Coordinated response of the Desulfovibrio desulfuricans 27774 transcriptome to nitrate, nitrite and nitric oxide

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

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

Microorganisms for the oxidation of nitrated cellulose in its effluents (review)

The processes of microbiological destruction of toxic and large-tonnage waste are the most attractive processes for protecting the environment. The review considers the results of studies of microbial decomposition of nitrate esters, including hardly decomposable nitrocellulose. The published data show that specific microorganisms are able to degrade nitrated cellulose compounds under both anaerobic and aerobic conditions. The most promising microorganisms in terms of the efficiency of the nitrocellulose degradation process are bacteria belonging to Desulfovibrio genera, fungi Fusarium solani and Sclerotium rolfsii, as well as their co-cultivation. Recently, the first information about the enzymes involved in the process of nitrocellulose degradation, possible mechanisms of reactions carried out by these enzymes, and the effect of electron donors and acceptors adding to the process have been obtained. Contamination of industrial wastewater with nitrocellulose leads to treatment necessity by using cost-effective, harmless methods. A combined aerobic-anaerobic system, including both bacteria and fungi, has shown hopeful results.

Structural and biochemical elucidation of class I hybrid cluster protein natively extracted from a marine methanogenic archaeon

Whilst widespread in the microbial world, the hybrid cluster protein (HCP) has been paradoxically a long-time riddle for microbiologists. During three decades, numerous studies on a few model organisms unravelled its structure and dissected its metal-containing catalyst, but the physiological function of the enzyme remained elusive. Recent studies on bacteria point towards a nitric oxide reductase activity involved in resistance during nitrate and nitrite reduction as well as host infection. In this study, we isolated and characterised a naturally highly produced HCP class I from a marine methanogenic archaeon grown on ammonia. The crystal structures of the enzyme in a reduced and partially oxidised state, obtained at a resolution of 1.45 and 1.36-Å, respectively, offered a precise picture of the archaeal enzyme intimacy. There are striking similarities with the well-studied enzymes from Desulfovibrio species regarding sequence, kinetic parameters, structure, catalyst conformations, and internal channelling systems. The close phylogenetic relationship between the enzymes from Methanococcales and many Bacteria corroborates this similarity. Indeed, Methanococcales HCPs are closer to these bacterial homologues than to any other archaeal enzymes. The relatively high constitutive production of HCP in M. thermolithotrophicus, in the absence of a notable nitric oxide source, questions the physiological function of the enzyme in these ancient anaerobes.

Evidence Supporting the Involvement of the Minority Compounds of Extra Virgin Olive Oil, through Gut Microbiota Modulation, in Some of the Dietary Benefits Related to Metabolic Syndrome in Comparison to Butter

Extra virgin olive oil (EVOO) has proven to yield a better health outcome than other saturated fats widely used in the Western diet, including a distinct dysbiosis-preventive modulation of gut microbiota. Besides its high content in unsaturated fatty acids, EVOO also has an unsaponifiable polyphenol-enriched fraction that is lost when undergoing a depurative process that gives place to refined olive oil (ROO). Comparing the effects of both oils on the intestinal microbiota of mice can help us determine which benefits of EVOO are due to the unsaturated fatty acids, which remain the same in both, and which benefits are a consequence of its minority compounds, mainly polyphenols. In this work, we study these variations after only six weeks of diet, when physiological changes are not appreciated yet but intestinal microbial alterations can already be detected. Some of these bacterial deviations correlate in multiple regression models with ulterior physiological values, at twelve weeks of diet, including systolic blood pressure. Comparison between the EVOO and ROO diets reveals that some of these correlations can be explained by the type of fat that is present in the diet, while in other cases, such as the genus Desulfovibrio, can be better understood if the antimicrobial role of the virgin olive oil polyphenols is considered.

