Response of Desulfovibrio vulgaris to alkaline stress

Genome-wide transcriptional response to silver stress in extremely halophilic archaeon Haloferax alexandrinus DSM 27206 T

BACKGROUND

The extremely halophilic archaeon Haloferax (Hfx.) alexandrinus DSM 27206 T was previously documented for the ability to biosynthesize silver nanoparticles while mechanisms underlying its silver tolerance were overlooked. In the current study, we aimed to assess the transcriptional response of this haloarchaeon to varying concentrations of silver, seeking a comprehensive understanding of the molecular determinants underpinning its heavy metal tolerance.

RESULTS

The growth curves confirmed the capacity of Hfx. alexandrinus to surmount silver stress, while the SEM-EDS analysis illustrated the presence of silver nanoparticles in cultures exposed to 0.5 mM silver nitrate. The RNA-Seq based transcriptomic analysis of Hfx. alexandrinus cells exposed to 0.1, 0.25, and 0.5 mM silver nitrate revealed the differential expression of multiple sets of genes potentially employed in heavy-metal stress response, genes mostly related to metal transporters, basic metabolism, oxidative stress response and cellular motility. The RT-qPCR analysis of selected transcripts was conducted to verify and validate the generated RNA-Seq data.

CONCLUSIONS

Our results indicated that copA, encoding the copper ATPase, is essential for the survival of Hfx. alexandrinus cells in silver-containing saline media. The silver-exposed cultures underwent several metabolic adjustments that enabled the activation of enzymes involved in the oxidative stress response and impairment of the cellular movement capacity. To our knowledge, this study represents the first comprehensive analysis of gene expression in halophillic archaea facing increased levels of heavy metals.

Syntrophic Interactions Ameliorate Arsenic Inhibition of Solvent-Dechlorinating Dehalococcoides mccartyi

Interactions and nutrient exchanges among members of microbial communities are important for understanding functional relationships in environmental microbiology. We can begin to elucidate the nature of these complex systems by taking a bottom-up approach utilizing simplified, but representative, community members. Here, we assess the effects of a toxic stress event, the addition of arsenite (As(III)), on a syntrophic co-culture containing lactate-fermenting Desulfovibrio vulgaris Hildenborough and solvent-dechlorinating Dehalococcoides mccartyi strain 195. Arsenic and trichloroethene (TCE) are two highly prevalent groundwater contaminants in the United States, and the presence of bioavailable arsenic is of particular concern at remediation sites in which reductive dechlorination has been employed. While we previously showed that low concentrations of arsenite (As(III)) inhibit the keystone TCE-reducing microorganism, D. mccartyi, this study reports the utilization of physiological analysis, transcriptomics, and metabolomics to assess the effects of arsenic on the metabolisms, gene expression, and nutrient exchanges in the described co-culture. It was found that the presence of D. vulgaris ameliorated arsenic stress on D. mccartyi, improving TCE dechlorination under arsenic-contaminated conditions. Nutrient and amino acid export by D. vulgaris may be a stress-ameliorating exchange in this syntrophic co-culture under arsenic stress, based on upregulation of transporters and increased extracellular nutrients like sarcosine and ornithine. These results broaden our knowledge of microbial community interactions and will support the further development and implementation of robust bioremediation strategies at multi-contaminant sites.

Microbial hydrogen consumption leads to a significant pH increase under high-saline-conditions: implications for hydrogen storage in salt caverns

Salt caverns have been successfully used for natural gas storage globally since the 1940s and are now under consideration for hydrogen (H2) storage, which is needed in large quantities to decarbonize the economy to finally reach a net zero by 2050. Salt caverns are not sterile and H2 is a ubiquitous electron donor for microorganisms. This could entail that the injected H2 will be microbially consumed, leading to a volumetric loss and potential production of toxic H2S. However, the extent and rates of this microbial H2 consumption under high-saline cavern conditions are not yet understood. To investigate microbial consumption rates, we cultured the halophilic sulphate-reducing bacteria Desulfohalobium retbaense and the halophilic methanogen Methanocalculus halotolerans under different H2 partial pressures. Both strains consumed H2, but consumption rates slowed down significantly over time. The activity loss correlated with a significant pH increase (up to pH 9) in the media due to intense proton- and bicarbonate consumption. In the case of sulphate reduction, this pH increase led to dissolution of all produced H2S in the liquid phase. We compared these observations to a brine retrieved from a salt cavern located in Northern Germany, which was then incubated with 100% H2 over several months. We again observed a H2 loss (up to 12%) with a concurrent increase in pH of up to 8.5 especially when additional nutrients were added to the brine. Our results clearly show that sulphate-reducing microbes present in salt caverns consume H2, which will be accompanied by a significant pH increase, resulting in reduced activity over time. This potentially self-limiting process of pH increase during sulphate-reduction will be advantageous for H2 storage in low-buffering environments like salt caverns.

Transcriptomic responses of haloalkalitolerant bacterium Egicoccus halophilus EGI 80432T to highly alkaline stress

The haloalkalitolerant bacterium Egicoccus halophilus EGI 80432^T exhibits high adaptability to saline-alkaline environment. The salinity adaptation mechanism of E. halophilus EGI 80432^T was fully understood based on transcriptome analyses and physiological responses; however, the alkaline response mechanism has not yet been investigated. Here, we investigated the alkaline response mechanism of E. halophilus EGI 80432^T by a transcriptomic comparison. In this study, the genes involved in the glycolysis, TCA cycle, starch, and trehalose metabolism for energy production and storage, were up-regulated under highly alkaline condition. Furthermore, genes responsible for the production of acidic and neutral metabolites, i.e., acetate, pyruvate, formate, glutamate, threonine, and ectoine, showed increased expression under highly alkaline condition, compared with the control pH condition. In contrast, the opposite results were observed in proton capture or retention gene expression profiles, i.e., cation/proton antiporters and ATP synthases. The above results revealed that E. halophilus EGI 80432^T likely tended to adopt an "acidic metabolites production" strategy in response to a highly alkaline condition. These findings would pave the way for further studies in the saline-alkaline adaptation mechanisms of E. halophilus EGI 80432^T, and hopefully provide a new insight into the foundational theory and application in ecological restoration with saline-alkaline strains.

