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Crop Residues in Wheat-Oilseed Rape Rotation System: a Pivotal, Shifting Platform for Microbial Meetings

  • Environmental Microbiology
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Abstract

Crop residues are a crucial ecological niche with a major biological impact on agricultural ecosystems. In this study, we used a combined diachronic and synchronic field experiment based on wheat-oilseed rape rotations to test the hypothesis that plant is a structuring factor of microbial communities in crop residues, and that this effect decreases over time with their likely progressive degradation and colonisation by other microorganisms. We characterised an entire fungal and bacterial community associated with 150 wheat and oilseed rape residue samples at a plurennial scale by metabarcoding. The impact of plant species on the residue microbiota decreased over time and our data revealed turnover, with the replacement of oligotrophs, often plant-specific genera (such as pathogens) by copiotrophs, belonging to more generalist genera. Within a single cropping season, the plant-specific genera and species were gradually replaced by taxa that are likely to originate from the soil. These changes occurred more rapidly for bacteria than for fungi, known to degrade complex compounds. Overall, our findings suggest that crop residues constitute a key fully-fledged microbial ecosystem. Taking into account this ecosystem, that has been neglected for too long, is essential, not only to improve the quantitative management of residues, the presence of which can be detrimental to crop health, but also to identify groups of beneficial microorganisms. Our findings are of particular importance, because the wheat-oilseed rape rotation, in which no-till practices are frequent, is particularly widespread in the European arable cropping systems.

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Data Availability

The raw sequencing data is available from the European Nucleotide Archive (ENA) under the study accession PRJEB27255 (sample SAMEA4723701 to SAMEA4724326). We provide the command-line script for data analysis and all necessary input files as Additional File 2.

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Acknowledgements

This study was performed in collaboration with the GeT core facility, Toulouse, France (http://get.genotoul.fr) and was supported by France Génomique National Infrastructure, funded as part of ‘Investissement d’avenir’ program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09). We thank Martial Briand (INRA, UMR IRHS) and Dr. Gautier Richard (INRA, UMR IGEPP) for assistance with bioinformatic analyses, and Dr. Thierry Rouxel (INRA, UMR BIOGER) for improving and clarifying this manuscript. We thank Julie Sappa for her help correcting our English. We finally thank the reviewers for their insightful comments on the paper, as these comments led us to improve the correctness of several analyses.

Funding

This study was supported by a grant from the European Union Horizon Framework 2020 Program (EMPHASIS Project, Grant Agreement No. 634179) covering the 2015–2019 period.

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Author notes

  1. Valérie Laval and Frédéric Suffert contributed equally to this work.

Authors and Affiliations

  1. UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850, Thiverval-Grignon, France

    Lydie Kerdraon, Marie-Hélène Balesdent, Valérie Laval & Frédéric Suffert

  2. UMR IRHS, INRA, Agrocampus Ouest, Université d’Angers, 49071, Beaucouzé, France

    Matthieu Barret

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  1. Lydie Kerdraon
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  2. Marie-Hélène Balesdent
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  3. Matthieu Barret
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Contributions

LK, FS, VL, MHB and MB conceived the study, participated in its design, and wrote the manuscript. LK conducted the experiments and analysed the data. FS and VL supervised the project. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Valérie Laval or Frédéric Suffert.

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Bacterial 16S sequence dataset (also deposited in GitHub: https://github.com/LydieKerdraon/Kerdraon_etal_CropResidues) (RDATA 26533 kb)

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Kerdraon, L., Balesdent, MH., Barret, M. et al. Crop Residues in Wheat-Oilseed Rape Rotation System: a Pivotal, Shifting Platform for Microbial Meetings. Microb Ecol 77, 931–945 (2019). https://doi.org/10.1007/s00248-019-01340-8

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