Bacterium Desulfovibrio Vulgaris Research Articles

Eco-friendly bifunctional antibacterial and anticorrosive broad-spectrum rosin thiourea iminazole quaternary ammonium salt against microbiologically influenced corrosion

Bifunctional antibacterial and anticorrosive broad-spectrum rosin thiourea iminazole quaternary ammonium salt (RTIQAS) was investigated to inhibit microbiologically influenced corrosion (MIC) caused by anaerobic gram-negative sulfate reducing bacterium (SRB) Desulfovibrio vulgaris against X80 carbon steel and aerobic gram-positive bacterium Bacillus licheniformis against 316L stainless steel. It also indicated that RTIQAS was more effective than common commercial biocides THPS (tetrakis hydroxymethyl phosphonium sulfate) and glutaraldehyde at the same concentration against X80 carbon steel corrosion by D. vulgaris. In the molecular simulation, the interaction energy confirmed the favorable adsorption of RTIQAS on the metal surfaces, indicating its potential as an effective corrosion inhibitor.

Antibiofilm assay for antimicrobial peptides combating the sulfate-reducing bacteria Desulfovibrio vulgaris.

In medical, environmental, and industrial processes, the accumulation of bacteria in biofilms can disrupt many processes. Antimicrobial peptides (AMPs) are receiving increasing attention in the development of new substances to avoid or reduce biofilm formation. There is a lack of parallel testing of the effect against biofilms in this area, as well as in the testing of other antibiofilm agents. In this paper, a high-throughput screening was developed for the analysis of the antibiofilm activity of AMPs, differentiated into inhibition and removal of a biofilm. The sulfate-reducing bacterium Desulfovibrio vulgaris was used as a model organism.D. vulgaris represents an undesirable bacterium, which is considered one of the major triggers of microbiologically influenced corrosion. The application of a 96-well plate and steel rivets as a growth surface realizes real-life conditions and at the same time establishes a flexible, simple, fast, and cost-effective assay. All peptides tested in this study demonstrated antibiofilm activity, although these peptides should be individually selected depending on the addressed aim. For biofilm inhibition, the peptide DASamP1 is the most suitable, with a sustained effect for up to 21 days. The preferred peptides for biofilm removal are S6L3-33, in regard to bacteria reduction, and Bactenecin, regarding total biomass reduction.

Microbiologically influenced corrosion of CoCrFeMnNi high entropy alloy by sulfate-reducing bacterium Desulfovibrio vulgaris

Sulfate-reducing bacterium Desulfovibrio vulgaris promoted the microbiologically influenced corrosion (MIC) of CoCrFeMnNi high entropy alloy (HEA) and led to pitting corrosion. D. vulgaris caused the formation of metal sulfides and thinning of passive film. The corrosion resistance decreased, and pit depths increased when the carbon source reduced to 40%. The relative expression of hydrogenase genes hydA and hydB in the biofilms under 40% carbon source significantly increased, indicating that the indirect electron transfer mediated by 2H+/H2 might play an important role in promoting the HEA MIC by D. vulgaris under starvation.

Enhanced pitting corrosion resistance of CoCrFeMnNi high entropy alloy in the presence of Desulfovibrio vulgaris via nitrogen doping

• Desulfovibrio vulgaris accelerates pitting corrosion of HEA without nitrogen. • Nitrogen doping significantly inhibits pitting corrosion induced by D. vulgaris . • Nitrogen strengthens passive film by increasing corrosion resistant species. • Nitrogen doped HEAs exhibits less defects in passive films. Corrosion-resistant high nitrogen high entropy alloys (HEAs) were manufactured by pressurized metallurgy. This work revealed the inhibitory effect of nitrogen on pitting corrosion of HEAs caused by sulfate reducing bacterium Desulfovibrio vulgaris . Results indicated that HEA-0N was susceptible to pitting corrosion and sulfidation under attack of D. vulgaris , whereas the addition of nitrogen significantly decreased the pitting sensitivity. Pitting potential of HEA-0.52N and HEA-1.23N increased by 133% and 171%, respectively compared to HEA-0N in the presence of SRB. X-ray photoelectron spectroscopy results unveiled that nitrogen enriched in passive film and strengthened it by increasing fraction of Cr 2 O 3 and Fe 3+ ox . Surface of the nitrogen-alloyed HEAs exhibited less defective passive films as revealed by Mott-Schottky results. Nitrogen doping provides a novel insight into the design of microbial corrosion resistant HEA.

