Two pathways for thiosulfate oxidation in the alphaproteobacterial chemolithotroph Paracoccus thiocyanatus SST

Sodium thiosulfate: A donor or carrier signaling molecule for hydrogen sulfide?

Sodium thiosulfate has been used for decades in the treatment of calciphylaxis and cyanide detoxification, and has recently shown initial therapeutic promise in critical diseases such as neuronal ischemia, diabetes mellitus, heart failure and acute lung injury. However, the precise mechanism of sodium thiosulfate remains incompletely defined and sometimes contradictory. Although sodium thiosulfate has been widely accepted as a donor of hydrogen sulfide (H2S), emerging findings suggest that it is the executive signaling molecule for H2S and that its effects may not be dependent on H2S. This article presents an overview of the current understanding of sodium thiosulfate, including its synthesis, biological characteristics, and clinical applications of sodium thiosulfate, as well as the underlying mechanisms in vivo. We also discussed the interplay of sodium thiosulfate and H2S. Our review highlights sodium thiosulfate as a key player in sulfide signaling with the broad clinical potential for the future.

First insight into the natural biodegradation of cyanide in a gold tailings environment enriched in cyanide compounds

The disposal of mining wastes that contain cyanide are dumped in tailings from gold extraction is a public concern in mining countries such as South Africa. Many studies have shown the potential of microorganisms to degrade cyanide. However, no in-situ exploration, in tailings contaminated with cyanide, of the capability of indigenous microorganisms to act as a natural barrier for cyanide attenuation has been performed. Here we aim to combine geochemical and metagenomics techniques to reveal the genomic machinery of indigenous bacteria to degrade cyanide in gold tailings. Indigenous bacteria (i.e., Alicyclobacillus, Sulfobacillus, Acinetobacter, Achromobacter, and among others) pose the genomic machinery to trigger hydrolytic cyanide degradation using enzymes such as nitrilase, nitrile hydratase (Nhase) and thiocyanate. It seems that the lack of nitrogen sources induces the use of cyanide, which would contribute to its natural attenuation in the gold tailings. Therefore, the bacteria identified could represent the first barrier for the detoxification and degradation of cyanide in the outermost layer of the tailings.

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.

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.

Copiotrophy in a Marine-Biofilm-Derived Roseobacteraceae Bacterium Can Be Supported by Amino Acid Metabolism and Thiosulfate Oxidation

Copiotrophic bacteria that respond rapidly to nutrient availability, particularly high concentrations of carbon sources, play indispensable roles in marine carbon cycling. However, the molecular and metabolic mechanisms governing their response to carbon concentration gradients are not well understood. Here, we focused on a new member of the family Roseobacteraceae isolated from coastal marine biofilms and explored the growth strategy at different carbon concentrations. When cultured in a carbon-rich medium, the bacterium grew to significantly higher cell densities than Ruegeria pomeroyi DSS-3, although there was no difference when cultured in media with reduced carbon. Genomic analysis showed that the bacterium utilized various pathways involved in biofilm formation, amino acid metabolism, and energy production via the oxidation of inorganic sulfur compounds. Transcriptomic analysis indicated that 28.4% of genes were regulated by carbon concentration, with increased carbon concentration inducing the expression of key enzymes in the EMP, ED, PP, and TCA cycles, genes responsible for the transformation of amino acids into TCA intermediates, as well as the sox genes for thiosulfate oxidation. Metabolomics showed that amino acid metabolism was enhanced and preferred in the presence of a high carbon concentration. Mutation of the sox genes decreased cell proton motive force when grown with amino acids and thiosulfate. In conclusion, we propose that copiotrophy in this Roseobacteraceae bacterium can be supported by amino acid metabolism and thiosulfate oxidation.

Microbes-mediated sulphur cycling in soil: Impact on soil fertility, crop production and environmental sustainability

