Sulfite Reductase Research Articles

Characterization of DsrD and its interaction with the DsrAB dissimilatory sulfite reductase.

Microbial dissimilatory sulfate reduction is a key process in the global sulfur and carbon cycles in anoxic ecosystems. In this anaerobic respiration, sulfate is phosphorylated and reduced to sulfite, which is further reduced to a DsrC-trisulfide by the dissimilatory sulfite reductase DsrAB. DsrD is a small protein that acts as an allosteric activator of DsrAB, increasing the efficiency of sulfite reduction. Here, we report a detailed study of DsrD and its interaction with DsrAB. Sequence similarity analyses show that there are three groups of DsrD in organisms with a reductive-type DsrAB. The protein regions involved in the DsrD-DsrAB interaction and activity-promoting effect were investigated through in vitro and in silico studies, including mutations of conserved DsrD residues. The results reveal that the conserved β-loop of DsrD is involved in the interaction, contributing to a better understanding of its mechanism of action.

High-throughput genetics enables identification of nutrient utilization and accessory energy metabolism genes in a model methanogen.

Archaea are widespread in the environment and play fundamental roles in diverse ecosystems; however, characterization of their unique biology requires advanced tools. This is particularly challenging when characterizing gene function. Here, we generate randomly barcoded transposon libraries in the model methanogenic archaeon Methanococcus maripaludis and use high-throughput growth methods to conduct fitness assays (RB-TnSeq) across over 100 unique growth conditions. Using our approach, we identified new genes involved in nutrient utilization and response to oxidative stress. We identified novel genes for the usage of diverse nitrogen sources in M. maripaludis including a putative regulator of alanine deamination and molybdate transporters important for nitrogen fixation. Furthermore, leveraging the fitness data, we inferred that M. maripaludis can utilize additional nitrogen sources including ʟ-glutamine, ᴅ-glucuronamide, and adenosine. Under autotrophic growth conditions, we identified a gene encoding a domain of unknown function (DUF166) that is important for fitness and hypothesize that it has an accessory role in carbon dioxide assimilation. Finally, comparing fitness costs of oxygen versus sulfite stress, we identified a previously uncharacterized class of dissimilatory sulfite reductase-like proteins (Dsr-LP; group IIId) that is important during growth in the presence of sulfite. When overexpressed, Dsr-LP conferred sulfite resistance and enabled use of sulfite as the sole sulfur source. The high-throughput approach employed here allowed for generation of a large-scale data set that can be used as a resource to further understand gene function and metabolism in the archaeal domain.IMPORTANCEArchaea are widespread in the environment, yet basic aspects of their biology remain underexplored. To address this, we apply randomly barcoded transposon libraries (RB-TnSeq) to the model archaeon Methanococcus maripaludis. RB-TnSeq coupled with high-throughput growth assays across over 100 unique conditions identified roles for previously uncharacterized genes, including several encoding proteins with domains of unknown function (DUFs). We also expand on our understanding of carbon and nitrogen metabolism and characterize a group IIId dissimilatory sulfite reductase-like protein as a functional sulfite reductase. This data set encompasses a wide range of additional conditions including stress, nitrogen fixation, amino acid supplementation, and autotrophy, thus providing an extensive data set for the archaeal community to mine for characterizing additional genes of unknown function.

The sewer advances: How to select eco-friendly pipe materials for environmental protection

Sewer pipe materials exhibit diverse inner-surface features, which can affect the attachment of biofilm and influence microbial metabolic processes. To investigate the role of the type of pipe material on the composition and metabolic capabilities of the adhering microorganisms, three sets of urban sewers (High-Density Polyethylene Pipe (HDPE), Ductile Iron Pipe (DIP), and Concrete Pipe (CP)) were constructed. Measurements of biofilm thickness and environmental factors revealed that the thickest biofilm in CP pipes reached 2000 μm, with ORP values as low as −325 mV, indicating a more suitable anaerobic microbial habitat. High-throughput sequencing showed similar relative abundances of genera related to carbon and sulfur metabolism in the DIP and CP pipes, whereas HDPE exhibited only half the relative abundance compared to that found in the other pipes. To explore the impact of pipe materials on the mechanisms of microbial response, a metagenomic approach was used to investigate the biological transformation of carbon and sulfur in wastewater. The annotations of the crucial enzyme-encoding genes related to methyl coenzyme M and sulfite reductase in DIP and CP were 50 and 110, respectively, whereas HDPE exhibited lower counts (25 and 70, respectively). This resulted in significantly lower carbon and sulfur metabolism capabilities in the HDPE biofilm than in the other two pipes. The stability of wastewater quality during the transmission process in HDPE pipes reduces the metabolic generation of toxic and harmful gases within the pipes, favoring the preservation of carbon sources for sewer systems. This study reveals the variations in carbon and sulfur metabolism in wastewater pipe systems influenced by pipe materials and provides insights for designing future sewers.

