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Title: Plant roots alter microbial functional genes supporting root litter decomposition

Abstract

Decomposition of soil organic carbon is central to the global carbon cycle and profoundly affected by plant roots. While root “priming” of decomposition has been extensively investigated, it is not known how plants alter the molecular ecology of soil microbial decomposers. We disentangled the effects of Avena fatua, a common annual grass, on 13C-labeled root litter decomposition and quantified multiple genetic characteristics of soil bacterial and fungal communities. In our study, plants consistently suppressed rates of root litter decomposition. Microbes from planted soils had relatively more genes coding for low molecular weight compound degradation enzymes, while those from unplanted had more macromolecule degradation genes. Higher abundances of “water stress” genes in planted soils suggested that microbes experienced plant-induced water stress. We developed a conceptual model based on Mantel analyses of our extensive data set. This model indicates that plant root effects on the multiple soil environmental and microbial mechanisms involved in root litter decomposition act through changing the functional gene profiles of microbial decomposers living near plant roots.

Authors:
 [1];  [2];  [3];  [4];  [3];  [5];  [2]
+ Show Author Affiliations
  1. Univ. of California, Berkeley, CA (United States); Univ. of Oklahoma, Norman, OK (United States)
  2. Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  3. Univ. of Oklahoma, Norman, OK (United States)
  4. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  5. Univ. of Oklahoma, Norman, OK (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Tsinghua Univ., Beijing (China)
Publication Date:
Research Org.:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE National Nuclear Security Administration (NNSA)
OSTI Identifier:
1526178
Alternate Identifier(s):
OSTI ID: 1636111
Report Number(s):
LLNL-JRNL-671996
Journal ID: ISSN 0038-0717; 794212
Grant/Contract Number:  
AC52-07NA27344; SC0004730; SC0010570; 00008322; SCW1060; SCW142
Resource Type:
Accepted Manuscript
Journal Name:
Soil Biology and Biochemistry
Additional Journal Information:
Journal Volume: 127; Journal Issue: C; Journal ID: ISSN 0038-0717
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Shi, Shengjing, Herman, Donald J., He, Zhili, Pett-Ridge, Jennifer, Wu, Liyou, Zhou, Jizhong, and Firestone, Mary K. Plant roots alter microbial functional genes supporting root litter decomposition. United States: N. p., 2018. Web. doi:10.1016/j.soilbio.2018.09.013.
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Shi, Shengjing, Herman, Donald J., He, Zhili, Pett-Ridge, Jennifer, Wu, Liyou, Zhou, Jizhong, & Firestone, Mary K. Plant roots alter microbial functional genes supporting root litter decomposition. United States. doi:10.1016/j.soilbio.2018.09.013.
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Shi, Shengjing, Herman, Donald J., He, Zhili, Pett-Ridge, Jennifer, Wu, Liyou, Zhou, Jizhong, and Firestone, Mary K. Tue . "Plant roots alter microbial functional genes supporting root litter decomposition". United States. doi:10.1016/j.soilbio.2018.09.013. https://www.osti.gov/servlets/purl/1526178.
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@article{osti_1526178,
title = {Plant roots alter microbial functional genes supporting root litter decomposition},
author = {Shi, Shengjing and Herman, Donald J. and He, Zhili and Pett-Ridge, Jennifer and Wu, Liyou and Zhou, Jizhong and Firestone, Mary K.},
abstractNote = {Decomposition of soil organic carbon is central to the global carbon cycle and profoundly affected by plant roots. While root “priming” of decomposition has been extensively investigated, it is not known how plants alter the molecular ecology of soil microbial decomposers. We disentangled the effects of Avena fatua, a common annual grass, on 13C-labeled root litter decomposition and quantified multiple genetic characteristics of soil bacterial and fungal communities. In our study, plants consistently suppressed rates of root litter decomposition. Microbes from planted soils had relatively more genes coding for low molecular weight compound degradation enzymes, while those from unplanted had more macromolecule degradation genes. Higher abundances of “water stress” genes in planted soils suggested that microbes experienced plant-induced water stress. We developed a conceptual model based on Mantel analyses of our extensive data set. This model indicates that plant root effects on the multiple soil environmental and microbial mechanisms involved in root litter decomposition act through changing the functional gene profiles of microbial decomposers living near plant roots.},
doi = {10.1016/j.soilbio.2018.09.013},
journal = {Soil Biology and Biochemistry},
number = C,
volume = 127,
place = {United States},
year = {2018},
month = {9}
}
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Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI:  10.1016/j.soilbio.2018.09.013
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Citation Metrics:
Cited by: 6 works
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Figures / Tables:

Table 1 Table 1: Total13C and13C associated with different soil fractions remaining in soil at the end of the experiment. Data are presented as means ± standard errors (n = 5). $P$ values shown in bold indicate significant changes in different 13C between planted and unplanted treatments ($P$ < 0.05).
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Works referencing / citing this record:

Plant presence reduces root and shoot litter decomposition rates of crops and wild relatives
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Plant presence reduces root and shoot litter decomposition rates of crops and wild relatives
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Massively parallel screening of synthetic microbial communities
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  • Kehe, Jared; Kulesa, Anthony; Ortiz, Anthony
  • Proceedings of the National Academy of Sciences, Vol. 116, Issue 26
  • DOI: 10.1073/pnas.1900102116

Simulating metagenomic stable isotope probing datasets with MetaSIPSim
journal, January 2020

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    Table 2 (p. 25)table
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    Figure 3 (p. 34)figure
    Figure 4 (p. 35)figure
    Figure 5 (p. 36)figure
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