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

Occurrence of Sphingomonas olei with elemental S oxidation capability in sodic soil: Potential role in sodicity reclamation and plant growth promotion

The success of the sodic soil reclamation using elemental S (S°) depends on the population of the native S° oxidizers. Augmenting the native flora of the sodic soils with effective S° oxidizers can enhance the success of the sodic soil reclamation. Present study reports for the first time the S° oxidation potential of the Sphingomonas olei strain 20UP7 isolated from sodic soils with pHs 9.8 and ECe 3.6 dS m-1. Inoculation with S. olei strain 20UP7 caused 13.0-24.2 % increase in S° oxidation in different sodic soils (pHs 9.1-10.5). It improved the concentration of the Ca2+, Mg2+, PO43- and declined the HCO3- and total alkalinity of the soil solution. This isolate also showed appreciable P and Zn solubilization, indole acetic acid, ammonia, and titratable acidity production in the growth media. It tended to the formation of biofilm around sulphur particles. The PCR amplification with gene-specific primers showed the occurrence of soxA, soxB, and soxY genes with a single band corresponding to length of 850, 460, and 360 base pairs, respectively. The integration of the S. olei strain 20UP7 with S° caused 21.7-25.4 % increase in the rice and wheat yield compared to the soil treated with S° alone. This study concludes that the S. olei, native to high saline-sodic soils can be utilized for improving the sodicity reclamation and plant growth promotion using elemental S based formulations.

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.

Controlling organic carbon increase in oxygenated marine sediment by using decarburization slag

The chemical oxygen demand (COD) in the Seto Inland Sea, Japan has increased in the recent decades due to the increase of bottom dissolved oxygen (DO) concentration which stimulated several autotrophic microorganisms, specially sulfur oxidizing bacteria (SOB). This increased SOB activity due to the oxygenation of the bottom sediment synthesized new organic matter (OM) which contributed dissolved organic carbon to the overlying seawater. This phenomenon further led to hypoxia in some subareas in the Seto Inland Sea. Higher pH or alkaline environment has been found to be an unfavorable condition for SOB. In this research, we used decarburization slag to elevate the pH of sediment to control the SOB activity and consequently reduce OM production in the sediment. Ignition loss of the surface sediment increased from 5.14% 6.38% after 21 days of incubation with aeration; whereas the sediment showed the less ignition loss of 5.71% after 21 days when the slag was incubated in the same experimental setup. Microbial community analysis showed less SOB activity in the slag added aerated sediment which accounts for the controlled increase of OM in the sediment. An additional experiment was conducted with magnesium oxide to confirm whether elevated pH can control the OM increase in sediment due to rising DO. All these results showed that decarburization slag can elevate the pH of the sediment to a certain level which can control the SOB activity followed by controlled increase of OM in the sediment. The findings may be beneficial to control accumulation of sedimentary OM which can act as a source of organic carbon in the overlying seawater.

A pan-genomic approach reveals novel Sulfurimonas clade in the ferruginous meromictic Lake Pavin

The permanently anoxic waters in meromictic lakes create suitable niches for the growth of bacteria using sulphur metabolisms like sulphur oxidation. In Lake Pavin, the anoxic water mass hosts an active cryptic sulphur cycle that interacts narrowly with iron cycling, however the metabolisms of the microorganisms involved are poorly known. Here we combined metagenomics, single-cell genomics, and pan-genomics to further expand our understanding of the bacteria and the corresponding metabolisms involved in sulphur oxidation in this ferruginous sulphide- and sulphate-poor meromictic lake. We highlighted two new species within the genus Sulfurimonas that belong to a novel clade of chemotrophic sulphur oxidisers exclusive to freshwaters. We moreover conclude that this genus holds a key-role not only in limiting sulphide accumulation in the upper part of the anoxic layer but also constraining carbon, phosphate and iron cycling.

