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Environmental Microbiology Jun 2018Biofilms of sulfate-reducing bacteria (SRB) produce H S, which contributes to corrosion. Although bacterial cells in biofilms are cemented together, they often dissolve...
Biofilms of sulfate-reducing bacteria (SRB) produce H S, which contributes to corrosion. Although bacterial cells in biofilms are cemented together, they often dissolve their own biofilm to allow the cells to disperse. Using Desulfovibrio vulgaris as a model SRB, we sought polysaccharide-degrading enzymes that disperse its biofilm. Using a whole-genome approach, we identified eight enzymes as putative extracellular glycoside hydrolases including DisH (DVU2239, dispersal hexosaminidase), an enzyme that we demonstrated here, by utilizing various p-nitrooligosaccharide substrates, to be an N-acetyl-β-D-hexosaminidase. For N-acetyl-β-D-galactosamine (GalNAc), V was 3.6 µmol of p-nitrophenyl/min (mg protein) and K was 0.8 mM; the specific activity for N-acetyl β-D-glucosamine (GlcNAc) was 7.8 µmol of p-nitrophenyl/min (mg protein) . Since GalNAc is one of the three exopolysaccharide matrix components of D. vulgaris, purified DisH was found to disperse 63 ± 2% biofilm as well as inhibit biofilm formation up to 47 ± 4%. The temperature and pH optima are 60°C and pH 6, respectively; DisH is also inhibited by copper and is secreted. In addition, since polymers of GalNAc and GlcNAc are found in the matrix of diverse bacteria, DisH dispersed biofilms of Pseudomonas aeruginosa, Escherichia coli and Bacillus subtilis. Therefore, DisH has the potential to inhibit and disperse a wide-range of biofilms.
Topics: Acetylgalactosamine; Bacteria; Bacterial Physiological Phenomena; Biofilms; Desulfovibrio vulgaris; Gene Expression Regulation, Bacterial; Gene Expression Regulation, Enzymologic; Glycoside Hydrolases; Nitrogen
PubMed: 29411481
DOI: 10.1111/1462-2920.14064 -
Microbiome Dec 2018Currently, the effect of the bacterial community on cast iron corrosion process does not reach consensus. Moreover, some studies have produced contrasting results,...
BACKGROUND
Currently, the effect of the bacterial community on cast iron corrosion process does not reach consensus. Moreover, some studies have produced contrasting results, suggesting that bacteria can either accelerate or inhibit corrosion.
RESULTS
The long-term effects of the bacterial community on cast iron corrosion in reclaimed wastewater distribution systems were investigated from both spatial (yellow layer vs. black layer) and temporal (1-year dynamic process) dimensions of the iron coupon-reclaimed wastewater microcosm using high-throughput sequencing and flow cytometry approaches. Cast iron coupons in the NON and UV reactors suffered more severe corrosion than did those in the NaClO reactor. The bacterial community significantly promoted cast iron corrosion, which was quantified for the first time in the practical reclaimed wastewater and found to account for at least 30.5% ± 9.7% of the total weight loss. The partition of yellow and black layers of cast iron corrosion provided more accurate information on morphology and crystal structures for corrosion scales. The black layer was dense, and the particles looked fusiform, while the yellow layer was loose, and the particles were ellipse or spherical. Goethite was the predominant crystalline phase in black layers, while corrosion products mainly existed as an amorphous phase in yellow layers. The bacterial community compositions of black layers were distinctly separated from yellow layers regardless of disinfection methods. The NON and UV reactors had a more similar microbial composition and variation tendency for the same layer type than did the NaClO reactor. Biofilm development can be divided into the initial start-up stage, mid-term development stage, and terminal stable stage. In total, 12 potential functional genera were selected to establish a cycle model for Fe, N, and S metabolism. Desulfovibrio was considered to accelerate the transfer of Fe to Fe and speed up weight loss.
CONCLUSION
The long-term effect of disinfection processes on corrosion behaviors of cast iron in reclaimed wastewater distribution systems and the hidden mechanisms were deciphered for the first time. This study established a cycle model for Fe, N, and S metabolism that involved 12 functional genera and discovered the significant contribution of Desulfovibrio in promoting corrosion.