Regulatory roles of extracellular polymeric substances in uranium reduction via extracellular electron transfer by Desulfovibrio vulgaris UR1

The pathway of reducing U(VI) to insoluble U(IV) using electroactive bacteria has become an effective and promising approach to address uranium-contaminated water caused by human activities. However, knowledge regarding the roles of extracellular polymeric substances (EPS) in the uranium reduction process involving in extracellular electron transfer (EET) mechanisms is limited. Here, this study isolated a novel U(VI)-reducing strain, Desulfovibrio vulgaris UR1, with a high uranium removal capacity of 2.75 mM/(g dry cell). Based on a reliable EPS extraction method (45 °C heating), manipulation of EPS in D. vulgaris UR1 suspensions (removal or addition of EPS) highlighted its critical role in facilitating uranium reduction efficiency. On the second day, U(VI) removal rates varied significantly across systems with different EPS contents: 60.8% in the EPS-added system, 48.5% in the pristine system, and 22.2% in the EPS-removed system. Characterization of biogenic solids confirmed the reduction of U(VI) by D. vulgaris UR1, and the main products were uraninite and UO2 (2.88–4.32 nm in diameter). As EPS formed a permeable barrier, these nanoparticles were primarily immobilized within the EPS in EPS-retained/EPS-added cells, and within the periplasm in EPS-removed cells. Multiple electroactive substances, such as tyrosine/tryptophan aromatic compounds, flavins, and quinone-like substances, were identified in EPS, which might be the reason for enhancement of uranium reduction via providing more electron shuttles. Furthermore, proteomics revealed that a large number of proteins in EPS were enriched in the subcategories of catalytic activity and electron transfer activity. Among these, iron-sulfur proteins, such as hydroxylamine reductase (P31101), pyruvate: ferredoxin oxidoreductase (A0A0H3A501), and sulfite reductase (P45574), played the most critical role in regulating EET in D. vulgaris UR1. This work highlighted the importance of EPS in the uranium reduction by D. vulgaris UR1, indicating that EPS functioned as both a reducing agent and a permeation barrier for access to heavy metal uranium.

Impact of Graphene Layers on Genetic Expression and Regulation within Sulfate-Reducing Biofilms.

Bacterial adhesion and biofilm maturation is significantly influenced by surface properties, encompassing both bare surfaces and single or multi-layered coatings. Hence, there is an utmost interest in exploring the intricacies of gene regulation in sulfate-reducing bacteria (SRB) on copper and graphene-coated copper surfaces. In this study, Oleidesulfovibrio alaskensis G20 was used as the model SRB to elucidate the pathways that govern pivotal roles during biofilm formation on the graphene layers. Employing a potent reporter green fluorescent protein (GFP) tagged to O. alaskensis G20, the spatial structure of O. alaskensis G20 biofilm on copper foil (CuF), single-layer graphene-coated copper (Cu-GrI), and double-layer graphene-coated copper (Cu-GrII) surfaces was investigated. Biofilm formation on CuF, Cu-GrI, and Cu-GrII surfaces was quantified using CLSM z-stack images within COMSTAT v2 software. The results revealed that CuF, Cu-GrI, and Cu-GrII did not affect the formation of the GFP-tagged O. alaskensis G20 biofilm architecture. qPCR expression showed insignificant fold changes for outer membrane components regulating the quorum-sensing system, and global regulatory proteins between the uncoated and coated surfaces. Notably, a significant expression was observed within the sulfate reduction pathway confined to dissimilatory sulfite reductases on the Cu-GrII surface compared to the CuF and Cu-GrI surfaces.

