scholarly journals Proteogenomic Insights into the Physiology of Marine, Sulfate-Reducing, Filamentous Desulfonema limicola and Desulfonema magnum

2021 ◽  
Vol 31 (1) ◽  
pp. 36-56
Author(s):  
Vanessa Schnaars ◽  
Lars Wöhlbrand ◽  
Sabine Scheve ◽  
Christina Hinrichs ◽  
Richard Reinhardt ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Gene Clusters ◽  
Transport Systems ◽  
Natural Habitats ◽  
Sulfate Reducing ◽  
Type Iv ◽  
Aromatic Compound Degradation ◽  
High Degree ◽  
Reducing Bacteria ◽  
Gliding Movement

The genus Desulfonema belongs to the deltaproteobacterial family Desulfobacteraceae and comprises marine, sulfate-reducing bacteria that form filaments and move by gliding. This study reports on the complete, manually annotated genomes of Dn. limicola 5ac10T (6.91 Mbp; 6,207 CDS) and Dn. magnum 4be13T (8.03 Mbp; 9,970 CDS), integrated with substrate-specific proteome profiles (8 vs. 11). The richness in mobile genetic elements is shared with other Desulfobacteraceae members, corroborating horizontal gene transfer as major driver in shaping the genomes of this family. The catabolic networks of Dn. limicola and Dn. magnum have the following general characteristics: 98 versus 145 genes assigned (having genomic shares of 1.7 vs. 2.2%), 92.5 versus 89.7% proteomic coverage, and scattered gene clusters for substrate degradation and energy metabolism. The Dn. magnum typifying capacity for aromatic compound degradation (e.g., p-cresol, 3-phenylpropionate) requires 48 genes organized in operon-like structures (87.7% proteomic coverage; no homologs in Dn. limicola). The protein complements for aliphatic compound degradation, central pathways, and energy metabolism are highly similar between both genomes and were identified to a large extent (69–96%). The differential protein profiles revealed a high degree of substrate-specificity for peripheral reaction sequences (forming central intermediates), agreeing with the high number of sensory/regulatory proteins predicted for both strains. By contrast, central pathways and modules of the energy metabolism were constitutively formed under the tested substrate conditions. In accord with their natural habitats that are subject to fluctuating changes of physicochemical parameters, both Desulfonema strains are well equipped to cope with various stress conditions. Next to superoxide dismutase and catalase also desulfoferredoxin and rubredoxin oxidoreductase are formed to counter exposure to molecular oxygen. A variety of proteases and chaperones were detected that function in maintaining cellular homeostasis upon heat or cold shock. Furthermore, glycine betaine/proline betaine transport systems can respond to hyperosmotic stress. Gliding movement probably relies on twitching motility via type-IV pili or adventurous motility. Taken together, this proteogenomic study demonstrates the adaptability of Dn. limicola and Dn. magnum to its dynamic habitats by means of flexible catabolism and extensive stress response capacities.

Activity of sulfate-reducing bacteria in human periodontal pocket

2002 ◽  
Vol 48 (12) ◽  
pp. 1099-1103 ◽  
Author(s):  
R Boopathy ◽  
M Robichaux ◽  
D LaFont ◽  
M Howell
Keyword(s):  
Electron Acceptor ◽  
Nitrogen Sources ◽  
Sulfate Reducing Bacteria ◽  
Sole Source ◽  
Periodontal Pocket ◽  
Sulfate Reducing ◽  
Optimum Growth Temperature ◽  
Dental Tissues ◽  
Type Iv ◽  
Reducing Bacteria

Samples of subgingival dental tissues were examined for the presence of sulfate-reducing bacteria (SRB). Using enrichment cultures, SRBs were detected in 9 of 17 individuals. A pure culture of SRB was obtained from one sample collected from a patient with type IV periodontal disease. The characterization of this isolate showed that it belongs to the genus Desulfovibrio. The isolate used pyruvate, lactate, glucose, fructose, and ethanol as the sole source of carbon. However, the isolate was unable to use acetate and methanol as a carbon source, indicating it as an incomplete oxidizer unable to carry out the terminal oxidation of substrates. Apart from using sulfate as electron acceptor, the isolate also used thiosulfate and nitrate as an electron acceptor. It has the ability to use a variety of nitrogen sources, including ammonium chloride, nitrate, and glutamate. The optimum growth temperature of the isolate was 37°C and the optimum pH for growth was 6.8. The SRB isolate contained the electron carrier desulfoviridin. The numbers of SRB in the mouth are assumed to be limited by sulfate. Potential sources of sulfate in the subgingival area include free sulfate in pocket fluid and glycosaminoglycans and sulfur-containing amino acids from periodontal tissues.Key words: sulfate-reducing bacteria, periodontal pocket, Desulfovibrio, subgingival tissues, electron acceptor.

