasonal temperature differences, including freezing winters, whereas Thioalkalivibrio nitratis ALJ2 was isolated from an East African Rift Valley soda lake with a constant warm temperature the year round. The strain AL2^T grew faster than ALJ2 at 10°C, likely due to its 3-fold-higher concentration of the osmolyte glycine betaine. Moreover, significant changes in the membrane lipid composition were observed for both strains, leading to an increase in their unsaturated fatty acid content via the Fab pathway to avoid membrane stiffness. Genes for the transcriptional and translational machinery, as well as for counteracting cold-induced hampering of nucleotides and proteins, were upregulated. Oxidative stress was reduced by induction of vitamin B₁₂ biosynthesis genes, and growth at 10°C provoked downregulation of genes involved in the second half of the sulfur oxidation pathway. Genes for intracellular signal transduction were differentially expressed, and interestingly, AL2^T upregulated flagellin expression, whereas ALJ2 downregulated it.

IMPORTANCE In addition to their haloalkaline conditions, soda lakes can also harbor a variety of other extreme parameters, to which their microbial communities need to adapt. However, for most of these supplementary stressors, it is not well known yet how haloalkaliphiles adapt and resist. Here, we studied the strategy for adaptation to low temperature in the haloalkaliphilic genus Thioalkalivibrio by using two strains isolated from soda lakes with different temperature regimes. Even though the strains showed a strong difference in growth rate at 10°C, they exhibited similar molecular and physiological adaptation responses. We hypothesize that they take advantage of resistance mechanisms against other stressors commonly found in soda lakes, which are therefore maintained in the bacteria living in the absence of low-temperature pressure. A major difference, however, was detected for their glycine betaine content at 10°C, highlighting the power of this osmolyte to also act as a key compound in cryoprotection.

Author Video: An author video summary of this article is available.

Bacterial community in saline farmland soil on the Tibetan plateau: responding to salinization while resisting extreme environments

Background

Salinization damages the health of soil systems and reduces crop yields. Responses of microbial communities to salinized soils and their functional maintenance under high salt stress are valuable scientific problems. Meanwhile, the microbial community of the salinized soil in the plateau environment is less understood. Here, we applied metagenomics technology to reveal the structure and function of microorganisms in salinized soil of the Tibetan Plateau.

Results

The diversity of composition and function of microbial community in saline soil have changed significantly. The abundances of chemoautotrophic and acidophilic bacteria comprising Rhodanobacter, Acidobacterium, Candidatus Nitrosotalea, and Candidatus Koribacter were significantly higher in saline soil. The potential degradation of organic carbon in the saline soil, as well as the production of NO and N₂O via denitrification, and the production of sulfate by sulfur oxidation were significantly higher than the non-saline soil. Both types of soils were rich in genes encoding resistance to environmental stresses (i.e., cold, ultraviolet light, and hypoxia in Tibetan Plateau). The resistance of the soil microbial communities to the saline environment is based on the absorption of K⁺ as the main mechanism, with cross-protection proteins and absorption buffer molecules as auxiliary mechanisms in our study area. Network analysis showed that functional group comprising chemoautotrophic and acidophilic bacteria had significant positive correlations with electrical conductivity and total sulfur, and significant negative correlations with the total organic carbon, pH, and available nitrogen. The soil moisture, pH, and electrical conductivity are likely to affect the bacterial carbon, nitrogen, and sulfur cycles.

Conclusions

These results indicate that the specific environment of the Tibetan Plateau and salinization jointly shape the structure and function of the soil bacterial community, and that the bacterial communities respond to complex and harsh living conditions. In addition, environmental feedback probably exacerbates greenhouse gas emissions and accelerates the reduction in the soil pH. This study will provide insights into the microbial responses to soil salinization and the potential ecological risks in the special plateau environment.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02190-6.

