Sulfide production and oxidation by heterotrophic bacteria under aerobic conditions

Biogeochemical Cycles in Plant-Soil Systems: Significance for Agriculture, Interconnections, and Anthropogenic Disruptions

Biogeochemical cycles are fundamental to the functioning of plant-soil systems, driving the availability and transfer of essential nutrients (like carbon (C), nitrogen (N), phosphorus (P), and sulfur (S)) as well as beneficial elements (like silicon (Si)). These interconnected cycles regulate ecosystem productivity, biodiversity, and resilience, forming the basis of critical ecosystem services. This review explores the mechanisms and dynamics of biogeochemical C, N, P, S, and Si cycles, emphasizing their roles in nutrient/element cycling, plant growth, and soil health, especially in agricultural plant-soil systems. The coupling between these cycles, facilitated mainly by microbial communities, highlights the complexity of nutrient/element interactions and corresponding implications for ecosystem functioning and stability. Human activities including industrial agriculture, deforestation, and pollution disrupt the underlying natural processes leading to nutrient/element imbalances, soil degradation, and susceptibility to climate impacts. Technological advancements such as artificial intelligence, remote sensing, and real-time soil monitoring offer innovative solutions for studying and managing biogeochemical cycles. These tools enable precise nutrient/element management, identification of ecosystem vulnerabilities, and the development of sustainable practices. Despite significant progress, research gaps remain, particularly in understanding the interlinkages between biogeochemical cycles and their responses to global change. This review underscores the need for integrated approaches that combine interdisciplinary research, technological innovation, and sustainable land-use strategies to mitigate human-induced disruptions and enhance ecosystem resilience. By addressing these challenges, biogeochemical processes and corresponding critical ecosystem services can be safeguarded, ensuring the sustainability of plant-soil systems in the face of environmental change.

Restoring tigecycline efficacy with lysine supplementation in tmexCD-toprJ-positive bacteria

OBJECTIVES

Antimicrobial resistance is one of the most pressing challenges to global public health. Tigecycline, a last-resort antibiotic, has been undermined by the emergence of the tmexCD1-toprJ1 gene cluster, a transferable RND-type efflux pump that confers resistance. Metabolite-enabled killing of antibiotic-resistant pathogens by antibiotics is an attractive strategy to tackle antibiotic resistance.

METHODS

The potentiation of lysine to tigecycline was evaluated through a series of in vitro studies, including bacterial viability assays, time-kill kinetics analysis, persister assays, and biofilm eradication experiments, as well as in vivo assessment using a murine systemic infection model. The underlying mechanisms of action were further explored through transcriptomic profiling and biochemical validation.

RESULTS

Herein, we show that lysine synergistically enhances the antibacterial efficacy of tigecycline against tmexCD-toprJ-positive bacteria. Mechanistic studies indicate that lysine supplementation promotes tigecycline uptake by upregulating ∆pH and disrupting membrane permeability. Transcriptomic analysis, coupled with phenotypic experiments, indicates that lysine not only triggers the generation of reactive oxygen species (ROS) by inhibiting hydrogen sulfide (H2S) production but also downregulates energy metabolism pathways essential for efflux pump function. These effects promote intracellular accumulation of tigecycline, thereby overcoming tmexCD-toprJ-mediated resistance. In mouse infection models, the combination of lysine and tigecycline shows improved therapeutic efficacy compared to tigecycline monotherapy.

CONCLUSION

Collectively, our findings indicate that lysine can serve as a promising tigecycline booster to tackle infections caused by tmexCD-toprJ-positive bacteria.

Overexpression of Tetrahymena Cysteine Synthetase 1 Promotes Cadmium Removal by Biosynthesizing Cadmium Sulfide Quantum Dots in Escherichia coli

Heavy metal cadmium causes significant contamination in aquatic ecosystems. The biomineralization of cadmium represents a vital biological mechanism for handling cadmium stress in diverse microorganisms. To improve the biomineralization capacity of cadmium by microorganisms in aquatic environments, Tetrahymena cysteine synthetase 1 (TtCsa1) was overexpressed in E. coli. The tolerance of E. coli/pET-28a-TtCSA1 to cadmium was enhanced by expressing TtCsa1. Upon addition of cysteine, E. coli/pET-28a-TtCSA1 generated more H2S, which reacted with Cd2+ to form CdS quantum dots (QDs), resulting in a stronger fluorescence signal. The UV-visible absorption and fluorescence spectra of the culture supernatant of E. coli/pET-28a-TtCSA1 showed characteristic peaks corresponding to CdS QDs. Transmission Electron Microscopy (TEM) images confirmed that the formation of CdS QDs and their agglomeration in the E. coli cells. X-ray Diffraction Analysis (XRD) analysis further confirmed the presence of QDs and their crystalline nature. In rich medium, E. coli/pET-28a-TtCSA1 achieved removal rates of 99.5%, 98.2%, 56.5%, and 49.4%, respectively, for Cd2+ concentrations of 0.15, 0.3, 0.45, and 0.6 mM within 48 h. In simulated wastewater, E. coli/pET-28a-TtCSA1 achieved removal rates of 99.4%, 94.3%, 90.1%, and 89.8%, respectively, for Cd2+ concentrations of 0.3, 0.45, 0.6, and 0.75 mM within 12 h. These results demonstrate that overexpressing TtCsa1 in E. coli can significantly enhance its ability to biomineralize Cd2+ in rich medium and simulated wastewater, which has potential applications in bioremediation of aquatic environments contaminated with heavy metals.

Correlation between quality change and hydrogen sulfide in aquatic product: Detection of hydrogen sulfide and its potential applications using bigeye tuna (Thunnus obesus) model during cold storage

Hydrogen sulfide (H2S) is an metabolic product of tuna during the spoilage, and relationship between H2S and tuna quality has not been specifically studied. This study detected changes in H2S content, H2S precursor substances, and related enzymes based on the formation pathway of H2S. H2S content increased of tuna resulted in significant increases in contents of cystathionine β-synthase, cystathionine γ-lyase, 3-mercapto pyruvate sulfotransferase, cysteine aminotransferase and methionine, while content of cysteine decreased which provided H2S formation. Cysteine and methionine metabolism, sulfur metabolism and histidine metabolism were metabolic pathways to assess H2S accumulation. Canonical correlation analysis showed that H2S content was significantly correlated with total volatile base nitrogen, total viable count (p < 0.05). This study elucidates the universality of H2S as an index for assessing seafood quality, utilizing quality indicators and modeling. Our findings offer a theoretical foundation and potential practical applications for improving the quality control of aquatic products.

Bioremediation of non-point hydrogen sulfide emissions using bacterial cellulose/activated carbon membrane

BACKGROUND

Hydrogen sulfide (H2S) gas, characterized by its low odor threshold and toxicity, poses significant challenges in non-point source odor management. Traditional biotechnologies are effective in removing malodorous gases from point sources but they are limited for non-point source odor control.

RESULTS

In this study, the sqr and pdo genes from Cupriavidus pinatubonensis JMP134 were introduced into the bacterial cellulose-producing strain Kosakonia oryzendophytica FY-07. This genetic modification enhanced the strain's sulfur oxidation capacity, which increased over time, with an average transformation capacity of approximately 275 mg·L- 1·day- 1. By incorporating 1% activated carbon, an efficient, naturally degradable bio-composite membrane was developed, achieving a maximum H2S adsorption capacity of 7.3 g·m- 3·day- 1. FY-07 remained stable in soil and improved the microbial community for H2S treatment.

CONCLUSION

The resulting bio-composite membrane is environment-friendly and efficient, making it suitable for emergency odor control in landfills. This study offers recommendations for using membrane materials in managing non-point hydrogen sulfide emissions.

Diversity of sulfur cycling halophiles within the Salton Sea, California's largest lake

BACKGROUND

Microorganisms are the biotic foundation for nutrient cycling across ecosystems, and their assembly is often based on the nutrient availability of their environment. Though previous research has explored the seasonal lake turnover and geochemical cycling within the Salton Sea, California's largest lake, the microbial community of this declining ecosystem has been largely overlooked. We collected seawater from a single location within the Salton Sea at 0 m, 3 m, 4 m, 5 m, 7 m, 9 m, 10 m, and 10.5 m depths in August 2021, December 2021, and April 2022.