Genetic Basis of Chromate Adaptation and the Role of the Pre-existing Genetic Divergence during an Experimental Evolution Study with Desulfovibrio vulgaris Populations

Hexavalent chromium [Cr(VI)] is a common environmental pollutant. However, little is known about the genetic basis of microbial evolution under Cr(VI) stress and the influence of the prior evolution histories on the subsequent evolution under Cr(VI) stress. In this study, Desulfovibrio vulgaris Hildenborough (DvH), a model sulfate-reducing bacterium, was experimentally evolved for 600 generations. By evolving the replicate populations of three genetically diverse DvH clones, including ancestor (AN, without prior experimental evolution history), non-stress-evolved EC3-10, and salt stress-evolved ES9-11, the contributions of adaptation, chance, and pre-existing genetic divergence to the evolution under Cr(VI) stress were able to be dissected. Significantly decreased lag phases under Cr(VI) stress were observed in most evolved populations, while increased Cr(VI) reduction rates were primarily observed in populations evolved from EC3-10 and ES9-11. The pre-existing genetic divergence in the starting clones showed strong influences on the changes in lag phases, growth rates, and Cr(VI) reduction rates. Additionally, the genomic mutation spectra in populations evolved from different starting clones were significantly different. A total of 14 newly mutated genes obtained mutations in at least two evolved populations, suggesting their importance in Cr(VI) adaptation. An in-frame deletion mutation of one of these genes, the chromate transporter gene DVU0426, demonstrated that it played an important role in Cr(VI) tolerance. Overall, our study identified potential key functional genes for Cr(VI) tolerance and demonstrated the important role of pre-existing genetic divergence in evolution under Cr(VI) stress conditions.

IMPORTANCE Chromium is one of the most common heavy metal pollutants of soil and groundwater. The potential of Desulfovibrio vulgaris Hildenborough in heavy metal bioremediation such as Cr(VI) reduction was reported previously; however, experimental evidence of key functional genes involved in Cr(VI) resistance are largely unknown. Given the genetic divergence of microbial populations in nature, knowledge on how this divergence affects the microbial adaptation to a new environment such as Cr(VI) stress is very limited. Taking advantage of our previous study, three groups of genetically diverse D. vulgaris Hildenborough populations with or without prior experimental evolution histories were propagated under Cr(VI) stress for 600 generations. Whole-population genome resequencing of the evolved populations revealed the genomic changes underlying the improved Cr(VI) tolerance. The strong influence of the pre-existing genetic divergence in the starting clones on evolution under Cr(VI) stress conditions was demonstrated at both phenotypic and genetic levels.

Sulphate-Reducing Bacteria’s Response to Extreme pH Environments and the Effect of Their Activities on Microbial Corrosion

Sulphate-reducing bacteria (SRB) are dominant species causing corrosion of various types of materials. However, they also play a beneficial role in bioremediation due to their tolerance of extreme pH conditions. The application of sulphate-reducing bacteria (SRB) in bioremediation and control methods for microbiologically influenced corrosion (MIC) in extreme pH environments requires an understanding of the microbial activities in these conditions. Recent studies have found that in order to survive and grow in high alkaline/acidic condition, SRB have developed several strategies to combat the environmental challenges. The strategies mainly include maintaining pH homeostasis in the cytoplasm and adjusting metabolic activities leading to changes in environmental pH. The change in pH of the environment and microbial activities in such conditions can have a significant impact on the microbial corrosion of materials. These bacteria strategies to combat extreme pH environments and their effect on microbial corrosion are presented and discussed.

Effect of Alkaline Artificial Seawater Environment on the Corrosion Behaviour of Duplex Stainless Steel 2205

Sulphate reducing bacteria (SRB) can be found in alkaline environments. Due to their metabolite products such as hydrogen sulphide, the corrosion behaviour of materials in alkaline environments may be affected by the presence of SRB. This study focuses on the investigation of corrosion behaviour of duplex stainless steel DSS 2205 in nutrient rich artificial seawater containing SRB species, Desulfovibrio vulgaris, at different alkaline conditions with pH range from 7 to 10. The open circuit potential value (OCP), sulphide level and pH were recorded daily. Confocal laser scanning microscopy (CLSM) was used to study the adhesion of SRB on the DSS 2205 surface. Electrochemical impedance spectroscopy (EIS) was used to study the properties of the biofilm. Potentiodynamic polarization was used to study the corrosion behaviour of material. Inductively coupled plasma mass was used to measure the concentration of cations Fe, Ni, Mo, Mn in the experimental solution after 28 days. Scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS) were used for surface analysis. The results showed that D. vulgaris are active in an alkaline environment with pH 7–9. However, at pH 10, D. vulgaris activity exhibited an 8-day lag. The corrosion rate of DSS 2205 at pH 9 was higher than at other pH environments due to a higher dissolved concentration of hydrogen sulphide.

