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Comparative analysis of the structure and function of rhizosphere microbiome of the Chinese medicinal herb Alisma in different regions

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Abstract

Rhizoma Alismatis, a commonly used traditional Chinese medicine, is the dried tuber of Alisma orientale and Alisma A. plantago-aquatica, mainly cultivated in Fujian and Sichuan provinces (China), respectively. Studies have shown that the rhizosphere microbiome is a key factor determining quality of Chinese medicinal plants. Here we applied metagenomics to investigate the rhizosphere microbiome of Alisma in Fujian and Sichuan, focusing on its structure and function and those genes involved in protostane triterpenes biosynthesis. The dominant phyla were Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes. Compared with Fujian, the rhizosphere of Sichuan has a greater α diversity and stronger microbial interactions but significantly lower relative abundance of archaea. Microbes with disease-suppressing functions were more abundant in Sichuan than Fujian, but vice versa for those with IAA-producing functions. Gemmatimonas, Anaeromyxobacter, and Pseudolabrys were the main contributors to the potential functional difference in two regions. Genes related to protostane triterpenes biosynthesis were enriched in Fujian. Steroidobacter, Pseudolabrys, Nevskia, and Nitrospira may contribute to the accumulation of protostane triterpenes in Alisma. This work fills a knowledge gap of Alisma’s rhizosphere microbiome, providing a valuable reference for studying its beneficial microorganisms.

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Data availability

All the sequences’ raw data were uploaded to NCBI’s Sequence Read Archive (SRA) database, under the following accession numbers: SRR17256002, SRR17256001, SRR17256000, SRR17255999, SRR17255998, SRR17255996, SRR17255995, SRR17255994, and SRR17255993.

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Funding

This research was supported by the National Natural Science Foundation of China (Grant No.82073958 and 81673534), Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization (Grant No. ZDXM-3-24), Qing Lan Project (Grant No. 2019), and Suzhou Science and Technology Development Plan (Grant No. SYSD2020248).

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Authors and Affiliations

  1. Nanjing University of Chinese Medicine School of Pharmacy, 138 Xianlin Avenue, Nanjing, 210023, China

    Chenbin Wei, Wei Gu, Rong Tian, Fei Xu, Yuanyuan Ji, Tao Li, Yu Zhu, Peilei Lang & Wenqing Wu

  2. Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, 210023, China

    Wei Gu

  3. Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine: Suzhou Hospital of Traditional Chinese Medicine, Suzhou, 215007, China

    Yun Han

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  1. Chenbin Wei
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  2. Wei Gu
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Correspondence to Wei Gu.

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Wei, C., Gu, W., Tian, R. et al. Comparative analysis of the structure and function of rhizosphere microbiome of the Chinese medicinal herb Alisma in different regions. Arch Microbiol 204, 448 (2022). https://doi.org/10.1007/s00203-022-03084-5

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