Reduction in soil fertility and depletion of natural resources due to current intensive agricultural practices along with climate changes are the major constraints for crop productivity and global food security. Diverse microbial populations' inhabiting the soil and rhizosphere participate in biogeochemical cycling of nutrients and thereby, improve soil fertility and plant health, and reduce the adverse impact of synthetic fertilizers on the environment. Sulphur is 4th most common crucial macronutrient required by all organisms including plants, animals, humans and microorganisms. Effective strategies are required to enhance sulphur content in crops for minimizing adverse effects of sulphur deficiency on plants and humans. Various microorganisms are involved in sulphur cycling in soil through oxidation, reduction, mineralization, and immobilization, and volatalization processes of diverse sulphur compounds. Some microorganisms possess the unique ability to oxidize sulphur compounds into plant utilizable sulphate (SO₄^2-) form. Considering the importance of sulphur as a nutrient for crops, many bacteria and fungi involved in sulphur cycling have been characterized from soil and rhizosphere. Some of these microbes have been found to positively affect plant growth and crop yield through multiple mechanisms including the enhanced mobilization of nutrients in soils (i.e., sulphate, phosphorus and nitrogen), production of growth-promoting hormones, inhibition of phytopathogens, protection against oxidative damage and mitigation of abiotic stresses. Application of these beneficial microbes as biofertilizers may reduce the conventional fertilizer application in soils. However, large-scale, well-designed, and long-term field trials are necessary to recommend the use of these microbes for increasing nutrient availability for growth and yield of crop plants. This review discusses the current knowledge regarding sulphur deficiency symptoms in plants, biogeochemical cycling of sulphur and inoculation effects of sulphur oxidizing microbes in improving plant biomass and crop yield in different crops.

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.

Metagenomic insights into comparative study of nitrogen metabolic potential and microbial community between primitive and urban river sediments

As a result of anthropogenic pollution, the nitrogen nutrients load in urban rivers has increased, potentially raising the risk of river eutrophication. Here, we studied how anthropogenic impacts alter nitrogen metabolism in river sediments by comparing the metagenomic function of microbial communities between relatively primitive and human-disturbed sediments. The contents of organic matter (OM), total nitrogen (TN), NO₃^--N and NO₂^--N were higher in primitive site than in polluted sites, which might be due to vegetation density, sediment type, hydrology, etc. Whereas, NH₄⁺-N content was higher in midstream and downstream, indicating that nitrogen loading increased in the anthropogenic regions and subsequently leading higher NH₄⁺-N. Hierarchical cluster analyses revealed significant changes in the community structure and functional potential between the primitive and human-affected sites. Metagenomic analysis demonstrated that Demequina, Streptomyces, Rubrobacter and Dechloromonas were the predominant denitrifiers. Ardenticatena and Dechloromonas species were the most important contributors to dissimilatory nitrate reduction. Furthermore, anthropogenic pollution significantly increased their abundance, and resulting in a decrease in NO₃^-, NO₂^--N and an increase in NH₄⁺-N contents. Additionally, the SOX metabolism of Dechloromonas and Sulfuritalea may involve in the sulfur-dependent autotrophic denitrification process by coupling the conversion of thiosulfate to sulfate with the reduction of NO₃^--N to N₂. From pristine to anthropogenic pollution sediments, the major nitrifying bacteria harboring Hao transitioned from Nitrospira to Nitrosomonas. This study sheds light on the consequences of anthropogenic activities on nitrogen metabolism in river sediments, allowing for better management of nitrogen pollution and eutrophication in river.

Heterotrophic Sulfur Oxidation of Halomonas titanicae SOB56 and Its Habitat Adaptation to the Hydrothermal Environment

Halomonas bacteria are ubiquitous in global marine environments, however, their sulfur-oxidizing abilities and survival adaptations in hydrothermal environments are not well understood. In this study, we characterized the sulfur oxidation ability and metabolic mechanisms of Halomonas titanicae SOB56, which was isolated from the sediment of the Tangyin hydrothermal field in the Southern Okinawa Trough. Physiological characterizations showed that it is a heterotrophic sulfur-oxidizing bacterium that can oxidize thiosulfate to tetrathionate, with the Na₂S₂O₃ degradation reaching 94.86%. Two potential thiosulfate dehydrogenase-related genes, tsdA and tsdB, were identified as encoding key catalytic enzymes, and their expression levels in strain SOB56 were significantly upregulated. Nine of fifteen examined Halomonas genomes possess TsdA- and TsdB-homologous proteins, whose amino acid sequences have two typical Cys-X2-Cys-His heme-binding regions. Moreover, the thiosulfate oxidation process in H. titanicae SOB56 might be regulated by quorum sensing, and autoinducer-2 synthesis protein LuxS was identified in its genome. Regarding the mechanisms underlying adaptation to hydrothermal environment, strain SOB56 was capable of forming biofilms and producing EPS. In addition, genes related to complete flagellum assembly system, various signal transduction histidine kinases, heavy metal transporters, anaerobic respiration, and variable osmotic stress regulation were also identified. Our results shed light on the potential functions of heterotrophic Halomonas bacteria in hydrothermal sulfur cycle and revealed possible adaptations for living at deep-sea hydrothermal fields by H. titanicae SOB56.

