Monofluorophosphate is a selective inhibitor of respiratory sulfate-reducing microorganisms

Potent and Selective Inhibition of Sulfate-Reducing Bacteria by Neutral Red

Sulfate-reducing bacteria (SRB) are anaerobic microorganisms that use sulfate as a terminal electron acceptor for the oxidation of organic compounds or H2. These organisms can cause a serious problem in, for example, the offshore oil industry, due to the production of sulfide. Thus, it is of fundamental and practical importance to identify potent and selective inhibitors of SRB. In this study, neutral red was identified as a previously unrecognized selective inhibitor of SRB, with several orders of magnitude higher potency than most commonly used industrial biocides and inorganic oxyanions. Neutral red remained a potent inhibitor of SRB growth under fermentative conditions and was tolerated by nitrate-reducing bacteria. After 30 days of exposure to 14.2 μM neutral red, the sulfidogenesis activity of SRB-enriched biomass was reduced by 98.3%, and the abundance of SRB populations declined from 25.5% to 0.76%. Transcriptomic analysis revealed that the inhibition of the central sulfate reduction pathway was implicated in the mechanism of neutral red toxicity against SRB growth. Furthermore, downregulation of two electron transport complexes (QmoABC and DsrMKJOP), ATP synthase, as well as cytoplasmic/periplasmic hydrogenase suggested the collapse of the proton gradient. These findings have implications for environmental control of SRB and may enhance economic benefits in industrial operations.

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

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

Simultaneous nitrate and sulfate biotransformation driven by different substrates: comparison of carbon sources and metabolic pathways at different C/N ratios

Nitrate (NO₃^-) and sulfate (SO₄^2-) often coexist in organic wastewater. The effects of different substrates on NO₃^- and SO₄^2- biotransformation pathways at various C/N ratios were investigated in this study. This study used an activated sludge process for simultaneous desulfurization and denitrification in an integrated sequencing batch bioreactor. The results revealed that the most complete removals of NO₃^- and SO₄^2- were achieved at a C/N ratio of 5 in integrated simultaneous desulfurization and denitrification (ISDD). Reactor Rb (sodium succinate) displayed a higher SO₄^2- removal efficiency (93.79%) with lower chemical oxygen demand (COD) consumption (85.72%) than reactor Ra (sodium acetate) on account of almost 100% removal of NO₃^- in both Ra and Rb. Ra produced more S^2- (5.96 mg L^-1) and H₂S (25 mg L^-1) than Rb, which regulated the biotransformation of NO₃^- from denitrification to dissimilatory nitrate reduction to ammonium (DNRA), whereas almost no H₂S accumulated in Rb which can avoid secondary pollution. Sodium acetate-supported systems were found to favor the growth of DNRA bacteria (Desulfovibrio); although denitrifying bacteria (DNB) and sulfate-reducing bacteria (SRB) were found to co-exist in both systems, Rb has a greater keystone taxa diversity. Furthermore, the potential carbon metabolic pathways of the two carbon sources have been predicted. Both succinate and acetate could be generated in reactor Rb through the citrate cycle and the acetyl-CoA pathway. The high prevalence of four-carbon metabolism in Ra suggests that the carbon metabolism of sodium acetate is significantly improved at a C/N ratio of 5. This study has clarified the biotransformation mechanisms of NO₃^- and SO₄^2- in the presence of different substrates and the potential carbon metabolism pathway, which is expected to provide new ideas for the simultaneous removal of NO₃^- and SO₄^2- from different media.

Niche Modification by Sulfate-Reducing Bacteria Drives Microbial Community Assembly in Anoxic Marine Sediments

Sulfate-reducing bacteria (SRB) are essential functional microbial taxa for degrading organic matter (OM) in anoxic marine environments. However, there are little experimental data regarding how SRB regulates microbial communities. Here, we applied a top-down microbial community management approach by inhibiting SRB to elucidate their contributions to the microbial community during OM degradation. Based on the highly replicated microcosms (n = 20) of five different incubation stages, we found that many microbial community properties were influenced after inhibiting SRB, including the composition, structure, network, and community assembly processes. We also found a strong coexistence pattern between SRB and other abundant phylogenetic lineages via positive frequency-dependent selection. The relative abundances of the families Synergistaceae, Peptostreptococcaceae, Dethiosulfatibacteraceae, Prolixibacteraceae, Marinilabiliaceae, and Marinifilaceae were simultaneously suppressed after inhibiting SRB during OM degradation. A close association between SRB and the order Marinilabiliales among coexisting taxa was most prominent. They contributed to preserved modules during network successions, were keystone nodes mediating the networked community, and contributed to homogeneous ecological selection. The molybdate tolerance test of the isolated strains of Marinilabiliales showed that inhibited SRB (not the inhibitor of SRB itself) triggered a decrease in the relative abundance of Marinilabiliales. We also found that inhibiting SRB resulted in reduced pH, which is unsuitable for the growth of most Marinilabiliales strains, while the addition of pH buffer (HEPES) in SRB-inhibited treatment microcosms restored the pH and the relative abundances of these bacteria. These data supported that SRB could modify niches to affect species coexistence. IMPORTANCE Our model offers insight into the ecological properties of SRB and identifies a previously undocumented dimension of OM degradation. This targeted inhibition approach could provide a novel framework for illustrating how functional microbial taxa associate the composition and structure of the microbial community, molecular ecological network, and community assembly processes. These findings emphasize the importance of SRB during OM degradation. Our results proved the feasibility of the proposed study framework, inhibiting functional taxa at the community level, for illustrating when and to what extent functional taxa can contribute to ecosystem services.