An assessment of sulfate reducing bacteria on treating sulfate-rich metal-laden wastewater from electroplating plant

Electroplating effluent contaminated with heavy metals posed a major threat on the aquatic ecosystems. The effect of the sulfate-reducing bacteria (SRB) enriched sludge on simultaneous removals of sulfate and nickel was identified. Batch tests showed that SRB biogenic precipitation could completely eliminate the nickel (100 %) with sodium lactate as carbon source at pH 7 within 3 d, and enhanced in the presence of Fe²⁺ and Fe³⁺, while inhibited at high concentrations. The formation of NiS₂ (confirmed by XRD, EDS and FTIR) indicated that the nickel was removed mainly through chemical bond. RDA analysis showed that COD/S ratios and the iron had the greatest influence on the performance. High-throughput sequencing indicated that the SRB enriched sludge was dominant with Desulfovibiro (43.3 %) at genus level. Finally, a pilot-scale experiment with SRB biological precipitation demonstrated that it could partially replace chemical precipitation for removing sulfate and nickel, and greatly improved the removals of ammonia-N, total nitrogen and total phosphorus in the sequential Anaerobic-Anoxic-Oxic process. This approach could greatly minimize the secondary contamination and chemicals dosing for pH adjusting and chemical coagulation. Therefore, SRB-based metal removal performance is a promising technology to realize a high-rate and low-cost process for treating practical sulfate rich metal-laden wastewater. This study is the first report about the comprehensive effect of SRB reactor with practical electroplating wastewater treatment system, which provides a new application template for electroplating wastewater treatment.

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.

LurR is a regulator of the central lactate oxidation pathway in sulfate-reducing Desulfovibrio species

The central carbon/lactate utilization pathway in the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough, is encoded by the highly conserved operon DVU3025-3033. Our earlier in vitro genome-wide study had suggested a network of four two-component system regulators that target this large operon; however, how these four regulators control this operon was not known. Here, we probe the regulation of the lactate utilization operon with mutant strains and DNA-protein binding assays. We show that the LurR response regulator is required for optimal growth and complete lactate utilization, and that it activates the DVU3025-3033 lactate oxidation operon as well as DVU2451, a lactate permease gene, in the presence of lactate. We show by electrophoretic mobility shift assays that LurR binds to three sites in the upstream region of DVU3025, the first gene of the operon. NrfR, a response regulator that is activated under nitrite stress, and LurR share similar binding site motifs and bind the same sites upstream of DVU3025. The DVU3025 promoter also has a binding site motif (Pho box) that is bound by PhoB, a two-component response regulator activated under phosphate limitation. The lactate utilization operon, the regulator LurR, and LurR binding sites are conserved across the order Desulfovibrionales whereas possible modulation of the lactate utilization genes by additional regulators such as NrfR and PhoB appears to be limited to D. vulgaris.

Recent advances in dissimilatory sulfate reduction: From metabolic study to application

Sulfate-reducing bacteria (SRB) are a group of diverse anaerobic microorganisms omnipresent in natural habitats and engineered environments that use sulfur compounds as the electron acceptor for energy metabolism. Dissimilatory sulfate reduction (DSR)-based techniques mediated by SRB have been utilized in many sulfate-containing wastewater treatment systems worldwide, particularly for acid mine drainage, groundwater, sewage and industrial wastewater remediation. However, DSR processes are often operated suboptimally and disturbances are common in practical application. To improve the efficiency and robustness of SRB-based processes, it is necessary to study SRB metabolism and operational conditions. In this review, the mechanisms of DSR processes are reviewed and discussed focusing on intracellular and extracellular electron transfer with different electron donors (hydrogen, organics, methane and electrodes). Based on the understanding of the metabolism of SRB, responses of SRB to environmental stress (pH-, temperature-, and salinity-related stress) are summarized at the species and community levels. Application in these stressed conditions is discussed and future research is proposed. The feasibility of recovering energy and resources such as biohydrogen, hydrocarbons, polyhydroxyalkanoates, magnetite and metal sulfides through the use of SRB were investigated but some long-standing questions remain unanswered. Linking the existing scientific understanding and observations to practical application is the challenge as always for promotion of SRB-based techniques.

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.

Evaluation of key parameters on simultaneous sulfate reduction and sulfide oxidation in an autotrophic biocathode

Bioelectrochemical systems (BESs) are being studied as an alternative technology for the treatment of several kinds of wastewaters with a lack of electron donor such as high-strength sulfate wastewaters. This study evaluates different parameters that influence the simultaneous sulfate reduction and sulfide oxidation in an autotrophic biocathode: ion-exchange membrane (IEM), cathodic pH and cathode potential. Two different membranes were studied to evaluate sulfate and sulfide adsorption and diffusion from the cathode to the anode, observing that a cation-exchange membrane (CEM) widely decreased these effects. Three different cathode pH (5.5, 7 and 8.5) were studied in a long-term operation observing that pH = 7 was the optimal for sulfate removal, achieving reduction rates around 150 mg S-SO₄^2- L^-1 d^-1. Microbial community analysis of the cathode biofilm demonstrated a high abundance of sulfate-reducing bacteria (SRB, 67% at pH 7, 60% at pH 8.5 and 42% at pH 5.5), mainly Desulfovibrio sp. at pH 5.5 and 7 and Desulfonatronum sp. at pH 8.5. The cathode potential also was studied from -0.7 to -1.2 V vs. SHE achieving sulfate removal rates higher than 700 mg S-SO₄^2- L^-1 d^-1 at cathode potentials from -1.0 to -1.2 V vs. SHE. Also, the highest cathodic recovery and the highest sulfur species imbalance were observed at a cathode potential of -1.0 V vs. SHE, which indicated a higher elemental sulfur production.

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.

