scholarly journals Anaerobic Microbial Communities in Lake Pavin, a Unique Meromictic Lake in France

2005 ◽  
Vol 71 (11) ◽  
pp. 7389-7400 ◽  
Author(s):  
Anne-C. Lehours ◽  
Corinne Bardot ◽  
Aurelie Thenot ◽  
Didier Debroas ◽  
Gerard Fonty
Keyword(s):  
16S Rrna ◽  
Microbial Communities ◽  
Restriction Fragment ◽  
Meromictic Lake ◽  
Heterogeneous Distribution ◽  
Sulfate Reducing ◽  
Microbial Group ◽  
Anoxic Layer ◽  
Lake Pavin ◽  
Reducing Bacteria

ABSTRACT The Bacteria and Archaea from the meromictic Lake Pavin were analyzed in samples collected along a vertical profile in the anoxic monimolimnion and were compared to those in samples from the oxic mixolimnion. Nine targeted 16S rRNA oligonucleotide probes were used to assess the distribution of Bacteria and Archaea and to investigate the in situ occurrence of sulfate-reducing bacteria and methane-producing Archaea involved in the terminal steps of the anaerobic degradation of organic material. The diversity of the complex microbial communities was assessed from the 16S rRNA polymorphisms present in terminal restriction fragment (TRF) depth patterns. The densities of the microbial community increased in the anoxic layer, and Archaea detected with probe ARCH915 represented the largest microbial group in the water column, with a mean Archaea/Eubacteria ratio of 1.5. Terminal restriction fragment length polymorphism (TRFLP) analysis revealed an elevated archaeal and bacterial phylotype richness in anoxic bottom-water samples. The structure of the Archaea community remained rather homogeneous, while TRFLP patterns for the eubacterial community revealed a heterogeneous distribution of eubacterial TRFs.

scholarly journals Whole-Cell versus Total RNA Extraction for Analysis of Microbial Community Structure with 16S rRNA-Targeted Oligonucleotide Probes in Salt Marsh Sediments

2000 ◽  
Vol 66 (7) ◽  
pp. 3037-3043 ◽  
Author(s):  
Marc E. Frischer ◽  
Jean M. Danforth ◽  
Michele A. Newton Healy ◽  
F. Michael Saunders
Keyword(s):  
Salt Marsh ◽  
16S Rrna ◽  
Microbial Communities ◽  
Rna Extraction ◽  
Oligonucleotide Probes ◽  
Whole Cell ◽  
Sulfate Reducing ◽  
Marsh Sediments ◽  
Salt Marsh Sediments ◽  
Reducing Bacteria

ABSTRACT rRNA-targeted oligonucleotide probes have become powerful tools for describing microbial communities, but their use in sediments remains difficult. Here we describe a simple technique involving homogenization, detergents, and dispersants that allows the quantitative extraction of cells from formalin-preserved salt marsh sediments. Resulting cell extracts are amenable to membrane blotting and hybridization protocols. Using this procedure, the efficiency of cell extraction was high (95.7% � 3.7% [mean � standard deviation]) relative to direct DAPI (4′,6′-diamidino-2-phenylindole) epifluorescence cell counts for a variety of salt marsh sediments. To test the hypothesis that cells were extracted without phylogenetic bias, the relative abundance (depth distribution) of five major divisions of the gram-negative mesophilic sulfate-reducing delta proteobacteria were determined in sediments maintained in a tidal mesocosm system. A suite of six 16S rRNA-targeted oligonucleotide probes were utilized. The apparent structure of sulfate-reducing bacteria communities determined from whole-cell and RNA extracts were consistent with each other (r 2 = 0.60), indicating that the whole-cell extraction and RNA extraction hybridization approaches for describing sediment microbial communities are equally robust. However, the variability associated with both methods was high and appeared to be a result of the natural heterogeneity of sediment microbial communities and methodological artifacts. The relative distribution of sulfate-reducing bacteria was similar to that observed in natural marsh systems, providing preliminary evidence that the mesocosm systems accurately simulate native marsh systems.

scholarly journals ANME-1 archaea drive methane accumulation and removal in estuarine sediments