RESULTS

We observed that the water column microbiome significantly varied by season (R2 = 0.59, P = 0.003). Temperature (R2 = 0.27, P = 0.004), dissolved organic matter (R2 = 0.13, P = 0.004), and dissolved oxygen (R2 = 0.089, P = 0.004) were significant drivers of seasonal changes in microbial composition. In addition, several halophilic mixotrophs and other extremotolerant bacteria were consistently identified in samples across depths and time points, though their relative abundances fluctuated by season. We found that while sulfur cycling genes were present in all metagenomes, their relative coverages fluctuated by pathway and season throughout the water column. Sulfur oxidation and incomplete sulfur oxidation pathways were conserved in the microbiome across seasons.

CONCLUSIONS

Our work demonstrates that the microbiome within the Salton Seawater has the capacity to metabolize sulfur species and utilize multiple trophic strategies, such as alternating between chemorganotrophy and chemolithoautrophy, to survive this harsh, fluctuating environment. Together, these results suggest that the Salton Sea microbiome is integral in the geochemical cycling of this ever-changing ecosystem and thus contributes to the seasonal dynamics of the Salton Sea. Further work is required to understand how these environmental bacteria are implicated relationship between the Salton Sea's sulfur cycle, dust proliferation, and respiratory distress experienced by the local population.

Roles of nitrite in facilitating nitrogen and sulfur conversion in the hybrid bioreactor of Sulfate-reduced ammonium oxidation and anaerobic ammonium oxidation

The hybrid bioreactor combining sulfate-reducing ammonium oxidation (Sulfammox) and Anammox offered potential for simultaneous nitrogen and sulfur removal, but the removal efficiency and microbial mechanism remain unclear. This study demonstrated that in the hybrid bioreactor, the ammonium utilization rate (AUR) of Sulfammox increased by 5.42 times. The promotion of NO2- on nitrogen and sulfur conversion in Sulfammox could be attributed to: 1) Increasing extracellular polymers substance (EPS) accelerated the stratification of granule sludge; 2) Increasing the relative abundance of Candidatus Brocadia by 29.55 times and Candidatus Anammoxoglobus by 3.17 times; 3) Upregulating the expression of nitrification (amo, hao and nxr) and sulfur metabolism (sat, aprAB dsr and sox) genes, associated with the pathways NH4+→NH2OH → NO2-→NO3- and SO42-→S2-→SO42-. Moreover, Candida Brocadia sapporoensis emerged as a potential specie of Sulfammox, mediating nitrification by hao and nxr, and sulfate reduction by sat and aprAB, thereby enabling electron transfer between nitrogen and sulfur.

Diversity and ecology of microbial sulfur metabolism

Sulfur plays a pivotal role in interactions within the atmosphere, lithosphere, pedosphere, hydrosphere and biosphere, and the functioning of living organisms. In the Earth's crust, mantle, and atmosphere, sulfur undergoes geochemical transformations due to natural and anthropogenic factors. In the biosphere, sulfur participates in the formation of amino acids, proteins, coenzymes and vitamins. Microorganisms in the biosphere are crucial for cycling sulfur compounds through oxidation, reduction and disproportionation reactions, facilitating their bioassimilation and energy generation. Microbial sulfur metabolism is abundant in both aerobic and anaerobic environments and is interconnected with biogeochemical cycles of important elements such as carbon, nitrogen and iron. Through metabolism, competition or cooperation, microorganisms metabolizing sulfur can drive the consumption of organic carbon, loss of fixed nitrogen and production of climate-active gases. Given the increasing significance of sulfur metabolism in environmental alteration and the intricate involvement of microorganisms in sulfur dynamics, a timely re-evaluation of the sulfur cycle is imperative. This Review explores our understanding of microbial sulfur metabolism, primarily focusing on the transformations of inorganic sulfur. We comprehensively overview the sulfur cycle in the face of rapidly changing ecosystems on Earth, highlighting the importance of microbially-mediated sulfur transformation reactions across different environments, ecosystems and microbiomes.

A distinct co-expressed sulfurtransferase extends the physiological role of mercaptopropionate dioxygenase in Pseudomonas aeruginosa PAO1

Oxidation and assimilation of persulfides in bacteria is often catalyzed by a persulfide dioxygenase and sulfurtransferase in consecutive reactions. Enzymes responsible for the oxidation of persulfides have not been clearly defined in Pseudomonas aeruginosa PAO1. The characterized mercaptopropionate dioxygenase (MDO) in P. aeruginosa PAO1 has been proposed to catalyze the oxidation of 3-mercaptopropionate. However, the physiological role of MDO is uncertain given the expression of a sulfurtransferase (ST) enzyme on the same operon as the thiol dioxygenase. The st gene had a co-occurrence frequency with mdo of 0.94 demonstrating the co-expression and physiological link of the two genes. There are four tandem rhodanese domains in the ST enzyme with two of the domains containing potential catalytic Cys residues (Cys191 and Cys435) capable of forming a persulfide. Only Cys435 was accessible in thiol quantification assays, and results from H/D-X MS analyses further established the accessibility of the domain containing Cys435. Both thiosulfate and mercaptopyruvate served as sulfur donors to the ST enzyme, with Cys435 forming the persulfide intermediate. Kinetic investigations of MDO suggested the enzyme had a broader substrate specificity than previously identified, oxidizing both mercaptopropionate and mercaptopyruvate thiol and persulfide substrates. The results obtained from these investigations provide insight into the overall mechanism and physiological role of the mdo operon in sulfide oxidation and assimilation.

Higher diversity of sulfur-oxidizing bacteria based on soxB gene sequencing in surface water than in spring in Wudalianchi volcanic group, NE China

INTRODUCTION

Sulfur-oxidizing bacteria (SOB) play a key role in the biogeochemical cycling of sulfur.

OBJECTIVES

To explore SOB diversity, distribution, and physicochemical drivers in five volcanic lakes and two springs in the Wudalianchi volcanic field, China.

METHODS

This study analyzed microbial communities in samples via high-throughput sequencing of the soxB gene. Physical-chemical parameters were measured, and QIIME 2 (v2019.4), R, Vsearch, MEGA7, and Mothur processed the data. Alpha diversity indices and UPGMA clustering assessed community differences, while heat maps visualized intra-sample variations. Canoco 5.0 analyzed community-environment correlations, and NMDS, Adonis, and PcoA explored sample dissimilarities and environmental factor correlations. SPSS v.18.0 tested for statistical significance.

RESULTS

The diversity of SOB in surface water was higher than in springs (more than 7.27 times). We detected SOB affiliated to β-proteobacteria (72.3 %), α-proteobacteria (22.8 %), and γ-proteobacteria (4.2 %) distributed widely in these lakes and springs. Rhodoferax and Cupriavidus were most frequent in all water samples, while Rhodoferax and Bradyrhizobium are dominant in surface waters but rare in springs. SOB genera in both habitats were positively correlated. Co-occurrence analysis identified Bradyrhizobium, Blastochloris, Methylibium, and Metyhlobacterium as potential keystone taxa. Redundancy analysis (RDA) revealed positive correlations between SOB diversity and total carbon (TC), Fe2+, and total nitrogen (TN) in all water samples.

CONCLUSION

The diversity and community structure of SOB in volcanic lakes and springs in the Wudalianchi volcanic group were clarified. Moreover, the diversity and abundance of SOB decreased with the variation of water openness, from open lakes to semi-enclosed lakes and enclosed lakes.

Microbial Cycling of Sulfur and Other Redox-Sensitive Elements in Porewaters of San Clemente Basin, California, and Cocos Ridge, Costa Rica

The microbial recycling of organic matter in marine sediments depends upon electron acceptors that are utilized based on availability and energetic yield. Since sulfate is the most abundant oxidant once oxygen has been depleted, the sulfide produced after sulfate reduction becomes an important electron donor for autotrophic microbes. The ability of sulfide to be re-oxidized through multiple metabolic pathways and intermediates with variable oxidation states prompts investigation into which species are preferentially utilized and what are the factors that determine the fate of reduced sulfur species. Quantifying these sulfur intermediates in porewaters is a critical first step towards achieving a more complete understanding of the oxidative sulfur cycle, yet this has been accomplished in very few studies, none of which include oligotrophic sedimentary environments in the open ocean. Here we present profiles of porewater sulfur intermediates from sediments underlying oligotrophic regions of the ocean, which encompass about 75% of the ocean's surface and are characterized by low nutrient levels and productivity. Aiming at addressing uncertainties about if and how sulfide produced by the degradation of scarce sedimentary organic matter plays a role in carbon fixation in the sediment, we determine depth profiles of redox-sensitive metals and sulfate isotope compositions and integrate these datasets with 16S rRNA microbial community composition data and solid-phase sulfur concentrations. We did not find significant correlations between sulfur species or trace metals and specific sulfur cycling taxa, which suggests that microorganisms in pelagic and oxic sediments may be generalists utilizing flexible metabolisms to oxidize organic matter through different electron acceptors.

