Microbial sulfite respiration

Unveiling microplastic's role in nitrogen cycling: Metagenomic insights from estuarine sediment microcosms

Marine microplastics (MPs) pollution, with rivers as a major source, leads to MPs accumulation in estuarine sediments, which are also nitrogen cycling hotspots. However, the impact of MPs on nitrogen cycling in estuarine sediments has rarely been documented. In this study, we conducted microcosm experiment to investigate the effects of commonly encountered polyethylene (PE) and polystyrene (PS) MPs, with two MPs concentrations (0.3% and 3% wet sediment weight) based on environmental concentration considerations and dose-response effects, on sediment dissolved oxygen (DO) diffusion capacity and microbial communities using microelectrode system and metagenomic analysis respectively. The results indicated that high concentrations of PE-MPs inhibited DO diffusion during the mid-phase of the experiment, an effect that dissipated in the later stages. Metagenomic analysis revealed that MP treatments reduced the relative abundance of dominant microbial colonies in the sediments. The PCoA results demonstrated that MPs altered the microbial community structure, particularly evident under high concentration PE-MPs treatments. Functional analysis related to the nitrogen cycle suggested that PS-MPs promoted the nitrification, denitrification, and DNRA processes, but inhibited the ANRA process, while PE-MPs had an inhibitory effect on the nitrate reduction process and the ANRA process. Additionally, the high concentration of PE-MPs treatment significantly stimulated the abundance of genus (Bacillus) by 34.1% and genes (lip, pnbA) by 100-187.5% associated with plastic degradation, respectively. Overall, in terms of microbial community structure and the abundance of nitrogen cycling functional genes, PE- and PS- MPs exhibit both similarities and differences in their impact on nitrogen cycling. Our findings highlight the complexity of MP effects on nitrogen cycling in estuarine sediments and high concentrations of PE-MP stimulated plastic-degrading genus and genes.

Intestinal melatonin levels and gut microbiota homeostasis are independent of the pineal gland in pigs

Introduction

Melatonin (MEL) is a crucial neuroendocrine hormone primarily produced by the pineal gland. Pinealectomy (PINX) has been performed on an endogenous MEL deficiency model to investigate the functions of pineal MEL and its relationship with various diseases. However, the effect of PINX on the gastrointestinal tract (GIT) MEL levels and gut microbiome in pigs has not been previously reported.

Methods

By using a newly established pig PINX model, we detected the levels of MEL in the GIT by liquid chromatography-tandem mass spectrometry. In addition, we examined the effects of PINX on the expression of MEL synthesis enzymes, intestinal histomorphology, and the intestinal barrier. Furthermore, 16S rRNA sequencing was performed to analyze the colonic microbiome.

Results

PINX reduced serum MEL levels but did not affect GIT MEL levels. Conversely, MEL supplementation increased MEL levels in the GIT and intestinal contents. Neither PINX nor MEL supplementation had any effect on weight gain, organ coefficient, serum biochemical indexes, or MEL synthetase arylalkylamine N-acetyltransferase (AANAT) expression in the duodenum, ileum, and colon. Furthermore, no significant differences were observed in the intestinal morphology or intestinal mucosal barrier function due to the treatments. Additionally, 16S rRNA sequencing revealed that PINX had no significant impact on the composition of the intestinal microbiota. Nevertheless, MEL supplementation decreased the abundance of Fibrobacterota and increased the abundance of Actinobacteriota, Desulfobacterota, and Chloroflexi.

Conclusion

We demonstrated that synthesis of MEL in the GIT is independent of the pineal gland. PINX had no influence on intestinal MEL level and microbiota composition in pigs, while exogenous MEL alters the structure of the gut microbiota.

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.

Exploring the synergistic interplay of sulfur metabolism and electron transfer in Cr(VI) and Cd(II) removal by Clostridium thiosulfatireducens: Genomic and mechanistic insights

In this study, a sulfate-reducing bacterium, Clostridium thiosulfatireducens (CT) was reported and the performance and removal mechanism of Cr(VI) and Cd(II) removal were investigated. It is noteworthy that the dsrAB gene is absent in this strain, but the strain is capable of producing sulfide. The conversion rate of Cr(VI) by CT was 84.24 % at a concentration of 25 mg/L, and the conversion rate of Cd(II) was 94.19 % at a concentration of 28 mg/L. The complete genome is 6,106,624 bp and the genome consisted of a single chromosome. The GC content of the chromosomes was 29.65 %. The mechanism of heavy metal removal by CT bacteria mainly includes biosorption, electron transfer and redox, with reduction combined with S2- precipitation as the main pathway. The product characterization results showed that the formation of mainly ionic crystals and precipitates (CdS, Cd(OH)2, Cr(OH)3, Cr2O3) after adsorption. Genome-wide techniques have shown that the clearance of Cr(VI) and Cd(II) by CT is largely dependent on sulfate transport, sulfur metabolism, and energy metabolism to some extent. In addition, genes related to ATP binding, electron carrier activity, transporter protein genes, and DNA repair are also important factors to improve the heavy metal resistance and transformation ability of CT strains. Both the Fe-S cycle and the ROS-resistant system can enhance the electron transfer activity and thus slow down the damage of heavy metals to microorganisms. This study fills the gap in the understanding of the basic properties and heavy metal transformation mechanism of CT.

Removal of nonylphenol ethoxylate surfactant in batch reactors: emphasis on methanogenic potential and microbial community characterization under optimized conditions

ABSTRACTNonylphenol ethoxylate (NPE) is an endocrine-disrupting chemical that has bioaccumulative, persistent and toxic characteristics in different environmental matrices and is difficult to remove in sewage treatment plants. In this study, the effects of the initial concentration of NPE (0.2 ± 0.03 - 3.0 ± 0.02 mg. L-1) and ethanol (73.9 ± 5.0-218.6 ± 10.6 mg. L-1) were investigated using factorial design. Assays were carried out in anaerobic batch reactors, using the Zinder basal medium, yeast extract (200 mg. L-1), vitamin solution and sodium bicarbonate (10% v/v). The optimal conditions were 218.56 mg.L-1 of ethanol and 1596.51 µg.L-1 of NPE, with 92% and 88% of NPE and organic matter removal, respectively, and methane yield (1689.8 ± 59.6 mmol) after 450 h of operation. In this condition, bacteria potentially involved in the degradation of this surfactant were identified in greater relative abundance, such as Acetoanaerobium (1.68%), Smithella (1.52%), Aminivibrio (0.91%), Petrimonas (0.57%) and Enterobacter (0.47%), as well as archaea Methanobacterium and Methanoregula, mainly involved in hydrogenotrophic pathway.

DsrMKJOP is the terminal reductase complex in anaerobic sulfate respiration

Microbial dissimilatory sulfate reduction (DSR) is a key process in the Earth biogeochemical sulfur cycle. In spite of its importance to the sulfur and carbon cycles, industrial processes, and human health, it is still not clear how reduction of sulfate to sulfide is coupled to energy conservation. A central step in the pathway is the reduction of sulfite by the DsrAB dissimilatory sulfite reductase, which leads to the production of a DsrC-trisulfide. A membrane-bound complex, DsrMKJOP, is present in most organisms that have DsrAB and DsrC, and its involvement in energy conservation has been inferred from sequence analysis, but its precise function was so far not determined. Here, we present studies revealing that the DsrMKJOP complex of the sulfate reducer Archaeoglobus fulgidus works as a menadiol:DsrC-trisulfide oxidoreductase. Our results reveal a close interaction between the DsrC-trisulfide and the DsrMKJOP complex and show that electrons from the quinone pool reduce consecutively the DsrM hemes b, the DsrK noncubane [4Fe-4S]3+/2+ catalytic center, and finally the DsrC-trisulfide with concomitant release of sulfide. These results clarify the role of this widespread respiratory membrane complex and support the suggestion that DsrMKJOP contributes to energy conservation upon reduction of the DsrC-trisulfide in the last step of DSR.

