Rhizosphere microbes play an essential role in supplying nutrients and maintaining plant health, functioning almost like a “second genome.” Their composition and activity depend on host plant traits and environmental signals such as light, temperature, and moisture. Circadian clocks are known to regulate plant physiology, including nutrient uptake and defense, but how these rhythms interact with microbial communities in agricultural soils remains poorly understood. For tea, a perennial crop with high economic value, soil nutrient cycling is critical for yield and quality. Yet the extent to which daily microbial rhythms shape nitrogen (N) and phosphorus (P) processes in the rhizosphere is unclear. Based on these challenges, further research is needed on circadian rhythms of tea rhizosphere microbes and nutrient cycling.
A research team from Zhejiang University and collaborators investigated this knowledge gap. Their study, published (DOI: 10.1093/hr/uhae267) on 9 October 2024 in Horticulture Research, analyzed microbial communities in the rhizospheres of two widely grown tea cultivars, Longjing43 (LJ43) and Zhongcha108 (ZC108). Using high-resolution sampling across day–night cycles in 20-year-old plantations, they profiled bacterial and fungal diversity and linked these to N and P cycling. The findings provide a rare window into how circadian rhythms orchestrate below-ground processes that support crop growth.
The study revealed that fungi exhibited stronger circadian patterns than bacteria: about 70% of fungal genera varied between midday and midnight, compared to 35–61% of bacterial genera. Fungal communities were more abundant and stable in darkness, suggesting resilience to environmental changes. Notably, cultivar differences shaped rhythmic nutrient cycling. In LJ43, enzymes such as urease and acidic phosphatase peaked at night, promoting organic N and P mineralization and supplying nutrients during the day. In contrast, ZC108 showed stronger midnight expression of genes linked to N fixation (nifH) and denitrification (nosZ, nirK), highlighting a greater microbial role in inorganic nutrient cycling. Morning hours also favored nitrification, evidenced by elevated AOA and AOB gene expression. Correlation analyses confirmed that microbial composition in ZC108 was closely tied to dynamic N and P cycling, while LJ43’s stability reflected more conservative resource use. These diel oscillations demonstrate that circadian-regulated microbes coordinate soil biogeochemical processes in ways highly dependent on plant genotype, with implications for productivity and ecological resilience in tea plantations.
“Our findings show that the timing of microbial activity is just as important as its composition,” said corresponding author Chunyang Li of Zhejiang University. “By mapping how bacteria and fungi respond to day–night rhythms, we reveal a hidden layer of regulation in soil nutrient cycling. The contrast between LJ43 and ZC108 demonstrates that plant genetics and microbial clocks interact in complex ways. This opens up opportunities to optimize soil management practices not only for tea but potentially for other perennial crops that depend on stable rhizosphere functions.”
Understanding circadian rhythms in soil microbes could pave the way for chronobiology-based agriculture. Adjusting the timing of fertilization, irrigation, or microbial inoculant application to align with peak microbial activity may enhance nutrient efficiency and crop health. For tea plantations, cultivar-specific management informed by microbial rhythms could reduce N loss, improve P availability, and support sustainable production. More broadly, integrating chronobiology into soil ecology offers a strategy to mitigate nutrient inefficiency and environmental impacts in agriculture. Future research should explore how microbial circadian functions interact with plant transcriptomes to improve yield and quality, creating resilient systems under changing climates.
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References
DOI
10.1093/hr/uhae267
Original Source URL
https://doi.org/10.1093/hr/uhae267
Funding information
The authors wish to thank Dr. Yingtao Sun (Guangzhou Institute of Geochemistry, Chinese Academy of Sciences) for assistance in data processing. This work was supported by the Talent Program of the Zhejiang University (0022112).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.