An Expanded Substrate Spectrum of Sulfide:Quinone Oxidoreductase Found in Pollutant Degrading Bacteria

Sulfide:Quinone Oxidoreductase (Sqr) Catalyzes The Initial Procedure On Sulfide Transformation, Alongside Sulfide (H2S, S2-) Oxidization Coupled With Coenzyme Q (CoQ) Reducing And Reactive Sulfur Species (RSS) Production. Here, We Assessed The Reactivity Of Propanethiol (PT) As An Alternative Substrate For Sqr To Maintain Intracellular Homeostasis In Strain S-1 Capable Of Degrading Emerging Sulfur-Containing Pollutants. We Deleted A Gene Encoding Sqr, And Serial Transcriptional Difference Induced By RSS Dynamics Was Therefore Revealed. Next, The Reaction Properties Of Two Sqr Homologs From Strains JMP134 And S-1 Were Comparatively Characterized, Respectively. As A Result, An Additional Role Of Sqr In Yielding RSS From PT Was Found In Reaction Mixture Prepared By Cell-Free Extracts Or Purified Enzymes. Interestingly, The Transformation Velocity Of PT By Sqr Was Slower Than That Of Sulfides. From This Scenario, It Was A Rate-Determining Step That PT As A Nucleophilic Compound Can Be Added Into Sqr Cysteine To Form Disulfide Bond And Likely Serve Nonoptimal Sulfur Recipient. In Addition, The Role Of Persulfidation Driven By RSS In Combating Oxidative And Sulfur Stresses Required To Be Further Clarified. Nevertheless, This Promiscuity Of Sqr-Binding Organosulfur Compounds And Its Catalytic Modulation Underscored That Expanded Substrates Might Benefit Sulfide Homeostasis In Thiol-Degrading Bacteria.

Enterobacter sp. HIT-SHJ4 isolated from wetland with carbon, nitrogen and sulfur co-metabolism and its implication for bioremediation

Both autotrophic and heterotrophic denitrification are known as important bioprocesses of microbe-mediated nitrogen cycle in natural ecosystems. Actually, mixotrophic denitrification co-driven by organic matter and reduced sulfur substances are also common, especially in hypoxic environments such as estuarine sediments. However, carbon, nitrogen and sulfur co-metabolism during mixotrophic denitrification in natural water ecosystems has rarely been reported in detail. Therefore, this study investigated the co-metabolism of carbon, nitrogen and sulfur using samples collected from four distinct natural water ecosystems. Results demonstrated that samples from various sources all exhibited the ability for co-metabolism of carbon, nitrogen and sulfur. Microbial community analysis showed that Pseudomonas and Paracoccus were dominant bacteria ranging from 65.6% to 75.5% in mixotrophic environment. Enterobacter sp. HIT-SHJ4, a mixotrophic denitrifying strain which owned the capacity for co-metabolism of carbon, nitrogen and sulfur, was isolated and reported here for the first time. The strain preferred methanol as its carbon source and demonstrated remarkable efficiency for removing sulfide and nitrate with below 100 mg/L sulfide. Under weak acid conditions (pH 6.5-7.0), it exhibited enhanced capability in converting sulfide to elemental sulfur. Its bioactivity was evident within a temperature from 25 °C to 40 °C and C/N ratios from 0.75 to 3. This study confirmed the widespread presence of microbial-mediated synergistic carbon, nitrogen and sulfur metabolism in natural aquatic ecosystems. HIT-SHJ4 emerges as a novel strain, shedding light on carbon, nitrogen and sulfur co-metabolism in natural water bodies. Furthermore, it also serves as a promising candidate microorganism for in-situ ecological remediation, particularly in dealing with contamination posed by nitrate, sulfide, and organic matter.

H2S scavenger as a broad-spectrum strategy to deplete bacteria-derived H2S for antibacterial sensitization

Bacteria-derived H2S plays multifunctional protective roles against antibiotics insult, and the H2S biogenesis pathway is emerging as a viable target for the antibacterial adjuvant design. However, the development of a pan-inhibitor against H2S-synthesizing enzymes is challenging and underdeveloped. Herein, we propose an alternative strategy to downregulate the H2S levels in H2S-producing bacteria, which depletes the bacteria-derived H2S chemically by H2S scavengers without acting on the synthesizing enzymes. After the screening of chemically diversified scaffolds and a structural optimization campaign, a potent and specific H2S scavenger is successfully identified, which displays efficient H2S depletion in several H2S-producing bacteria, potentiates both bactericidal agents and photodynamic therapy, enhances the bacterial clearance of macrophages and polymorphonuclear neutrophils, disrupts the formation of bacterial biofilm and increases the sensitivity of bacterial persister cells to antibiotics. Most importantly, such an H2S scavenger exhibits sensitizing effects with gentamicin in Pseudomonas aeruginosa -infected pneumonia and skin wound female mouse models. In aggregate, our results not only provide an effective strategy to deplete bacteria-derived H2S and establish the H2S biogenesis pathway as a viable target for persisters and drug-resistant bacteria, but also deliver a promising antibacterial adjuvant for potential clinical translation.

Mechanism of Intracellular Elemental Sulfur Oxidation in Beggiatoa leptomitoformis, Where Persulfide Dioxygenase Plays a Key Role

Representatives of the colorless sulfur bacteria of the genus Beggiatoa use reduced sulfur compounds in the processes of lithotrophic growth, which is accompanied by the storage of intracellular sulfur. However, it is still unknown how the transformation of intracellular sulfur occurs in Beggiatoa representatives. Annotation of the genome of Beggiatoa leptomitoformis D-402 did not identify any genes for the oxidation or reduction of elemental sulfur. By searching BLASTP, two putative persulfide dioxygenase (PDO) homologs were found in the genome of B. leptomitoformis. In some heterotrophic prokaryotes, PDO is involved in the oxidation of sulfane sulfur. According to HPLC-MS/MS, the revealed protein was reliably detected in a culture sample grown only in the presence of endogenous sulfur and CO2. The recombinant protein from B. leptomitoformis was active in the presence of glutathione persulfide. The crystal structure of recombinant PDO exhibited consistency with known structures of type I PDO. Thus, it was shown that B. leptomitoformis uses PDO to oxidize endogenous sulfur. Additionally, on the basis of HPLC-MS/MS, RT-qPCR, and the study of PDO reaction products, we predicted the interrelation of PDO and Sox-system function in the oxidation of endogenous sulfur in B. leptomitoformis and the connection of this process with energy metabolism.

The Effects of Different Thiol-Containing Compounds on the Degradation of Sulforaphene

Sulforaphene (4-methylsufinyl-3-butenyl isothiocyanate, SFE), produced by myrosinase hydrolysis of glucoraphenin (4-methylsulfinyl-3-butenyl glucosinolate) found in radish seeds, is strongly associated with cancer prevention. In this study, we investigated the stability of SFE (purity above 98%) under various thiol-containing compounds at 25 °C, such as sodium hydrosulfide (NaHS), glutathione (GSH), and cysteine (Cys). We observed that the degradation of SFE was closely related to the presence and dissociation capacity of thiol-containing compounds in the solution, particularly the thiol group. We found that the degradation rate of SFE was influenced by incubation with NaHS, GSH, and Cys, with distinct degradation products detected for each of these thiol-containing compounds. Compared to GSH, sulfide and Cys played important roles in promoting the degradation of SFE. Furthermore, we found substantial quantities of hydrogen sulfide in conjunction with SFE during the hydrolysis process of seeds, and a heat treatment of the seeds resulted in increased production of SFE. However, the introduction of sulfide-oxidizing bacteria to the hydrolytic system did not exhibit any inhibitory effect on the degradation of SFE. These results provided a guideline for industries to improve the stability of SFE during preparation.

Adaptive modifications in plant sulfur metabolism over evolutionary time

Sulfur (S) is an essential element for life on Earth. Plants are able to take up and utilize sulfate (SO42-), the most oxidized inorganic form of S compounds on Earth, through the reductive S assimilatory pathway that couples with photosynthetic energy conversion. Organic S compounds are subsequently synthesized in plants and made accessible to animals, primarily as the amino acid methionine. Thus, plant S metabolism clearly has nutritional importance in the global food chain. S metabolites may be part of redox regulation and drivers of essential metabolic pathways as cofactors and prosthetic groups, such as Fe-S centers, CoA, thiamine, and lipoic acid. The evolution of the S metabolic pathways and enzymes reflects the critical importance of functional innovation and diversifications. Here we review the major evolutionary alterations that took place in S metabolism across different scales and outline research directions that may take advantage of understanding the evolutionary adaptations.