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

BackgroundH2S 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.ResultsOur 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.ConclusionsOur 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.Dka3P5uGJeBhH66pkNJcogVideo

Integrated multi-omics analyses reveal microbial community resilience to fluctuating low oxygen in the East China sea

Climate change and eutrophication are accelerating ocean deoxygenation, leading to a global decline in oxygen levels. The East China Sea, frequently experiencing deoxygenation events, harbors diverse microbial communities. However, the response of these communities to the changing deoxygenation dynamics remains poorly understood. Here, we explored the composition and function of microbial communities inhabiting seawaters of the Changjiang Estuary and offshore areas. Our findings suggested that neutral processes significantly influenced the assembly of these communities. The overall bacterial composition demonstrated remarkable high stability across the oxygen gradient. Salinity exhibited a significantly stronger correlation with bacterial community structure than dissolved oxygen. Both metagenomics and metaproteomics revealed that all of the samples exhibited similar functional community structures. Heterotrophic metabolism dominated these sites, as evidenced by a diverse array of transporters and metabolic enzymes for organic matter uptake and utilization, which constituted a significant portion of the expressed proteins. O2 was the primary electron acceptor in bacteria even under hypoxic conditions, evidenced by expression of low- and high-affinity cytochrome oxidases. Proteins associated with anaerobic processes, such as dissimilatory sulfite reductases, were virtually undetectable. Untargeted liquid chromatography with tandem mass spectrometry analysis of seawater samples revealed a diverse range of dissolved organic matter (DOM) components in amino acids, lipids, organic acids, peptides, and carbohydrates, potentially fueling dominant taxa growth. Despite fluctuations in the abundance of specific genera, the remarkable similarity in community structure, function, and DOM suggests that this ecosystem possesses robust adaptive mechanisms that buffer against abrupt changes, even below the well-defined hypoxic threshold in marine ecosystem.

Integrating double-labeling HCR-FISH into a multidisciplinary pipeline for biofouling assessment on austenitic stainless steel in brackish seawater circuit

This study modified and integrated a bioimaging method of hybridization chain reaction fluorescence in situ hybridization (HCR-FISH) into a pipeline for assessing biofouling on stainless steel (SS). A modified protocol of double-labeling HCR-FISH was directly applied to two surface types of SS grade EN 1.4404 to detect localized bacteria and sulfate-reducing bacteria (SRB) by targeting bacterial 16 S rRNA genes and dissimilatory sulfite reductase (dsrB) genes, respectively. The protocol was first validated using microbial pure cultures and materials before being integrated into a biofouling assessment pipeline of SS in a laboratory-scale brackish water circuit, incorporating electrochemical, surface, and molecular biology characterization analyses. The double-labeling HCR-FISH improved bioimaging of surface biofilm morphology and microbial distribution, surpassing monochrome staining methods. This method was compatible and complemented other microscopy techniques and molecular biological analyses, providing additional insights into the biofilms and deposits on the alloy surfaces. The implemented assessment pipeline for biofouling determination frequently detected the ennoblement phenomenon in the evolution of marine biofilm on SS surfaces. However, within the experimental timeframe, microbial activities in the brackish seawater circuit did not flourish significantly, resulting in minimal impact on the steel material. Additionally, surface type and roughness may correlate with microbial adhesion, biofilm growth, and the deformation of passivation layers in SS. Despite abundant sessile bacteria, particularly opportunistic microorganisms, on the steel surfaces, no direct correlations with biodeterioration phenomena or influences of surface roughness of an alloy and the presence of biofilm were conclusively established.

Comparative analysis of microbial community under acclimation of linear alkylbenzene sulfonate (LAS) surfactants and degradation mechanisms of functional strains

Linear alkylbenzene sulfonate (LAS) is one of the most widely used anionic surfactants and a common toxic pollutant in wastewater. This study employed high throughput sequencing to explore the microbial community structure within activated sludge exposed to a high concentration of LAS. Genera such as Pseudomonas, Aeromonas, Thauera and Klebsiella exhibited a significant positive correlation with LAS concentrations. Furthermore, Comamonas and Klebsiella were significantly enriched under the stress of LAS. Moreover, bacterial strains with LAS-degrading capability were isolated and characterized to elucidate the degradation pathways. The Klebsiella pneumoniae isolate L1 could effectively transform more than 60 % of 25 mg/L of LAS within 72 h. Chemical analyses revealed that L1 utilized the LAS sulfonyl group as a sulfur source to support its growth. Genomic and transcriptomic analyses suggested that strain L1 may uptake LAS through the sulfate ABC transport system and remove sulfonate with sulfate and sulfite reductases.