Redox loops in anaerobic respiration - The role of the widespread NrfD protein family and associated dimeric redox module

In prokaryotes, the proton or sodium motive force required for ATP synthesis is produced by respiratory complexes that present an ion-pumping mechanism or are involved in redox loops performed by membrane proteins that usually have substrate and quinone-binding sites on opposite sides of the membrane. Some respiratory complexes include a dimeric redox module composed of a quinone-interacting membrane protein of the NrfD family and an iron‑sulfur protein of the NrfC family. The QrcABCD complex of sulfate reducers, which includes the QrcCD module homologous to NrfCD, was recently shown to perform electrogenic quinone reduction providing the first conclusive evidence for energy conservation among this family. Similar redox modules are present in multiple respiratory complexes, which can be associated with electroneutral, energy-driven or electrogenic reactions. This work discusses the presence of the NrfCD/PsrBC dimeric redox module in different bioenergetics contexts and its role in prokaryotic energy conservation mechanisms.

Transcriptional response of Thialkalivibrio versutus D301 to different sulfur sources and identification of the sulfur oxidation pathways

The genus Thialkalivibrio plays an essential role in the biological desulfurization system. However, to date, the sulfur oxidation pathways of Thialkalivibrio are not clearly understood. Here, we performed transcriptomic analysis on Thialkalivibrio versutus D301 with either thiosulfate or chemical sulfur as the sulfur source to understand it. The results show that T. versutus D301 has a higher growth rate and sulfur oxidation activity when thiosulfate is utilized. The use of chemical sulfur as sulfur source leads to decreased expression of genes involved in carbon metabolism, ribosome synthesis and oxidative phosphorylation in T. versutus D301. Potentially due to the adsorption to sulfur particles, the genes related to flagellum assembly and motivation are significantly induced in T. versutus D301 in the presence of chemical sulfur. In the periplasm, both thiosulfate and polysulfide from the chemical sulfur are oxidized to sulfate via the similar truncated Sox system (SoxAXYZB). Then, part of polysulfide reached to cytoplasm through an unidentified route is oxidized to sulfite by the Dsr-like system. The sulfite in the cytoplasm is further catalyzed to sulfate by SoxB or SoeABC. Overall, the difference in the oxidation rates of D301 can be mainly attributed to the bioavailability of the two sulfur sources, not the sulfur oxidation pathways.

Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis

The hydrothermal vent tubeworm Riftia pachyptila hosts a single 16S rRNA phylotype of intracellular sulfur-oxidizing symbionts, which vary considerably in cell morphology and exhibit a remarkable degree of physiological diversity and redundancy, even in the same host. To elucidate whether multiple metabolic routes are employed in the same cells or rather in distinct symbiont subpopulations, we enriched symbionts according to cell size by density gradient centrifugation. Metaproteomic analysis, microscopy, and flow cytometry strongly suggest that Riftia symbiont cells of different sizes represent metabolically dissimilar stages of a physiological differentiation process: While small symbionts actively divide and may establish cellular symbiont-host interaction, large symbionts apparently do not divide, but still replicate DNA, leading to DNA endoreduplication. Moreover, in large symbionts, carbon fixation and biomass production seem to be metabolic priorities. We propose that this division of labor between smaller and larger symbionts benefits the productivity of the symbiosis as a whole.

Improving confirmed nanometric sulfur bioproduction using engineered Thioalkalivibrio versutus

Complicated production procedures and superior characteristics of nano-sized sulfur elevate its price to 25-40 fold higher than micrograde kind. Also, natural gas hydrogen sulfide levels are restricted because of its toxic environmental consequences. Thioalkalivibrio versutus is a polyextremophilic industrial autotroph with high natural gas desulfurization capability. Here, nanometric (>50 nm) sulfur bioproduction using T. versutus while desulfurizing natural gas was validated. Also, this production was enhanced by 166.7% via lowering sulfate production by 55.1%. A specially-developed CRISPR system, with 42% editing efficiency, simplified the genome editing workflow scheme for this challenging bacterium. In parallel, sulfur metabolism was uncovered using proteins mining and transcriptome studies for defining sulfate-producing key genes (heterodisulfide reductase-like complex, sulfur dioxygenase, sulfite dehydrogenase and sulfite oxidase). This study provided cost-effective nanometric sulfur production and improved this production using a novel CRISPR strategy, which could be suitable for industrial polyextremophiles, after uncovering sulfur pathways in T. versutus.