How a Formate Dehydrogenase Responds to Oxygen: Unexpected O2 Insensitivity of an Enzyme Harboring Tungstopterin, Selenocysteine, and [4Fe–4S] Clusters

The reversible two-electron interconversion of formate and CO2 is catalyzed by both nonmetallo- and metallo-formate dehydrogenases (FDHs). The latter group comprises molybdenum- or tungsten-containing enzymes with the metal coordinated by two equivalents of a pyranopterin cofactor, a cysteinyl or selenocysteinyl (Sec) ligand supplied by the polypeptide, and a catalytically essential terminal sulfido ligand. In addition, these biocatalysts incorporate one or more [4Fe–4S] clusters for facilitating long-distance electron transfer. However, an interesting dichotomy arises when attempting to understand how the metallo-FDHs react with O2. Whereas existing scholarship portrays these enzymes as being unable to perform in air due to extreme O2 lability of their metal centers, studies dating as far back as the 1930s emphasize that some of these systems exhibit formate oxidase (FOX) activity, coupling formate oxidation to O2 reduction. Therefore, to reconcile these conflicting views, we explored context-dependent functional linkages between metallo-FDHs and their cognate electron acceptors within the same organism vis-à-vis catalysis under atmospheric O2. Here, we report the discovery and characterization of an O2-insensitive FDH2 from the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH) that ligates tungsten, Sec, and four [4Fe–4S] clusters. By advancing a robust expression platform for its recombinant production, we eliminate both the requirement of nitrate or azide during purification and reductive activation with thiols and/or formate prior to catalysis. Because the distinctive spectral signatures of formate-reduced DvH-FDH2 remain invariant under anaerobic and aerobic conditions, we benchmarked the enzyme activity in air, identifying CO2 as the catalytic product. Full reaction progress curve analysis discloses a high catalytic efficiency when probed with a high-potential artificial electron acceptor. Furthermore, we show that DvH-FDH2 enables near-stoichiometric hydrogen peroxide production without superoxide release to achieve O2 insensitivity. Notably, simultaneous electron transfer to cytochrome c and O2 reveals that metal-based electron bifurcation is operational in this system. Taken together, our work proves the co-occurrence of redox bifurcated FDH and FOX activities within a metalloenzyme scaffold. These findings set the stage for uncovering previously unknown O2-insensitive flavin-based electron bifurcation mechanisms, as well as for developing authentic formate/air biofuel cells, engineering O2-stable FDHs and biohybrid metallocatalysts, and discerning formate bioenergetics of gut microbiota.

Influence of Sulfate Reduction on Arsenic Migration and Transformation in Groundwater Environment

The sulfate-reducing bacteria-mediated reduction process is considered to be an important mechanism affecting arsenic migration and transformation in anaerobic environments. To investigate the effect of sulfate-reducing bacteria in a high-arsenic aquifer on arsenic migration and transformation, the typical sulfate-reducing bacteria Desulfovibrio vulgaris was selected for micro-cosmic experiments to simulate a groundwater environment with or without sulfate amendment. The reduction of Fe(III) and As(V) by Desulfovibrio vulgaris was identified, and Fe(III) and As(V) were reduced in both sulfate-free and sulfate-containing systems. However, the addition of 1 mM sulfate significantly enhanced Fe(III) and As(V) reduction. Compared with no sulfate addition, 1 mM sulfate increased the reduction rates of Fe(III) and As(V) by 111.9% and 402.2%, respectively. The sulfate process mediated by Desulfovibrio vulgaris also remarkably promoted arsenic release in sediments. These results indicated that sulfate concentration should be considered when sulfate reduction is used as a remediation method for arsenic pollution in groundwater.

