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Evidence from GC-TRFLP that bacterial communities in soil are lognormally distributed.

Doroghazi JR, Buckley DH - PLoS ONE (2008)

Bottom Line: As a result, few microbial systems have been sampled with sufficient depth to generate reliable estimates of the community SAD.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 distribution for studying the SAD of bacterial communities as for plant and animal communities.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Cornell University, Ithaca, New York, United States of America.

ABSTRACT
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 distribution for studying the SAD of bacterial communities as for plant and animal communities.

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Plot of GC-TRFLP data for a soil sample indicating TRFLP results for CsCl gradient fractions containing DNA of different G+C content.Peaks are colored based on height to increase contrast between peaks.
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pone-0002910-g001: Plot of GC-TRFLP data for a soil sample indicating TRFLP results for CsCl gradient fractions containing DNA of different G+C content.Peaks are colored based on height to increase contrast between peaks.

Mentions: A single soil sample was subjected to both TRFLP and GC-TRFLP analysis of bacterial 16S rRNA genes. GC-TRFLP identified 731 OTUs, defined by genome G+C content and TRF size (Figures 1 and 2). In contrast, TRFLP analysis of the same DNA sample resulted in 173 discrete TRFs (Figures 2 and 3). To facilitate comparison with TRFLP, the TRFs from GC-TRFLP were composited without respect to genome G+C content and their cumulative peak heights summed (Figure 3). GC-TRFLP generated a total of 359 distinct TRFs demonstrating that GC-TRFLP enhanced recovery of TRFs not accessible through conventional TRFLP; as has been previously suggested for a similar method [17]. A total of 85.5% of the TRFs detected in TRFLP were also detected in GC-TRFLP (Figure 3). Variation between TRFLP and composite GC-TRFLP increased as a function of rank abundance suggesting a relationship between peak height and variance in peak height which might be expected for these data (Figure 4).


Evidence from GC-TRFLP that bacterial communities in soil are lognormally distributed.

Doroghazi JR, Buckley DH - PLoS ONE (2008)

Plot of GC-TRFLP data for a soil sample indicating TRFLP results for CsCl gradient fractions containing DNA of different G+C content.Peaks are colored based on height to increase contrast between peaks.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2483420&req=5

pone-0002910-g001: Plot of GC-TRFLP data for a soil sample indicating TRFLP results for CsCl gradient fractions containing DNA of different G+C content.Peaks are colored based on height to increase contrast between peaks.
Mentions: A single soil sample was subjected to both TRFLP and GC-TRFLP analysis of bacterial 16S rRNA genes. GC-TRFLP identified 731 OTUs, defined by genome G+C content and TRF size (Figures 1 and 2). In contrast, TRFLP analysis of the same DNA sample resulted in 173 discrete TRFs (Figures 2 and 3). To facilitate comparison with TRFLP, the TRFs from GC-TRFLP were composited without respect to genome G+C content and their cumulative peak heights summed (Figure 3). GC-TRFLP generated a total of 359 distinct TRFs demonstrating that GC-TRFLP enhanced recovery of TRFs not accessible through conventional TRFLP; as has been previously suggested for a similar method [17]. A total of 85.5% of the TRFs detected in TRFLP were also detected in GC-TRFLP (Figure 3). Variation between TRFLP and composite GC-TRFLP increased as a function of rank abundance suggesting a relationship between peak height and variance in peak height which might be expected for these data (Figure 4).

Bottom Line: As a result, few microbial systems have been sampled with sufficient depth to generate reliable estimates of the community SAD.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 distribution for studying the SAD of bacterial communities as for plant and animal communities.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Cornell University, Ithaca, New York, United States of America.

ABSTRACT
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 distribution for studying the SAD of bacterial communities as for plant and animal communities.

Show MeSH