Topics: Bacteria; Biofilms; Bioreactors; Corrosion; DNA, Bacterial; Desulfovibrio; High-Throughput Nucleotide Sequencing; Iron; Iron Compounds; Minerals; Sequence Analysis, DNA; Spatio-Temporal Analysis; Wastewater
PubMed: 30545419
DOI: 10.1186/s40168-018-0610-5 -
Bioresource Technology Apr 2024A robust modeling approach for predicting heavy metal removal by sulfate-reducing bacteria (SRB) is currently missing. In this study, four machine learning models were...
A robust modeling approach for predicting heavy metal removal by sulfate-reducing bacteria (SRB) is currently missing. In this study, four machine learning models were constructed and compared to predict the removal of Cd, Cu, Pb, and Zn as individual ions by SRB. The CatBoost model exhibited the best predictive performance across the four subsets, achieving R values of 0.83, 0.91, 0.92, and 0.83 for the Cd, Cu, Pb, and Zn models, respectively. Feature analysis revealed that temperature, pH, sulfate concentration, and C/S (the mass ratio of chemical oxygen demand to sulfate) had significant impacts on the outcomes. These features exhibited the most effective metal removal at 35 °C and sulfate concentrations of 1000-1200 mg/L, with variations observed in pH and C/S ratios. This study introduced a new modeling approach for predicting the treatment of metal-containing wastewater by SRB, offering guidance for optimizing operational parameters in the biological sulfidogenic process.
Topics: Cadmium; Lead; Metals, Heavy; Desulfovibrio; Sulfates
PubMed: 38417462
DOI: 10.1016/j.biortech.2024.130501 -
Journal of Applied Microbiology Sep 2021Sulphate-reducing bacteria (SRB) are ecologically important group of anaerobic micro-organisms that can reduce sulphate to form hydrogen sulphide-a toxic gas causing...
AIMS
Sulphate-reducing bacteria (SRB) are ecologically important group of anaerobic micro-organisms that can reduce sulphate to form hydrogen sulphide-a toxic gas causing iron corrosion on metal surfaces. In this work, SRB strains were isolated from aquatic environments in the country of Georgia to determine their lysogenicity and the role of temperate phages in host metabolism.
METHODS AND RESULTS
SRB strains were isolated in samples from the Black Sea coast of Georgia. Based on their genetic, cytological and physiological properties of bacteria, 10 Georgian isolates were assigned to the genus Desulfovibrio. Temperate bacteriophages were induced from three out of ten strains by UV-exposure. Comparison of metal (Fe and Cr) reduction and utilization of various carbon sources by the wild-type (lysogenic) bacterial strains and their UV-irradiated counterparts was done.
CONCLUSIONS
Temperate phage in the cells of SRB could alter significant functions of bacteria and may have a contribution in the acquisition of different traits by SRB.
SIGNIFICANCE AND IMPACT OF THE STUDY
This article pointed to a significant role for temperate bacteriophages in the metabolism and metabolic potential of host strains of SRB, which were first isolated from the aquatic environment of Georgia.
Topics: Aquatic Organisms; Bacteriophages; Desulfovibrio; Georgia; Lysogeny; Seawater; Sulfates; Water Microbiology
PubMed: 33555060
DOI: 10.1111/jam.15030 -
Methods in Enzymology 2011Sulfate reducing bacteria (SRB) are physiologically important given their nearly ubiquitous presence and have important applications in the areas of bioremediation and...
Sulfate reducing bacteria (SRB) are physiologically important given their nearly ubiquitous presence and have important applications in the areas of bioremediation and bioenergy. This chapter provides details on the steps used for homologous-recombination mediated chromosomal manipulation of Desulfovibrio vulgaris Hildenborough, a well-studied sulfate reducer. More specifically, we focus on the implementation of a "parts" based approach for suicide vector assembly, important aspects of anaerobic culturing, choices for antibiotic selection, electroporation-based DNA transformation, as well as tools for screening and verifying genetically modified constructs. These methods, which in principle may be extended to other SRB, are applicable for functional genomics investigations, as well as metabolic engineering manipulations.
Topics: Biodegradation, Environmental; Cell Culture Techniques; Chromosomes, Bacterial; DNA, Bacterial; Desulfovibrio; Electroporation; Gene Deletion; Genetic Engineering; Genetic Vectors; Plasmids; Recombination, Genetic; Sulfates
PubMed: 21601101
DOI: 10.1016/B978-0-12-385075-1.00022-6 -
Current Microbiology Sep 2021Hot springs harbour diverse and interesting groups of microorganisms adapted to extreme conditions. However, due to limitations in the culture-dependent approach, most...
