Discovery of genes associated with sulfate-reducing bacteria biofilm using text mining and biological network analysis

Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range ofDeltaproteobacteriadiversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co-occurrences containing putatively heterotrophic, candidate phyla such as OD1,Atribacteria, MBG-B, and Hyd24-12 and the potential for complex sulfur cycling involvingEpsilon-,Delta-, andGammaproteobacteriain methane seep ecosystems.

Download Full-text

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

Mikrobiolohichnyi Zhurnal ◽

10.15407/microbiolj82.05.011 ◽

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.

Download Full-text

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

Ecology and Noospherology ◽

10.15421/031708 ◽

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.

Download Full-text

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

Vietnam Journal of Biotechnology ◽

10.15625/1811-4989/14/3/9873 ◽

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.

Download Full-text