scholarly journals Analysis of Diversity and Activity of Sulfate-Reducing Bacterial Communities in Sulfidogenic Bioreactors Using 16S rRNA and dsrB Genes as Molecular Markers

2006 ◽  
Vol 73 (2) ◽  
pp. 594-604 ◽  
Author(s):  
Shabir A. Dar ◽  
Li Yao ◽  
Udo van Dongen ◽  
J. Gijs Kuenen ◽  
Gerard Muyzer
Keyword(s):  
16S Rrna ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Populations ◽  
Sulfate Reducing ◽  
Dna And Rna ◽  
Dissimilatory Sulfite Reductase ◽  
Pcr Products ◽  
Gradient Gel Electrophoresis ◽  
Reducing Bacteria

ABSTRACTHere we describe the diversity and activity of sulfate-reducing bacteria (SRB) in sulfidogenic bioreactors by using the simultaneous analysis of PCR products obtained from DNA and RNA of the 16S rRNA and dissimilatory sulfite reductase (dsrAB) genes. We subsequently analyzed the amplified gene fragments by using denaturing gradient gel electrophoresis (DGGE). We observed fewer bands in the RNA-based DGGE profiles than in the DNA-based profiles, indicating marked differences in the populations present and in those that were metabolically active at the time of sampling. Comparative sequence analyses of the bands obtained from rRNA anddsrBDGGE profiles were congruent, revealing the same SRB populations. Bioreactors that received either ethanol or isopropanol as an energy source showed the presence of SRB affiliated withDesulfobulbus rhabdoformisand/orDesulfovibrio sulfodismutans, as well as SRB related to the acetate-oxidizingDesulfobacca acetoxidans. The reactor that received wastewater containing a diverse mixture of organic compounds showed the presence of nutritionally versatile SRB affiliated withDesulfosarcina variabilisand another acetate-oxidizing SRB, affiliated withDesulfoarculus baarsii. In addition to DGGE analysis, we performed whole-cell hybridization with fluorescently labeled oligonucleotide probes to estimate the relative abundances of the dominant sulfate-reducing bacterial populations.Desulfobacca acetoxidans-like populations were most dominant (50 to 60%) relative to the total SRB communities, followed byDesulfovibrio-like populations (30 to 40%), andDesulfobulbus-like populations (15 to 20%). This study is the first to identify metabolically active SRB in sulfidogenic bioreactors by using the functional genedsrABas a molecular marker. The same approach can also be used to infer the ecological role of coexisting SRB in other habitats.

scholarly journals Cr(VI) Reduction by Sulfidogenic and Nonsulfidogenic Microbial Consortia

2003 ◽  
Vol 69 (3) ◽  
pp. 1847-1853 ◽  
Author(s):  
Y. Meriah Arias ◽  
Bradley M. Tebo
Keyword(s):  
Gel Electrophoresis ◽  
Time Course ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Small Subunit ◽  
Ribosomal Genes ◽  
Microbial Consortia ◽  
Sulfate Reducing ◽  
Pcr Products ◽  
Gradient Gel Electrophoresis ◽  
Reducing Bacteria

ABSTRACT In time course experiments, bacterial community compositions were compared between a sulfidogenic and two nonsulfidogenic Cr(VI)-reducing consortia enriched from metal-contaminated sediments. The consortia were subjected to 0 and 0.85 mM or 1.35 mM Cr(VI), and Cr(VI) reduction, growth, and denaturing gradient gel electrophoresis profiles of PCR products of small-subunit (16S) ribosomal genes were compared. Results showed that although Cr(VI) was completely reduced by the three consortia, Cr(VI) inhibited cell growth, with sulfate-reducing bacteria being particularly sensitive to Cr(VI) toxicity relative to other bacteria in the consortia.

Identification of a Bacterial Consortium with Biotechnological Potential for Arsenic Bioremediation

2013 ◽  
Vol 825 ◽  
pp. 540-543
Author(s):  
Mariana Moreira ◽  
Silvana de Queiroz Silva ◽  
Mônica Cristina Teixeira
Keyword(s):  
Burkholderia Cepacia ◽  
Iron Sulfide ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Dna Amplification ◽  
Bacterial Consortium ◽  
Universal Primers ◽  
Ribosomal Database Project ◽  
Sulfate Reducing ◽  
Gradient Gel Electrophoresis ◽  
Reducing Bacteria

