Sulfate reduction in microorganisms-recent advances and biotechnological applications

Bacterial community composition and metabolic characteristics of three representative marine areas in northern China

Bacteria are essential components of ecosystems, participating in nutrient cycling and biogeochemical processes, and playing a crucial role in maintaining the stability of marine ecosystems. However, the biogeographic distribution patterns of bacterial diversity and metabolic functions in the estuarine and coastal areas of northern China remain unclear. Here, we used metagenomic sequencing to investigate the bacterial community composition and metabolic functions in sediments from the adjacent waters of the Yellow River Estuary, the Yellow Sea Cold Water Mass, and the adjacent waters of the Yangtze River Estuary. Among the 9164 species that were found, the most dominant microbial communities are Pseudomonadota, Actinomycetota, Bacteroidota, and Bacillota, but there are significant differences in the species composition in these three typical habitats. Amino acid metabolism and carbohydrate metabolic pathways were highly enriched. Glycoside hydrolases (GHs) predominate in carbon metabolism across all samples. In nitrogen metabolic pathway, genes related to organic degradation and synthesis are more abundant in the Yellow River Estuary than the other two habitats. In sulfur metabolic pathway, genes involved in assimilatory sulfate reduction are significantly enriched. Assimilatory sulfate reduction might be crucial for sulfur metabolism in coastal regions, with a full assimilatory nitrate reduction pathway found in Desulfobacterota. This research offers insights into the compositional diversity, metabolic functions, and biogeographic distribution patterns of bacterial communities in sediments from typical marine areas of northern China.

Deciphering the microbial interactions and metabolic shifts at different COD/sulfate ratios in electro-assisted anaerobic digestion

This research aims to investigate the influence of sulfate on the performance of microbial electrolysis cell-assisted anaerobic digester (MEC-AD) across varying sulfate conditions, including no sulfate and reduced COD/sulfate ratios from 20 to 1. The principal results indicate a gradual decline in methane yield in the MEC-AD from 78.7 ± 2.3 % under no sulfate conditions to 56.2 ± 2.0 % at a COD/sulfate ratio of 1, contrasting with a more substantial decrease in the control reactor (69.9 ± 3.6 % to 32.8 ± 1.5 %). The MEC-AD reactor exhibits heightened resilience to sulfide toxicity, showcasing higher specific methanogenic activities. Key findings suggest that the MEC-AD reactor maintains lower free sulfide concentrations, attributed to its higher pH and potential anodic sulfide oxidation. Additionally, the study reveals the promotion of syntrophic partnerships in the MEC-AD reactor, particularly between sulfate-reducing bacteria (SRB) such as Desulfovibrio, Desulfomicrobium, and Desulfobulbus, and other microbial groups, including hydrogenotrophic methanogens and electroactive bacteria. The integration of these mechanisms highlights the MEC-AD reactor's ability to effectively mitigate sulfate-induced challenges and enhance overall anaerobic digestion performance. This study presents a significant step forward in the development of resilient anaerobic digestion systems capable of efficiently handling sulfate stress.

Insights into the role of electrochemical stimulation on sulfur-driven biodegradation of antibiotics in wastewater treatment

The presence of antibiotics in wastewater poses significant threat to our ecosystems and health. Traditional biological wastewater treatment technologies have several limitations in treating antibiotic-contaminated wastewaters, such as low removal efficiency and poor process resilience. Here, a novel electrochemical-coupled sulfur-mediated biological system was developed for treating wastewater co-contaminated with several antibiotics (e.g., ciprofloxacin (CIP), sulfamethoxazole (SMX), chloramphenicol (CAP)). Superior removal of CIP, SMX, and CAP with efficiencies ranging from 40.6 ± 2.6 % to 98.4 ± 1.6 % was achieved at high concentrations of 1000 μg/L in the electrochemical-coupled sulfur-mediated biological system, whereas the efficiencies ranged from 30.4 ± 2.3 % to 98.2 ± 1.4 % in the control system (without electrochemical stimulation). The biodegradation rates of CIP, SMX, and CAP increased by 1.5∼1.9-folds under electrochemical stimulation compared to the control. The insights into the role of electrochemical stimulation for multiple antibiotics biodegradation enhancement was elucidated through a combination of metagenomic and electrochemical analyses. Results showed that sustained electrochemical stimulation significantly enriched the sulfate-reducing and electroactive bacteria (e.g., Desulfobulbus, Longilinea, and Lentimicrobiumin on biocathode and Geobactor on bioanode), and boosted the secretion of electron transport mediators (e.g., cytochrome c and extracellular polymeric substances), which facilitated the microbial extracellular electron transfer processes and subsequent antibiotics removal in the sulfur-mediated biological system. Furthermore, under electrochemical stimulation, functional genes associated with sulfur and carbon metabolism and electron transfer were more abundant, and the microbial metabolic processes were enhanced, contributing to antibiotics biodegradation. Our study for the first time demonstrated that the synergistic effects of electrochemical-coupled sulfur-mediated biological system was capable of overcoming the limitations of conventional biological treatment processes. This study shed light on the mechanism of enhanced antibiotics biodegradation via electrochemical stimulation, which could be employed in sulfur-mediated bioprocess for treating antibiotic-contaminated wastewaters.

Hydrogen sulfide produced by the gut microbiota impairs host metabolism via reducing GLP-1 levels in male mice

Dysbiosis of the gut microbiota has been implicated in the pathogenesis of metabolic syndrome (MetS) and may impair host metabolism through harmful metabolites. Here, we show that Desulfovibrio, an intestinal symbiont enriched in patients with MetS, suppresses the production of the gut hormone glucagon-like peptide 1 (GLP-1) through the production of hydrogen sulfide (H2S) in male mice. Desulfovibrio-derived H2S is found to inhibit mitochondrial respiration and induce the unfolded protein response in intestinal L cells, thereby hindering GLP-1 secretion and gene expression. Remarkably, blocking Desulfovibrio and H2S with an over-the-counter drug, bismuth subsalicylate, improves GLP-1 production and ameliorates diet-induced metabolic disorder in male mice. Together, our study uncovers that Desulfovibrio-derived H2S compromises GLP-1 production, shedding light on the gut-relayed mechanisms by which harmful microbiota-derived metabolites impair host metabolism in MetS and suggesting new possibilities for treating MetS.

