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Title: Differences in substrate use linked to divergent carbon flow during litter decomposition

Abstract

ABSTRACT Discovering widespread microbial processes that create variation in soil carbon (C) cycling within ecosystems may improve soil C modeling. Toward this end, we screened 206 soil communities decomposing plant litter in a common garden microcosm environment and examined features linked to divergent patterns of C flow. C flow was measured as carbon dioxide (CO2) and dissolved organic carbon (DOC) from 44-days of litter decomposition. Two large groups of microbial communities representing ‘high’ and ‘low’ DOC phenotypes from original soil and 44-day microcosm samples were down-selected for fungal and bacterial profiling. Metatranscriptomes were also sequenced from a smaller subset of communities in each group. The two groups exhibited differences in average rate of CO2 production, demonstrating that the divergent patterns of C flow arose from innate functional constraints on C metabolism, not a time-dependent artefact. To infer functional constraints, we identified features – traits at the organism, pathway or gene level – linked to the high and low DOC phenotypes using RNA-Seq approaches and machine learning approaches. Substrate use differed across the high and low DOC phenotypes. Additional features suggested that divergent patterns of C flow may be driven in part by differences in organism interactions that affect DOC abundancemore » directly or indirectly by controlling community structure.« less

Authors:
ORCiD logo [1];  [2];  [1];  [1];  [1];  [1];  [3];  [1]
  1. Biosciences Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA
  2. Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA
  3. Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA, School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE Office of Science (SC). Biological and Environmental Research (BER)
OSTI Identifier:
1641872
Alternate Identifier(s):
OSTI ID: 1716813
Report Number(s):
LA-UR-20-22813
Journal ID: ISSN 1574-6941; fiaa135
Grant/Contract Number:  
89233218CNA000001; F255LANL2018
Resource Type:
Published Article
Journal Name:
FEMS Microbiology Ecology (Online)
Additional Journal Information:
Journal Name: FEMS Microbiology Ecology (Online) Journal Volume: 96 Journal Issue: 8; Journal ID: ISSN 1574-6941
Publisher:
Federation of European Microbiological Societies
Country of Publication:
Netherlands
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; soil; carbon cycling; microbiome; dissolved organic carbon; carbon dioxide; physiology; effect traits; machine learning; metatranscriptome; oligotrophs; fungivores; bacteriovores

Citation Formats

Albright, Michaeline B. N., Thompson, Jaron, Kroeger, Marie E., Johansen, Renee, Ulrich, Danielle E. M., Gallegos-Graves, La Verne, Munsky, Brian, and Dunbar, John. Differences in substrate use linked to divergent carbon flow during litter decomposition. Netherlands: N. p., 2020. Web. https://doi.org/10.1093/femsec/fiaa135.
Albright, Michaeline B. N., Thompson, Jaron, Kroeger, Marie E., Johansen, Renee, Ulrich, Danielle E. M., Gallegos-Graves, La Verne, Munsky, Brian, & Dunbar, John. Differences in substrate use linked to divergent carbon flow during litter decomposition. Netherlands. https://doi.org/10.1093/femsec/fiaa135
Albright, Michaeline B. N., Thompson, Jaron, Kroeger, Marie E., Johansen, Renee, Ulrich, Danielle E. M., Gallegos-Graves, La Verne, Munsky, Brian, and Dunbar, John. Mon . "Differences in substrate use linked to divergent carbon flow during litter decomposition". Netherlands. https://doi.org/10.1093/femsec/fiaa135.
@article{osti_1641872,
title = {Differences in substrate use linked to divergent carbon flow during litter decomposition},
author = {Albright, Michaeline B. N. and Thompson, Jaron and Kroeger, Marie E. and Johansen, Renee and Ulrich, Danielle E. M. and Gallegos-Graves, La Verne and Munsky, Brian and Dunbar, John},
abstractNote = {ABSTRACT Discovering widespread microbial processes that create variation in soil carbon (C) cycling within ecosystems may improve soil C modeling. Toward this end, we screened 206 soil communities decomposing plant litter in a common garden microcosm environment and examined features linked to divergent patterns of C flow. C flow was measured as carbon dioxide (CO2) and dissolved organic carbon (DOC) from 44-days of litter decomposition. Two large groups of microbial communities representing ‘high’ and ‘low’ DOC phenotypes from original soil and 44-day microcosm samples were down-selected for fungal and bacterial profiling. Metatranscriptomes were also sequenced from a smaller subset of communities in each group. The two groups exhibited differences in average rate of CO2 production, demonstrating that the divergent patterns of C flow arose from innate functional constraints on C metabolism, not a time-dependent artefact. To infer functional constraints, we identified features – traits at the organism, pathway or gene level – linked to the high and low DOC phenotypes using RNA-Seq approaches and machine learning approaches. Substrate use differed across the high and low DOC phenotypes. Additional features suggested that divergent patterns of C flow may be driven in part by differences in organism interactions that affect DOC abundance directly or indirectly by controlling community structure.},
doi = {10.1093/femsec/fiaa135},
journal = {FEMS Microbiology Ecology (Online)},
number = 8,
volume = 96,
place = {Netherlands},
year = {2020},
month = {7}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1093/femsec/fiaa135

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