Diversity at single nucleotide to pangenome scales among sulfur cycling bacteria in salt marshes

IMPORTANCE

Salt marshes are known for their significant carbon storage capacity, and sulfur cycling is closely linked with the ecosystem-scale carbon cycling in these ecosystems. Sulfate reducers are key for the decomposition of organic matter, and sulfur oxidizers remove toxic sulfide, supporting the productivity of marsh plants. To date, the complexity of coastal environments, heterogeneity of the rhizosphere, high microbial diversity, and uncultured majority hindered our understanding of the genomic diversity of sulfur-cycling microbes in salt marshes. Here, we use comparative genomics to overcome these challenges and provide an in-depth characterization of sulfur-cycling microbial diversity in salt marshes. We characterize communities across distinct sites and plant species and uncover extensive genomic diversity at the taxon level and specific genomic features present in MAGs affiliated with uncultivated sulfur-cycling lineages. Our work provides insights into the partnerships in salt marshes and a roadmap for multiscale analyses of diversity in complex biological systems.

Shotgun Metagenomics Reveals Impacts of Copper and Water Heater Anodes on Pathogens and Microbiomes in Hot Water Plumbing Systems

Hot water building plumbing systems are vulnerable to the proliferation of opportunistic pathogens (OPs), including Legionella pneumophila and Mycobacterium avium. Implementation of copper as a disinfectant could help reduce OPs, but a mechanistic understanding of the effects on the microbial community under real-world plumbing conditions is lacking. Here, we carried out a controlled pilot-scale study of hot water systems and applied shotgun metagenomic sequencing to examine the effects of copper dose (0-2 mg/L), orthophosphate corrosion control agent, and water heater anode materials (aluminum vs magnesium vs powered anode) on the bulk water and biofilm microbiome composition. Metagenomic analysis revealed that, even though a copper dose of 1.2 mg/L was required to reduce Legionella and Mycobacterium numbers, lower doses (e.g., ≤0.6 mg/L) measurably impacted the broader microbial community, indicating that the OP strains colonizing these systems were highly copper tolerant. Orthophosphate addition reduced bioavailability of copper, both to OPs and to the broader microbiome. Functional gene analysis indicated that both membrane damage and interruption of nucleic acid replication are likely at play in copper inactivation mechanisms. This study identifies key factors (e.g., orthophosphate, copper resistance, and anode materials) that can confound the efficacy of copper for controlling OPs in hot water plumbing.

A meta-analysis of tissue microbial biomarkers for recurrence and metastasis in multiple cancer types

Background. Local recurrence and distant metastasis are the main causes of death in patients with cancer. Only considering species abundance changes when identifying markers of recurrence and metastasis in patients hinders finding solutions.Hypothesis. Consideration of microbial abundance changes and microbial interactions facilitates the identification of microbial markers of tumour recurrence and metastasis.Aim. This study aims to simultaneously consider microbial abundance changes and microbial interactions to identify microbial markers of recurrence and metastasis in multiple cancer types.Method. One thousand one hundred and six non-RM (patients without recurrence and metastasis within 3 years after initial surgery) tissue samples and 912 RM (patients with recurrence or metastasis within 3 years after initial surgery) tissue samples representing 11 cancer types were collected from The Cancer Genome Atlas (TCGA).Results. Tumour tissue bacterial composition differed significantly among 11 cancers. Among them, the tissue microbiome of four cancers, head and neck squamous cell carcinoma (HNSC), lung squamous cell carcinoma (LUSC), stomach adenocarcinoma (STAD) and uterine corpus endometrial carcinoma (UCEC), showed relatively good performance in predicting recurrence and metastasis in patients, with areas under the receiver operating characteristic curve (AUCs) of 0.78, 0.74, 0.91 and 0.93, respectively. Considering both species abundance changes and microbial interactions for the four cancers, a combination of nine genera (Niastella, Schlesneria, Thioalkalivibrio, Phaeobacter, Sphaerotilus, Thiomonas, Lawsonia, Actinobacillus and Spiroplasma) performed best in predicting patient survival.Conclusion. Taken together, our results imply that comprehensive consideration of microbial abundance changes and microbial interactions is helpful for mining bacterial markers that carry prognostic information.

