Abstract
Phyllosphere and rhizosphere are unique and wide‐ranging habitats that harbor various microbial communities, which influence plant growth and health, and the productivity of the ecosystems. In this study, we characterized the shared microbiome of the phyllosphere and rhizosphere among three plants (Ipomoea pes‐caprae, Wedelia chinensis, and Cocos nucifera), to obtain an insight into the relationships between bacteria (including diazotrophic bacteria) and fungi, present on these host plants. Quantitative PCR showed that the abundances of the microbiome in the soil samples were significantly higher than those in the phyllosphere samples, though there was an extremely low abundance of fungi in bulk soil. High‐throughput sequencing showed that the alpha‐diversity of bacteria and fungi was higher in the rhizosphere than the phyllosphere samples associated with the same plant, while there was no obvious shift in the alpha‐diversity of diazotrophic communities between all the tested phyllosphere and soil samples. Results of the microbial composition showed that sample‐specific bacteria and fungi were found among the phyllosphere and rhizosphere of the different host plants. About 10%–27% of bacteria, including diazotrophs, and fungi overlapped between the phyllosphere and the rhizosphere of these host plants. No significant difference in microbial community structure was found among the tested rhizosphere samples, and soil properties had a higher influence on the soil microbial community structures than the host plant species.
Highlights
The leaf surface, known as the phyllosphere, is a large and extremely diverse habitat for terrestrial microorganisms
Heip's evenness index of the Cocos nucifera (CN)-R rhizosphere were significantly higher than that of Ipomoea pes-caprae (IP)-R and Wedelia chinensis (WC)-R. These three bacterial and fungal indices were mostly lower in the phyllosphere samples, compared to soil samples, the Shannon index and Chao1 of fungi in rhizosphere IP-R were slightly lower than that of phyllosphere IP. These results revealed that the sampled soils harbored a higher diversity, richness, and evenness of bacteria and fungi than the tested phyllosphere samples
To compare the similarities and differences among the test samples, between the bacterial, fungal, and diazotrophic community structures, including phyllosphere (Bao et al, 2019), rhizosphere, and bulk soil samples, we used hierarchical clustering analysis, principal coordinates analysis (PCoA), and analysis of similarity (ANOSIM), based on the operational taxonomic units (OTUs) composition. These analyses showed that fungal, bacterial, and diazotrophic communities were different between all the phyllosphere and soil samples (Figure 2)
Summary
The leaf surface, known as the phyllosphere, is a large and extremely diverse habitat for terrestrial microorganisms. A recent study of the common grapevine (Vitis vinifera) microbiota showed that the root-associated bacterial communities differed significantly from the aboveground communities, yet the microbiota of the leaves, flowers, and grapes shared a greater proportion of taxa with the soil communities than with each other. This suggests that soil may serve as a common bacterial reservoir for belowground and aboveground plant microbiota (Zarraonaindia et al, 2015). We used high-throughput amplicon sequencing to compare the microbial community composition, structure, and interaction, especially the shared microbes between the phyllosphere and rhizosphere, among the different host plant species in this tropical island
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