Influence of potassium dichromate on the reduction of sulfur, nitrate and nitrite ions by bacteria Desulfuromonas sp

This article presents the regularities of reduction of sulfur, nitrate and nitrite ions by sulfur reducing bacteria Desulfuromonas sp., which were isolated from the water of the man-made Yavorivske Lake (Lviv Region, Ukraine), under the influence of potassium dichromate. This bacteria in the process of anaerobic respiration can use and reduce different electron acceptors, such as sulfur, nitrates, nitrites, oxidized forms of heavy metals, in particular, hexavalent chromium. Technogenically altered ecotopes are characterized by complex pollution, so several electron acceptors are available to bacteria at the same time. Strains of microorganisms isolated from such ecotopes are adapted to unfavourable conditions and therefore have high biotechnological potential. The purpose of this work was to investigate the regularities of elemental sulfur, nitrate or nitrite ion usage by sulfidogenic bacteria of Desulfuromonas genus in conditions of simultaneous presence in the medium of another electron acceptor – Cr(VI), to establish the succession of reduction of electron acceptors by strains of these bacteria and to evaluate the efficiency of their possible application in technologies of complex purification of the environment from metal compounds and other inorganic toxicants. Bacteria were grown under anaerobic conditions in Kravtsov-Sorokin medium without SO42– and without Mohr’s salt for 10 days. To study the efficiency of sulfur, nitrate or nitrite ions’ reduction at simultaneous presence in the medium of Cr(VI) bacteria were sown in media with elemental sulfur, NaNO3, NaNO2 or K2Cr2O7 to final S0, NO3–, NO2–or Cr(VI) concentration in the medium of 3.47 (concentration of SO42– in medium of standard composition) or 1.74, 3.47, 5.21, 6.94 and 10.41 mM. Biomass was determined by the turbidimetric method, and the concentrations of nitrate, nitrite, ammonium ions, hydrogen sulfide, Cr(VI), Cr(ІІІ) in cultural liquid were determined spectrophotometrically. It has been established that Cr(VI) inhibits the biomass accumulation and hydrogen sulfide production by bacteria of Desulfuromonas sp. after simultaneous addition into the medium of 3.47 mM S0 and 1.74–10.41 mM Cr(VI). In the medium with the same initial content (3.47 mM) of S0 and Cr(VI) bacteria produced Cr(III) at concentrations 3.3–3.4 times higher than that of hydrogen sulfide. It has been shown that K2Cr2O7 inhibits biomass accumulation, nitrate ions’ reduction and ammonium ions’ production by bacteria after simultaneous addition into the medium of 3.47 mM NO3– and 1.74–10.41 mM Cr(VI) or 1.74–10.41 mM NO3– and 3.47 mM Cr(VI). In the medium with the same initial content (3.47 mM) of NO3– and Cr(VI) bacteria reduced up to 1.2 times more nitrate ions than Cr(VI) with the production of ammonium ions at concentrations the same times higher than those of Cr(III). It has been established that K2Cr2O7 inhibits biomass accumulation, nitrite ions’ reduction and ammonium ions’ production by bacteria after simultaneous addition into the medium of 3.47 mM NO2– and 1.74–10.41 mM Cr(VI) or 1.74–10.41 mM NO2– and 3.47 mM Cr(VI). In the medium with the same initial content of (3.47 mM) NO2– and Cr(VI) the reduction of Cr(VI) by bacteria was only slightly, up to 1.1 times, lower than the reduction of nitrite ions, almost the same concentrations of trivalent chromium and ammonium ions were detected in the cultural liquid. The processes of nitrate and nitride reduction carried out by bacteria of Desulfuromonas genus were revealed to be less sensitive to the negative influence of sodium dichromate, as compared with the process of sulfur reduction, because in the media with the same initial content (3.47 mM) of NO3– or NO2– and Cr(VI) bacteria produced 1.1–1.2 times more NH4+ than Cr(III), but in the medium with the same initial content (3.47 mM) of S0 and Cr(VI) ) bacteria produced over than three times more Cr(III) than hydrogen sulfide. Our data allow us to conclude that bacteria of Desulfuromonas genus, the investigated strains of which are adapted to high concentrations (up to 10.41 mM) of inorganic toxicants, play an important role in the geochemical cycles of sulfur, nitrogen and chromium in aquatic environments that have been under anthropogenic influence.