Alkaline Response of a Halotolerant Alkaliphilic Halomonas Strain and Functional Diversity of Its Na+(K+)/H+ Antiporters

Halomonas sp. Y2 is a halotolerant alkaliphilic strain from Na⁺-rich pulp mill wastewater with high alkalinity (pH >11.0). Transcriptome analysis of this isolate revealed this strain may use various transport systems for pH homeostasis. In particular, the genes encoding four putative Na⁺/H⁺ antiporters were differentially expressed upon acidic or alkaline conditions. Further evidence, from heterologous expression and mutant studies, suggested that Halomonas sp. Y2 employs its Na⁺/H⁺ antiporters in a labor division way to deal with saline and alkaline environments. Ha-NhaD2 displayed robust Na⁺(Li⁺) resistance and high transport activities in Escherichia coli; a ΔHa-nhaD2 mutant exhibited growth inhibition at high Na⁺(Li⁺) concentrations at pH values of 6.2, 8.0, and 10.0, suggesting its physiological role in osmotic homeostasis. In contrast, Ha-NhaD1 showed much weaker activities in ion exporting and pH homeostasis. Ha-Mrp displayed a combination of properties similar to those of Mrp transporters from some Bacillus alkaliphiles and neutrophiles. This conferred obvious Na⁺(Li⁺, K⁺) resistance in E. coli-deficient strains, as those ion transport spectra of some neutrophil Mrp antiporters. Conversely, similar to the Bacillus alkaliphiles, Ha-Mrp showed central roles in the pH homeostasis of Halomonas sp. Y2. An Ha-mrp-disrupted mutant was seriously inhibited by high concentrations of Na⁺(Li⁺, K⁺) but only under alkaline conditions. Ha-NhaP was determined to be a K⁺/H⁺ antiporter and shown to confer strong K⁺ resistance both at acidic and alkaline stresses.

Adaptation of an abundant Roseobacter RCA organism to pelagic systems revealed by genomic and transcriptomic analyses

The RCA (Roseobacter clade affiliated) cluster, with an internal 16S rRNA gene sequence similarity of >98%, is the largest cluster of the marine Roseobacter clade and most abundant in temperate to (sub)polar oceans, constituting up to 35% of total bacterioplankton. The genome analysis of the first described species of the RCA cluster, Planktomarina temperata RCA23, revealed that this phylogenetic lineage is deeply branching within the Roseobacter clade. It shares not >65.7% of homologous genes with any other organism of this clade. The genome is the smallest of all closed genomes of the Roseobacter clade, exhibits various features of genome streamlining and encompasses genes for aerobic anoxygenic photosynthesis (AAP) and CO oxidation. In order to assess the biogeochemical significance of the RCA cluster we investigated a phytoplankton spring bloom in the North Sea. This cluster constituted 5.1% of the total, but 10-31% (mean 18.5%) of the active bacterioplankton. A metatranscriptomic analysis showed that the genome of P. temperata RCA23 was transcribed to 94% in the bloom with some variations during day and night. The genome of P. temperata RCA23 was also retrieved to 84% from metagenomic data sets from a Norwegian fjord and to 82% from stations of the Global Ocean Sampling expedition in the northwestern Atlantic. In this region, up to 6.5% of the total reads mapped on the genome of P. temperata RCA23. This abundant taxon appears to be a major player in ocean biogeochemistry.

Application of phenotypic microarrays to environmental microbiology

Environmental organisms are extremely diverse and only a small fraction has been successfully cultured in the laboratory. Culture in micro wells provides a method for rapid screening of a wide variety of growth conditions and commercially available plates contain a large number of substrates, nutrient sources, and inhibitors, which can provide an assessment of the phenotype of an organism. This review describes applications of phenotype arrays to anaerobic and thermophilic microorganisms, use of the plates in stress response studies, in development of culture media for newly discovered strains, and for assessment of phenotype of environmental communities. Also discussed are considerations and challenges in data interpretation and visualization, including data normalization, statistics, and curve fitting.

Global transcriptomic and proteomic responses of Dehalococcoides ethenogenes strain 195 to fixed nitrogen limitation

Bacteria of the genus Dehalococcoides play an important role in the reductive dechlorination of chlorinated ethenes. A systems-level approach was taken in this study to examine the global transcriptomic and proteomic responses of exponentially growing cells of Dehalococcoides ethenogenes strain 195 to fixed nitrogen limitation (FNL), as dechlorination activity and cell yield both decrease during FNL. As expected, the nitrogen-fixing (nif) genes were differentially upregulated in the transcriptome and proteome of strain 195 during FNL. Aside from the nif operon, a putative methylglyoxal synthase-encoding gene (DET1576), the product of which is predicted to catalyze the formation of the toxic electrophile methylglyoxal and is implicated in the uncoupling of anabolism from catabolism in bacteria, was strongly upregulated in the transcriptome and could potentially play a role in the observed growth inhibition during FNL. Carbon catabolism genes were generally downregulated in response to FNL, and a number of transporters were differentially regulated in response to nitrogen limitation, with some playing apparent roles in nitrogen acquisition, while others were associated with general stress responses. A number of genes related to the functions of nucleotide synthesis, replication, transcription, translation, and posttranslational modifications were also differentially expressed. One gene coding for a putative reductive dehalogenase (DET1545) and a number of genes coding for oxidoreductases, which have implications in energy generation and redox reactions, were also differentially regulated. Interestingly, most of the genes within the multiple integrated elements were not differentially expressed. Overall, this study elucidates the molecular responses of strain 195 to FNL and identifies differentially expressed genes that are potential biomarkers to evaluate environmental cellular nitrogen status.

Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium

Background

Two component regulatory systems are the primary form of signal transduction in bacteria. Although genomic binding sites have been determined for several eukaryotic and bacterial transcription factors, comprehensive identification of gene targets of two component response regulators remains challenging due to the lack of knowledge of the signals required for their activation. We focused our study on Desulfovibrio vulgaris Hildenborough, a sulfate reducing bacterium that encodes unusually diverse and largely uncharacterized two component signal transduction systems.