Sulfate adenylyl transferase kinetics and mechanisms of metabolic inhibitors of microbial sulfate respiration

Sulfate analog oxyanions that function as selective metabolic inhibitors of dissimilatory sulfate reducing microorganisms (SRM) are widely used in ecological studies and industrial applications. As such, it is important to understand the mode of action and mechanisms of tolerance or adaptation to these compounds. Different oxyanions vary widely in their inhibitory potency and mechanism of inhibition, but current evidence suggests that the sulfate adenylyl transferase/ATP sulfurylase (Sat) enzyme is an important target. We heterologously expressed and purified the Sat from the model SRM, Desulfovibrio alaskensis G20. With this enzyme we determined the turnover kinetics (kcat, KM) for alternative substrates (molybdate, selenate, arsenate, monofluorophosphate, and chromate) and inhibition constants (KI) for competitive inhibitors (perchlorate, chlorate, and nitrate). These measurements enable the first quantitative comparisons of these compounds as substrates or inhibitors of a purified Sat from a respiratory sulfate reducer. We compare predicted half-maximal inhibitory concentrations (IC50) based on Sat kinetics with measured IC50 values against D. alaskensis G20 growth and discuss our results in light of known mechanisms of sensitivity or resistance to oxyanions. This analysis helps with the interpretation of recent adaptive laboratory evolution studies and illustrates the value of interpreting gene-microbe-environment interactions through the lens of enzyme kinetics.

Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology

Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.

Tungstate Control of Microbial Sulfidogenesis and Souring of the Engineered Environment

Sulfide accumulation in oil reservoir fluids (souring) from the activity of sulfate-reducing microorganisms (SRM) is of grave concern because of the associated health and facility failure risks. Here, we present an assessment of tungstate as a selective and potent inhibitor of SRM. Dose-response inhibitor experiments were conducted with a number of SRM isolates and enrichments at 30-80 °C and an increase in the effectiveness of tungstate treatment at higher temperatures was observed. To explore mixed inhibitor treatment modes, we tested synergy or antagonism between several inhibitors with tungstate, and found synergism between WO₄^2- and NO₂^-, while additive effects were observed with ClO₄^- and NO₃^-. We also evaluated SRM inhibition by tungstate in advective upflow oil-sand-packed columns. Although 2 mM tungstate was initially sufficient to inhibit sulfidogenesis, subsequent temporal CaWO₄ precipitation resulted in loss of the bioavailable inhibitor from solution and a concurrent increase in effluent sulfide. Mixing 4 mM sodium carbonate with the 2 mM tungstate was enough to promote tungstate solubility to reach inhibitory concentrations, without precipitation, and completely inhibit SRM activity. Overall, we demonstrate the effectiveness of tungstate as a potent SRM inhibitor, particularly at higher temperatures, and propose a novel carbonate-tungstate formulation for application to soured oil reservoirs.

Novel Mode of Molybdate Inhibition of Desulfovibrio vulgaris Hildenborough

Sulfate-reducing microorganisms (SRM) are found in multiple environments and play a major role in global carbon and sulfur cycling. Because of their growth capabilities and association with metal corrosion, controlling the growth of SRM has become of increased interest. One such mechanism of control has been the use of molybdate (MoO4 2-), which is thought to be a specific inhibitor of SRM. The way in which molybdate inhibits the growth of SRM has been enigmatic. It has been reported that molybdate is involved in a futile energy cycle with the sulfate-activating enzyme, sulfate adenylyl transferase (Sat), which results in loss of cellular ATP. However, we show here that a deletion of this enzyme in the model SRM, Desulfovibrio vulgaris Hildenborough, remained sensitive to molybdate. We performed several subcultures of the ∆sat strain in the presence of increasing concentrations of molybdate and obtained a culture with increased resistance to the inhibitor (up to 3 mM). The culture was re-sequenced and three single nucleotide polymorphisms (SNPs) were identified that were not present in the parental strain. Two of the SNPs seemed unlikely candidates for molybdate resistance due to a lack of conservation of the mutated residues in homologous genes of closely related strains. The remaining SNP was located in DVU2210, a protein containing two domains: a YcaO-like domain and a tetratricopeptide-repeat domain. The SNP resulted in a change of a serine residue to arginine in the ATP-hydrolyzing motif of the YcaO-like domain. Deletion mutants of each of the three genes apparently enriched with SNPs in the presence of inhibitory molybdate and combinations of these genes were generated in the Δsat and wild-type strains. Strains lacking both sat and DVU2210 became more resistant to molybdate. Deletions of the other two genes in which SNPs were observed did not result in increased resistance to molybdate. YcaO-like proteins are distributed across the bacterial and archaeal domains, though the function of these proteins is largely unknown. The role of this protein in D. vulgaris is unknown. Due to the distribution of YcaO-like proteins in prokaryotes, the veracity of molybdate as a specific SRM inhibitor should be reconsidered.