Dissimilatory reduction of sulfate, nitrate and nitrite ions by bacteria Desulfovibrio sp. under the influence of potassium dichromate

In the process of anaerobic respiration, sulfate reducing bacteria, besides sulfates, can use other electron acceptors: nitrates, nitrites, oxidized forms of heavy metals, in particular, hexavalent chromium, which are harmful for organisms. Selection of pollutant-resistant stains of this kind of bacteria isolated from technogenically altered ecotopes, capable of reductive transformation of various nature pollutants, is an especially relevant task for the creation of new effective remediation biotechnologies. The purpose of this work was to investigate the regularities of usage of sulfate, nitrate or nitrite ions by bacteria of the Desulfovibrio genus, isolated from Yavorivske Lake, at conditions of simultaneous presence in the medium of another electron acceptor – Cr(VI), to establish a succession of electron acceptors’ reduction by investigated sulfidogenic bacteria and to evaluate the efficiency of their possible application in technologies of complex purification of the environment from metal, sulfur and nitrogen compounds. Bacteria were grown under anaerobic conditions for 10 days in Kravtsov-Sorokin medium without Mohr’s salt. To study the efficiency of sulfate, nitrate, or nitrite ions’ reduction at simultaneous presence in the medium of Cr(VI), bacteria were sown in media with Na2SO4×10H2O, NaNO3, NaNO2 or K2Cr2O7 to final SO42–, NO3–, NO2– or Cr(VI) concentration in the medium of 3.47 (concentration of SO42– in medium of standard composition) or 1.74, 3.47, 5.21, 6.94, 10.41 mM. Biomass was determined turbidimetrically, and the concentrations of sulfate, nitrate, nitrite, ammonium ions, hydrogen sulfide, Cr(VI), Cr(ІІІ) in cultural liquid were determined by spectrophotometric method. It has been established that Cr(VI) inhibits the biomass accumulation, sulfate ions’ reduction and hydrogen sulfide production by Desulfovibrio sp. after simultaneous introduction into the medium of 3.47 mM SO42– and 1.74–10.41 mM Cr(VI). In the medium with the same initial content (3.47 mM) of SO42– and Cr(VI), bacteria reduced 2.1–2.3 times more Cr(VI) than sulfate ions with Cr(III) production at concentrations up to 2.2 times higher than hydrogen sulfide. It has been shown that K2Cr2O7 inhibits the biomass accumulation, the nitrate ions reduction and the ammonium ions production by bacteria after simultaneous addition into the medium of 3.47 mM NO3– and 1.74–10.41 mM Cr(VI) or 1.74–10.41 mM NO3– and 3.47 mM Cr(VI). In the medium with the same initial content (3.47 mM) of NO3– and Cr(VI) bacteria reduced 1.1–1.3 times more nitrate ions than Cr(VI) with the production of ammonium ions at concentrations up to 1.3 times higher than that of Cr(III). It has been established that K2Cr2O7 inhibits the biomass accumulation, the nitrite ions’ reduction and the ammonium ions’ production by bacteria after simultaneous addition into the medium of 3.47 mM NO2– and 1.74–10.41 mM Cr(VI) or 1.74–10.41 mM NO2– and 3.47 mM Cr(VI). In the medium with the same initial content (3.47 mM) NO2– and Cr(VI) the reduction of Cr(VI) by bacteria practically did not differ from the reduction of nitrite ions (was only slightly lower – up to 1.1 times), almost the same concentrations of trivalent chromium and ammonium ions in the cultural liquid were detected. The processes of nitrate and nitride reduction, carried out by bacteria of Desulfovibrio genus, were revealed to be less sensitive to the negative influence of sodium dichromate, as compared with the process of sulfate ions’ reduction, which in the medium with 3.47 mM SO42– and 1.74–10.41 mM Cr(VІ) decreased by 3.2–4.6 times as compared with this process in the medium with only Na2SO4×10H2O. The investigated strains of bacteria are adapted to high concentrations of toxic pollutants (up to 10.41 mM) and therefore are promising for application in technologies of complex environment purification from hexavalent chromium, sulfur and nitrogen compounds.