scholarly journals A Comparative Genomic Analysis of Energy Metabolism in Sulfate Reducing Bacteria and Archaea

2011 ◽  
Vol 2 ◽  
Author(s):  
Inês A. Cardoso Pereira ◽  
Ana Raquel Ramos ◽  
Fabian Grein ◽  
Marta Coimbra Marques ◽  
Sofia Marques da Silva ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Genomic Analysis ◽  
Sulfate Reducing Bacteria ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Sulfate Reducing ◽  
Reducing Bacteria

scholarly journals Energy metabolism and uranium (VI) reduction by Desulfovibrio

2005 ◽  
Author(s):  
◽  
Rayford B. Payne
Keyword(s):  
Energy Source ◽  
Energy Metabolism ◽  
Organic Compounds ◽  
Hydrogen Gas ◽  
Contaminated Groundwater ◽  
Human Beings ◽  
Cytochrome C3 ◽  
Uranium Reduction ◽  
Sulfate Reducing ◽  
Reducing Bacteria

Sulfate reducing bacteria (SRB) of the genus Desulfovibrio can breathe uranium in a manner similar to the way in which we (human beings) breathe oxygen. In respiration, we transfer electrons from food to oxygen, producing water, SRB transfer electrons of uranium (VI) to uranium (IV). (This transfer of electrons is also called reduction.) The reduction of U(VI) to U(IV) alters the solubility state of the uranium from a soluble to an insoluble, and therefore less biologically available, form. Because SRB are commonly found in uranium contaminated groundwater and soil, it is theoretically possible that we could use them to bioremediate uranium contaminated environments. However, before we attempt to use SRB to bioremediate uranium contaminated environments, we must first understand the SRB genes and enzymes involved in the process of uranium reduction. We have determined that the enzyme cytochrome c3 can act as a U(VI) reductase by Desulfovibrio when hydrogen gas is the energy source; however, alternate pathways utilizing organic compounds for U(VI) reduction exist. In addition, we have observed that Desulfovibrio that have been previously exposed to uranium (such as those bacteria that would be found in a uranium contaminated environment) are impaired in utilizing some organic compounds, but not hydrogen gas, as an energy source for uranium (VI) reduction. This suggests that in order for us to use SRB to treat uranium contaminated environments, it would be more efficient to add hydrogen gas, not organic compounds, as an energy source for the SRB.

scholarly journals Selenium Is Involved in Regulation of Periplasmic Hydrogenase Gene Expression in Desulfovibrio vulgaris Hildenborough

2006 ◽  
Vol 188 (9) ◽  
pp. 3228-3235 ◽  
Author(s):  
Filipa M. A. Valente ◽  
Cláudia C. Almeida ◽  
Isabel Pacheco ◽  
João Carita ◽  
Lígia M. Saraiva ◽  
...  
Keyword(s):  
Model Organism ◽  
Physiological Role ◽  
Major Effect ◽  
Electron Donors ◽  
Strong Increase ◽  
Desulfovibrio Vulgaris ◽  
Hydrogen Metabolism ◽  
Natural Habitats ◽  
Sulfate Reducing ◽  
Reducing Bacteria

ABSTRACT Desulfovibrio vulgaris Hildenborough is a good model organism to study hydrogen metabolism in sulfate-reducing bacteria. Hydrogen is a key compound for these organisms, since it is one of their major energy sources in natural habitats and also an intermediate in the energy metabolism. The D. vulgaris Hildenborough genome codes for six different hydrogenases, but only three of them, the periplasmic-facing [FeFe], [FeNi]1, and [FeNiSe] hydrogenases, are usually detected. In this work, we studied the synthesis of each of these enzymes in response to different electron donors and acceptors for growth as well as in response to the availability of Ni and Se. The formation of the three hydrogenases was not very strongly affected by the electron donors or acceptors used, but the highest levels were observed after growth with hydrogen as electron donor and lowest with thiosulfate as electron acceptor. The major effect observed was with inclusion of Se in the growth medium, which led to a strong repression of the [FeFe] and [NiFe]1 hydrogenases and a strong increase in the [NiFeSe] hydrogenase that is not detected in the absence of Se. Ni also led to increased formation of the [NiFe]1 hydrogenase, except for growth with H2, where its synthesis is very high even without Ni added to the medium. Growth with H2 results in a strong increase in the soluble forms of the [NiFe]1 and [NiFeSe] hydrogenases. This study is an important contribution to understanding why D. vulgaris Hildenborough has three periplasmic hydrogenases. It supports their similar physiological role in H2 oxidation and reveals that element availability has a strong influence in their relative expression.