Selective carbon sources influence the end products of microbial nitrate respiration

Respiratory and catabolic genes are differentially distributed across microbial genomes. Thus, specific carbon sources may favor different respiratory processes. We profiled the influence of 94 carbon sources on the end products of nitrate respiration in microbial enrichment cultures from diverse terrestrial environments. We found that some carbon sources consistently favor dissimilatory nitrate reduction to ammonium (DNRA/nitrate ammonification) while other carbon sources favor nitrite accumulation or denitrification. For an enrichment culture from aquatic sediment, we sequenced the genomes of the most abundant strains, matched these genomes to 16S rDNA exact sequence variants (ESVs), and used 16S rDNA amplicon sequencing to track the differential enrichment of functionally distinct ESVs on different carbon sources. We found that changes in the abundances of strains with different genetic potentials for nitrite accumulation, DNRA or denitrification were correlated with the nitrite or ammonium concentrations in the enrichment cultures recovered on different carbon sources. Specifically, we found that either L-sorbose or D-cellobiose enriched for a Klebsiella nitrite accumulator, other sugars enriched for an Escherichia nitrate ammonifier, and citrate or formate enriched for a Pseudomonas denitrifier and a Sulfurospirillum nitrate ammonifier. Our results add important nuance to the current paradigm that higher concentrations of carbon will always favor DNRA over denitrification or nitrite accumulation, and we propose that, in some cases, carbon composition can be as important as carbon concentration in determining nitrate respiratory end products. Furthermore, our approach can be extended to other environments and metabolisms to characterize how selective parameters influence microbial community composition, gene content, and function.

Growth inhibition of sulfate-reducing bacteria for trichloroethylene dechlorination enhancement

Trichloroethylene (TCE) is a frequently found organic contaminant in polluted-groundwater. In this microcosm study, effects of hydrogen-producing bacteria [Clostridium butyricum (Clostridium sp.)] and inhibitor of sulfate-reducing bacteria (SRB) addition on the enhancement of TCE dechlorination were evaluated. Results indicate that Clostridium sp. supplement could effectively enhance TCE reductive dechlorination (97.4% of TCE removal) due to increased hydrogen concentration and Dehalococcoides (DHC) populations (increased to 1 × 10⁴ gene copies/L). However, addition of Clostridium sp. also caused the increase in dsrA (dissimilatory sulfide reductase subunit A) (increased to 2 × 10⁸ gene copies/L), and thus, part of the hydrogen was consumed by SRB, which would limit the effective application of hydrogen by DHC. Control of Clostridium sp. addition is a necessity to minimize the adverse impact of Clostridium sp. on DHC growth. Ferric citrate caused the slight raise of the oxidation-reduction state, which resulted in growth inhibition of SRB. Molybdate addition inhibited the growth of SRB, and thus, the dsrA concentrations (dropped from 4 × 10⁷ to 9 × 10⁵ gene copies/L) and sulfate reduction efficiency were decreased. Increased DHC populations (increased from 8 × 10³ to 1 × 10⁵ gene copies/L) were due to increased available hydrogen (increased from 0 to 2 mg/L), which enhanced TCE dechlorination (99.3% TCE removal). Metagenomic analyses show that a significant microbial diversity was detected in microcosms with different treatments. Clostridium sp., ferric citrate, and molybdate addition caused a decreased SRB communities and increased fatty acid production microbial communities (increased from 4.9% to 20.2%), which would be beneficial to the hydrogen production and TCE dechlorination processes.

Homoacetogenesis and microbial community composition are shaped by pH and total sulfide concentration

Biological CO2 sequestration through acetogenesis with H2 as electron donor is a promising technology to reduce greenhouse gas emissions. Today, a major issue is the presence of impurities such as hydrogen sulfide (H2 S) in CO2 containing gases, as they are known to inhibit acetogenesis in CO2 -based fermentations. However, exact values of toxicity and inhibition are not well-defined. To tackle this uncertainty, a series of toxicity experiments were conducted, with a mixed homoacetogenic culture, total dissolved sulfide concentrations ([TDS]) varied between 0 and 5 mM and pH between 5 and 7. The extent of inhibition was evaluated based on acetate production rates and microbial growth. Maximum acetate production rates of 0.12, 0.09 and 0.04 mM h-1 were achieved in the controls without sulfide at pH 7, pH 6 and pH 5. The half-maximal inhibitory concentration (IC50 qAc ) was 0.86, 1.16 and 1.36 mM [TDS] for pH 7, pH 6 and pH 5. At [TDS] above 3.33 mM, acetate production and microbial growth were completely inhibited at all pHs. 16S rRNA gene amplicon sequencing revealed major community composition transitions that could be attributed to both pH and [TDS]. Based on the observed toxicity levels, treatment approaches for incoming industrial CO2 streams can be determined.

