Plant Compartments and Developmental Stages Modulate the Balance between Niche-Based and Neutral Processes in Soybean Microbiome

Abstract

Understanding the dynamics of plant-associated microbial communities within agriculture is well documented. However, the ecological processes that assemble the plant microbiome are not well understood. This study elucidates the relative dominance of assembly processes across plant compartments (root, stem, and leaves) and developmental stages (emergence, growth, flowering, and maturation). Bacterial community composition and assembly processes were assessed using 16S rRNA gene amplicon sequencing. Null models that couple phylogenetic community composition and species distribution models were used to evaluate ecological assembly processes of bacterial communities. All models highlighted that the balance between the assembly process was modulated by compartments and developmental stages. Dispersal limitation dominated amongst the epiphytic communities and at the maturation stage. Homogeneous selection dominated assembly across plant compartments and development stages. Overall, both sets of models were mostly in agreement in predicting the prevailing assembly processes. Our results show, for the first time, that even though niche-based processes dominate in the plant environment, the relative influence of dispersal limitation in community assembly is important.

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Acknowledgements

The authors would like to thank Benjamin Mimee from Agriculture and Agri-Food Canada for providing the seeds used in the study. We also wish to acknowledge Compute Canada for access to the University of Waterloo’s High-Performance Computing (HPC) infrastructure (Graham system) through a resources allocation granted to EY.

Funding

This work was supported by a Discovery Grant from the Natural Sciences and Engineering Research Council (NSERC) grant RGPIN 2014-05274 to EY. IM was supported by the Innovation and Scarce Skills scholarship from the South African National Research Foundation (NRF), Fonds de Recherche du Québec (FRQNT), and partly by Foundation Armand-Frappier.

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Correspondence to É. Yergeau.

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Moroenyane, I., Mendes, L., Tremblay, J. et al. Plant Compartments and Developmental Stages Modulate the Balance between Niche-Based and Neutral Processes in Soybean Microbiome. Microb Ecol (2021). https://doi.org/10.1007/s00248-021-01688-w

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Keywords

  • Soybean microbiome
  • Niche-based assembly
  • Community assembly
  • Phylogenetic community structure