Intermediates involved in the reduction of SO2: insight into the mechanism of sulfite reductases.

Sulfite reductases (SiRs) catalyze the reduction of SO32- to H2S in biosynthetic sulfur assimilation and dissimilation of sulfate. The mechanism of the 6e-/6H+ reduction of SO32- at the siroheme cofactor is debated, and proposed intermediates involved in this 6e- reduction are yet to be spectroscopically characterized. The reaction of SO2 with a ferrous iron porphyrin is investigated, and two intermediates are trapped and characterized: an initial Fe(III)-SO22- species, which undergoes proton-assisted S-O bond cleavage to form an Fe(III)-SO species. These species are characterized using a combination of resonance Raman (with 34S-labelled SO2), EPR and DFT calculations. Results obtained help reconcile the different proposed mechanisms for the SiRs.

Dimerization of assimilatory NADPH-dependent sulfite reductase reveals elements for diflavin reductase binding at a minimal interface.

Escherichia coli NADPH-dependent assimilatory sulfite reductase is responsible for fixing sulfur for incorporation into sulfur-containing biomolecules. The oxidoreductase is composed of two subunits, an NADPH, FMN, and FAD-binding diflavin reductase and an iron siroheme and Fe4S4-containing oxidase. How they interact has been an unknown for over 50 years because the complex is highly flexible, thus has been intransigent for traditional X-ray or cryo-EM structural analysis. Using a combination of the chameleon plunging system with a fluorinated lipid we overcame the challenge of preserving the minimal dimer between the subunits for high-resolution cryo-EM analysis. Here, we report the first structure of the complex between the reductase and oxidase, revealing how they interact in a minimal interface. Further, we determined the structural elements that discriminate between the pairing of a siroheme-containing oxidase with a diflavin reductase or a ferredoxin partner to channel the six electrons that reduce sulfite to sulfide.

The coexistence of arbuscular mycorrhizal fungi and dark septate endophytes synergistically enhanced the cadmium tolerance of maize

IntroductionArbuscular mycorrhizal fungi (AMF) and dark septate endophytic fungi (DSEs) generally coexist in the roots of plants. However, our understanding of the effects of their coexistence on plant growth and stress resistance is limited.MethodsIn the present study, the effects of single and dual inoculation of AMF and DSE on the growth, photosynthetic physiology, glutathione (GSH) metabolism, endogenous hormones, and cadmium (Cd) content of maize under 25 mg•kg-1 Cd stress were investigated.ResultsCompared with that after the non-inoculation treatment, AMF+DSE co-inoculation significantly increased the photosynthetic rate (Pn) of maize leaves; promoted root GSH metabolism; increased the root GSH concentration and activity of γ-glutamyl cysteine synthase (γ-GCS), ATP sulfatase (ATPS) and sulfite reductase (SIR) by 215%, 117%, 50%, and 36%, respectively; and increased the concentration of endogenous hormones in roots, with increases in zeatin (ZR), indole-3 acetic acid (IAA), and abscisic acid (ABA) by 81%, 209%, and 72%, respectively. AMF inoculation, DSE inoculation and AMF+DSE co-inoculation significantly increased maize biomass, and single inoculation with AMF or DSE increased the Cd concentration in roots by 104% or 120%, respectively. Moreover, significant or highly significant positive correlations were observed between the contents of ZR, IAA, and ABA and the activities of γ-GCS, ATPS, and SIR and the glutathione (GSH) content. There were significant or highly significant positive interactions between AMF and DSE on the Pn of leaves, root GSH metabolism, and endogenous hormone contents according to two-way analysis of variance. Therefore, the coexistence of AMF and DSE synergistically enhanced the Cd tolerance of maize.

Reaction Mechanism Catalyzed by the Dissimilatory Sulfite Reductase - The Role of the Siroheme-[4FeS4] Cofactor.

