Metabolism of sulfate-reducing prokaryotes

Gated Nanosensor for Sulphate-Reducing Bacteria Detection

Desulfovibrio vulgaris is an anaerobic microorganism belonging to the group of sulphate-reducing bacteria (SRB). SRB form biofilms on metal surfaces in water supply networks, producing a microbiologically influenced corrosion (MIC). This process produces the deterioration of metal surfaces, leading to high economic costs and different environmental safety and health problems related to its chemical treatment. For that reason, rapid and accurate detection methods of SRB are needed. In this work, a new detection system for Desulfovibrio has been developed using gated nanoporous materials. The probe is based on hybrid nanoporous alumina films encapsulating a fluorescent molecule (rhodamine B), whose release is controlled by an oligonucleotide gate. Upon exposure to Desulfovibrio's genomic material, a movement of the oligonucleotide gatekeeper happens, resulting in the selective delivery of the entrapped rhodamine B. The developed material shows high selectivity and sensitivity for detecting Desulfovibrio DNA in aqueous buffer and biological media. The implementation of this technology for the detection of Desulfovibrio as a tool for monitoring water supply networks is innovative and allows real-time in situ monitoring, making it possible to detect the growth of Desulfovibrio inside of pipes at an early stage and perform timely interventions to reverse it.

Bacteria and Methanogens in the Human Microbiome: a Review of Syntrophic Interactions

Methanogens are microorganisms belonging to the Archaea domain and represent the primary source of biotic methane. Methanogens encode a series of enzymes which can convert secondary substrates into methane following three major methanogenesis pathways. Initially recognized as environmental microorganisms, methanogens have more recently been acknowledged as host-associated microorganisms after their detection and initial isolation in ruminants in the 1950s. Methanogens have also been co-detected with bacteria in various pathological situations, bringing their role as pathogens into question. Here, we review reported associations between methanogens and bacteria in physiological and pathological situations in order to understand the metabolic interactions explaining these associations. To do so, we describe the origin of the metabolites used for methanogenesis and highlight the central role of methanogens in the syntrophic process during carbon cycling. We then focus on the metabolic abilities of co-detected bacterial species described in the literature and infer from their genomes the probable mechanisms of their association with methanogens. The syntrophic interactions between bacteria and methanogens are paramount to gut homeostasis. Therefore, any dysbiosis affecting methanogens might impact human health. Thus, the monitoring of methanogens may be used as a bio-indicator of dysbiosis. Moreover, new therapeutic approaches can be developed based on their administration as probiotics. We thus insist on the importance of investigating methanogens in clinical microbiology.

Mussels and Local Conditions Interact to Influence Microbial Communities in Mussel Beds

Microbiomes are increasingly recognized as widespread regulators of function from individual organism to ecosystem scales. However, the manner in which animals influence the structure and function of environmental microbiomes has received considerably less attention. Using a comparative field study, we investigated the relationship between freshwater mussel microbiomes and environmental microbiomes. We used two focal species of unionid mussels, Amblema plicata and Actinonaias ligamentina, with distinct behavioral and physiological characteristics. Mussel microbiomes, those of the shell and biodeposits, were less diverse than both surface and subsurface sediment microbiomes. Mussel abundance was a significant predictor of sediment microbial community composition, but mussel species richness was not. Our data suggest that local habitat conditions which change dynamically along streams, such as discharge, water turnover, and canopy cover, work in tandem to influence environmental microbial community assemblages at discreet rather than landscape scales. Further, mussel burrowing activity and mussel shells may provide habitat for microbial communities critical to nutrient cycling in these systems.

Microbiota Metabolites in Health and Disease

Metabolism is one of the strongest drivers of interkingdom interactions-including those between microorganisms and their multicellular hosts. Traditionally thought to fuel energy requirements and provide building blocks for biosynthetic pathways, metabolism is now appreciated for its role in providing metabolites, small-molecule intermediates generated from metabolic processes, to perform various regulatory functions to mediate symbiotic relationships between microbes and their hosts. Here, we review recent advances in our mechanistic understanding of how microbiota-derived metabolites orchestrate and support physiological responses in the host, including immunity, inflammation, defense against infections, and metabolism. Understanding how microbes metabolically communicate with their hosts will provide us an opportunity to better describe how a host interacts with all microbes-beneficial, pathogenic, and commensal-and an opportunity to discover new ways to treat microbial-driven diseases.

Environmental characteristics of a tundra river system in Svalbard. Part 2: Chemical stress factors

Bacterial communities in the Arctic environment are subject to multiple stress factors, including contaminants, although typically their concentrations are small. The Arctic contamination research has focused on persistent organic pollutants (POPs) because they are bioaccumulative, resistant to degradation and toxic for all organisms. Pollutants have entered the Arctic predominantly by atmospheric and oceanic long-range transport, and this was facilitated by their volatile or semi-volatile properties, while their chemical stability extended their lifetimes following emission. Chemicals present in the Arctic at detectable and quantifiable concentrations testify to their global impact. Chemical contamination may induce serious disorders in the integrity of polar ecosystems influencing the growth of bacterial communities. In this study, the abundance and the types of bacteria in the Arctic freshwater were examined and the microbial characteristics were compared to the amount of potentially harmful chemical compounds in particular elements of the Arctic catchment. The highest concentrations of all determined PAHs were observed in two samples in the vicinity of the estuary both in June and September 2016 and were 1964 ng L^-1 (R12) and 3901 ng L^-1 (R13) in June, and 2179 ng L^-1 (R12) and 1349 ng L^-1 (R13) in September. Remarkable concentrations of the sum of phenols and formaldehyde were detected also at the outflow of the Revelva river into the sea (R12) and were 0.24 mg L^-1 in June and 0.35 mg L^-1 in September 2016. The elevated concentrations of chemical compounds near the estuary suggest a potential impact of the water from the lower tributaries (including the glacier-fed stream measured at R13) or the sea currents and the sea aerosol as pollutant sources. The POPs' degradation at low temperature is not well understood but bacteria capable to degrading such compounds were noted in each sampling point.

