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      Comparison of Microbial Community Compositions of Injection and Production Well Samples in a Long-Term Water-Flooded Petroleum Reservoir

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          Abstract

          Water flooding plays an important role in recovering oil from depleted petroleum reservoirs. Exactly how the microbial communities of production wells are affected by microorganisms introduced with injected water has previously not been adequately studied. Using denaturing gradient gel electrophoresis (DGGE) approach and 16S rRNA gene clone library analysis, the comparison of microbial communities is carried out between one injection water and two production waters collected from a working block of the water-flooded Gudao petroleum reservoir located in the Yellow River Delta. DGGE fingerprints showed that the similarities of the bacterial communities between the injection water and production waters were lower than between the two production waters. It was also observed that the archaeal composition among these three samples showed no significant difference. Analysis of the 16S rRNA gene clone libraries showed that the dominant groups within the injection water were Betaproteobacteria, Gammaproteobacteria and Methanomicrobia, while the dominant groups in the production waters were Gammaproteobacteria and Methanobacteria. Only 2 out of 54 bacterial operational taxonomic units (OTUs) and 5 out of 17 archaeal OTUs in the injection water were detected in the production waters, indicating that most of the microorganisms introduced by the injection water may not survive to be detected in the production waters. Additionally, there were 55.6% and 82.6% unique OTUs in the two production waters respectively, suggesting that each production well has its specific microbial composition, despite both wells being flooded with the same injection water.

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          Most cited references44

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          Biological activity in the deep subsurface and the origin of heavy oil.

          At temperatures up to about 80 degrees C, petroleum in subsurface reservoirs is often biologically degraded, over geological timescales, by microorganisms that destroy hydrocarbons and other components to produce altered, denser 'heavy oils'. This temperature threshold for hydrocarbon biodegradation might represent the maximum temperature boundary for life in the deep nutrient-depleted Earth. Most of the world's oil was biodegraded under anaerobic conditions, with methane, a valuable commodity, often being a major by-product, which suggests alternative approaches to recovering the world's vast heavy oil resource that otherwise will remain largely unproduced.
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            Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'.

            Although it has been recognized that PCR amplification of mixed templates may generate sequence artifacts, the mechanisms of their formation, frequency and potential elimination have not been fully elucidated. Here evidence is presented for heteroduplexes as a major source of artifacts in mixed-template PCR. Nearly equal proportions of homoduplexes and heteroduplexes were observed after co-amplifying 16S rDNA from three bacterial genomes and analyzing products by constant denaturing capillary electrophoresis (CDCE). Heteroduplexes became increasingly prevalent as primers became limiting and/or template diversity was increased. A model exploring the fate of cloned heteroduplexes during MutHLS-mediated mismatch repair in the Escherichia coli host demonstrates that the diversity of artifactual sequences increases exponentially with the number of both variable nucleotides and of original sequence variants. Our model illustrates how minimization of heteroduplex molecules before cloning may reduce artificial genetic diversity detected during sequence analysis by clone screening. Thus, we developed a method to eliminate heteroduplexes from mixed-template PCR products by subjecting them to 'reconditioning PCR', a low cycle number re-amplification of a 10-fold diluted mixed-template PCR product. This simple modification to the protocol may ensure that sequence richness encountered in clone libraries more closely reflects genetic diversity in the original sample.
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              Bacterial metabolism of long-chain n-alkanes.

              Degradation of alkanes is a widespread phenomenon in nature, and numerous microorganisms, both prokaryotic and eukaryotic, capable of utilizing these substrates as a carbon and energy source have been isolated and characterized. In this review, we summarize recent advances in the understanding of bacterial metabolism of long-chain n-alkanes. Bacterial strategies for accessing these highly hydrophobic substrates are presented, along with systems for their enzymatic degradation and conversion into products of potential industrial value. We further summarize the current knowledge on the regulation of bacterial long-chain n-alkane metabolism and survey progress in understanding bacterial pathways for utilization of n-alkanes under anaerobic conditions.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2011
                15 August 2011
                : 6
                : 8
                : e23258
                Affiliations
                [1 ]State Key Laboratory of Microbial Metabolism and School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
                [2 ]Institute of Oil Recovery Research, Shengli Oil Field Ltd., Dongying, China
                Université Paris Sud, France
                Author notes

                Conceived and designed the experiments: XZ LZ SG. Performed the experiments: HR WR GG. Analyzed the data: HR XZ. Contributed reagents/materials/analysis tools: ZS. Wrote the paper: HR XZ LZ.

                [¤]

                Current address: University of Groningen, Groningen, The Netherlands

                Article
                PONE-D-11-05728
                10.1371/journal.pone.0023258
                3156122
                21858049
                32658ebe-cf2e-41ff-9c80-e87a4f8e4e98
                Ren et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
                History
                : 29 March 2011
                : 10 July 2011
                Page count
                Pages: 9
                Categories
                Research Article
                Biology
                Ecology
                Community Ecology
                Community Structure
                Microbial Ecology
                Microbiology
                Archaeans
                Archaeal Biochemistry
                Applied Microbiology
                Bacteriology
                Microbial Ecology
                Chemistry
                Organic Chemistry
                Organic Materials
                Petroleum Products
                Earth Sciences
                Energy and Power
                Fossil Fuels
                Environmental Sciences
                Environmental Engineering
                Geochemistry
                Biogeochemistry
                Geology
                Petrology
                Engineering
                Geological Engineering

                Uncategorized
                Uncategorized

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