The objective of this work was to identify one bacterial consortium adapted to the cultivation in the presence of trivalent arsenic (AsIII). Samples were cultured in flasks containing modified Postgate C liquid medium (selective for sulfate-reducing bacteria, SRB). Six different As concentrations were used: 0.5, 1.0, 2.0, 4.0, 8.0 and 16 mg l-1. The growth of sulfate reducing microorganisms was indirectly observed by the formation of an iron sulfide black precipitate and also by the Eh measures.100 ml aliquots of cultured media were centrifuged and stored at-20°C for DNA extraction by phenol/chloroform method. Universal primers 968F-GC 1392R (Bacteria domain) were used for 16S ribosomal DNA amplification. Microbial diversity was evaluated by denaturing gradient gel electrophoresis (DGGE). After DGGE analysis 7 different bands were selected, cut, sequenced and analyzed using the Ribosomal Database Project Release. Consortium microorganisms identified were: Pantoea agglomerans, Enterobacter sp, Citrobacter sp, Cupriavidusmetallidurans, Ralstonia sp, Burkholderia cepacia and Bacillus sp. Thus the microbial consortium here identified is a good candidate for bioremediation of arsenic contaminated areas and effluents.

scholarly journals Nested PCR-Denaturing Gradient Gel Electrophoresis Approach To Determine the Diversity of Sulfate-Reducing Bacteria in Complex Microbial Communities

2005 ◽  
Vol 71 (5) ◽  
pp. 2325-2330 ◽  
Author(s):  
Shabir A. Dar ◽  
J. Gijs Kuenen ◽  
Gerard Muyzer
Keyword(s):  
Microbial Communities ◽  
Nested Pcr ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Sulfate Reducing Bacteria ◽  
Comparative Sequence Analysis ◽  
Rrna Gene ◽  
Sulfate Reducing ◽  
Gradient Gel Electrophoresis ◽  
Reducing Bacteria

ABSTRACT Here, we describe a three-step nested-PCR-denaturing gradient gel electrophoresis (DGGE) strategy to detect sulfate-reducing bacteria (SRB) in complex microbial communities from industrial bioreactors. In the first step, the nearly complete 16S rRNA gene was amplified using bacterial primers. Subsequently, this product was used as a template in a second PCR with group-specific SRB primers. A third round of amplification was conducted to obtain fragments suitable for DGGE. The largest number of bands was observed in DGGE patterns of products obtained with primers specific for the Desulfovibrio-Desulfomicrobium group, indicating a large diversity of these SRBs. In addition, members of other phylogenetic SRB groups, i.e., Desulfotomaculum, Desulfobulbus, and Desulfococcus-Desulfonema-Desulfosarcina, were detected. Bands corresponding to Desulfobacterium and Desulfobacter were not detected in the bioreactor samples. Comparative sequence analysis of excised DGGE bands revealed the identity of the community members. The developed three-step PCR-DGGE strategy is a welcome tool for studying the diversity of sulfate-reducing bacteria.

scholarly journals Analysis of Bacterial Communities in the Rhizosphere of Chrysanthemum via Denaturing Gradient Gel Electrophoresis of PCR-Amplified 16S rRNA as Well as DNA Fragments Coding for 16S rRNA

2001 ◽  
Vol 67 (1) ◽  
pp. 172-178 ◽  
Author(s):  
Bernadette M. Duineveld ◽  
George A. Kowalchuk ◽  
Anneke Keijzer ◽  
Jan Dirk van Elsas ◽  
Johannes A. van Veen
Keyword(s):  
16S Rrna ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bulk Soil ◽  
Root Tip ◽  
Rt Pcr ◽  
Root Tips ◽  
Bacterial Populations ◽  
Gradient Gel Electrophoresis ◽  
Species Specific

ABSTRACT The effect of developing chrysanthemum roots on the presence and activity of bacterial populations in the rhizosphere was examined by using culture-independent methods. Nucleic acids were extracted from rhizosphere soil samples associated with the bases of roots or root tips of plants harvested at different stages of development. PCR and reverse transcriptase (RT) PCR were used to amplify 16S ribosomal DNA (rDNA) and 16S rRNA, respectively, and the products were subjected to denaturing gradient gel electrophoresis (DGGE). Prominent DGGE bands were excised and sequenced to gain insight into the identities of predominantly present (PCR) and predominantly active (RT-PCR) bacterial populations. The majority of DGGE band sequences were related to bacterial genera previously associated with the rhizosphere, such asPseudomonas, Comamonas, Variovorax, and Acetobacter, or typical of root-free soil environments, such as Bacillus and Arthrobacter. The PCR-DGGE patterns observed for bulk soil were somewhat more complex than those obtained from rhizosphere samples, and the latter contained a subset of the bands present in bulk soil. DGGE analysis of RT-PCR products detected a subset of bands visible in the rDNA-based analysis, indicating that some dominantly detected bacterial populations did not have high levels of metabolic activity. The sequences detected by the RT-PCR approach were, however, derived from a wide taxonomic range, suggesting that activity in the rhizosphere was not determined at broad taxonomic levels but rather was a strain- or species-specific phenomenon. Comparative analysis of DGGE profiles grouped all DNA-derived root tip samples together in a cluster, and within this cluster the root tip samples from young plants formed a separate subcluster. Comparison of rRNA-derived bacterial profiles showed no grouping of root tip samples versus root base samples. Rather, all profiles derived from 2-week-old plant rhizosphere soils grouped together regardless of location along the root.