Dr. NO and Mr. Toxic - the versatile role of nitric oxide

Nitric oxide (NO) is present in various organisms from humans, to plants, fungus and bacteria. NO is a fundamental signaling molecule implicated in major cellular functions. The role of NO ranges from an essential molecule to a potent mediator of cellular damages. The ability of NO to react with a broad range of biomolecules allows on one hand its regulation and a gradient concentration and on the other hand to exert physiological as well as pathological functions. In humans, NO is implicated in cardiovascular homeostasis, neurotransmission and immunity. However, NO can also contribute to cardiovascular diseases (CVDs) or septic shock. For certain denitrifying bacteria, NO is part of their metabolism as a required intermediate of the nitrogen cycle. However, for other bacteria, NO is toxic and harmful. To survive, those bacteria have developed processes to resist this toxic effect and persist inside their host. NO also contributes to maintain the host/microbiota homeostasis. But little is known about the impact of NO produced during prolonged inflammation on microbiota integrity, and some pathogenic bacteria take advantage of the NO response to colonize the gut over the microbiota. Taken together, depending on the environmental context (prolonged production, gradient concentration, presence of partners for interaction, presence of oxygen, etc.), NO will exert its beneficial or detrimental function. In this review, we highlight the dual role of NO for humans, pathogenic bacteria and microbiota, and the mechanisms used by each organism to produce, use or resist NO.

Anaerobic bacterial response to nitric oxide stress: Widespread misconceptions and physiologically relevant responses

How anaerobic bacteria protect themselves against nitric oxide-induced stress is controversial, not least because far higher levels of stress were used in the experiments on which most of the literature is based than bacteria experience in their natural environments. This results in chemical damage to enzymes that inactivates their physiological function. This review illustrates how transcription control mechanisms reveal physiological roles of the encoded gene products. Evidence that the hybrid cluster protein, Hcp, is a major high affinity NO reductase in anaerobic bacteria is reviewed: if so, its trans-nitrosation activity is a nonspecific secondary consequence of chemical inactivation. Whether the flavorubredoxin, NorV, is equally effective at such low [NO] is unknown. YtfE is proposed to be an enzyme rather than a source of iron for the repair of iron-sulfur proteins damaged by nitrosative stress. Any reaction catalyzed by YtfE needs to be revealed. The concentration of NO that accumulates in the cytoplasm of anaerobic bacteria is unknown, but indirect evidence indicates that it is in the pM to low nM range. Also unknown are the functions of the NO-inducible cytoplasmic proteins YgbA, YeaR, or YoaG. Experiments to resolve some of these questions are proposed.

OrpR is a σ54 -dependent activator using an iron-sulfur cluster for redox sensing in Desulfovibrio vulgaris Hildenborough

Enhancer binding proteins (EBPs) are key players of σ⁵⁴ -regulation that control transcription in response to environmental signals. In the anaerobic microorganism Desulfovibrio vulgaris Hildenborough (DvH), orp operons have been previously shown to be coregulated by σ⁵⁴ -RNA polymerase, the integration host factor IHF and a cognate EBP, OrpR. In this study, ChIP-seq experiments indicated that the OrpR regulon consists of only the two divergent orp operons. In vivo data revealed that (i) OrpR is absolutely required for orp operons transcription, (ii) under anaerobic conditions, OrpR binds on the two dedicated DNA binding sites and leads to high expression levels of the orp operons, (iii) increasing the redox potential of the medium leads to a drastic down-regulation of the orp operons expression. Moreover, combining functional and biophysical studies on the anaerobically purified OrpR leads us to propose that OrpR senses redox potential variations via a redox-sensitive [4Fe-4S]²⁺ cluster in the sensory PAS domain. Overall, the study herein presents the first characterization of a new Fe-S redox regulator belonging to the σ⁵⁴ -dependent transcriptional regulator family probably advantageously selected by cells adapted to the anaerobic lifestyle to monitor redox stress conditions.

