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Front. Microbiol. | doi: 10.3389/fmicb.2018.01635

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

  • 1Department of Microbiology, University of Massachusetts Amherst, United States
  • 2Department of Medicine, University of Chicago, United States
  • 3Josephine Bay Paul Center, Marine Biological Laboratory (MBL), United States
  • 4Institute for Ecology and Evolution, University of Oregon, United States
  • 5Center for Microbial Ecology, Michigan State University, United States
  • 6Department of Land, Air, and Water Resources, University of California, Davis, United States
  • 7Joint Genome Institute (JGI), United States
  • 8Centro de Energia Nuclear na Agricultura, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Brazil

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 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 metagenome-assembled genomes 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.

Keywords: Amazon rainforest soil, land-use change, Metagenome assembled genomes, rare biosphere, soil metagenomics

Received: 16 Apr 2018; Accepted: 30 Jun 2018.

Edited by:

Etienne Yergeau, Institut national de la recherche scientifique (INRS), Canada

Reviewed by:

Terrence H. Bell, Pennsylvania State University, United States
Carl-Eric Wegner, Friedrich-Schiller-Universität Jena, Germany
Erick Cardenas Poire, Microbiome Insights, Canada  

Copyright: © 2018 Kroeger, Delmont, Eren, Meyer, Guo, Khan, Rodrigues, Bohannan, Tringe, Borges, Tiedje, Tsai and Nüsslein. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Prof. Klaus Nüsslein, University of Massachusetts Amherst, Department of Microbiology, 639 North Pleasant St., N203 Morrill Science Center IV N, Amherst, 01003-9298, MA, United States,