Dissimilatory sulfate reduction in the cake layer of a full-scale anaerobic dynamic membrane bioreactor for hotel laundry wastewater treatment: Bacterial community and functional genes

Dissimilatory sulfate reduction (DSR) in cake layer of full-scale anaerobic dynamic membrane bioreactor for treating hotel laundry wastewater was studied. Change (Δ) of sulfate concentration (ΔSO₄^2-) was positively correlated to dynamic cake layer (DCL) development, while ΔS^2- was negatively correlated. ΔSO₃^2- and ΔS_{organic sulfur} remained around 1.5-2.5 and 1.2-2.3 mg-S/L, respectively. Thus, DSR was the predominant sulfate reduction process in DCL. 33 binned genomes from DCL microbiome samples possessed one or more DSR functional genes. But only four binned genomes possess all functional genes, and thus can achieve complete DSR. However, no significant variations of these DSR bacteria was obseared during DCL development. Metagenomic analysis predicted that sulfate reduction in DCL was mainly carried out by collaborations between bacteria with incomplete DSR pathways. Among which, sulfite → sulfide by dissimilatory-sulfite-reductase expression bacteria was the key process. Overall results suggested that controlling dissimilatory-sulfite-reductase activities could prevent sulfide buildup in the effluent.

Metabolism of the Genus Guyparkeria Revealed by Pangenome Analysis

Halophilic sulfur-oxidizing bacteria belonging to the genus Guyparkeria occur at both marine and terrestrial habitats. Common physiological characteristics displayed by Guyparkeria isolates have not yet been linked to the metabolic potential encoded in their genetic inventory. To provide a genetic basis for understanding the metabolism of Guyparkeria, nine genomes were compared to reveal the metabolic capabilities and adaptations. A detailed account is given on Guyparkeria’s ability to assimilate carbon by fixation, to oxidize reduced sulfur, to oxidize thiocyanate, and to cope with salinity stress.

Microbial diversity in a military impacted lagoon (Vieques, Puerto Rico) and description of "Candidatus Biekeibacterium resiliens" gen. nov., sp. nov. comprising a new bacterial family

The Anones Lagoon, located in the Island Municipality of Vieques, Puerto Rico (PR), received extensive bombing by the US Navy during military exercises for decades until 2003 when military activities ceased. Here, we employed shotgun metagenomic sequencing to investigate how microbial communities responded to pollution by heavy metals and explosives at this lagoon. Sediment samples (0-5 cm) from Anones were collected in 2005 and 2014 and compared to samples from two reference lagoons, i.e., Guaniquilla, Cabo Rojo (a natural reserve) and Condado, San Juan (PR's capital city). Consistent with low anthropogenic inputs, Guaniquilla exhibited the highest degree of diversity with a lower frequency of genes related to xenobiotics metabolism between the three lagoons. Notably, a clear shift was observed in Anones, with Euryarchaeota becoming enriched (9% of total) and a concomitant increase in community diversity, by about one order of magnitude, after almost 10 years without bombing activities. In contrast, genes associated with explosives biodegradation and heavy metal transformation significantly decreased in abundance in Anones 2014 (by 91.5%). Five unique metagenome-assembled genomes (MAGs) were recovered from the Anones 2005 sample that encoded genetic determinants implicated in biodegradation of contaminants, and we propose to name one of them as "Candidatus Biekeibacterium resiliens" gen. nov., sp. nov. within the Gammaproteobacteria class. Collectively, these results provide new insights into the natural attenuation of explosive contaminants by the benthic microbial communities of the Anones lagoon and provide a reference point for assessing other similarly impacted sites and associated bioremediation efforts.