Distribution and Activity of Sulfur-Metabolizing Bacteria along the Temperature Gradient in Phototrophic Mats of the Chilean Hot Spring Porcelana

In terrestrial hot springs, some members of the microbial mat community utilize sulfur chemical species for reduction and oxidization metabolism. In this study, the diversity and activity of sulfur-metabolizing bacteria were evaluated along a temperature gradient (48-69 °C) in non-acidic phototrophic mats of the Porcelana hot spring (Northern Patagonia, Chile) using complementary meta-omic methodologies and specific amplification of the aprA (APS reductase) and soxB (thiosulfohydrolase) genes. Overall, the key players in sulfur metabolism varied mostly in abundance along the temperature gradient, which is relevant for evaluating the possible implications of microorganisms associated with sulfur cycling under the current global climate change scenario. Our results strongly suggest that sulfate reduction occurs throughout the whole temperature gradient, being supported by different taxa depending on temperature. Assimilative sulfate reduction is the most relevant pathway in terms of taxonomic abundance and activity, whereas the sulfur-oxidizing system (Sox) is likely to be more diverse at low rather than at high temperatures. Members of the phylum Chloroflexota showed higher sulfur cycle-related transcriptional activity at 66 °C, with a potential contribution to sulfate reduction and oxidation to thiosulfate. In contrast, at the lowest temperature (48 °C), Burkholderiales and Acetobacterales (both Pseudomonadota, also known as Proteobacteria) showed a higher contribution to dissimilative sulfate reduction/oxidation as well as to thiosulfate metabolism. Cyanobacteriota and Planctomycetota were especially active in assimilatory sulfate reduction. Analysis of the aprA and soxB genes pointed to members of the order Burkholderiales (Gammaproteobacteria) as the most dominant and active along the temperature gradient for these genes. Changes in the diversity and activity of different sulfur-metabolizing bacteria in photoautotrophic microbial mats along a temperature gradient revealed their important role in hot spring environments, especially the main primary producers (Chloroflexota/Cyanobacteriota) and diazotrophs (Cyanobacteriota), showing that carbon, nitrogen, and sulfur cycles are highly linked in these extreme systems.

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

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

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.

Simultaneous sulfide and methane oxidation by an extremophile

Hydrogen sulfide (H₂S) and methane (CH₄) are produced in anoxic environments through sulfate reduction and organic matter decomposition. Both gases diffuse upwards into oxic zones where aerobic methanotrophs mitigate CH₄ emissions by oxidizing this potent greenhouse gas. Although methanotrophs in myriad environments encounter toxic H₂S, it is virtually unknown how they are affected. Here, through extensive chemostat culturing we show that a single microorganism can oxidize CH₄ and H₂S simultaneously at equally high rates. By oxidizing H₂S to elemental sulfur, the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV alleviates the inhibitory effects of H₂S on methanotrophy. Strain SolV adapts to increasing H₂S by expressing a sulfide-insensitive ba₃-type terminal oxidase and grows as chemolithoautotroph using H₂S as sole energy source. Genomic surveys revealed putative sulfide-oxidizing enzymes in numerous methanotrophs, suggesting that H₂S oxidation is much more widespread in methanotrophs than previously assumed, enabling them to connect carbon and sulfur cycles in novel ways.

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.

Vertically stratified methane, nitrogen and sulphur cycling and coupling mechanisms in mangrove sediment microbiomes

BACKGROUND

Mangrove ecosystems are considered as hot spots of biogeochemical cycling, yet the diversity, function and coupling mechanism of microbially driven biogeochemical cycling along the sediment depth of mangrove wetlands remain elusive. Here we investigated the vertical profile of methane (CH₄), nitrogen (N) and sulphur (S) cycling genes/pathways and their potential coupling mechanisms using metagenome sequencing approaches.

RESULTS

Our results showed that the metabolic pathways involved in CH₄, N and S cycling were mainly shaped by pH and acid volatile sulphide (AVS) along a sediment depth, and AVS was a critical electron donor impacting mangrove sediment S oxidation and denitrification. Gene families involved in S oxidation and denitrification significantly (P < 0.05) decreased along the sediment depth and could be coupled by S-driven denitrifiers, such as Burkholderiaceae and Sulfurifustis in the surface sediment (0-15 cm). Interestingly, all S-driven denitrifier metagenome-assembled genomes (MAGs) appeared to be incomplete denitrifiers with nitrate/nitrite/nitric oxide reductases (Nar/Nir/Nor) but without nitrous oxide reductase (Nos), suggesting such sulphide-utilizing groups might be an important contributor to N₂O production in the surface mangrove sediment. Gene families involved in methanogenesis and S reduction significantly (P < 0.05) increased along the sediment depth. Based on both network and MAG analyses, sulphate-reducing bacteria (SRB) might develop syntrophic relationships with anaerobic CH₄ oxidizers (ANMEs) by direct electron transfer or zero-valent sulphur, which would pull forward the co-existence of methanogens and SRB in the middle and deep layer sediments.

