Tea leaves shape their microbial world: metabolites drive phyllosphere microbiome assembly

Using five distinct tea cultivars, researchers combined metabolomic profiling, metagenomics, and machine learning to identify eight key microbial genes associated with leaf secondary compounds, particularly epigallocatechin gallate (EGCG) and gallic acid. These findings uncover how plant metabolites shape microbial functions, offering new opportunities to enhance crop health and quality through microbiome optimization.

Plants and microbes have co-evolved through complex interactions influenced by physiology, biochemistry, and the surrounding environment. The phyllosphere, the leaf surface habitat for microbes, plays a vital role in biogeochemical cycles and plant health. In this niche, microbial colonization is often guided by leaf-derived metabolites such as sugars, amino acids, and antimicrobial compounds. While root and seed microbiomes have been widely studied, the phyllosphere’s microbial drivers—particularly the influence of leaf metabolites—remain underexplored. Tea plants (Camellia sinensis), with their diverse chemical profiles shaped by artificial selection, provide an ideal model. Due to these unresolved questions, deeper investigation is required to unravel how specific leaf metabolites influence the structure and function of microbial communities in the phyllosphere.

A study (DOI: 10.48130/bpr-0025-0002) published in Beverage Plant Research on 7 May 2025 by Ping Xu’s team, Zhejiang University, provides fresh insights into how plant metabolites direct microbial community composition and gene expression, particularly genes involved in sulfur cycling and microbial adaptation.

To investigate how leaf metabolites influence the taxonomic and functional composition of the phyllosphere microbiome in tea plants, researchers employed a combination of metabolomic profiling, metagenomic sequencing, and advanced statistical and machine learning methods. Principal Component Analysis (PCA) and PERMANOVA revealed that amino acid and secondary metabolite compositions varied significantly across five tea cultivars. In particular, the amino acids theanine (THEA), glutamine (GLN), and arginine (ARG) were differentially abundant, with etiolated cultivars (AB, HJ, YJ) showing significantly higher THEA levels than non-etiolated ones (FD, LJ). While several catechins, including EGCG, varied between cultivars, differences did not strictly align with etiolation status. Microbial diversity analysis indicated significant differences in both alpha and beta diversity among cultivars, with dominant microbial phyla including Proteobacteria and Bacteroidota. At the genus level, Sphingomonas and Methylobacterium were among the most abundant. Functional gene annotation uncovered 414 genes linked to nitrogen, phosphorus, sulfur, and methane cycling, with sulfur transformation pathways showing the highest relative abundance. Random Forest analysis identified eight key genes—four of which were involved in sulfur cycling—that strongly correlated with variations in 12 secondary metabolites. Notably, cysK, metZ, betB, and sulP were associated with sulfur metabolism and showed distinct correlations with EGCG and gallic acid levels. Taxonomic mapping revealed that Sphingomonas, Methylobacterium, and Chryseobacterium harbored all eight key genes, underscoring their central role in metabolite-responsive microbial functions. Overall, the study demonstrated that tea leaf metabolites—particularly secondary compounds—play a crucial role in shaping not just the microbial community structure, but also its functional gene landscape.

This research bridges the gap between tea plant breeding and ecological microbiome engineering. The identification of microbial genes responsive to leaf metabolites offers new biomarkers for selecting beneficial microbial partners in agricultural systems. In particular, sulfur cycling genes could serve as targets for developing bioinoculants to enhance tea plant nutrition and stress tolerance. Additionally, by tailoring tea cultivars to favor desirable microbial functions, producers may be able to enhance flavor profiles and crop health naturally.

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References

DOI

10.48130/bpr-0025-0002

Original Source URL

https://doi.org/10.48130/bpr-0025-0002

Funding information

This research was supported by the Natural Science Foundation of China (32072632).

About Beverage Plant Research

Beverage Plant Research (e-ISSN 2769-2108) is the official journal of Tea Research Institute, Chinese Academy of Agricultural Sciences and China Tea Science Society. Beverage Plant Research is an open access, online-only journal published by Maximum Academic Press which publishing original research, methods, reviews, editorials, and perspectives, which advance the biology, chemistry, processing, and health functions of tea and other important beverage plants.