The concept of the holobiont has been proposed for plants. The term ‘holobiont’ was first defined by Lynn Margulis in 1991, as a simple biological unit involving a host and a single inherited symbiont. Zilberg-Rosenberg and Rosenberg (2008) expanded this definition to the entire microbiota. These authors have further proposed the holobiont to be a selection unit, which underlies the hologenome based theory of evolution.

This Research Topic is one of two volumes on the Plant Holobiont:
The Plant Holobiont Volume I: Microbiota as part of the holobiont; challenges for agriculture
The Plant Holobiont Volume II: Impacts of the Rhizosphere on Plant Health

Promoting beneficial interactions between plants and their associated microbiota is a way to ensure the sustainability of a cropping system in agroecology. The hologenomic view of crop-microbe interactions allows us to better consider the plant-microbe interactions and their results on plant growth, ecology and evolution. This represents a major issue in the concept of the so-called crop ideotype, defined as a plant genotype chosen for its capacity to better exploit a given environment and to adapt to abiotic and biotic stressors. The next step will be to consider interactions between plants within a plant canopy (mono- or pluri-species) as interactions between holobionts when taking into account ecosystem services expected from agroecosystems (e.g. food production, climate mitigation, water biofiltration).

Thus, new plant genotypes need to be selected in order to better exploit rhizodeposits and plant-microbiota interactions in the rhizosphere. This will require the identification of plant traits involved in the recruitment of beneficial microbial populations/functions.

To reach that target, further research is needed to (i) identify plant and microbiota determinants for a beneficial interaction, (ii) define functional crop holobionts, (iii) design cropping systems that value the best the corresponding holobionts, and (iv) understand and predict the co-evolution of the beneficial plant-microbe interactions.
This Research Topic focuses on studies (including e.g. original research, perspectives, minireviews, commentaries and opinion papers) that will address:

1. Methods of characterizing healthy and functional holobionts; taxonomic and phenotypic/functional diversity, structure, microbial networks.
2. Interactions within the holobiont: plant legacy effect, selection and succession of beneficial microbiota, microbe-microbe interactions.
3. Role of microbiota in the interaction among holobionts.
4. Holobiont co-adaptation and co-evolution.
5. Agricultural practices and their impact on the holobiont: conventional and organic farming, crop rotation, intercropping, agroforestry.
6. Engineering holobionts towards sustainable agriculture.

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Frontiers in Plant Science

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