Biosynthesis and function of microbial methylmenaquinones

The membranous quinone/quinol pool is essential for the majority of life forms and its composition has been widely used as a biomarker in microbial taxonomy. The most abundant quinone is menaquinone (MK), which serves as an essential redox mediator in various electron transport chains of aerobic and anaerobic respiration. Several methylated derivatives of MK, designated methylmenaquinones (MMKs), have been reported to be present in members of various microbial phyla possessing either the classical MK biosynthesis pathway (Men) or the futalosine pathway (Mqn). Due to their low redox midpoint potentials, MMKs have been proposed to be specifically involved in appropriate electron transport chains of anaerobic respiration. The class C radical SAM methyltransferases MqnK, MenK and MenK2 have recently been shown to catalyse specific MK methylation reactions at position C-8 (MqnK/MenK) or C-7 (MenK2) to synthesise 8-MMK, 7-MMK and 7,8-dimethylmenaquinone (DMMK). MqnK, MenK and MenK2 from organisms such as Wolinella succinogenes, Adlercreutzia equolifaciens, Collinsella tanakaei, Ferrimonas marina and Syntrophus aciditrophicus have been functionally produced in Escherichia coli, enabling extensive quinone/quinol pool engineering of the native MK and 2-demethylmenaquinone (DMK). Cluster and phylogenetic analyses of available MK and MMK methyltransferase sequences revealed signature motifs that allowed the discrimination of MenK/MqnK/MenK2 family enzymes from other radical SAM enzymes and the identification of C-7-specific menaquinone methyltransferases of the MenK2 subfamily. It is envisaged that this knowledge will help to predict the methylation status of the menaquinone/menaquinol pool of any microbial species (or even a microbial community) from its (meta)genome.

Continuous single-stage elemental sulfur reduction and copper sulfide precipitation under thermoacidophilic conditions

Metal sulfide precipitation is a viable technology for high-yield metal recovery from hydrometallurgical streams, with the potential to streamline the process design. A single-stage elemental sulfur (S⁰)-reducing and metal sulfide precipitating process can optimize the operational and capital costs associated with this technology, boosting the competitiveness of this technology for wider industrial application. However, limited research is available on biological sulfur reduction at high temperature and low pH, frequent conditions of hydrometallurgical process waters. Here we assessed the sulfidogenic activity of an industrial granular sludge previously shown to reduce S⁰ under hot (60-80 °C) and acidic conditions (pH 3.6). A 4 L gas-lift reactor was operated for 206 days and fed continuously with culture medium and copper. During the reactor operation, we explored the effect of the hydraulic retention time, copper loading rates, temperature, and H₂ and CO₂ flow rates on the volumetric sulfide production rates (VSPR). A maximum VSPR of 274 ± 6 mg·L^-1·d^-1 was reached, a 3.9-fold increase of the VSPR previously reported with this inoculum in batch operation. Interestingly, the maximum VSPR was achieved at the highest copper loading rates. At the maximum copper loading rate (509 mg·L^-1·d^-1), a 99.96% copper removal efficiency was observed. 16 s rRNA gene amplicon sequencing revealed an increased abundance of reads assigned to Desulfurella and Thermoanaerobacterium in periods of higher sulfidogenic activity.

Novel insight into the role of sulfur dioxide in fruits and vegetables: Chemical interactions, biological activity, metabolism, applications, and safety

Sulfur dioxide (SO₂) are a category of chemical compounds widely used as additives in food industry. So far, the use of SO₂ in fruit and vegetable industry has been indispensable although its safety concerns have been controversial. This article comprehensively reviews the chemical interactions of SO₂ with the components of fruit and vegetable products, elaborates its mechanism of antimicrobial, anti-browning, and antioxidation, discusses its roles in regulation of sulfur metabolism, reactive oxygen species (ROS)/redox, resistance induction, and quality maintenance in fruits and vegetables, summarizes the application technology of SO₂ and its safety in human (absorption, metabolism, toxicity, regulation), and emphasizes the intrinsic metabolism of SO₂ and its consequences for the postharvest physiology and safety of fresh fruits and vegetables. In order to fully understand the benefits and risks of SO₂, more research is needed to evaluate the molecular mechanisms of SO₂ metabolism in the cells and tissues of fruits and vegetables, and to uncover the interaction mechanisms between SO₂ and the components of fruits and vegetables as well as the efficacy and safety of bound SO₂. This review has important guiding significance for adjusting an applicable definition of maximum residue limit of SO₂ in food.

Anaerobic degradation of organic carbon supports uncultured microbial populations in estuarine sediments

BACKGROUND

A large proportion of prokaryotic microbes in marine sediments remains uncultured, hindering our understanding of their ecological functions and metabolic features. Recent environmental metagenomic studies suggested that many of these uncultured microbes contribute to the degradation of organic matter, accompanied by acetogenesis, but the supporting experimental evidence is limited.

RESULTS

Estuarine sediments were incubated with different types of organic matters under anaerobic conditions, and the increase of uncultured bacterial populations was monitored. We found that (1) lignin stimulated the increase of uncultured bacteria within the class Dehalococcoidia. Their ability to metabolize lignin was further supported by the presence of genes associated with a nearly complete degradation pathway of phenolic monomers in the Dehalococcoidia metagenome-assembled genomes (MAGs). (2) The addition of cellulose stimulated the increase of bacteria in the phylum Ca. Fermentibacterota and family Fibrobacterales, a high copy number of genes encoding extracellular endoglucanase or/and 1,4-beta-cellobiosidase for cellulose decomposition and multiple sugar transporters were present in their MAGs. (3) Uncultured lineages in the order Bacteroidales and the family Leptospiraceae were enriched by the addition of casein and oleic acid, respectively, a high copy number of genes encoding extracellular peptidases, and the complete β-oxidation pathway were found in those MAGs of Bacteroidales and Leptospiraceae, respectively. (4) The growth of unclassified bacteria of the order Clostridiales was found after the addition of both casein and cellulose. Their MAGs contained multiple copies of genes for extracellular peptidases and endoglucanase. Additionally, ¹³C-labeled acetate was produced in the incubations when ¹³C-labeled dissolved inorganic carbon was provided.

CONCLUSIONS

Our results provide new insights into the roles of microorganisms during organic carbon degradation in anaerobic estuarine sediments and suggest that these macro and single molecular organic carbons support the persistence and increase of uncultivated bacteria. Acetogenesis is an additional important microbial process alongside organic carbon degradation. Video Abstract.

