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Structure and community assembly of rare bacterial community in sediments of Sancha Lake

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Abstract

To explore the structure and assembly of the rare bacterial community within sediment samples, as well as their responses their responses to environmental influencing factors, we collected surface sediment and overlying water samples from Sancha Lake across four seasons. MiSeq high-throughput sequencing was applied to the V3-V4 hypervariable regions of the 16 S rRNA genes, and the β – Nearest Taxon index (βNTI) was utilized to analyze the bacterial community assembly in the sediment samples. Our findings uncovered abundant bacterial diversity within the sediment samples of Sancha Lake, with 9314 operational taxonomic units (OTUs) identified, encompassing 59 phyla, 198 classes, 279 orders, 447 families, and 758 genera of bacteria. Proteobacteria and Chloroflexi were the dominant rare bacteria at the phylum level, whereas Coxiella and hgcl_clade were the principal rare bacteria at the genus level. The variety index of rare communities across diverse seasons was notably higher than that of abundant ones (P < 0.01). Bacterial community structure differed between spring and other seasons, and the rare bacterial community exhibited substantial seasonal alterations during non-spring periods. pH, dissolved oxygen (DO), total phosphorus (TP), and soluble reactive phosphorus (SRP) were the predominant environmental factors, exerting an even greater influence on rare bacteria. Within the co-occurrence network, rare bacteria constituted the majority of nodes and connections and were the dominant key species throughout all seasons. The assembly of their community was chiefly deterministic in autumn and random in other seasons. This study indicated that rare bacteria in Sancha Lake were diverse. They were keystone taxa for maintaining community interactions and stable operation, and their assembly process was influenced by both stochastic and deterministic factors.

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Data availability

The datasets analysed during the current study are available in the NCBI repository (https://www.ncbi.nlm.nih.gov/). The BioProject accession number is PRJNA1336117.

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Acknowledgements

This research was funded by Student Research Training Program(242005).

Funding

This research was funded by Student Research Training Program(242005).

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Authors and Affiliations

  1. School of Environmental Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China

    Yong Li, Yajie Li, Yihan Wu, Zuguang Liu, Shiqi Luo & Sidan Gong

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  1. Yong Li
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  4. Zuguang Liu
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Contributions

Y.L. writing – review & editing, investigation, conceptualization. Y.L. and Y.W. writing – original draft, visualization, project administration. Z.L. and S.L. writing – original draft, visualization. S.G. and Y.L. methodology, investigation. All authors read and approved the final manuscript.

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Li, Y., Li, Y., Wu, Y. et al. Structure and community assembly of rare bacterial community in sediments of Sancha Lake.
Sci Rep (2025). https://doi.org/10.1038/s41598-025-31889-z

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  • DOI: https://doi.org/10.1038/s41598-025-31889-z

Keywords

  • Sancha Lake sediments
  • Eutrophication
  • Rare bacteria
  • Diversity
  • Community assembly

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