The effect of developmental stages on microbiome assembly in the phyllosphere and rhizosphere of rice grown in urban area soil.

Background: The plant microbiome can support plant health and fitness in the face of biotic and abiotic stress. Research has mostly focused on plant growth in natural and agricultural soils. However, as urban areas continue to expand and soils change in the Anthropocene, microbiome assembly during development of plants grown in urban area soil remains largely elusive. Here, we examined the effect of developmental stages on the phyllosphere and rhizosphere microbiomes of rice grown in soil from an urban area during the vegetative growth stages.

Results: We found that the microbial alpha and beta diversity, networks, and functions of the phyllosphere and rhizosphere microbiomes significantly differed among rice seedling, tillering, and elongation stages. Notably, we observed that bacteria assigned to potential animal parasites or symbionts not only exhibited significantly higher relative abundances in the phyllosphere compared to the rhizosphere but are also influenced by the developmental stages. Plants grown in the urban area soil had a higher relative abundance of Bacteroidales and enriched bacteria assigned to potential animal parasites or symbionts in the phyllosphere in contrast to plants grown in field. Some of these bacteria were shown to significantly influence the assembly of the phyllosphere microbiome and to prevalently engage in negative interactions with other microbes.

Conclusion: Our study provides new insights into developmental stage-resolved microbiome assembly of plants grown in urban areas. The insights could help in the development of strategies for promoting 'One Health' by highlighting the role of plants as alternative host for bacterial groups that are prevalently associated with animals.