Plant selection and ecological microhabitat drive the shrub-associated microbiome selection in revegetated shrub ecosystems

Shrubs are commonly used for revegetation in degraded dryland ecosystems worldwide, and their introduction can recruit a large number of microbes from the soil. However, the assembly of plant-associated microbiomes and the effect of the introduction of plants on soil and plant-associated microbiomes remain unclear. In this study, we investigated shrub-associated microbes from five ecological microhabitats, including the leaves, litter, roots, rhizosphere, and root zone, across four xeric shrub plantations (Artemisia ordosica, Caragana korshinskii, Hedysarum mongolicum, and Salix psammophila), using 16S and internal transcribed spacer2 rRNA gene sequencing. We found that the changes in the bacterial and fungal communities were more influenced by the microhabitats than by the plant species, with distinct niche differentiation. Microbial source tracking and nestedness analysis showed that the shrub-associated bacteria primarily originated from the bulk soils and were slightly selected in the different microhabitats; this similar pattern was not observed in the shrub-associated fungi. Furthermore, the surrounding zone of roots was a hot spot for microbial recruitment in revegetated shrubs. Null model analysis indicated that the deterministic and stochastic process dominated the assembly of bacterial and fungal communities, respectively. Our findings suggest that ecological microhabitats of revegetated shrublands strongly influence the bacterial and fungal compositions of the plant microbiome. This study enhances our understanding of the mechanism underlying the plant-soil microbiome feedback during the initial plant-establishment period in dryland ecosystems. Furthermore, our insights can assist in the development of effective strategies for establishing and managing vegetation sustainably in drylands. •Microbiomes in five microhabitats in four xeric shrubs were studied.•Microhabitats primarily influence the changes in bacterial and fungal communities.•Shrub-associated bacteria primarily originated from the bulk soil.•Determinism and stochasticity dominate bacterial and fungal community assembly, respectively.