CONCLUSIONS

In addition to offering a perspective on the vertical distribution of microbially driven CH₄, N and S cycling genes/pathways, this study emphasizes the important role of S-driven denitrifiers on N₂O emissions and various possible coupling mechanisms of ANMEs and SRB along the mangrove sediment depth. The exploration of potential coupling mechanisms provides novel insights into future synthetic microbial community construction and analysis. This study also has important implications for predicting ecosystem functions within the context of environmental and global change. Video Abstract.

Potential of biological sulphur recovery from thiosulphate by haloalkaliphilic Thioalkalivibrio denitrificans

The aim of this study was to investigate the potential for elemental sulphur recovery from sulphurous solutions under aerobic and anoxic conditions by haloalkalophilic Thioalkalivibrio denitrificans at 0.8-19.6 g S₂O₃^2--S L^-1 and 0.2-0.58 g NO₂ L^-1, respectively. The experiments were conducted as batch assays with haloalkaline (pH 10 and ≥ 14 g Na⁺ L^-1) thiosulphate solution. Aerobically, the highest biotransformation rate of thiosulphate obtained was 0.03 h^-1 at 8.5 g L S₂O₃^2--S. Based on Monod model, the maximum substrate utilisation rate (q_m) was 0.024 h^-1 with half saturation constant (K_s) 0.42 g S₂O₃^2--S L^-1 at initial [S₂O₃^2--S] of 14 g L^-1. S⁰ accumulated at [S₂O₃^2--S] ≥ 1.5 g L^-1 (10% yield at initial 9.5 g S₂O₃^2--S L^-1) and the highest S⁰ yield estimated with the model was 61% with initial [S₂O₃^2--S] of 16.5 g L^-1. Anoxically, the maximum nitrite removal rate based on Monod modelling was 0.011 h^-1 with K_s= 0.84 g NO₂^- L^-1. Aerobically and anoxically the maximum specific growth rates (µ_m) were 0.046 and 0.022 h^-1, respectively. In summary, high-rate aerobic biotransformation kinetics of thiosulphate were demonstrated, whereas the rates were slower and no S⁰ accumulated under anoxic conditions. Thus, future developments of biotechnical applications for the recovery of S⁰ from haloalkaline streams from the process industry should focus on aerobic treatment.HighlightsHaloalkaline S₂O₃^2- biotransformations kinetics by Thioalkalivibrio denitrificansAerobic thiosulphate-S bioconversion up to 0.024 h^-1 with K_s = 0.42 g S₂O₃^2--S L^-110% S⁰ yield with initial 9.5 g S₂O₃^2--S L^-1 in aerobic conditionAnoxic NO₂ removal up to 0.01 h^-1 with K_s = 0.84 g NO₂^- L^-1.

Drivers of Pb, Sb and As release from spent gunshot in wetlands: Enhancement by organic matter and native microorganisms

In many countries the use of lead-based ammunition is prevalent, and results in exposure and poisoning of waterfowl and other species of birds. In waterfowl hunting areas large quantities of spent shot may be deposited in wetland and terrestrial habitats. These pellets can undergo transformations, which are influenced by various abiotic and biotic factors. In addition to lead (Pb), other elements like antimony (Sb) and arsenic (As) can be leached from Pb shot into the environment. In vitro simulations that included organic matter and microorganisms were utilized to examine elemental leaching from gunshot. We found that leaching efficiency was the greatest in solutions rich in organic matter derived from artificial root exudates (2.69 % for Pb, 1.16 % for Sb, 1.83 % for As), while leaching efficiency was considerably lower in river water (0.04 %). In vitro simulations containing native microorganisms also exhibited greater leaching efficiency (0.49 % for Pb, 0.52 % for Sb, 1.32 % for As) than in ultrapure deionized water and river water. Surface alterations in gunshot included the formation of a weathering crust and secondary phases dominated by carbonates. Spent gunshot is a source of Pb, Sb and As in wetlands that could affect aquatic ecosystems.

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.