Microbial assimilatory sulfate reduction-mediated H2S: an overlooked role in Crohn's disease development

BACKGROUND

H2S imbalances in the intestinal tract trigger Crohn's disease (CD), a chronic inflammatory gastrointestinal disorder characterized by microbiota dysbiosis and barrier dysfunction. However, a comprehensive understanding of H2S generation in the gut, and the contributions of both microbiota and host to systemic H2S levels in CD, remain to be elucidated. This investigation aimed to enhance comprehension regarding the sulfidogenic potential of both the human host and the gut microbiota.

RESULTS

Our analysis of a treatment-naive CD cohorts' fecal metagenomic and biopsy metatranscriptomic data revealed reduced expression of host endogenous H2S generation genes alongside increased abundance of microbial exogenous H2S production genes in correlation with CD. While prior studies focused on microbial H2S production via dissimilatory sulfite reductases, our metagenomic analysis suggests the assimilatory sulfate reduction (ASR) pathway is a more significant contributor in the human gut, given its high prevalence and abundance. Subsequently, we validated our hypothesis experimentally by generating ASR-deficient E. coli mutants ∆cysJ and ∆cysM through the deletion of sulfite reductase and L-cysteine synthase genes. This alteration significantly affected bacterial sulfidogenic capacity, colon epithelial cell viability, and colonic mucin sulfation, ultimately leading to colitis in murine model. Further study revealed that gut microbiota degrade sulfopolysaccharides and assimilate sulfate to produce H2S via the ASR pathway, highlighting the role of sulfopolysaccharides in colitis and cautioning against their use as food additives.

CONCLUSIONS

Our study significantly advances understanding of microbial sulfur metabolism in the human gut, elucidating the complex interplay between diet, gut microbiota, and host sulfur metabolism. We highlight the microbial ASR pathway as an overlooked endogenous H2S producer and a potential therapeutic target for managing CD. Video Abstract.

Microbial life in preferential flow paths in subsurface clayey till revealed by metataxonomy and metagenomics

BACKGROUND

Subsurface microorganisms contribute to important ecosystem services, yet little is known about how the composition of these communities is affected by small scale heterogeneity such as in preferential flow paths including biopores and fractures. This study aimed to provide a more complete characterization of microbial communities from preferential flow paths and matrix sediments of a clayey till to a depth of 400 cm by using 16S rRNA gene and fungal ITS2 amplicon sequencing of environmental DNA. Moreover, shotgun metagenomics was applied to samples from fractures located 150 cm below ground surface (bgs) to investigate the bacterial genomic adaptations resulting from fluctuating exposure to nutrients, oxygen and water.

RESULTS

The microbial communities changed significantly with depth. In addition, the bacterial/archaeal communities in preferential flow paths were significantly different from those in the adjacent matrix sediments, which was not the case for fungal communities. Preferential flow paths contained higher abundances of 16S rRNA and ITS gene copies than the corresponding matrix sediments and more aerobic bacterial taxa than adjacent matrix sediments at 75 and 150 cm bgs. These findings were linked to higher organic carbon and the connectivity of the flow paths to the topsoil as demonstrated by previous dye tracer experiments. Moreover, bacteria, which were differentially more abundant in the fractures than in the matrix sediment at 150 cm bgs, had higher abundances of carbohydrate active enzymes, and a greater potential for mixotrophic growth.

CONCLUSIONS

Our results demonstrate that the preferential flow paths in the subsurface are unique niches that are closely connected to water flow and the fluctuating ground water table. Although no difference in fungal communities were observed between these two niches, hydraulically active flow paths contained a significantly higher abundance in fungal, archaeal and bacterial taxa. Metagenomic analysis suggests that bacteria in tectonic fractures have the genetic potential to respond to fluctuating oxygen levels and can degrade organic carbon, which should result in their increased participation in subsurface carbon cycling. This increased microbial abundance and activity needs to be considered in future research and modelling efforts of the soil subsurface.

α-Ketoglutarate downregulates thiosulphate metabolism to enhance antibiotic killing

Potentiation of the effects of currently available antibiotics is urgently required to tackle the rising antibiotics resistance. The pyruvate (P) cycle has been shown to play a critical role in mediating aminoglycoside antibiotic killing, but the mechanism remains unexplored. In this study, we investigated the effects of intermediate metabolites of the P cycle regarding the potentiation of gentamicin. We found that α-ketoglutarate (α-KG) has the best synergy with gentamicin compared to the other metabolites. This synergistic killing effect was more effective with aminoglycosides than other types of antibiotics, and it was effective against various types of bacterial pathogens. Using fish and mouse infection models, we confirmed that the synergistic killing effect occurred in vivo. Furthermore, functional proteomics showed that α-KG downregulated thiosulphate metabolism. Upregulation of thiosulphate metabolism by exogenous thiosulphate counteracted the killing effect of gentamicin. The role of thiosulphate metabolism in antibiotic resistance was further confirmed using thiosulphate reductase knockout mutants. These mutants were more sensitive to gentamicin killing, and less tolerant to antibiotics compared to their parental strain. Thus, our study highlights a strategy for potentiating antibiotic killing by using a metabolite that reduces antibiotic resistance.

MarR family proteins sense sulfane sulfur in bacteria

Members of the multiple antibiotic resistance regulator (MarR) protein family are ubiquitous in bacteria and play critical roles in regulating cellular metabolism and antibiotic resistance. MarR family proteins function as repressors, and their interactions with modulators induce the expression of controlled genes. The previously characterized modulators are insufficient to explain the activities of certain MarR family proteins. However, recently, several MarR family proteins have been reported to sense sulfane sulfur, including zero-valent sulfur, persulfide (R-SSH), and polysulfide (R-SnH, n ≥ 2). Sulfane sulfur is a common cellular component in bacteria whose levels vary during bacterial growth. The changing levels of sulfane sulfur affect the expression of many MarR-controlled genes. Sulfane sulfur reacts with the cysteine thiols of MarR family proteins, causing the formation of protein thiol persulfide, disulfide bonds, and other modifications. Several MarR family proteins that respond to reactive oxygen species (ROS) also sense sulfane sulfur, as both sulfane sulfur and ROS induce the formation of disulfide bonds. This review focused on MarR family proteins that sense sulfane sulfur. However, the sensing mechanisms reviewed here may also apply to other proteins that detect sulfane sulfur, which is emerging as a modulator of gene regulation.

Organic matter degradation in the deep, sulfidic waters of the Black Sea: insights into the ecophysiology of novel anaerobic bacteria

BACKGROUND

Recent studies have reported the identity and functions of key anaerobes involved in the degradation of organic matter (OM) in deep (> 1000 m) sulfidic marine habitats. However, due to the lack of available isolates, detailed investigation of their physiology has been precluded. In this study, we cultivated and characterized the ecophysiology of a wide range of novel anaerobes potentially involved in OM degradation in deep (2000 m depth) sulfidic waters of the Black Sea.

RESULTS

We have successfully cultivated a diverse group of novel anaerobes belonging to various phyla, including Fusobacteriota (strain S5), Bacillota (strains A1T and A2), Spirochaetota (strains M1T, M2, and S2), Bacteroidota (strains B1T, B2, S6, L6, SYP, and M2P), Cloacimonadota (Cloa-SY6), Planctomycetota (Plnct-SY6), Mycoplasmatota (Izemo-BS), Chloroflexota (Chflx-SY6), and Desulfobacterota (strains S3T and S3-i). These microorganisms were able to grow at an elevated hydrostatic pressure of up to 50 MPa. Moreover, this study revealed that different anaerobes were specialized in degrading specific types of OM. Strains affiliated with the phyla Fusobacteriota, Bacillota, Planctomycetota, and Mycoplasmatota were found to be specialized in the degradation of cellulose, cellobiose, chitin, and DNA, respectively, while strains affiliated with Spirochaetota, Bacteroidota, Cloacimonadota, and Chloroflexota preferred to ferment less complex forms of OM. We also identified members of the phylum Desulfobacterota as terminal oxidizers, potentially involved in the consumption of hydrogen produced during fermentation. These results were supported by the identification of genes in the (meta)genomes of the cultivated microbial taxa which encode proteins of specific metabolic pathways. Additionally, we analyzed the composition of membrane lipids of selected taxa, which could be critical for their survival in the harsh environment of the deep sulfidic waters and could potentially be used as biosignatures for these strains in the sulfidic waters of the Black Sea.