scholarly journals Evaluations of Different Hypervariable Regions of Archaeal 16S rRNA Genes in Profiling of Methanogens by Archaea-Specific PCR and Denaturing Gradient Gel Electrophoresis

2007 ◽  
Vol 74 (3) ◽  
pp. 889-893 ◽  
Author(s):  
Zhongtang Yu ◽  
Rubén García-González ◽  
Floyd L. Schanbacher ◽  
Mark Morrison
Keyword(s):  
16S Rrna ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Specific Pcr ◽  
Pcr Products ◽  
Gradient Gel Electrophoresis ◽  
V Region

ABSTRACT Different hypervariable (V) regions of the archaeal 16S rRNA gene (rrs) were compared systematically to establish a preferred V region(s) for use in Archaea-specific PCR-denaturing gradient gel electrophoresis (DGGE). The PCR products of the V3 region produced the most informative DGGE profiles and permitted identification of common methanogens from rumen samples from sheep. This study also showed that different methanogens might be detected when different V regions are targeted by PCR-DGGE. Dietary fat appeared to transiently stimulate Methanosphaera stadtmanae but inhibit Methanobrevibacter sp. strain AbM4 in rumen samples.

scholarly journals Microbial Ecology of Anaerobic Digesters: The Key Players of Anaerobiosis

2014 ◽  
Vol 2014 ◽  
pp. 1-21 ◽  
Author(s):  
Fayyaz Ali Shah ◽  
Qaisar Mahmood ◽  
Mohammad Maroof Shah ◽  
Arshid Pervez ◽  
Saeed Ahmad Asad
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Methanogenic Bacteria ◽  
Molecular Techniques ◽  
Anaerobic Digesters ◽  
Sulfate Reducing ◽  
Anaerobic Microorganisms ◽  
Gradient Gel Electrophoresis ◽  
Reducing Bacteria ◽  
Complex Organic

Anaerobic digestion is the method of wastes treatment aimed at a reduction of their hazardous effects on the biosphere. The mutualistic behavior of various anaerobic microorganisms results in the decomposition of complex organic substances into simple, chemically stabilized compounds, mainly methane andCO2. The conversions of complex organic compounds toCH4andCO2are possible due to the cooperation of four different groups of microorganisms, that is, fermentative, syntrophic, acetogenic, and methanogenic bacteria. Microbes adopt various pathways to evade from the unfavorable conditions in the anaerobic digester like competition between sulfate reducing bacteria (SRB) and methane forming bacteria for the same substrate.Methanosarcinaare able to use both acetoclastic and hydrogenotrophic pathways for methane production. This review highlights the cellulosic microorganisms, structure of cellulose, inoculum to substrate ratio, and source of inoculum and its effect on methanogenesis. The molecular techniques such as DGGE (denaturing gradient gel electrophoresis) utilized for dynamic changes in microbial communities and FISH (fluorescentin situhybridization) that deal with taxonomy and interaction and distribution of tropic groups used are also discussed.

scholarly journals Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms

1998 ◽  
Vol 64 (10) ◽  
pp. 3731-3739 ◽  
Author(s):  
Cecilia M. Santegoeds ◽  
Timothy G. Ferdelman ◽  
Gerard Muyzer ◽  
Dirk de Beer
Keyword(s):  
Sulfate Reduction ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Sulfate Reducing Bacteria ◽  
Molecular Techniques ◽  
Bacterial Biofilm ◽  
Bacterial Populations ◽  
Sulfate Reducing ◽  
Combined Application ◽  
Biofilm Development ◽  
Reducing Bacteria

ABSTRACT We describe the combined application of microsensors and molecular techniques to investigate the development of sulfate reduction and of sulfate-reducing bacterial populations in an aerobic bacterial biofilm. Microsensor measurements for oxygen showed that anaerobic zones developed in the biofilm within 1 week and that oxygen was depleted in the top 200 to 400 μm during all stages of biofilm development. Sulfate reduction was first detected after 6 weeks of growth, although favorable conditions for growth of sulfate-reducing bacteria (SRB) were present from the first week. In situ hybridization with a 16S rRNA probe for SRB revealed that sulfate reducers were present in high numbers (approximately 108 SRB/ml) in all stages of development, both in the oxic and anoxic zones of the biofilm. Denaturing gradient gel electrophoresis (DGGE) showed that the genetic diversity of the microbial community increased during the development of the biofilm. Hybridization analysis of the DGGE profiles with taxon-specific oligonucleotide probes showed thatDesulfobulbus and Desulfovibrio were the main sulfate-reducing bacteria in all biofilm samples as well as in the bulk activated sludge. However, different Desulfobulbus andDesulfovibrio species were found in the 6th and 8th weeks of incubation, respectively, coinciding with the development of sulfate reduction. Our data indicate that not all SRB detected by molecular analysis were sulfidogenically active in the biofilm.

