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Title: Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations

Abstract

To understand the forces driving differentiation and diversification in wild bacterial populations, we must be able to delineate and track ecologically relevant units through space and time. Mapping metagenomic sequences to reference genomes derived from the same environment can reveal genetic heterogeneity within populations, and in some cases, be used to identify boundaries between genetically similar, but ecologically distinct, populations. Here we examine population-level heterogeneity within abundant and ubiquitous freshwater bacterial groups such as the acI Actinobacteria and LD12 Alphaproteobacteria (the freshwater sister clade to the marine SAR11) using 33 single-cell genomes and a 5-year metagenomic time series. The single-cell genomes grouped into 15 monophyletic clusters (termed "tribes") that share at least 97.9% 16S rRNA identity. Distinct populations were identified within most tribes based on the patterns of metagenomic read recruitments to single-cell genomes representing these tribes. Genetically distinct populations within tribes of the acI Actinobacterial lineage living in the same lake had different seasonal abundance patterns, suggesting these populations were also ecologically distinct. In contrast, sympatric LD12 populations were less genetically differentiated. This suggests that within one lake, some freshwater lineages harbor genetically discrete (but still closely related) and ecologically distinct populations, while other lineages are composed of lessmore » differentiated populations with overlapping niches. Our results point at an interplay of evolutionary and ecological forces acting on these communities that can be observed in real time.« less

Authors:
 [1]; ORCiD logo [2];  [2];  [3]; ORCiD logo [4];  [5]; ORCiD logo [5];  [6];  [6];  [5]; ORCiD logo [2]
  1. Univ. of Wisconsin-Madison, Madison, WI (United States); Uppsala Univ., Uppsala (Sweden)
  2. Univ. of Wisconsin-Madison, Madison, WI (United States)
  3. Univ. of Alicante, Alicante (Spain)
  4. Bigelow Lab for Ocean Sciences, East Boothbay, ME (United States)
  5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  6. Uppsala Univ., Uppsala (Sweden)
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:
1459402
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
The ISME Journal
Additional Journal Information:
Journal Volume: 12; Journal Issue: 3; Related Information: © 2017 The Author(s) 2017, under exclusive licence to Macmillan Publishers Limited, part of Springer Nature.; Journal ID: ISSN 1751-7362
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Garcia, Sarahi L., Stevens, Sarah L. R., Crary, Benjamin, Martinez-Garcia, Manuel, Stepanauskas, Ramunas, Woyke, Tanja, Tringe, Susannah G., Andersson, Siv G. E., Bertilsson, Stefan, Malmstrom, Rex R., and McMahon, Katherine D. Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations. United States: N. p., 2017. Web. doi:10.1038/s41396-017-0001-0.
Garcia, Sarahi L., Stevens, Sarah L. R., Crary, Benjamin, Martinez-Garcia, Manuel, Stepanauskas, Ramunas, Woyke, Tanja, Tringe, Susannah G., Andersson, Siv G. E., Bertilsson, Stefan, Malmstrom, Rex R., & McMahon, Katherine D. Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations. United States. doi:10.1038/s41396-017-0001-0.
Garcia, Sarahi L., Stevens, Sarah L. R., Crary, Benjamin, Martinez-Garcia, Manuel, Stepanauskas, Ramunas, Woyke, Tanja, Tringe, Susannah G., Andersson, Siv G. E., Bertilsson, Stefan, Malmstrom, Rex R., and McMahon, Katherine D. Fri . "Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations". United States. doi:10.1038/s41396-017-0001-0. https://www.osti.gov/servlets/purl/1459402.
@article{osti_1459402,
title = {Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations},
author = {Garcia, Sarahi L. and Stevens, Sarah L. R. and Crary, Benjamin and Martinez-Garcia, Manuel and Stepanauskas, Ramunas and Woyke, Tanja and Tringe, Susannah G. and Andersson, Siv G. E. and Bertilsson, Stefan and Malmstrom, Rex R. and McMahon, Katherine D.},
abstractNote = {To understand the forces driving differentiation and diversification in wild bacterial populations, we must be able to delineate and track ecologically relevant units through space and time. Mapping metagenomic sequences to reference genomes derived from the same environment can reveal genetic heterogeneity within populations, and in some cases, be used to identify boundaries between genetically similar, but ecologically distinct, populations. Here we examine population-level heterogeneity within abundant and ubiquitous freshwater bacterial groups such as the acI Actinobacteria and LD12 Alphaproteobacteria (the freshwater sister clade to the marine SAR11) using 33 single-cell genomes and a 5-year metagenomic time series. The single-cell genomes grouped into 15 monophyletic clusters (termed "tribes") that share at least 97.9% 16S rRNA identity. Distinct populations were identified within most tribes based on the patterns of metagenomic read recruitments to single-cell genomes representing these tribes. Genetically distinct populations within tribes of the acI Actinobacterial lineage living in the same lake had different seasonal abundance patterns, suggesting these populations were also ecologically distinct. In contrast, sympatric LD12 populations were less genetically differentiated. This suggests that within one lake, some freshwater lineages harbor genetically discrete (but still closely related) and ecologically distinct populations, while other lineages are composed of less differentiated populations with overlapping niches. Our results point at an interplay of evolutionary and ecological forces acting on these communities that can be observed in real time.},
doi = {10.1038/s41396-017-0001-0},
journal = {The ISME Journal},
number = 3,
volume = 12,
place = {United States},
year = {2017},
month = {12}
}

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    Works referencing / citing this record:

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