The assembly of phyllosphere microbial communities is under the control of stochastic and deterministic processes. In neotropical forests, the tree host identity and physiology together with strong heterogeneities of the environment within the canopy and at the leaf scale could potentially drive the assembly of phyllosphere microbial communities. We analyzed the assembly processes shaping the microbial communities living in the endophytic and epiphytic phyllosphere in tree species across vertical environmental gradients present from the top of the canopy to the ground. We used DNA metabarcoding to characterize microbial communities and described the microhabitats along the gradient by measuring morphological and chemical foliar traits of host trees. The results revealed that the assembly of both communities resulted from a balance of deterministic and stochastic effects with strong discrepancies between fungal and bacterial communities. Different effects of the host and of the vertical environmental gradient shaped epiphytic and endophytic communities. If fungal communities were mainly shaped by the host identity, different leaf morphological and chemical leaf traits drove the epi- and endophytic bacterial communities. Taken together, the phyllosphere represent a global selective pressure of the plant on microbial communities but the microhabitat at the leaf scale contribute also significantly to drive the assembly of microbial communities.

Funding : Agence Nationale de la Recherche (FR) ANR-10-LABX-25-01 In accordance with Article 17, paragraph 2 of the Nagoya Protocol, this work benefits of the Access and Benefit Sharing Agreement ABSCH-IRCC-FR-245926-1.