Characterization of sulfur-compound metabolism underlying wax-ester fermentation in Euglena gracilis

Euglena gracilis is a microalga, which has been used as a model organism for decades. Recent technological advances have enabled mass cultivation of this species for industrial applications such as feedstock in nutritional foods and cosmetics. E. gracilis degrades its storage polysaccharide (paramylon) under hypoxic conditions for energy acquisition by an oxygen-independent process and accumulates high amount of wax-ester as a by-product. Using this sequence of reactions referred to as wax-ester fermentation, E. gracilis is studied for its application in biofuel production. Although the wax-ester production pathway is well characterized, little is known regarding the biochemical reactions underlying the main metabolic route, especially, the existence of an unknown sulfur-compound metabolism implied by the nasty odor generation accompanying the wax-ester fermentation. In this study, we show sulfur-metabolomics of E. gracilis in aerobic and hypoxic conditions, to reveal the biochemical reactions that occur during wax-ester synthesis. Our results helped us in identifying hydrogen sulfide (H2S) as the nasty odor-producing component in wax-ester fermentation. In addition, the results indicate that glutathione and protein degrades during hypoxia, whereas cysteine, methionine, and their metabolites increase in the cells. This indicates that this shift of abundance in sulfur compounds is the cause of H2S synthesis.

How to tackle the stringent sulfate removal requirements in mine water treatment-A review of potential methods

Sulfate (SO₄^2-) is a ubiquitous anion in natural waters. It is not considered toxic, but it may be detrimental to freshwater species at elevated concentrations. Mining activities are one significant source of anthropogenic sulfate into natural waters, mainly due to the exposure of sulfide mineral ores to weathering. There are several strategies for mitigating sulfate release, starting from preventing sulfate formation in the first place and ending at several end-of-pipe treatment options. Currently, the most widely used sulfate-removal process is precipitation as gypsum (CaSO₄·2H₂O). However, the lowest reachable concentration is theoretically 1500 mg L^-1 SO₄^2- due to gypsum's solubility. At the same time, several mines worldwide have significantly more stringent sulfate discharge limits. The purpose of this review is to examine the process options to reach low sulfate levels (< 1500 mg L^-1) in mine effluents. Examples of such processes include alternative chemical precipitation methods, membrane technology, biological treatment, ion exchange, and adsorption. In addition, aqueous chemistry and current effluent standards concerning sulfate together with concentrate treatment and sulfur recovery are discussed.

The role of sulfate in aerobic granular sludge process for emerging sulfate-laden wastewater treatment

Sulfate-rich wastewaters pose a major threat to mainstream wastewater treatment due to the unpreventable production of sulfide and associated shift in functional bacteria. Aerobic granular sludge could mitigate these challenges in view of its high tolerance and resilience against changes in various environmental conditions. This study aims to confirm the feasibility of aerobic granular sludge in the treatment of sulfate containing wastewater, investigate the impact of sulfate on nutrient removal and granulation, and reveal metabolic relationships in the above processes. Experiments were conducted using five sequencing batch reactors with different sulfate concentrations operated under alternating anoxic/aerobic condition. Results showed that effect of sulfate on chemical oxygen demand (COD) removal is negligible, while phosphate removal was enhanced from 12% to 87% with an increase in sulfate from 0 to 200 mg/L. However, a long acclimatization of the biomass (more than 70 days) is needed at a sulfate concentration of 500 mg/L and a total deterioration of phosphate removal at 1000 mg/L. Batch tests revealed that sulfide promoted volatile fatty acids (VFAs) uptake, producing more energy for phosphate uptake when sulfate concentrations were beneath 200 mg/L. However, sulfide detoxification became energy dominating, leaving insufficient energy for Polyhydroxyalkanoate (PHA) synthesis and phosphate uptake when sulfate content was further increased. Granulation accelerated with increasing sulfate levels by enhanced production of N-Acyl homoserine lactones (AHLs), a kind of quorum sensing (QS) auto-inducer, using S-Adenosyl Methionine (SAM) as primer. The current study demonstrates interactions among sulfate metabolism, nutrients removal and granulation, and confirms the feasibility of using the aerobic granular sludge process for sulfate-laden wastewaters treatment with low to medium sulfate content.

Physiological handling of dietary fructose-containing sugars: implications for health

Fructose has always been present in our diet, but its consumption has increased markedly over the past 200 years. This is mainly due to consumption of sucrose or high-fructose corn syrup in industrial foods and beverages. Unlike glucose, fructose cannot be directly used as an energy source by all cells of the human body and needs first to be converted into glucose, lactate or fatty acids in the liver, intestine and kidney. Because of this specific two-step metabolism, some energy is consumed in splanchnic organs to convert fructose into other substrates, resulting in a lower net energy efficiency of fructose compared with glucose. A high intake of fructose-containing sugars is associated with body weight gain in large cohort studies, and fructose can certainly contribute to energy imbalance leading to obesity. Whether fructose-containing foods promote obesity more than other energy-dense foods remains controversial, however. A short-term (days-weeks) high-fructose intake is not associated with an increased fasting glycemia nor to an impaired insulin-mediated glucose transport in healthy subjects. It, however, increases hepatic glucose production, basal and postprandial blood triglyceride concentrations and intrahepatic fat content. Whether these metabolic alterations are early markers of metabolic dysfunction or merely adaptations to the specific two-step fructose metabolism remain unknown.

Resonance assignment of DVU2108 that is part of the Orange Protein complex in Desulfovibrio vulgaris Hildenborough

We report the 94 % assignment of DVU2108, a protein belonging to the Orange Protein family, that in Desulfovibrio vulgaris Hildenborough forms a protein complex named the Orange Protein complex. This complex has been shown to be implicated in the cell division of this organism. DVU2108 is a conserved protein in anaerobic microorganisms and in Desulfovibrio gigas the homologous protein was isolated with a novel Mo-Cu cluster non-covalently attached to the polypeptide chain. However, the heterologously produced DVU2108 did not contain any bound metal. These assignments provide the means to characterize the interaction of DVU2108 with the proteins that form the Orange Protein complex using NMR methods.

