Genomic Characterization and Environmental Distribution of a Thermophilic Anaerobe Dissulfurirhabdus thermomarina SH388T Involved in Disproportionation of Sulfur Compounds in Shallow Sea Hydrothermal Vents

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

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

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

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

A metagenomic insight into the microbiomes of geothermal springs in the Subantarctic Kerguelen Islands

The Kerguelen Islands, located in the southern part of the Indian Ocean, are very isolated geographically. The microbial diversity and communities present on the island, especially associated to geothermal springs, have never been analyzed with high-throughput sequencing methods. In this article, we performed the first metagenomics analysis of microorganisms present in Kerguelen hot springs. From four hot springs, we assembled metagenomes and recovered 42 metagenome-assembled genomes, mostly associated with new putative taxa based on phylogenomic analyses and overall genome relatedness indices. The 42 MAGs were studied in detail and showed putative affiliations to 13 new genomic species and 6 new genera of Bacteria or Archaea according to GTDB. Functional potential of MAGs suggests the presence of thermophiles and hyperthermophiles, as well as heterotrophs and primary producers possibly involved in the sulfur cycle, notably in the oxidation of sulfur compounds. This paper focused on only four of the dozens of hot springs in the Kerguelen Islands and should be considered as a preliminary study of the microorganisms inhabiting the hot springs of these isolated islands. These results show that more efforts should be made towards characterization of Kerguelen Islands ecosystems, as they represent a reservoir of unknown microbial lineages.

Genome analysis of a new sulphur disproportionating species Thermosulfurimonas strain F29 and comparative genomics of sulfur-disproportionating bacteria from marine hydrothermal vents

This paper reports on the genome analysis of strain F29 representing a new species of the genus Thermosulfurimonas. This strain, isolated from the Lucky Strike hydrothermal vent field on the Mid-Atlantic Ridge, is able to grow by disproportionation of S⁰ with CO₂ as a carbon source. Strain F29 possesses a genome of 2,345,565 bp, with a G+C content of 58.09%, and at least one plasmid. The genome analysis revealed complete sets of genes for CO₂ fixation via the Wood-Ljungdahl pathway, for sulphate-reduction and for hydrogen oxidation, suggesting the involvement of the strain into carbon, sulphur, and hydrogen cycles of deep-sea hydrothermal vents. Strain F29 genome encodes also several CRISPR sequences, suggesting that the strain may be subjected to viral attacks. Comparative genomics was carried out to decipher sulphur disproportionation pathways. Genomes of sulphur-disproportionating bacteria from marine hydrothermal vents were compared to the genomes of non-sulphur-disproportionating bacteria. This analysis revealed the ubiquitous presence in these genomes of a molybdopterin protein consisting of a large and a small subunit, and an associated chaperone. We hypothesize that these proteins may be involved in the process of elemental sulphur disproportionation.

Sulfur disproportionation is exergonic in the vicinity of marine hydrothermal vents

Sulfur is abundant in different oxidation states in hydrothermal ecosystems, where it plays a central role in microbial energy production. The contribution of microbially catalyzed disproportionation of elemental sulfur (S⁰ ) to the energy fluxes of this ecosystem is unknown. Indeed, within the current knowledge it is impossible to study this process in a global way due to the lack of specific genetic markers and because of the difficulties in unraveling the isotopic signals from the different reactions of the sulfur cycle. In this context, calculations of the Gibbs energy (∆Gr) of sulfur disproportionation can identify whether this process is thermodynamically favorable and provides sufficient energy yields for growth at the temperatures, pressures, and chemical compositions found in the various niches of the hydrothermal ecosystem. Herein, free energy yield calculations were performed using internally consistent thermodynamic properties and geochemical data from four different hydrothermal systems. These calculations showed that S⁰ -disproportionation is sufficiently exergonic to allow growth in most niches of the hydrothermal ecosystems, regardless of the geological and geochemical context, and depth; it is most favorable at elevated temperatures and alkaline pH, at low sulfide and sulfate concentrations, and in the presence of sulfide-chelating minerals, which are common in these environments. This article is protected by copyright. All rights reserved.

Genetic Potential of Dissulfurimicrobium hydrothermale, an Obligate Sulfur-Disproportionating Thermophilic Microorganism

The biochemical pathways of anaerobic sulfur disproportionation are only partially deciphered, and the mechanisms involved in the first step of S⁰-disproportionation remain unknown. Here, we present the results of sequencing and analysis of the complete genome of Dissulfurimicrobium hydrothermale strain Sh68^T, one of two strains isolated to date known to grow exclusively by anaerobic disproportionation of inorganic sulfur compounds. Dissulfurimicrobium hydrothermale Sh68^T is a motile, thermophilic, anaerobic, chemolithoautotrophic microorganism isolated from a hydrothermal pond at Uzon caldera, Kamchatka, Russia. It is able to produce energy and grow by disproportionation of elemental sulfur, sulfite and thiosulfate. Its genome consists of a circular chromosome of 2,025,450 base pairs, has a G + C content of 49.66% and a completion of 97.6%. Genomic data suggest that CO₂ assimilation is carried out by the Wood–Ljungdhal pathway and that central anabolism involves the gluconeogenesis pathway. The genome of strain Sh68^T encodes the complete gene set of the dissimilatory sulfate reduction pathway, some of which are likely to be involved in sulfur disproportionation. A short sequence protein of unknown function present in the genome of strain Sh68^T is conserved in the genomes of a large panel of other S⁰-disproportionating bacteria and was absent from the genomes of microorganisms incapable of elemental sulfur disproportionation. We propose that this protein may be involved in the first step of elemental sulfur disproportionation, as S⁰ is poorly soluble and unable to cross the cytoplasmic membrane in this form.

