Endogenous isolation of replicon probes for assessing plasmid ecology of marine sediment microbial communities

Cook, M. A., Osborn, A. M., Bettandorff, J. and Sobecky, P. A. (2001) Endogenous isolation of replicon probes for assessing plasmid ecology of marine sediment microbial communities. Microbiology, 147 (8). pp. 2089-2101. ISSN 1350-0872

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Item Type:Article
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Six functional replication origins (repGA14, repGA33, repGA70, repSD41, repSD164 and repSD172), obtained from endogenously isolated, broad-host-range (BHR) marine plasmids ranging in size from 5 to 60 kb, were used to determine plasmid occurrence in three coastal marine sediment sites (in California, Georgia and South Carolina, USA). The plasmid-specific replicons were isolated from plasmid-bearing marine sediment bacteria belonging to the α and γ subclasses of the Proteobacteria. The plasmid sources of the endogenous replicons were considered to be cryptic due to a lack of identifiable phenotypic traits. The putative Rep proteins from a number of these replicons showed similarity to replicons of two recognized families: RCR group III (repSD164) and the FIA family of theta group A (repSD41, repSD121, repGA33 and repGA14). Plasmids isolated from marine bacteria belonging to the genera Pseudoalteromonas, Shewanella and Vibrio cultivated from geographically different coastal sites exhibited homology to two of the marine plasmid replicons, repSD41 and repGA70, obtained from a Vibrio sp. The repGA33 plasmid origin, obtained from a Shewanella sp. isolated from coastal Georgia, was detected in 7 of the Georgia marine sediment Shewanella sp. isolates. Microbial community DNA extracted from marine sediments was also screened for the presence of the plasmid replication sequences. Community DNA samples amplified by PCR yielded a positive signal for the repSD172 and repGA14 replication sequences. The replication origin of BHR plasmid RK2 (IncP) was also detected in marine Vibrio sp. and microbial community DNA extracted from the three coastal sites. These findings provide molecular evidence that marine sediment bacteria harbour an untapped population of BHR plasmids.

Keywords:bacterial DNA, helicase, article, controlled study, ecology, gene replication, geographic distribution, Gram negative bacterium, host, marine environment, microbiology, molecular biology, nonhuman, nucleotide sequence, phenotype, plasmid, polymerase chain reaction, population, priority journal, Pseudoalteromonas, replicon, screening, seashore, sediment, sequence homology, Shewanella, United States, Vibrio, Alphaproteobacteria, Amino Acid Sequence, Cloning, Molecular, DNA Helicases, DNA Probes, DNA, Bacterial, DNA-Binding Proteins, Ecosystem, Gammaproteobacteria, Geologic Sediments, Molecular Sequence Data, Plasmids, Replication Origin, Seawater, Trans-Activators, Bacteria (microorganisms), Negibacteria, Prokaryota, Proteobacteria, Shewanella sp., Vibrio, Vibrio sp.
Subjects:C Biological Sciences > C180 Ecology
C Biological Sciences > C500 Microbiology
Divisions:College of Science > School of Life Sciences
ID Code:8966
Deposited On:22 Apr 2013 12:32

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