Hot springs harbour diverse and interesting groups of microorganisms adapted to extreme conditions. However, due to limitations in the culture-dependent approach, most of such thermophiles remain uncultured and unexplored. Hence, this study was conducted to gain a comprehensive understanding of the bacterial diversity of Mahapelessa hot spring, Sri Lanka using both culture-dependent and culture-independent approaches. The in situ temperature of the water sample was 44.5 °C and the pH was 8.14. 16S rRNA Sanger sequencing of DNA extracted from the 18 bacterial isolates revealed the presence of eight genera belonging to two phyla: Proteobacteria (84%) and Firmicutes (16%) and the most abundant genus being Klebsiella. A total of 23 bacterial phyla representing 80 classes, 43 orders, 123 families, 205 genera and 83 species were detected by 16S rRNA V3-V4 region by amplicon metagenome sequencing of DNA extracted from water samples, where the most abundant phylum was the Proteobacteria (57.39%), followed by Firmicutes (23.7%) and Chloroflexi (4.14%). The three phyla Actinobacteria, Planctomycetes and Bacteroidetes were also detected less than 3% in abundance while 4.48% of bacteria could not be fit into any known phylum. The most abundant genera were Burkholderia (14.87%), Desulfotomaculum (7.23%) and Stenotrophomonas (6.1%). Four strictly anaerobic bacteria, Anaerosolibacter carboniphilus (0.71%), Bellilinea caldifistulae (0.04%), Salimesophilobacter vulgaris (0.1%), Anaerobacterium chartisolvens (0.12%); two potential plant growth-promoting bacteria, Azospirillum halopraeferens (0.04%) and Bradyrhizobium liaoningense (0.16%) and one potential alkali tolerant and sulphate-reducing bacterium, Desulfovibrio alkalitolerans (0.45%) were recorded. Pigmentiphaga sp. was isolated from Mahapelessa hot spring and to the best of our knowledge, this is the first record of this genus from a hot spring. This study gives insight into the vast bacterial diversity present in the Mahapelessa hot spring from the culture-independent approach which could not be identified using standard culturing techniques.
Topics: Azospirillum; Bacteria; Bradyrhizobium; Chloroflexi; Clostridiaceae; Clostridiales; Desulfovibrionaceae; Hot Springs; Humans; Phylogeny; RNA, Ribosomal, 16S
PubMed: 34258683
DOI: 10.1007/s00284-021-02608-4 -
Antonie Van Leeuwenhoek Sep 2021The diversity of anaerobic microorganisms in terrestrial mud volcanoes is largely unexplored. Here we report the isolation of a novel sulfate-reducing alkaliphilic...
The diversity of anaerobic microorganisms in terrestrial mud volcanoes is largely unexplored. Here we report the isolation of a novel sulfate-reducing alkaliphilic bacterium (strain F-1) from a terrestrial mud volcano located at the Taman peninsula, Russia. Cells of strain F-1 were Gram-negative motile vibrios with a single polar flagellum; 2.0-4.0 µm in length and 0.5 µm in diameter. The temperature range for growth was 6-37 °C, with an optimum at 24 °C. The pH range for growth was 7.0-10.5, with an optimum at pH 9.5. Strain F-1 utilized lactate, pyruvate, and molecular hydrogen as electron donors and sulfate, sulfite, thiosulfate, elemental sulfur, fumarate or arsenate as electron acceptors. In the presence of sulfate, the end products of lactate oxidation were acetate, HS and CO Lactate and pyruvate could also be fermented. The major product of lactate fermentation was acetate. The main cellular fatty acids were anteiso-C, C, C, and iso-Cω8. Phylogenetic analysis revealed that strain F-1 was most closely related to Pseudodesulfovibrio aespoeensis (98.05% similarity). The total size of the genome of the novel isolate was 3.23 Mb and the genomic DNA G + C content was 61.93 mol%. The genome contained all genes essential for dissimilatory sulfate reduction. We propose to assign strain F-1 to the genus Pseudodesulfovibrio, as a new species, Pseudodesulfovibrio alkaliphilus sp. nov. The type strain is F-1 (= KCTC 15918 = VKM B-3405).
