Dynamic variation of Paris polyphylla root-associated microbiome assembly with planting years

Abstract

Paris polyphylla var. yunnanensi ( P. polyphylla ) is an important perennial Chinese traditional medicine.  However, studies focusing on P. polyphylla and related microbes are scarce, especially on the assembly mechanisms and dynamics of the P. polyphylla microbiome. High-throughput sequencing of the 16S rRNA genes was implemented to investigate the diversity, community assembly process and molecular ecological network of the bacterial communities in three root compartments (bulk soil, rhizosphere, and root endosphere) across three years. Our results demonstrated that the composition and assembly process of the microbial community in different compartments varied greatly and were strongly affected by planting years. Bacterial diversity reduced from bulk soils to rhizosphere soils to root endosphere and varied over time. Microorganisms benefit to plants were selectively enriched in P. polyphylla roots as its core microbiome, including Pseudomonas, Rhizobium, Steroidobacter, Sphingobium and Agrobacterium. And nitrogen metabolism, carbon metabolism, phosphonate and phosphinate metabolism genes in bulk soils increased over time, and the network’s complexity and the proportion of stochasticity in the community assembly process increased. These findings suggest that P. polyphylla exerts the selective effect to enrich the beneficial microorganisms and proves the sequential increasing selection pressure with P. polyphylla growth. Our work adds to the understanding of the dynamic processes of plant-associated microbial community assembly, guides the selection and application timing of P. polyphylla -associated microbial inoculants and is vital for sustainable agriculture.

Keywords: Paris polyphylla var. yunnanensi, Compartments, Community assembly, Dynamic variation.