Anaerobic ammonium oxidation coupled with sulfate reduction links nitrogen with sulfur cycle

Sulfate-dependent ammonium oxidation (Sulfammox) is a critical process linking nitrogen and sulfur cycles. However, the metabolic pathway of microbes driven Sulfammox is still in suspense. The study demonstrated that ammonium was not consumed with sulfate as the sole electron acceptor during long-term enrichment, probably due to inhibition from sulfide accumulation, while ammonium was removed at ∼ 10 mg N/L/d with sulfate and nitrate as electron acceptors. Ammonium and sulfate were converted into nitrogen gas, sulfide, and elemental sulfur. Sulfammox was mainly performed by Candidatus Brocadia sapporoensis and Candidatus Brocadia fulgida, both of which encoded ammonium oxidation pathway and dissimilatory sulfate reduction pathway. Not sulfide-driven autotrophic denitrifiers but Candidatus Kuenenia stuttgartiensis converted nitrate to nitrite with sulfide. The results of this study reveal the specialized metabolism of Sulfammox bacteria (Candidatus Brocadia sapporoensis and Candidatus Brocadia fulgida) and provide insight into microbial relationships during the nitrogen and sulfur cycles.

Comparative study of the removal of sulfate by UASB in light and dark environment

At present, the application of sewage treatment technologies is restricted by high sulfate concentrations. In the present work, the sulfate removal was biologically treated using an upflow anaerobic sludge blanket (UASB) in the absence/presence of light. First, the start-up of UASB for the sulfate removal was studied in terms of COD degradation, sulfate removal, and effluent pH. Second, the impacts of different operation parameters (i.e., COD/SO42- ratio, temperature and illumination time) on the UASB performance were explored. Third, the properties of sludge derived from the UASB at different time were analyzed. Results show that after 28 days of start-up, the COD removal efficiencies in both the photoreactor and non-photoreactor could reach a range of 85-90% while such reactors could achieve > 90% of sulfate being removed. Besides, higher illumination time could facilitate the removal of pollutants in the photoreactor. To sum up, the present study can provide technical support for the clean removal of sulfate from wastewater using photoreactors.

The Cambrian microfossil Qingjiangonema reveals the co-evolution of sulfate-reducing bacteria and the oxygenation of Earth's surface

Sulfate reduction is an essential metabolism that maintains biogeochemical cycles in marine and terrestrial ecosystems. Sulfate reducers are exclusively prokaryotic, phylogenetically diverse, and may have evolved early in Earth's history. However, their origin is elusive and unequivocal fossils are lacking. Here we report a new microfossil, Qingjiangonema cambria, from ∼518-million-year-old black shales that yield the Qingjiang biota. Qingjiangonema is a long filamentous form comprising hundreds of cells filled by equimorphic and equidimensional pyrite microcrystals with a light sulfur isotope composition. Multiple lines of evidence indicate Qingjiangonema was a sulfate-reducing bacterium that exhibits similar patterns of cell organization to filamentous forms within the phylum Desulfobacterota, including the sulfate-reducing Desulfonema and sulfide-oxidizing cable bacteria. Phylogenomic analyses confirm separate, independent origins of multicellularity in Desulfonema and in cable bacteria. Molecular clock analyses infer that the Desulfobacterota, which encompass a majority of sulfate-reducing taxa, diverged ∼2.41 billion years ago during the Paleoproterozoic Great Oxygenation Event, while cable bacteria diverged ∼0.56 billion years ago during or immediately after the Neoproterozoic Oxygenation Event. Taken together, we interpret Qingjiangonema as a multicellular sulfate-reducing microfossil and propose that cable bacteria evolved from a multicellular filamentous sulfate-reducing ancestor. We infer that the diversification of the Desulfobacterota and the origin of cable bacteria may have been responses to oxygenation events in Earth's history.

Evolution and multiple functions of sulfonation and cytosolic sulfotransferases across species

Organisms have conversion systems for sulfate ion to take advantage of the chemical features. The use of biologically converted sulfonucleotides varies in an evolutionary manner, with the universal use being that of sulfonate donors. Sulfotransferases have the ability to transfer the sulfonate group of 3'-phosphoadenosine 5'-phosphosulfate to a variety of molecules. Cytosolic sulfotransferases (SULTs) play a role in the metabolism of low-molecular-weight compounds in response to the host organism's living environment. This review will address the diverse functions of the SULT in evolution, including recent findings. In addition to the diversity of vertebrate sulfotransferases, the molecular aspects and recent studies on bacterial and plant sulfotransferases are also addressed.

Deciphering the spatial distribution and function profiles of soil bacterial community in Liao River estuarine wetland, Northeast China

Soil microbes play vital roles in estuarine wetlands. Understanding the soil bacterial community structure and function profiles is essential to reveal the ecological functions of microbes in estuarine wetlands. Herein, soil samples were collected from Liao River estuarine wetland, Northeast China, along the river to the estuarine mouth, and soil bacterial communities were explored. Results showed that soil physiochemical properties, bacterial community structure and functions exhibited distinct variations influenced by geographical location. Bacterial phyla in soils were dominated by Proteobacteria and Bacteroidetes, while Gillisia and Woeseia were the predominant genera. Soil pH, electrical conductivity and nitrogen-related nutrients were the important factors affecting bacterial community structure. Based on PICRUSt prediction, the genes related to metabolism of nitrogen, sulfur and methane showed spatial distribution patterns, and the abundances of most biomarker genes increased as the distance from estuarine mouth extended. These findings could enrich the understanding of soil microbiome in estuarine wetlands.

Large-scale genetic characterization of the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough

Sulfate-reducing bacteria (SRB) are obligate anaerobes that can couple their growth to the reduction of sulfate. Despite the importance of SRB to global nutrient cycles and their damage to the petroleum industry, our molecular understanding of their physiology remains limited. To systematically provide new insights into SRB biology, we generated a randomly barcoded transposon mutant library in the model SRB Desulfovibrio vulgaris Hildenborough (DvH) and used this genome-wide resource to assay the importance of its genes under a range of metabolic and stress conditions. In addition to defining the essential gene set of DvH, we identified a conditional phenotype for 1,137 non-essential genes. Through examination of these conditional phenotypes, we were able to make a number of novel insights into our molecular understanding of DvH, including how this bacterium synthesizes vitamins. For example, we identified DVU0867 as an atypical L-aspartate decarboxylase required for the synthesis of pantothenic acid, provided the first experimental evidence that biotin synthesis in DvH occurs via a specialized acyl carrier protein and without methyl esters, and demonstrated that the uncharacterized dehydrogenase DVU0826:DVU0827 is necessary for the synthesis of pyridoxal phosphate. In addition, we used the mutant fitness data to identify genes involved in the assimilation of diverse nitrogen sources and gained insights into the mechanism of inhibition of chlorate and molybdate. Our large-scale fitness dataset and RB-TnSeq mutant library are community-wide resources that can be used to generate further testable hypotheses into the gene functions of this environmentally and industrially important group of bacteria.