Sulfoquinovose is a widespread organosulfur substrate for Roseobacter clade bacteria in the ocean

Sulfoquinovose (SQ) is one of the most abundant organosulfur compounds in the biosphere, and its biosynthesis and degradation can represent an important contribution to the sulfur cycle. To data, in marine environments, the microorganisms capable of metabolising SQ have remained unidentified and the sources of SQ are still uncertain. Herein, the marine Roseobacter clade bacteria (RCB) Dinoroseobacter shibae DFL 12 and Roseobacter denitrificans OCh 114 were found to grow using SQ as the sole source of carbon and energy. In the presence of SQ, we identified a set of highly up-regulated proteins encoded by gene clusters in these two organisms, of which four homologues to proteins in the SQ monooxygenase pathway of Agrobacterium fabrum C58 may confer the ability to metabolise SQ to these marine bacteria. The sulfite released from SQ desulfonation by FMN-dependent SQ monooxygenase (SmoC) may provide bacteria with reduced sulfur for assimilation, while proteins associated with sulfite production via assimilatory sulfate reduction were significantly down-regulated. Such SQ catabolic genes are restricted to a limited number of phylogenetically diverse bacterial taxa with the predominate genera belonging to the Roseobacter clade (Roseobacteraceae). Moreover, transcript analysis of Tara Oceans project and coastal Bohai Sea samples provided additional evidence for SQ metabolism by RCB. SQ was found to be widely distributed in marine phytoplankton and cyanobacteria with variable intracellular concentrations ranging from micromolar to millimolar levels, and the amounts of SQ on particulate organic matter in field samples were, on average, lower than that of dimethylsulfoniopropionate (DMSP) by one order of magnitude. Together, the phototroph-derived SQ actively metabolised by RCB represents a previously unidentified link in the marine sulfur cycle.

Iron carbon particle dosing for odor control in sewers: Laboratory tests

Treatment of malodor in the sewer system is a priority in many municipalities for human health concerns, sewer pipe corrosion prevention. In this study, the removal effects of iron-carbon (Fe-C) particles on the inhibition of sulfide in the liquid phase, as well as hydrogen sulfide (H₂S) and methyl mercaptan (MeSH) in the headspace were investigated using laboratory-scale reactors simulating gravity-flow sewer system. The results indicated that the sulfide in the liquid phase can be reduced from 15.1 to 16.5 mg S/L to 0.05 and 0.14 mg S/L after 70 g/L and 50 g/L Fe-C particles dosing. The flux of H₂S and MeSH in the headspace was also inhibited, and its flux decreased by up to 99%. Meanwhile, the microbial community structures of sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) in the sediment surface and water were also analyzed, and the results revealed that the relative abundance of SRB in the water and sediment surface was inhibited greatly after adding Fe-C particles, especially for Sulfurospirillum, Clostridium, and Desulfovibrio, while Fe-C particles promoted the growth of SOB. Moreover, the surface deposition was collected and analyzed through X-ray photoelectron spectroscopy (XPS), and the results indicated that sulfide can be removed by co-precipitation with ferrous ions formed through micro-electrolysis of Fe-C. This study provides a new approach to control the in-situ odor pollution for sewage systems.

Submerged zone and vegetation drive distribution of heavy metal fractions and microbial community structure: Insights into stormwater biofiltration system

Biofiltration system is a widely used stormwater treatment option that is effective in removing heavy metals. The concentration and distribution of heavy metal fractions in biofiltration filter media, as well as the microbiota composition affected by the design parameters, are relatively novel concepts that require further research. A laboratory-scale column study was conducted to investigate the microbial community and the fractionation of heavy metals (Pb, Cu, Cr, and Cd) extracted from filter media samples, subjected to the presence of vegetation, submerged zone (SZ), and major environmental parameters (pH, water content). Sequential extractions revealed that, compared to the three other fractions (exchangeable fraction, reducible fraction, and oxidizable fraction), the residual fraction was the most represented for each metal (41 - 82 %). As a result, vegetation was found to reduce pH value, and significantly decrease the concentration of the exchangeable fraction of Pb in the middle layer, and the oxidizable fraction of Pb, Cu, Cd, and Cr in the middle and bottom layers (p < 0.05). The formation of an anoxic environment by submerged zone settlements resulted in a significant decrease in the concentration of reducible fractions and a significant increase in the concentration of oxidizable fractions for four heavy metals (p < 0.05). In addition, the analysis of the microbiota showed that the diversity and richness of microorganisms increased in the presence of SZ and plants. The dominant phylum in biofiltration was Proteobacteria, followed by Firmicutes, Bacteroidetes, Acidobacteria, and Actinobacteria as major phyla. Heavy metal fractions could regulate the structure of microbial communities in biofiltration. The findings of this study would enrich our understanding of the improvement of multi-metal-contaminated runoff treatment and highlight the impact of design parameters and heavy metal fractionation on microbial community structure in the biofiltration system.

Generation and Physiology of Hydrogen Sulfide and Reactive Sulfur Species in Bacteria

Sulfur is not only one of the most abundant elements on the Earth, but it is also essential to all living organisms. As life likely began and evolved in a hydrogen sulfide (H₂S)-rich environment, sulfur metabolism represents an early form of energy generation via various reactions in prokaryotes and has driven the sulfur biogeochemical cycle since. It has long been known that H₂S is toxic to cells at high concentrations, but now this gaseous molecule, at the physiological level, is recognized as a signaling molecule and a regulator of critical biological processes. Recently, many metabolites of H₂S, collectively called reactive sulfur species (RSS), have been gradually appreciated as having similar or divergent regulatory roles compared with H₂S in living organisms, especially mammals. In prokaryotes, even in bacteria, investigations into generation and physiology of RSS remain preliminary and an understanding of the relevant biological processes is still in its infancy. Despite this, recent and exciting advances in the fields are many. Here, we discuss abiotic and biotic generation of H₂S/RSS, sulfur-transforming enzymes and their functioning mechanisms, and their physiological roles as well as the sensing and regulation of H₂S/RSS.

Unveiling changes of microbial community involved in N and P removal in constructed wetlands with exposing to silver nanoparticles

Constructed wetlands (CWs) are environmentally friendly engineered systems to purify wastewater, with low-cost and easy maintenance. However, it is not clear on responses of functional microbes for nitrogen (N) and phosphorus (P) biotransformation in CWs to silver nanoparticles (Ag NPs). The high throughput sequencings were employed to reveal microbial communities in vertical flow subsurface CWs with stable operation for 120 days. The results indicated that NH₄⁺-N, TN and TP removal of soil layer decreased by 43.56%, 15.7% and 22.7% under stress of Ag NPs. Microbial richness index and compositions were affected, and control wetland enriched Sulfurospirillum, Desulfarculaceae and Flavobacterium whereas CWs exposed to Ag NPs enriched Desulfosporosinus and Desulfurispora from LEfSe analysis. Moreover, after dosing Ag NPs, relative abundances of functional genes amoA and hao for nitrification, nirK and norB for denitrification and ppx and phoA/phoD for phosphorus conversions in upper soil were significantly downregulated. Inhibition on functional bacteria and genes of Ag NPs explained poor removal efficiencies of nitrogen and phosphorus pollutants in CWs. Our findings give an insight into ecological toxicity of Ag NPs on CWs with N and P bioconversions and provide the understanding of response of nitrifiers, denitrifies and PAOs.