The Heterotrophic Bacterium Cupriavidus pinatubonensis JMP134 Oxidizes Sulfide to Sulfate with Thiosulfate as a Key Intermediate

Heterotrophic bacteria actively participate in the biogeochemical cycle of sulfur on Earth. The heterotrophic bacterium Cupriavidus pinatubonensis JMP134 contains several enzymes involved in sulfur oxidation, but how these enzymes work together to oxidize sulfide in the bacterium has not been studied. Using gene-deletion and whole-cell assays, we determined that the bacterium uses sulfide:quinone oxidoreductase to oxidize sulfide to polysulfide, which is further oxidized to sulfite by persulfide dioxygenase. Sulfite spontaneously reacts with polysulfide to produce thiosulfate. The sulfur-oxidizing (Sox) system oxidizes thiosulfate to sulfate. Flavocytochrome c sulfide dehydrogenase enhances thiosulfate oxidation by the Sox system but couples with the Sox system for sulfide oxidation to sulfate in the absence of sulfide:quinone oxidoreductase. Thus, C. pinatubonensis JMP134 contains a main pathway and a contingent pathway for sulfide oxidation.IMPORTANCE We establish a new pathway of sulfide oxidation with thiosulfate as a key intermediate in Cupriavidus pinatubonensis JMP134. The bacterium mainly oxidizes sulfide by using sulfide:quinone oxidoreductase, persulfide dioxygenase, and the Sox system with thiosulfate as a key intermediate. Although the purified and reconstituted Sox system oxidizes sulfide, its rate of sulfide oxidation in C. pinatubonensis JMP134 is too low to be physiologically relevant. The findings reveal how these sulfur-oxidizing enzymes participate in sulfide oxidation in a single bacterium.

Phylogeny resolved, metabolism revealed: functional radiation within a widespread and divergent clade of sponge symbionts

The symbiosis between bacteria and sponges has arguably the longest evolutionary history for any extant metazoan lineage, yet little is known about bacterial evolution or adaptation in this process. An example of often dominant and widespread bacterial symbionts of sponges is a clade of uncultured and uncharacterised Proteobacteria. Here we set out to characterise this group using metagenomics, in-depth phylogenetic analyses, metatranscriptomics, and fluorescence in situ hybridisation microscopy. We obtained five metagenome-assembled-genomes (MAGs) from different sponge species that, together with a previously published MAG (AqS2), comprise two families within a new gammaproteobacterial order that we named ^UTethybacterales. Members of this order share a heterotrophic lifestyle but vary in their predicted ability to use various carbon, nitrogen and sulfur sources, including taurine, spermidine and dimethylsulfoniopropionate. The deep branching of the ^UTethybacterales within the Gammaproteobacteria and their almost exclusive presence in sponges suggests they have entered a symbiosis with their host relatively early in evolutionary time and have subsequently functionally radiated. This is reflected in quite distinct lifestyles of various species of ^UTethybacterales, most notably their diverse morphologies, predicted substrate preferences, and localisation within the sponge tissue. This study provides new insight into the evolution of metazoan-bacteria symbiosis.

Comparative Genomic Analysis Reveals the Metabolism and Evolution of the Thermophilic Archaeal Genus Metallosphaera

