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

Schmidt, Jennifer E.; Kent, Angela D.; Brisson, Vanessa L.; Gaudin, Amélie C.  M.

doi:10.1186/s40168-019-0756-9

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

Journal Article · Thu Nov 07 00:00:00 EST 2019 · Microbiome

DOI:https://doi.org/10.1186/s40168-019-0756-9· OSTI ID:1599819

Schmidt, Jennifer E. ^[1]; Kent, Angela D. ^[2]; Brisson, Vanessa L. ^[3]; Gaudin, Amélie C. M. ^[1]

Univ. of California, Davis, CA (United States)
Univ. of Illinois at Urbana-Champaign, IL (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); USDA; University of California, Davis

Grant/Contract Number:: AC02-05CH11231; CA-D-PLS-2332-H

OSTI ID:: 1599819

Journal Information:: Microbiome, Vol. 7, Issue 1; ISSN 2049-2618

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 167 works

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
rhizosphere
agricultural management
soil microbial community
nitrogen cycling
quantitative PCR
agroecosystem
adaptive feedbacks

MOESM10 of Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling Schmidt, Jennifer; Kent, Angela; Brisson, Vanessa https://doi.org/10.6084/m9.figshare.10270727 The current record is supplemented by this image	image	January 2019
MOESM10 of Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling Schmidt, Jennifer; Kent, Angela; Brisson, Vanessa https://doi.org/10.6084/m9.figshare.10270727.v1 The current record is supplemented by this image	image	January 2019
MOESM11 of Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling Schmidt, Jennifer; Kent, Angela; Brisson, Vanessa https://doi.org/10.6084/m9.figshare.10270736 The current record is supplemented by this image	image	January 2019
MOESM11 of Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling Schmidt, Jennifer; Kent, Angela; Brisson, Vanessa https://doi.org/10.6084/m9.figshare.10270736.v1 The current record is supplemented by this image	image	January 2019
MOESM1 of Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling Schmidt, Jennifer; Kent, Angela; Brisson, Vanessa https://doi.org/10.6084/m9.figshare.10270742 The current record is supplemented by this dataset	dataset	January 2019
MOESM2 of Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling Schmidt, Jennifer; Kent, Angela; Brisson, Vanessa https://doi.org/10.6084/m9.figshare.10270745 The current record is supplemented by this text	text	January 2019
MOESM3 of Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling Schmidt, Jennifer; Kent, Angela; Brisson, Vanessa https://doi.org/10.6084/m9.figshare.10270748 The current record is supplemented by this text	text	January 2019
MOESM4 of Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling Schmidt, Jennifer; Kent, Angela; Brisson, Vanessa https://doi.org/10.6084/m9.figshare.10270754.v1 The current record is supplemented by this dataset	dataset	January 2019
MOESM5 of Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling Schmidt, Jennifer; Kent, Angela; Brisson, Vanessa https://doi.org/10.6084/m9.figshare.10270760 The current record is supplemented by this dataset	dataset	January 2019
MOESM5 of Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling Schmidt, Jennifer; Kent, Angela; Brisson, Vanessa https://doi.org/10.6084/m9.figshare.10270760.v1 The current record is supplemented by this dataset	dataset	January 2019
MOESM6 of Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling Schmidt, Jennifer; Kent, Angela; Brisson, Vanessa https://doi.org/10.6084/m9.figshare.10270763 The current record is supplemented by this dataset	dataset	January 2019
MOESM6 of Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling Schmidt, Jennifer; Kent, Angela; Brisson, Vanessa https://doi.org/10.6084/m9.figshare.10270763.v1 The current record is supplemented by this dataset	dataset	January 2019
MOESM7 of Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling Schmidt, Jennifer; Kent, Angela; Brisson, Vanessa https://doi.org/10.6084/m9.figshare.10270769 The current record is supplemented by this text	text	January 2019
MOESM8 of Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling Schmidt, Jennifer; Kent, Angela; Brisson, Vanessa https://doi.org/10.6084/m9.figshare.10270772 The current record is supplemented by this image	image	January 2019
MOESM8 of Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling Schmidt, Jennifer; Kent, Angela; Brisson, Vanessa https://doi.org/10.6084/m9.figshare.10270772.v1 The current record is supplemented by this image	image	January 2019
MOESM9 of Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling Schmidt, Jennifer; Kent, Angela; Brisson, Vanessa https://doi.org/10.6084/m9.figshare.10270778 The current record is supplemented by this image	image	January 2019
MOESM9 of Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling Schmidt, Jennifer; Kent, Angela; Brisson, Vanessa https://doi.org/10.6084/m9.figshare.10270778.v1 The current record is supplemented by this image	image	January 2019
Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling Schmidt, Jennifer; Kent, Angela; Brisson, Vanessa https://doi.org/10.6084/m9.figshare.c.4729757 The current record is supplemented by this collection	collection	January 2019
Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling Schmidt, Jennifer; Kent, Angela; Brisson, Vanessa https://doi.org/10.6084/m9.figshare.c.4729757.v1 The current record is supplemented by this collection	collection	January 2019
MOESM3 of Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling Schmidt, Jennifer; Kent, Angela; Brisson, Vanessa https://doi.org/10.6084/m9.figshare.10270748.v1 The current record is supplemented by this text	text	January 2019
MOESM4 of Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling Schmidt, Jennifer; Kent, Angela; Brisson, Vanessa https://doi.org/10.6084/m9.figshare.10270754 The current record is supplemented by this dataset	dataset	January 2019
MOESM1 of Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling Schmidt, Jennifer; Kent, Angela; Brisson, Vanessa https://doi.org/10.6084/m9.figshare.10270742.v1 The current record is supplemented by this dataset	dataset	January 2019
MOESM7 of Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling Schmidt, Jennifer; Kent, Angela; Brisson, Vanessa https://doi.org/10.6084/m9.figshare.10270769.v1 The current record is supplemented by this text	text	January 2019
MOESM2 of Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling Schmidt, Jennifer; Kent, Angela; Brisson, Vanessa https://doi.org/10.6084/m9.figshare.10270745.v1 The current record is supplemented by this text	text	January 2019

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

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