Extracellular electron transfer-dependent Cr(VI)/sulfate reduction mediated by iron sulfide nanoparticles

The slow electron transfer rate is a bottleneck to the biological wastewater treatment. This study evaluated the concomitant biotransformation and nonenzymatic reduction of Cr(VI) mediated by sulfate reducing bacteria (SRB), especially for the reinforcing Cr(VI) reduction via accelerating the electron transfer by the in-situ biosynthesized iron sulfide nanoparticles (FeS NPs). The kinetic results showed that 10 mg/L Cr(VI) was completely removed by pre-cultured FeS NPs within 7 h with k_Cr(VI) of 2.6 × 10^-4 s^-1, one magnitude higher than that without FeS NPs. Despite its competing electron to postpone sulfate reduction, the reduction of Cr(VI) was markedly improved via nonenzymatic reactions by the sulfide, the product of sulfate reduction. In the reinforcing system (bio-FeS NP@SRB), the bio-FeS NPs served as an electronic bypass conduit for CoQ could significantly amplify the electron flux, and switch the Cr(VI) reduction from intracellular space to extracellular environment, which had a great detoxification effect on the microorganisms, eventually markedly promoted electron transfer extracellularly and the reduction of Cr(VI). After the long-term acclimatization, Desulfovibrio became the dominant bacteria at the genus level and accounted for the relative abundance of 32%. This study provides an alternative to use biogenic FeS NPs for Cr(VI) remediation.

Bacterial Dynamics and Their Influence on the Biogeochemical Cycles in a Subtropical Hypereutrophic Lake During the Rainy Season

Lakes in subtropical regions are highly susceptible to eutrophication due to the heavy rainfall, which causes significant runoff of pollutants (e.g., nutrients) to reach surface waters, altering the water quality and influencing the microbial communities that regulate the biogeochemical cycles within these ecosystems. Lake Cajititlán is a shallow, subtropical, and endorheic lake in western Mexico. Nutrient pollution from agricultural activity and wastewater discharge have affected the lake’s water quality, leading the reservoir to a hypereutrophic state, resulting in episodes of fish mortality during the rainy season. This study investigated the temporal dynamics of bacterial communities within Lake Cajititlán and their genes associated with the nitrogen, phosphorus, sulfur, and carbon biogeochemical cycles during the rainy season, as well as the influences of physicochemical and environmental variables on such dynamics. Significant temporal variations were observed in the composition of bacterial communities, of which Flavobacterium and Pseudomonas were the dominant genera. The climatological parameters that were most correlated with the bacterial communities and their functional profiles were pH, DO, ORP, turbidity, TN, EC, NH₄⁺, and NO₃^–. The bacterial communities displayed variations in their functional composition for nitrogen, phosphorus, and sulfur metabolisms during the sampling months. The bacterial communities within the lake are highly susceptible to nutrient loads and low DO levels during the rainy season. Bacterial communities had a higher relative abundance of genes associated with denitrification, nitrogen fixation, assimilatory sulfate reduction, cysteine, SOX system, and all phosphorus metabolic pathways. The results obtained here enrich our understanding of the bidirectional interactions between bacterial communities and major biogeochemical processes in eutrophic subtropical lakes.

Into the darkness: The ecologies of novel 'microbial dark matter' phyla in an Antarctic lake

Uncultivated microbial clades ("microbial dark matter") are inferred to play important, but uncharacterized roles in nutrient cycling. Using Antarctic lake (Ace Lake, Vestfold Hills) metagenomes, 12 metagenome-assembled genomes (MAGs; 88-100% complete) were generated for four "dark matter" phyla: six MAGs from Candidatus Auribacterota (= Aureabacteria, SURF-CP-2), inferred to be hydrogen- and sulfide-producing fermentative heterotrophs, with individual MAGs encoding bacterial microcompartments (BMCs), gas vesicles, and type IV pili; one MAG (100% complete) from Candidatus Hinthialibacterota (= OLB16), inferred to be a facultative anaerobe capable of dissimilatory nitrate reduction to ammonia, specialized for mineralization of complex organic matter (e.g., sulfated polysaccharides), and encoding BMCs, flagella, and Tad pili; three MAGs from Candidatus Electryoneota (= AABM5-125-24), previously reported to include facultative anaerobes capable of dissimilatory sulfate reduction, and here inferred to perform sulfite oxidation, reverse tricarboxylic acid cycle for autotrophy, and possess numerous proteolytic enzymes; two MAGs from Candidatus Lernaellota (= FEN-1099), inferred to be capable of formate oxidation, amino acid fermentation, and possess numerous enzymes for protein and polysaccharide degradation. The presence of 16S rRNA gene sequences in public metagenome datasets (88-100% identity) suggests these "dark matter" phyla contribute to sulfur cycling, degradation of complex organic matter, ammonification and/or chemolithoautrophic CO₂ fixation in diverse global environments. This article is protected by copyright. All rights reserved.

The DsrD functional marker protein is an allosteric activator of the DsrAB dissimilatory sulfite reductase

Metagenomic data have recently transformed our view of the role played by sulfur metabolism in anoxic environments by showing that this trait is much more widespread than previously believed. A key enzyme in sulfur metabolism is the dissimilatory sulfite reductase DsrAB that is ubiquitous in organisms with a reductive, oxidative, or disproportionating activity. However, the function of some dsr genes, such as dsrD, has so far been unknown despite its use as a functional marker to genomically assign the type of sulfur energy metabolism, sometimes with unclear results. Here, we disclose the function of DsrD as an activator of DsrAB that significantly increases its activity, providing important insights into the mechanism of this enzyme in different types of sulfur metabolism.

Dissimilatory sulfur metabolism was recently shown to be much more widespread among bacteria and archaea than previously believed. One of the key pathways involved is the dsr pathway that is responsible for sulfite reduction in sulfate-, sulfur-, thiosulfate-, and sulfite-reducing organisms, sulfur disproportionators and organosulfonate degraders, or for the production of sulfite in many photo- and chemotrophic sulfur-oxidizing prokaryotes. The key enzyme is DsrAB, the dissimilatory sulfite reductase, but a range of other Dsr proteins is involved, with different gene sets being present in organisms with a reductive or oxidative metabolism. The dsrD gene codes for a small protein of unknown function and has been widely used as a functional marker for reductive or disproportionating sulfur metabolism, although in some cases this has been disputed. Here, we present in vivo and in vitro studies showing that DsrD is a physiological partner of DsrAB and acts as an activator of its sulfite reduction activity. DsrD is expressed in respiratory but not in fermentative conditions and a ΔdsrD deletion strain could be obtained, indicating that its function is not essential. This strain grew less efficiently during sulfate and sulfite reduction. Organisms with the earliest forms of dsrAB lack the dsrD gene, revealing that its activating role arose later in evolution relative to dsrAB.

Ubiquitous Occurrence of a Biogenic Sulfonate in Marine Environment

The biogenic sulfonate 2,3-dihydroxypropane-1-sulfonate (DHPS) is a vital metabolic currency between phytoplankton and bacteria in marine environments. However, the occurrence and quantification of DHPS in the marine environment has not been well-characterized. In this study, we used targeted metabolomics to determine the concentration of DHPS in the Pearl River Estuary, an in situ costal mesocosm ecosystem and a hydrothermal system off Kueishantao Island. The results suggested that DHPS occurred ubiquitously in the marine environment, even in shallow-sea hydrothermal systems, at a level comparable to that of dimethylsulfoniopropionate. The concentration of DHPS was closely related to phytoplankton community composition and was especially associated with the abundance of diatoms. Epsilonproteobacteria were considered as the most likely producers of DHPS in shallow-sea hydrothermal systems. This work expands current knowledge on sulfonates and presents a new viewpoint on the sulfur cycle in hydrothermal systems.

