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Evidence from GC-TRFLP that Bacterial Communities in Soil Are Lognormally Distributed

The Species Abundance Distribution (SAD) is a fundamental property of ecological communities and the form and formation of SADs have been examined for a wide range of communities including those of microorganisms. Progress in understanding microbial SADs, however, has been limited by the remarkable...

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Detalles Bibliográficos
Autores principales: Doroghazi, James R., Buckley, Daniel H.
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2483420/
https://www.ncbi.nlm.nih.gov/pubmed/18682841
http://dx.doi.org/10.1371/journal.pone.0002910
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author Doroghazi, James R.
Buckley, Daniel H.
author_facet Doroghazi, James R.
Buckley, Daniel H.
author_sort Doroghazi, James R.
collection PubMed
description The Species Abundance Distribution (SAD) is a fundamental property of ecological communities and the form and formation of SADs have been examined for a wide range of communities including those of microorganisms. Progress in understanding microbial SADs, however, has been limited by the remarkable diversity and vast size of microbial communities. As a result, few microbial systems have been sampled with sufficient depth to generate reliable estimates of the community SAD. We have used a novel approach to characterize the SAD of bacterial communities by coupling genomic DNA fractionation with analysis of terminal restriction fragment length polymorphisms (GC-TRFLP). Examination of a soil microbial community through GC-TRFLP revealed 731 bacterial operational taxonomic units (OTUs) that followed a lognormal distribution. To recover the same 731 OTUs through analysis of DNA sequence data is estimated to require analysis of 86,264 16S rRNA sequences. The approach is examined and validated through construction and analysis of simulated microbial communities in silico. Additional simulations performed to assess the potential effects of PCR bias show that biased amplification can cause a community whose distribution follows a power-law function to appear lognormally distributed. We also show that TRFLP analysis, in contrast to GC-TRFLP, is not able to effectively distinguish between competing SAD models. Our analysis supports use of the lognormal as the null distribution for studying the SAD of bacterial communities as for plant and animal communities.
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spelling pubmed-24834202008-08-06 Evidence from GC-TRFLP that Bacterial Communities in Soil Are Lognormally Distributed Doroghazi, James R. Buckley, Daniel H. PLoS One Research Article The Species Abundance Distribution (SAD) is a fundamental property of ecological communities and the form and formation of SADs have been examined for a wide range of communities including those of microorganisms. Progress in understanding microbial SADs, however, has been limited by the remarkable diversity and vast size of microbial communities. As a result, few microbial systems have been sampled with sufficient depth to generate reliable estimates of the community SAD. We have used a novel approach to characterize the SAD of bacterial communities by coupling genomic DNA fractionation with analysis of terminal restriction fragment length polymorphisms (GC-TRFLP). Examination of a soil microbial community through GC-TRFLP revealed 731 bacterial operational taxonomic units (OTUs) that followed a lognormal distribution. To recover the same 731 OTUs through analysis of DNA sequence data is estimated to require analysis of 86,264 16S rRNA sequences. The approach is examined and validated through construction and analysis of simulated microbial communities in silico. Additional simulations performed to assess the potential effects of PCR bias show that biased amplification can cause a community whose distribution follows a power-law function to appear lognormally distributed. We also show that TRFLP analysis, in contrast to GC-TRFLP, is not able to effectively distinguish between competing SAD models. Our analysis supports use of the lognormal as the null distribution for studying the SAD of bacterial communities as for plant and animal communities. Public Library of Science 2008-08-06 /pmc/articles/PMC2483420/ /pubmed/18682841 http://dx.doi.org/10.1371/journal.pone.0002910 Text en Doroghazi et al. http://creativecommons.org/licenses/by/4.0/ 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 properly credited.
spellingShingle Research Article
Doroghazi, James R.
Buckley, Daniel H.
Evidence from GC-TRFLP that Bacterial Communities in Soil Are Lognormally Distributed
title Evidence from GC-TRFLP that Bacterial Communities in Soil Are Lognormally Distributed
title_full Evidence from GC-TRFLP that Bacterial Communities in Soil Are Lognormally Distributed
title_fullStr Evidence from GC-TRFLP that Bacterial Communities in Soil Are Lognormally Distributed
title_full_unstemmed Evidence from GC-TRFLP that Bacterial Communities in Soil Are Lognormally Distributed
title_short Evidence from GC-TRFLP that Bacterial Communities in Soil Are Lognormally Distributed
title_sort evidence from gc-trflp that bacterial communities in soil are lognormally distributed
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2483420/
https://www.ncbi.nlm.nih.gov/pubmed/18682841
http://dx.doi.org/10.1371/journal.pone.0002910
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