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Article: Evaluation of terminal-restriction fragment length polymorphism analysis in contrasting marine environments

TitleEvaluation of terminal-restriction fragment length polymorphism analysis in contrasting marine environments
Authors
Issue Date2008
PublisherWiley-Blackwell Publishing Ltd.. The Journal's web site is located at http://www.wiley.com/bw/journal.asp?ref=0168-6496
Citation
Fems Microbiology Ecology, 2008, v. 65 n. 1, p. 169-178 How to Cite?
AbstractTerminal-restriction fragment length polymorphism (T-RFLP) analysis is widely used in microbial ecology studies. In the present study, T-RFLP analysis of PCR products digested by five restriction enzymes (AluI, HaeIII, MspI, Sau3AI and TaqI) was applied for 20 samples from three contrasting coastal environments to assess the biases associated with the choice of enzyme digestion and T-RF analysis. The five enzyme digestions produced highly variable species richness (in terms of number of T-RFs). Analysis of peak areas with a threshold of 0.5% of the total peak area, which recovered 92-96% of the total peak area, revealed different diversity indexes from the five enzyme digestions. Multidimensional scaling, based on matrices that were generated by scoring peak presence/absence and area, revealed similar bacterial community structure patterns among the 20 samples, regardless of the choice of restriction enzymes. Our results strongly argue that the choice of different digestion enzymes in the T-RFLP technique generated valid and consistent bacterial community structures but highly variable species richness and diversity indices. The biases associated with the choice of digestion enzymes needs to be evaluated carefully or at least to be addressed when using T-RFLP analysis. © 2008 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.
Persistent Identifierhttp://hdl.handle.net/10722/179059
ISSN
2015 Impact Factor: 3.53
2015 SCImago Journal Rankings: 1.687
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorZhang, Ren_US
dc.contributor.authorThiyagarajan, Ven_US
dc.contributor.authorQian, PYen_US
dc.date.accessioned2012-12-19T09:51:42Z-
dc.date.available2012-12-19T09:51:42Z-
dc.date.issued2008en_US
dc.identifier.citationFems Microbiology Ecology, 2008, v. 65 n. 1, p. 169-178en_US
dc.identifier.issn0168-6496en_US
dc.identifier.urihttp://hdl.handle.net/10722/179059-
dc.description.abstractTerminal-restriction fragment length polymorphism (T-RFLP) analysis is widely used in microbial ecology studies. In the present study, T-RFLP analysis of PCR products digested by five restriction enzymes (AluI, HaeIII, MspI, Sau3AI and TaqI) was applied for 20 samples from three contrasting coastal environments to assess the biases associated with the choice of enzyme digestion and T-RF analysis. The five enzyme digestions produced highly variable species richness (in terms of number of T-RFs). Analysis of peak areas with a threshold of 0.5% of the total peak area, which recovered 92-96% of the total peak area, revealed different diversity indexes from the five enzyme digestions. Multidimensional scaling, based on matrices that were generated by scoring peak presence/absence and area, revealed similar bacterial community structure patterns among the 20 samples, regardless of the choice of restriction enzymes. Our results strongly argue that the choice of different digestion enzymes in the T-RFLP technique generated valid and consistent bacterial community structures but highly variable species richness and diversity indices. The biases associated with the choice of digestion enzymes needs to be evaluated carefully or at least to be addressed when using T-RFLP analysis. © 2008 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.en_US
dc.languageengen_US
dc.publisherWiley-Blackwell Publishing Ltd.. The Journal's web site is located at http://www.wiley.com/bw/journal.asp?ref=0168-6496en_US
dc.relation.ispartofFEMS Microbiology Ecologyen_US
dc.subject.meshBacteria - Classification - Genetics - Isolation & Purificationen_US
dc.subject.meshDna, Bacterial - Analysis - Genetics - Isolation & Purificationen_US
dc.subject.meshEcosystemen_US
dc.subject.meshGenes, Rrnaen_US
dc.subject.meshGenetic Variationen_US
dc.subject.meshPhylogenyen_US
dc.subject.meshPolymerase Chain Reaction - Methodsen_US
dc.subject.meshPolymorphism, Restriction Fragment Lengthen_US
dc.subject.meshRna, Ribosomal, 16S - Geneticsen_US
dc.subject.meshSeawater - Microbiologyen_US
dc.subject.meshSpecies Specificityen_US
dc.titleEvaluation of terminal-restriction fragment length polymorphism analysis in contrasting marine environmentsen_US
dc.typeArticleen_US
dc.identifier.emailThiyagarajan, V: rajan@hkucc.hku.hken_US
dc.identifier.authorityThiyagarajan, V=rp00796en_US
dc.description.naturelink_to_OA_fulltexten_US
dc.identifier.doi10.1111/j.1574-6941.2008.00493.xen_US
dc.identifier.pmid18503550-
dc.identifier.scopuseid_2-s2.0-45149092660en_US
dc.identifier.hkuros223068-
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-45149092660&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume65en_US
dc.identifier.issue1en_US
dc.identifier.spage169en_US
dc.identifier.epage178en_US
dc.identifier.isiWOS:000256717200015-
dc.publisher.placeUnited Kingdomen_US
dc.identifier.scopusauthoridZhang, R=7404865691en_US
dc.identifier.scopusauthoridThiyagarajan, V=6602476830en_US
dc.identifier.scopusauthoridQian, PY=35240648600en_US

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