Nature's nitrite-to-ammonia expressway, with no stop at dinitrogen

Since the characterization of cytochrome c₅₅₂ as a multiheme nitrite reductase, research on this enzyme has gained major interest. Today, it is known as pentaheme cytochrome c nitrite reductase (NrfA). Part of the NH₄⁺ produced from NO₂^- is released as NH₃ leading to nitrogen loss, similar to denitrification which generates NO, N₂O, and N₂. NH₄⁺ can also be used for assimilatory purposes, thus NrfA contributes to nitrogen retention. It catalyses the six-electron reduction of NO₂^- to NH₄⁺, hosting four His/His ligated c-type hemes for electron transfer and one structurally differentiated active site heme. Catalysis occurs at the distal side of a Fe(III) heme c proximally coordinated by lysine of a unique CXXCK motif (Sulfurospirillum deleyianum, Wolinella succinogenes) or, presumably, by the canonical histidine in Campylobacter jejeuni. Replacement of Lys by His in NrfA of W. succinogenes led to a significant loss of enzyme activity. NrfA forms homodimers as shown by high resolution X-ray crystallography, and there exist at least two distinct electron transfer systems to the enzyme. In γ-proteobacteria (Escherichia coli) NrfA is linked to the menaquinol pool in the cytoplasmic membrane through a pentaheme electron carrier (NrfB), in δ- and ε-proteobacteria (S. deleyianum, W. succinogenes), the NrfA dimer interacts with a tetraheme cytochrome c (NrfH). Both form a membrane-associated respiratory complex on the extracellular side of the cytoplasmic membrane to optimize electron transfer efficiency. This minireview traces important steps in understanding the nature of pentaheme cytochrome c nitrite reductases, and discusses their structural and functional features.

Microbial sulfur metabolism and environmental implications

Sulfur as a macroelement plays an important role in biochemistry in both natural environments and engineering biosystems, which can be further linked to other important element cycles, e.g. carbon, nitrogen and iron. Consequently, the sulfur cycling primarily mediated by sulfur compounds oxidizing microorganisms and sulfur compounds reducing microorganisms has enormous environmental implications, particularly in wastewater treatment and pollution bioremediation. In this review, to connect the knowledge in microbial sulfur metabolism to environmental applications, we first comprehensively review recent advances in understanding microbial sulfur metabolisms at molecular-, cellular- and ecosystem-levels, together with their energetics. We then discuss the environmental implications to fight against soil and water pollution, with four foci: (1) acid mine drainage, (2) water blackening and odorization in urban rivers, (3) SANI® and DS-EBPR processes for sewage treatment, and (4) bioremediation of persistent organic pollutants. In addition, major challenges and further developments toward elucidation of microbial sulfur metabolisms and their environmental applications are identified and discussed.

Integrated approach in LDPE degradation - An application using Winogradsky column, computational modeling, and pathway prediction

Plastic pollution in the current scenario requires a sustainable and eco-friendly treatment process. Single-use plastics accumulate more than recyclable plastic wastes. Low-Density Polyethylene (LDPE) is one among the plastic family with inert characteristics. The traditional method, such as landfilling, develops pollution resistant micro-organisms. It is involved in the exploitation of the native microbes to the fullest. The soil of the Kodungaiyur, agriculture site, and Otteri dumpyard were used, which resulted in nearly 22.97 ± 2.7115%, 15.91667 ± 2.73775%, and 10.74 ± 0.502925% of LDPE degradation in 30 days without nutrient supplements. The enrichment of the column by organic nutrients increased the degradation of LDPE. The column enrichment was confirmed by the sulfur oxidizing bacteria (SOB) Escherichia coli and Pseudomonas stutzeri, which produced 195 mg/mL of sulfate ions. The FTIR of the LDPE degradation showed the polymer's oxygenation, while the electron microscopic images revealed cracks. In addition, an attempt was made to fit the experimental time-series data into suitable mathematical models to look at prediction and elementary forecasting. Three mathematical models, namely the customized moving averages model (CMAM), simple liinear regression model (SLRM), and a modified linear regression model (MLRM) with a lag, were able to represent the real experimental data complementarily.

Genomic characterization of three novel Desulfobacterota classes expand the metabolic and phylogenetic diversity of the phylum

We report on the genomic characterization of three novel classes in the phylum Desulfobacterota. One class (proposed name Candidatus 'Anaeroferrophillalia') was characterized by heterotrophic growth capacity, either fermentatively or utilizing polysulfide, tetrathionate or thiosulfate as electron acceptors. In the absence of organic carbon sources, autotrophic growth via the Wood-Ljungdahl (WL) pathway and using hydrogen or Fe(II) as an electron donor is also inferred for members of the 'Anaeroferrophillalia'. The second class (proposed name Candidatus 'Anaeropigmentia') was characterized by its capacity for growth at low oxygen concentration, and the capacity to synthesize the methyl/alkyl carrier CoM, an ability that is prevalent in the archaeal but rare in the bacterial domain. Pigmentation is inferred from the capacity for carotenoid (lycopene) production. The third class (proposed name Candidatus 'Zymogenia') was characterized by fermentative heterotrophic growth capacity, broad substrate range and the adaptation of some of its members to hypersaline habitats. Analysis of the distribution pattern of all three classes showed their occurrence as rare community members in multiple habitats, with preferences for anaerobic terrestrial, freshwater and marine environments over oxygenated (e.g. pelagic ocean and agricultural land) settings. Special preference for some members of the class Candidatus 'Zymogenia' for hypersaline environments such as hypersaline microbial mats and lagoons was observed.

Transcriptomics analysis of the metabolic mechanisms of iron reduction induced by sulfate reduction mediated by sulfate-reducing bacteria

Sulfate-reducing bacteria (SRB) play an important role in sulfur, iron and carbon cycling. The majority of studies have illustrated the role of SRB in biogeochemical cycling in pure cultures. In this study, we established three SRB enrichment cultures (designated HL, NB and WC) from different paddy soils and conducted a transcriptomic analysis of their metabolic characteristics under sulfate and sulfate-free conditions. In the HL cultures, there was no sulfate consumption but ferrihydrite was reduced. This indicated that bacteria in the HL samples can reduce ferrihydrite and preferentially utilize ferrihydrite as the electron acceptor in the absence of both ferrihydrite and sulfate. Sulfate consumption was equal in the NB and the WC cultures, although more ferrihydrite was reduced in the NB cultures. Transcriptomics analysis showed that (i) upregulation of O-acetylserine sulfhydrylase gene expression indicating sulfate assimilation in the WC samples; (ii) the energy conservation trithionate pathway is commonly employed by SRB and (iii) sulfate not only enhanced iron reduction by its conversion to sulfide but also promoted enzymatic electron transfer via c-type cytochromes.