Results

We report the first systematic mapping of the genes regulated by all transcriptionally acting response regulators in a single bacterium. Our results enabled functional predictions for several response regulators and include key processes of carbon, nitrogen and energy metabolism, cell motility and biofilm formation, and responses to stresses such as nitrite, low potassium and phosphate starvation. Our study also led to the prediction of new genes and regulatory networks, which found corroboration in a compendium of transcriptome data available for D. vulgaris. For several regulators we predicted and experimentally verified the binding site motifs, most of which were discovered as part of this study.

Conclusions

The gene targets identified for the response regulators allowed strong functional predictions to be made for the corresponding two component systems. By tracking the D. vulgaris regulators and their motifs outside the Desulfovibrio spp. we provide testable hypotheses regarding the functions of orthologous regulators in other organisms. The in vitro array based method optimized here is generally applicable for the study of such systems in all organisms.

Generalized schemes for high-throughput manipulation of the Desulfovibrio vulgaris genome

The ability to conduct advanced functional genomic studies of the thousands of sequenced bacteria has been hampered by the lack of available tools for making high-throughput chromosomal manipulations in a systematic manner that can be applied across diverse species. In this work, we highlight the use of synthetic biological tools to assemble custom suicide vectors with reusable and interchangeable DNA "parts" to facilitate chromosomal modification at designated loci. These constructs enable an array of downstream applications, including gene replacement and the creation of gene fusions with affinity purification or localization tags. We employed this approach to engineer chromosomal modifications in a bacterium that has previously proven difficult to manipulate genetically, Desulfovibrio vulgaris Hildenborough, to generate a library of over 700 strains. Furthermore, we demonstrate how these modifications can be used for examining metabolic pathways, protein-protein interactions, and protein localization. The ubiquity of suicide constructs in gene replacement throughout biology suggests that this approach can be applied to engineer a broad range of species for a diverse array of systems biological applications and is amenable to high-throughput implementation.

Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough

Protein-protein interactions offer an insight into cellular processes beyond what may be obtained by the quantitative functional genomics tools of proteomics and transcriptomics. The aforementioned tools have been extensively applied to study Escherichia coli and other aerobes and more recently to study the stress response behavior of Desulfovibrio vulgaris Hildenborough, a model obligate anaerobe and sulfate reducer and the subject of this study. Here we carried out affinity purification followed by mass spectrometry to reconstruct an interaction network among 12 chromosomally encoded bait and 90 prey proteins based on 134 bait-prey interactions identified to be of high confidence. Protein-protein interaction data are often plagued by the lack of adequate controls and replication analyses necessary to assess confidence in the results, including identification of potential false positives. We addressed these issues through the use of biological replication, exponentially modified protein abundance indices, results from an experimental negative control, and a statistical test to assign confidence to each putative interacting pair applicable to small interaction data studies. We discuss the biological significance of metabolic features of D. vulgaris revealed by these protein-protein interaction data and the observed protein modifications. These include the distinct role of the putative carbon monoxide-induced hydrogenase, unique electron transfer routes associated with different oxidoreductases, and the possible role of methylation in regulating sulfate reduction.

How sulphate-reducing microorganisms cope with stress: lessons from systems biology

Sulphate-reducing microorganisms (SRMs) are a phylogenetically diverse group of anaerobes encompassing distinct physiologies with a broad ecological distribution. As SRMs have important roles in the biogeochemical cycling of carbon, nitrogen, sulphur and various metals, an understanding of how these organisms respond to environmental stresses is of fundamental and practical importance. In this Review, we highlight recent applications of systems biology tools in studying the stress responses of SRMs, particularly Desulfovibrio spp., at the cell, population, community and ecosystem levels. The syntrophic lifestyle of SRMs is also discussed, with a focus on system-level analyses of adaptive mechanisms. Such information is important for understanding the microbiology of the global sulphur cycle and for developing biotechnological applications of SRMs for environmental remediation, energy production, biocorrosion control, wastewater treatment and mineral recovery.

Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover

Staphylococcus aureus pathogenesis can be attributed partially to its ability to adapt to otherwise deleterious host-associated stresses. Here, Affymetrix GeneChips® were used to examine the S. aureus responses to inorganic acid and alkaline shock and to assess whether stress-dependent changes in mRNA turnover are likely to facilitate the organism's ability to tolerate a pH challenge. The results indicate that S. aureus adapts to pH shock by eliciting responses expected of cells coping with pH alteration, including neutralizing cellular pH, DNA repair, amino acid biosynthesis, and virulence factor expression. Further, the S. aureus response to alkaline conditions is strikingly similar to that of stringent response-induced cells. Indeed, we show that alkaline shock stimulates the accumulation of the stringent response activator (p)ppGpp. The results also revealed that pH shock significantly alters the mRNA properties of the cell. A comparison of the mRNA degradation properties of transcripts whose titers either increased or decreased in response to a sudden pH change revealed that alterations in mRNA degradation may, in part, account for the changes in the mRNA levels of factors predicted to mediate pH tolerance. A set of small stable RNA molecules were induced in response to acid- or alkaline-shock conditions and may mediate adaptation to pH stress.