Microbial transcriptome profiling of black band disease in a Faviid coral during a seasonal disease peak

The etiology of black band disease (BBD), a persistent, globally distributed coral disease characterized by a dark microbial mat, is still unclear. A metatranscriptomics approach was used to unravel the roles of the major mat constituents in the disease process. By comparing the transcriptomes of the mat constituents with those of the surface microbiota of diseased and healthy corals, we showed a shift in bacterial composition and function in BBD-affected corals. mRNA reads of Cyanobacteria, Bacteroidetes and Firmicutes phyla were prominent in the BBD mat. Cyanobacterial adenosylhomocysteinase, involved in cyanotoxin production, was the most transcribed gene in the band consortium. Pathogenic and non-pathogenic forms of Vibrio spp., mainly transcribing the thiamine ABC transporter, were abundant and highly active in both the band and surface tissues. Desulfovibrio desulfuricans was the primary producer of sulfide in the band. Members of the Bacilli class expressed high levels of rhodanese, an enzyme responsible for cyanide and sulfide detoxification. These results offer a first look at the varied functions of the microbiota in the disease mat and surrounding coral surface and enabled us to develop an improved functional model for this disease.

Sulfate-reducing bacteria impairs working memory in mice

The ability of gut microbes to bi-directionally communicate with the brain and vice versa form the basis of the gut microbiome-central nervous system axis. It has been shown that inoculation with pathogenic gut bacteria alters the behavior of mice; however, it is not known whether or not non-pathogenic resident microbes have similar effects. In this study, we tested the hypothesis that the administration of sulfate-reducing bacteria (SRB), a specific group of resident gut bacteria that generate hydrogen sulfide (H2S), impair learning and memory performance in mice tested in an 8-arm radial maze and Morris water maze. We found that mice spent more time in the center of the maze when they were gavaged with live SRB as compared to mice given saline (control), lactulose+mannitol (L/M), or killed SRB. SRB-gavaged mice were also tested using the Morris water maze and were found to take longer to complete the test, spend more time further from the platform, and have a longer path length to reach the platform. This effect of SRB on maze performance was associated with a higher concentration of H2S in the small intestine and cecum. We conclude that SRB, a specific resident gut bacterial species, could impair cognitive function in mice.

Patterns of sulfur isotope fractionation during microbial sulfate reduction

Studies of microbial sulfate reduction have suggested that the magnitude of sulfur isotope fractionation varies with sulfate concentration. Small apparent sulfur isotope fractionations preserved in Archean rocks have been interpreted as suggesting Archean sulfate concentrations of <200 μm, while larger fractionations thereafter have been interpreted to require higher concentrations. In this work, we demonstrate that fractionation imposed by sulfate reduction can be a function of concentration over a millimolar range, but that nature of this relationship depends on the organism studied. Two sulfate-reducing bacteria grown in continuous culture with sulfate concentrations ranging from 0.1 to 6 mm showed markedly different relationships between sulfate concentration and isotope fractionation. Desulfovibrio vulgaris str. Hildenborough showed a large and relatively constant isotope fractionation ((34) εSO 4-H2S ≅ 25‰), while fractionation by Desulfovibrio alaskensis G20 strongly correlated with sulfate concentration over the same range. Both data sets can be modeled as Michaelis-Menten (MM)-type relationships but with very different MM constants, suggesting that the fractionations imposed by these organisms are highly dependent on strain-specific factors. These data reveal complexity in the sulfate concentration-fractionation relationship. Fractionation during MSR relates to sulfate concentration but also to strain-specific physiological parameters such as the affinity for sulfate and electron donors. Previous studies have suggested that the sulfate concentration-fractionation relationship is best described with a MM fit. We present a simple model in which the MM fit with sulfate concentration and hyperbolic fit with growth rate emerge from simple physiological assumptions. As both environmental and biological factors influence the fractionation recorded in geological samples, understanding their relationship is critical to interpreting the sulfur isotope record. As the uptake machinery for both sulfate and electrons has been subject to selective pressure over Earth history, its evolution may complicate efforts to uniquely reconstruct ambient sulfate concentrations from a single sulfur isotopic composition.

The complete genome sequence and emendation of the hyperthermophilic, obligate iron-reducing archaeon "Geoglobus ahangari" strain 234(T)

“Geoglobus ahangari” strain 234^T is an obligate Fe(III)-reducing member of the Archaeoglobales, within the archaeal phylum Euryarchaeota, isolated from the Guaymas Basin hydrothermal system. It grows optimally at 88 °C by coupling the reduction of Fe(III) oxides to the oxidation of a wide range of compounds, including long-chain fatty acids, and also grows autotrophically with hydrogen and Fe(III). It is the first archaeon reported to use a direct contact mechanism for Fe(III) oxide reduction, relying on a single archaellum for locomotion, numerous curled extracellular appendages for attachment, and outer-surface heme-containing proteins for electron transfer to the insoluble Fe(III) oxides. Here we describe the annotation of the genome of “G. ahangari” strain 234^T and identify components critical to its versatility in electron donor utilization and obligate Fe(III) respiratory metabolism at high temperatures. The genome comprises a single, circular chromosome of 1,770,093 base pairs containing 2034 protein-coding genes and 52 RNA genes. In addition, emended descriptions of the genus “Geoglobus” and species “G. ahangari” are described.

Remediation of nitrate-contaminated water by solid-phase denitrification process-a review

The paper presents a compilation of various autotrophic and heterotrophic ways of solid-phase denitrification. It covers a complete understanding of various pathways followed during denitrification process. The paper gives a brief review on various governing factors on which the process depends. It focuses mainly on the solid-phase denitrification process, its applicability, efficiency, and disadvantages associated. It presents a critical review on various methodologies associated with denitrification process reported in past years. A comparative study has also been carried out to have a better understanding of advantages and disadvantages of a particular method. We summarize the various organic and inorganic substances and various techniques that have been used for enhancing denitrification process and suggest possible gaps in the research areas whi'ch are worthy of future research.