Unraveling the mechanism of sulfur nutrition in pigeonpea inoculated with sulfur-oxidizing bacteria

An investigation was carried out to understand the mechanism(s) involved in the uptake of sulfur (S) as sulfate in pigeonpea following single inoculation of two sulfur-oxidizing bacteria (SOB), Stenotrophomonas maltophilia and Stenotrophomonas pavanii in the treatments amended with either elemental sulfur (S0) or sulfate (S6). Colonization potential and biofilm formation were analyzed through confocal laser scanning microscope (CLSM) and scanning electron microscope (SEM). Furthermore, the effect of seed inoculation on root architecture, expression of genes involved in sulfur oxidation (sox) in bacterial inoculants, and genes involved in sulfate transport in pigeonpea (PpSULTR) were analyzed to correlate with the higher uptake of S in roots and shoots of pigeonpea. Both the SOB exhibited a good colonization potential and biofilm formation on the roots of pigeonpea. Among the 11 sox genes targeted in rhizosphere of pigeonpea, expression was achieved for seven genes, which showed 2-fold increase in treatments inoculated with S. maltophilia and amended with either S6 or S0. The inoculation of S. maltophilia and amendment of S0 led to increased expression of PpSULTR genes by several folds in roots. The inoculation of SOB had a significant influence on non-enzymatic (osmolytes like proline) and enzymatic (PAL, peroxidase, superoxide dismutase, and catalase) levels. The results revealed a significant increase in sulfur uptake in roots and shoots in treatment inoculated with S. maltophilia and amended with S6. The investigation showed that the SOB-mediated over-expression of PpSULTR genes in roots of pigeonpea and sox genes in the rhizosphere were acting synergistically in facilitating higher uptake and translocation of S in roots and shoots of pigeonpea plants.

HMS-S-S: a tool for the identification of sulfur metabolism-related genes and analysis of operon structures in genome and metagenome assemblies

Sulfur compounds are used in a variety of biological processes including respiration and photosynthesis. Sulfide and sulfur compounds of intermediary oxidation state can serve as electron donors for lithotrophic growth while sulfate, thiosulfate and sulfur are used as electron acceptors in anaerobic respiration. The biochemistry underlying the manifold transformations of inorganic sulfur compounds occurring in sulfur metabolizing prokaryotes is astonishingly complex and knowledge about it has immensely increased over the last years. The advent of next-generation sequencing approaches as well as the significant increase of data availability in public databases has driven focus of environmental microbiology to probing the metabolic capacity of microbial communities by analysis of this sequence data. To facilitate these analyses, we created HMS-S-S, a comprehensive equivalogous hidden Markov model (HMM)-supported tool. Protein sequences related to sulfur compound oxidation, reduction, transport and intracellular transfer are efficiently detected and related enzymes involved in dissimilatory sulfur oxidation as opposed to sulfur compound reduction can be confidently distinguished. HMM search results are coupled to corresponding genes, which allows analysis of co-occurrence, synteny and genomic neighborhood. The HMMs were validated on an annotated test dataset and by cross-validation. We also proved its performance by exploring meta-assembled genomes isolated from samples from environments with active sulfur cycling, including members of the cable bacteria, novel Acidobacteria and assemblies from a sulfur-rich glacier, and were able to replicate and extend previous reports.

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.

Phylogeny and Metabolic Potential of the Candidate Phylum SAR324

Simple Summary

SAR324, newly proposed as its own candidate phylum, is a diverse and globally abundant bacterial group living in a wide range of environments, from deep-sea hydrothermal vents and brine pools to the epipelagic regions of the global oceans and terrestrial aquifers. The different SAR324 clades harbor a diverse array of genes and pathways well adapted to their respective environments. This metabolic flexibility explains the ubiquitous presence and the importance of SAR324 in global biogeochemical cycles.