Simultaneous removal of sulphur dioxide and nitric oxide at different oxygen concentrations in a thermophilic biotrickling filter (BTF): Evaluation of removal efficiency, intermediates interaction and characterisation of microbial communities

Simultaneous flue gas desulphurisation and denitrification in biotrickling filter was investigated under different O₂ concentrations (0%, 3%, 5%, 8% and 10%) at 45 °C. NO and SO₂ removal efficiency, intermediates (NO₃^-, NO₂^-, NO₂, SO₄^2- and S^2-) interaction and accumulation, S⁰ recovery and microbial community structure were investigated. Results indicated the highest NO removal efficiency was 96.5% at 5% O₂. Maximum SO₂ removal efficiency was 95.6% at 3% O₂. Moreover, N intermediates accumulation increased when O₂ concentration increased from 0% to 10%. The lowest S^2- concentration of 61 mg/L and the maximum S⁰ recovery of 76.9% were achieved at 5% O₂. The bioreactor at 10% O₂ contained less bacterial OTUs richness and evenness compared with other conditions. Illumina analysis indicated Proteobacteria, Firmicutes and Bacteroidetes were the dominant members. Overall, microbial community structure differs significantly under different O₂ concentrations.

Anion transport as a target of adaption to perchlorate in sulfate-reducing communities

Inhibitors can be used to control the functionality of microbial communities by targeting specific metabolisms. The targeted inhibition of dissimilatory sulfate reduction limits the generation of toxic and corrosive hydrogen sulfide across several industrial systems. Sulfate-reducing microorganisms (SRM) are specifically inhibited by sulfate analogs, such as perchlorate. Previously, we showed pure culture SRM adaptation to perchlorate stress through mutation of the sulfate adenylyltransferase, a central enzyme in the sulfate reduction pathway. Here, we explored adaptation to perchlorate across unconstrained SRM on a community scale. We followed natural and bio-augmented sulfidogenic communities through serial transfers in increasing concentrations of perchlorate. Our results demonstrated that perchlorate stress altered community structure by initially selecting for innately more resistant strains. Isolation, whole-genome sequencing, and molecular biology techniques allowed us to define subsequent genetic mechanisms of adaptation that arose across the dominant adapting SRM. Changes in the regulation of divalent anion:sodium symporter family transporters led to increased intracellular sulfate to perchlorate ratios, allowing SRM to escape the effects of competitive inhibition. Thus, in contrast to pure-culture results, SRM in communities cope with perchlorate stress via changes in anion transport and its regulation. This highlights the value of probing evolutionary questions in an ecological framework, bridging the gap between ecology, evolution, genomics, and physiology.

Sulfate-reducing bacteria and methanogens are involved in arsenic methylation and demethylation in paddy soils

Microbial arsenic (As) methylation and demethylation are important components of the As biogeochemical cycle. Arsenic methylation is enhanced under flooded conditions in paddy soils, producing mainly phytotoxic dimethylarsenate (DMAs) that can cause rice straighthead disease, a physiological disorder occurring widely in some rice growing regions. The key microbial groups responsible for As methylation and demethylation in paddy soils are unknown. Three paddy soils were incubated under flooded conditions. DMAs initially accumulated in the soil porewater, followed by a rapid disappearance coinciding with the production of methane. The soil from a rice straighthead disease paddy field produced a much larger amount of DMAs than the other two soils. Using metabolic inhibition, quantification of functional gene transcripts, microbial enrichment cultures and 13C-labeled DMAs, we show that sulfate-reducing bacteria (SRB) and methanogenic archaea are involved in As methylation and demethylation, respectively, controlling the dynamics of DMAs in paddy soils. We present a model of As biogeochemical cycle in paddy soils, linking the dynamics of changing soil redox potential with arsenite mobilization, arsenite methylation and subsequent demethylation driven by different microbial groups. The model provides a basis for controlling DMAs accumulation and incidence of straighthead disease in rice.

Resistance and Resilience of Sulfidogenic Communities in the Face of the Specific Inhibitor Perchlorate

Hydrogen sulfide is a toxic and corrosive gas, produced by the activity of sulfate-reducing microorganisms (SRM). Owing to the environmental, economic and human-health consequences of sulfide, there is interest in developing specific inhibitors of SRM. Recent studies have identified perchlorate as a promising emerging inhibitor. The aim of this work is to quantitatively dissect the inhibitory dynamics of perchlorate. Sulfidogenic mixed continuous-flow systems were treated with perchlorate. SRM number, sulfide production and community structure were monitored pre-, during and post-treatment. The data generated was compared to a simple mathematical model, where SRM growth slows as a result of inhibition. The experimental data supports the interpretation that perchlorate largely acts to suppress SRM growth rates, rendering planktonic SRM increasingly susceptible to wash-out. Surface-attachment was identified as an important parameter preventing SRM wash-out and thus governing inhibitory dynamics. Our study confirmed the lesser depletion of surface-attached SRM as compared to planktonic SRM during perchlorate treatment. Indirect effects of perchlorate (bio-competitive exclusion of SRM by dissimilatory perchlorate-reducing bacteria, DPRB) were also assayed by amending reactors with DPRB. Indeed, low concentrations of perchlorate coupled with DRPB amendment can drive sulfide concentrations to zero. Further, inhibition in a complex community was compared to that in a pure culture, highlighting similarities and differences between the two scenarios. Finally, we quantified susceptibility to perchlorate across SRM in various culture conditions, showing that prediction of complex behavior in continuous systems from batch results is possible. This study thus provides an overview of the sensitivity of sulfidogenic communities to perchlorate, as well as mechanisms underlying these patterns.