A genomic view on syntrophic versus non-syntrophic lifestyle in anaerobic fatty acid degrading communities

In sulfate-reducing and methanogenic environments complex biopolymers are hydrolyzed and degraded by fermentative micro-organisms that produce hydrogen, carbon dioxide and short chain fatty acids. Degradation of short chain fatty acids can be coupled to methanogenesis or to sulfate-reduction. Here we study from a genome perspective why some of these micro-organisms are able to grow in syntrophy with methanogens and others are not. Bacterial strains were selected based on genome availability and upon their ability to grow on short chain fatty acids alone or in syntrophic association with methanogens. Systematic functional domain profiling allowed us to shed light on this fundamental and ecologically important question. Extra-cytoplasmic formate dehydrogenases (InterPro domain number; IPR006443), including their maturation protein FdhE (IPR024064 and IPR006452) is a typical difference between syntrophic and non-syntrophic butyrate and propionate degraders. Furthermore, two domains with a currently unknown function seem to be associated with the ability of syntrophic growth. One is putatively involved in capsule or biofilm production (IPR019079) and a second in cell division, shape-determination or sporulation (IPR018365). The sulfate-reducing bacteria Desulfobacterium autotrophicum HRM2, Desulfomonile tiedjei and Desulfosporosinus meridiei were never tested for syntrophic growth, but all crucial domains were found in their genomes, which suggests their possible ability to grow in syntrophic association with methanogens. In addition, profiling domains involved in electron transfer mechanisms revealed the important role of the Rnf-complex and the formate transporter in syntrophy, and indicate that DUF224 may have a role in electron transfer in bacteria other than Syntrophomonas wolfei as well. This article is a part of a Special Issue entitled: 18th European Bioenergetics Conference (Biochim. Biophys. Acta, Volume 1837, Issue 7, July 2014).

IHF is required for the transcriptional regulation of the Desulfovibrio vulgaris Hildenborough orp operons

Transcriptional activation of σ(54)-dependent promoters is usually tightly regulated in response to environmental cues. The high abundance of potential σ(54)-dependent promoters in the anaerobe bacteria, Desulfovibrio vulgaris Hildenborough, reflects the high versatility of this bacteria suggesting that σ(54) factor is the nexus of a large regulatory network. Understanding the key players of σ(54)-regulation in this organism is therefore essential to gain insights into the adaptation to anaerobiosis. Recently, the D. vulgaris orp genes, specifically found in anaerobe bacteria, have been shown to be transcribed by the RNA polymerase coupled to the σ(54) alternative sigma factor. In this study, using in vitro binding experiments and in vivo reporter fusion assays in the Escherichia coli heterologous host, we showed that the expression of the divergent orp promoters is strongly dependent on the integration host factor IHF. Bioinformatic and mutational analysis coupled to reporter fusion activities and mobility shift assays identified two functional IHF binding site sequences located between the orp1 and orp2 promoters. We further determined that the D. vulgaris DVU0396 (IHFα) and DVU1864 (IHFβ) subunits are required to control the expression of the orp operons suggesting that they form a functionally active IHF heterodimer. Interestingly results obtained from the in vivo inactivation of DVU0396, which is required for orp operons transcription, suggest that several functionally IHF active homodimer or heterodimer are present in D. vulgaris.

Structural, biochemical and genetic characterization of dissimilatory ATP sulfurylase from Allochromatium vinosum

ATP sulfurylase (ATPS) catalyzes a key reaction in the global sulfur cycle by reversibly converting inorganic sulfate (SO4 (2-)) with ATP to adenosine 5'-phosphosulfate (APS) and pyrophosphate (PPi). In this work we report on the sat encoded dissimilatory ATP sulfurylase from the sulfur-oxidizing purple sulfur bacterium Allochromatium vinosum. In this organism, the sat gene is located in one operon and co-transcribed with the aprMBA genes for membrane-bound APS reductase. Like APS reductase, Sat is dispensible for growth on reduced sulfur compounds due to the presence of an alternate, so far unidentified sulfite-oxidizing pathway in A. vinosum. Sulfate assimilation also proceeds independently of Sat by a separate pathway involving a cysDN-encoded assimilatory ATP sulfurylase. We produced the purple bacterial sat-encoded ATP sulfurylase as a recombinant protein in E. coli, determined crucial kinetic parameters and obtained a crystal structure in an open state with a ligand-free active site. By comparison with several known structures of the ATPS-APS complex in the closed state a scenario about substrate-induced conformational changes was worked out. Despite different kinetic properties ATPS involved in sulfur-oxidizing and sulfate-reducing processes are not distinguishable on a structural level presumably due to the interference between functional and evolutionary processes.

Microbial sulfite respiration

Despite its reactivity and hence toxicity to living cells, sulfite is readily converted by various microorganisms using distinct assimilatory and dissimilatory metabolic routes. In respiratory pathways, sulfite either serves as a primary electron donor or terminal electron acceptor (yielding sulfate or sulfide, respectively), and its conversion drives electron transport chains that are coupled to chemiosmotic ATP synthesis. Notably, such processes are also seen to play a general role in sulfite detoxification, which is assumed to have an evolutionary ancient origin. The diversity of sulfite conversion is reflected by the fact that the range of microbial sulfite-converting enzymes displays different cofactors such as siroheme, heme c, or molybdopterin. This chapter aims to summarize the current knowledge of microbial sulfite metabolism and focuses on sulfite catabolism. The structure and function of sulfite-converting enzymes and the emerging picture of the modular architecture of the corresponding respiratory/detoxifying electron transport chains is emphasized.

