Abstract
Plant-associated microbiomes are key determinants of host-plant fitness, productivity, and function. However, compared to bacterial community, we still lack fundamental knowledge concerning the variation in the fungal microbiome at the plant niche level. In this study, we quantified the fungal communities in the rhizosphere soil, as well as leaf and root endosphere compartments of a subtropical island shrub, Mussaenda kwangtungensis, using high-throughput DNA sequencing. We found that fungal microbiomes varied significantly across different plant compartments. Rhizosphere soil exhibited the highest level of fungal diversity, whereas the lowest level was found in the leaf endosphere. Further, the fungal communities inhabiting the root endosphere shared a greater proportion of fungal operational taxonomic units (OTUs) with rhizosphere communities than with leaf fungal endophyte communities, despite significant separation in community structure between the two belowground compartments. The fungal co-occurrence networks in the three compartments of M. kwangtungensis showed scale-free features and non-random co-occurrence patterns and matched the topological properties of small-world and evidently modular structure. Additionally, the rhizosphere network was more complex and showed higher centrality and connectedness than the leaf and root endosphere networks. Overall, our findings provide comprehensive insights into the structural variability, niche differentiation, and co-occurrence patterns in the plant associated fungal microbiome.
Highlights
Plant associated fungal communities exert profound and crucial influence on plant survival, health, productivity and even ecosystem functions (Berg et al, 2005; Rodriguez et al, 2009)
The plant holobiome is gaining increased attention, little work has been conducted to explore the niche differentiation in their community structure and co-occurrence patterns associated with the leaf endosphere, root endosphere, and the rhizosphere compartments
We removed operational taxonomic units (OTUs) that have fewer than 10 reads, and kept 2,242,941 fungal internal transcribed spacer 2 (ITS2) reads
Summary
Plant associated fungal communities exert profound and crucial influence on plant survival, health, productivity and even ecosystem functions (Berg et al, 2005; Rodriguez et al, 2009). The plant holobiome is gaining increased attention, little work has been conducted to explore the niche differentiation in their community structure and co-occurrence patterns associated with the leaf endosphere, root endosphere, and the rhizosphere compartments. Understanding the composition, dynamics, and activity of the endophytic and rhizosphere fungal community is critical for the development of new strategies to promote plant growth and health in both agro-ecosystems and natural ecosystems (Raaijmakers et al, 2009). Network analysis of taxa co-occurrence patterns revealing potential biotic interactions, habitat affinities, or shared physiologies among members, can offer new insights into the structure and assembly of complex microbial communities that cannot be obtained by the traditional suite of analytical approaches (Barberan et al, 2012; Zhang et al, 2018). This study will advance our understanding in assembly principles and ecological interactions of plant associated fungal communities, and may lay the foundation for further exploitation and optimization of the community for human advantage
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