QbD Based Media Development for the Production of Fab Fragments in E. coli

Ranibizumab is a biotherapeutic Fab fragment used for the treatment of age-related macular degeneration and macular oedema. It is currently expressed in the gram-negative bacterium, Escherichia coli. However, low expression levels result in a high manufacturing cost. The protein expression can be increased by manipulating nutritional requirements (carbon source, nitrogen source, buffering agent), process parameters (pH, inducer concentration, agitation, temperature), and the genetic make-up of the producing strain. Further, understanding the impact of these factors on product quality is a requirement as per the principles of Quality by Design (QbD). In this paper, we examine the effect of various media components and process parameters on the expression level and quality of the biotherapeutic. First, risk analysis was performed to shortlist different media components based on the literature. Next, experiments were performed to screen these components. Eight components were identified for further investigation and were examined for their effect and interactions using a Fractional Factorial experimental design. Sucrose, biotin, and pantothenate were found to have the maximum effect during Fab production. Furthermore, cyanocobalamin glutathione and biotin-glutathione were the most significant interactions observed. Product identification was performed with Liquid Chromatography–Mass Spectrometry (LC-MS), the expression level was quantified using Bio-layer Interferometry, Reverse Phase-HPLC, and SDS-PAGE, and product quality were measured by RP-HPLC. Overall, a five-fold enhancement of the target protein titer was obtained (from 5 mg/L to 25 mg/L) using the screened medium components vis-a-vis the basal medium, thereby demonstrating the efficacy of the systematic approach purported by QbD.

Specific inhibitors of respiratory sulfate reduction: towards a mechanistic understanding

Microbial sulfate reduction (SR) by sulfate-reducing micro-organisms (SRM) is a primary environmental mechanism of anaerobic organic matter mineralization, and as such influences carbon and sulfur cycling in many natural and engineered environments. In industrial systems, SR results in the generation of hydrogen sulfide, a toxic, corrosive gas with adverse human health effects and significant economic and environmental consequences. Therefore, there has been considerable interest in developing strategies for mitigating hydrogen sulfide production, and several specific inhibitors of SRM have been identified and characterized. Specific inhibitors are compounds that disrupt the metabolism of one group of organisms, with little or no effect on the rest of the community. Putative specific inhibitors of SRM have been used to control sulfidogenesis in industrial and engineered systems. Despite the value of these inhibitors, mechanistic and quantitative studies into the molecular mechanisms of their inhibition have been sparse and unsystematic. The insight garnered by such studies is essential if we are to have a more complete understanding of SR, including the past and current selective pressures acting upon it. Furthermore, the ability to reliably control sulfidogenesis - and potentially assimilatory sulfate pathways - relies on a thorough molecular understanding of inhibition. The scope of this review is to summarize the current state of the field: how we measure and understand inhibition, the targets of specific SR inhibitors and how SRM acclimatize and/or adapt to these stressors.

The selective pressures on the microbial community in a metal-contaminated aquifer

In many environments, toxic compounds restrict which microorganisms persist. However, in complex mixtures of inhibitory compounds, it is challenging to determine which specific compounds cause changes in abundance and prevent some microorganisms from growing. We focused on a contaminated aquifer in Oak Ridge, Tennessee, USA that has large gradients of pH and widely varying concentrations of uranium, nitrate, and many other inorganic ions. In the most contaminated wells, the microbial community is enriched in the Rhodanobacter genus. Rhodanobacter abundance is positively correlated with low pH and high concentrations of uranium and 13 other ions and we sought to determine which of these ions are selective pressures that favor the growth of Rhodanobacter over other taxa. Of these ions, low pH and high UO₂²⁺, Mn²⁺, Al³⁺, Cd²⁺, Zn²⁺, Co²⁺, and Ni²⁺ are both (a) selectively inhibitory of a Pseudomonas isolate from an uncontaminated well vs. a Rhodanobacter isolate from a contaminated well, and (b) reach toxic concentrations (for the Pseudomonas isolate) in the Rhodanobacter-dominated wells. We used mixtures of ions to simulate the groundwater conditions in the most contaminated wells and verified that few isolates aside from Rhodanobacter can tolerate these eight ions. These results clarify which ions are likely causal factors that impact the microbial community at this field site and are not merely correlated with taxonomic shifts. Furthermore, our general high-throughput approach can be applied to other environments, isolates, and conditions to systematically help identify selective pressures on microbial communities.