Bioremediation of mine water

Caused by the oxidative dissolution of sulfide minerals, mine waters are often acidic and contaminated with high concentrations of sulfates, metals, and metalloids. Because the so-called acid mine drainage (AMD) affects the environment or poses severe problems for later use, treatment of these waters is required. Therefore, various remediation strategies have been developed to remove soluble metals and sulfates through immobilization using physical, chemical, and biological approaches. Conventionally, iron and sulfate-the main pollutants in mine waters-are removed by addition of neutralization reagents and subsequent chemical iron oxidation and sulfate mineral precipitation. Biological treatment strategies take advantage of the ability of microorganisms that occur in mine waters to metabolize iron and sulfate. As a rule, these can be grouped into oxidative and reductive processes, reflecting the redox state of mobilized iron (reduced form) and sulfur (oxidized form) in AMD. Changing the redox states of iron and sulfur results in iron and sulfur compounds with low solubility, thus leading to their precipitation and removal. Various techniques have been developed to enhance the efficacy of these microbial processes, as outlined in this review.

Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes

Accurate detection of transcriptional regulatory elements is essential for high-quality genome annotation, metabolic reconstruction, and modeling of regulatory networks. We developed a computational approach for reconstruction of regulons operated by transcription factors (TFs) from large protein families and applied this novel approach to three TF families in 10 Desulfovibrionales genomes. Phylogenetic analyses of 125 regulators from the ArsR, Crp/Fnr, and GntR families revealed that 65% of these regulators (termed reference TFs) are well conserved in Desulfovibrionales, while the remaining 35% of regulators (termed singleton TFs) are species specific and show a mosaic distribution. For regulon reconstruction in the group of singleton TFs, the standard orthology-based approach was inefficient, and thus, we developed a novel approach based on the simultaneous study of all homologous TFs from the same family in a group of genomes. As a result, we identified binding for 21 singleton TFs and for all reference TFs in all three analyzed families. Within each TF family we observed structural similarities between DNA-binding motifs of different reference and singleton TFs. The collection of reconstructed regulons is available at the RegPrecise database (http://regprecise.lbl.gov/RegPrecise/Desulfovibrionales.jsp).

Revisiting the dissimilatory sulfate reduction pathway

Sulfur isotopes in the geological record integrate a combination of biological and diagenetic influences, but a key control on the ratio of sulfur isotopes in sedimentary materials is the magnitude of isotope fractionation imparted during dissimilatory sulfate reduction. This fractionation is controlled by the flux of sulfur through the network of chemical reactions involved in sulfate reduction and by the isotope effect associated with each of these chemical reactions. Despite its importance, the network of reactions constituting sulfate reduction is not fully understood, with two principle networks underpinning most isotope models. In this study, we build on biochemical data and recently solved crystal structures of enzymes to propose a revised network topology for the flow of sulfur through the sulfate reduction metabolism. This network is highly branched and under certain conditions produces results consistent with the observations that motivated previous sulfate reduction models. Our revised network suggests that there are two main paths to sulfide production: one that involves the production of thionate intermediates, and one that does not. We suggest that a key factor in determining sulfur isotope fractionation associated with sulfate reduction is the ratio of the rate at which electrons are supplied to subunits of Dsr vs. the rate of sulfite delivery to the active site of Dsr. This reaction network may help geochemists to better understand the relationship between the physiology of sulfate reduction and the isotopic record it produces.

Genetics and molecular biology of the electron flow for sulfate respiration in desulfovibrio

Progress in the genetic manipulation of the Desulfovibrio strains has provided an opportunity to explore electron flow pathways during sulfate respiration. Most bacteria in this genus couple the oxidation of organic acids or ethanol with the reduction of sulfate, sulfite, or thiosulfate. Both fermentation of pyruvate in the absence of an alternative terminal electron acceptor, disproportionation of fumarate and growth on H₂ with CO₂ during sulfate reduction are exhibited by some strains. The ability to produce or consume H₂ provides Desulfovibrio strains the capacity to participate as either partner in interspecies H₂ transfer. Interestingly the mechanisms of energy conversion, pathways of electron flow and the parameters determining the pathways used remain to be elucidated. Recent application of molecular genetic tools for the exploration of the metabolism of Desulfovibrio vulgaris Hildenborough has provided several new datasets that might provide insights and constraints to the electron flow pathways. These datasets include (1) gene expression changes measured in microarrays for cells cultured with different electron donors and acceptors, (2) relative mRNA abundances for cells growing exponentially in defined medium with lactate as carbon source and electron donor plus sulfate as terminal electron acceptor, and (3) a random transposon mutant library selected on medium containing lactate plus sulfate supplemented with yeast extract. Studies of directed mutations eliminating apparent key components, the quinone-interacting membrane-bound oxidoreductase (Qmo) complex, the Type 1 tetraheme cytochrome c₃ (Tp1-c₃), or the Type 1 cytochrome c₃:menaquinone oxidoreductase (Qrc) complex, suggest a greater flexibility in electron flow than previously considered. The new datasets revealed the absence of random transposons in the genes encoding an enzyme with homology to Coo membrane-bound hydrogenase. From this result, we infer that Coo hydrogenase plays an important role in D. vulgaris growth on lactate plus sulfate. These observations along with those reported previously have been combined in a model showing dual pathways of electrons from the oxidation of both lactate and pyruvate during sulfate respiration. Continuing genetic and biochemical analyses of key genes in Desulfovibrio strains will allow further clarification of a general model for sulfate respiration.