CyPhyRNA-seq: a genome-scale RNA-seq method to detect active self-cleaving ribozymes by capturing RNAs with 2ʹ,3ʹ cyclic phosphates and 5ʹ hydroxyl ends

ABSTRACT Self-cleaving ribozymes are catalytically active RNAs that cleave themselves into a 5′-fragment with a 2′,3′-cyclic phosphate and a 3′-fragment with a 5′-hydroxyl. They are widely applied for the construction of synthetic RNA devices and RNA-based therapeutics. However, the targeted discovery of self-cleaving ribozymes remains a major challenge. We developed a transcriptome-wide method, called cyPhyRNA-seq, to screen for ribozyme cleavage fragments in total RNA extract. This approach employs the specific ligation-based capture of ribozyme 5′-fragments using a variant of the Arabidopsis thaliana tRNA ligase we engineered. To capture ribozyme 3′-fragments, they are enriched from total RNA by enzymatic treatments. We optimized and enhanced the individual steps of cyPhyRNA-seq in vitro and in spike-in experiments. Then, we applied cyPhyRNA-seq to total RNA isolated from the bacterium Desulfovibrio vulgaris and detected self-cleavage of the three predicted type II hammerhead ribozymes, whose activity had not been examined to date. cyPhyRNA-seq can be used for the global analysis of active self-cleaving ribozymes with the advantage to capture both ribozyme cleavage fragments from total RNA. Especially in organisms harbouring many self-cleaving RNAs, cyPhyRNA-seq facilitates the investigation of cleavage activity. Moreover, this method has the potential to be used to discover novel self-cleaving ribozymes in different organisms.

Feasibility of cleaning As- and U-containing soil of a gold mine by using biologically nano-sized FeS: Implications for soil remediation technology

Gold and uranium mining has resulted in elevated concentrations of As and U contaminants in groundwater and soil, which has become a paramount concern for the environment and public health. Nanocleaning technology is one of the few permanent treatment alternatives to remove metal contaminants from soils. In recent years, nano-sized FeS, a washing solution that uses nanocleaning technology, has elicited extensive interest in environmental remediation because it does not produce secondary pollution. In this study, As and U were removed from contaminated soil by employing nano-sized FeS washing solution biologically synthesized by the iron-reducing bacteria Acidiphilium cryputum JF-5 and sulphate-reducing bacteria Desulfovibrio vulgaris miyazaki SRB. After cleaning with a nano-sized FeS suspension solution, culture-medium and pure-water for three cycles, the concentration of As in the nano-sized FeS experiment was higher than that of U, suggesting that the cleaning effect for As was better than that for U. The As and U removal rates of the nano-sized FeS cleaning experiment were 12% and 1.59%, respectively, over the three cycles. By using the sequential extraction method, the nano-sized FeS cleaning experiments mainly removed the As fraction bound to Fe/Al oxides. An ATR-FTIR spectral analysis indicated that the band observed at 461 cm −1 was attributed to the ν 4 symmetric stretching mode of AsO 4 3 − . The obvious vibrations observed at 798 cm −1 and 778 cm −1 , were assigned to the ν 1 vibration of AsO 3 3 − . The band at 834 cm −1 was assigned to the weak vibration of UO 2 while the band at 949 cm −1 was attributed to the Fe–O–D bending vibration. The results of this study provide helpful information and references for designing long-term and efficient bioremediation strategies for As- and U-containing soils. • The cleaning performance of biologically-formed nano-sized FeS for As is better than U. • As in soil was extracted by nano-sized FeS as reductive dissolution and re-adsorption. • The main removal species of As is the bound to Fe/Al oxides state. • The cleaning of biologically FeS can be used for a low-cost in-situ remediation technology.

Deletion Mutants, Archived Transposon Library, and Tagged Protein Constructs of the Model Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough.

The dissimilatory sulfate-reducing deltaproteobacterium Desulfovibrio vulgaris Hildenborough (ATCC 29579) was chosen by the research collaboration ENIGMA to explore tools and protocols for bringing this anaerobe to model status. Here, we describe a collection of genetic constructs generated by ENIGMA that are available to the research community.