Shotgun proteomic analysis of nanoparticle-synthesizing Desulfovibrio alaskensis in response to platinum and palladium

Platinum and palladium are much sought-after metals of critical global importance in terms of abundance and availability. At the nano-scale these metals are of even higher value due to their catalytic abilities for industrial applications. Desulfovibrio alaskensis is able to capture ionic forms of both of these metals, reduce them and synthesize elemental nanoparticles. Despite this ability, very little is known about the biological pathways involved in the formation of these nanoparticles. Proteomic analysis of D. alaskensis in response to platinum and palladium has highlighted those proteins involved in both the reductive pathways and the wider stress-response system. A core set of 13 proteins was found in both treatments and consisted of proteins involved in metal transport and reduction. There were also seven proteins that were specific to either platinum or palladium. Overexpression of one of these platinum-specific genes, a NiFe hydrogenase small subunit (Dde_2137), resulted in the formation of larger nanoparticles. This study improves our understanding of the pathways involved in the metal resistance mechanism of Desulfovibrio and is informative regarding how we can tailor the bacterium for nanoparticle production, enhancing its application as a bioremediation tool and as a way to capture contaminant metals from the environment.

A comparative proteomic analysis of Desulfovibrio vulgaris Hildenborough in response to the antimicrobial agent free nitrous acid

Sulfate reducing bacteria (SRB) can contribute to facilitating serious concrete corrosion through the production of hydrogen sulfide in sewers. Recently, free nitrous acid (FNA) was discovered as a promising antimicrobial agent to inhibit SRB activities thereby limiting hydrogen sulfide production in sewers. However, knowledge of the bacterial response to increasing levels of the antimicrobial agent is unknown. Here we report the proteomic response of Desulfovibrio vulgaris Hildenborough and reveal that the antimicrobial effect of FNA is multi-targeted and dependent on the FNA levels. This was achieved using a sequential window acquisition of all theoretical mass spectrometry analysis to determine protein abundance variations in D. vulgaris during exposure to different FNA concentrations. When exposed to 1.0 μg N/L FNA, nitrite reduction (nitrite reductase) related proteins and nitrosative stress related proteins, including the hybrid cluster protein, showed distinct increased abundances. When exposed to 4.0 and 8.0 μg N/L FNA, increased abundance was detected for proteins putatively involved in nitrite reduction. Abundance of proteins involved in the sulfate reduction pathway (from adenylylphophosulfate to sulfite) and lactate oxidation pathway (from pyruvate to acetate) were initially inhibited in response to FNA at 8 h incubation, and then recovered at 12 h incubation. Lowered ribosomal protein abundance in D. vulgaris was detected, however, total cellular protein levels were mostly constant in the presence or absence of FNA. In addition, this study indicates that proteins coded by genes DVU2543, DVU0772, and DVU3212 potentially participate in resisting oxidative stress with FNA exposure. These findings share new insights for understanding the dynamic responses of D. vulgaris to FNA and could be useful to guide and improve the practical applications of FNA-based technologies for control of sewer corrosion.

Nitrosative stress sensing in Porphyromonas gingivalis: structure of and heme binding by the transcriptional regulator HcpR

Although the HcpR regulator plays a vital step in initiation of the nitrosative stress response in many Gram-negative anaerobic bacteria, the molecular mechanisms that it uses to mediate gas sensing are not well understood. Here, a 2.6 Å resolution crystal structure of the N-terminal sensing domain of the anaerobic periodontopathogen Porphyromonas gingivalis HcpR is presented. The protein has classical features of the regulators belonging to the FNR-CRP family and contains a hydrophobic pocket in its N-terminal sensing domain. It is shown that heme bound to HcpR exhibits heme iron as a hexacoordinate system in the absence of nitric oxide (NO) and that upon nitrosylation it transitions to a pentacoordinate system. Finally, small-angle X-ray scattering experiments on full-length HcpR reveal that the C-terminal DNA-binding domain of HcpR has a high degree of interdomain flexibility.