Members of the genus Metallosphaera are widely found in sulfur-rich and metal-laden environments, but their physiological and ecological roles remain poorly understood. Here, we sequenced Metallosphaera tengchongensis Ric-A, a strain isolated from the Tengchong hot spring in Yunnan Province, China, and performed a comparative genome analysis with other Metallosphaera genomes. The genome of M. tengchongensis had an average nucleotide identity (ANI) of approximately 70% to that of Metallosphaera cuprina. Genes sqr, tth, sir, tqo, hdr, tst, soe, and sdo associated with sulfur oxidation, and gene clusters fox and cbs involved in iron oxidation existed in all Metallosphaera genomes. However, the adenosine-5'-phosphosulfate (APS) pathway was only detected in Metallosphaera sedula and Metallosphaera yellowstonensis, and several subunits of fox cluster were lost in M. cuprina. The complete 3-hydroxypropionate/4-hydroxybutyrate cycle and dicarboxylate/4-hydroxybutyrate cycle involved in carbon fixation were found in all Metallosphaera genomes. A large number of gene family gain events occurred in M. yellowstonensis and M. sedula, whereas gene family loss events occurred frequently in M. cuprina. Pervasive strong purifying selection was found acting on the gene families of Metallosphaera, of which transcription-related genes underwent the strongest purifying selection. In contrast, genes related to prophages, transposons, and defense mechanisms were under weaker purifying pressure. Taken together, this study expands knowledge of the genomic traits of Metallosphaera species and sheds light on their evolution.

Synechococcus sp. Strain PCC7002 Uses Sulfide:Quinone Oxidoreductase To Detoxify Exogenous Sulfide and To Convert Endogenous Sulfide to Cellular Sulfane Sulfur

Eutrophication and deoxygenation possibly occur in coastal waters due to excessive nutrients from agricultural and aquacultural activities, leading to sulfide accumulation. Cyanobacteria, as photosynthetic prokaryotes, play significant roles in carbon fixation in the ocean. Although some cyanobacteria can use sulfide as the electron donor for photosynthesis under anaerobic conditions, little is known on how they interact with sulfide under aerobic conditions. In this study, we report that Synechococcus sp. strain PCC7002 (PCC7002), harboring an sqr gene encoding sulfide:quinone oxidoreductase (SQR), oxidized self-produced sulfide to S0, present as persulfide and polysulfide in the cell. The Δsqr mutant contained less cellular S0 and had increased expression of key genes involved in photosynthesis, but it was less competitive than the wild type in cocultures. Further, PCC7002 with SQR and persulfide dioxygenase (PDO) oxidized exogenous sulfide to tolerate high sulfide levels. Thus, SQR offers some benefits to cyanobacteria even under aerobic conditions, explaining the common presence of SQR in cyanobacteria.IMPORTANCE Cyanobacteria are a major force for primary production via oxygenic photosynthesis in the ocean. A marine cyanobacterium, PCC7002, is actively involved in sulfide metabolism. It uses SQR to detoxify exogenous sulfide, enabling it to survive better than its Δsqr mutant in sulfide-rich environments. PCC7002 also uses SQR to oxidize endogenously generated sulfide to S0, which is required for the proper expression of key genes involved in photosynthesis. Thus, SQR has at least two physiological functions in PCC7002. The observation provides a new perspective for the interplays of C and S cycles.

Thiocyanate Degradation by a Highly Enriched Culture of the Neutrophilic Halophile Thiohalobacter sp. Strain FOKN1 from Activated Sludge and Genomic Insights into Thiocyanate Metabolism

Thiocyanate (SCN^-) is harmful to a wide range of organisms, and its removal is essential for environmental protection. A neutrophilic halophile capable of thiocyanate degradation, Thiohalobacter sp. strain FOKN1, was highly enriched (relative abundance; 98.4%) from activated sludge collected from a bioreactor receiving thiocyanate-rich wastewater. The enrichment culture degraded 3.38 mM thiocyanate within 140 h, with maximum activity at pH 8.8, 37°C, and 0.18 M sodium chloride. Thiocyanate degradation was inhibited by 30 mg L^-1 phenol, but not by thiosulfate. Microbial thiocyanate degradation is catalyzed by thiocyanate dehydrogenase, while limited information is currently available on the molecular mechanisms underlying thiocyanate degradation by the thiocyanate dehydrogenase of neutrophilic halophiles. Therefore, (meta)genomic and proteomic analyses of enrichment cultures were performed to elucidate the whole genome sequence and proteome of Thiohalobacter sp. strain FOKN1. The 3.23-Mb circular Thiohalobacter sp. strain FOKN1 genome was elucidated using a PacBio RSII sequencer, and the expression of 914 proteins was identified by tandem mass spectrometry. The Thiohalobacter sp. strain FOKN1 genome had a gene encoding thiocyanate dehydrogenase, which was abundant in the proteome, suggesting that thiocyanate is degraded by thiocyanate dehydrogenase to sulfur and cyanate. The sulfur formed may be oxidized to sulfate by the sequential oxidation reactions of dissimilatory sulfite reductase, adenosine-5'-phosphosulfate reductase, and dissimilatory ATP sulfurylase. Although the Thiohalobacter sp. strain FOKN1 genome carried a gene encoding cyanate lyase, its protein expression was not detectable. The present study advances the understanding of the molecular mechanisms underlying thiocyanate degradation by the thiocyanate dehydrogenase of neutrophilic halophiles.