Insights into the effects of operating parameters on sulfate reduction performance and microbial pathways in the anaerobic sequencing batch reactor

Sulfate-reducing bacteria (SRB)-based anaerobic process has aroused wide concern in the treatment of sulfate-containing wastewater. Chemical oxygen demand-to-sulfate ratio (COD/SO42-) and HRT are two key factors that affect not only the anaerobic treatment performance but also the activity of SRB. In this study, an anaerobic sequencing batch reactor was constructed, and the effects of different operating parameters (COD/SO42-, HRT) on the relationship of sulfate (SO42-) reduction performance, microbial communities, and metabolic pathways were comprehensively investigated. The results indicated that the SO42- removal rates could achieve above 95% under different operating parameters. Bioinformatics analysis revealed that microbial community changed with reactor operation. At the genus level, the enrichment of Propionicclava and Peptoclostridium contributed to the establishment of a homotrophic relationship with Desulfobulbus, the dominant SRB in the reactor, which indicated that they took vital part in maintaining the structural and functional stability of the bacterial community under different operating parameters. In particular, an increasing trend of the relative abundance of functional genes encoding dissimilatory sulfate reduction was detected with the increase of COD/SO42-, which indicated high SO42- reduction potentials. This knowledge will help to reveal the mechanism of the effect of operating parameters on the anaerobic sulfate removal process, thus providing effective guidance for the targeted regulation of anaerobic sequencing batch bioreactors treating SO42--containing wastewater.

The tongue biofilm metatranscriptome identifies metabolic pathways associated with the presence or absence of halitosis

Intra-oral halitosis usually results from the production of volatile sulfur compounds, such as methyl mercaptan and hydrogen sulfide, by the tongue microbiota. There are currently no reports on the microbial gene-expression profiles of the tongue microbiota in halitosis. In this study, we performed RNAseq of tongue coating samples from individuals with and without halitosis. The activity of Streptococcus (including S. parasanguinis), Veillonella (including V. dispar) and Rothia (including R. mucilaginosa) was associated with halitosis-free individuals while Prevotella (including P. shahi), Fusobacterium (including F. nucleatum) and Leptotrichia were associated with halitosis. Interestingly, the metatranscriptome of patients that only had halitosis levels of methyl mercaptan was similar to that of halitosis-free individuals. Finally, gene expression profiles showed a significant over-expression of genes involved in L-cysteine and L-homocysteine synthesis, as well as nitrate reduction genes, in halitosis-free individuals and an over-expression of genes responsible for cysteine degradation into hydrogen sulfide in halitosis patients.

Insight of the bio-cathode biofilm construction in microbial electrolysis cell dealing with sulfate-containing wastewater

Signaling molecules are useful in biofilm formation, but the mechanism for biofilm construction still needs to be explored. In this study, a signaling molecule, N-butyryl-l-Homoserine lactone (C₄-HSL), was supplied to enhance the construction of the sulfate-reducing bacteria (SRB) bio-cathode biofilm in microbial electrolysis cell (MEC). The sulfate reduction efficiency was more than 90% in less time under the system with C₄-HSL addition. The analysis of SRB bio-cathode biofilms indicated that the activity, distribution, microbial population, and secretion of extracellular polymers prompted by C₄-HSL, which accelerate the sulfate reduction, in particular for the assimilatory sulfate reduction pathway. Specifically, the relative abundance of acidogenic fermentation bacteria increased, and Desulfovibrio was co-metabolized with acidogenic fermentation bacteria. This knowledge will help to reveal the potential of signaling molecules to enhance the SRB bio-cathode biofilm MEC construction and improve the performance of treating sulfate-containing wastewater.

Metagenomic and metatranscriptomic insights into sulfate-reducing bacteria in a revegetated acidic mine wasteland

The widespread occurrence of sulfate-reducing microorganisms (SRMs) in temporarily oxic/hypoxic aquatic environments indicates an intriguing possibility that SRMs can prevail in constantly oxic/hypoxic terrestrial sulfate-rich environments. However, little attention has been given to this possibility, leading to an incomplete understanding of microorganisms driving the terrestrial part of the global sulfur (S) cycle. In this study, genome-centric metagenomics and metatranscriptomics were employed to explore the diversity, metabolic potential, and gene expression profile of SRMs in a revegetated acidic mine wasteland under constantly oxic/hypoxic conditions. We recovered 16 medium- to high-quality metagenome-assembled genomes (MAGs) containing reductive dsrAB. Among them, 12 and four MAGs belonged to Acidobacteria and Deltaproteobacteria, respectively, harboring three new SRM genera. Comparative genomic analysis based on seven high-quality MAGs (completeness >90% and contamination <10%; including six acidobacterial and one deltaproteobacterial) and genomes of three additional cultured model species showed that Acidobacteria-related SRMs had more genes encoding glycoside hydrolases, oxygen-tolerant hydrogenases, and cytochrome c oxidases than Deltaproteobacteria-related SRMs. The opposite pattern was observed for genes encoding superoxide reductases and thioredoxin peroxidases. Using VirSorter, viral genome sequences were found in five of the 16 MAGs and in all three cultured model species. These prophages encoded enzymes involved in glycoside hydrolysis and antioxidation in their hosts. Moreover, metatranscriptomic analysis revealed that 15 of the 16 SRMs reported here were active in situ. An acidobacterial MAG containing a prophage dominated the SRM transcripts, expressing a large number of genes involved in its response to oxidative stress and competition for organic matter.

