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Phosphorus mining activities alter endophytic bacterial communities and metabolic functions of surrounding vegetables and crops

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Abstract

[Aims] The goal was to evaluate the effect of phosphorus mining on the endophytic bacterial community of surrounding crops and vegetables and screen beneficial bacteria. [Methods] 16S rRNA sequencing was used to assess endophytic bacterial diversity, community, and metabolic function variations in surrounding plants, including Glycine max, Triticum aestivum, and Lactuca sativa. [Results] The results showed that phosphorus mining caused a decline in the endophytic bacterial diversity of plants, including the Shannon and Simpson indices (P < 0.05). Rhizobium was significantly enriched in lettuce, soybean, and wheat roots in the phosphate mining area compared with corresponding samples from a nonphosphate mining area (P < 0.05). The metabolic function prediction based on Phylogenetic Investigation of Communities by Reconstruction of Unobserved States showed that endophytic bacteria in lettuce, soybean, and wheat roots developed various strategies to cope with phosphorus mining stress. We further isolated 11 endophytic bacteria from the three plant types, of which Enterobacter sp. P35, Pseudomonas aeruginosa P33, and Rhizobium pusense P25 showed strong resistance to multiple heavy metals. Several endophytic bacteria, including Pseudomonas aeruginosa P33, Sphingomonas panni P15, and Bacillus cereus P3, showed multiple growth-promoting properties for plants. [Conclusions] To our knowledge, this is the first study to examine the effects of phosphate mining on endophytic bacteria in human food sources (vegetables and crops), providing a comprehensive understanding of the ecological effects of phosphate mining. The results also highlight the need to pay attention to the easily neglected effect of phosphorus mining on the microecology and provide a basis for screening bacteria for remediation.

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Data Availability

The datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request.

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Funding

This work was supported by the National Natural Science Foundation of China (grant no. 42107233), Sichuan Natural Science Foundation Project (2023NSFSC1229), the CAS Key Laboratory of Environmental and Applied Microbiology & Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences (No. KLCAS-2021–3), and the Open Research Fund Program of the State Environmental Protection Key Laboratory of Food Chain Pollution Control (No. FC2021YB08).

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Authors and Affiliations

  1. Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China

    Qiang Li, Peng **ang, Lijiao Li, Ting Zhang, Qian Wu, Zhijie Bao & Wenying Tu

  2. School of Public Health, Chengdu Medical College, Chengdu, Sichuan, China

    Changsong Zhao

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Contributions

Conceived and designed the experiments: Q.L., and C.Z. Analyzed the data: P.X., T.Z., Q.W., Z.B., L.L., and W.T. Wrote and reviewed the paper: Q.L., and P.X..

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Correspondence to Changsong Zhao.

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Fig. S1

Rarefaction curves of bacterial OTUs in different samples. Gma, endophytic bacteria associated with soybean roots from the nonphosphorus mining area; Lsa, endophytic bacteria associated with lettuce roots from the nonphosphorus mining area; Tae, endophytic bacteria associated with wheat roots from the nonphosphorus mining area; Gma.P, endophytic bacteria associated with soybean roots from the phosphorus mining area; Lsa.P, endophytic bacteria associated with lettuce roots from the phosphorus mining area; Tae.P, endophytic bacteria associated with wheat roots from the phosphorus mining area (DOC 525 KB)

Fig. S2

Unique and shared operational taxonomic units (OTUs) of different samples. Gma, endophytic bacteria associated with soybean roots from the nonphosphorus mining area; Lsa, endophytic bacteria associated with lettuce roots from the nonphosphorus mining area; Tae, endophytic bacteria associated with wheat roots from the nonphosphorus mining area; Gma.P, endophytic bacteria associated with soybean roots from the phosphorus mining area; Lsa.P, endophytic bacteria associated with lettuce roots from the phosphorus mining area; Tae.P, endophytic bacteria associated with wheat roots from the phosphorus mining area (DOC 1188 KB)

Fig. S3

Overall Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation of endophytic bacteria from different samples (DOC 792 KB)

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Li, Q., **ang, P., Li, L. et al. Phosphorus mining activities alter endophytic bacterial communities and metabolic functions of surrounding vegetables and crops. Plant Soil 497, 155–174 (2024). https://doi.org/10.1007/s11104-023-05961-4

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