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Title: Genome-reconstruction for eukaryotes from complex natural microbial communities

Microbial eukaryotes are integral components of natural microbial communities, and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, we propose a method to recover eukaryotic genomes from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. We developed a k-mer-based strategy, EukRep, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation, and prediction of metabolic potential. We used this approach to test the effect of addition of organic carbon on a geyser-associated microbial community and detected a substantial change of the community metabolism, with selection against almost all candidate phyla bacteria and archaea and for eukaryotes. Near complete genomes were reconstructed for three fungi placed within the Eurotiomycetes and an arthropod. While carbon fixation and sulfur oxidation were important functions in the geyser community prior to carbon addition, the organic carbon-impacted community showed enrichment for secreted proteases, secreted lipases, cellulose targeting CAZymes, and methanol oxidation. We demonstrate the broader utility of EukRep by reconstructing and evaluating relatively high-quality fungal, protist, and rotifer genomes from complexmore » environmental samples. This approach opens the way for cultivation-independent analyses of whole microbial communities.« less
Authors:
 [1] ;  [2] ;  [3] ;  [2] ;  [4]
  1. Univ. of California, Berkeley, CA (United States). Department of Plant and Microbial Biology
  2. Univ. of California, Berkeley, CA (United States). Department of Earth and Planetary Science
  3. Univ. of California, Berkeley, CA (United States). Department of Plant and Microbial Biology ; USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. Univ. of California, Berkeley, CA (United States). Department of Earth and Planetary Science and Department of Environmental Science, Policy, and Management; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Division
Publication Date:
Grant/Contract Number:
AC02-05CH11231
Type:
Accepted Manuscript
Journal Name:
Genome Research
Additional Journal Information:
Journal Volume: 28; Journal Issue: 4; Journal ID: ISSN 1088-9051
Publisher:
Cold Spring Harbor Laboratory Press
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES
OSTI Identifier:
1477272

West, Patrick T., Probst, Alexander J., Grigoriev, Igor V., Thomas, Brian C., and Banfield, Jillian F.. Genome-reconstruction for eukaryotes from complex natural microbial communities. United States: N. p., Web. doi:10.1101/gr.228429.117.
West, Patrick T., Probst, Alexander J., Grigoriev, Igor V., Thomas, Brian C., & Banfield, Jillian F.. Genome-reconstruction for eukaryotes from complex natural microbial communities. United States. doi:10.1101/gr.228429.117.
West, Patrick T., Probst, Alexander J., Grigoriev, Igor V., Thomas, Brian C., and Banfield, Jillian F.. 2018. "Genome-reconstruction for eukaryotes from complex natural microbial communities". United States. doi:10.1101/gr.228429.117. https://www.osti.gov/servlets/purl/1477272.
@article{osti_1477272,
title = {Genome-reconstruction for eukaryotes from complex natural microbial communities},
author = {West, Patrick T. and Probst, Alexander J. and Grigoriev, Igor V. and Thomas, Brian C. and Banfield, Jillian F.},
abstractNote = {Microbial eukaryotes are integral components of natural microbial communities, and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, we propose a method to recover eukaryotic genomes from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. We developed a k-mer-based strategy, EukRep, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation, and prediction of metabolic potential. We used this approach to test the effect of addition of organic carbon on a geyser-associated microbial community and detected a substantial change of the community metabolism, with selection against almost all candidate phyla bacteria and archaea and for eukaryotes. Near complete genomes were reconstructed for three fungi placed within the Eurotiomycetes and an arthropod. While carbon fixation and sulfur oxidation were important functions in the geyser community prior to carbon addition, the organic carbon-impacted community showed enrichment for secreted proteases, secreted lipases, cellulose targeting CAZymes, and methanol oxidation. We demonstrate the broader utility of EukRep by reconstructing and evaluating relatively high-quality fungal, protist, and rotifer genomes from complex environmental samples. This approach opens the way for cultivation-independent analyses of whole microbial communities.},
doi = {10.1101/gr.228429.117},
journal = {Genome Research},
number = 4,
volume = 28,
place = {United States},
year = {2018},
month = {3}
}

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