Anaerobic treatment of sulfate-rich wastewater in an anaerobic sequential batch reactor (AnSBR) using butanol as the carbon source

Biological sulfate reduction was studied in a laboratory-scale anaerobic sequential batch reactor (14 L) containing mineral coal for biomass attachment. The reactor was fed industrial wastewater with increasingly high sulfate concentrations to establish its application limits. Special attention was paid to the use of butanol in the sulfate reduction that originated from melamine resin production. This product was used as the main organic amendment to support the biological process. The reactor was operated for 65 cycles (48 h each) at sulfate loading rates ranging from 2.2 to 23.8 g SO(4)(2-)/cycle, which corresponds to sulfate concentrations of 0.25, 0.5, 1.0, 2.0 and 3.0 g SO(4)(2-) L(-1). The sulfate removal efficiency reached 99% at concentrations of 0.25, 0.5 and 1.0 g SO(4)(2-) L(-1). At higher sulfate concentrations (2.0 and 3.0 g SO(4)(2-) L(-1)), the sulfate conversion remained in the range of 71-95%. The results demonstrate the potential applicability of butanol as the carbon source for the biological treatment of sulfate in an anaerobic batch reactor.

The anaerobe-specific orange protein complex of Desulfovibrio vulgaris hildenborough is encoded by two divergent operons coregulated by σ54 and a cognate transcriptional regulator

Analysis of sequenced bacterial genomes revealed that the genomes encode more than 30% hypothetical and conserved hypothetical proteins of unknown function. Among proteins of unknown function that are conserved in anaerobes, some might be determinants of the anaerobic way of life. This study focuses on two divergent clusters specifically found in anaerobic microorganisms and mainly composed of genes encoding conserved hypothetical proteins. We show that the two gene clusters DVU2103-DVU2104-DVU2105 (orp2) and DVU2107-DVU2108-DVU2109 (orp1) form two divergent operons transcribed by the σ(54)-RNA polymerase. We further demonstrate that the σ(54)-dependent transcriptional regulator DVU2106, located between orp1 and orp2, collaborates with σ(54)-RNA polymerase to orchestrate the simultaneous expression of the divergent orp operons. DVU2106, whose structural gene is transcribed by the σ(70)-RNA polymerase, negatively retrocontrols its own expression. By using an endogenous pulldown strategy, we identify a physiological complex composed of DVU2103, DVU2104, DVU2105, DVU2108, and DVU2109. Interestingly, inactivation of DVU2106, which is required for orp operon transcription, induces morphological defects that are likely linked to the absence of the ORP complex. A putative role of the ORP proteins in positioning the septum during cell division is discussed.

Sulfate reduction, molecular diversity, and copper amendment effects in bacterial communities enriched from sediments exposed to copper mining residues

Sulfate-reducing bacterial communities from coastal sediments with a long-term exposure to copper (Cu)-mining residues were studied in lactate enrichments. The toxicity of excess copper may affect sulfate-reducing bacterial communities. Sulfate reduction was monitored by sulfate and organic acid measurements. Molecular diversity was analyzed by 16S rRNA, dissimilatory sulfate reduction dsrAB, and Cu translocating phospho-type adenosine triphosphatases (P-ATPases) cop-like gene sequence profiling. The influence of Cu amendment was tested in these enrichments. Results showed fast sulfate reduction mostly coupled to incomplete organic carbon oxidation and partial sulfate reduction inhibition due to copper amendment. The 16S rRNA clonal libraries analysis indicated that delta- and gamma-Proteobacteria and Cytophaga-Flexibacter-Bacteroides dominated the enrichments. The dsrAB libraries revealed the presence of Desulfobacteraceae and Desulfovibrionaceae families-related sequences. Copper produced significant shifts (i.e., a decrease in the relative abundance of sulfate-reducing microorganisms) in the enriched bacterial community structure as determined by terminal-restriction fragment length polymorphism (T-RFLP) profiling and multivariate analyses. Clonal libraries of cop-like sequences showed low richness in the enriched microbial communities, and a strong effect of copper on its relative abundance. Novel Cu-P(IB)-ATPase sequences encoding Cu resistance were detected. The present study indicates that Cu does not significantly affect sulfate reduction and genetic diversity of taxonomic and dissimilatory sulfate-reduction molecular markers. However, the diversity of Cu resistance genetic determinants was strongly modified by this toxic metal.

Response of the sulfate-reducing community to the re-establishment of estuarine conditions in two contrasting soils: a mesocosm approach

We studied the response of the sulfate-reducing prokaryote (SRP) communities to the experimental variation of salinity and tide in an outdoor mesocosm setup. Intact soil monoliths were collected at two areas of the Haringvliet lagoon (The Netherlands): one sampling location consisted of agricultural grassland, drained and fertilized for at least the last century; the other of a freshwater marshland with more recent sea influence. Two factors, i.e., "salinity" (freshwater/oligohaline) and "tide" (nontidal/tidal), were tested in a full-factorial design. Soil samples were collected after 5 months (June-October). Dissimilatory (bi)sulfite reductase beta subunit-based denaturing gradient gel electrophoresis (dsrB-DGGE) analysis revealed that the SRP community composition in the agricultural grassland and in the freshwater marshland was represented mainly by microorganisms related to the Desulfobulbaceae and the Desulfobacteraceae, respectively. Desulfovibrio-related dsrB were detected only in the tidal treatments; Desulfomonile-related dsrB occurrence was related to the presence of oligohaline conditions. Treatments did have an effect on the overall SRP community composition of both soils, but not on the sulfate depletion rates in sulfate-amended anoxic slurry incubations. However, initiation of sulfate reduction upon sulfate addition was clearly different between the two soils.

Citric acid wastewater as electron donor for biological sulfate reduction

Citrate-containing wastewater is used as electron donor for sulfate reduction in a biological treatment plant for the removal of sulfate. The pathway of citrate conversion coupled to sulfate reduction and the microorganisms involved were investigated. Citrate was not a direct electron donor for the sulfate-reducing bacteria. Instead, citrate was fermented to mainly acetate and formate. These fermentation products served as electron donors for the sulfate-reducing bacteria. Sulfate reduction activities of the reactor biomass with acetate and formate were sufficiently high to explain the sulfate reduction rates that are required for the process. Two citrate-fermenting bacteria were isolated. Strain R210 was closest related to Trichococcus pasteurii (99.5% ribosomal RNA (rRNA) gene sequence similarity). The closest relative of strain S101 was Veillonella montepellierensis with an rRNA gene sequence similarity of 96.7%. Both strains had a complementary substrate range.