Topics: Bacterial Typing Techniques; DNA, Bacterial; Desulfovibrionaceae; Fatty Acids; Oxidation-Reduction; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sulfates
PubMed: 34212258
DOI: 10.1007/s10482-021-01608-5 -
Journal of the American Chemical Society May 2012When enzymes are optimized for biotechnological purposes, the goal often is to increase stability or catalytic efficiency. However, many enzymes reversibly convert their...
When enzymes are optimized for biotechnological purposes, the goal often is to increase stability or catalytic efficiency. However, many enzymes reversibly convert their substrate and product, and if one is interested in catalysis in only one direction, it may be necessary to prevent the reverse reaction. In other cases, reversibility may be advantageous because only an enzyme that can operate in both directions can turnover at a high rate even under conditions of low thermodynamic driving force. Therefore, understanding the basic mechanisms of reversibility in complex enzymes should help the rational engineering of these proteins. Here, we focus on NiFe hydrogenase, an enzyme that catalyzes H(2) oxidation and production, and we elucidate the mechanism that governs the catalytic bias (the ratio of maximal rates in the two directions). Unexpectedly, we found that this bias is not mainly determined by redox properties of the active site, but rather by steps which occur on sites of the proteins that are remote from the active site. We evidence a novel strategy for tuning the catalytic bias of an oxidoreductase, which consists in modulating the rate of a step that is limiting only in one direction of the reaction, without modifying the properties of the active site.
Topics: Catalytic Domain; Desulfovibrio; Hydrogenase; Models, Molecular; Mutation; Oxidation-Reduction; Thermodynamics
PubMed: 22540997
DOI: 10.1021/ja301802r -
Chemical Record (New York, N.Y.) Jan 2022Sulfate reducing bacteria (SRB) are blamed as main culprits in triggering huge corrosion damages by microbiologically influenced corrosion. They obtained their energy...
Sulfate reducing bacteria (SRB) are blamed as main culprits in triggering huge corrosion damages by microbiologically influenced corrosion. They obtained their energy through enzymatic conversion of sulfates to sulfides which are highly corrosive. However, conventional SRB detection methods are complex, time-consuming and are not enough sensitive for reliable detection. The advanced biosensing technologies capable of overcoming the aforementioned drawbacks are in demand. So, nanomaterials being economical, environmental friendly and showing good electrocatalytic properties are promising candidates for electrochemical detection of SRB as compared with antibody based assays. Here, we summarize the recent advances in the detection of SRB using different techniques such as PCR, UV visible method, fluorometric method, immunosensors, electrochemical sensors and photoelectrochemical sensors. We also discuss the SRB detection based on determination of sulfide, typical metabolic product of SRB.
Topics: Biosensing Techniques; Corrosion; Desulfovibrio; Immunoassay; Oxidation-Reduction; Sulfates
PubMed: 34415677
DOI: 10.1002/tcr.202100166 -
Microbiological Research Mar 2023Solidesulfovibrio fructosivorans (formely Desulfovibrio fructosovorans), an anaerobic sulfate-reducing bacterium, possesses six gene clusters encoding six hydrogenases...
Solidesulfovibrio fructosivorans (formely Desulfovibrio fructosovorans), an anaerobic sulfate-reducing bacterium, possesses six gene clusters encoding six hydrogenases catalyzing the reversible oxidation of hydrogen gas (H) into protons and electrons. One of these, named Hnd, was demonstrated to be an electron-bifurcating hydrogenase Hnd (Kpebe et al., 2018). It couples the exergonic reduction of NAD to the endergonic reduction of a ferredoxin with electrons derived from H and whose function has been recently shown to be involved in ethanol production under pyruvate fermentation (Payne 2022). To understand further the physiological role of Hnd in S. fructosivorans, we compared the mutant deleted of part of the hnd gene with the wild-type strain grown on pyruvate without sulfate using NMR-based metabolomics. Our results confirm that Hnd is profoundly involved in ethanol metabolism, but also indirectly intervenes in global carbon metabolism and additional metabolic processes such as the biosynthesis of branched-chain amino acids. We also highlight the metabolic reprogramming induced by the deletion of hndD that leads to the upregulation of several NADP-dependent pathways.
Topics: Electrons; Fermentation; Hydrogen; Hydrogenase; Oxidation-Reduction; Pyruvic Acid; Desulfovibrionaceae
PubMed: 36592576
DOI: 10.1016/j.micres.2022.127279