Mitigating Sulfidogenesis With Simultaneous Perchlorate and Nitrate Treatments

Sulfide biogenesis (souring) in oil reservoirs is an extensive and costly problem. Nitrate is currently used as a souring inhibitor but often requires high concentrations and yields inconsistent results. Recently, perchlorate has displayed promise as a more potent inhibitor in lab scale studies. However, combining the two treatments to determine synergy and effectiveness in a dynamic system has never been tested. Nitrate inhibits perchlorate consumption by perchlorate reducing bacteria, suggesting that the combined treatment may allow deeper penetration of the perchlorate into the reservoir matrix. Furthermore, the metabolic intermediates of perchlorate and nitrate reduction (nitrite and chlorite, respectively) are synergistic with the primary electron acceptors for inhibition of sulfate reduction. To assess the possible synergies between nitrate and perchlorate treatments, triplicate glass columns packed with pre-soured marine sediment were flushed with media containing sulfate and an inhibitor treatment [(i) perchlorate; (ii) nitrate; (iii) perchlorate and nitrate; or (iv) none]. Internal geochemistry and microbial community changes were monitored along the length of the columns during six phases of increasing treatment concentrations. In a final phase all treatments were removed. Sulfide production decreased in all treated columns in conjunction with increased inhibitor concentrations relative to the untreated control. Interestingly, the potency of the "mixed" treatment was additive relative to the individual treatments suggesting no interaction. Microbial community analyses indicated community shifts and clustering by treatment. The mixed treatment column community's trajectory closely resembled that of the community found in the perchlorate only treatment, suggesting that perchlorate was the dominant control on the "mixed" community structure. In contrast, the nitrate and untreated column communities had unique trajectories. This study indicates that concurrent nitrate and perchlorate treatment is not more effective than perchlorate treatment alone but is more effective than nitrate treatment. As such, treatment decisions may be based on economic factors.

Dissimilatory Sulfate Reduction Under High Pressure by Desulfovibrio alaskensis G20

Biosouring results from production of H₂S by sulfate-reducing microorganisms (SRMs) in oil reservoirs. H₂S is toxic, corrosive, and explosive, and as such, represents a significant threat to personnel, production facilities, and transportation pipelines. Since typical oil reservoir pressures can range from 10 to 50 MPa, understanding the role that pressure plays in SRM metabolism is important to improving souring containment strategies. To explore the impact of pressure, we grew an oil-field SRM isolate, Desulfovibrio alaskensis G20, under a range of pressures (0.1–14 MPa) at 30°C. The observed microbial growth rate was an inverse function of pressure with an associated slight reduction in sulfate and lactate consumption rate. Competitive fitness experiments with randomly bar-coded transposon mutant library sequencing (RB-TnSeq) identified several genes associated with flagellar biosynthesis and assembly that were important at high pressure. The fitness impact of specific genes was confirmed using individual transposon mutants. Confocal microscopy revealed that enhanced cell aggregation occurs at later stages of growth under pressure. We also assessed the effect of pressure on SRM inhibitor potency. Dose-response experiments showed a twofold decrease in the sensitivity of D. alaskensis to the antibiotic chloramphenicol at 14 MPa. Fortuitously, pressure had no significant influence on the inhibitory potency of the common souring controlling agent nitrate, or the emerging SRM inhibitors perchlorate, monofluorophosphate, or zinc pyrithione. Our findings improve the conceptual model of microbial sulfate reduction in high-pressure environments and the influence of pressure on souring inhibitor efficacy.

Microbial Processes Mediating the Evolution of Methylarsine Gases from Dimethylarsenate in Paddy Soils

Arsenic (As) biovolatilization is an important component of the global As biogeochemical cycle. Soils can emit various methylarsine gases, but the underlying microbial processes remain unclear. Here, we show that the addition of molybdate (Mo), an inhibitor of sulfate-reducing bacteria, greatly enhanced dimethylarsine evolution from dimethylarsenate [DMAs(V)] added to two paddy soils. Molybdate addition significantly affected the microbial community structure. The aerobic enrichment cultures from both soils volatilized substantial amounts of dimethylarsine from DMAs(V) in the presence of Mo, whereas the anaerobic enrichment cultures did not. A Bacillus strain (CZ-2) capable of reducing DMAs(V) to dimethylarsine was isolated from the aerobic enrichment culture, and its volatilization ability was enhanced by Mo. RNA-seq analysis identified 10 reductase genes upregulated by Mo. Addition of the reducing agent NADH increased dimethylarsine volatilization by strain CZ-2, suggesting that DMAs(V) reductase is an NADH-dependent enzyme. The strain could not methylate arsenite or convert monomethylarsenate and DMAs(V) to trimethylarsine. Our results show that dimethylarsine evolution from DMAs(V) is independent of the As methylation pathway and that Mo enhances dimethylarsine evolution from paddy soils by shifting the microbial community structure and enhancing the reduction of DMAs(V) to dimethylarsine, possibly through upregulating the expression of DMAs(V) reductase gene(s).

Iron-Coupled Anaerobic Oxidation of Methane Performed by a Mixed Bacterial-Archaeal Community Based on Poorly Reactive Minerals

Anaerobic oxidation of methane (AOM) was shown to reduce methane emissions by over 50% in freshwater systems, its main natural contributor to the atmosphere. In these environments iron oxides can become main agents for AOM, but the underlying mechanism for this process has remained enigmatic. By conducting anoxic slurry incubations with lake sediments amended with ¹³C-labeled methane and naturally abundant iron oxides the process was evidenced by significant ¹³C-enrichment of the dissolved inorganic carbon pool and most pronounced when poorly reactive iron minerals such as magnetite and hematite were applied. Methane incorporation into biomass was apparent by strong uptake of ¹³C into fatty acids indicative of methanotrophic bacteria, associated with increasing copy numbers of the functional methane monooxygenase pmoA gene. Archaea were not directly involved in full methane oxidation, but their crucial participation, likely being mediators in electron transfer, was indicated by specific inhibition of their activity that fully stopped iron-coupled AOM. By contrast, inhibition of sulfur cycling increased ¹³C-methane turnover, pointing to sulfur species involvement in a competing process. Our findings suggest that the mechanism of iron-coupled AOM is accomplished by a complex microbe-mineral reaction network, being likely representative of many similar but hidden interactions sustaining life under highly reducing low energy conditions.