Enceladus as a Potential Niche for Methanogens and Estimation of Its Biomass

Enceladus is a potential target for future astrobiological missions. NASA's Cassini spacecraft demonstrated that the Saturnian moon harbors a salty ocean beneath its icy crust and the existence and analysis of the plume suggest water-rock reactions, consistent with the possible presence of hydrothermal vents. Particularly, the plume analysis revealed the presence of molecular hydrogen, which may be used as an energy source by microorganisms ( e.g., methanogens). This could support the possibility that populations of methanogens could establish in such environments if they exist on Enceladus. We took a macroscale approximation using ecological niche modeling to evaluate whether conditions suitable for methanogenic archaea on Earth are expected in Enceladus. In addition, we employed a new approach for computing the biomass using the Monod growth model. The response curves for the environmental variables performed well statistically, indicating that simple correlative models may be used to approximate large-scale distributions of these genera on Earth. We found that the potential hydrothermal conditions on Enceladus fit within the macroscale conditions identified as suitable for methanogens on Earth, and estimated a concentration of 1010-1011 cells/cm3.

Acidisoma silvae sp. nov. and Acidisomacellulosilytica sp. nov., Two Acidophilic Bacteria Isolated from Decaying Wood, Hydrolyzing Cellulose and Producing Poly-3-hydroxybutyrate

Two novel strains, HW T2.11^T and HW T5.17^T, were isolated from decaying wood (forest of Champenoux, France). Study of the 16S rRNA sequence similarity indicated that the novel strains belong to the genus Acidisoma. The sequence similarity of the 16S rRNA gene of HW T2.11^T with the corresponding sequences of A. tundrae and A. sibiricum was 97.30% and 97.25%, while for HW T5.17^T it was 96.85% and 97.14%, respectively. The DNA G+C contents of the strains were 62.32–62.50%. Cells were Gram-negative coccobacilli that had intracellular storage granules (poly-3-hydroxybutyrate (P3HB)) that confer resistance to environmental stress conditions. They were mesophilic and acidophilic organisms growing at 8–25 °C, at a pH of 2.0–6.5, and were capable of using a wide range of organic compounds and complex biopolymers such as starch, fucoidan, laminarin, pectin and cellulose, the latter two being involved in wood composition. The major cellular fatty acid was cyclo C_19:0ω8c and the major quinone was Q-10. Overall, genome relatedness indices between genomes of strains HW T2.11^T and HW T5.17^T (Orthologous Average Nucleotide Identity (OrthoANI) value = 83.73% and digital DNA-DNA hybridization score = 27.5%) confirmed that they belonged to two different species. Genetic predictions indicate that the cyclopropane fatty acid (CFA) pathway is present, conferring acid-resistance properties to the cells. The two novel strains might possess a class IV polyhydroxyalcanoate (PHA) synthase operon involved in the P3HB production pathway. Overall, the polyphasic taxonomic analysis shows that these two novel strains are adapted to harsh environments such as decaying wood where the organic matter is difficult to access, and can contribute to the degradation of dead wood. These strains represent novel species of the genus Acidisoma, for which the names Acidisoma silvae sp. nov. and Acidisomacellulosilytica sp. nov. are proposed. The type strains of Acidisoma silvae and Acidisomacellulosilytica are, respectively, HW T2.11^T (DSM 111006^T; UBOCC-M-3364^T) and HW T5.17^T (DSM 111007^T; UBOCC-M-3365^T).

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.

Community composition and functional prediction of prokaryotes associated with sympatric sponge species of southwestern Atlantic coast

Prokaryotes contribute to the health of marine sponges. However, there is lack of data on the assembly rules of sponge-associated prokaryotic communities, especially for those inhabiting biodiversity hotspots, such as ecoregions between tropical and warm temperate southwestern Atlantic waters. The sympatric species Aplysina caissara, Axinella corrugata, and Dragmacidon reticulatum were collected along with environmental samples from the north coast of São Paulo (Brazil). Overall, 64 prokaryotic phyla were detected; 51 were associated with sponge species, and the dominant were Proteobacteria, Bacteria (unclassified), Cyanobacteria, Crenarchaeota, and Chloroflexi. Around 64% and 89% of the unclassified operational taxonomical units (OTUs) associated with Brazilian sponge species showed a sequence similarity below 97%, with sequences in the Silva and NCBI Type Strain databases, respectively, indicating the presence of a large number of unidentified taxa. The prokaryotic communities were species-specific, ranging 56%-80% of the OTUs and distinct from the environmental samples. Fifty-four lineages were responsible for the differences detected among the categories. Functional prediction demonstrated that Ap. caissara was enriched for energy metabolism and biosynthesis of secondary metabolites, whereas D. reticulatum was enhanced for metabolism of terpenoids and polyketides, as well as xenobiotics' biodegradation and metabolism. This survey revealed a high level of novelty associated with Brazilian sponge species and that distinct members responsible from the differences among Brazilian sponge species could be correlated to the predicted functions.