2020 ◽  
Author(s):  
Richard Kevorkian ◽  
Sean Callahan ◽  
Rachel Winstead ◽  
Karen G. Lloyd
Keyword(s):  
16S Rrna ◽  
Sulfate Reducing Bacteria ◽  
Low Energy ◽  
Estuarine Sediments ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sulfate Reducing ◽  
Hydrogenotrophic Methanogenesis ◽  
Natural Settings ◽  
Reducing Bacteria

AbstractUncultured members of the Methanomicrobia called ANME-1 perform the anaerobic oxidation of methane (AOM) through a process that uses much of the methanogenic pathway. It is unknown whether ANME-1 obligately perform AOM, or whether some of them can perform methanogenesis when methanogenesis is exergonic. Most marine sediments lack advective transport of methane, so AOM occurs in the sulfate methane transition zone (SMTZ) where sulfate-reducing bacteria consume hydrogen produced by fermenters, making hydrogenotrophic methanogenesis exergonic in the reverse direction. When sulfate is depleted deeper in the sediments, hydrogen accumulates making hydrogenotrophic methanogenesis exergonic, and methane accumulates in the methane zone (MZ). In White Oak River estuarine sediments, we found that ANME-1 comprised 99.5% of 16S rRNA genes from amplicons and 100% of 16S rRNA genes from metagenomes of the Methanomicrobia in the SMTZ and 99.9% and 98.3%, respectively, in the MZ. Each of the 16 ANME-1 OTUs (97% similarity) had peaks in the SMTZ that coincided with peaks of putative sulfate-reducing bacteria Desulfatiglans sp. and SEEP-SRB1. In the MZ, ANME-1, but no putative sulfate-reducing bacteria or cultured methanogens, increased with depth. Using publicly available data, we found that ANME-1 was the only group expressing methanogenic genes during both net AOM and net methanogenesis in an enrichment. The commonly-held belief that ANME-1 perform AOM is based on the fact that they dominate natural settings and enrichments where net AOM is measured. We found that ANME-1 also dominate natural settings and enrichment where net methanogenesis is measured, so we conclude that ANME-1 perform methane production. Alternating between AOM and methanogenesis, either in a single ANME-1 cell or between different subclades with similar 16S rRNA sequences of ANME-1, may confer a competitive advantage, explaining the predominance of low-energy adapted ANME-1 in methanogenic sediments worldwide.Abstract ImportanceLife may operate differently at very low energy levels. Natural populations of microbes that make methane survive on some of the lowest energy yields of all life. From all available data, we infer that these microbes alternate between methane production and oxidation, depending on which process is energy-yielding in the environment. This means that much of the methane produced naturally in marine sediments occurs through an organism that is also capable of destroying it under different circumstances.

scholarly journals Production of biogas: relationship between methanogenic and sulfate-reducing microorganisms

2017 ◽  
Vol 12 (1) ◽  
pp. 82-91 ◽  
Author(s):  
Ivan Kushkevych ◽  
Monika Vítězová ◽  
Tomáš Vítěz ◽  
Milan Bartoš
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Biogas Production ◽  
Sulfate Reducing Bacteria ◽  
Quantitative Composition ◽  
Rrna Gene ◽  
Sulfate Reducing ◽  
Relationship Of ◽  
Reducing Bacteria

AbstractThe production of high-quality methane depends on many factors, including temperature, pH, substrate, composition and relationship of the microorganisms. The qualitative and quantitative composition of methanogenic and sulfate-reducing microorganisms and their relationship in the experimental bioreactors has never been studied. The aim of this research was to characterize, for the first time, the diversity of the methanogenic microorganisms and sulfate-reducing bacteria, and study their relationship and biogas production in experimental bioreactors. Amplification of 16S rRNA gene fragments was carried out. Purified amplicons were paired-end sequenced on an Illumina Mi-Seq platform. The dominant morphotypes of these microorganisms in the bioreactor were homologous (99%) by the sequences of 16S rRNA gene to theMethanosarcina,Thermogymnomonas,Methanoculleusgenera andArchaeondeposited in GenBank. Three dominant genera of sulfate-reducing bacteria,Desulfomicrobium,DesulfobulbusandDesulfovibrio, were detected in the bioreactor. The phylogenetic trees showing their genetic relationship were constructed. The diversity and number of the genera, production of methane, hydrogen sulfide and hydrogen in the bioreactor was investigated. This research is important for understanding the relationship between methanogenic microbial populations and other bacterial physiological groups, their substrate competition and, in turn, can be helpful for controlling methanogenesis in bioreactors.

