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Title: Deforestation impacts network co-occurrence patterns of microbial communities in Amazon soils

Abstract

Co-occurrence networks allow for the identification of potential associations among species, which may be important for understanding community assembly and ecosystem functions. We employed this strategy to examine prokaryotic co-occurrence patterns in the Amazon soils and the response of these patterns to land use change to pasture, with the hypothesis that altered microbial composition due to deforestation will mirror the co-occurrence patterns across prokaryotic taxa. In this study, we calculated Spearman correlations between operational taxonomic units (OTUs) as determined by 16S rRNA gene sequencing, and only robust correlations were considered for network construction (-0.80 ≥ ρ ≥ 0.80, adjusted P <0.01). The constructed network represents distinct forest and pasture components, with altered compositional and topological features. A comparative analysis between two representative modules of these contrasting ecosystems revealed novel information regarding changes to metabolic pathways related to nitrogen cycling. Our results showed that soil physicochemical properties such as temperature, C/N and H ++Al 3+ had a significant impact on prokaryotic communities, with alterations to network topologies. Taken together, changes in co-occurrence patterns and physicochemical properties may contribute to ecosystem processes including nitrification and denitrification, two important biogeochemical processes occurring in tropical forest systems.

Authors:
 [1];  [2];  [3];  [4];  [5];  [6];  [7]; ORCiD logo [8]
  1. Univ. of Texas, Arlington, TX (United States). Dept. of Biology
  2. Univ. of Oregon, Eugene, OR (United States). Inst. of Ecology and Evolution
  3. Univ. of Massachusetts, Amherst, MA (United States). Dept. of Microbiology
  4. Michigan State Univ., East Lansing, MI (United States). Center for Microbial Ecology
  5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division
  6. Univ. of California, Davis, CA (United States). Dept. of Land, Air and Water Resources
  7. Univ. of Arizona, Tucson, AZ (United States). Dept. of Soil,Water and Environmental Science
  8. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division; Univ. of California, Davis, CA (United States). Dept. of Land, Air and Water Resources
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), Biological Systems Science Division (SC-23.2 )
OSTI Identifier:
1487088
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
FEMS Microbiology Ecology (Online)
Additional Journal Information:
Journal Volume: 95; Journal Issue: 2; Journal ID: ISSN 1574-6941
Publisher:
Federation of European Microbiological Societies
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; forest; land use change; microorganisms; ecological network; pasture; amazon; physicochemical properties; nitrification, denitrification

Citation Formats

Khan, M. A. Wadud, Bohannan, Brendan J. M., Nüsslein, Klaus, Tiedje, James M., Tringe, Susannah G., Parlade, Eloi, Barberán, Albert, and Rodrigues, Jorge L. M.. Deforestation impacts network co-occurrence patterns of microbial communities in Amazon soils. United States: N. p., 2018. Web. doi:10.1093/femsec/fiy230.
Khan, M. A. Wadud, Bohannan, Brendan J. M., Nüsslein, Klaus, Tiedje, James M., Tringe, Susannah G., Parlade, Eloi, Barberán, Albert, & Rodrigues, Jorge L. M.. Deforestation impacts network co-occurrence patterns of microbial communities in Amazon soils. United States. doi:10.1093/femsec/fiy230.
Khan, M. A. Wadud, Bohannan, Brendan J. M., Nüsslein, Klaus, Tiedje, James M., Tringe, Susannah G., Parlade, Eloi, Barberán, Albert, and Rodrigues, Jorge L. M.. Tue . "Deforestation impacts network co-occurrence patterns of microbial communities in Amazon soils". United States. doi:10.1093/femsec/fiy230. https://www.osti.gov/servlets/purl/1487088.
@article{osti_1487088,
title = {Deforestation impacts network co-occurrence patterns of microbial communities in Amazon soils},
author = {Khan, M. A. Wadud and Bohannan, Brendan J. M. and Nüsslein, Klaus and Tiedje, James M. and Tringe, Susannah G. and Parlade, Eloi and Barberán, Albert and Rodrigues, Jorge L. M.},
abstractNote = {Co-occurrence networks allow for the identification of potential associations among species, which may be important for understanding community assembly and ecosystem functions. We employed this strategy to examine prokaryotic co-occurrence patterns in the Amazon soils and the response of these patterns to land use change to pasture, with the hypothesis that altered microbial composition due to deforestation will mirror the co-occurrence patterns across prokaryotic taxa. In this study, we calculated Spearman correlations between operational taxonomic units (OTUs) as determined by 16S rRNA gene sequencing, and only robust correlations were considered for network construction (-0.80 ≥ ρ ≥ 0.80, adjusted P <0.01). The constructed network represents distinct forest and pasture components, with altered compositional and topological features. A comparative analysis between two representative modules of these contrasting ecosystems revealed novel information regarding changes to metabolic pathways related to nitrogen cycling. Our results showed that soil physicochemical properties such as temperature, C/N and H++Al3+ had a significant impact on prokaryotic communities, with alterations to network topologies. Taken together, changes in co-occurrence patterns and physicochemical properties may contribute to ecosystem processes including nitrification and denitrification, two important biogeochemical processes occurring in tropical forest systems.},
doi = {10.1093/femsec/fiy230},
journal = {FEMS Microbiology Ecology (Online)},
issn = {1574-6941},
number = 2,
volume = 95,
place = {United States},
year = {2018},
month = {11}
}

Journal Article:
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