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Microbial Community Analysis (microbial + community_analysis)
Selected AbstractsImpact of animal waste lagoon effluents on chlorpyrifos degradation in soilsENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 12 2000Xinjiang Huang Abstract Animal-derived lagoon effluents are a good source of inorganic nutrients and organic matter; however, they may impact the degradation and transport of soil-applied pesticides. The degradation of chlorpyrifos in poultry-, swine-, and cow-derived effluents and effluent-soil matrices were studied using batch and column incubation studies. Chlorpyrifos was degraded by aerobic microbial processes in animal-derived lagoon effluents. Microbial community analysis by denaturing gradient gel electrophoresis of polymerase chain reaction-amplified 16S ribosomal ribonucleic acid genes showed that a single band became dominant in effluent during chlorpyrifos degradation. In soils, both biotic and abiotic degradation contributed significantly to the overall dissipation of chlorpyrifos. Large differences in degradation rates were observed between soils, with the fastest rate observed in soil with higher pH and cation-exchange capacity. Effluents appeared to have only a minor effect on chlorpyrifos degradation in soils, although effluent-induced increases in soil-solution pH over time may enhance hydrolysis by a few percent in low-pH soils. Soil properties, not effluent properties, appear to control chlorpyrifos degradation under laboratory conditions; however, the impact on changes in soil properties and microbial ecology with long-term effluent irrigation warrants further investigation. [source] Microbial community analysis at crude oil-contaminated soils targeting the 16S ribosomal RNA, xylM, C23O, and bcr genesJOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2009Y. Higashioka Abstract Aims:, The analyses targeting multiple functional genes were performed on the samples of crude oil-contaminated soil, to investigate community structures of organisms involved in monoaromatic hydrocarbon degradation. Methods and Results:, Environmental samples were obtained from two sites that were contaminated with different components of crude oil. The analysis on 16S rRNA gene revealed that bacterial community structures were clearly different between the two sites. The cloning analyses were performed by using primers specific for the catabolic genes involved in the aerobic or anaerobic degradation of monoaromatic hydrocarbons, i.e. xylene monooxygenase (xylM), catechol 2,3-dioxygenase (C23O), and benzoyl-CoA reductase (bcr) genes. From the result of xylM gene, it was suggested that there are lineages specific to the respective sites, reflecting the differences of sampling sites. In the analysis of the C23O gene, the results obtained with two primer sets were distinct from each other. A comparison of these suggested that catabolic types of major bacteria carrying this gene were different between the two sites. As for the bcr gene, no amplicon was obtained from one sample. Phylogenetic analysis revealed that the sequences obtained from the other sample were distinct from the known sequences. Conclusions:, The differences between the two sites were demonstrated in the analyses of all tested genes. As for aerobic cleavage of the aromatic ring, it was also suggested that analysis using two primer sets provide more detailed information about microbial communities in the contaminated site. Significance and Impact of the Study:, The present study demonstrated that analysis targeting multiple functional genes as molecular markers is practical to examine microbial community in crude oil-contaminated environments. [source] Hydrolysis and microbial community analyses in two-stage anaerobic digestion of energy cropsJOURNAL OF APPLIED MICROBIOLOGY, Issue 3 2007D.G. Cirne Abstract Aims:, The roles of the diverse populations of micro-organisms responsible for biodegradation of organic matter to form methane and carbon dioxide are rudimentarily understood. To expand the knowledge on links between microbial communities and the rate limiting, hydrolytic stage of two-stage biogas production from energy crops, this study was performed. Methods and Results:, The process performance and microbial communities (as determined by fluorescence in situ hybridization) in two separate two-stage batch digestions of sugar beets and grass/clover were studied. The microbial populations developed in the hydrolytic stage of anaerobic digestion of beets and grass/clover showed very few similarities, despite that the hydrolysis dynamics were similar. In both substrates, the solubilization of organic material was rapid for the first 10 days and accompanied by a build-up of volatile fatty acids (VFAs) and lactate. Between days 10 and 15, VFA and lactate concentrations decreased, as did the solubilization rates. For both substrates, Archaea started to appear in the hydrolytic stage between days 10 and 15, and the fraction of Bacteria decreased. The major bacterial group detected in the leachate fraction for beets was Alphaproteobacteria, whereas for grass/clover it was Firmicutes. The number of cells that bound to probes specifically targeting bacteria with cellulolytic activity was higher in the digestion of grass than in the digestion of beet. Conclusions:, This study allowed the identification of the general bacterial groups involved, and the identification of a clear shift in the microbial population when hydrolysis rate became limiting for each of the substrates investigated. Significance and Impact of the Study:, The findings from this study could be considered as a first step towards the development of strategies to stimulate hydrolysis further and ultimately increasing the methane production rates and yields from reactor-based digestion of these substrates. [source] Use of rpoB and 16S rRNA genes to analyse bacterial diversity of a tropical soil using PCR and DGGELETTERS IN APPLIED MICROBIOLOGY, Issue 4 2002R.S. Peixoto Aim: To evaluate the rpoB gene as a biomarker for PCR-DGGE microbial analyses using soil DNA from the Cerrado, Brazil. Methods: DNA extraction from soil was followed by Polymerase Chain Reaction (PCR) amplification of rpoB and 16S rRNA genes. PCR products were compared by Denaturing Gradient Gel Electrophoresis (DGGE) to compare gene/community profiles. Results: The rpoB DGGE profiles comprised fewer bands than the 16S rDNA profiles and were easier to delineate and therefore to analyse. Comparison of the community profiles revealed that the methods were complementary. Conclusions, Significance and Impact of the Study: The gene for the beta subunit of the RNA polymerase, rpoB, is a single copy gene unlike 16S rDNA. Multiple copies of 16S rRNA genes in bacterial genomes complicate diversity assessments made from DGGE profiles. Using the rpoB gene offers a better alternative to the commonly used 16S rRNA gene for microbial community analyses based on DGGE. [source] Quantification of microbial communities in near-surface and deeply buried marine sediments on the Peru continental margin using real-time PCRENVIRONMENTAL MICROBIOLOGY, Issue 7 2006Axel Schippers Summary Deeply buried marine sediments harbour a large fraction of all prokaryotes on Earth but it is still unknown which phylogenetic and physiological microbial groups dominate the deep biosphere. In this study real-time PCR allowed a comparative quantitative microbial community analysis in near-surface and deeply buried marine sediments from the Peru continental margin. The 16S rRNA gene copy numbers of prokaryotes and Bacteria were almost identical with a maximum of 108,1010 copies cm,3 in the near-surface sediments. Archaea exhibited one to three orders of magnitude lower 16S rRNA gene copy numbers. The 18S rRNA gene of Eukarya was always at least three orders of magnitude less abundant than the 16S rRNA gene of prokaryotes. The 16S rRNA gene of the Fe(III)- and Mn(IV)-reducing bacterial family Geobacteraceae and the dissimilatory (bi)sulfite reductase gene (dsrA) of sulfate-reducing prokaryotes were abundant with 106,108 copies cm,3 in near-surface sediments but showed lower numbers and an irregular distribution in the deep sediments. The copy numbers of all genes decreased with sediment depth exponentially. The depth gradients were steeper for the gene copy numbers than for numbers of total prokaryotes (acridine orange direct counts), which reflects the ongoing degradation of the high-molecular-weight DNA with sediment age and depth. The occurrence of eukaryotic DNA also suggests DNA preservation in the deeply buried sediments. [source] | ||||||||||