Specificity of Lectins Labeled with Colloidal Gold to the Exopolymeric Matrix Carbohydrates of the Sulfate-Reducing Bacteria Biofilm Formed on Steel

2020 ◽  
Vol 82 (5) ◽  
pp. 11-20
Author(s):  
D.R. Abdulina ◽  
◽  
L.M. Purish ◽  
G.O. Iutynska ◽  
◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Colloidal Gold ◽  
Steel Surface ◽  
Lectin Binding ◽  
Sulfate Reducing Bacteria ◽  
Gold Particles ◽  
Sulfate Reducing ◽  
Transmission Electron ◽  
Reducing Bacteria

The studies of the carbohydrate composition of the sulfate-reducing bacteria (SRB) biofilms formed on the steel surface, which are a factor of microbial corrosion, are significant. Since exopolymers synthesized by bacteria could activate corrosive processes. The aim of the study was to investigate the specificity of commercial lectins, labeled with colloidal gold to carbohydrates in the biofilm exopolymeric matrix produced by the corrosive-relevant SRB strains from man-caused ecotopes. Methods. Microbiological methods (obtaining of the SRB biofilms during cultivation in liquid Postgate B media under microaerophilic conditions), biochemical methods (lectin-binding analysis of 10 commercial lectins, labeled with colloidal gold), transmission electron microscopy using JEM-1400 JEOL. Results. It was shown using transmission electron microscopy that the binding of lectins with carbohydrates in the biofilm of the studied SRB strains occurred directly in the exopolymerіс matrix, as well as on the surfaces of bacterial cells, as seen by the presence of colloidal gold particles. For detection of the neutral carbohydrates (D-glucose and D-mannose) in the biofilm of almost all studied bacterial strains PSA lectin was the most specific. This lectin binding in biofilms of Desulfotomaculum sp. К1/3 and Desulfovibrio sp. 10 strains was higher in 90.8% and 94.4%, respectively, then for ConA lectin. The presence of fucose in the SRB biofilms was detected using LABA lectin, that showed specificity to the biofilm EPS of all the studied strains. LBA lectin was the most specific to N-аcetyl-D-galactosamine for determination of amino sugars in the biofilm. The amount of this lectin binding in D. vulgaris DSM644 biofilm was 30.3, 10.1 and 9.3 times higher than SBA, SNA and PNA lectins, respectively. STA, LVA and WGA lectins were used to detect the N-acetyl-Dglucosamine and sialic acid in the biofilm. WGA lectin showed specificity to N-acetyl-D-glucosamine in the biofilm of all the studied SRB; maximum number of bounded colloidal gold particles (175 particles/μm2) was found in the Desulfotomaculum sp. TC3 biofilm. STA lectin was interacted most actively with N-acetyl-D-glucosamine in Desulfotomaculum sp. TC3 and Desulfomicrobium sp. TC4 biofilms. The number of bounded colloidal gold particles was in 9.2 and 7.4 times higher, respectively, than using LVA lectin. The lowest binding of colloidal gold particles was observed for LVA lectin. Conclusions. It was identified the individual specificity of the 10 commercial lectins to the carbohydrates of biofilm matrix on the steel surface, produced by SRB. It was estimated that lectins with identical carbohydrates specificity had variation in binding to the biofilm carbohydrates of different SRB strains. Establishing of the lectin range selected for each culture lead to the reduction of the scope of studies and labor time in the researching of the peculiarities of exopolymeric matrix composition of biofilms formed by corrosiverelevant SRB.

The influence of potassium dichromate on dissimilatory reduction of sulfate and nitrate ions by bacteria Desulfovibrio sp.

2017 ◽  
Vol 28 (1-2) ◽  
pp. 84-95
Author(s):  
O. M. Moroz ◽  
S. O. Hnatush ◽  
Ch. I. Bohoslavets ◽  
T. M. Hrytsun’ ◽  
B. M. Borsukevych
Keyword(s):  
Electron Acceptor ◽  
Potassium Dichromate ◽  
Anaerobic Respiration ◽  
Sulfate Reducing Bacteria ◽  
Negative Influence ◽  
Electron Acceptors ◽  
Metal Compounds ◽  
Nitrate Ions ◽  
Sulfate Reducing ◽  
Reducing Bacteria

