Core rhizosphere microbiomes of dryland wheat are influenced by location and land use history

Authors: Schlatter, Daniel; YIN, CHUNTAO - Washington State University; HULBERT, SCOT - Washington State University; Paulitz, Timothy

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/10/2019
Publication Date: 2/18/2020
Citation: Schlatter, D.C., Yin, C., Hulbert, S., Paulitz, T.C. 2020. Core rhizosphere microbiomes of dryland wheat are influenced by location and land use history. Applied and Environmental Microbiology. 86(5):e02135-19. https://doi.org/10.1128/AEM.02135-19.
DOI: https://doi.org/10.1128/AEM.02135-19

Interpretive Summary: Bacterial and fungal communities are highly variable across different locations and wheat cropping system zones in Eastern Washington. Using next-generation sequencing, we identified the key core communities in the bulk soil and rhizosphere of wheat. Many of the taxa were common to both bulk soil and rhizosphere samples, but only a small core were present in almost all the rhizosphere samples across all locations. Core bacteria were Bradyrhizobium, Sphingomonadaceae, Massilia, Variovorax, Oxalobacteraceae, and Caulobacteraceae. Key core fungal taxa in the rhizosphere included Nectriaceae, Pleosporaceae, Trichocomaceae, Mortierellaceae and Ulocladium, Microdochium, Macroventuria, and Cadophora.

Technical Abstract: The Inland Pacific Northwest is one of the most productive dryland wheat production areas in the United States. It encompasses a range of soil types and annual precipitation zones from 200 to 600 mm/yr. We explored the bacterial and fungal communities among multiple locations across this gradient using next-generation sequencing to identify the taxa that consistently associated with wheat roots, to determine how land use history influences this community, and how microbial co-occurrence networks vary with location, land use history and root proximity. Location and land use history (long-term no-till vs non-cropped Conservation Reserve Program (CRP) were the strongest drivers of bacterial and fungal communities. Members of Burkholderiaceae, Oxalobacteraceae, Sphingomonadaceae, Sphingobacteriaceae, Xanthomonadaceae, Flavobacteriaceae, Micrococcaceae, and Streptomycetaceae tended to be more prevalent in soils cultivated to wheat with a history of no-till. In CRP soils, members of Solirobrobacteraceae, Rubrobacteraceae, Propionibacteriaceae, Opitutaceae, and Cytophagaceae tended to be relatively more abundant. Contrasting bulk and rhizosphere soil, rhizospheres were especially enriched in the bacterial families Burkholderiaceae, Caulobacteraceae, Comamonadaceae, Cytophagaceae, Flavobacteriaceae, Microbacteriaceae, Mycobacteriacee, Oxalobacteraceae, Phyllobacteriaceae, Pseudomonadaceae, Rhizobiaceae, and Sphingobacteriaceae. Bulk soil, in contrast, was enriched in only a few families, such as Gaiellaceae, Kineosporiaceae, Micromonospora, and Pseudonocardiaceae. Members of the fungal families Chaetomiaceae, Hyaloscyphaceae, Nectriaceae, Coniochaetaceae, Pleosporaceae, and Xylariaceae were significantly more abundant in soils with a history of wheat production in no-till. In contrast, Helotiales, Ceratobasidiaceae, Sebacinales, and Sporomiacae were enriched in soils with a history of CRP. There was a core set of bacteria and fungi that was found in >95% of rhizosphere or bulk soil samples. The most abundant core bacteria in the wheat rhizosphere were members of Bradyrhizobium, Sphingomonadaceae, Massilia, Variovorax, Oxalobacteraceae, and Caulobacteraceae. Fungal taxa in the rhizosphere included Nectriaceae, Pleosporaceae, Trichocomaceae, Mortierellaceae and Ulocladium, Microdochium, Macroventuria, and Cadophora. There was a large overlap between fungal and bacterial taxa found in the bulk soil compared to rhizosphere. Richness and diversity of bacteria was higher in bulk soil compared to rhizosphere soil, and higher in CRP vs no-till soils. In one location, a virgin soil that was never cropped had a distinct bacterial and fungal community. Bacterial co-occurrence networks were more complex in CRP compared to cropped no-till (NT) fields. Hub taxa included Acidobacteria GP1, Massilia, and Variovorax in NT soil and Bacillus, Microvirga, Actinobacteria, Nocardioides, Chitinophaga, and Xanthomonadaceae in CRP soil. Key fungal hub taxa in NT soils were Penicillium, Herpotrichiellaceae, Humicola, and Mortierella but only an OTU of Chytridiomycetes was a hub in the CRP soil.