A deep-sea sulfate-reducing bacterium generates zero-valent sulfur via metabolizing thiosulfate

Zero-valent sulfur (ZVS) is a crucial intermediate in the sulfur geobiochemical circulation and is widespread in deep-sea cold seeps. Sulfur-oxidizing bacteria are thought to be the major contributors to the formation of ZVS. However, ZVS production mediated by sulfate-reducing bacteria (SRB) has rarely been reported. In this study, we isolated and cultured a typical SRB designated Oceanidesulfovibrio marinus CS1 from deep-sea cold seep sediment in the South China Sea. We show that O. marinus CS1 forms ZVS in the medium supplemented with thiosulfate. Proteomic and protein activity assays revealed that thiosulfate reductase (PhsA) and the sulfide:quinone oxidoreductase (SQR) played key roles in driving ZVS formation in O. marinus CS1. During this process, thiosulfate firstly was reduced by PhsA to form sulfide, then sulfide was oxidized by SQR to produce ZVS. The expressions of PhsA and SQR were significantly upregulated when O. marinus CS1 was cultured in a deep-sea cold seep, strongly indicating that strain CS1 might form ZVS in the deep-sea environment. Notably, homologs of phsA and sqr were widely identified from microbes living in sediments of deep-sea cold seep in the South China Sea by the metagenomic analysis. We thus propose that SRB containing phsA and sqr genes potentially contribute to the formation of ZVS in deep-sea cold seep environments.

Core carbon fixation pathways associated with cake layer development in an anoxic-oxic biofilm-membrane bioreactor treating textile wastewater

Microbial carbon fixation pathways have not yet been adequately understood for their role in membrane case layer formation processes. Carbon fixation bacteria can play critical roles in either causing or enhancing cake layer formation in some autotrophic-prone anoxic conditions, such as sulfur-cycling conditions. Understanding the microbes capable of carbon fixation can potentially guide the design of membrane biofouling mitigation strategies in scientific ways. Thus, we used meta-omics methods to query carbon fixation pathways in the cake layers of a full-scale anoxic-oxic biofilm-MBR system treating textile wastewater in this study. Based on the wastewater constituents and other properties, such as anoxic conditions, sulfide-reducing and sulfur-oxidizing bacteria could co-exist in the membrane unit. In addition, low-light radiation conditions could also happen to the membrane unit. However, we could not quantify the light intensity or total energy input accurately because the whole experimental setup was a full-scale system. Potentially complete carbon fixation pathways in the cake layer included the Calvin-Benson-Bassham cycle, Wood-Ljungdahl pathway, and the 3-hydroxypropionate bicycle. We discovered that using aeration could effectively inhibit carbon fixation, which resulted in mitigating membrane cake layer development. However, the aeration resulted in the 3-hydroxypropionate bicycle pathway, presumably used by aerobic sulfur-oxidizing prokaryotes, to become a more abundant carbon fixation pathway in the cake layer under aerobic conditions.

A biosynthetic pathway for the selective sulfonation of steroidal metabolites by human gut bacteria

Members of the human gut microbiome enzymatically process many bioactive molecules in the gastrointestinal tract. Most gut bacterial modifications characterized so far are hydrolytic or reductive in nature. Here we report that abundant human gut bacteria from the phylum Bacteroidetes perform conjugative modifications by selectively sulfonating steroidal metabolites. While sulfonation is a ubiquitous biochemical modification, this activity has not yet been characterized in gut microbes. Using genetic and biochemical approaches, we identify a widespread biosynthetic gene cluster that encodes both a sulfotransferase (BtSULT, BT0416) and enzymes that synthesize the sulfonate donor adenosine 3'-phosphate-5'-phosphosulfate (PAPS), including an APS kinase (CysC, BT0413) and an ATP sulfurylase (CysD and CysN, BT0414-BT0415). BtSULT selectively sulfonates steroidal metabolites with a flat A/B ring fusion, including cholesterol. Germ-free mice monocolonized with Bacteroides thetaiotaomicron ΔBT0416 exhibited reduced gastrointestinal levels of cholesterol sulfate (Ch-S) compared with wild-type B. thetaiotaomicron-colonized mice. The presence of BtSULT and BtSULT homologues in bacteria inhibited leucocyte migration in vitro and in vivo, and abundances of cluster genes were significantly reduced in patients with inflammatory bowel disease. Together, these data provide a mechanism by which gut bacteria sulfonate steroidal metabolites and suggest that these compounds can modulate immune cell trafficking in the host.

Phosphorylation and sulfation share a common biosynthetic pathway, but extend biochemical and evolutionary diversity of biological macromolecules in distinct ways

Phosphate and sulfate groups are integral to energy metabolism and introduce negative charges into biological macromolecules. One purpose of such modifications is to elicit precise binding/activation of protein partners. The physico-chemical properties of the two groups, while superficially similar, differ in one important respect—the valency of the central (phosphorus or sulfur) atom. This dictates the distinct properties of their respective esters, di-esters and hence their charges, interactions with metal ions and their solubility. These, in turn, determine the contrasting roles for which each group has evolved in biological systems. Biosynthetic links exist between the two modifications; the sulfate donor 3′-phosphoadenosine-5′-phosphosulfate being formed from adenosine triphosphate (ATP) and adenosine phosphosulfate, while the latter is generated from sulfate anions and ATP. Furthermore, phosphorylation, by a xylosyl kinase (Fam20B, glycosaminoglycan xylosylkinase) of the xylose residue of the tetrasaccharide linker region that connects nascent glycosaminoglycan (GAG) chains to their parent proteoglycans, substantially accelerates their biosynthesis. Following observations that GAG chains can enter the cell nucleus, it is hypothesized that sulfated GAGs could influence events in the nucleus, which would complete a feedback loop uniting the complementary anionic modifications of phosphorylation and sulfation through complex, inter-connected signalling networks and warrants further exploration.

Oxytetracycline co-metabolism with denitrification/desulfurization in SRB mediated system

Aquaculture wastewater contained a high remnant of oxytetracycline (OTC) and nitrate. In this study, OTC co-metabolized with denitrification/desulfurization was investigated in terms of kinetic analysis, pathway, microbial communities and produces analysis in sulfate-reducing bacteria (SRB) mediated system. Long-term acclimatization with sulfate (300 mg-S/L) could markedly accelerate the removed rate of OTC from 0.9 to 1.4 mg/g-SS/d, with the kinetic constants increasing from 0.2760 to 0.5232 d^-1, mainly via enzymes including adenosine-5'-phos-phosulfate reductase and cytochrome P450, and non-enzymatic process related to intermediates (adenosine-5'-phos-phosulfate and S⁰). Furthermore, OTC was likely detoxified by SRB enriched sludge mainly via hydrolysis, dehydration, oxidation and reduction. The denitrification process would postpone the OTC degradation via outcompeting electron donors with the desulfurization process. Redundancy analysis suggested that sulfur-oxidizing bacteria (Acidithiobacillus, Ochrobactrum) were highly related to OTC degradation processes. This study provides deep insight and a new opportunity for the treatment of aquaculture wastewater containing OTC, sulfate and nitrate by SRB sludge.

