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

James R Doroghazi,Daniel H Buckley,Jerome Chave

doi:10.1371/journal.pone.0002910

James R Doroghazi, Daniel H Buckley + Show 1 more

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https://doi.org/10.1371/journal.pone.0002910

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Journal: PloS one	Publication Date: Aug 6, 2008
Citations: 29	License type: CC BY 4.0

Affiliation: Cornell University

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

Highlights

The hollow curve of a species abundance distribution which results when most species are rare and a few are abundant is one of the few ecological patterns exhibited by almost all communities
We have used GC-terminal restriction fragment length polymorphism (TRFLP) to analyze the distribution of 731 bacterial operational taxonomic units (OTUs) from one gram of soil and found that the lognormal distribution provides the best fit to the data, and was the only distribution tested that could not be rejected as significantly different from the GC-TRFLP data
It is important to note that a traditional TRFLP approach was insufficient for this purpose due to the inability to effectively distinguish between the different distributions tested (Table 3)

Summary

Introduction

The hollow curve of a species abundance distribution which results when most species are rare and a few are abundant is one of the few ecological patterns exhibited by almost all communities. A range of factors such as birth, death, migration, niche adaptation, lifestyle, chance, resource partitioning, and history can all contribute to the formation of this characteristic hollow curve (see [1] for review). The universality of this phenomenon is worthy of study in its own right, but SADs can be useful in making predictions about community properties such as diversity and migration [2]. The ecological processes that create these patterns, remain nebulous and require further investigation

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