CONCLUSIONS

This is the first report that demonstrates the cultivation and ecophysiology of such a diverse group of microorganisms from any sulfidic marine habitat. Collectively, this study provides a step forward in our understanding of the microbes thriving in the extreme conditions of the deep sulfidic waters of the Black Sea. Video Abstract.

Exogenous additive ferric sulfate regulates sulfur-oxidizing bacteria in cow manure composting to promote carbon fixation

Enhancing carbon fixation in the composting process was of great significance in the era of massive generation of organic solid waste. In this study, the experimental results showed that the contents of dissolved organic matter (DOM) in the experimental group (CT) were 37.58% higher than those in the control group (CK). The CO2 emission peaked on day 5, and the value of CK was 1.34 times that of CT. Significant differences were observed between the contents of sulfur fractions in CT and CK. This phenomenon may be due to the suppression of sulfur-reducing gene expression in CT. On day 51 of composting, the abundance of sulfur-oxidizing bacteria (SOB) Rhodobacter (5.33%), Rhodovulum (14.76%), and Thioclava (23.83%) in CT was higher than that in CK. In summary, the composting fermentation regulated by Fe2(SO4)3 increased the sulfate content, enhanced the expression of sulfur-oxidizing genes and SOB, and ultimately promoted carbon sequestration during composting.

Elemental sulfur biorecovery from phosphogypsum using oxygen-membrane biofilm reactor: Bioreactor parameters optimization, metagenomic analysis and metabolic prediction of the biofilm activity

This work investigated elemental sulfur (S0) biorecovery from Phosphogypsum (PG) using sulfur-oxidizing bacteria in an O2-based membrane biofilm reactor (MBfR). The system was first optimized using synthetic sulfide medium (SSM) as influent, then switched to biogenic sulfide medium (BSM) generated by biological reduction of PG alkaline leachate. The results using SSM had high sulfide-oxidation efficiency (98 %), sulfide to S0 conversion (∼90 %), and S0 production rate up to 2.7 g S0/(m2.d), when the O2/S ratio was ∼0.5 g O2/g S. With the BSM influent, the system maintained high sulfide-to-S0 conversion rate (97 %), and S0-production rate of 1.6 g S0/(m2.d). Metagenomic analysis revealed that Thauera was the dominant genus in SSM and BSM biofilms. Furthermore, influent composition affected the bacterial community structure and abundances of functional microbial sulfur genes, modifying the sulfur-transformation pathways in the biofilms. Overall, this work shows promise for O2-MBfR usage in S0 biorecovery from PG-leachate and other sulfidogenic effluents.

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

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

Deep-sea in situ and laboratory multi-omics provide insights into the sulfur assimilation of a deep-sea Chloroflexota bacterium

Chloroflexota bacteria are abundant and globally distributed in various deep-sea ecosystems. It has been reported based on metagenomics data that two deep-sea Chloroflexota lineages (the SAR202 group and Dehalococcoidia class) have the potential to drive sulfur cycling. However, the absence of cultured Chloroflexota representatives is a significant bottleneck toward understanding their contribution to the deep-sea sulfur cycling. In this study, we find that Phototrophicus methaneseepsis ZRK33 isolated from deep-sea sediment has a heterotrophic lifestyle and can assimilate sulfate and thiosulfate. Using combined physiological, genomic, proteomic, and in situ transcriptomic methods, we find that strain ZRK33 can perform assimilatory sulfate reduction in both laboratory and deep-sea conditions. Metabolism of sulfate or thiosulfate by strain ZRK33 significantly promotes the transport and degradation of various macromolecules and thereby stimulates the energy production. In addition, metagenomic results show that genes associated with assimilatory and dissimilatory sulfate reduction are ubiquitously distributed in the metagenome-assembled genomes of Chloroflexota members derived from deep-sea sediments. Metatranscriptomic results also show that the expression levels of related genes are upregulated, strongly suggesting that Chloroflexota bacteria may play undocumented roles in deep-sea sulfur cycling.

IMPORTANCE

The cycling of sulfur is one of Earth's major biogeochemical processes and is closely related to the energy metabolism of microorganisms living in the deep-sea cold seep and hydrothermal vents. To date, some of the members of Chloroflexota are proposed to play a previously unrecognized role in sulfur cycling. However, the sulfur metabolic characteristics of deep-sea Chloroflexota bacteria have never been reported, and remain to be verified in cultured deep-sea representatives. Here, we show that the deep-sea Chloroflexota bacterium ZRK33 can perform sulfate assimilation in both laboratory and deep-sea conditions, which expands our knowledge of the sulfur metabolic potential of deep-sea Chloroflexota bacteria. We also show that the genes associated with assimilatory and dissimilatory sulfate reduction ubiquitously distribute in the deep-sea Chloroflexota members, providing hints to the roles of Chloroflexota bacteria in deep-sea sulfur biogeochemical cycling.

Hydrogen sulfide production does not affect antibiotic resistance in Pseudomonas aeruginosa

Hydrogen sulfide (H2S) has been proposed to protect bacteria from antibiotics, pointing to H2S-producing enzymes as possible targets for the development of antibiotic adjuvants. Here, MIC assays performed with Pseudomonas aeruginosa mutants producing altered H2S levels demonstrate that H2S does not affect antibiotic resistance in this bacterium. Moreover, correlation analyses in a large collection of P. aeruginosa cystic fibrosis isolates argue against the protective role of H2S from antibiotic activity during chronic lung infection.

Removal of sulfur and nitrogen pollutants in a sediment microbial fuel cell coupled with Vallisneria natans: Efficiency, microbial community structure, and functional genes

The rapid development of the economy has led to an increase in the sulfur and nitrogen load in surface water, which has the potential to cause river eutrophication and the emission of malodorous gases. A lab-scale sediment microbial fuel cell coupled with Vallisneria natans (P-SMFC) was designed for surface water remediation. The enhancement of pollutant removal performance of P-SMFC was evaluated in contrast to the SMFC system without plants (SMFC), the open-circuit control system with plants (C-P), and the open-circuit control system without plants (C-S), while illustrating the mechanisms of the sulfur and nitrogen transformation process. The results demonstrated that the effluent and sediment of P-SMFC had lower concentrations of sulfide compared to other systems. Furthermore, P-SMFC exhibited higher removal efficiency for COD (73.1 ± 8.7%), NH4+-N (80.5 ± 19.8%), and NO3--N (88.5 ± 11.8%) compared to other systems. The closed-circuit conditions and growth of Vallisneria natans create a favorable ecological niche for functional microorganisms involved in power generation, sulfur oxidation, and nitrogen transformation. Additionally, metagenomic analysis revealed that multifunctional bacteria possessing both denitrification and sulfur oxidation genes, such as Thiobacillus, Dechloromonas, and Bacillus, may play simultaneous roles in metabolizing sulfur and nitrogen, thus serving as integral factors in maintaining the performance of P-SMFC. In summary, these findings provide a theoretical reference for the concurrent enhancement of sulfur and nitrogen pollutants removal in P-SMFC and will facilitate its practical application in the remediation of contaminated surface water.

Dual-channel versatile molecular sensing platform for individual and successive HClO and H2S detection: Applicable in toxic alerts of environmental samples and living organisms

In this study, we have successfully developed a novel dual-response fluorescent probe, NACou, designed for the visual and quantitative detection of HClO/H2S in real water samples and liquid beverages by a thin-film sensing platform. Additionally, NACou demonstrated efficacy for sensing HClO/H2S in HeLa cells, plants and zebrafish through distinct fluorescent channels, yielding satisfactory results. NACou exhibited a multi-modal fluorescence response mechanism for detecting HClO and H2S with remarkable low detection limits of 27.8 nM and 34.4 nM, accompanied by outstanding fluorescent enhancement (209-fold and 148-fold, respectively). These advantages position NACou as a potent molecular tool for HClO and H2S sensing. The specific recognition performance of NACou towards HClO/H2S were confirmed through fluorescence spectroscopy, mass analysis and UV-vis spectroscopy. Importantly, the thin-film sensing platform with the visible fluorescence change can enable rapid assays for water quality and food safety monitoring, showcasing significant practical application value. Impressively, NACou has been employed in warning against liver injury induced by multiple drugs, allowing for the exploration of the pathogenesis and degree of drug-induced injury.