Effect of the deletion of qmoABC and the promoter-distal gene encoding a hypothetical protein on sulfate reduction in Desulfovibrio vulgaris Hildenborough

The pathway of electrons required for the reduction of sulfate in sulfate-reducing bacteria (SRB) is not yet fully characterized. In order to determine the role of a transmembrane protein complex suggested to be involved in this process, a deletion in Desulfovibrio vulgaris Hildenborough was created by marker exchange mutagenesis that eliminated four genes putatively encoding the QmoABC complex and a hypothetical protein (DVU0851). The Qmo (quinone-interacting membrane-bound oxidoreductase) complex is proposed to be responsible for transporting electrons to the dissimilatory adenosine-5'-phosphosulfate reductase in SRB. In support of the predicted role of this complex, the deletion mutant was unable to grow using sulfate as its sole electron acceptor with a range of electron donors. To explore a possible role for the hypothetical protein in sulfate reduction, a second mutant was constructed that had lost only the gene that codes for the DVU0851 protein. The second constructed mutant grew with sulfate as the sole electron acceptor; however, there was a lag that was not present with the wild-type or complemented strain. Neither deletion strain was significantly impaired for growth with sulfite or thiosulfate as the terminal electron acceptor. Complementation of the Delta(qmoABC-DVU0851) mutant with all four genes or only the qmoABC genes restored its ability to grow by sulfate respiration. These results confirmed the prediction that the Qmo complex is in the electron pathway for sulfate reduction and revealed that no other transmembrane complex could compensate when Qmo was lacking.

The Qrc membrane complex, related to the alternative complex III, is a menaquinone reductase involved in sulfate respiration

Biological sulfate reduction is a process with high environmental significance due to its major contribution to the carbon and sulfur cycles in anaerobic environments. However, the respiratory chain of sulfate-reducing bacteria is still poorly understood. Here we describe a new respiratory complex that was isolated as a major protein present in the membranes of Desulfovibrio vulgaris Hildenborough. The complex, which was named Qrc, is the first representative of a new family of redox complexes. It has three subunits related to the complex iron-sulfur molybdoenzyme family and a multiheme cytochrome c and binds six hemes c, one [3Fe-4S](+1/0) cluster, and several interacting [4Fe-4S](2+/1+) clusters but no molybdenum. Qrc is related to the alternative complex III, and we show that it has the reverse catalytic activity, acting as a Type I cytochrome c(3):menaquinone oxidoreductase. The qrc genes are found in the genomes of deltaproteobacterial sulfate reducers, which have periplasmic hydrogenases and formate dehydrogenases that lack a membrane subunit for reduction of the quinone pool. In these organisms, Qrc acts as a menaquinone reductase with electrons from periplasmic hydrogen or formate oxidation. Binding of a menaquinone analogue affects the EPR spectrum of the [3Fe-4S](+1/0) cluster, indicating the presence of a quinone-binding site close to the periplasmic subunits. Qrc is the first respiratory complex from sulfate reducers to have its physiological function clearly elucidated.

Impact of elevated nitrate on sulfate-reducing bacteria: a comparative study of Desulfovibrio vulgaris

Sulfate-reducing bacteria have been extensively studied for their potential in heavy-metal bioremediation. However, the occurrence of elevated nitrate in contaminated environments has been shown to inhibit sulfate reduction activity. Although the inhibition has been suggested to result from the competition with nitrate-reducing bacteria, the possibility of direct inhibition of sulfate reducers by elevated nitrate needs to be explored. Using Desulfovibrio vulgaris as a model sulfate-reducing bacterium, functional genomics analysis reveals that osmotic stress contributed to growth inhibition by nitrate as shown by the upregulation of the glycine/betaine transporter genes and the relief of nitrate inhibition by osmoprotectants. The observation that significant growth inhibition was effected by 70 mM NaNO(3) but not by 70 mM NaCl suggests the presence of inhibitory mechanisms in addition to osmotic stress. The differential expression of genes characteristic of nitrite stress responses, such as the hybrid cluster protein gene, under nitrate stress condition further indicates that nitrate stress response by D. vulgaris was linked to components of both osmotic and nitrite stress responses. The involvement of the oxidative stress response pathway, however, might be the result of a more general stress response. Given the low similarities between the response profiles to nitrate and other stresses, less-defined stress response pathways could also be important in nitrate stress, which might involve the shift in energy metabolism. The involvement of nitrite stress response upon exposure to nitrate may provide detoxification mechanisms for nitrite, which is inhibitory to sulfate-reducing bacteria, produced by microbial nitrate reduction as a metabolic intermediate and may enhance the survival of sulfate-reducing bacteria in environments with elevated nitrate level.

F1F0-ATP synthases of alkaliphilic bacteria: lessons from their adaptations

This review focuses on the ATP synthases of alkaliphilic bacteria and, in particular, those that successfully overcome the bioenergetic challenges of achieving robust H+-coupled ATP synthesis at external pH values>10. At such pH values the protonmotive force, which is posited to provide the energetic driving force for ATP synthesis, is too low to account for the ATP synthesis observed. The protonmotive force is lowered at a very high pH by the need to maintain a cytoplasmic pH well below the pH outside, which results in an energetically adverse pH gradient. Several anticipated solutions to this bioenergetic conundrum have been ruled out. Although the transmembrane sodium motive force is high under alkaline conditions, respiratory alkaliphilic bacteria do not use Na+- instead of H+-coupled ATP synthases. Nor do they offset the adverse pH gradient with a compensatory increase in the transmembrane electrical potential component of the protonmotive force. Moreover, studies of ATP synthase rotors indicate that alkaliphiles cannot fully resolve the energetic problem by using an ATP synthase with a large number of c-subunits in the synthase rotor ring. Increased attention now focuses on delocalized gradients near the membrane surface and H+ transfers to ATP synthases via membrane-associated microcircuits between the H+ pumping complexes and synthases. Microcircuits likely depend upon proximity of pumps and synthases, specific membrane properties and specific adaptations of the participating enzyme complexes. ATP synthesis in alkaliphiles depends upon alkaliphile-specific adaptations of the ATP synthase and there is also evidence for alkaliphile-specific adaptations of respiratory chain components.

Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation

The response of Desulfovibrio vulgaris Hildenborough to salt adaptation (long-term NaCl exposure) was examined by performing physiological, global transcriptional, and metabolite analyses. Salt adaptation was reflected by increased expression of genes involved in amino acid biosynthesis and transport, electron transfer, hydrogen oxidation, and general stress responses (e.g., heat shock proteins, phage shock proteins, and oxidative stress response proteins). The expression of genes involved in carbon metabolism, cell growth, and phage structures was decreased. Transcriptome profiles of D. vulgaris responses to salt adaptation were compared with transcriptome profiles of D. vulgaris responses to salt shock (short-term NaCl exposure). Metabolite assays showed that glutamate and alanine accumulated under salt adaptation conditions, suggesting that these amino acids may be used as osmoprotectants in D. vulgaris. Addition of amino acids (glutamate, alanine, and tryptophan) or yeast extract to the growth medium relieved salt-related growth inhibition. A conceptual model that links the observed results to currently available knowledge is proposed to increase our understanding of the mechanisms of D. vulgaris adaptation to elevated NaCl levels.

Cytoplasmic pH measurement and homeostasis in bacteria and archaea

Of all the molecular determinants for growth, the hydronium and hydroxide ions are found naturally in the widest concentration range, from acid mine drainage below pH 0 to soda lakes above pH 13. Most bacteria and archaea have mechanisms that maintain their internal, cytoplasmic pH within a narrower range than the pH outside the cell, termed "pH homeostasis." Some mechanisms of pH homeostasis are specific to particular species or groups of microorganisms while some common principles apply across the pH spectrum. The measurement of internal pH of microbes presents challenges, which are addressed by a range of techniques under varying growth conditions. This review compares and contrasts cytoplasmic pH homeostasis in acidophilic, neutralophilic, and alkaliphilic bacteria and archaea under conditions of growth, non-growth survival, and biofilms. We present diverse mechanisms of pH homeostasis including cell buffering, adaptations of membrane structure, active ion transport, and metabolic consumption of acids and bases.

Cation/proton antiporter complements of bacteria: why so large and diverse?

Most bacterial genomes have five to nine distinct genes predicted to encode transporters that exchange cytoplasmic Na(+) and/or K(+) for H(+) from outside the cell, i.e. monovalent cation/proton antiporters. By contrast, pathogens that live primarily inside host cells usually possess zero to one such antiporter while other stress-exposed bacteria exhibit even higher numbers. The monovalent cation/proton antiporters encoded by these diverse genes fall into at least eight different transporter protein families based on sequence similarity. They enable bacteria to meet challenges of high or fluctuating pH, salt, temperature or osmolarity, but we lack explanations for why so many antiporters are needed and for the value added by specific antiporter types in specific settings. In this issue of Molecular Microbiology, analyses of the pH dependence of cytoplasmic [Na(+)], [K(+)], pH and transmembrane electrical potential in the 'poly extremophile'Natranaerobius thermophilus are the context for assessment of the catalytic properties of 12 predicted monovalent cation/proton antiporters in the genome of this thermophilic haloalkaliphile. The results provide a profile of adaptations of the poly extremophilic anaerobe, including a proposed role of cytoplasmic buffering capacity. They also provide new perspectives on two large monovalent cation/proton antiporter families, the NhaC and the cation/proton antiporter-3 antiporter families.

Characterization of pNC1, a small and mobilizable plasmid for use in genetic manipulation of Desulfovibrio africanus

To develop a vector system that facilitates genetic manipulation in Desulfovibrio species, we screened native sulfate-reducing bacteria for small plasmids. A self-replicating plasmid was discovered in Desulfovibrio africanus SR-1. Sequence analysis of this 8568-bp plasmid (pNC1) revealed a G+C content of 47.2% and nine open reading frames. This plasmid has a copy number of six. Compatible hosts include D. africanus and Pseudomonas aeruginosa PA14. Genetic characterization of pNC1 revealed that 53.6% of the plasmid contains genes associated with replication, mobilization, and partitioning. The 1123-bp replicon is composed of a rep gene and four 22-bp iterons. The mobilization operon is composed of three genes with a putative 144-bp oriT. The partitioning operon is composed of parA and parB with a downstream parS. We report the construction of a small pNC1-based cloning vector which transforms D. africanus at high frequencies (approximately 1.5 x 10(3) CFU/microg DNA), is mobilizable at high transfer frequency (4.8 x 10(-4) transconjugants/donor), and is stably maintained under non-selective pressure. This study provides a potential host-vector system for Desulfovibrio gene functional analyses.

Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation

Hypothetical (HyP) and conserved HyP genes account for >30% of sequenced bacterial genomes. For the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough, 347 of the 3634 genes were annotated as conserved HyP (9.5%) along with 887 HyP genes (24.4%). Given the large fraction of the genome, it is plausible that some of these genes serve critical cellular roles. The study goals were to determine which genes were expressed and provide a more functionally based annotation. To accomplish this, expression profiles of 1234 HyP and conserved genes were used from transcriptomic datasets of 11 environmental stresses, complemented with shotgun LC–MS/MS and AMT tag proteomic data. Genes were divided into putatively polycistronic operons and those predicted to be monocistronic, then classified by basal expression levels and grouped according to changes in expression for one or multiple stresses. One thousand two hundred and twelve of these genes were transcribed with 786 producing detectable proteins. There was no evidence for expression of 17 predicted genes. Except for the latter, monocistronic gene annotation was expanded using the above criteria along with matching Clusters of Orthologous Groups. Polycistronic genes were annotated in the same manner with inferences from their proximity to more confidently annotated genes. Two targeted deletion mutants were used as test cases to determine the relevance of the inferred functional annotations.