Abstract

The bacterial SAR324 cluster is ubiquitous and abundant in the ocean, especially around hydrothermal vents and in the deep sea, where it can account for up to 30% of the whole bacterial community. According to a new taxonomy generated using multiple universal protein-coding genes (instead of the previously used 16S rRNA single gene marker), the former Deltaproteobacteria cluster SAR324 has been classified since 2018 as its own phylum. Yet, very little is known about its phylogeny and metabolic potential. We downloaded all publicly available SAR324 genomes (65) from all natural environments and reconstructed 18 new genomes using publicly available oceanic metagenomic data and unpublished data from the waters underneath the Ross Ice Shelf. We calculated a global SAR324 phylogenetic tree and identified six clusters (namely 1A, 1B, 2A, 2B, 2C and 2D) within this clade. Genome annotation and metatranscriptome read mapping showed that SAR324 clades possess a flexible array of genes suited for survival in various environments. Clades 2A and 2C are mostly present in the surface mesopelagic layers of global oceans, while clade 2D dominates in deeper regions. Our results show that SAR324 has a very versatile and broad metabolic potential, including many heterotrophic, but also autotrophic pathways. While one surface water associated clade (2A) seems to use proteorhodopsin to gain energy from solar radiation, some deep-sea genomes from clade 2D contain the complete Calvin–Benson–Bassham cycle gene repertoire to fix carbon. This, in addition to a variety of other genes and pathways for both oxic (e.g., dimethylsulfoniopropionate degradation) and anoxic (e.g., dissimilatory sulfate reduction, anaerobic benzoate degradation) conditions, can help explain the ubiquitous presence of SAR324 in aquatic habitats.

Comparative analysis of microbial communities from different full-scale haloalkaline biodesulfurization systems

Abstract

In biodesulfurization (BD) at haloalkaline and dO₂-limited conditions, sulfide-oxidizing bacteria (SOB) effectively convert sulfide into elemental sulfur that can be used in agriculture as a fertilizer and fungicide. Here we show which bacteria are present in this biotechnological process. 16S rRNA gene amplicon sequencing of biomass from ten reactors sampled in 2018 indicated the presence of 444 bacterial Amplicon Sequence Variants (ASVs). A core microbiome represented by 30 ASVs was found in all ten reactors, with Thioalkalivibrio sulfidiphilus as the most dominant species. The majority of these ASVs are phylogenetically related to bacteria previously identified in haloalkaline BD processes and in natural haloalkaline ecosystems. The source and composition of the feed gas had a great impact on the microbial community composition followed by alkalinity, sulfate, and thiosulfate concentrations. The halophilic SOB of the genus Guyparkeria (formerly known as Halothiobacillus) and heterotrophic SOB of the genus Halomonas were identified as potential indicator organisms of sulfate and thiosulfate accumulation in the BD process.

Key points

• Biodesulfurization (BD) reactors share a core microbiome

• The source and composition of the feed gas affects the microbial composition in the BD reactors

• Guyparkeria and Halomonas indicate high concentrations of sulfate and thiosulfate in the BD process

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-022-11771-y.

Complete Genome Sequence of Halomonas sp. Strain FeN2, a Novel Cathode-Oxidizing Bacterium Isolated from Catalina Harbor Sediments

We report the complete, closed, circular genome of Halomonas sp. strain FeN2, a metabolically versatile electrotroph that was isolated from Catalina Harbor sediments. The 4.8-Mb genome contains 4,286 protein-coding genes and has complete glycolytic, tricarboxylic acid, glyoxylate, pentose phosphate, and reductive pentose phosphate pathways. FeN2 also contains genes for aerobic and anaerobic (denitrification) respiration.

Presence of Fe(II) and nitrate shapes aquifer-originating communities leading to an autotrophic enrichment dominated by an Fe(II)-oxidizing Gallionellaceae sp

Autotrophic nitrate reduction coupled to Fe(II) oxidation is an important nitrate removal process in anoxic aquifers. However, it remains unknown how changes of O2 and carbon availability influence the community structure of nitrate-reducing Fe(II)-oxidizing (NRFeOx) microbial assemblages and what the genomic traits of these NRFeOx key players are. We compared three metabolically distinct denitrifying assemblages, supplemented with acetate, acetate/Fe(II) or Fe(II), enriched from an organic-poor, pyrite-rich aquifer. The presence of Fe(II) promoted the growth of denitrifying Burkholderiaceae spp. and an unclassified Gallionellaceae sp. This Gallionellaceae sp. was related to microaerophilic Fe(II) oxidizers; however, it did not grow under microoxic conditions. Furthermore, we explored a metagenome and 15 metagenome-assembled genomes from an aquifer-originating, autotrophic NRFeOx culture. The dominant Gallionellaceae sp. revealed the potential to oxidize Fe(II) (e.g. cyc2), fix CO2 (e.g. rbcL) and perform near-complete denitrification leading to N2O formation (e.g. narGHJI,nirK/S and norBC). In addition, Curvibacter spp.,Methyloversatilis sp. and Thermomonas spp. were identified as novel putative NRFeOx taxa. Our findings provide first insights into the genetic traits of the so far only known autotrophic NRFeOx culture originating from an organic-poor aquifer, providing the genomic basis to study mechanisms of nitrate removal in organic-poor subsurface ecosystems.