scholarly journals Suspension Array Analysis of 16S rRNA from Fe- and SO42-Reducing Bacteria in Uranium-Contaminated Sediments Undergoing Bioremediation

2006 ◽  
Vol 72 (7) ◽  
pp. 4672-4687 ◽  
Author(s):  
Darrell P. Chandler ◽  
Ann E. Jarrell ◽  
Eric R. Roden ◽  
Julia Golova ◽  
Boris Chernov ◽  
...  
Keyword(s):  
16S Rrna ◽  
Total Rna ◽  
Iron Reducing Bacteria ◽  
Suspension Array ◽  
Sulfate Reducing ◽  
Subsurface Sediments ◽  
Reducing Bacteria ◽  
Bead Arrays ◽  
Microbiological Analyses

ABSTRACT A 16S rRNA-targeted tunable bead array was developed and used in a retrospective analysis of metal- and sulfate-reducing bacteria in contaminated subsurface sediments undergoing in situ U(VI) bioremediation. Total RNA was extracted from subsurface sediments and interrogated directly, without a PCR step. Bead array validation studies with total RNA derived from 24 isolates indicated that the behavior and response of the 16S rRNA-targeted oligonucleotide probes could not be predicted based on the primary nucleic acid sequence. Likewise, signal intensity (absolute or normalized) could not be used to assess the abundance of one organism (or rRNA) relative to the abundance of another organism (or rRNA). Nevertheless, the microbial community structure and dynamics through time and space and as measured by the rRNA-targeted bead array were consistent with previous data acquired at the site, where indigenous sulfate- and iron-reducing bacteria and near neighbors of Desulfotomaculum were the organisms that were most responsive to a change in injected acetate concentrations. Bead array data were best interpreted by analyzing the relative changes in the probe responses for spatially and temporally related samples and by considering only the response of one probe to itself in relation to a background (reference) environmental sample. By limiting the interpretation of the data in this manner and placing it in the context of supporting geochemical and microbiological analyses, we concluded that ecologically relevant and meaningful information can be derived from direct microarray analysis of rRNA in uncharacterized environmental samples, even with the current analytical uncertainty surrounding the behavior of individual probes on tunable bead arrays.

scholarly journals Sulfate-Reducing Bacteria in Tubes Constructed by the Marine Infaunal Polychaete Diopatra cuprea

2004 ◽  
Vol 70 (12) ◽  
pp. 7053-7065 ◽  
Author(s):  
George Y. Matsui ◽  
David B. Ringelberg ◽  
Charles R. Lovell
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Phospholipid Fatty Acid ◽  
Rrna Gene ◽  
Sandy Sediment ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Sulfate Reducing

ABSTRACT Marine infaunal burrows and tubes greatly enhance solute transport between sediments and the overlying water column and are sites of elevated microbial activity. Biotic and abiotic controls of the compositions and activities of burrow and tube microbial communities are poorly understood. The microbial communities in tubes of the marine infaunal polychaete Diopatria cuprea collected from two different sediment habitats were examined. The bacterial communities in the tubes from a sandy sediment differed from those in the tubes from a muddy sediment. The difference in community structure also extended to the sulfate-reducing bacterial (SRB) assemblage, although it was not as pronounced for this functional group of species. PCR-amplified 16S rRNA gene sequences recovered from Diopatra tube SRB by clonal library construction and screening were all related to the family Desulfobacteriaceae. This finding was supported by phospholipid fatty acid analysis and by hybridization of 16S rRNA probes specific for members of the genera Desulfosarcina, Desulfobacter, Desulfobacterium, Desulfobotulus, Desulfococcus, and Desulfovibrio and some members of the genera Desulfomonas, Desulfuromonas, and Desulfomicrobium with 16S rRNA gene sequences resolved by denaturing gradient gel electrophoresis. Two of six SRB clones from the clone library were not detected in tubes from the sandy sediment. The habitat in which the D. cuprea tubes were constructed had a strong influence on the tube bacterial community as a whole, as well as on the SRB assemblage.