Using the sulfide-oxidizing bacterium Geobacillus thermodenitrificans to restrict H2S release during chicken manure composting

Hydrogen sulfide (H2S) is a toxic gas massively released during chicken manure composting. Diminishing its release requires efficient and low cost methods. In recent years, heterotrophic bacteria capable of rapid H2S oxidation have been discovered but their applications in environmental improvement are rarely reported. Herein, we investigated H2S oxidation activity of a heterotrophic thermophilic bacterium Geobacillus thermodenitrificans DSM465, which contains a H2S oxidation pathway composed by sulfide:quinone oxidoreductase (SQR) and persulfide dioxygenase (PDO). This strain rapidly oxidized H2S to sulfane sulfur and thiosulfate. The oxidation rate reached 5.73 μmol min-1·g-1 of cell dry weight. We used G. thermodenitrificans DSM465 to restrict H2S release during chicken manure composting. The H2S emission during composting process reduced by 27.5% and sulfate content in the final compost increased by 34.4%. In addition, this strain prolonged the high temperature phase by 7 days. Thus, using G. thermodenitrificans DSM465 to control H2S release was an efficient and economic method. This study provided a new strategy for making waste composting environmental friendly and shed light on perspective applications of heterotrophic H2S oxidation bacteria in environmental improvements.

Low cost and renewable H2S-biofilter inoculated with Trichoderma harzianum

The use of biogas to produce hydrogen is currently gaining more attention. One of the drawbacks for the valorization of biogas is the presence of H2S, a hazardous molecule that can cause damage in the metallic internal structures of industries. In this study, the H2S-removal performance of a fungi-based biofilter was investigated. First, an H2S-resistant fungal species was isolated from an industrial digestate and identified as Trichoderma harzianum. The capacity of this microorganism to metabolize H2S in a mineral medium was confirmed. Then, a bioreactor was constructed and put in place to monitor the elimination of gaseous H2S. A mix of cardboard, perlite, woodchips, and wood pellets was used as filling. Microbial development and the outlet gas composition were monitored during a 60-day experimental process during which H2S was completely removed. 97% of the introduced sulphur was detected in the used filling material (fungal species + packing material) by elemental analysis. 24% of the detected sulphur was identified by ion-exchange chromatography as SO42-. Elemental analysis, gas chromatography, and ion-exchange chromatography were used to determine the bioreactor sulphur balance. Metagenomic analysis underlined that H2S elimination was due to the presence of Trichoderma harzianum with a H2S-specific bacterial consortium.

The Microbial Ecology of Estuarine Ecosystems

Human civilization relies on estuaries, and many estuarine ecosystem services are provided by microbial communities. These services include high rates of primary production that nourish harvests of commercially valuable species through fisheries and aquaculture, the transformation of terrestrial and anthropogenic materials to help ensure the water quality necessary to support recreation and tourism, and mutualisms that maintain blue carbon accumulation and storage. Research on the ecology that underlies microbial ecosystem services in estuaries has expanded greatly across a range of estuarine environments, including water, sediment, biofilms, biological reefs, and stands of seagrasses, marshes, and mangroves. Moreover, the application of new molecular tools has improved our understanding of the diversity and genomic functions of estuarine microbes. This review synthesizes recent research on microbial habitats in estuaries and the contributions of microbes to estuarine food webs, elemental cycling, and interactions with plants and animals, and highlights novel insights provided by recent advances in genomics.

Reversed oxidative TCA (roTCA) for carbon fixation by an Acidimicrobiia strain from a saline lake

Acidimicrobiia are widely distributed in nature and suggested to be autotrophic via the Calvin-Benson-Bassham (CBB) cycle. However, direct evidence of chemolithoautotrophy in Acidimicrobiia is lacking. Here, we report a chemolithoautotrophic enrichment from a saline lake, and the subsequent isolation and characterization of a chemolithoautotroph, Salinilacustristhrix flava EGI L10123T, which belongs to a new Acidimicrobiia family. Although strain EGI L10123T is autotrophic, neither its genome nor Acidimicrobiia metagenome-assembled genomes from the enrichment culture encode genes necessary for the CBB cycle. Instead, genomic, transcriptomic, enzymatic, and stable-isotope probing data hinted at the activity of the reversed oxidative TCA (roTCA) coupled with the oxidation of sulfide as the electron donor. Phylogenetic analysis and ancestral character reconstructions of Acidimicrobiia suggested that the essential CBB gene rbcL was acquired through multiple horizontal gene transfer events from diverse microbial taxa. In contrast, genes responsible for sulfide- or hydrogen-dependent roTCA carbon fixation were already present in the last common ancestor of extant Acidimicrobiia. These findings imply the possibility of roTCA carbon fixation in Acidimicrobiia and the ecological importance of Acidimicrobiia. Further research in the future is necessary to confirm whether these characteristics are truly widespread across the clade.

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

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

A biological strategy for sulfide control in sewers: Removing sulfide by sulfur-oxidizing bacteria

Sulfide produced from sewers is considered one of the dominant threats to public health and sewer lifespan due to its toxicity and corrosiveness. In this study, we developed an environmentally friendly strategy for gaseous sulfide control by enriching indigenous sulfur-oxidizing bacteria (SOB) from sewer sediment. Ceramics acted as bio-carriers for immobilizing SOB for practical use in a lab-scale sewer reactor. 16 S rRNA gene sequences revealed that the SOB consortium was successfully enriched, with Thiobacillus, Pseudomonas, and Alcaligenes occupying a dominant abundance of 64.7% in the microbial community. Metabolic pathway analysis in different acclimatization stages indicates that microorganisms could convert thiosulfate and sulfide into elemental sulfur after enrichment and immobilization. A continuous experiment in lab-scale sewer reactors confirmed an efficient result for sulfide removal with hydrogen sulfide reduction of 43.9% and 85.1% under high-sulfur load and low-sulfur load conditions, respectively. This study shed light on the promising application for sewer sulfide control by biological sulfur oxidation strategy.

Microbial Ecosystems in Movile Cave: An Environment of Extreme Life

Movile Cave, situated in Romania close to the Black Sea, constitutes a distinct and challenging environment for life. Its partially submerged ecosystem depends on chemolithotrophic processes for its energetics, which are fed by a continuous hypogenic inflow of mesothermal waters rich in reduced chemicals such as hydrogen sulfide and methane. We sampled a variety of cave sublocations over the course of three years. Furthermore, in a microcosm experiment, minerals were incubated in the cave waters for one year. Both endemic cave samples and extracts from the minerals were subjected to 16S rRNA amplicon sequencing. The sequence data show specific community profiles in the different subenvironments, indicating that specialized prokaryotic communities inhabit the different zones in the cave. Already after one year, the different incubated minerals had been colonized by specific microbial communities, indicating that microbes in Movile Cave can adapt in a relatively short timescale to environmental opportunities in terms of energy and nutrients. Life can thrive, diversify and adapt in remote and isolated subterranean environments such as Movile Cave.

Soil depth exerts a stronger impact on microbial communities and the sulfur biological cycle than salinity in salinized soils

The distribution of microbial communities along salinity gradients in the surface layer of salinized soils has been widely studied. However, it is unknown whether microbial communities exhibit similar distribution patterns in surface and deep soils. Additionally, the relationship between soil depth, salinity, and sulfur metabolism remains unclear. Herein, bulk soils in the surface (S, 5-10 cm) and deep (D, 20-25 cm) layers from high- and low-salinity soils were analyzed using metagenomic and physicochemical analyses. Soil depth was significantly correlated to the concentration of sulfur compounds in the soil and exerted a stronger effect than salinity. Non-metric multidimensional scaling analysis revealed significant differences in microbial community structure with varying soil depths and salinities. However, soil depth clearly influenced microbial community abundance, homogeneity, and diversity, while salinity had a limited effect on microbial abundance. Archaea and bacteria were enriched in the surface and deep soils, respectively. Gene abundance analysis revealed significant differences in the abundance of sulfur-related genes at different soil depths. The abundance of sulfur oxidation genes was lower in deep soil than in surface soil, whereas the abundance of other sulfur-related genes showed the opposite trend. Redundancy analysis (RDA) showed that environmental factors and sulfur compounds have a significant impact on sulfur metabolism genes, with sulfide significantly affecting low-salinity soils in the surface and deep layers, whereas salinity and sulfane sulfur had a greater correlation with high-salinity soils. Correlation analysis further showed that Euryarchaeota clustered with Bacteroidetes and Balneolaeota, while Proteobacteria clustered with many phyla, such as Acidobacteria. Various sulfur metabolism genes were widely distributed in both clusters. Our results indicate that microorganisms actively participate in the sulfur cycle in saline soils and that soil depth can affect these processes and the structure of microbial communities to a greater extent than soil salinity.