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

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

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

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

Early-stage response in anaerobic bioreactors due to high sulfate loads: Hydrogen sulfide yield and other organic volatile sulfur compounds as a sign of microbial community modifications

In this work, the early-stage response of six lab-scale biogas bioreactors fed with different amounts of a sulfate-rich organic agro-industrial effluent was investigated. Biogas characterization, gas chromatography selective for sulfur compounds and high-throughput sequencing of 16S rRNA gene were performed. Hydrogen sulfide (H₂S) yield went from transient to steady state in ∼ 2 weeks for all the studied conditions. In addition, volatile sulfur compounds (VSCs), like methanethiol (MeSH) and dimethyl sulfide (DMS), were generated at high sulfate loads. Changes were evidenced in the microbial community structures, with a higher abundance of genes involved in the dissimilatory sulfate-reduction pathway in high loaded sulfate bioreactors, as determined by PICRUSt analysis. Principal component analysis (PCA) and correlation analyses evidenced strong relationships between H₂S, VSCs and the microbial community. Sulfate-reducing bacteria (SRB) like Desulfocarbo, Desulfocella and Desulfobacteraceae might be possibly linked with methylation processes of H₂S.

Metagenomic and metabolic analyses of poly-extreme microbiome from an active crater volcano lake

El Chichón volcano is one of the most active volcanoes in Mexico. Previous studies have described its poly-extreme conditions and its bacterial composition, although the functional features of the complete microbiome have not been characterized yet. By using metabarcoding analysis, metagenomics, metabolomics and enzymology techniques, the microbiome of the crater lake was characterized in this study. New information is provided on the taxonomic and functional diversity of the representative Archaea phyla, Crenarchaeota and Euryarchaeota, as well as those that are representative of Bacteria, Thermotogales and Aquificae. With culture of microbial consortia and with the genetic information collected from the natural environment sampling, metabolic interactions were identified between prokaryotes, which can withstand multiple extreme conditions. The existence of a close relationship between the biogeochemical cycles of carbon and sulfur in an active volcano has been proposed, while the relationship in the energy metabolism of thermoacidophilic bacteria and archaea in this multi-extreme environment was biochemically revealed for the first time. These findings contribute towards understanding microbial metabolism under extreme conditions, and provide potential knowledge pertaining to "microbial dark matter", which can be applied to biotechnological processes and evolutionary studies.

Bioactive small molecules produced by the human gut microbiome modulate Vibrio cholerae sessile and planktonic lifestyles

Humans live in symbiosis with a diverse community of microorganisms, which has evolved to carry out many specific tasks that benefit the host, including protection against invading pathogens. Within the chemical diversity of the gastrointestinal tract, small molecules likely constitute chemical cues for the communication between the microbiota and pathogens. Therefore, we sought to investigate if molecules produced by the human gut microbiota show biological activity against the human pathogen Vibrio cholerae. To probe the effects of the gut metabolome on V. cholerae, we investigated its response to small-molecule extracts from human feces, from a complex bacterial community cultivated in vitro, and from culture supernatants of Enterocloster citroniae, Bacteroides thetaiotaomicron, and Bacteroides vulgatus. Using RNA sequencing, we determined the impact of the human gut metabolome on V. cholerae global gene expression. Among the genes downregulated in the presence of the fecal extract, the most overrepresented functional category was cell motility, which accounted for 39% of repressed genes. Repression of V. cholerae motility by the fecal extract was confirmed phenotypically, and E. citroniae extracts reproduced this phenotype. A complex in vitro microbial community led to increased motility, as did extracts from B. vulgatus, a species present in this community. Accordingly, mucin penetration was also repressed by fecal and E. citroniae extracts, suggesting that the phenotypes observed may have implications for host colonization. Together with previous studies, this work shows that small molecules from the gut metabolome may have a widespread, significant impact on microbe-microbe interactions established in the gut environment.

Decoupling mechanism of Acid Orange 7 decolorization and sulfate reduction by a Caldanaerobacter dominated extreme-thermophilic consortium

The biological treatment of textile wastewater discharged from the dye baths and rinsing processes are challenged by both high temperatures of 50-80 °C and sulfate reduction. At present, most studies report azo dyes can be removed under mesophilic conditions, but the sulfate reduction is inevitable, consuming extra electron donors and producing undesirable sulfide. In this work, a Caldanaerobacter (> 97%) dominated extreme-thermophilic consortium (EX-AO7) was enriched using xylose as the substrate. The typical sulfate-reducing enzymes such as sulfite oxidase and sulfite reductase were not identified in enriched EX-AO7 by the metagenomic analysis. Then, the decolorization and sulfate reduction were expectedly decoupled by enriched EX-AO7 in extreme-thermophilic conditions, in which no sulfide was detected during the AO7 decolorization process. AO7 of 100 and 200 mg/L could be totally decolorized by EX-AO7. However, when 400 mg/L AO7 was added, the residual AO7 concentration was 22 ± 19 mg/L after 24 h, which was mainly due to the toxicity of AO7. Dosing zero-valent iron (ZVI) could also promote AO7 decolorization by 1.7 times since the addition of ZVI could provide a proliferative environment for EX-AO7 growth. Thereby, our work provides a new paradigm to promote the AZO dyes decolorization and minimize sulfate reduction.

Comparative metabolic modeling of multiple sulfate-reducing prokaryotes reveals versatile energy conservation mechanisms

Sulfate-reducing prokaryotes (SRPs) are crucial participants in the cycling of sulfur, carbon, and various metals in the natural environment and in engineered systems. Despite recent advances in genetics and molecular biology bringing a huge amount of information about the energy metabolism of SRPs, little effort has been made to link this important information with their biotechnological studies. This study aims to construct multiple metabolic models of SRPs that systematically compile genomic, genetic, biochemical, and molecular information about SRPs to study their energy metabolism. Pan-genome analysis was conducted to compare the genomes of SRPs, from which a list of orthologous genes related to central and energy metabolism was obtained. Twenty-four SRP metabolic models via the inference of pan-genome analysis were efficiently constructed. The metabolic model of the well-studied model SRP Desulfovibrio vulgaris Hildenborough (DvH) was validated via flux balance analysis (FBA). The DvH model predictions matched reported experimental growth and energy yields, which demonstrated that the core metabolic model worked successfully. Further, steady-state simulation of SRP metabolic models under different growth conditions showed how the use of different electron transfer pathways leads to energy generation. Three energy conservation mechanisms were identified, including menaquinone-based redox loop, hydrogen cycling, and proton pumping. Flavin-based electron bifurcation (FBEB) was also demonstrated to be an essential mechanism for supporting energy conservation. The developed models can be easily extended to other species of SRPs not examined in this study. More importantly, the present work develops an accurate and efficient approach for constructing metabolic models of multiple organisms, which can be applied to other critical microbes in environmental and industrial systems, thereby enabling the quantitative prediction of their metabolic behaviors to benefit relevant applications.

Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens

BACKGROUND

Viruses are the most abundant biological entities on Earth, known to be crucial components of microbial ecosystems. However, there is little information on the viral community within agricultural waste. There are currently ~ 2.7 million dairy cattle in the UK producing 7-8% of their own bodyweight in manure daily, and 28 million tonnes annually. To avoid pollution of UK freshwaters, manure must be stored and spread in accordance with guidelines set by DEFRA. Manures are used as fertiliser, and widely spread over crop fields, yet little is known about their microbial composition. We analysed the virome of agricultural slurry over a 5-month period using short and long-read sequencing.

RESULTS

Hybrid sequencing uncovered more high-quality viral genomes than long or short-reads alone; yielding 7682 vOTUs, 174 of which were complete viral genomes. The slurry virome was highly diverse and dominated by lytic bacteriophage, the majority of which represent novel genera (~ 98%). Despite constant influx and efflux of slurry, the composition and diversity of the slurry virome was extremely stable over time, with 55% of vOTUs detected in all samples over a 5-month period. Functional annotation revealed a diverse and abundant range of auxiliary metabolic genes and novel features present in the community, including the agriculturally relevant virulence factor VapE, which was widely distributed across different phage genera that were predicted to infect several hosts. Furthermore, we identified an abundance of phage-encoded diversity-generating retroelements, which were previously thought to be rare on lytic viral genomes. Additionally, we identified a group of crAssphages, including lineages that were previously thought only to be found in the human gut.

CONCLUSIONS

The cattle slurry virome is complex, diverse and dominated by novel genera, many of which are not recovered using long or short-reads alone. Phages were found to encode a wide range of AMGs that are not constrained to particular groups or predicted hosts, including virulence determinants and putative ARGs. The application of agricultural slurry to land may therefore be a driver of bacterial virulence and antimicrobial resistance in the environment. Video abstract.

Hydrogen sulfide toxicity in the gut environment: Meta-analysis of sulfate-reducing and lactic acid bacteria in inflammatory processes

BACKGROUND

Hydrogen sulfide is the final product of sulfate-reducing bacteria metabolism. Its high concentration in the gut can affect adversely bowel environment and intestinal microbiota by toxicity and pH lowering.

AIM OF REVIEW

The aim of the review was to give observations related to the properties of bacterial communities inhabiting the gut, with the emphasis on sulfate-reducing bacteria and lactic acid bacteria.

KEY SCIENTIFIC CONCEPTS OF REVIEW

The conduction of meta-analysis was another goal, since it gave statistical observation of the relevant studies. The review literature consisted of more than 160 studies, published from 1945 to 2019. Meta-analysis included 16 studies and they were chosen from the Web of Science database. The systematic review gave important information about the development of gut inflammation, with emphasis on sulfate-reducing and lactic acid bacteria. Oppositely from sulfate-reducing bacteria, probiotic properties of lactic acid bacteria are effective inhibitors against inflammatory bowel disease development, including ulcerative colitis. These facts were confirmed by the conducted meta-analysis. The results and observations gained from the systematic review represent the emphasized importance of gut microbiota for bowel inflammation. On the other side, it should be stated that more studies in the future will provide even better confirmations.

Metagenomic insights into aniline effects on microbial community and biological sulfate reduction pathways during anaerobic treatment of high-sulfate wastewater

For comprehensive insights into the change of sulfate reduction pathway responding to the toxic stress and the shift of microbial community and performance of sulfate reduction, we built a laboratory-scale expanded granular sludge bed reactor (EGSB) treating high-sulfate wastewater with elevated aniline concentrations from 0 to 480 mg/L. High-throughput sequencing and metagenomic approaches were applied to decipher the molecular mechanisms of sulfate reduction under aniline stress through taxonomic and functional profiles. The increasing aniline in the anaerobic system induced the accumulation of volatile fatty acids (VFA), further turned the bioreactor into acidification, which was the principal reason for the deterioration of system performance and finally resulted in the accumulation of toxic free sulfide. Moreover, aniline triggered the change of bacterial community and genes relating to sulfate reduction pathways. The increase of aniline from 0 to 320 mg/L enriched total sulfate-reducing bacteria (SRB), and the most abundant genus was Desulfomicrobium, accounting for 66.85-91.25% of total SRB. The assimilatory sulfate reduction pathway was obviously inhibited when aniline was over 160 mg/L, while genes associated with dissimilatory sulfate reduction pathways all exhibited an upward tendency with the increasing aniline content. The enrichment of aniline-resistant SRB (e.g. Desulfomicrobium) carrying genes associated with the dissimilatory sulfate reduction pathway also confirmed the underlying mechanism that sulfate reduction turned into dissimilation under high aniline condition. Taken together, these results comprehensively provided solid evidence for the effects of aniline on the biological sulfate reduction processes treating high-sulfate wastewater and the underlying molecular mechanisms which may highlight the important roles of SRB and related sulfate reduction genes during treatment.