The Porphyromonas gingivalis Hybrid Cluster Protein Hcp Is Required for Growth with Nitrite and Survival with Host Cells

Although the periodontal pathogen Porphyromonas gingivalis must withstand high levels of nitrosative stress while in the oral cavity, the mechanisms of nitrosative stress defense are not well understood in this organism. Previously we showed that the transcriptional regulator HcpR plays a significant role in defense, and here we further defined its regulon. Our study shows that hcp (PG0893), a putative nitric oxide (NO) reductase, is the only gene significantly upregulated in response to nitrite (NO₂) and that this regulation is dependent on HcpR. An isogenic mutant deficient in hcp is not able to grow with 200 μM nitrite, demonstrating that the sensitivity of the HcpR mutant is mediated through Hcp. We further define the molecular mechanisms of HcpR interaction with the hcp promoter through mutational analysis of the inverted repeat present within the promoter. Although other putative nitrosative stress protection mechanisms present on the nrfAH operon are also found in the P. gingivalis genome, we show that their gene products play no role in growth of the bacterium with nitrite. As growth of the hcp-deficient strain was also significantly diminished in the presence of a nitric oxide-producing compound, S-nitrosoglutathione (GSNO), Hcp appears to be the primary means by which P. gingivalis responds to NO₂ ^--based stress. Finally, we show that Hcp is required for survival with host cells but that loss of Hcp has no effect on association and entry of P. gingivalis into human oral keratinocytes.

Integrating Bacterial ChIP-seq and RNA-seq Data With SnakeChunks

Next-generation sequencing (NGS) is becoming a routine approach in most domains of the life sciences. To ensure reproducibility of results, there is a crucial need to improve the automation of NGS data processing and enable forthcoming studies relying on big datasets. Although user-friendly interfaces now exist, there remains a strong need for accessible solutions that allow experimental biologists to analyze and explore their results in an autonomous and flexible way. The protocols here describe a modular system that enable a user to compose and fine-tune workflows based on SnakeChunks, a library of rules for the Snakemake workflow engine. They are illustrated using a study combining ChIP-seq and RNA-seq to identify target genes of the global transcription factor FNR in Escherichia coli, which has the advantage that results can be compared with the most up-to-date collection of existing knowledge about transcriptional regulation in this model organism, extracted from the RegulonDB database. © 2019 by John Wiley & Sons, Inc.

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.

Anaerobic Bacterial Response to Nitrosative Stress

This chapter provides an overview of current knowledge of how anaerobic bacteria protect themselves against nitrosative stress. Nitric oxide (NO) is the primary source of this stress. Aerobically its removal is an oxidative process, whereas reduction is required anaerobically. Mechanisms required to protect aerobic and anaerobic bacteria are therefore different. Several themes recur in the review. First, how gene expression is regulated often provides clues to the physiological function of the gene products. Second, the physiological significance of reports based upon experiments under extreme conditions that bacteria do not encounter in their natural environment requires reassessment. Third, responses to the primary source of stress need to be distinguished from secondary consequences of chemical damage due to failure of repair mechanisms to cope with extreme conditions. NO is generated by many mechanisms, some of which remain undefined. An example is the recent demonstration that the hybrid cluster protein combines with YtfE (or RIC protein, for repair of iron centres damaged by nitrosative stress) in a new pathway to repair key iron-sulphur proteins damaged by nitrosative stress. The functions of many genes expressed in response to nitrosative stress remain either controversial or are completely unknown. The concentration of NO that accumulates in the bacterial cytoplasm is essentially unknown, so dogmatic statements cannot be made that damage to transcription factors (Fur, FNR, SoxRS, MelR, OxyR) occurs naturally as part of a physiologically relevant signalling mechanism. Such doubts can be resolved by simple experiments to meet six proposed criteria.