Nickel ferrite/MXene-coated carbon felt anodes for enhanced microbial fuel cell performance

In recent years, the modification of electrode materials for enhancing the power generation of microbial fuel cells (MFCs) has attracted considerable attention. In this study, a conventional carbon felt (CF) electrode was modified by NiFe₂O₄ (NiFe₂O₄@CF), MXene (MXene@CF), and NiFe₂O₄-MXene (NiFe₂O₄-MXene@CF) using facile dip-and-dry and hydrothermal methods. In these modified CF electrodes, the electrochemical performance considerably improved, while the highest power density (1385 mW/m²), which was 5.6, 2.8, and 1.4 times higher than those of CF, NiFe₂O₄@CF, and MXene@CF anodes, respectively, was achieved using NiFe₂O₄-MXene@CF. Furthermore, electrochemical impedance spectroscopy and cyclic voltammetry results confirmed the superior bioelectrochemical activity of a NiFe₂O₄-MXene@CF anode in a MFC. The improved performance could be attributed to the low charge transfer resistance, high conductivity and number of catalytically active sites of the NiFe₂O₄-MXene@CF anode. Microbial community analysis demonstrated the relative abundance of electroactive bacteria on a NiFe₂O₄-MXene@CF anodic biofilm rather than CF, MXene@CF, and NiFe₂O₄@CF anodes. Therefore, these results suggest that combining the favorable properties of composite materials such as NiFe₂O₄-MXene@CF anodes can open up new directions for fabricating novel electrodes for renewable energy-related applications.

Redox loops in anaerobic respiration - The role of the widespread NrfD protein family and associated dimeric redox module

In prokaryotes, the proton or sodium motive force required for ATP synthesis is produced by respiratory complexes that present an ion-pumping mechanism or are involved in redox loops performed by membrane proteins that usually have substrate and quinone-binding sites on opposite sides of the membrane. Some respiratory complexes include a dimeric redox module composed of a quinone-interacting membrane protein of the NrfD family and an iron‑sulfur protein of the NrfC family. The QrcABCD complex of sulfate reducers, which includes the QrcCD module homologous to NrfCD, was recently shown to perform electrogenic quinone reduction providing the first conclusive evidence for energy conservation among this family. Similar redox modules are present in multiple respiratory complexes, which can be associated with electroneutral, energy-driven or electrogenic reactions. This work discusses the presence of the NrfCD/PsrBC dimeric redox module in different bioenergetics contexts and its role in prokaryotic energy conservation mechanisms.

The Iron-Sulfur Flavoprotein DsrL as NAD(P)H:Acceptor Oxidoreductase in Oxidative and Reductive Dissimilatory Sulfur Metabolism

DsrAB-type dissimilatory sulfite reductase is a key enzyme of microbial sulfur-dependent energy metabolism. Sulfur oxidizers also contain DsrL, which is essential for sulfur oxidation in Allochromatium vinosum. This NAD(P)H oxidoreductase acts as physiological partner of oxidative-type rDsrAB. Recent analyses uncovered that DsrL is not confined to sulfur oxidizers but also occurs in (probable) sulfate/sulfur-reducing bacteria. Here, phylogenetic analysis revealed a separation into two major branches, DsrL-1, with two subgroups, and DsrL-2. When present in organisms with reductive-type DsrAB, DsrL is of type 2. In the majority of cases oxidative-type rDsrAB occurs with DsrL-1 but combination with DsrL-2-type enzymes is also observed. Three model DsrL proteins, DsrL-1A and DsrL-1B from the sulfur oxidizers A. vinosum and Chlorobaculum tepidum, respectively, as well as DsrL-2 from thiosulfate- and sulfur-reducing Desulfurella amilsii were kinetically characterized. DaDsrL-2 is active with NADP(H) but not with NAD(H) which we relate to a conserved YRR-motif in the substrate-binding domains of all DsrL-2 enzymes. In contrast, AvDsrL-1A has a strong preference for NAD(H) and the CtDsrL-1B enzyme is completely inactive with NADP(H). Thus, NAD⁺ as well as NADP⁺ are suitable in vivo electron acceptors for rDsrABL-1-catalyzed sulfur oxidation, while NADPH is required as electron donor for sulfite reduction. This observation can be related to the lower redox potential of the NADPH/NADP⁺ than the NADH/NAD⁺ couple under physiological conditions. Organisms with a rdsrAB and dsrL-1 gene combination can be confidently identified as sulfur oxidizers while predictions for organisms with other combinations require much more caution and additional information sources.

Sulfites in meat: Occurrence, activity, toxicity, regulation, and detection. A comprehensive review

Sulfites are a class of chemical compounds, SO₂ releasers, widely used as additives in food industry, due to their antimicrobial, color stabilizing, antibrowning, and antioxidant properties. As the results of these pleiotropic functions they can be added to a broad range of products including dried fruits and vegetables, seafood, juices, alcoholic and nonalcoholic beverage, and in few meat products. Sulfites ingestion has been correlated with several adverse and toxic reactions, such as hypersensitivity, allergic diseases, vitamin deficiency, and may lead to dysbiotic events of gut and oral microbiota. In many countries, these additives are closely regulated and in meat products the legislation restricts their usage. Several studies have been conducted to investigate the sulfites contents in meat and meat products, and many of them have revealed that some meat preparations represent one of the main sources of SO₂ exposure, especially in adults and young people. This review discusses properties, technological functions, regulation, and health implications of sulfites in meat-based foods, and lays a special emphasis on the chemical mechanisms involved in their interactions with organic and inorganic meat components.

Metagenomics-Guided Discovery of Potential Bacterial Metallothionein Genes from the Soil Microbiome That Confer Cu and/or Cd Resistance

Metallothionein (MT) genes are valuable genetic materials for developing metal bioremediation tools. Currently, a limited number of prokaryotic MTs have been experimentally identified, which necessitates the expansion of bacterial MT diversity. In this study, we conducted a metagenomics-guided analysis for the discovery of potential bacterial MT genes from the soil microbiome. More specifically, we combined resistance gene enrichment through diversity loss, metagenomic mining with a dedicated MT database, evolutionary trace analysis, DNA chemical synthesis, and functional genomic validation to identify novel MTs. Results showed that Cu stress induced a compositional change in the soil microbiome, with an enrichment of metal-resistant bacteria in soils with higher Cu concentrations. Shotgun metagenomic sequencing was performed to obtain the gene pool of environmental DNA (eDNA), which was subjected to a local BLAST search against an MT database for detecting putative MT genes. Evolutional trace analysis led to the identification of 27 potential MTs with conserved cysteine/histidine motifs different from those of known prokaryotic MTs. Following chemical synthesis of these 27 potential MT genes and heterologous expression in Escherichia coli, six of them were found to improve the hosts' growth substantially and enhanced the hosts' sorption of Cu, Cd, and Zn, among which MT5 led to a 13.7-fold increase in Cd accumulation. Furthermore, four of them restored Cu and/or Cd resistance in two metal-sensitive E. coli strains.IMPORTANCE The metagenomics-guided procedure developed here bypasses the difficulties encountered in classic PCR-based approaches and led to the discovery of novel MT genes, which may be useful in developing bioremediation tools. The procedure used here expands our knowledge on the diversity of bacterial MTs in the environment and may also be applicable to identify other functional genes from eDNA.

Structural evidence for a reaction intermediate mimic in the active site of a sulfite dehydrogenase

We provide structural and spectroscopic evidence for a molybdenum–phosphate adduct mimicking a proposed reaction intermediate in the active site of a prokaryotic sulfite oxidizing enzyme.