Sulfate reducing bacteria, capable to reductive transformation of different nature pollutants, used in biotechnologies of purification of sewage, contaminated by carbon, sulfur, nitrogen and metal compounds. H2S formed by them sediment metals to form of insoluble sulfides. Number of metals can be used by these microorganisms as electron acceptors during anaerobic respiration. Because under the influence of metal compounds observed slowing of bacteria metabolism, selection isolated from technologically modified ecotops resistant to pollutions strains is important task to create a new biotechnologies of purification. That’s why the purpose of this work was to study the influence of potassium dichromate, present in medium, on reduction of sulfate and nitrate ions by sulfate reducing bacteria Desulfovibrio desulfuricans IMV K-6, Desulfovibrio sp. Yav-6 and Desulfovibrio sp. Yav-8, isolated from Yavorivske Lake, to estimate the efficiency of possible usage of these bacteria in technologies of complex purification of environment from dangerous pollutants. Bacteria were cultivated in modified Kravtsov-Sorokin medium without SO42- and FeCl2×4H2O for 10 days. To study the influence of K2Cr2O7 on usage by bacteria SO42- or NO3- cells were seeded to media with Na2SO4×10H2O or NaNO3 and K2Cr2O7 at concentrations of 1.74 mM for total content of electron acceptors in medium 3.47 mM (concentration of SO42- in medium of standard composition). Cells were also seeded to media with 3.47 mM Na2SO4×10H2O, NaNO3 or K2Cr2O7 to investigate their growth in media with SO42-, NO3- or Cr2O72- as sole electron acceptor (control). Biomass was determined by turbidymetric method, content of sulfate, nitrate, dichromate, chromium (III) ions, hydrogen sulfide or ammonia ions in cultural liquid – by spectrophotometric method. It was found that K2Cr2O7 inhibits growth (2.2 and 1.3 times) and level of reduction by bacteria sulfate or nitrate ions (4.2 and 3.0 times, respectively) at simultaneous addition into cultivation medium of 1.74 mM SO42- or NO3- and 1.74 mM Cr2O72-, compared with growth and level of reduction of sulfate or nitrate ions in medium only with SO42- or NO3- as sole electron acceptor. Revealed that during cultivation of bacteria in presence of equimolar amount of SO42- or NO3- and Cr2O72-, last used by bacteria faster, content of Cr3+ during whole period of bacteria cultivation exceeded content H2S or NH4+. K2Cr2O7 in medium has most negative influence on dissimilatory reduction by bacteria SO42- than NO3-, since level of nitrate ions reduction by cells in medium with NO3- and Cr2O72- was a half times higher than level of sulfate ions reduction by it in medium with SO42- and Cr2O72-. The ability of bacteria Desulfovibrio sp. to priority reduction of Cr2O72- and after their exhaustion − NO3- and SO42- in the processes of anaerobic respiration can be used in technologies of complex purification of environment from toxic compounds.

Removal of lead by sulfate-reducing bacteria in anaerobic continuous stirred tank reactors

2016 ◽  
Vol 14 (3) ◽  
pp. 557-561
Author(s):  
Nguyễn Thị Yên ◽  
Kiều Thị Quỳnh Hoa
Keyword(s):  
Sulfate Reducing Bacteria ◽  
Stirred Tank ◽  
Synthetic Wastewater ◽  
Terminal Electron Acceptor ◽  
Stirred Tank Reactors ◽  
Sulfate Reducing ◽  
Sulfide Production ◽  
Continuous Stirred Tank ◽  
Continuous Stirred Tank Reactors ◽  
Reducing Bacteria

Lead contaminated wastewater negatively impacts to living organisms as well as humans. In recent years, a highly promising biological process using the anaerobic production of sulfide ions by sulfate-reducing bacteria has presented itself as an alternative option for the removal of lead. This process is based on microbial utilization of electron donors, such as organic compounds (carbon sources), and sulfate as the terminal electron acceptor for sulfide production. The biogenic hydrogen sulfide reacts with dissolved heavy metals to form insoluble metal sulfide precipitates Removal of lead by an enriched consortium of sulfate-reducing bacteria (DM10) was evaluated sulfate reduction, sulfide production and lead precipitation. Four parallel anaerobic continuous stirred tank reactors (CSTR, V = 2L) (referred as R1 - R4) were fed with synthetic wastewater containing Pb2+ in the concentrations of 0, 100, 150 and 200 mg L-1 of lead and operated with a hydraulic retention time of 5 days for 40 days. The loading rates of each metal in R1- R4 were 0, 20, 30 and 40 mg L-1 d-1, respectively. The results showed that there was no inhibition of SRB growth and that lead removal efficiencies of 99-100% for Pb2+ were achieved in R2 (100 mg L-1) and R3 (150 mg L-1) throughout the experiment. For the highest lead concentration of  200 mg L-1, a decrease in efficiency of removal (from 100 to 96%) was observed at the end of the experiment. The obtained result of this study might help for a better control operation and performance improvements of reactors.

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