Seed or soil: Tracing back the plant mycobiota primary sources | Graine ou sol : déterminer les sources primaires du mycobiote végétal

Sequencing data are publicly available in GenBank (accession number: PRJNA1028866 for bulk soil, rhizosphere, and roots in situ and PRJNA1035432 for leaves, seeds in situ, and seedling's leaves and roots). The bioinformatics pipeline can be found at: https://github.com/BPerezLamarque/Scripts.

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English. Abstract: Plants host diverse communities of fungi (the mycobiota), playing crucial roles in their development. The assembly processes of the mycobiota, however, remain poorly understood, in particular, whether it is transmitted by parents through the seeds (vertical transmission) or recruited in the environment (horizontal transmission). Here we attempt to quantify the relative contributions of horizontal and vertical transmission in the mycobiota assembly of a desert shrub, Haloxylon salicornicum, by comparing the mycobiota of in situ bulk soil and seeds to that of (i) in situ adult individuals and (ii) in vitro-germinated seedlings in soil collected in situ. We show that the mycobiota are partially vertically transmitted through the seeds to seedlings, whereas bulk soil has a limited contribution to the seedling's mycobiota. In adults, root and bulk soil mycobiota tend to resemble each other, suggesting a compositional turnover in plant mycobiota during plant development due to horizontal transmission. Thus, the mycobiota are transmitted both horizontally and vertically depending on the plant tissue and developmental stage. Understanding the respective contribution of these transmission pathways to the plant mycobiota is fundamental to deciphering potential coevolutionary processes between plants and fungi. Our findings particularly emphasize the importance of vertical transmission in desert ecosystems.Graphical Abstract: https://enviromicro-journals.onlinelibrary.wiley.com/cms/asset/6ece3818-87a9-428d-b07f-8659320c1a34/emi413301-toc-0001-m.jpgThe plant microbiota is essential to plant functioning, but the assembly process shaping it is poorly understood, in particular for fungal partners. Here, by coupling in situ sampling and in vitro experiment, we show that the fungal microbiota of Haloxylon salicornicum, a desert shrub, is transmitted both vertically through seeds and horizontally through soil depending on the plant compartment and the developmental stage, highlighting the importance of both transmission paths.

French. Les plantes hébergent diverses communautés de champignons (le mycobiote), qui jouent un rôle crucial dans leur développement. Les processus d'assemblage du mycobiote restent cependant mal compris. En particulier nous ne savons pas s'il est transmis par les parents via les graines (transmission verticale) ou recruté dans l'environnement (transmission horizontale). Nous tentons ici de quantifier la contribution relative de la transmission horizontale et verticale dans l'assemblage du mycobiote d'un arbuste du désert, Haloxylon salicornicum, en comparant le mycobiote du sol et des graines in situ à celui (i) d'individus adultes in situ et (ii) de plantules germées in vitro dans un sol prélevé in situ. Nous montrons que le mycobiote est partiellement transmis verticalement par les graines aux plantules, alors que le sol a une contribution limitée au mycobiote des plantules. Chez les adultes, le mycobiote des racines et du sol tendent à se ressembler, ce qui suggère un renouvellement de la composition des mycobiotes des plantes au cours de leur développement en raison de la transmission horizontale. Ainsi, le mycobiote est transmis à la fois horizontalement et verticalement en fonction du tissu végétal et du stade de développement. Comprendre la contribution respective de ces voies de transmission au mycobiote végétal est fondamental pour déchiffrer les processus potentiels de coévolution entre les plantes et les champignons. Nos résultats soulignent en particulier l'importance de la transmission verticale dans les écosystèmes désertiques.