The present work is another part of our investigation on the pathway of dissimilatory sulfate reduction and covers a theoretical study on the reaction catalyzed by dissimilatory sulfite reductase (dSIR). dSIR is the terminal enzyme involved in this metabolic pathway, which uses the siroheme-[4Fe4S] cofactor for six-electron reduction of sulfite to sulfide. In this study we use a large cluster model containing siroheme-[4Fe4S] cofactor and protein residues involved in the direct interactions with the substrate, to get insight into the most feasible reaction mechanism and to understand the role of each considered active site component. In combination with earlier studies reported in the literature, our results lead to several interesting insights. One of the most important conclusions is that the reaction mechanism consists of three steps of two-electron reduction of sulfur and the probable role of the siroheme-[4Fe4S] cofactor is to ensure the delivery of packages of two electrons to the reactant.

Pathways and contributions of sulfate reducing-bacteria to arsenic cycling in landfills

Sulfate-reducing bacteria (SRB) are generally found in sanitary landfills and play a role in sulfur (S) and metal/metalloid geochemical cycling. In this study, we investigated the influence of SRB on arsenic (As) metabolic pathways in refuse-derived cultures. The results indicated that SRB promote As(III) methylation and are beneficial for controlling As levels. Heterotrophic and autotrophic SRB showed significant differences during As cycling. In heterotrophic SRB cultures, the As methylation rate increased with As(III) concentration in the medium and reached a peak (85.1%) in cultures containing 25 mg L−1 As(III). Moreover, 4.0–12.6% of SO42− was reduced to S2−, which then reacted with As(III) to form realgar (AsS). In contrast, autotrophic SRB oxidized As(III) to less toxic As(V) under anaerobic conditions. Heterotrophic arsM-harboring SRB, such as Desulfosporosinus, Desulfocurvibacter, and Desulfotomaculum, express As-related genes and are considered key genera for As methylation in landfills. Thiobacillus are the main autotrophic SRB in landfills and can derive energy by oxidizing sulfur compounds and metal(loid)s. These results suggest that different types of SRB drive As methylation, redox reaction, and mineral formation in landfills. These study findings have implications for the management of As pollutants in landfills and other contaminated environments.

Pungency related gene network in Allium sativum L., response to sulfur treatments

Pungency of garlic (Allium sativum L.) is generated from breakdown of the alk(en)yl cysteine sulphoxide (CSO), alliin and its subsequent breakdown to allicin under the activity of alliinase (All). Based on recent evidence, two other important genes including Sulfite reductase (SiR) and Superoxide dismutase (SOD) are thought to be related to sulfur metabolism. These three gene functions are in sulfate assimilation pathway. However, whether it is involved in stress response in crops is largely unknown. In this research, the order and priority of simultaneous expression of three genes including All, SiR and SOD were measured on some garlic ecotypes of Iran, collected from Zanjan, Hamedan and Gilan, provinces under sulfur concentrations (0, 6, 12, 24 and 60 g/ per experimental unit: pot) using real-time quantitative PCR (RT-qPCR) analysis. For understanding the network interactions between studied genes and other related genes, in silico gene network analysis was constructed to investigate various mechanisms underlying stimulation of A. sativum L. to cope with imposed sulfur. Complicated network including TF-TF, miRNA-TF, and miRNA-TF-gene, was split into sub-networks to have a deeper insight. Analysis of q-RT-PCR data revealed the highest expression in All and SiR genes respectively. To distinguish and select significant pathways in sulfur metabolism, RESNET Plant database of Pathway Studio software v.10 (Elsevier), and other relative data such as chemical reactions, TFs, miRNAs, enzymes, and small molecules were extracted. Complex sub-network exhibited plenty of routes between stress response and sulfate assimilation pathway. Even though Alliinase did not display any connectivity with other stress response genes, it showed binding relation with lectin functional class, as a result of which connected to leucine zipper, exocellulase, peroxidase and ARF functional class indirectly. Integration network of these genes revealed their involvement in various biological processes such as, RNA splicing, stress response, gene silencing by miRNAs, and epigenetic. The findings of this research can be used to extend further research on the garlic metabolic engineering, garlic stress related genes, and also reducing or enhancing the activity of the responsible genes for garlic pungency for health benefits and industry demands.

Reconstruction of the genome-scale metabolic network model of Sinorhizobium fredii CCBAU45436 for free-living and symbiotic states.