Preferential reduction of the thermodynamically less favorable electron acceptor, sulfate, by a nitrate-reducing strain of the sulfate-reducing bacterium Desulfovibrio desulfuricans 27774

Desulfovibrio desulfuricans strain 27774 is one of a relative small group of sulfate-reducing bacteria that can also grow with nitrate as an alternative electron acceptor, but how nitrate reduction is regulated in any sulfate-reducing bacterium is controversial. Strain 27774 grew more rapidly and to higher yields of biomass with nitrate than with sulfate or nitrite as the only electron acceptor. In the presence of both sulfate and nitrate, sulfate was used preferentially, even when cultures were continuously gassed with nitrogen and carbon dioxide to prevent sulfide inhibition of nitrate reduction. The napC transcription start site was identified 112 bases upstream of the first base of the translation start codon. Transcripts initiated at the napC promoter that were extended across the napM-napA boundary were detected by reverse transcription-PCR, confirming that the six nap genes can be cotranscribed as a single operon. Real-time PCR experiments confirmed that nap operon expression is regulated at the level of mRNA transcription by at least two mechanisms: nitrate induction and sulfate repression. We speculate that three almost perfect inverted-repeat sequences located upstream of the transcription start site might be binding sites for one or more proteins of the CRP/FNR family of transcription factors that mediate nitrate induction and sulfate repression of nitrate reduction by D. desulfuricans.

Characterization of the Functionally Critical AXAXAXA and PXXEXXP Motifs of the ATP Synthase c-Subunit from an Alkaliphilic Bacillus

The membrane-embedded rotor in the F(0) sector of proton-translocating ATP synthases is formed from hairpin-like c-subunits that are protonated and deprotonated during energization of ATP synthesis. This study focuses on two c-subunit motifs that are unique to synthases of extremely alkaliphilic Bacillus species. One motif is the AXAXAXA sequence found in the N-terminal helix-1 instead of the GXGXGXG of non-alkaliphiles. Quadruple A-->G chromosomal mutants of alkaliphilic Bacillus pseudofirmus OF4 retain 50% of the wild-type hydrolytic activity (ATPase) but <18% of the ATP synthase capacity at high pH. Consistent with a structural impact of the four alanine replacements, the mutant ATPase activity showed enhanced inhibition by dicyclohexylcarbodiimide, which blocks the helix-2 carboxylate. Single, double, or triple A-->G mutants exhibited more modest defects, as monitored by malate growth. The key carboxylate is in the second motif, which is P(51)XXE(54)XXP in extreme alkaliphiles instead of the (A/G)XX(E/D)XXP found elsewhere. Mutation of Pro(51) to alanine had been shown to severely reduce malate growth and ATP synthesis at high pH. Here, two Pro(51) to glycine mutants of different severities retained ATP synthase capacity but exhibited growth deficits and proton leakiness. A Glu(54) to Asp(54) change increased proton leakiness and reduced malate growth 79-90%. The Pro(51) and the Glu(54) mutants were both more dicyclohexylcarbodiimide-sensitive than wild type. The results highlight the requirement for c-subunit adaptations to achieve alkaliphile ATP synthesis with minimal cytoplasmic proton loss and suggest partial suppression of some mutations by changes outside the atp operon.

Acid and base stress and transcriptomic responses in Bacillus subtilis

Acid and base environmental stress responses were investigated in Bacillus subtilis. B. subtilis AG174 cultures in buffered potassium-modified Luria broth were switched from pH 8.5 to pH 6.0 and recovered growth rapidly, whereas cultures switched from pH 6.0 to pH 8.5 showed a long lag time. Log-phase cultures at pH 6.0 survived 60 to 100% at pH 4.5, whereas cells grown at pH 7.0 survived <15%. Cells grown at pH 9.0 survived 40 to 100% at pH 10, whereas cells grown at pH 7.0 survived <5%. Thus, growth in a moderate acid or base induced adaptation to a more extreme acid or base, respectively. Expression indices from Affymetrix chip hybridization were obtained for 4,095 protein-encoding open reading frames of B. subtilis grown at external pH 6, pH 7, and pH 9. Growth at pH 6 upregulated acetoin production (alsDS), dehydrogenases (adhA, ald, fdhD, and gabD), and decarboxylases (psd and speA). Acid upregulated malate metabolism (maeN), metal export (czcDO and cadA), oxidative stress (catalase katA; OYE family namA), and the SigX extracytoplasmic stress regulon. Growth at pH 9 upregulated arginine catabolism (roc), which generates organic acids, glutamate synthase (gltAB), polyamine acetylation and transport (blt), the K(+)/H(+) antiporter (yhaTU), and cytochrome oxidoreductases (cyd, ctaACE, and qcrC). The SigH, SigL, and SigW regulons were upregulated at high pH. Overall, greater genetic adaptation was seen at pH 9 than at pH 6, which may explain the lag time required for growth shift to high pH. Low external pH favored dehydrogenases and decarboxylases that may consume acids and generate basic amines, whereas high external pH favored catabolism-generating acids.

Important discoveries from analysing bacterial phenotypes

The ability to test hundreds to thousands of cellular phenotypes in a single experiment has opened up new avenues of investigation and exploration and led to important discoveries in very diverse applications of microbiological research and development. The information provided by global phenotyping is complementary to, and often more easily interpretable than information provided by global molecular analytical methods such as gene chips and proteomics. This report summarizes advances presented by scientists brought together to share their experiences and knowledge gained with high-throughput phenotyping.