scholarly journals Sulfate-Reducing Bacteria and Their Activities in Cyanobacterial Mats of Solar Lake (Sinai, Egypt)

1998 ◽  
Vol 64 (8) ◽  
pp. 2943-2951 ◽  
Author(s):  
Andreas Teske ◽  
Niels B. Ramsing ◽  
Kirsten Habicht ◽  
Manabu Fukui ◽  
Jan Küver ◽  
...  
Keyword(s):  
Surface Layer ◽  
Sulfate Reduction ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Sulfate Reducing Bacteria ◽  
Cyanobacterial Mat ◽  
Sulfate Reducing ◽  
Gradient Gel Electrophoresis ◽  
Solar Lake ◽  
Sulfate Reduction Rates ◽  
Reducing Bacteria

ABSTRACT The sulfate-reducing bacteria within the surface layer of the hypersaline cyanobacterial mat of Solar Lake (Sinai, Egypt) were investigated with combined microbiological, molecular, and biogeochemical approaches. The diurnally oxic surface layer contained between 106 and 107 cultivable sulfate-reducing bacteria ml−1 and showed sulfate reduction rates between 1,000 and 2,200 nmol ml−1 day−1, both in the same range as and sometimes higher than those in anaerobic deeper mat layers. In the oxic surface layer and in the mat layers below, filamentous sulfate-reducing Desulfonema bacteria were found in variable densities of 104 to 106cells ml−1. A Desulfonema-related, diurnally migrating bacterium was detected with PCR and denaturing gradient gel electrophoresis within and below the oxic surface layer. Facultative aerobic respiration, filamentous morphology, motility, diurnal migration, and aggregate formation were the most conspicuous adaptations of Solar Lake sulfate-reducing bacteria to the mat matrix and to diurnal oxygen stress. A comparison of sulfate reduction rates within the mat and previously published photosynthesis rates showed that CO2 from sulfate reduction in the upper 5 mm accounted for 7 to 8% of the total photosynthetic CO2 demand of the mat.

Oral administration of kefiran exerts a bifidogenic effect on BALB/c mice intestinal microbiota

2016 ◽  
Vol 7 (2) ◽  
pp. 237-246 ◽  
Author(s):  
M.F. Hamet ◽  
M. Medrano ◽  
P.F. Pérez ◽  
A.G. Abraham
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Profile Analysis ◽  
In Situ Hybridisation ◽  
Gc Content ◽  
Principal Component ◽  
Distal Colon ◽  
Bacterial Populations ◽  
Pcr Products ◽  
Gradient Gel Electrophoresis

The activity of kefiran, the exopolysaccharide present in kefir grains, was evaluated on intestinal bacterial populations in BALB/c mice. Animals were orally administered with kefiran and Eubacteria, lactobacilli and bifidobacteria populations were monitored in faeces of mice at days 0, 2, 7, 14 and 21. Profiles obtained by Denaturing Gradient Gel Electrophoresis (DGGE) with primers for Eubacteria were compared by principal component analysis and clearly defined clusters, correlating with the time of kefiran consumption, were obtained. Furthermore, profile analysis of PCR products amplified with specific oligonucleotides for bifidobacteria showed an increment in the number of DGGE bands in the groups administered with kefiran. Fluorescent In Situ Hybridisation (FISH) with specific probes for bifidobacteria showed an increment of this population in faeces, in accordance to DGGE results. The bifidobacteria population was also studied on distal colon content after 0, 2 and 7 days of kefiran administration. Analysis of PCR products by DGGE with Eubacteria primers showed an increment in the number and intensity of bands with high GC content of mice administered with kefiran. Sequencing of DGGE bands confirmed that bifidobacteria were one of the bacterial populations modified by kefiran administration. DGGE profiles of PCR amplicons obtained by using Bifidobacterium or Lactobacillus specific primers confirmed that kefiran administration enhances bifidobacteria, however no changes were observed in Lactobacillus populations. The results of the analysis of bifidobacteria populations assessed on different sampling sites in a murine model support the use of this exopolysaccharide as a bifidogenic functional ingredient.

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