Post-translational modifications of Desulfovibrio vulgaris Hildenborough sulfate reduction pathway proteins

Recent developments in shotgun proteomics have enabled high-throughput studies of a variety of microorganisms at a proteome level and provide experimental validation for predicted open reading frames in the corresponding genome. More importantly, advances in mass spectrometric data analysis now allow mining of large proteomics data sets for the presence of post-translational modifications (PTMs). Although PTMs are a critical aspect of cellular activity, such information eludes cell-wide studies conducted at the transcript level. Here, we analyze several mass spectrometric data sets acquired using two-dimensional liquid chromatography tandem mass spectrometry, 2D-LC/MS/MS, for the sulfate reducing bacterium, Desulfovibrio vulgaris Hildenborough. Our searches of the raw spectra led us to discover several post-translationally modified peptides in D. vulgaris. Of these, several peptides containing a lysine with a +42 Da modification were found reproducibly across all data sets. Both acetylation and trimethylation have the same nominal +42 Da mass, and are therefore candidates for this modification. Several spectra were identified having markers for trimethylation, while one is consistent with an acetylation. Surprisingly, these modified peptides predominantly mapped to proteins involved in sulfate respiration. Other highly expressed proteins in D. vulgaris, such as enzymes involved in electron transport and other central metabolic processes, did not contain this modification. Decoy database searches were used to control for random spectrum/sequence matches. Additional validation for these modifications was provided by alternate workflows, for example, two-dimensional gel electrophoresis followed by mass spectrometry analysis of the dissimilatory sulfite reductase gamma-subunit (DsrC) protein. MS data for DsrC in this alternate workflow also contained the +42 Da modification at the same loci. Furthermore, the DsrC homologue in another sulfate reducing bacterium, Desulfovibrio desulfuricans G20, also showed similar +42 Da modifications in the same pathway. Here, we discuss our methods and implications of potential trimethylation in the D. vulgaris sulfate reduction pathway.

Quantitative analysis of three hydrogenotrophic microbial groups, methanogenic archaea, sulfate-reducing bacteria, and acetogenic bacteria, within plaque biofilms associated with human periodontal disease

Human subgingival plaque biofilms are highly complex microbial ecosystems that may depend on H(2)-metabolizing processes. Here we investigated the ubiquity and proportions of methanogenic archaea, sulfate reducers, and acetogens in plaque samples from 102 periodontitis patients. In contrast to the case for 65 healthy control subjects, hydrogenotrophic groups were almost consistently detected in periodontal pockets, with the proportions of methanogens and sulfate reducers being significantly elevated in severe cases. In addition, antagonistic interactions among the three microbial groups indicated that they may function as alternative syntrophic partners of secondary fermenting periodontal pathogens.

Quantitative analysis of three hydrogenotrophic microbial groups, methanogenic archaea, sulfate-reducing bacteria, and acetogenic bacteria, within plaque biofilms associated with human periodontal disease

Human subgingival plaque biofilms are highly complex microbial ecosystems that may depend on H(2)-metabolizing processes. Here we investigated the ubiquity and proportions of methanogenic archaea, sulfate reducers, and acetogens in plaque samples from 102 periodontitis patients. In contrast to the case for 65 healthy control subjects, hydrogenotrophic groups were almost consistently detected in periodontal pockets, with the proportions of methanogens and sulfate reducers being significantly elevated in severe cases. In addition, antagonistic interactions among the three microbial groups indicated that they may function as alternative syntrophic partners of secondary fermenting periodontal pathogens.

Effect of solvents on obligately anaerobic bacteria

Growth of Acetobacterium woodii and Clostridium sporogenes was studied in the presence of water-immiscible solvents. Nitrogen purging, vacuum distillation or distillation under nitrogen were all suitable as methods to remove oxygen from the solvents, since growth rates and yields of A. woodii were unaffected in the presence of tetradecane which had been degassed by these methods. Varying the solvent volume from 20% to 80% of the culture volume had little effect on growth rate of A. woodii. A.woodii was relatively sensitive to organic solvents since growth was inhibited by alkanes with logP(octanol/water) values below 7.1. C. sporogenes was less solvent sensitive, since it grew without inhibition when the logP of the solvent was > or = 6.6. Nevertheless, both A. woodii and C. sporogenes were more sensitive to solvent polarity than aerobic bacteria.

Homology modeling of dissimilatory APS reductases (AprBA) of sulfur-oxidizing and sulfate-reducing prokaryotes

Background

The dissimilatory adenosine-5′-phosphosulfate (APS) reductase (cofactors flavin adenine dinucleotide, FAD, and two [4Fe-4S] centers) catalyzes the transformation of APS to sulfite and AMP in sulfate-reducing prokaryotes (SRP); in sulfur-oxidizing bacteria (SOB) it has been suggested to operate in the reverse direction. Recently, the three-dimensional structure of the Archaeoglobus fulgidus enzyme has been determined in different catalytically relevant states providing insights into its reaction cycle.

Methodology/Principal Findings

Full-length AprBA sequences from 20 phylogenetically distinct SRP and SOB species were used for homology modeling. In general, the average accuracy of the calculated models was sufficiently good to allow a structural and functional comparison between the beta- and alpha-subunit structures (78.8–99.3% and 89.5–96.8% of the AprB and AprA main chain atoms, respectively, had root mean square deviations below 1 Å with respect to the template structures). Besides their overall conformity, the SRP- and SOB-derived models revealed the existence of individual adaptations at the electron-transferring AprB protein surface presumably resulting from docking to different electron donor/acceptor proteins. These structural alterations correlated with the protein phylogeny (three major phylogenetic lineages: (1) SRP including LGT-affected Archaeoglobi and SOB of Apr lineage II, (2) crenarchaeal SRP Caldivirga and Pyrobaculum, and (3) SOB of the distinct Apr lineage I) and the presence of potential APS reductase-interacting redox complexes. The almost identical protein matrices surrounding both [4Fe-4S] clusters, the FAD cofactor, the active site channel and center within the AprB/A models of SRP and SOB point to a highly similar catalytic process of APS reduction/sulfite oxidation independent of the metabolism type the APS reductase is involved in and the species it has been originated from.

