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Fungal Communities of the Canola Rhizosphere: Keystone Species and Substantial Between-Year Variation of the Rhizosphere Microbiome

  • Fungal Microbiology
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Abstract

Rhizosphere microbes influence one another, forming extremely complex webs of interactions that may determine plant success. Identifying the key factors that structure the fungal microbiome of the plant rhizosphere is a necessary step in optimizing plant production. In a long-term field experiment conducted at three locations in the Canadian prairies, we tested the following hypotheses: (1) diversification of cropping systems influences the fungal microbiome of the canola (Brassica napus) rhizosphere; (2) the canola rhizosphere has a core fungal microbiome, i.e., a set of fungi always associated with canola; and (3) some taxa within the rhizosphere microbiome of canola are highly interrelated and fit the description of hub taxa. Our results show that crop diversification has a significant effect on the structure of the rhizosphere fungal community but not on fungal diversity. We also discovered and described a canola core microbiome made up of one zero-radius operational taxonomic unit (ZOTU), cf. Olpidium brassicae, and an eco-microbiome found only in 2013 consisting of 47 ZOTUs. Using network analysis, we identified four hub taxa in 2013: ZOTU14 (Acremonium sp.), ZOTU28 (Sordariomycetes sp.), ZOTU45 (Mortierella sp.) and ZOTU179 (cf. Ganoderma applanatum), and one hub taxon, ZOTU17 (cf. Mortierella gamsii) in 2016. None of these most interacting taxa belonged to the core microbiome or eco-microbiome for each year of sampling. This temporal variability puts into question the idea of a plant core fungal microbiome and its stability. Our results provide a basis for the development of ecological engineering strategies for the improvement of canola production systems in Canada.

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Acknowledgments

We are grateful to Mario Laterrière and David Gagné for their assistance with the bio-informatic analysis and thank the technical staff of the AAFC research centers in Lacombe, Lethbridge and Scott for carrying out the sampling and providing useful advice.

Funding

This study received funding from the following sources: the Agricultural Bioproducts Innovation Program (ABIP), the Prairie Canola Agronomic Research Program (PCARP), the Agriculture and Agri-Food Canada Canada Canola Cluster Growing Forward Initiative, the Alberta Canola Producers Commission, the Saskatchewan Canola Development Commission, the Manitoba Canola Growers Association, the Canola Council of Canada, the Western Grains Research Foundation, and the Natural Sciences and Engineering Research Council of Canada.

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  1. Institut de recherche en biologie végétale, ,Université de Montréal, 4101 East, Sherbrooke Street, Montréal, QC, H1X 2B2, Canada

    Jean-Baptiste Floc’h, Chantal Hamel & Marc St-Arnaud

  2. Jardin Botanique de Montréal, Montreal, Canada

    Jean-Baptiste Floc’h, Chantal Hamel & Marc St-Arnaud

  3. Québec Research and Development Centre of Quebec, Agriculture and Agri-Food Canada, Quebec City, QC, Canada

    Jean-Baptiste Floc’h & Chantal Hamel

  4. Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada

    K. Neil Harker

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  1. Jean-Baptiste Floc’h
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  2. Chantal Hamel
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  3. K. Neil Harker
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Correspondence to Marc St-Arnaud.

Electronic Supplementary Material

Figure S1

Cumulative precipitation proportion at each site in 2013 and 2016. The fungal communities in the canola rhizosphere may have been influenced by moisture availability in July 2016. (PNG 55 kb)

High resolution image (EPS 1234 kb)

Figure S2

Rarefaction curves for each rhizosphere soil sample, showing the relationship between the number of ZOTUs and the abundance of ITS sequences reads, in the 2013 dataset. The vertical black line indicates the plateau threshold for all curves. (PNG 152 kb)

High resolution image (EPS 7997 kb)

Figure S3

Rarefaction curves for each rhizosphere soil sample, showing the relationship between the number of ZOTUs and the abundance of ITS sequences reads, in the 2016 dataset. The vertical black line indicates the plateau threshold for all curves. (PNG 166 kb)

High resolution image (EPS 4188 kb)

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Floc’h, JB., Hamel, C., Harker, K.N. et al. Fungal Communities of the Canola Rhizosphere: Keystone Species and Substantial Between-Year Variation of the Rhizosphere Microbiome. Microb Ecol 80, 762–777 (2020). https://doi.org/10.1007/s00248-019-01475-8

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