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Title: Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments

Abstract

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 electronmore » 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.« less

Authors:
 [1];  [2];  [3];  [3];  [3];  [3];  [4]
  1. Univ. of California, Berkeley, CA (United States); Univ. of Colorado Denver, Denver, CO (United States)
  2. Univ. of Chicago, Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States); Univ. of California, Berkeley, CA (United States)
  3. Univ. of California, Berkeley, CA (United States)
  4. Argonne National Lab. (ANL), Argonne, IL (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1511353
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 8; Journal Issue: 2; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Ribosomal RNA; Sequence databases; Sequence assembly tools; Taxonomy; Sequence analysis; Phylogenetic analysis; Sediment; Sulfates

Citation Formats

Miller, Christopher S., Handley, Kim M., Wrighton, Kelly C., Frischkorn, Kyle R., Thomas, Brian C., Banfield, Jillian F., and Gilbert, Jack Anthony. Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments. United States: N. p., 2013. Web. doi:10.1371/journal.pone.0056018.
Miller, Christopher S., Handley, Kim M., Wrighton, Kelly C., Frischkorn, Kyle R., Thomas, Brian C., Banfield, Jillian F., & Gilbert, Jack Anthony. Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments. United States. doi:10.1371/journal.pone.0056018.
Miller, Christopher S., Handley, Kim M., Wrighton, Kelly C., Frischkorn, Kyle R., Thomas, Brian C., Banfield, Jillian F., and Gilbert, Jack Anthony. Wed . "Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments". United States. doi:10.1371/journal.pone.0056018. https://www.osti.gov/servlets/purl/1511353.
@article{osti_1511353,
title = {Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments},
author = {Miller, Christopher S. and Handley, Kim M. and Wrighton, Kelly C. and Frischkorn, Kyle R. and Thomas, Brian C. and Banfield, Jillian F. and Gilbert, Jack Anthony},
abstractNote = {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.},
doi = {10.1371/journal.pone.0056018},
journal = {PLoS ONE},
issn = {1932-6203},
number = 2,
volume = 8,
place = {United States},
year = {2013},
month = {2}
}

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Works referenced in this record:

A Molecular View of Microbial Diversity and the Biosphere
journal, May 1997


Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
journal, July 2006

  • DeSantis, T. Z.; Hugenholtz, P.; Larsen, N.
  • Applied and Environmental Microbiology, Vol. 72, Issue 7, p. 5069-5072
  • DOI: 10.1128/AEM.03006-05

Search and clustering orders of magnitude faster than BLAST
journal, August 2010