Conclusions

Based on the comparative models, there are no significant structural differences between dissimilatory APS reductases from SRP and SOB; this might be indicative for a similar catalytic process of APS reduction/sulfite oxidation.

Heavy metal removal from synthetic wastewaters in an anaerobic bioreactor using stillage from ethanol distilleries as a carbon source

This work was conducted to investigate the possibility of using stillage from ethanol distilleries as substrate for sulfate reducing bacteria (SRB) growth and to evaluate the removal efficiency of heavy metals present in wastewaters containing sulfates. The experiments were carried out in a continuous bench-scale Upflow Anaerobic Sludge Blanket reactor (13 l) operated with a hydraulic retention time of 18 h. The bioreactor was inoculated with 7 l of anaerobic sludge. Afterwards, an enrichment procedure to increase SRB numbers was started. After this, cadmium and zinc were added to the synthetic wastewater, and their removal as metal sulfide was evaluated. The synthetic wastewater used represented the drainage from a dam of a metallurgical industry to which a carbon source (stillage) was added. The results showed that high percentages of removal (>99%) of Cd and Zn were attained in the bioreactor, and that the removal as sulfide precipitates was not the only form of metal removal occurring in the bioreactor environment.

Unusual starch degradation pathway via cyclodextrins in the hyperthermophilic sulfate-reducing archaeon Archaeoglobus fulgidus strain 7324

The hyperthermophilic archaeon Archaeoglobus fulgidus strain 7324 has been shown to grow on starch and sulfate and thus represents the first sulfate reducer able to degrade polymeric sugars. The enzymes involved in starch degradation to glucose 6-phosphate were studied. In extracts of starch-grown cells the activities of the classical starch degradation enzymes, alpha-amylase and amylopullulanase, could not be detected. Instead, evidence is presented here that A. fulgidus utilizes an unusual pathway of starch degradation involving cyclodextrins as intermediates. The pathway comprises the combined action of an extracellular cyclodextrin glucanotransferase (CGTase) converting starch to cyclodextrins and the intracellular conversion of cyclodextrins to glucose 6-phosphate via cyclodextrinase (CDase), maltodextrin phosphorylase (Mal-P), and phosphoglucomutase (PGM). These enzymes, which are all induced after growth on starch, were characterized. CGTase catalyzed the conversion of starch to mainly beta-cyclodextrin. The gene encoding CGTase was cloned and sequenced and showed highest similarity to a glucanotransferase from Thermococcus litoralis. After transport of the cyclodextrins into the cell by a transport system to be defined, these molecules are linearized via a CDase, catalyzing exclusively the ring opening of the cyclodextrins to the respective maltooligodextrins. These are degraded by a Mal-P to glucose 1-phosphate. Finally, PGM catalyzes the conversion of glucose 1-phosphate to glucose 6-phosphate, which is further degraded to pyruvate via the modified Embden-Meyerhof pathway.

Hydrogen metabolism in Desulfovibrio desulfuricans strain New Jersey (NCIMB 8313)--comparative study with D. vulgaris and D. gigas species

This article aims to study hydrogen production/consumption in Desulfovibrio (D.) desulfuricans strain New Jersey, a sulfate reducer isolated from a medium undergoing active biocorrosion and to compare its hydrogen metabolism with two other Desulfovibrio species, D. gigas and D. vulgaris Hildenborough. Hydrogen production was followed during the growth of these three bacterial species under different growth conditions: no limitation of sulfate and lactate, sulfate limitation, lactate limitation, pyruvate/sulfate medium and in the presence of molybdate. Hydrogen production/consumption by D. desulfuricans shows a behavior similar to that of D. gigas but a different one from that of D. vulgaris, which produces higher quantities of hydrogen on lactate/sulfate medium. The three species are able to increase the hydrogen production when the sulfate became limiting. Moreover, in a pyruvate/sulfate medium hydrogen production was lower than on lactate/sulfate medium. Hydrogen production by D. desulfuricans in presence of molybdate is extremely high. Hydrogenases are key enzymes on production/consumption of hydrogen in sulfate reducing organisms. The specific activity, number and cellular localization of hydrogenases vary within the three Desulfovibrio species used in this work, which could explain the differences observed on hydrogen utilization.

Chemolithotrophic denitrification with elemental sulfur for groundwater treatment

Denitrification for the treatment of nitrates in wastewater typically relies on organic electron donating substrates. However, for groundwater treatment, inorganic compounds such as elemental sulfur (S0) are being considered as alternative electron donors in order to overcome concerns that residual organics can cause biofouling. In this study, a packed-bed bioreactor supplied with S0:limestone granules (1:1, v/v) was started up utilizing a chemolithotrophic denitrifying enrichment culture in the form of biofilm granules that was pre-cultivated on thiosulfate. The granular enrichment culture enabled a rapid start-up of the bioreactor. A nearly complete removal of nitrate (7.3 mM) was NO3- attained by the bioreactor at nitrate loading rates of up to 21.6 mmol/(L(reactor)d). With lower influent concentrations (1.3 mM nitrate) comparable to those found in contaminated groundwater, high nitrate loads of 18.1 mmol/(L(reactor)d) were achieved with an average nitrate removal efficiency of 95.9%. The recovery of nitrogen as benign N2 gas was nearly stoichiometric. The concentration of undesirable products from S0-based denitrification such as nitrite and sulfide were low. Comparison of bioreactor results with batch kinetic studies revealed that denitrification rates were dependent on the surface area of the added S0. The surface area normalized denitrification rate was determined to be 26.4 mmol /(m2 S0 d).