Introduction

In microbial ecology, a fundamental question relates to how community diversity and composition change in response to perturbation. Most studies have had limited ability to deeply sample community structure (e.g. Sanger-sequenced 16S rRNA libraries), or have had limited taxonomic resolution (e.g. studies based on 16S rRNA hypervariable region sequencing). Here, we combine the higher taxonomic resolution of near-full-length 16S rRNA gene amplicons with the economics and sensitivity of short-read sequencing to assay the abundance and identity of organisms that represent as little as 0.01% of sediment bacterial communities. We used a new version of EMIRGE optimized for large data size to reconstruct near-full-length 16S rRNA genes from amplicons sheared and sequenced with Illumina technology. The approach allowed us to differentiate the community composition among samples acquired before perturbation, after acetate amendment shifted the predominant metabolism to iron reduction, and once sulfate reduction began. Results were highly reproducible across technical replicates, and identified specific taxa that responded to the perturbation. All samples contain very high alpha diversity and abundant organisms from phyla without cultivated representatives. Surprisingly, at the time points measured, there was no strong loss of evenness, despite the selective pressure of acetate amendment and change in the terminal electron accepting process. However, community membership was altered significantly. The method allows for sensitive, accurate profiling of the "long tail" of low abundance organisms that exist in many microbial communities, and can resolve population dynamics in response to environmental change.

Publications

  1. Short-read assembly of full-length 16S amplicons reveals bacterial diversity in subsurface sediments.
    Cite this
    Miller CS, Handley KM, Wrighton KC, Frischkorn KR, Thomas BC, Banfield JF, 2013-01-01 - PloS one
  2. EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data.
    Cite this
    Miller CS, Baker BJ, Thomas BC, Singer SW, Banfield JF, 2011-01-01 - Genome biology

Credits

  1. Christopher S Miller
    Developer

  2. Kim M Handley
    Developer

  3. Kelly C Wrighton
    Developer

  4. Kyle R Frischkorn
    Developer

  5. Brian C Thomas
    Developer

  6. Jillian F Banfield
    Investigator

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Summary
AccessionBT006334
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByJillian F Banfield