Assessment of 2,2-Dibromo-3-Nitrilopropionamide Biocide Enhanced by D-Tyrosine against Zinc Corrosion by a Sulfate Reducing Bacterium

The biocorrosion of pure zinc by sulfate reducing bacterium (SRB) Desulfovibrio vulgaris was found to be very severe (2.3 ± 0.1 mm/y) after 7 d incubation in 100 mL of ATCC 1249 medium at 37 °C in ...

Sulfate reducing bacterium Desulfovibrio vulgaris caused severe microbiologically influenced corrosion of zinc and galvanized steel

The microbiologically influenced corrosion (MIC) of zinc and galvanized steel caused by a sulfate reducing bacterium (SRB) was investigated. After 7 days of incubation of Desulfovibrio vulgaris in 125 mL anaerobic vials (100 mL culture medium) at 37 °C, the sessile cell coverage on the galvanized steel was slightly higher than that on pure zinc: (1.9 ± 0.2) × 109 cells/cm2 vs. (9.0 ± 1.8) × 108 cells/cm2. The weight losses for galvanized steel and pure zinc were 31.5 ± 2.5 mg/cm2 and 35.4 ± 4.5 mg/cm2, respectively, which were 101 higher than that for carbon steel. The corrosion current densities of galvanized and pure zinc were 25.5 μA/cm2 and 100 μA/cm2, respectively after the 7-day incubation, confirming that galvanized steel was less prone to SRB MIC despite having a slightly higher sessile cell count. In both cases, the corrosion product was mainly ZnS. Three MIC mechanisms were possible for the severe corrosion against the two metals. Extracellular electron transfer MIC (EET-MIC) was thermodynamically favorable for zinc. Furthermore, in the presence of Zn coupons, H2 evolution in the headspace was 5.5 times higher than without Zn coupons, which suggested that proton attack and/or H2S attack also occurred in the corrosion process.

Oxygen isotope effects during microbial sulfate reduction: applications to sediment cell abundances

The majority of anaerobic biogeochemical cycling occurs within marine sediments. To understand these processes, quantifying the distribution of active cells and gross metabolic activity is essential. We present an isotope model rooted in thermodynamics to draw quantitative links between cell-specific sulfate reduction rates and active sedimentary cell abundances. This model is calibrated using data from a series of continuous culture experiments with two strains of sulfate reducing bacteria (freshwater bacterium Desulfovibrio vulgaris strain Hildenborough, and marine bacterium Desulfovibrio alaskensis strain G-20) grown on lactate across a range of metabolic rates and ambient sulfate concentrations. We use a combination of experimental sulfate oxygen isotope data and nonlinear regression fitting tools to solve for unknown kinetic, step-specific oxygen isotope effects. This approach enables identification of key isotopic reactions within the metabolic pathway, and defines a new, calibrated framework for understanding oxygen isotope variability in sulfate. This approach is then combined with porewater sulfate/sulfide concentration data and diagenetic modeling to reproduce measured 18O/16O in porewater sulfate. From here, we infer cell-specific sulfate reduction rates and predict abundance of active cells of sulfate reducing bacteria, the result of which is consistent with direct biological measurements.

Effects of ferrous ion concentration on microbiologically influenced corrosion of carbon steel by sulfate reducing bacterium Desulfovibrio vulgaris

Ferrous ion (Fe2+) in a sulfate reducing bacteria (SRB) culture medium is known to enhance microbiologically influenced corrosion (MIC) of carbon steel, but the underlining mechanism is controversial. This work showed that it was due to better sessile cell growth that was likely attributed to Fe2+ detoxification of H2S. Two hundred ppm (w/w) initial Fe2+ in the ATCC 1249 medium achieved a 4.7 times higher Desulfovibrio vulgaris sessile cell count and 5.0 times higher C1018 carbon steel weight loss, compared to 20 ppm. Linear polarization resistance, electrochemical impedance spectroscopy and potentiodynamic polarization measurements corroborated weight loss and pitting data trends.