Bacterial nitrous oxide respiration: electron transport chains and copper transfer reactions

Biologically catalyzed nitrous oxide (N₂O, laughing gas) reduction to dinitrogen gas (N₂) is a desirable process in the light of ever-increasing atmospheric concentrations of this important greenhouse gas and ozone depleting substance. A diverse range of bacterial species produce the copper cluster-containing enzyme N₂O reductase (NosZ), which is the only known enzyme that converts N₂O to N₂. Based on phylogenetic analyses, NosZ enzymes have been classified into clade I or clade II and it has turned out that this differentiation is also applicable to nos gene clusters (NGCs) and some physiological traits of the corresponding microbial cells. The NosZ enzyme is the terminal reductase of anaerobic N₂O respiration, in which electrons derived from a donor substrate are transferred to NosZ by means of an electron transport chain (ETC) that conserves energy through proton motive force generation. This chapter presents models of the ETCs involved in clade I and clade II N₂O respiration as well as of the respective NosZ maturation and maintenance processes. Despite differences in NGCs and growth yields of N₂O-respiring microorganisms, the deduced bioenergetic framework in clade I and clade II N₂O respiration is assumed to be equivalent. In both cases proton motive quinol oxidation by N₂O is thought to be catalyzed by the Q cycle mechanism of a membrane-bound Rieske/cytochrome bc complex. However, clade I and clade II organisms are expected to differ significantly in terms of auxiliary electron transport processes as well as NosZ active site maintenance and repair.

Desulphurisation of Biogas: A Systematic Qualitative and Economic-Based Quantitative Review of Alternative Strategies

The desulphurisation of biogas for hydrogen sulphide (H2S) removal constitutes a significant challenge in the area of biogas research. This is because the retention of H2S in biogas presents negative consequences on human health and equipment durability. The negative impacts are reflective of the potentially fatal and corrosive consequences reported when biogas containing H2S is inhaled and employed as a boiler biofuel, respectively. Recognising the importance of producing H2S-free biogas, this paper explores the current state of research in the area of desulphurisation of biogas. In the present paper, physical–chemical, biological, in-situ, and post-biogas desulphurisation strategies were extensively reviewed as the basis for providing a qualitative comparison of the strategies. Additionally, a review of the costing data combined with an analysis of the inherent data uncertainties due underlying estimation assumptions have also been undertaken to provide a basis for quantitative comparison of the desulphurisation strategies. It is anticipated that the combination of the qualitative and quantitative comparison approaches employed in assessing the desulphurisation strategies reviewed in the present paper will aid in future decisions involving the selection of the preferred biogas desulphurisation strategy to satisfy specific economic and performance-related targets.

Control of Bacterial Sulfite Detoxification by Conserved and Species-Specific Regulatory Circuits

Although sulfite, a by-product of the degradation of many sulfur compounds, is highly reactive and can cause damage to DNA, proteins and lipids, comparatively little is known about the regulation of sulfite-oxidizing enzyme (SOEs) expression. Here we have investigated the regulation of SOE-encoding genes in two species of α-Proteobacteria, Sinorhizobium meliloti and Starkeya novella, that degrade organo- and inorganic sulfur compounds, respectively, and contain unrelated types of SOEs that show different expression patterns. Our work revealed that in both cases, the molecular signal that triggers SOE gene expression is sulfite, and strong up-regulation depends on the presence of a sulfite-responsive, cognate Extracytoplasmic function (ECF) sigma factor, making sulfite oxidation a bacterial stress response. An additional RpoE1-like ECF sigma factor was also involved in the regulation, but was activated by different molecular signals, taurine (Sm) and tetrathionate (Sn), respectively, targeted different gene promoters, and also differed in the magnitude of the response generated. We therefore propose that RpoE1 is a secondary, species-specific regulator of SOE gene expression rather than a general, conserved regulatory circuit. Sulfite produced by major dissimilatory processes appeared to be the trigger for SOE gene expression in both species, as we were unable to find evidence for an increase of SOE activity in stationary growth phase. The basic regulation of bacterial sulfite oxidation by cognate ECF sigma factors is likely to be applicable to three groups of alpha and beta-Proteobacteria in which we identified similar SOE operon structures.

The function, biogenesis and regulation of the electron transport chains in Campylobacter jejuni: New insights into the bioenergetics of a major food-borne pathogen

Campylobacter jejuni is a zoonotic Epsilonproteobacterium that grows in the gastrointestinal tract of birds and mammals, and is the most frequent cause of food-borne bacterial gastroenteritis worldwide. As an oxygen-sensitive microaerophile, C. jejuni has to survive high environmental oxygen tensions, adapt to oxygen limitation in the host intestine and resist host oxidative attack. Despite its small genome size, C. jejuni is a versatile and metabolically active pathogen, with a complex and highly branched set of respiratory chains allowing the use of a wide range of electron donors and alternative electron acceptors in addition to oxygen, including fumarate, nitrate, nitrite, tetrathionate and N- or S-oxides. Several novel enzymes participate in these electron transport chains, including a tungsten containing formate dehydrogenase, a Complex I that uses flavodoxin and not NADH, a periplasmic facing fumarate reductase and a cytochrome c tetrathionate reductase. This review presents an updated description of the composition and bioenergetics of these various respiratory chains as they are currently understood, including recent work that gives new insights into energy conservation during electron transport to various alternative electron acceptors. The regulation of synthesis and assembly of the electron transport chains is also discussed. A deeper appreciation of the unique features of the respiratory systems of C. jejuni may be helpful in informing strategies to control this important pathogen.

The bioenergetics mechanisms and applications of sulfate-reducing bacteria in remediation of pollutants in drainage: A review

Sulfate-reducing bacteria (SRB), a group of anaerobic prokaryotes, can use sulfur species as a terminal electron acceptor for the oxidation of organic compounds. They not only have significant ecological functions, but also play an important role in bioremediation of contaminated sites. Although numerous studies on metabolism and applications of SRB have been conducted, they still remain incompletely understood and even controversial. Fully understanding the metabolism of SRB paves the way for allowing the microorganisms to provide more beneficial services in bioremediation. Here we review progress in bioenergetics mechanisms and application of SRB including: (1) electron acceptors and donors for SRB; (2) pathway for sulfate reduction; (3) electron transfer in sulfate reduction; (4) application of SRB for economical and concomitant treatment of heavy metal, organic contaminants and sulfates. Moreover, current knowledge gaps and further research needs are identified.

Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle

A critical step in the biogeochemical cycle of sulfur on Earth is microbial sulfate reduction, yet organisms from relatively few lineages have been implicated in this process. Previous studies using functional marker genes have detected abundant, novel dissimilatory sulfite reductases (DsrAB) that could confer the capacity for microbial sulfite/sulfate reduction but were not affiliated with known organisms. Thus, the identity of a significant fraction of sulfate/sulfite-reducing microbes has remained elusive. Here we report the discovery of the capacity for sulfate/sulfite reduction in the genomes of organisms from 13 bacterial and archaeal phyla, thereby more than doubling the number of microbial phyla associated with this process. Eight of the 13 newly identified groups are candidate phyla that lack isolated representatives, a finding only possible given genomes from metagenomes. Organisms from Verrucomicrobia and two candidate phyla, Candidatus Rokubacteria and Candidatus Hydrothermarchaeota, contain some of the earliest evolved dsrAB genes. The capacity for sulfite reduction has been laterally transferred in multiple events within some phyla, and a key gene potentially capable of modulating sulfur metabolism in associated cells has been acquired by putatively symbiotic bacteria. We conclude that current functional predictions based on phylogeny significantly underestimate the extent of sulfate/sulfite reduction across Earth's ecosystems. Understanding the prevalence of this capacity is integral to interpreting the carbon cycle because sulfate reduction is often coupled to turnover of buried organic carbon. Our findings expand the diversity of microbial groups associated with sulfur transformations in the environment and motivate revision of biogeochemical process models based on microbial community composition.

