Environmental adaptation of root-associated microbiomes

Root-associated microbial communities play important roles in plant growth, health and environmental adaptability. However, it remains unknown which microbial taxa possibly help their hosts adapt to shady environment and the ecological mechanisms that lead to changes of root-associated microbial communities. Here, we investigated the bacterial and fungal communities of rhizosphere and endosphere associated with saplings of Abies faxoniana, a dormant tree species in the vast southwest area in China, and bulk soil from both semi-cloudy and semi-sunny slopes using deep high-throughput sequencing techniques. The growth-promoting bacteria Burkholderia and mycorrhizal fungi Piloderma were enriched in the endosphere of the semi-cloudy slopes. Notably, pH was the dominant factor determining the alpha diversity of bulk and rhizosphere bacterial communities, whereas the plant aboveground water content (AWC) mostly influenced endosphere bacteria. By contrast, the bulk and endosphere fungal community alpha diversity were mostly influenced by plant height, while the soil available N had the highest contributions for rhizosphere fungal alpha diversity. In addition, the most impacting factors that determine the beta diversity of bulk, endosphere and rhizosphere bacterial communities were pH, sapling biomass and slope aspect, respectively. Variance partitioning analysis (VPA) showed that soil properties explained the most variation (14.2%) of bulk bacterial community structures, while plant traits mostly explained endosphere (5.5%) or rhizosphere (2.8%) bacterial communities. For fungi, slope aspect was the most explanation factor for fungal communities irrespective of sample types. Structural equation model (SEM) analysis indicated that fungi rather than bacteria influence tree sapling biomass. Our finding provides a mechanistic understanding for plant adaptation to shady environment from microbiome perspectives and related ecological mechanisms that determine belowground community assembly patterns. Thus, the management of forest microbial ecology needs to simultaneously consider slope aspect, sample types and microbial taxa for improving ecosystem function and service.