Thiosulfate oxidation in sulfur-reducing Shewanella oneidensis and its unexpected influences on the cytochrome c content

Thiosulfate, an important form of sulfur compounds, can serve as both electron donor and acceptor in various microorganisms. In Shewanella oneidensis, a bacterium renowned for respiratory versatility, thiosulfate reduction has long been recognized but whether it can catalyse thiosulfate oxidation remains elusive. In this study, we discovered that S. oneidensis is capable of thiosulfate oxidation, a process specifically catalysed by two periplasmic cytochrome c (cyt c) proteins, TsdA and TsdB, which act as the catalytic subunit and the electron transfer subunit respectively. In the presence of oxygen, oxidation of thiosulfate has priority over reduction. Intriguingly, thiosulfate oxidation negatively regulates the cyt c content in S. oneidensis cells, largely by reducing intracellular levels of cAMP, which as the cofactor modulates activity of global regulator Crp required for transcription of many cyt c genes. This unexpected finding provides an additional dimension to interplays between the respiration regulator and the respiratory pathways in S. oneidensis. Moreover, the data presented here identified S. oneidensis as the first bacterium known to date owning both functional thiosulfate reductase and dehydrogenase, and importantly, genomics analyses suggested that the number of bacterial species possessing this feature is rather limited.

34S enrichment as a signature of thiosulfate oxidation in the "Proteobacteria"

Kinetics of thiosulfate oxidation, product and intermediate formation, and 34S fractionation, were studied for the members of Alphaproteobacteria Paracoccus sp. SMMA5 and Mesorhizobium thiogangeticum SJTT, the Betaproteobacteria member Pusillimonas ginsengisoli SBO3, and the Acidithiobacillia member Thermithiobacillus sp. SMMA2, during chemolithoautotrophic growth in minimal salts media supplemented with 20 mM thiosulfate. The two Alphaproteobacteria oxidized thiosulfate directly to sulfate, progressively enriching the end-product with 34S; Δ34Sthiosulfate-sulfate values recorded at the end of the two processes (when no thiosulfate was oxidized any further) were -2.9‰ and -3.5‰, respectively. Pusillimonas ginsengisoli SBO3 and Thermithiobacillus sp. SMMA2, on the other hand, oxidized thiosulfate to sulfate via tetrathionate intermediate formation, with progressive 34S enrichment in the end-product sulfate throughout the incubation period; Δ34Sthiosulfate-sulfate, at the end of the two processes (when no further oxidation took place), reached -3.5‰ and -3.8‰, respectively. Based on similar 34S fractionation patterns recorded previously during thiosulfate oxidation by strains of Paracoccus pantotrophus, Advenella kashmirensis and Hydrogenovibrio crunogenus, it was concluded that progressive reverse fractionation, enriching the end-product sulfate with 34S, could be a characteristic signature of bacterial thiosulfate oxidation.

The Mechanisms of Thiosulfate Toxicity against Saccharomyces cerevisiae

Elemental sulfur and sulfite have been used to inhibit the growth of yeasts, but thiosulfate has not been reported to be toxic to yeasts. We observed that thiosulfate was more inhibitory than sulfite to Saccharomyces cerevisiae growing in a common yeast medium. At pH < 4, thiosulfate was a source of elemental sulfur and sulfurous acid, and both were highly toxic to the yeast. At pH 6, thiosulfate directly inhibited the electron transport chain in yeast mitochondria, leading to reductions in oxygen consumption, mitochondrial membrane potential and cellular ATP. Although thiosulfate was converted to sulfite and H₂S by the mitochondrial rhodanese Rdl1, its toxicity was not due to H₂S as the rdl1-deletion mutant that produced significantly less H₂S was more sensitive to thiosulfate than the wild type. Evidence suggests that thiosulfate inhibits cytochrome c oxidase of the electron transport chain in yeast mitochondria. Thus, thiosulfate is a potential agent against yeasts.

Structural-genetic insight and optimization of protease production from a novel strain of Aeromonas veronii CMF, a gut isolate of Chrysomya megacephala

Structural-genetic characterization of protease producing genes and enzymes from microbial sources are seldom appreciated despite having its substantial utilization in protein engineering or genetic manipulation for biotechnological applications. Aeromonas veronii CMF, a mesophilic bacterium isolated from the gut of Chrysomya megacephala, was found to exhibited significant level of protease activity. For the revelation of genetic potential in relation to protease production, whole genome of this organism was sequenced and analysed while structure-function of different protease enzyme was predicated using various in silico analysis. The 4.5 mb CMF genome was found to encompass various types of protease and mostly they are neutral in nature. Enzyme production was highest in an optimum pH and temperature of 6.0 (32.09 ± 1.015 U/ml) and 35ºC (41.65 ± 1.152 U/ml), respectively. Other culture parameters for optimum production of protease were determined to be inoculum size (1%), incubation period (72 h), shaking condition (125 rpm), carbon and nitrogen source [2% lactose (92.21 ± 3.16 U/ml) and 0.5% urea (163.62 ± 4.31 U/ml), respectively] and effect of surfactants [0.02 mg/ml Tween 80 (174.72 ± 4.48 U/ml)]. Furthermore, A. veronii CMF exhibited significant enzyme production like serine protease (15.22 ± 0.563 U/ml), aspartate protease (33.16 ± 0.762 U/ml) and collagenase (17.26 ± 0.626 U/ml). Genomic information and results of physio-biochemical assays indicate its cost-effective potential use in different enzyme-industry.