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

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

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.

The Rhodanese PspE Converts Thiosulfate to Cellular Sulfane Sulfur in Escherichia coli

Hydrogen sulfide (H₂S) and its oxidation product zero-valent sulfur (S⁰) play important roles in animals, plants, and bacteria. Inside cells, S⁰ exists in various forms, including polysulfide and persulfide, which are collectively referred to as sulfane sulfur. Due to the known health benefits, the donors of H₂S and sulfane sulfur have been developed and tested. Among them, thiosulfate is a known H₂S and sulfane sulfur donor. We have previously reported that thiosulfate is an effective sulfane sulfur donor in Escherichia coli; however, it is unclear how it converts thiosulfate to cellular sulfane sulfur. In this study, we showed that one of the various rhodaneses, PspE, in E. coli was responsible for the conversion. After the thiosulfate addition, the ΔpspE mutant did not increase cellular sulfane sulfur, but the wild type and the complemented strain ΔpspE::pspE increased cellular sulfane sulfur from about 92 μM to 220 μM and 355 μM, respectively. LC-MS analysis revealed a significant increase in glutathione persulfide (GSSH) in the wild type and the ΔpspE::pspE strain. The kinetic analysis supported that PspE was the most effective rhodanese in E. coli in converting thiosulfate to glutathione persulfide. The increased cellular sulfane sulfur alleviated the toxicity of hydrogen peroxide during E. coli growth. Although cellular thiols might reduce the increased cellular sulfane sulfur to H₂S, increased H₂S was not detected in the wild type. The finding that rhodanese is required to convert thiosulfate to cellular sulfane sulfur in E. coli may guide the use of thiosulfate as the donor of H₂S and sulfane sulfur in human and animal tests.

Potential Auxiliary Metabolic Capabilities and Activities Reveal Biochemical Impacts of Viruses in Municipal Wastewater Treatment Plants

Viruses influence biogeochemical cycles in oceans, freshwater, soil, and human gut through infection and by modulating virocell metabolism through virus-encoded auxiliary metabolic genes (vAMGs). However, the geographical distribution, potential metabolic function, and engineering significance of vAMGs in wastewater treatment plants (WWTPs) remain to be explored. Here, 752 single-contig viral genomes with high confidence, 510 of which belonged to Caudovirales, were recovered from the activated sludge metagenomes of 32 geographically distributed WWTPs. A total of 101 vAMGs involved in various metabolic pathways were identified, the most common of which were the queuosine biosynthesis genes folE, queD, and queE and the sulfur metabolism gene cysH. Phylogenetic analysis and virus-host relationship prediction revealed the probable evolutionary histories of vAMGs involved in carbon (acpP and prsA), nitrogen (amoC), sulfur (cysH), and phosphate (phoH) metabolism, which potentially mediate microbial carbon and nutrient cycling. Notably, 11 of the 38 (28.3%) vAMGs identified in the metagenomes with corresponding metatranscriptomes were transcriptionally expressed, implying an active functional state. This meta-analysis provides the first broad catalog of vAMGs in municipal WWTPs and how they may assist in the basic physiological reactions of their microbial hosts or nutrient cycling in the WWTPs, and therefore, may have important effects on the engineering of wastewater treatment processes.

Recent Advances in Biotechnologies for the Treatment of Environmental Pollutants Based on Reactive Sulfur Species

The definition of reactive sulfur species (RSS) is inspired by the reactivity and variable chemical valence of sulfur. Sulfur is an essential element for life and is a part of global geochemical cycles. Wastewater treatment bioreactors can be divided into two major categories: sulfur reduction and sulfur oxidation. We review the origins of the definition of RSS and related biotechnological processes in environmental management. Sulfate reduction, sulfide oxidation, and sulfur-based redox reactions are key to driving the coupled global carbon, nitrogen, and sulfur co-cycles. This shows the coupling of the sulfur cycle with the carbon and nitrogen cycles and provides insights into the global material-chemical cycle. We also review the biological classification and RSS metabolic mechanisms of functional microorganisms involved in the biological processes, such as sulfate-reducing and sulfur-oxidizing bacteria. Developments in molecular biology and genomic technologies have allowed us to obtain detailed information on these bacteria. The importance of RSS in environmental technologies requires further consideration.

New microbial electrosynthesis system for methane production from carbon dioxide coupled with oxidation of sulfide to sulfate

Microbial electrosynthesis system (MES) is a promising method that can use carbon dioxide, which is a greenhouse gas, to produce methane which acts as an energy source, without using organic substances. However, this bioelectrical reduction reaction can proceed at a certain high applied voltage when coupled with water oxidation in the anode coated with metallic catalyst. When coupled with the oxidation of HS^- to SO₄^2-, methane production is thermodynamically more feasible, thus implying its production at a considerably lower applied voltage. In this study, we demonstrated the possibility of electrotrophic methane production coupled with HS^- oxidation in a cost-effective bioanode chamber in the MES without organic substrates at a low applied voltage of 0.2 V. In addition, microbial community analyses of biomass enriched in the bioanode and biocathode were used to reveal the most probable pathway for methane production from HS^- oxidation. In the bioanode, electroautotrophic SO₄^2- production accompanied with electron donation to the electrode is performed mainly by the following two steps: first, incomplete sulfide oxidation to sulfur cycle intermediates (SCI) is performed; then the produced SCI are disproportionated to HS^- and SO₄^2-. In the biocathode, methane is produced mainly via H₂ and acetate by electron-accepting syntrophic bacteria, homoacetogens, and acetoclastic archaea. Here, a new eco-friendly MES with biological H₂S removal is established.

Riddles of Lost City: Chemotrophic Prokaryotes Drives Carbon, Sulfur, and Nitrogen Cycling at an Extinct Cold Seep, South China Sea

Deep-sea cold seeps are one of the most productive ecosystems that sustained by hydrocarbons carried by the fluid. Once the seep fluid ceases, the thriving autotrophic communities die out, terming as the extinct seep. But heterotrophic fauna can still survive even for thousands of years. The critical role of prokaryotes in active seeps are well defined, but their functions in extinct seeps are poorly understood to date. Here, we clarified the diversity, taxonomic specificity, interspecies correlation, and metabolic profiles of sediment prokaryotes at an extinct seep site of Haima cold seep, South China Sea. Alpha diversity of archaea significantly increased, while that of bacteria remained unchanged in extinct seep compared to active seep. However, archaea composition did not differ significantly at extinct seep from active or nonseep sites based on weighted-unifrac dissimilarity, while bacteria composition exhibited significant difference. Distribution of archaea and bacteria showed clear specificity to extinct seeps, indicating the unique life strategies here. Prokaryotes might live chemolithoautotrophically on cycling of inorganic carbon, sulfur, and nitrogen, or chemoorganotrophically on recycling of hydrocarbons. Notably, many of the extinct seep specific species and networked keystone lineages are classified as Proteobacteria. Regarding the functional diversity and metabolic flexibility of this clade, Proteobacteria is supposed to integrate the geochemical cycles and play a critical role in energy and resource supplement for microbiome in extinct seep. Collectively, our findings shed lights on the microbial ecology and functional diversity in extinct seeps, providing new understanding of biogeochemical cycling after fluid cessation. IMPORTANCE This research paper uncovered the potential mechanisms for microbiota mediated geochemical cycling in extinct cold seep, advancing our understanding in deep sea microbiology ecology.

A sulfide-sensor and a sulfane sulfur-sensor collectively regulate sulfur-oxidation for feather degradation by Bacillus licheniformis

Bacillus licheniformis MW3 degrades bird feathers. Feather keratin is rich in cysteine, which is metabolized to produce hazardous sulfide and sulfane sulfur. A challenge to B. licheniformis MW3 growing on feathers is to detoxify them. Here we identified a gene cluster in B. licheniformis MW3 to deal with these toxicity. The cluster contains 11 genes: the first gene yrkD encodes a repressor, the 8^th and 9^th genes nreB and nreC encode a two-component regulatory system, and the 10th and 11th genes encode sulfide: quinone reductase (SQR) and persulfide oxygenase (PDO). SQR and PDO collectively oxidize sulfide and sulfane sulfur to sulfite. YrkD sensed sulfane sulfur to derepress the 11 genes. The NreBC system sensed sulfide and further amplified the transcription of sqr and pdo. The two regulatory systems synergistically controlled the expression of the gene cluster, which was required for the bacterium to grow on feather. The findings highlight the necessity of removing sulfide and sulfane sulfur during feather degradation and may help with bioremediation of feather waste and sulfide pollution.