Why does sulfate inhibit selenate reduction: Molybdenum deprivation from Mo-dependent selenate reductase

Selenium pollution has become an increasingly serious global concern. Methane-fed selenate reduction has proven to be of great interest for the bioremediation of selenate-contaminated waters even with the coexistence of nitrate and dissolved oxygen. However, it is unclear if the common concurrent sulfate anion affects selenate removal. To address this question, we first introduced selenate (SeO₄^2-) as the sole influent electron acceptor in a CH₄-fed membrane biofilm reactor (CH₄-MBfR); then we added different concentrations of sulfate (SO₄^2-). The initial selenate removal efficiency (∼90%) was decreased by 50% in the presence of 15.6 μM of sulfate and completely inhibited after loading with 171.9 μM of sulfate. 16S rRNA gene sequencing showed that the selenate-reducing bacteria decreased after the addition of sulfate. Metagenomic sequencing showed that the abundance of genes encoding molybdenum (Mo)-dependent selenate reductase reduced by >50% when exposed to high concentrations of sulfate. Furthermore, the decrease in the total genes encoding all Mo-oxidoreductases was much greater than that of the genes encoding molybdate transporters, suggesting that the inhibition of selenate reduction by sulfate was most likely via the direct competition with molybdate for the transport system, leading to a lack of available Mo for Mo-dependent selenate reductases and thus reducing their activities. This result was confirmed by a batch test wherein the supplementation of molybdate mitigated the sulfate effect. Overall, this study shed light on the underlying mechanism of sulfate inhibition on selenate reduction and laid the foundation for applying the technology to practical wastewaters.

Depth-related variability in viral communities in highly stratified sulfidic mine tailings

BACKGROUND

Recent studies have significantly expanded our knowledge of viral diversity and functions in the environment. Exploring the ecological relationships between viruses, hosts, and the environment is a crucial first step towards a deeper understanding of the complex and dynamic interplays among them.

RESULTS

Here, we obtained extensive 16S rRNA gene amplicon, metagenomics sequencing, and geochemical datasets from different depths of two highly stratified sulfidic mine tailings cores with steep geochemical gradients especially pH, and explored how variations in viral community composition and functions were coupled to the co-existing prokaryotic assemblages and the varying environmental conditions. Our data showed that many viruses in the mine tailings represented novel genera, based on gene-sharing networks. Siphoviridae, Podoviridae, and Myoviridae dominated the classified viruses in the surface tailings and deeper layers. Both viral richness and normalized coverage increased with depth in the tailings cores and were significantly correlated with geochemical properties, for example, pH. Viral richness was also coupled to prokaryotic richness (Pearson's r = 0.65, P = 0.032). The enrichment of prophages in the surface mine tailings suggested a preference of lysogenic viral lifestyle in more acidic conditions. Community-wide comparative analyses clearly showed that viruses in the surface tailings encoded genes mostly with unknown functions while viruses in the deeper layers contained genes mainly annotated as conventional functions related to metabolism and structure. Notably, significantly abundant assimilatory sulfate reduction genes were identified from the deeper tailings layers and they were widespread in viruses predicted to infect diverse bacterial phyla.

CONCLUSIONS

Overall, our results revealed a depth-related distribution of viral populations in the extreme and heterogeneous tailings system. The viruses may interact with diverse hosts and dynamic environmental conditions and likely play a role in the functioning of microbial community and modulate sulfur cycles in situ. Video Abstract.

Insights into pharmaceuticals removal in an anaerobic sulfate-reducing bacteria sludge system

In this study, we examined eight typical and widely detected pharmaceuticals (PhAs) removal in an anaerobic sulfate-reducing bacteria (SRB) sludge system (five antibiotics: sulfadiazine (SD), sulfamethoxazole (SMX), trimethoprim (TMP), ciprofloxacin (CIP) and enoxacin (ENO), and three nonsteroidal anti-inflammatory drugs (NSAIDs): ibuprofen (IBU), ketoprofen (KET) and diclofenac (DIC)). The results showed that the SRB sludge had the higher removal efficacy (20 to 90%) for antibiotics (SD, SMX, TMP, CIP and ENO) than NSAIDs (<20%) via adsorption and biodegradation under different operating conditions. Based on a series of batch studies, fluoroquinolone antibiotics (CIP and ENO) were instantly (<15 min) removed (∼98%) via adsorption on SRB sludge with adsorption coefficient (K_d) as high as 25.3 ± 1.8 L/g-suspended solids (SS). And thermodynamics results indicated that the adsorption of CIP and ENO on SRB sludge was spontaneous (Gibbs free energy change (ΔG°) <0 kJ/mol), exothermic (enthalpy change (ΔH°) <0 kJ/mol), and the adsorption process involved both physisorption and chemisorption (absolute value of ΔH° = 20 to 80 kJ/mol). Three widely prescribed antibiotics (SMX, TMP and CIP) were further investigated for their possible biodegradation pathways along with functional enzymes involved through a series of batch experiments. The biotransformation intermediates indicated that biotransformations of SMX and CIP in SRB sludge system could be initiated from the cleavage of isoxazole and piperazinyl rings catalyzed by sulfite reductase (SR) and cytochrome P450 (CYP450) enzymes, respectively. TMP was likely biotransformed via O-demethylation and N-acetylation coupled with hydroxylation reactions with CYP450 enzymes as the main functional enzymes. This study provided new insight into PhAs removal in SRB sludge system, and has significant potential of implementing sulfur-mediated biological process for the treatment of PhAs containing wastewater.

Formation of Large Native Sulfur Deposits Does Not Require Molecular Oxygen

Large native (i.e., elemental) sulfur deposits can be part of caprock assemblages found on top of or in lateral position to salt diapirs and as stratabound mineralization in gypsum and anhydrite lithologies. Native sulfur is formed when hydrocarbons come in contact with sulfate minerals in presence of liquid water. The prevailing model for native sulfur formation in such settings is that sulfide produced by sulfate-reducing bacteria is oxidized to zero-valent sulfur in presence of molecular oxygen (O2). Although possible, such a scenario is problematic because: (1) exposure to oxygen would drastically decrease growth of microbial sulfate-reducing organisms, thereby slowing down sulfide production; (2) on geologic timescales, excess supply with oxygen would convert sulfide into sulfate rather than native sulfur; and (3) to produce large native sulfur deposits, enormous amounts of oxygenated water would need to be brought in close proximity to environments in which ample hydrocarbon supply sustains sulfate reduction. However, sulfur stable isotope data from native sulfur deposits emplaced at a stage after the formation of the host rocks indicate that the sulfur was formed in a setting with little solute exchange with the ambient environment and little supply of dissolved oxygen. We deduce that there must be a process for the formation of native sulfur in absence of an external oxidant for sulfide. We hypothesize that in systems with little solute exchange, sulfate-reducing organisms, possibly in cooperation with other anaerobic microbial partners, drive the formation of native sulfur deposits. In order to cope with sulfide stress, microbes may shift from harmful sulfide production to non-hazardous native sulfur production. We propose four possible mechanisms as a means to form native sulfur: (1) a modified sulfate reduction process that produces sulfur compounds with an intermediate oxidation state, (2) coupling of sulfide oxidation to methanogenesis that utilizes methylated compounds, acetate or carbon dioxide, (3) ammonium oxidation coupled to sulfate reduction, and (4) sulfur comproportionation of sulfate and sulfide. We show these reactions are thermodynamically favorable and especially useful in environments with multiple stressors, such as salt and dissolved sulfide, and provide evidence that microbial species functioning in such environments produce native sulfur. Integrating these insights, we argue that microbes may form large native sulfur deposits in absence of light and external oxidants such as O2, nitrate, and metal oxides. The existence of such a process would not only explain enigmatic occurrences of native sulfur in the geologic record, but also provide an explanation for cryptic sulfur and carbon cycling beneath the seabed.