scholarly journals Desulfoplanes formicivorans gen. nov., sp. nov., a novel sulfate-reducing bacterium isolated from a blackish meromictic lake, and emended description of the family Desulfomicrobiaceae

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1902-1907 ◽  
Author(s):  
Miho Watanabe ◽  
Hisaya Kojima ◽  
Manabu Fukui
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Meromictic Lake ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
The Novel ◽  
Sulfate Reducing ◽  
The Family ◽  
The 16S Rrna Gene

A novel sulfate-reducing bacterium, designated strain Pf12BT, was isolated from sediment of meromictic Lake Harutori in Japan. Cells were vibroid (1.0 × 3.0–4.0 μm), motile and Gram-stain-negative. For growth, the optimum pH was 7.0–7.5 and the optimum temperature was 42–45 °C. Strain Pf12BT used sulfate, thiosulfate and sulfite as electron acceptors. The G+C content of the genomic DNA was 55.4 mol%. Major cellular fatty acids were C16 : 0 and C18 : 0. The strain was desulfoviridin-positive. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belonged to the order Desulfovibrionales in the class Deltaproteobacteria. The closest relative was Desulfomicrobium baculatum DSM 4028T with which it shared 91  % 16S rRNA gene sequence similarity. On the basis of phylogenetic and phenotypic characterization, a novel species of a new genus belonging to the family Desulfomicrobiaceae is proposed, Desulfoplanes formicivorans gen. nov., sp. nov. The type strain of Desulfoplanes formicivorans is Pf12BT ( = NBRC 110391T = DSM 28890T).

scholarly journals Improved dsrA-Based Terminal Restriction Fragment Length Polymorphism Analysis of Sulfate-Reducing Bacteria

2010 ◽  
Vol 76 (15) ◽  
pp. 5308-5311 ◽  
Author(s):  
Daniel Santillano ◽  
Antje Boetius ◽  
Alban Ramette
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Sulfate Reducing Bacteria ◽  
Polymorphism Analysis ◽  
Sulfate Reducing ◽  
Reducing Bacteria ◽  
Restriction Fragment Length

ABSTRACT To better describe the community structure of sulfate-reducing bacteria in environmental systems, we compared several dissimilatory sulfite reductase (dsr) primer sets for terminal restriction fragment length polymorphism application. A new reverse primer that increased allelic diversity estimates up to 5-fold was applied to hydrocarbon seep samples to examine the relationship between guild activity and diversity.

scholarly journals In Situ Analysis of Sulfate-Reducing Bacteria Related to Desulfocapsa thiozymogenes in the Chemocline of Meromictic Lake Cadagno (Switzerland)

2000 ◽  
Vol 66 (2) ◽  
pp. 820-824 ◽  
Author(s):  
Mauro Tonolla ◽  
Antonella Demarta ◽  
Sandro Peduzzi ◽  
Dittmar Hahn ◽  
Raffaele Peduzzi
Keyword(s):  
Sulfate Reducing Bacteria ◽  
Comparative Sequence Analysis ◽  
Potential Interaction ◽  
Meromictic Lake ◽  
Rrna Gene ◽  
Sulfate Reducing ◽  
Sulfur Bacteria ◽  
The Family ◽  
Reducing Bacteria

ABSTRACT Comparative sequence analysis of a 16S rRNA gene clone library from the chemocline of the meromictic Lake Cadagno (Switzerland) retrieved two clusters of sequences resembling sulfate-reducing bacteria within the family Desulfovibrionaceae. In situ hybridization showed that, similar to sulfate-reducing bacteria of the familyDesulfobacteriaceae, bacteria of one cluster with similarity values to the closest cultured relatives of between 92.6 and 93.1% resembled free cells or cells loosely attached to other cells or debris. Bacteria of the second cluster closely related toDesulfocapsa thiozymogenes DSM7269 with similarity values between 97.9 and 98.4% were generally associated with aggregates of different small-celled phototrophic sulfur bacteria, suggesting a potential interaction between the two groups of bacteria.

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