Sinorhizobium fredii CCBAU45436 is an excellent rhizobium that plays an important role in agricultural production. However, there still needs more comprehensive understanding of the metabolic system of S. fredii CCBAU45436, which hinders its application in agriculture. Therefore, based on the first-generation metabolic model iCC541 we developed a new genome-scale metabolic model iAQY970, which contains 970 genes, 1,052 reactions, 942 metabolites and is scored 89% in the MEMOTE test. Cell growth phenotype predicted by iAQY970 is 81.7% consistent with the experimental data. The results of mapping the proteome data under free-living and symbiosis conditions to the model showed that the biomass production rate in the logarithmic phase was faster than that in the stable phase, and the nitrogen fixation efficiency of rhizobia parasitized in cultivated soybean was higher than that in wild-type soybean, which was consistent with the actual situation. In the symbiotic condition, there are 184 genes that would affect growth, of which 94 are essential; In the free-living condition, there are 143 genes that influence growth, of which 78 are essential. Among them, 86 of the 94 essential genes in the symbiotic condition were consistent with the prediction of iCC541, and 44 essential genes were confirmed by literature information; meanwhile, 30 genes were identified by DEG and 33 genes were identified by Geptop. In addition, we extracted four key nitrogen fixation modules from the model and predicted that sulfite reductase (EC 1.8.7.1) and nitrogenase (EC 1.18.6.1) as the target enzymes to enhance nitrogen fixation by MOMA, which provided a potential focus for strain optimization. Through the comprehensive metabolic model, we can better understand the metabolic capabilities of S. fredii CCBAU45436 and make full use of it in the future.

Effect of target gene sequence evenness and dominance on real-time PCR quantification of artificial sulfate-reducing microbial communities.

Quantitative real-time PCR of phylogenetic and functional marker genes is among the most commonly used techniques to quantify the abundance of microbial taxa in environmental samples. However, in most environmental applications, the approach is a rough assessment of population abundance rather than an exact absolute quantification method because of PCR-based estimation biases caused by multiple factors. Previous studies on these technical issues have focused on primer or template sequence features or PCR reaction conditions. However, how target gene sequence characteristics (e.g., evenness and dominance) in environmental samples affect qPCR quantifications has not been well studied. Here, we compared three primer sets targeting the beta subunit of the dissimilatory sulfite reductase (dsrB) to investigate qPCR quantification performance under different target gene sequence evenness and dominance conditions using artificial gBlock template mixtures designed accordingly. Our results suggested that the qPCR quantification performance of all tested primer sets was determined by the comprehensive effect of the target gene sequence evenness and dominance in environmental samples. Generally, highly degenerate primer sets have equivalent or better qPCR quantification results than a more target-specific primer set. Low template concentration in this study (~105 copies/L) will exaggerate the qPCR quantification results difference among tested primer sets. Improvements to the accuracy and reproducibility of qPCR assays for gene copy number quantification in environmental microbiology and microbial ecology studies should be based on prior knowledge of target gene sequence information acquired by metagenomic analysis or other approaches, careful selection of primer sets, and proper reaction conditions optimization.

Racial and Ethnic Minorities With Acute Pancreatitis Live in Neighborhoods With Higher Social Vulnerability Scores.

The primary objective was to determine differences in Social Vulnerability Index (SVI) scores among minorities (African-Americans and Hispanics) with acute pancreatitis (AP) compared with non-Hispanic whites (NHWs) with AP. The secondary objectives were to determine differences in diet, sulfidogenic bacteria gene copy numbers (gcn) and hydrogen sulfide (H2S) levels between the 2 groups. Patients with AP were enrolled during hospitalization (n = 54). Patient residential addresses were geocoded, and the Centers for Disease Control and Prevention's SVI scores were appended. Dietary intake and serum H2S levels were determined. Microbial DNAs were isolated from stool, and gcn of sulfidogenic bacteria were determined. Minorities had higher SVI scores compared with NHWs ( P = 0.006). They also had lower consumption of beneficial nutrients such as omega-3 fatty acids [stearidonic ( P = 0.019), and eicosapentaenoic acid ( P = 0.042)], vitamin D ( P = 0.025), and protein from seafood ( P = 0.031). Lastly, minorities had higher pan-dissimilatory sulfite reductase A ( pan-dsrA ) gcn ( P = 0.033) but no significant differences in H2S levels ( P = 0.226). Minorities with AP have higher SVI compared with NHWs with AP. Higher SVI scores, lower consumption of beneficial nutrients, and increased gcn of pan-dsrA in minorities with AP suggest that neighborhood vulnerability could be contributing to AP inequities.