Formate cross-feeding and cooperative metabolic interactions revealed by transcriptomics in co-cultures of acetogenic and amylolytic human colonic bacteria

Interspecies cross-feeding is a fundamental factor in anaerobic microbial communities. In the human colon, formate is produced by many bacterial species but is normally detected only at low concentrations. Ruminococcus bromii produces formate, ethanol and acetate in approximately equal molar proportions in pure culture on RUM-RS medium with 0.2% Novelose resistant starch (RS3) as energy source. Batch co-culturing on starch with the acetogen Blautia hydrogenotrophica however led to the disappearance of formate and increased levels of acetate, which is proposed to occur through the routing of formate via the Wood Ljungdahl pathway of B. hydrogenotrophica. We investigated these inter-species interactions further using RNAseq to examine gene expression in continuous co-cultures of R. bromii and B. hydrogenotrophica. Transcriptome analysis revealed upregulation of B. hydrogenotrophica genes involved in the Wood-Ljungdahl pathway and of a 10 gene cluster responsible for increased branched chain amino acid fermentation in the co-cultures. Cross-feeding between formate-producing species and acetogens may be a significant factor in short chain fatty acid formation in the colon contributing to high rates of acetate production. Transcriptome analysis also indicated competition for the vitamin thiamine and downregulation of dissimilatory sulfate reduction and key redox proteins in R. bromii in the co-cultures, thus demonstrating the wide-ranging consequences of inter-species interactions in this model system.

Electrochemical Bioreactor Technology for Biocatalysis and Microbial Electrosynthesis

Two seemingly distinct fields, industrial biocatalysis and microbial electrosynthesis, can be viewed together through the lens of electrochemical bioreactor technology in order to highlight the challenges that exist in creating a versatile platform technology for use in chemical and biological applications. Industrial biocatalysis applications requiring NAD(P)H to perform redox transformations often necessitate convoluted coupled-enzyme regeneration systems to regenerate reduced cofactor, NAD(P)H from oxidized cofactor, NAD(P). Renewed interest in continuously recycling the cofactor via electrochemical reduction is motivated by the low cost of performing electrochemical reactions, easy monitoring of the reaction progress, and straightforward product recovery. However, electrochemical cofactor regeneration methods invariably produce adventitious reduced cofactor side products which result in unproductive loss of input NAD(P). Microbial electrosynthesis is a form of microbially driven catalysis in which electricity is supplied to living microorganisms for the production of industrially relevant chemical products at higher carbon efficiencies and yields compared with traditional, nonelectrically driven, fermentations. The fundamental biochemistry of these organisms as related to selected biochemical redox processes will be explored in order to highlight opportunities to devise strategies for taking advantage of these biochemical processes in engineered systems.

Heavy metal and sulfate removal from sulfate-rich synthetic mine drainages using sulfate reducing bacteria

The removals of heavy metals and sulfate in the synthetic acid mine drainages (AMDs) by Desulfovibrio desulfuricans, sulfate-reducing bacteria (SRB), and the indigenous bacteria isolated from the mine area soil sample were studied to compare the AMD treatment efficiencies. The AMD treatment by the D. desulfuricans grown in the Desulfovibrio medium was used to represent bioaugmentation, while the AMD treatment by the indigenous bacteria grown in the Desulfovibrio medium was used to represent biostimulation. The consumption of lactate and sulfate suggested that the zinc (Zn) removal in the Zn-spiked Desulfovibrio medium by D. desulfuricans involved chemical precipitation and biosorption. The complete Zn removal by D. desulfuricans took 24 h, while the indigenous bacteria took 360 h. The significantly lower rate can probably be attributed to the composition of the culture. The removal of Zn in the sulfate-rich synthetic AMD-containing Desulfovibrio medium (i.e., AMD) was adversely affected by the presence of other heavy metals. Also, the sulfate reduction by D. desulfuricans and the indigenous bacteria was reduced from 47% to 20% and from 36% to 6%, respectively. The inhibitive effects on the removal of heavy metals and sulfate were greater with the Zn/Cu-spiked AMD than the Zn-spiked AMD. Overall, the indigenous bacteria showed potential for removing heavy metals and sulfate in AMDs, while the removal efficiency was lower than D. desulfuricans. The continuous supply of carbon sources with an adaptation period may be required to enhance the AMD treatment efficiency by the indigenous bacteria.

Current understanding of sulfur assimilation metabolism to biosynthesize L-cysteine and recent progress of its fermentative overproduction in microorganisms

To all organisms, sulfur is an essential and important element. The assimilation of inorganic sulfur molecules such as sulfate and thiosulfate into organic sulfur compounds such as L-cysteine and L-methionine (essential amino acid for human) is largely contributed by microorganisms. Of these, special attention is given to thiosulfate (S₂O₃^2-) assimilation, because thiosulfate relative to often utilized sulfate (SO₄^2-) as a sulfur source is proposed to be more advantageous in microbial growth and biotechnological applications like L-cysteine fermentative overproduction toward industrial manufacturing. In Escherichia coli as well as other many bacteria, the thiosulfate assimilation pathway is known to depend on O-acetyl-L-serine sulfhydrylase B. Recently, another yet-unidentified CysM-independent thiosulfate pathway was found in E. coli. This pathway is expected to consist of the initial part of the thiosulfate to sulfite (SO₃^2-) conversion, and the latter part might be shared with the final part of the known sulfate assimilation pathway [sulfite → sulfide (S^2-) → L-cysteine]. The catalysis of thiosulfate to sulfite is at least partly mediated by thiosulfate sulfurtransferase (GlpE). In this mini-review, we introduce updated comprehensive information about sulfur assimilation in microorganisms, including this topic. Also, we introduce recent advances of the application study about L-cysteine overproduction, including the GlpE overexpression.