Genome-Based Metabolic Reconstruction of a Novel Uncultivated Freshwater Magnetotactic coccus "Ca. Magnetaquicoccus inordinatus" UR-1, and Proposal of a Candidate Family "Ca. Magnetaquicoccaceae"

Magnetotactic bacteria are widely represented microorganisms that have the ability to synthesize magnetosomes. The magnetotactic cocci of the order Magnetococcales are the most frequently identified, but their classification remains unclear due to the low number of cultivated representatives. This paper reports the analysis of an uncultivated magnetotactic coccus UR-1 collected from the Uda River (in eastern Siberia). Genome analyses of this bacterium and comparison to the available Magnetococcales genomes identified a novel species called "Ca. Magnetaquicoccus inordinatus," and a delineated candidate family "Ca. Magnetaquicoccaceae" within the order Magnetococcales is proposed. We used average amino acid identity values <55-56% and <64-65% as thresholds for the separation of families and genera, respectively, within the order Magnetococcales. Analyses of the genome sequence of UR-1 revealed a potential ability for a chemolithoautotrophic lifestyle, with the oxidation of a reduced sulfur compound and carbon assimilation by rTCA. A nearly complete magnetosome genome island, containing a set of mam and mms genes, was also identified. Further comparative analyses of the magnetosome genes showed vertical inheritance as well as horizontal gene transfer as the evolutionary drivers of magnetosome biomineralization genes in strains of the order Magnetococcales.

Sulfur metabolites in the pelagic ocean

Marine microorganisms play crucial roles in Earth's element cycles through the production and consumption of organic matter. One of the elements whose fate is governed by microbial activities is sulfur, an essential constituent of biomass and a crucial player in climate processes. With sulfur already being well studied in the ocean in its inorganic forms, organic sulfur compounds are emerging as important chemical links between marine phytoplankton and bacteria. The high concentration of inorganic sulfur in seawater, which can readily be reduced by phytoplankton, provides a freely available source of sulfur for biomolecule synthesis. Mechanisms such as exudation and cell lysis release these phytoplankton-derived sulfur metabolites into seawater, from which they are rapidly assimilated by marine bacteria and archaea. Energy-limited bacteria use scavenged sulfur metabolites as substrates or for the synthesis of vitamins, cofactors, signalling compounds and antibiotics. In this Review, we examine the current knowledge of sulfur metabolites released into and taken up from the marine dissolved organic matter pool by microorganisms, and the ecological links facilitated by their diversity in structures, oxidation states and chemistry.

Transcriptomic Analysis of Two Thioalkalivibrio Species Under Arsenite Stress Revealed a Potential Candidate Gene for an Alternative Arsenite Oxidation Pathway

