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Title: New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes

Abstract

Deforestation in the Brazilian Amazon occurs at an alarming rate, which has broad effects on global greenhouse gas emissions, carbon storage, and biogeochemical cycles. In this study, soil metagenomes and metagenome-assembled genomes (MAGs) were analyzed for alterations to microbial community composition, functional groups, and putative physiology as it related to land-use change and tropical soil. A total of 28 MAGs were assembled encompassing 10 phyla, including both dominant and rare biosphere lineages. Amazon Acidobacteria subdivision 3, Melainabacteria, Microgenomates, and Parcubacteria were found exclusively in pasture soil samples, while Candidatus Rokubacteria was predominant in the adjacent rainforest soil. These shifts in relative abundance between land-use types were supported by the different putative physiologies and life strategies employed by the taxa. This research provides unique biological insights into candidate phyla in tropical soil and how deforestation may impact the carbon cycle and affect climate change.

Authors:
 [1];  [2];  [3];  [4];  [5];  [1];  [6];  [4];  [7];  [8];  [5];  [8];  [1]
  1. Univ. of Massachusetts, Amherst, MA (United States). Dept. of Microbiology
  2. Univ. of Chicago, IL (United States). Dept. of Medicine
  3. Univ. of Chicago, IL (United States). Dept. of Medicine; Marine Biological Lab., Woods Hole, MA (United States). Josephine Bay Paul Center
  4. Univ. of Oregon, Eugene, OR (United States). Inst. of Ecology and Evolution
  5. Michigan State Univ., East Lansing, MI (United States). Center for Microbial Ecology
  6. Univ. of California, Davis, CA (United States). Dept. of Land, Air, and Water Resources
  7. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  8. Univ. of São Paulo, Piracicaba (Brazil). Center for Nuclear Energy in Agriculture
Publication Date:
Research Org.:
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of Massachusetts, Amherst, MA (United States); Univ. of São Paulo, Piracicaba (Brazil)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); National Science Foundation (NSF); USDA National Inst. of Food and Agriculture (NIFA); São Paulo Research Foundation (FAPESP) (Brazil)
OSTI Identifier:
1461209
Alternate Identifier(s):
OSTI ID: 1477343
Grant/Contract Number:  
AC02-05CH11231; DEB 14422214; 2009-447 35319-05186; 2014/50320-4
Resource Type:
Journal Article: Published Article
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 9; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Amazon rainforest soil; land-use change; metagenome assembled genomes; rare biosphere; soil metagenomics

Citation Formats

Kroeger, Marie E., Delmont, Tom O., Eren, A. M., Meyer, Kyle M., Guo, Jiarong, Khan, Kiran, Rodrigues, Jorge L. M., Bohannan, Brendan J. M., Tringe, Susannah G., Borges, Clovis D., Tiedje, James M., Tsai, Siu M., and Nüsslein, Klaus. New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes. United States: N. p., 2018. Web. doi:10.3389/fmicb.2018.01635.
Kroeger, Marie E., Delmont, Tom O., Eren, A. M., Meyer, Kyle M., Guo, Jiarong, Khan, Kiran, Rodrigues, Jorge L. M., Bohannan, Brendan J. M., Tringe, Susannah G., Borges, Clovis D., Tiedje, James M., Tsai, Siu M., & Nüsslein, Klaus. New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes. United States. doi:10.3389/fmicb.2018.01635.
Kroeger, Marie E., Delmont, Tom O., Eren, A. M., Meyer, Kyle M., Guo, Jiarong, Khan, Kiran, Rodrigues, Jorge L. M., Bohannan, Brendan J. M., Tringe, Susannah G., Borges, Clovis D., Tiedje, James M., Tsai, Siu M., and Nüsslein, Klaus. Mon . "New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes". United States. doi:10.3389/fmicb.2018.01635.
@article{osti_1461209,
title = {New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes},
author = {Kroeger, Marie E. and Delmont, Tom O. and Eren, A. M. and Meyer, Kyle M. and Guo, Jiarong and Khan, Kiran and Rodrigues, Jorge L. M. and Bohannan, Brendan J. M. and Tringe, Susannah G. and Borges, Clovis D. and Tiedje, James M. and Tsai, Siu M. and Nüsslein, Klaus},
abstractNote = {Deforestation in the Brazilian Amazon occurs at an alarming rate, which has broad effects on global greenhouse gas emissions, carbon storage, and biogeochemical cycles. In this study, soil metagenomes and metagenome-assembled genomes (MAGs) were analyzed for alterations to microbial community composition, functional groups, and putative physiology as it related to land-use change and tropical soil. A total of 28 MAGs were assembled encompassing 10 phyla, including both dominant and rare biosphere lineages. Amazon Acidobacteria subdivision 3, Melainabacteria, Microgenomates, and Parcubacteria were found exclusively in pasture soil samples, while Candidatus Rokubacteria was predominant in the adjacent rainforest soil. These shifts in relative abundance between land-use types were supported by the different putative physiologies and life strategies employed by the taxa. This research provides unique biological insights into candidate phyla in tropical soil and how deforestation may impact the carbon cycle and affect climate change.},
doi = {10.3389/fmicb.2018.01635},
journal = {Frontiers in Microbiology},
number = ,
volume = 9,
place = {United States},
year = {Mon Jul 23 00:00:00 EDT 2018},
month = {Mon Jul 23 00:00:00 EDT 2018}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.3389/fmicb.2018.01635

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