Host genetic variation drives the differentiation in the ecological role of the native Miscanthus root-associated microbiome

Ji, Niuniu; Liang, Di; Clark, Lindsay V.; Sacks, Erik J.; Kent, Angela D.

doi:10.1186/s40168-023-01646-3

Host genetic variation drives the differentiation in the ecological role of the native Miscanthus root-associated microbiome

Journal Article · Sat Sep 30 00:00:00 EDT 2023 · Microbiome

DOI:https://doi.org/10.1186/s40168-023-01646-3· OSTI ID:2007154

Ji, Niuniu ^[1]; Liang, Di ^[2]; Clark, Lindsay V. ^[2]; Sacks, Erik J. ^[2]; Kent, Angela D. ^[2]

University of Illinois at Urbana-Champaign, IL (United States); CABBI
University of Illinois at Urbana-Champaign, IL (United States)

Microbiome recruitment is influenced by plant host, but how host plant impacts the assembly, functions, and interactions of perennial plant root microbiomes is poorly understood. Here we examined prokaryotic and fungal communities between rhizosphere soils and the root endophytic compartment in two native Miscanthus species (Miscanthus sinensis and Miscanthus floridulus) of Taiwan and further explored the roles of host plant on root-associated microbiomes. Our results suggest that host plant genetic variation, edaphic factors, and site had effects on the root endophytic and rhizosphere soil microbial community compositions in both Miscanthus sinensis and Miscanthus floridulus, with a greater effect of plant genetic variation observed for the root endophytic communities. Host plant genetic variation also exerted a stronger effect on core prokaryotic communities than on non-core prokaryotic communities in each microhabitat of two Miscanthus species. From rhizosphere soils to root endophytes, prokaryotic co-occurrence network stability increased, but fungal co-occurrence network stability decreased. Furthermore, we found root endophytic microbial communities in two Miscanthus species were more strongly driven by deterministic processes rather than stochastic processes. Root-enriched prokaryotic OTUs belong to Gammaproteobacteria, Alphaproteobacteria, Betaproteobacteria, Sphingobacteriia, and [Saprospirae] both in two Miscanthus species, while prokaryotic taxa enriched in the rhizosphere soil are widely distributed among different phyla. We provide empirical evidence that host genetic variation plays important roles in root-associated microbiome in Miscanthus. The results of this study have implications for future bioenergy crop management by providing baseline data to inform translational research to harness the plant microbiome to sustainably increase agriculture productivity.

View Accepted Manuscript (DOE)

Research Organization:: Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Urbana, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0018420

OSTI ID:: 2007154

Journal Information:: Microbiome, Journal Name: Microbiome Journal Issue: 1 Vol. 11; ISSN 2049-2618

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Root-associated microbiomes of wheat under the combined effect of plant development and nitrogen fertilization Chen, Shuaimin; Waghmode, Tatoba; Sun, Ruibo figshare https://doi.org/10.6084/m9.figshare.c.4708817.v1	collection	January 2019
Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula Brown, Shawn P.; Grillo, Michael A.; Podowski, Justin C. figshare https://doi.org/10.6084/m9.figshare.c.5135614.v1	collection	January 2020

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Additional file 1 of Host genotype-specific rhizosphere fungus enhances drought resistance in wheat Yue, Hong; Sun, Xuming; Wang, Tingting figshare https://doi.org/10.6084/m9.figshare.25333388	dataset	January 2024

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54 ENVIRONMENTAL SCIENCES
Core microbiome
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Microbial co-occurrence networks
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Rhizosphere soil

Host genetic variation drives the differentiation in the ecological role of the native Miscanthus root-associated microbiome

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