Impact of microplastics on microbial-mediated soil sulfur transformations in flooded conditions

As emerging environmental pollutants, microplastics have become a crucial focus in environmental science research. Despite this, the impact of microplastics on soil in flooding conditions remains largely unexplored. Addressing this gap, our study examined the influence of polystyrene (PS) and polyphenylene sulfide (PPS) on the microbial populations in black soil, meadow soil, and paddy soil under flooded conditions. Given the significant regulatory influence exerted by microorganisms on sulfur transformations, our study was primarily focused on evaluating the microbial contributions to alterations in soil sulfur species. Our findings revealed several notable trends: In black soil, both PS and PPS led to a marked increase in the abundance of γ-proteobacteria and Subgroup_6, while reducing Clostridia. Ignavibacteria were found to be lower under PPS compared to PS. In meadow soil, the introduction of PPS resulted in increased levels of KD4–96 and γ-proteobacteria, while α-proteobacteria decreased. Chloroflexia under PPS was observed to be lower than under PS conditions. In paddy soil, our study identified a significant rise in Bacteroidia and Ignavibacteria, accompanied by a decrease in α-proteobacteria and γ-proteobacteria. γ-proteobacteria levels under PPS were notably higher than those under PS conditions. These shifts in microbial communities induced by both PS and PPS had a direct impact on adenosine 5′-phosphosulfate reductase, sulfite reductase, and polysulfide dioxygenase. Consequently, these changes led to soil organic sulfur decrease and sulfide increase. This study not only offers a theoretical framework but also provides empirical evidence for understanding the effects of microplastics on soil microorganisms and their role in regulating nutrient cycling, particularly in flood-prone conditions. Furthermore, this study underscores the importance of ensuring an adequate supply of sulfur in agricultural practices, such as rice and lotus root cultivation, to support optimal crop growth in the presence of microplastic pollution.

A novel mechanism for dissimilatory nitrate reduction to ammonium in Acididesulfobacillus acetoxydans.

The biological route of nitrate reduction has important implications for the bioavailability of nitrogen within ecosystems. Nitrate reduction via nitrite, either to ammonium (ammonification) or to nitrous oxide or dinitrogen (denitrification), determines whether nitrogen is retained within the system or lost as a gas. The acidophilic sulfate-reducing bacterium (aSRB) Acididesulfobacillus acetoxydans can perform dissimilatory nitrate reduction to ammonium (DNRA). While encoding a Nar-type nitrate reductase, A. acetoxydans lacks recognized nitrite reductase genes. In this study, A. acetoxydans was cultivated under conditions conducive to DNRA. During cultivations, we monitored the production of potential nitrogen intermediates (nitrate, nitrite, nitric oxide, hydroxylamine, and ammonium). Resting cell experiments were performed with nitrate, nitrite, and hydroxylamine to confirm their reduction to ammonium, and formed intermediates were tracked. To identify the enzymes involved in DNRA, comparative transcriptomics and proteomics were performed with A. acetoxydans growing under nitrate- and sulfate-reducing conditions. Nitrite is likely reduced to ammonia by the previously undescribed nitrite reductase activity of the NADH-linked sulfite reductase AsrABC, or by a putatively ferredoxin-dependent homolog of the nitrite reductase NirA (DEACI_1836), or both. We identified enzymes and intermediates not previously associated with DNRA and nitrosative stress in aSRB. This increases our knowledge about the metabolism of this type of bacteria and helps the interpretation of (meta)genome data from various ecosystems on their DNRA potential and the nitrogen cycle.IMPORTANCENitrogen is crucial to any ecosystem, and its bioavailability depends on microbial nitrogen-transforming reactions. Over the recent years, various new nitrogen-transforming reactions and pathways have been identified, expanding our view on the nitrogen cycle and metabolic versatility. In this study, we elucidate a novel mechanism employed by Acididesulfobacillus acetoxydans, an acidophilic sulfate-reducing bacterium, to reduce nitrate to ammonium. This finding underscores the diverse physiological nature of dissimilatory reduction to ammonium (DNRA). A. acetoxydans was isolated from acid mine drainage, an extremely acidic environment where nitrogen metabolism is poorly studied. Our findings will contribute to understanding DNRA potential and variations in extremely acidic environments.