The genus Thioalkalivibrio includes haloalkaliphilic chemolithoautotrophic sulfur-oxidizing bacteria isolated from various soda lakes worldwide. Some of these lakes possess in addition to their extreme haloalkaline environment also other harsh conditions, to which Thioalkalivibrio needs to adapt. An example is arsenic in soda lakes in eastern California, which is found there in concentrations up to 3000 μM. Arsenic is a widespread element that can be an environmental issue, as it is highly toxic to most organisms. However, resistance mechanisms in the form of detoxification are widespread and some prokaryotes can even use arsenic as an energy source. We first screened the genomes of 76 Thioalkalivibrio strains for the presence of known arsenic oxidoreductases and found 15 putative ArxA (arsenite oxidase) and two putative ArrA (arsenate reductase). Subsequently, we studied the resistance to arsenite in detail in Thioalkalivibrio jannaschii ALM2^T, and Thioalkalivibrio thiocyanoxidans ARh2^T by comparative genomics and by growing them at different arsenite concentrations followed by arsenic species and transcriptomic analysis. Tv. jannaschii ALM2^T, which has been isolated from Mono Lake, an arsenic-rich soda lake, could resist up to 5 mM arsenite, whereas Tv. thiocyanoxidans ARh2^T, which was isolated from a Kenyan soda lake, could only grow up to 0.1 mM arsenite. Interestingly, both species oxidized arsenite to arsenate under aerobic conditions, although Tv. thiocyanoxidans ARh2^T does not contain any known arsenite oxidases, and in Tv. jannaschii ALM2^T, only arxB2 was clearly upregulated. However, we found the expression of a SoeABC-like gene, which we assume might have been involved in arsenite oxidation. Other arsenite stress responses for both strains were the upregulation of the vitamin B₁₂ synthesis pathway, which can be linked to antioxidant activity, and the up- and downregulation of different DsrE/F-like genes whose roles are still unclear. Moreover, Tv. jannaschii ALM2^T induced the ars gene operon and the Pst system, and Tv. thiocanoxidans ARh2^T upregulated the sox and apr genes as well as different heat shock proteins. Our findings for Thioalkalivibrio confirm previously observed adaptations to arsenic, but also provide new insights into the arsenic stress response and the connection between the arsenic and the sulfur cycle.

Comparative Genomics of Thiohalobacter thiocyanaticus HRh1T and Guyparkeria sp. SCN-R1, Halophilic Chemolithoautotrophic Sulfur-Oxidizing Gammaproteobacteria Capable of Using Thiocyanate as Energy Source

The genomes of Thiohalobacter thiocyanaticus and Guyparkeria (formerly known as Halothiobacillus) sp. SCN-R1, two gammaproteobacterial halophilic sulfur-oxidizing bacteria (SOB) capable of thiocyanate oxidation via the "cyanate pathway", have been analyzed with a particular focus on their thiocyanate-oxidizing potential and sulfur oxidation pathways. Both genomes encode homologs of the enzyme thiocyanate dehydrogenase (TcDH) that oxidizes thiocyanate via the "cyanate pathway" in members of the haloalkaliphilic SOB of the genus Thioalkalivibrio. However, despite the presence of conservative motives indicative of TcDH, the putative TcDH of the halophilic SOB have a low overall amino acid similarity to the Thioalkalivibrio enzyme, and also the surrounding genes in the TcDH locus were different. In particular, an alternative copper transport system Cus is present instead of Cop and a putative zero-valent sulfur acceptor protein gene appears just before TcDH. Moreover, in contrast to the thiocyanate-oxidizing Thioalkalivibrio species, both genomes of the halophilic SOB contained a gene encoding the enzyme cyanate hydratase. The sulfur-oxidizing pathway in the genome of Thiohalobacter includes a Fcc type of sulfide dehydrogenase, a rDsr complex/AprAB/Sat for oxidation of zero-valent sulfur to sulfate, and an incomplete Sox pathway, lacking SoxCD. The sulfur oxidation pathway reconstructed from the genome of Guyparkeria sp. SCN-R1 was more similar to that of members of the Thiomicrospira-Hydrogenovibrio group, including a Fcc type of sulfide dehydrogenase and a complete Sox complex. One of the outstanding properties of Thiohalobacter is the presence of a Na+-dependent ATP synthase, which is rarely found in aerobic Prokaryotes.Overall, the results showed that, despite an obvious difference in the general sulfur-oxidation pathways, halophilic and haloalkaliphilic SOB belonging to different genera within the Gammaproteobacteria developed a similar unique thiocyanate-degrading mechanism based on the direct oxidative attack on the sulfane atom of thiocyanate.