Highly integrated adaptive mechanisms in Spiribacter halalkaliphilus, a bacterium abundant in Chinese soda-saline lakes

Soda-saline lakes are polyextreme environments inhabited by many haloalkaliphiles, including one of the most abundant Spiribacter species. However, its mechanisms of adaptation are not ecophysiologically characterized. Based on a large-scale cultivation strategy, we obtained a representative isolate of this Spiribacter species whose relative abundance was the highest (up to 15.63%) in a wide range of salinities in the soda-saline lakes in Inner Mongolia, China. This species is a chemoorganoheterotrophic haloalkaliphile. It has a small and streamlined genome and utilizes a wide variety of compatible solutes to resist osmotic pressure and multiple monovalent cation/proton antiporters for pH homeostasis. In addition to growth enhancement by light under microaerobic conditions, cell growth, organic substrate consumption and polyhydroxybutyrate biosynthesis were also improved by inorganic sulfide. Both quantitative RT-PCR and enzymatic assays verified that sulfide:quinone oxidoreductase was upregulated during this process. Metatranscriptomic analysis indicated that all genes related to environmental adaptation were transcribed in natural environments. Overall, this study has identified a novel abundant haloalkaliphile with multiple and highly integrated adaptive strategies and found that inorganic sulfide was able to improve the adaptation of a heterotroph to polyextreme environments.

Catalytic Properties of Flavocytochrome c Sulfide Dehydrogenase from Haloalkaliphilic Bacterium Thioalkalivibrio paradoxus

Flavocytochrome c sulfide dehydrogenase (FCC) is one of the central enzymes of the respiratory chain in sulfur-oxidizing bacteria. FCC catalyzes oxidation of sulfide and polysulfide ions to elemental sulfur accompanied by electron transfer to cytochrome c. The catalytically active form of the enzyme is a non-covalently linked heterodimer composed of flavin- and heme-binding subunits. The Thioalkalivibrio paradoxus ARh1 genome contains five copies of genes encoding homologous FCCs with an amino acid sequence identity from 36 to 54%. When growing on thiocyanate or thiosulfate as the main energy source, the bacterium synthesizes products of different copies of FCC genes. In this work, we isolated and characterized FCC synthesized during the growth of Tv. paradoxus on thiocyanate. FCC was shown to oxidize exclusively sulfide but not other reduced sulfur compounds, such as thiosulfate, sulfite, tetrathionate, and sulfur, and it also does not catalyze the reverse reaction of sulfur reduction to sulfide. Kinetic parameters of the sulfide oxidation reaction are characterized.

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.

Autotrophic denitrification in constructed wetlands: Achievements and challenges

The use of constructed wetlands for wastewater treatment is rapidly increasing worldwide due to their advantages of low operating and maintenance costs. Denitrification in constructed wetlands is dependent on the presence of organic carbon sources, and the shortage of organic carbon is the primary hurdle for nitrate removal. Therefore, the use of inorganic electronic donors has emerged as an alternative. This paper provides a comprehensive review of nitrate removal pathways using various inorganic electron donors and the performance and development of autotrophic denitrification in constructed wetlands. The main environmental parameters and operating conditions for nitrate removal in wetlands are discussed, and the challenges currently faced in the application of enhanced autotrophic denitrification wetlands are emphasized. Overall, this review illustrates the need for a deep understanding of the complex interrelationships among environmental and operational parameters and wetland substrates for improving the wastewater treatment performance of constructed wetlands.

