Genetic diversity within mer genes directly amplified from communities of noncultivated soil and sediment bacteria

Bruce, K. D. and Osborn, A. M. and Pearson, A. J. and Strike, P. and Ritchie, D. A. (1995) Genetic diversity within mer genes directly amplified from communities of noncultivated soil and sediment bacteria. Molecular Ecology, 4 (5). pp. 605-612. ISSN 0962-1083

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Item Type:Article
Item Status:Live Archive

Abstract

Individual merRT delta P regions were amplified from DNA directly isolated from soil and sediment samples using consensus primers derived from the conserved mer sequences of Tn501, Tn21 and pMER419. Soil and sediment samples were taken from four sites in the British Isles; one 'pristine' (SB) and three polluted (SO, SE, T2) with respect to mercury. The sizes of the PCR products amplified (approximately 1 kb) were consistent with their generation from mer determinants related to the archetypal elements found in Gram negative bacteria. Forty-five individual clones of sequences obtained from these four sites were isolated which hybridized (> 70 homology) to a merRT delta P probe from Tn501. The diversity of these amplified mer genes was analysed using Restriction Fragment Length Polymorphism (RFLP) profiling. Fourteen RFLP classes were distinguished, 12 of which proved to be novel and only two of which had been identified in an earlier study of 40 Gram negative mercury resistant bacteria cultured from the same four sites. UPGMA analysis was used to examine the relationships between the 22 classes of determinant identified. The T2 site, which has the longest history of mercury exposure, was found to have the greatest level of diversity in terms of numbers of classes of determinant, while the SO site, which had the highest mercury levels showed relatively low variation. Variation of mer genes within and between the sequences from cultivated bacteria and from total bacterial DNA shows clearly that analysing only sequences from cultivated organisms results in a gross underestimation of genetic variation.

Additional Information:Pubmed ID: 7582168
Keywords:bacterial DNA, bacterial protein, mercury, primer DNA, article, bacterial gene, bacterium, comparative study, consensus sequence, genetic variability, genetics, isolation and purification, microbiology, molecular cloning, molecular genetics, nucleotide sequence, oligonucleotide probe, phylogeny, plasmid, restriction fragment length polymorphism, soil pollutant, transposon, water pollution, Bacteria, Bacterial Proteins, Base Sequence, Cloning, Molecular, Conserved Sequence, DNA Primers, DNA Transposable Elements, DNA, Bacterial, Genes, Bacterial, Molecular Sequence Data, Oligonucleotide Probes, Plasmids, Polymorphism, Restriction Fragment Length, Soil Microbiology, Soil Pollutants, Support, Non-U.S. Gov't, Variation (Genetics), Water Microbiology, Water Pollution, Chemical
Subjects:C Biological Sciences > C180 Ecology
C Biological Sciences > C500 Microbiology
Divisions:College of Science > School of Life Sciences
ID Code:8976
Deposited On:13 May 2013 09:39

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