Aerobic microbial communities in the sediments of a marine oxygen minimum zone

The ecology of aerobic microorganisms is never explored in marine oxygen minimum zone (OMZ) sediments. Here we reveal aerobic bacterial communities along ∼3 m sediment-horizons of the eastern Arabian Sea OMZ. Sulfide-containing sediment-cores retrieved from 530 mbsl (meters beneath the sea-level) and 580 mbsl were explored at 15–30 cm intervals, using metagenomics, pure-culture-isolation, genomics and metatranscriptomics. Genes for aerobic respiration, and oxidation of methane/ammonia/alcohols/thiosulfate/sulfite/organosulfur-compounds, were detected in the metagenomes from all 25 sediment-samples explored. Most probable numbers for aerobic chemolithoautotrophs and chemoorganoheterotrophs at individual sample-sites were up to 1.1 × 10⁷ (g sediment)^-1. The sediment-sample collected from 275 cmbsf (centimeters beneath the seafloor) of the 530-mbsl-core yielded many such obligately aerobic isolates belonging to Cereibacter, Guyparkeria, Halomonas, Methylophaga, Pseudomonas and Sulfitobacter which died upon anaerobic incubation, despite being provided with all possible electron acceptors and fermentative substrates. High percentages of metatranscriptomic reads from the 275 cmbsf sediment-sample, and metagenomic reads from all 25 sediment-samples, matched the isolates’ genomic sequences including those for aerobic metabolisms, genetic/environmental information processing and cell division, thereby illustrating the bacteria's in-situ activity, and ubiquity across the sediment-horizons, respectively. The findings hold critical implications for organic carbon sequestration/remineralization, and inorganic compounds oxidation, within the sediment realm of global marine OMZs.

Molecular mechanism of sulfur chemolithotrophy in the betaproteobacterium Pusillimonas ginsengisoli SBSA

Chemolithotrophic sulfur oxidation represents a significant part of the biogeochemical cycling of this element. Due to its long evolutionary history, this ancient metabolism is well known for its extensive mechanistic and phylogenetic diversification across a diverse taxonomic spectrum. Here we carried out whole-genome sequencing and analysis of a new betaproteobacterial isolate, Pusillimonas ginsengisoli SBSA, which is found to oxidize thiosulfate via the formation of tetrathionate as an intermediate. The 4.7 Mb SBSA genome was found to encompass a soxCDYZAXOB operon, plus single thiosulfate dehydrogenase (tsdA) and sulfite : acceptor oxidoreductase (sorAB) genes. Recombination-based knockout of tsdA revealed that the entire thiosulfate is first converted to tetrathionate by the activity of thiosulfate dehydrogenase (TsdA) and the Sox pathway is not functional in this bacterium despite the presence of all necessary sox genes. The ∆soxYZ and ∆soxXA knockout mutants exhibited a wild-type-like phenotype for thiosulfate/tetrathionate oxidation, whereas ∆soxB, ∆soxCD and soxO::Kan^R mutants only oxidized thiosulfate up to tetrathionate intermediate and had complete impairment in tetrathionate oxidation. The substrate-dependent O₂ consumption rate of whole cells and the sulfur-oxidizing enzyme activities of cell-free extracts, measured in the presence/absence of thiol inhibitors/glutathione, indicated that glutathione plays a key role in SBSA tetrathionate oxidation. The present findings collectively indicate that the potential glutathione : tetrathionate coupling in P. ginsengisoli involves a novel enzymatic component, which is different from the dual-functional thiol dehydrotransferase (ThdT), while subsequent oxidation of the sulfur intermediates produced (e.g. glutathione : sulfodisulfane molecules) may proceed via the iterative action of soxBCD .