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

Miller, Christopher S.; Handley, Kim M.; Wrighton, Kelly C.; Frischkorn, Kyle R.; Thomas, Brian C.; Banfield, Jillian F.; Gilbert, Jack Anthony

doi:10.1371/journal.pone.0056018

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

Journal Article · Wed Feb 06 00:00:00 EST 2013 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0056018· OSTI ID:1511353

Miller, Christopher S. ^[1]; Handley, Kim M. ^[2]; Wrighton, Kelly C. ^[3]; Frischkorn, Kyle R. ^[3]; Thomas, Brian C. ^[3]; Banfield, Jillian F. ^[3]; Gilbert, Jack Anthony ^[4]

Univ. of California, Berkeley, CA (United States); Univ. of Colorado Denver, Denver, CO (United States)
Univ. of Chicago, Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States); Univ. of California, Berkeley, CA (United States)
Univ. of California, Berkeley, CA (United States)
Argonne National Lab. (ANL), Argonne, IL (United States)

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1511353

Journal Information:: PLoS ONE, Vol. 8, Issue 2; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 149 works

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Utilizing novel diversity estimators to quantify multiple dimensions of microbial biodiversity across domains Doll, Hannah M.; Armitage, David W.; Daly, Rebecca A. BMC Microbiology, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2180-13-259	journal	January 2013
Exploring the Shift in Structure and Function of Microbial Communities Performing Biological Phosphorus Removal Mao, Yanping; Wang, Zhiping; Li, Liguan PLOS ONE, Vol. 11, Issue 8 https://doi.org/10.1371/journal.pone.0161506	journal	August 2016
Bioremediation of Wastewaters from Local Textile Industries in Ilorin, Nigeria Ajao, Abdullahi; Awe, Sunday; Sulugambari, Zulukarnain https://doi.org/10.20944/preprints201811.0458.v1	posted_content	November 2018
Dynamic transition of chemolithotrophic sulfur-oxidizing bacteria in response to amendment with nitrate in deposited marine sediments Aoyagi, Tomo; Kimura, Makoto; Yamada, Namiha Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.00426	journal	May 2015

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59 BASIC BIOLOGICAL SCIENCES
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Sulfates