The Transcriptional Repressor PerR Senses Sulfane Sulfur by Cysteine Persulfidation at the Structural Zn2+ Site in Synechococcus sp. PCC7002

Cyanobacteria can perform both anoxygenic and oxygenic photosynthesis, a characteristic which ensured that these organisms were crucial in the evolution of the early Earth and the biosphere. Reactive oxygen species (ROS) produced in oxygenic photosynthesis and reactive sulfur species (RSS) produced in anoxygenic photosynthesis are closely related to intracellular redox equilibrium. ROS comprise superoxide anion (O₂^●-), hydrogen peroxide (H₂O₂), and hydroxyl radicals (^●OH). RSS comprise H₂S and sulfane sulfur (persulfide, polysulfide, and S₈). Although the sensing mechanism for ROS in cyanobacteria has been explored, that of RSS has not been elucidated. Here, we studied the function of the transcriptional repressor PerR in RSS sensing in Synechococcus sp. PCC7002 (PCC7002). PerR was previously reported to sense ROS; however, our results revealed that it also participated in RSS sensing. PerR repressed the expression of prxI and downregulated the tolerance of PCC7002 to polysulfide (H₂S_n). The reporter system indicated that PerR sensed H₂S_n. Cys¹²¹ of the Cys4:Zn²⁺ site, which contains four cysteines (Cys¹²¹, Cys¹²⁴, Cys¹⁶⁰, and Cys¹⁶³) bound to one zinc atom, could be modified by H₂S_n to Cys¹²¹-SSH, as a result of which the zinc atom was released from the site. Moreover, Cys¹⁹ could also be modified by polysulfide to Cys¹⁹-SSH. Thus, our results reveal that PerR, a representative of the Cys₄ zinc finger proteins, senses H₂S_n. Our findings provide a new perspective to explore the adaptation strategy of cyanobacteria in Proterozoic and contemporary sulfurization oceans.

Cupriavidus pinatubonensis JMP134 Alleviates Sulfane Sulfur Toxicity after the Loss of Sulfane Dehydrogenase through Oxidation by Persulfide Dioxygenase and Hydrogen Sulfide Release

An incomplete Sox system lacking sulfane dehydrogenase SoxCD may produce and accumulate sulfane sulfur when oxidizing thiosulfate. However, how bacteria alleviate the pressure of sulfane sulfur accumulation remains largely unclear. In this study, we focused on the bacterium Cupriavidus pinatubonensis JMP134, which contains a complete Sox system. When soxCD was deleted, this bacterium temporarily produced sulfane sulfur when oxidizing thiosulfate. Persulfide dioxygenase (PDO) in concert with glutathione oxidizes sulfane sulfur to sulfite. Sulfite can spontaneously react with extra persulfide glutathione (GSSH) to produce thiosulfate, which can feed into the incomplete Sox system again and be oxidized to sulfate. Furthermore, the deletion strain lacking PDO and SoxCD produced volatile H₂S gas when oxidizing thiosulfate. By comparing the oxidized glutathione (GSSG) between the wild-type and deletion strains, we speculated that H₂S is generated during the interaction between sulfane sulfur and the glutathione/oxidized glutathione (GSH/GSSG) redox couple, which may reduce the oxidative stress caused by the accumulation of sulfane sulfur in bacteria. Thus, PDO and H₂S release play a critical role in alleviating sulfane sulfur toxicity after the loss of soxCD in C. pinatubonensis JMP134.

Production of selenium nanoparticles occurs through an interconnected pathway of sulphur metabolism and oxidative stress response in Pseudomonas putida KT2440

The soil bacterium Pseudomonas putida KT2440 has been shown to produce selenium nanoparticles aerobically from selenite; however, the molecular actors involved in this process are unknown. Here, through a combination of genetic and analytical techniques, we report the first insights into selenite metabolism in this bacterium. Our results suggest that the reduction of selenite occurs through an interconnected metabolic network involving central metabolic reactions, sulphur metabolism, and the response to oxidative stress. Genes such as sucA, D2HGDH and PP_3148 revealed that the 2-ketoglutarate and glutamate metabolism is important to convert selenite into selenium. On the other hand, mutations affecting the activity of the sulphite reductase decreased the bacteria's ability to transform selenite. Other genes related to sulphur metabolism (ssuEF, sfnCE, sqrR, sqr and pdo2) and stress response (gqr, lsfA, ahpCF and sadI) were also identified as involved in selenite transformation. Interestingly, suppression of genes sqrR, sqr and pdo2 resulted in the production of selenium nanoparticles at a higher rate than the wild-type strain, which is of biotechnological interest. The data provided in this study brings us closer to understanding the metabolism of selenium in bacteria and offers new targets for the development of biotechnological tools for the production of selenium nanoparticles.

Interactions among deep-sea mussels and their epibiotic and endosymbiotic chemoautotrophic bacteria: Insights from multi-omics analysis

Endosymbiosis with Gammaproteobacteria is fundamental for the success of bathymodioline mussels in deep-sea chemosynthesis-based ecosystems. However, the recent discovery of Campylobacteria on the gill surfaces of these mussels suggests that these host-bacterial relationships may be more complex than previously thought. Using the cold-seep mussel ( Gigantidas haimaensis) as a model, we explored this host-bacterial system by assembling the host transcriptome and genomes of its epibiotic Campylobacteria and endosymbiotic Gammaproteobacteria and quantifying their gene and protein expression levels. We found that the epibiont applies a sulfur oxidizing (SOX) multienzyme complex with the acquisition of soxB from Gammaproteobacteria for energy production and switched from a reductive tricarboxylic acid (rTCA) cycle to a Calvin-Benson-Bassham (CBB) cycle for carbon assimilation. The host provides metabolic intermediates, inorganic carbon, and thiosulfate to satisfy the materials and energy requirements of the epibiont, but whether the epibiont benefits the host is unclear. The endosymbiont adopts methane oxidation and the ribulose monophosphate pathway (RuMP) for energy production, providing the major source of energy for itself and the host. The host obtains most of its nutrients, such as lysine, glutamine, valine, isoleucine, leucine, histidine, and folate, from the endosymbiont. In addition, host pattern recognition receptors, including toll-like receptors, peptidoglycan recognition proteins, and C-type lectins, may participate in bacterial infection, maintenance, and population regulation. Overall, this study provides insights into the complex host-bacterial relationships that have enabled mussels and bacteria to thrive in deep-sea chemosynthetic ecosystems.

An Optimized Transformation Protocol for Escherichia coli BW3KD with Supreme DNA Assembly Efficiency

DNA cloning requires two steps: the assembly of recombinant DNA molecules and the transformation of the product into a host organism for replication. High efficiencies in both processes can increase the success rate. Recently, we developed an Escherichia coli BW3KD strain with higher transformation efficiency than commonly used cloning strains. Here, we further developed a simple method named TSS-HI (transformation storage solution optimized by Hannahan and Inoue method) for competent cell preparation, which combined the advantages of three common methods for operational simplicity and high transformation efficiency. When competent BW3KD cells were prepared using this developed method, the transformation efficiency reached up to (7.21 ± 1.85) × 10⁹ CFU/μg DNA, which exceeded the levels of commercial chemically competent cells and homemade electrocompetent cells. BW3KD cells formed colonies within 7 h on lysogeny broth agar plates, quicker than the well-known fast-growing E. coli cloning strain Mach1. The competent cells worked effectively for the transformation of assembled DNA of 1 to 7 fragments in one step and promoted efficiencies of transformation or cloning with large plasmids. The cloning efficiency of BW3KD cells prepared by this method increased up to 828-fold over that of E. coli XL1-Blue MRF' cells prepared by a common method. Thus, competent cells are suitable for different cloning jobs and should help with the increased demand for DNA assembly in biological studies and biotechnology. IMPORTANCE DNA transformation is commonly used in cloning; however, high transformation efficiency becomes a limiting factor in many applications, such as the construction of CRISPR and DNA libraries, the assembly of multiple fragments, and the transformation of large plasmids. We developed a new competent cell preparation method with unmatched transformation efficiency. When the BW3KD strain, derived from Escherichia coli BW25113 cells, was prepared by this method, its transformation efficiency reached up to (7.21 ± 1.85) × 10⁹ CFU/μg DNA, which broke the record for chemically prepared competent cells. Routine cloning could be completed in 1 day due to the high growth rate of this strain. The competent cells were shown to be highly efficient for transformation or cloning with large plasmids and for the assembly of multiple fragments. The results highlight the effectiveness of the new protocol and the usefulness of the BW3KD strain as the host.