Electrochemical investigation of increased carbon steel corrosion via extracellular electron transfer by a sulfate reducing bacterium under carbon source starvation

Microbiologically influenced corrosion (MIC) of carbon steel by sulfate reducing bacterium (SRB) Desulfovibrio vulgaris under organic carbon starvation was investigated using electrochemical methods to support weight loss and pitting data. 20% carbon source led to the highest weight loss (6.6 mg/cm2), while 100% had the lowest (3.3 mg/cm2) after 10 days. Linear polarization resistance and electrochemical impedance spectrometry data confirmed the weight loss and pitting data trends. The data in this work support the theory that carbon steel corrosion by SRB is due to electron harvest from extracellular iron oxidation by SRB, which belongs to extracellular electron transfer MIC (EET-MIC).

Migration and Transformation of Adsorbed Arsenic Mediated by Sulfate Reducing Bacteria

In the natural environment, arsenic (As) is mainly adsorbed on iron oxide minerals. The release of adsorbed arsenic from iron oxide minerals to the water is the main source of arsenic pollution. Microbes play a crucial role for this process. The purpose of this study was to investigate the effect of the sulfate-reducing bacteria Desulfovibrio vulgaris DP4 on the transformation and mobilization of As. The experimental results show that the released As concentration of the two systems is 0 μmol·L-1 at 0 h. Compared with the control, DP4 promotes the desorption of As(Ⅴ) before the 84 h incubation process. The released As concentration reaches the maximum value of 12.6 μmol·L-1 at 13 h, accounting for~79% of the initial total adsorbed As (16 μmol·L-1). The maximum released As concentration is~8.4 times higher than that of the control (1.5 μmol·L-1). After 84 hours, the concentration of the released As in the DP4 system is lower than the abiotic control, which suggests that the released As is readsorbed on the solid surface. During the incubation process, the As mobility is significantly correlated with Eh. The XRD results show that the crystallinity of the solid samples in the DP4 system decreases by~50%. In general, a lower crystallinity of the adsorbent indicates a higher adsorption capacity. This may be one important reason for the As readsorption after 84 h. In addition, the SEM shows that goethite is agglomerated by DP4 and the EDS results indicate that goethite is partially transformed to an Fe-S mineral. Based on XANES, arsenic-sulfur minerals were not detected in the solid phase, which further confirms the SEM-EDS results, that is, that Fe-S minerals formed in the solid phase, rather than As2S3 (AsS). The released As was readsorbed on the secondary iron mineral, resulting in a lower dissolved As concentration in the DP4 system than in the abiotic control. Furthermore, 19% As(Ⅲ) was detected in the solid phase while dissolved As(Ⅲ) was not determined during the incubation process. The results suggest that sulfate-reducing bacteria may directly reduce adsorbed As(Ⅴ) to As(Ⅲ).

Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics.

For many bacteria with sequenced genomes, we do not understand how they synthesize some amino acids. This makes it challenging to reconstruct their metabolism, and has led to speculation that bacteria might be cross-feeding amino acids. We studied heterotrophic bacteria from 10 different genera that grow without added amino acids even though an automated tool predicts that the bacteria have gaps in their amino acid synthesis pathways. Across these bacteria, there were 11 gaps in their amino acid biosynthesis pathways that we could not fill using current knowledge. Using genome-wide mutant fitness data, we identified novel enzymes that fill 9 of the 11 gaps and hence explain the biosynthesis of methionine, threonine, serine, or histidine by bacteria from six genera. We also found that the sulfate-reducing bacterium Desulfovibrio vulgaris synthesizes homocysteine (which is a precursor to methionine) by using DUF39, NIL/ferredoxin, and COG2122 proteins, and that homoserine is not an intermediate in this pathway. Our results suggest that most free-living bacteria can likely make all 20 amino acids and illustrate how high-throughput genetics can uncover previously-unknown amino acid biosynthesis genes.

Autophagy counters LPS-mediated suppression of lysozyme.

