Indigenous microbial communities in Albertan sediments are capable of anaerobic benzene biodegradation under methanogenic, sulfate‐reducing, nitrate‐reducing, and iron‐reducing redox conditions

2020 ◽  
Author(s):  
Korris Lee ◽  
Ania Ulrich
Keyword(s):  
Microbial Communities ◽  
Redox Conditions ◽  
Sulfate Reducing

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.

Molecular assessment of the sensitivity of sulfate-reducing microbial communities remediating mine drainage to aerobic stress

2013 ◽  
Vol 47 (14) ◽  
pp. 5316-5325 ◽  
Author(s):  
Emilie Lefèvre ◽  
Luciana P. Pereyra ◽  
Sage R. Hiibel ◽  
Elizabeth M. Perrault ◽  
Susan K. De Long ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Mine Drainage ◽  
Sulfate Reducing ◽  
Molecular Assessment

scholarly journals Particle-associated and free-living microbial assemblages are distinct in a permanently redox-stratified freshwater lake

2021 ◽  
Author(s):  
Ashley B. Cohen ◽  
Vanja Klepac-Ceraj ◽  
Kristen Butler ◽  
Felix Weber ◽  
Arkadiy I. Garber ◽  
...  
Keyword(s):  
Organic Carbon ◽  
Seasonal Variability ◽  
Inorganic Nitrogen ◽  
Niche Partitioning ◽  
Green Sulfur Bacteria ◽  
Redox Conditions ◽  
Substrate Availability ◽  
Free Living ◽  
Sulfate Reducing ◽  
Green Lake

Microbial assemblages associated with biogenic particles are phylogenetically distinct from free-living counterparts, yet biogeochemically coupled. Compositions may vary with organic carbon and inorganic substrate availability and with redox conditions, which determine reductant and oxidant availability. To explore microbial assemblage compositional responses to steep oxygen and redox gradients and seasonal variability in particle and substrate availability, we analyzed taxonomic compositions of particle-associated (PA) and free-living (FL) bacteria and archaea in permanently redox-stratified Fayetteville Green Lake. PA and FL assemblages (> 2.7 μm and 0.2-2.7 μm) were surveyed at the peak (July) and end (October) of concurrent cyanobacteria, purple and green sulfur bacteria blooms that result in substantial vertical fluxes of particulate organic carbon. Assemblage compositions varied significantly among redox conditions and size fractions (PA or FL). Temporal differences were only apparent among samples from the mixolimnion and oxycline, coinciding with seasonal hydrographic changes. PA assemblages of the mixolimnion and oxycline shifted from aerobic heterotrophs in July to fermenters, iron-reducers, and denitrifiers in October, likely reflecting seasonal variability in photoautotroph biomass and inorganic nitrogen. Within a light-scattering layer spanning the lower oxycline and upper monimolimnion, photoautotrophs were more abundant in July than in October, when Desulfocapsa, a sulfate-reducing and sulfur-disproportionating bacterium, and Chlorophyte chloroplasts were abundant in PA assemblages. In this layer, microbial activity and cell concentrations were also highest. Below, the most abundant resident taxa were sulfate-reducing bacteria and anaerobic respirers. Results suggest PA and FL assemblage niche partitioning interconnects multiple elemental cycles that involve particulate and dissolved phases.

Comparative Analysis of the Sulfate-Reducing Performance and Microbial Colonisation of Three Continuous Reactor Configurations with Varying Degrees of Biomass Retention

2017 ◽  
Vol 262 ◽  
pp. 638-642
Author(s):  
Tomas Hessler ◽  
Tynan Marais ◽  
Robert J. Huddy ◽  
Robert van Hille ◽  
Susan T.L. Harrison
Keyword(s):  
Microbial Communities ◽  
Sulfate Reduction ◽  
Retention Time ◽  
Packed Bed Reactor ◽  
Continuous Reactor ◽  
Hydraulic Residence Time ◽  
Acid Rock ◽  
Sulfate Reducing ◽  
Biomass Retention ◽  
Biological Sulfate Reduction

Biological sulfate reduction represents an alternative and sustainable option to reduce the high sulfate load, precipitate heavy metals and neutralise the acidity associated with acid rock drainage (ARD). Sulfate-reducing enrichment cultures have been developed on simple and complex electron donors from several environmental samples and used to inoculate three reactor configurations, namely a continuous stirred tank bioreactor, up-flow anaerobic packed bed reactor and a linear flow channel reactor, with varying degrees of biomass retention provided by carbon microfibres and polyurethane foam. These matrices are included to enhance microbial attachment and colonisation, allowing for the decoupling of hydraulic retention time and biomass retention time. The bioreactor systems are operated under increasingly stringent conditions through the reduction in the hydraulic residence time. The biological sulfate reduction performance and the biomass concentration of planktonic, matrix-attached and matrix-associated communities are routinely monitored. This investigation makes use of biomass quantification of the planktonic community and, following detachment, the matrix-associated community to investigate the resultant microbial communities in these reactor systems. Evaluation of these mixed microbial communities, and their link to process performance, provides an opportunity to impact the design and operation of pilot- and industrial-scale bioprocesses.

34S/32S fractionation by sulfate-reducing microbial communities in estuarine sediments

2011 ◽  
Vol 75 (14) ◽  
pp. 3903-3914 ◽  
Author(s):  
Marjolijn C. Stam ◽  
Paul R.D. Mason ◽  
Anniet M. Laverman ◽  
Céline Pallud ◽  
Philippe Van Cappellen
Keyword(s):  
Microbial Communities ◽  
Estuarine Sediments ◽  
Sulfate Reducing

Use of ribosomal RNA-based molecular probes for characterization of complex microbial communities in anaerobic biofilms

1995 ◽  
Vol 31 (1) ◽  
pp. 261-272 ◽  
Author(s):  
Lutgarde Raskin ◽  
Rudolf I. Amann ◽  
Lars K. Poulsen ◽  
Bruce E. Rittmann ◽  
David A. Stahl
Keyword(s):  
Microbial Communities ◽  
Ribosomal Rna ◽  
Fixed Bed ◽  
Molecular Probes ◽  
Biofilm Reactor ◽  
Sulfate Reducing ◽  
Biofilm Reactors ◽  
Functional Behavior ◽  
Long Term Study

The use of ribosomal RNA (rRNA) probe technology for the characterization of complex microbial communities is reviewed and illustrated by discussing the results of a long-term study of four anaerobic fixed-bed biofilm reactors. Two distinct approaches were used to characterize the microbial community structure in these biofilm reactors. The first used a collection of phylogenetically defined oligonucleotide rRNA probes for methanogens and sulfate-reducing bacteria (SRB) to quantify their populations. Population abundance was linked to the functional behavior of the biofilm reactor community by determining the effluent concentrations of the substrates, intermediates, and final products of microbial metabolism. This analysis indicated that the presence of SRB (especially Desulfovibrio-species) was not dependent upon the presence of sulfate. Methanobacteriales-species were the major competitors for hydrogen with these SRB in the absence of sulfate. The second approach involved selective amplification, cloning, sequencing, and whole cell hybridization to identify, visualize, and isolate a biofilm community member (strain PT-2). Subsequently, it was determined that the growth rate of strain PT-2 was significantly higher in young biofilms than in established biofilms.

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.

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