Genomes of Neutrophilic Sulfur-Oxidizing Chemolithoautotrophs Representing 9 Proteobacterial Species From 8 Genera

Even in the current era of metagenomics, the interpretation of nucleotide sequence data is primarily dependent on knowledge obtained from a limited number of microbes isolated in pure culture. Thus, it is of fundamental importance to expand the variety of strains available in pure culture, to make reliable connections between physiological characteristics and genomic information. In this study, two sulfur oxidizers that potentially represent two novel species were isolated and characterized. They were subjected to whole-genome sequencing together with 7 neutrophilic and chemolithoautotrophic sulfur-oxidizing bacteria. The genes for sulfur oxidation in the obtained genomes were identified and compared with those of isolated sulfur oxidizers in the classes Betaproteobacteria and Gammaproteobacteria. Although the combinations of these genes in the respective genomes are diverse, typical combinations corresponding to three types of core sulfur oxidation pathways were identified. Each pathway involves one of three specific sets of proteins, SoxCD, DsrABEFHCMKJOP, and HdrCBAHypHdrCB. All three core pathways contain the SoxXYZAB proteins, and a cytoplasmic sulfite oxidase encoded by soeABC is a conserved component in the core pathways lacking SoxCD. Phylogenetically close organisms share same core sulfur oxidation pathway, but a notable exception was observed in the family ‘Sulfuricellaceae’. In this family, some strains have either core pathway involving DsrABEFHCMKJOP or HdrCBAHypHdrCB, while others have both pathways. A proteomics analysis showed that proteins constituting the core pathways were produced at high levels. While hypothesized function of HdrCBAHypHdrCB is similar to that of Dsr system, both sets of proteins were detected with high relative abundances in the proteome of a strain possessing genes for these proteins. In addition to the genes for sulfur oxidation, those for arsenic metabolism were searched for in the sequenced genomes. As a result, two strains belonging to the families Thiobacillaceae and Sterolibacteriaceae were observed to harbor genes encoding ArxAB, a type of arsenite oxidase that has been identified in a limited number of bacteria. These findings were made with the newly obtained genomes, including those from 6 genera from which no genome sequence of an isolated organism was previously available. These genomes will serve as valuable references to interpret nucleotide sequences.

Diversity and Distribution of Sulfur Oxidation-Related Genes in Thioalkalivibrio, a Genus of Chemolithoautotrophic and Haloalkaliphilic Sulfur-Oxidizing Bacteria

Soda lakes are saline alkaline lakes characterized by high concentrations of sodium carbonate/bicarbonate which lead to a stable elevated pH (>9), and moderate to extremely high salinity. Despite this combination of extreme conditions, biodiversity in soda lakes is high, and the presence of diverse microbial communities provides a driving force for highly active biogeochemical cycles. The sulfur cycle is one of the most important of these and bacterial sulfur oxidation is dominated by members of the obligately chemolithoautotrophic genus Thioalkalivibrio. Currently, 10 species have been described in this genus, but over one hundred isolates have been obtained from soda lake samples. The genomes of 75 strains were sequenced and annotated previously, and used in this study to provide a comprehensive picture of the diversity and distribution of genes related to dissimilatory sulfur metabolism in Thioalkalivibrio. Initially, all annotated genes in 75 Thioalkalivibrio genomes were placed in ortholog groups and filtered by bi-directional best BLAST analysis. Investigation of the ortholog groups containing genes related to sulfur oxidation showed that flavocytochrome c (fcc), the truncated sox system, and sulfite:quinone oxidoreductase (soe) are present in all strains, whereas dissimilatory sulfite reductase (dsr; which catalyzes the oxidation of elemental sulfur) was found in only six strains. The heterodisulfide reductase system (hdr), which is proposed to oxidize sulfur to sulfite in strains lacking both dsr and soxCD, was detected in 73 genomes. Hierarchical clustering of strains based on sulfur gene repertoire correlated closely with previous phylogenomic analysis. The phylogenetic analysis of several sulfur oxidation genes showed a complex evolutionary history. All in all, this study presents a comprehensive investigation of sulfur metabolism-related genes in cultivated Thioalkalivibrio strains and provides several avenues for future research.