Proteome-Scale Detection of Differential Conservation Patterns at Protein and Subprotein Levels with BLUR

In the multiomics era, comparative genomics studies based on gene repertoire comparison are increasingly used to investigate evolutionary histories of species, to study genotype–phenotype relations, species adaptation to various environments, or to predict gene function using phylogenetic profiling. However, comparisons of orthologs have highlighted the prevalence of sequence plasticity among species, showing the benefits of combining protein and subprotein levels of analysis to allow for a more comprehensive study of genotype/phenotype correlations. In this article, we introduce a new approach called BLUR (BLAST Unexpected Ranking), capable of detecting genotype divergence or specialization between two related clades at different levels: gain/loss of proteins but also of subprotein regions. These regions can correspond to known domains, uncharacterized regions, or even small motifs. Our method was created to allow two types of research strategies: 1) the comparison of two groups of species with no previous knowledge, with the aim of predicting phenotype differences or specializations between close species or 2) the study of specific phenotypes by comparing species that present the phenotype of interest with species that do not. We designed a website to facilitate the use of BLUR with a possibility of in-depth analysis of the results with various tools, such as functional enrichments, protein–protein interaction networks, and multiple sequence alignments. We applied our method to the study of two different biological pathways and to the comparison of several groups of close species, all with very promising results. BLUR is freely available at http://lbgi.fr/blur/.

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.

A New Thioalkalivibrio sp. Strain Isolated from Petroleum-Contaminated Brackish Estuary Sediments: A New Candidate for Bio-Based Application for Sulfide Oxidation in Halo-Alkaline Conditions

A new halo-alkaline sulfur-oxidising bacterial strain was isolated from brackish estuary sediments contaminated by total petroleum hydrocarbon. The isolate was classified as a new strain of Thioalkalivibrio sulfidiphilus sp., showing a higher capability of adaptation to pH and a higher optimal sodium concentration for growth, when compared to Thioalkalivibrio sulfidiphilus sp. HL-EbGr7, type strain of the species. The strain was capable to grow in saline concentrations up to 1.5 M Na+ and pH up to 10. The genome of the new isolate was sequenced and annotated. The comparison with the genome of Thioalkalivibrio sulfidiphilus sp. HL-EbGr7 showed a duplication of an operon encoding for a putative primary sodium extruding pump and the presence of a sodium/proton antiporter with optimal efficiency at halo-alkaline conditions. The new strain was able to oxidize sulfide at halo-alkaline conditions at the rate of 1 mmol/mg-N/h, suitable for industrial applications dedicated to the recovery of alkaline scrubber for H2S emission absorption and abatement.

Trinuclear copper biocatalytic center forms an active site of thiocyanate dehydrogenase

Biocatalytic copper centers are generally involved in the activation and reduction of dioxygen, with only few exceptions known. Here we report the discovery and characterization of a previously undescribed copper center that forms the active site of a copper-containing enzyme thiocyanate dehydrogenase (suggested EC 1.8.2.7) that was purified from the haloalkaliphilic sulfur-oxidizing bacterium of the genus Thioalkalivibrio ubiquitous in saline alkaline soda lakes. The copper cluster is formed by three copper ions located at the corners of a near-isosceles triangle and facilitates a direct thiocyanate conversion into cyanate, elemental sulfur, and two reducing equivalents without involvement of molecular oxygen. A molecular mechanism of catalysis is suggested based on high-resolution three-dimensional structures, electron paramagnetic resonance (EPR) spectroscopy, quantum mechanics/molecular mechanics (QM/MM) simulations, kinetic studies, and the results of site-directed mutagenesis.

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.

The functional diversity of the prokaryotic sulfur carrier protein TusA

Persulfide groups participate in a wide array of biochemical pathways and are chemically very versatile. The TusA protein has been identified as a central element supplying and transferring sulfur as persulfide to a number of important biosynthetic pathways, like molybdenum cofactor biosynthesis or thiomodifications in nucleosides of tRNAs. In recent years, it has furthermore become obvious that this protein is indispensable for the oxidation of sulfur compounds in the cytoplasm. Phylogenetic analyses revealed that different TusA protein variants exists in certain organisms, that have evolved to pursue specific roles in cellular pathways. The specific TusA-like proteins thereby cannot replace each other in their specific roles and are rather specific to one sulfur transfer pathway or shared between two pathways. While certain bacteria like Escherichia coli contain several copies of TusA-like proteins, in other bacteria like Allochromatium vinosum a single copy of TusA is present with an essential role for this organism. Here, we give an overview on the multiple roles of the various TusA-like proteins in sulfur transfer pathways in different organisms to shed light on the remaining mysteries of this versatile protein.