Arsenic Methylation Dynamics in a Rice Paddy Soil Anaerobic Enrichment Culture

Methylated arsenic (As) species represent a significant fraction of the As accumulating in rice grains, and there are geographic patterns in the abundance of methylated arsenic in rice that are not understood. The microorganisms driving As biomethylation in paddy environments, and thus the soil conditions conducive to the accumulation of methylated arsenic, are unknown. We tested the hypothesis that sulfate-reducing bacteria (SRB) are key drivers of arsenic methylation in metabolically versatile mixed anaerobic enrichments from a Mekong Delta paddy soil. We used molybdate and monofluorophosphate as inhibitors of sulfate reduction to evaluate the contribution of SRB to arsenic biomethylation, and developed degenerate primers for the amplification of arsM genes to identify methylating organisms. Enrichment cultures converted 63% of arsenite into methylated products, with dimethylarsinic acid as the major product. While molybdate inhibited As biomethylation, this effect was unrelated to its inhibition of sulfate reduction and instead inhibited the methylation pathway. Based on arsM sequences and the physiological response of cultures to media conditions, we propose that amino acid fermenting organisms are potential drivers of As methylation in the enrichments. The lack of a demethylating capacity may have contributed to the robust methylation efficiencies in this mixed culture.

Microbial metal resistance and metabolism across dynamic landscapes: high-throughput environmental microbiology

Multidimensional gradients of inorganic compounds influence microbial activity in diverse pristine and anthropogenically perturbed environments. Here, we suggest that high-throughput cultivation and genetics can be systematically applied to generate quantitative models linking gene function, microbial community activity, and geochemical parameters. Metal resistance determinants represent a uniquely universal set of parameters around which to study and evaluate microbial fitness because they represent a record of the environment in which all microbial life evolved. By cultivating microbial isolates and enrichments in laboratory gradients of inorganic ions, we can generate quantitative predictions of limits on microbial range in the environment, obtain more accurate gene annotations, and identify useful strategies for predicting and engineering the trajectory of natural ecosystems.

High-Throughput Screening To Identify Potent and Specific Inhibitors of Microbial Sulfate Reduction

The selective perturbation of complex microbial ecosystems to predictably influence outcomes in engineered and industrial environments remains a grand challenge for geomicrobiology. In some industrial ecosystems, such as oil reservoirs, sulfate reducing microorganisms (SRM) produce hydrogen sulfide which is toxic, explosive, and corrosive. Despite the economic cost of sulfidogenesis, there has been minimal exploration of the chemical space of possible inhibitory compounds, and very little work has quantitatively assessed the selectivity of putative souring treatments. We have developed a high-throughput screening strategy to identify potent and selective inhibitors of SRM, quantitatively ranked the selectivity and potency of hundreds of compounds and identified previously unrecognized SRM selective inhibitors and synergistic interactions between inhibitors. Zinc pyrithione is the most potent inhibitor of sulfidogenesis that we identified, and is several orders of magnitude more potent than commonly used industrial biocides. Both zinc and copper pyrithione are also moderately selective against SRM. The high-throughput (HT) approach we present can be readily adapted to target SRM in diverse environments and similar strategies could be used to quantify the potency and selectivity of inhibitors of a variety of microbial metabolisms. Our findings and approach are relevant to efforts to engineer environmental ecosystems and also to understand the role of natural gradients in shaping microbial niche space.

Diversity and Composition of Sulfate-Reducing Microbial Communities Based on Genomic DNA and RNA Transcription in Production Water of High Temperature and Corrosive Oil Reservoir

Deep subsurface petroleum reservoir ecosystems harbor a high diversity of microorganisms, and microbial influenced corrosion is a major problem for the petroleum industry. Here, we used high-throughput sequencing to explore the microbial communities based on genomic 16S rDNA and metabolically active 16S rRNA analyses of production water samples with different extents of corrosion from a high-temperature oil reservoir. Results showed that Desulfotignum and Roseovarius were the most abundant genera in both genomic and active bacterial communities of all the samples. Both genomic and active archaeal communities were mainly composed of Archaeoglobus and Methanolobus. Within both bacteria and archaea, the active and genomic communities were compositionally distinct from one another across the different oil wells (bacteria p = 0.002; archaea p = 0.01). In addition, the sulfate-reducing microorganisms (SRMs) were specifically assessed by Sanger sequencing of functional genes aprA and dsrA encoding the enzymes adenosine-5'-phosphosulfate reductase and dissimilatory sulfite reductase, respectively. Functional gene analysis indicated that potentially active Archaeoglobus, Desulfotignum, Desulfovibrio, and Thermodesulforhabdus were frequently detected, with Archaeoglobus as the most abundant and active sulfate-reducing group. Canonical correspondence analysis revealed that the SRM communities in petroleum reservoir system were closely related to pH of the production water and sulfate concentration. This study highlights the importance of distinguishing the metabolically active microorganisms from the genomic community and extends our knowledge on the active SRM communities in corrosive petroleum reservoirs.

