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Title: Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling

Abstract

BACKGROUND: Rhizosphere microbial communities are key regulators of plant performance, yet few studies have assessed the impact of different management approaches on the rhizosphere microbiomes of major crops. Rhizosphere microbial communities are shaped by interactions between agricultural management and host selection processes, but studies often consider these factors individually rather than in combination. We tested the impacts of management (M) and rhizosphere effects (R) on microbial community structure and co-occurrence networks of maize roots collected from long-term conventionally and organically managed maize-tomato agroecosystems. We also explored the interaction between these factors (M × R) and how it impacts rhizosphere microbial diversity and composition, differential abundance, indicator taxa, co-occurrence network structure, and microbial nitrogen-cycling processes. RESULTS: Host selection processes moderate the influence of agricultural management on rhizosphere microbial communities, although bacteria and fungi respond differently to plant selection and agricultural management. We found that plants recruit management-system-specific taxa and shift N-cycling pathways in the rhizosphere, distinguishing this soil compartment from bulk soil. Rhizosphere microbiomes from conventional and organic systems were more similar in diversity and network structure than communities from their respective bulk soils, and community composition was affected by both M and R effects. In contrast, fungal community composition wasmore » affected only by management, and network structure only by plant selection. Quantification of six nitrogen-cycling genes (nifH, amoA [bacterial and archaeal], nirK, nrfA, and nosZ) revealed that only nosZ abundance was affected by management and was higher in the organic system. CONCLUSIONS: Plant selection interacts with conventional and organic management practices to shape rhizosphere microbial community composition, co-occurrence patterns, and at least one nitrogen-cycling process. Reframing research priorities to better understand adaptive plant-microbe feedbacks and include roots as a significant moderating influence of management outcomes could help guide plant-oriented strategies to improve productivity and agroecosystem sustainability.« less

Authors:
 [1];  [2];  [3];  [1]
  1. Univ. of California, Davis, CA (United States)
  2. Univ. of Illinois at Urbana-Champaign, IL (United States)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); USDA; University of California, Davis
OSTI Identifier:
1599819
Grant/Contract Number:  
AC02-05CH11231; CA-D-PLS-2332-H
Resource Type:
Accepted Manuscript
Journal Name:
Microbiome
Additional Journal Information:
Journal Volume: 7; Journal Issue: 1; Journal ID: ISSN 2049-2618
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; rhizosphere; agricultural management; soil microbial community; nitrogen cycling; quantitative PCR; agroecosystem; adaptive feedbacks

Citation Formats

Schmidt, Jennifer E., Kent, Angela D., Brisson, Vanessa L., and Gaudin, Amélie C. M. Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling. United States: N. p., 2019. Web. doi:10.1186/s40168-019-0756-9.
Schmidt, Jennifer E., Kent, Angela D., Brisson, Vanessa L., & Gaudin, Amélie C. M. Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling. United States. doi:10.1186/s40168-019-0756-9.
Schmidt, Jennifer E., Kent, Angela D., Brisson, Vanessa L., and Gaudin, Amélie C. M. Thu . "Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling". United States. doi:10.1186/s40168-019-0756-9. https://www.osti.gov/servlets/purl/1599819.
@article{osti_1599819,
title = {Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling},
author = {Schmidt, Jennifer E. and Kent, Angela D. and Brisson, Vanessa L. and Gaudin, Amélie C. M.},
abstractNote = {BACKGROUND: Rhizosphere microbial communities are key regulators of plant performance, yet few studies have assessed the impact of different management approaches on the rhizosphere microbiomes of major crops. Rhizosphere microbial communities are shaped by interactions between agricultural management and host selection processes, but studies often consider these factors individually rather than in combination. We tested the impacts of management (M) and rhizosphere effects (R) on microbial community structure and co-occurrence networks of maize roots collected from long-term conventionally and organically managed maize-tomato agroecosystems. We also explored the interaction between these factors (M × R) and how it impacts rhizosphere microbial diversity and composition, differential abundance, indicator taxa, co-occurrence network structure, and microbial nitrogen-cycling processes. RESULTS: Host selection processes moderate the influence of agricultural management on rhizosphere microbial communities, although bacteria and fungi respond differently to plant selection and agricultural management. We found that plants recruit management-system-specific taxa and shift N-cycling pathways in the rhizosphere, distinguishing this soil compartment from bulk soil. Rhizosphere microbiomes from conventional and organic systems were more similar in diversity and network structure than communities from their respective bulk soils, and community composition was affected by both M and R effects. In contrast, fungal community composition was affected only by management, and network structure only by plant selection. Quantification of six nitrogen-cycling genes (nifH, amoA [bacterial and archaeal], nirK, nrfA, and nosZ) revealed that only nosZ abundance was affected by management and was higher in the organic system. CONCLUSIONS: Plant selection interacts with conventional and organic management practices to shape rhizosphere microbial community composition, co-occurrence patterns, and at least one nitrogen-cycling process. Reframing research priorities to better understand adaptive plant-microbe feedbacks and include roots as a significant moderating influence of management outcomes could help guide plant-oriented strategies to improve productivity and agroecosystem sustainability.},
doi = {10.1186/s40168-019-0756-9},
journal = {Microbiome},
number = 1,
volume = 7,
place = {United States},
year = {2019},
month = {11}
}

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