Peatland Acidobacteria with a dissimilatory sulfur metabolism

Sulfur-cycling microorganisms impact organic matter decomposition in wetlands and consequently greenhouse gas emissions from these globally relevant environments. However, their identities and physiological properties are largely unknown. By applying a functional metagenomics approach to an acidic peatland, we recovered draft genomes of seven novel Acidobacteria species with the potential for dissimilatory sulfite (dsrAB, dsrC, dsrD, dsrN, dsrT, dsrMKJOP) or sulfate respiration (sat, aprBA, qmoABC plus dsr genes). Surprisingly, the genomes also encoded DsrL, which so far was only found in sulfur-oxidizing microorganisms. Metatranscriptome analysis demonstrated expression of acidobacterial sulfur-metabolism genes in native peat soil and their upregulation in diverse anoxic microcosms. This indicated an active sulfate respiration pathway, which, however, might also operate in reverse for dissimilatory sulfur oxidation or disproportionation as proposed for the sulfur-oxidizing Desulfurivibrio alkaliphilus. Acidobacteria that only harbored genes for sulfite reduction additionally encoded enzymes that liberate sulfite from organosulfonates, which suggested organic sulfur compounds as complementary energy sources. Further metabolic potentials included polysaccharide hydrolysis and sugar utilization, aerobic respiration, several fermentative capabilities, and hydrogen oxidation. Our findings extend both, the known physiological and genetic properties of Acidobacteria and the known taxonomic diversity of microorganisms with a DsrAB-based sulfur metabolism, and highlight new fundamental niches for facultative anaerobic Acidobacteria in wetlands based on exploitation of inorganic and organic sulfur molecules for energy conservation.

Sulfur Cycling and the Intestinal Microbiome

In this review, we focus on the activities transpiring in the anaerobic segment of the sulfur cycle occurring in the gut environment where hydrogen sulfide is produced. While sulfate-reducing bacteria are considered as the principal agents for hydrogen sulfide production, the enzymatic desulfhydration of cysteine by heterotrophic bacteria also contributes to production of hydrogen sulfide. For sulfate-reducing bacteria respiration, molecular hydrogen and lactate are suitable as electron donors while sulfate functions as the terminal electron acceptor. Dietary components provide fiber and macromolecules that are degraded by bacterial enzymes to monomers, and these are fermented by intestinal bacteria with the production to molecular hydrogen which promotes the metabolic dominance by sulfate-reducing bacteria. Sulfate is also required by the sulfate-reducing bacteria, and this can be supplied by sulfate- and sulfonate-containing compounds that are hydrolyzed by intestinal bacterial with the release of sulfate. While hydrogen sulfide in the intestinal biosystem may be beneficial to bacteria by increasing resistance to antibiotics, and protecting them from reactive oxygen species, hydrogen sulfide at elevated concentrations may become toxic to the host.

The life sulfuric: microbial ecology of sulfur cycling in marine sediments

Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes. Sulfur-transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate-rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep-subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle.

Implications from distinct sulfate-reducing bacteria populations between cattle manure and digestate in the elucidation of H2S production during anaerobic digestion of animal slurry

Biogas produced from the anaerobic digestion of animal slurry consists mainly of methane (CH₄) and carbon dioxide (CO₂), but also includes other minor gases, such as hydrogen sulfide (H₂S). Since it can act as a potent corrosive agent and presents a health hazard even at low concentrations, H₂S is considered an undesirable by-product of anaerobic digestion. Sulfate-reducing bacteria (SRBs) have been identified as the main biological source of H₂S in a number of natural, biological, and human-made habitats, and thus represent likely candidate microorganisms responsible for the production of H₂S in anaerobic manure digesters. Phylogenetically, SRBs form a divergent group of bacteria that share a common anaerobic respiration pathway that allows them to use sulfate as a terminal electron acceptor. While the composition and activity of SRBs have been well documented in other environments, their metabolic potential remains largely uncharacterized and their populations poorly defined in anaerobic manure digesters. In this context, a combination of in vitro culture-based studies and DNA-based approaches, respectively, were used to gain further insight. Unexpectedly, only low to nondetectable levels of H₂S were produced by digestate collected from a manure biogas plant documented to have persistently high concentrations of H₂S in its biogas (2000-3000 ppm). In contrast, combining digestate with untreated manure (a substrate with comparatively lower sulfate and SRB cell densities than digestate) was found to produce elevated H₂S levels in culture. While a 16S rRNA gene-based community composition approach did not reveal likely candidate SRBs in digestate or untreated manure, the use of the dsrAB gene as a phylogenetic marker provided more insight. In digestate, the predominant SRBs were found to be uncharacterized species likely belonging to the genus Desulfosporosinus (Peptococcaceae, Clostridiales, Firmicutes), while Desulfovibrio-related SRBs (Desulfovibrionaceae, Desulfovibrionales, Proteobacteria) were the most highly represented in untreated manure. Intriguingly, the same species-level OTUs with a similar pattern of opposite relative abundance were also found in two other digesters with lower H₂S levels in their biogas. Together, our results suggest that elevated H₂S production in anaerobic digesters requires the combination of biological and nutritional factors from both untreated manure and digestate.

Thermodesulfitimonas autotrophica gen. nov., sp. nov., a thermophilic, obligate sulfite-reducing bacterium isolated from a terrestrial hot spring

A novel thermophilic, anaerobic, chemolithoautotrophic bacterium, strain SF97T, was isolated from a terrestrial hot spring (Kuril Islands, Russia). Cells of strain SF97T were rod-shaped and motile with a Gram-positive cell-wall type. The novel isolate grew at 45-72 °C (optimum 65 °C) and pH 5.5-8.5 (optimum 6.0-6.5). The strain grew chemolithoautotrophically with molecular hydrogen as an electron donor, sodium sulfite or SO2 gas as an electron acceptor and bicarbonate/CO2 as a carbon source. Sulfate, thiosulfate, elemental sulfur, Fe(III) or nitrate were not used as electron acceptors either with H2 or organic electron donors. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belonged to the family Thermoanaerobacteraceae, order Thermoanaerobacterales, and was distantly related to species of the genus Ammonifex (92-93 % sequence similarity). On the basis of its physiological properties and results of phylogenetic analyses, strain SF97T is considered to represent a novel species of a new genus, for which the name Thermodesulfitimonas autotrophica gen. nov., sp. nov. is proposed. The type strain of Thermodesulfitimonas autotrophica is SF97T (=DSM 102936T=VKM B-2961T). T. autotrophica is the first reported obligate sulfite-reducing micro-organism.