Assembly-Driven Community Genomics of a Hypersaline Microbial Ecosystem
Abstract
Microbial populations inhabiting a natural hypersaline lake ecosystem in Lake Tyrrell, Victoria, Australia, have been characterized using deep metagenomic sampling, iterative de novo assembly, and multidimensional phylogenetic binning. Composite genomes representing habitat-specific microbial populations were reconstructed for eleven different archaea and one bacterium, comprising between 0.6 and 14.1% of the planktonic community. Eight of the eleven archaeal genomes were from microbial species without previously cultured representatives. These new genomes provide habitat-specific reference sequences enabling detailed, lineage-specific compartmentalization of predicted functional capabilities and cellular properties associated with both dominant and less abundant community members, including organisms previously known only by their 16S rRNA sequences. Together, these data provide a comprehensive, culture-independent genomic blueprint for ecosystem-wide analysis of protein functions, population structure, and lifestyles of co-existing, co-evolving microbial groups within the same natural habitat. The ‘‘assembly-driven’’ community genomic approach demonstrated in this study advances our ability to push beyond single gene investigations, and promotes genome-scale reconstructions as a tangible goal in the quest to define the metabolic, ecological, and evolutionary dynamics that underpin environmental microbial diversity.
- Authors:
-
- Univ. of California, San Diego, CA (United States). Scripps Inst. of Oceanography. Marine Biology Research Division
- Univ. of California, Berkeley, CA (United States). Dept. of Earth and Planetary Sciences; Univ. of California, Berkeley, CA (United States). Dept. of Environmental Science, Policy, and Management
- Univ. of Southern California, Los Angeles, CA (United States). Dept. of Biological Sciences
- Univ. of California, San Diego, CA (United States). Scripps Inst. of Oceanography. Marine Biology Research Division; Univ. of California, San Diego, CA (United States). Division of Biological Sciences
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
- OSTI Identifier:
- 1627601
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- PLoS ONE
- Additional Journal Information:
- Journal Volume: 8; Journal Issue: 4; Journal ID: ISSN 1932-6203
- Publisher:
- Public Library of Science
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; Science & Technology - Other Topics
Citation Formats
Podell, Sheila, Ugalde, Juan A., Narasingarao, Priya, Banfield, Jillian F., Heidelberg, Karla B., and Allen, Eric E. Assembly-Driven Community Genomics of a Hypersaline Microbial Ecosystem. United States: N. p., 2013.
Web. doi:10.1371/journal.pone.0061692.
Podell, Sheila, Ugalde, Juan A., Narasingarao, Priya, Banfield, Jillian F., Heidelberg, Karla B., & Allen, Eric E. Assembly-Driven Community Genomics of a Hypersaline Microbial Ecosystem. United States. https://doi.org/10.1371/journal.pone.0061692
Podell, Sheila, Ugalde, Juan A., Narasingarao, Priya, Banfield, Jillian F., Heidelberg, Karla B., and Allen, Eric E. Thu .
"Assembly-Driven Community Genomics of a Hypersaline Microbial Ecosystem". United States. https://doi.org/10.1371/journal.pone.0061692. https://www.osti.gov/servlets/purl/1627601.
@article{osti_1627601,
title = {Assembly-Driven Community Genomics of a Hypersaline Microbial Ecosystem},
author = {Podell, Sheila and Ugalde, Juan A. and Narasingarao, Priya and Banfield, Jillian F. and Heidelberg, Karla B. and Allen, Eric E.},
abstractNote = {Microbial populations inhabiting a natural hypersaline lake ecosystem in Lake Tyrrell, Victoria, Australia, have been characterized using deep metagenomic sampling, iterative de novo assembly, and multidimensional phylogenetic binning. Composite genomes representing habitat-specific microbial populations were reconstructed for eleven different archaea and one bacterium, comprising between 0.6 and 14.1% of the planktonic community. Eight of the eleven archaeal genomes were from microbial species without previously cultured representatives. These new genomes provide habitat-specific reference sequences enabling detailed, lineage-specific compartmentalization of predicted functional capabilities and cellular properties associated with both dominant and less abundant community members, including organisms previously known only by their 16S rRNA sequences. Together, these data provide a comprehensive, culture-independent genomic blueprint for ecosystem-wide analysis of protein functions, population structure, and lifestyles of co-existing, co-evolving microbial groups within the same natural habitat. The ‘‘assembly-driven’’ community genomic approach demonstrated in this study advances our ability to push beyond single gene investigations, and promotes genome-scale reconstructions as a tangible goal in the quest to define the metabolic, ecological, and evolutionary dynamics that underpin environmental microbial diversity.},
doi = {10.1371/journal.pone.0061692},
journal = {PLoS ONE},
number = 4,
volume = 8,
place = {United States},
year = {Thu Apr 18 00:00:00 EDT 2013},
month = {Thu Apr 18 00:00:00 EDT 2013}
}
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