Impaired Paneth cell expression of antimicrobial protein (AMP) lysozyme is found in patients with Crohn's disease with the autophagy gene ATG16L1 risk allele, in mice with mutations in autophagy genes Atg16L1, Atg5 and Atg7, and in Irgm1 knockout mice. Defective autophagy is also associated with expansion of resident Gram-negative bacteria in the intestinal lumen. These findings suggest that autophagy may control extracellular resident microbes by governing expression of lysozyme. To test the hypothesis that autophagy may have a defensive role in host response to resident extracellular microbes, we investigated the relationship between gut microbes, autophagy, and lysozyme. RAW 264.7 macrophages were treated with fecal slurry (FS), representing the resident microbial community; lipopolysaccharide (LPS); or butyrate, representing microbial products; or a representative resident Gram-negative bacterium Desulfovibrio vulgaris (DSV). FS, LPS, and DSV inhibited lysozyme expression, whereas butyrate had no effect. Induction of autophagy by rapamycin countered this inhibition, whereas silencing of the autophagy gene Irgm1 exacerbated the inhibitory effects of LPS on lysozyme expression. LPS also inhibited lysozyme activity against DSV and autophagy reversed this effect. Our results provide a novel insight into an interaction between gut bacteria, autophagy and AMP whereby autophagy may defend the host by countering the suppression of antimicrobial protein by Gram-negative bacteria.

Regulation, sensory domains and roles of two Desulfovibrio desulfuricans ATCC27774 Crp family transcription factors, HcpR1 and HcpR2, in response to nitrosative stress.

In silico analyses identified a Crp/Fnr family transcription factor (HcpR) in sulfate-reducing bacteria that controls expression of the hcp gene, which encodes the hybrid cluster protein and contributes to nitrosative stress responses. There is only one hcpR gene in the model sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough, but two copies in Desulfovibrio desulfuricans 27774, which can use nitrate as an alternative electron acceptor to sulfate. Structures of the D. desulfuricans hcpR1, hcpR2 and hcp operons are reported. We present evidence that hcp expression is regulated by HcpR2, not by HcpR1, and that these two regulators differ in both their DNA-binding site specificity and their sensory domains. HcpR1 is predicted to be a b-type cytochrome. HcpR1 binds upstream of the hcpR1 operon and its synthesis is regulated coordinately with hcp in response to NO. In contrast, hcpR2 expression was not induced by nitrate, nitrite or NO. HcpR2 is an iron-sulfur protein that reacts with NO and O2 . We propose that HcpR1 and HcpR2 use different sensory mechanisms to regulate subsets of genes required for defense against NO-induced nitrosative stress, and that diversification of signal perception and DNA recognition by these two proteins is a product of D. desulfuricans adaptation to its particular environmental niche.

Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported

Numerous affinity purification-mass spectrometry (AP-MS) and yeast two-hybrid screens have each defined thousands of pairwise protein-protein interactions (PPIs), most of which are between functionally unrelated proteins. The accuracy of these networks, however, is under debate. Here, we present an AP-MS survey of the bacterium Desulfovibrio vulgaris together with a critical reanalysis of nine published bacterial yeast two-hybrid and AP-MS screens. We have identified 459 high confidence PPIs from D. vulgaris and 391 from Escherichia coli Compared with the nine published interactomes, our two networks are smaller, are much less highly connected, and have significantly lower false discovery rates. In addition, our interactomes are much more enriched in protein pairs that are encoded in the same operon, have similar functions, and are reproducibly detected in other physical interaction assays than the pairs reported in prior studies. Our work establishes more stringent benchmarks for the properties of protein interactomes and suggests that bona fide PPIs much more frequently involve protein partners that are annotated with similar functions or that can be validated in independent assays than earlier studies suggested.

Quantitative comparison of anaerobic pitting patterns and damage risks by chloride versus Desulfovibrio vulgaris using a fast pitting-characterization method

Anaerobic carbon steel corrosion induced by chloride and a sulfate reducing bacterium (SRB) Desulfovibrio vulgaris was compared using a fast pitting-characterization method based on Infinite Focus Microscopy. This method was found to be significantly less labor-intensive and more reproducible for determination of maximum and average pit depths and pitted area percentage than manual pit identification and measurement. Graphic diagrams were developed with these parameters to show pitting patterns and compare damage risks. Results showed that this SRB was more damaging than chloride by forming deep pit clusters with larger maximum pit depths. Pit geometry and size were also compared for the two corrosion causes. The fast pitting-characterization method was validated to work well for corrosion with different pitting patterns and pit geometries induced by the chloride and D. vulgaris systems.