Pyrosequencing reveals microbial community dynamics in integrated simultaneous desulfurization and denitrification process at different influent nitrate concentrations

Integrated simultaneous desulfurization and denitrification (ISDD) process has proven to be feasible for the coremoval of sulfate, nitrate, and chemical oxygen demand (COD). In this study, we aimed to reveal the microbial community dynamics in the ISDD process with different influent nitrate (NO₃^-) concentrations. For all tested scenarios, full denitrification was accomplished while sulfate removal efficiency decreased along with increased influent NO₃^- concentrations. The proportion of S⁰ to influent SO₄^2- maintained a low level (5.6-17.0%) regardless of the increased influent NO₃^- concentrations. Microbial community analysis results showed that higher influent NO₃^- concentrations affected the microbial community structure greatly. Phyla Proteobacteria, Spirochaetae, Firmicutes, Synergistetes, and Chloroflexi dominated in all the community compositions, of which Proteobacteria exhibited a clear difference among eight microbial samples. Members of δ-Proteobacteria, with 16S rRNA gene sequences related to Desulfobulbus, were clearly decreased at influent NO₃^- = 3000 and 3500 mg/L, suggesting an inhibitory effect of NO₃^- on sulfate reduction. In contrast, as influent NO₃^- concentration increased, microbial community was notably enriched in γ-Proteobacteria and ε-Proteobacteria, which revealed the enrichment of 16S rRNA gene sequences related to Pseudomonas (γ-Proteobacteria), and Arcobacteria and Sulfurospirillum (ε-Proteobacteria).

System-Wide Adaptations of Desulfovibrio alaskensis G20 to Phosphate-Limited Conditions

The prevalence of lipids devoid of phosphorus suggests that the availability of phosphorus limits microbial growth and activity in many anoxic, stratified environments. To better understand the response of anaerobic bacteria to phosphate limitation and starvation, this study combines microscopic and lipid analyses with the measurements of fitness of pooled barcoded transposon mutants of the model sulfate reducing bacterium Desulfovibrio alaskensis G20. Phosphate-limited G20 has lower growth rates and replaces more than 90% of its membrane phospholipids by a mixture of monoglycosyl diacylglycerol (MGDG), glycuronic acid diacylglycerol (GADG) and ornithine lipids, lacks polyphosphate granules, and synthesizes other cellular inclusions. Analyses of pooled and individual mutants reveal the importance of the high-affinity phosphate transport system (the Pst system), PhoR, and glycolipid and ornithine lipid synthases during phosphate limitation. The phosphate-dependent synthesis of MGDG in G20 and the widespread occurrence of the MGDG/GADG synthase among sulfate reducing ∂-Proteobacteria implicate these microbes in the production of abundant MGDG in anaerobic environments where the concentrations of phosphate are lower than 10 μM. Numerous predicted changes in the composition of the cell envelope and systems involved in transport, maintenance of cytoplasmic redox potential, central metabolism and regulatory pathways also suggest an impact of phosphate limitation on the susceptibility of sulfate reducing bacteria to other anthropogenic or environmental stresses.

Microbial Biotechnology 2020; microbiology of fossil fuel resources

This roadmap examines the future of microbiology research and technology in fossil fuel energy recovery. Globally, the human population will be reliant on fossil fuels for energy and chemical feedstocks for at least the medium term. Microbiology is already important in many areas relevant to both upstream and downstream activities in the oil industry. However, the discipline has struggled for recognition in a world dominated by geophysicists and engineers despite widely known but still poorly understood microbially mediated processes e.g. reservoir biodegradation, reservoir souring and control, microbial enhanced oil recovery. The role of microbiology is even less understood in developing industries such as shale gas recovery by fracking or carbon capture by geological storage. In the future, innovative biotechnologies may offer new routes to reduced emissions pathways especially when applied to the vast unconventional heavy oil resources formed, paradoxically, from microbial activities in the geological past. However, despite this potential, recent low oil prices may make industry funding hard to come by and recruitment of microbiologists by the oil and gas industry may not be a high priority. With regards to public funded research and the imperative for cheap secure energy for economic growth in a growing world population, there are signs of inherent conflicts between policies aimed at a low carbon future using renewable technologies and policies which encourage technologies which maximize recovery from our conventional and unconventional fossil fuel assets.

Sulfate reduction in microorganisms-recent advances and biotechnological applications

Sulfur, the least common of the five macroelements, plays an important role in biochemistry due to its ability to be easily reduced or oxidized, leading to a great amount of research concerning sulfur bioconversion. Interestingly, new studies concerning microbial sulfate reduction pathways in the last half decade have become increasingly sparse, indicating that most of the pathways involved have been discovered and studied. Despite this, systems biology approaches to model these pathways are often missing or not used. As the products of microbial sulfate reduction play important roles in the environment, biotechnology, and industry, modeling sulfur bioconversion remains an untapped research space for future work.

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.