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Distinct Composition and Assembly Processes of Bacterial Communities in a River from the Arid Area: Ecotypes or Habitat Types?

Abstract

The composition, function, and assembly mechanism of the bacterial community are the focus of microbial ecology. Unsupervised machine learning may be a better way to understand the characteristics of bacterial metacommunities compared to the empirical habitat types. In this study, the composition, potential function, and assembly mechanism of the bacterial community in the arid river were analysed. The Dirichlet multinomial mixture method recognised four ecotypes across the three habitats (biofilm, water, and sediment). The bacterial communities in water are more sensitive to human activities. Bacterial diversity and richness in water decreased as the intensity of human activities increased from the region of water II to water I. Significant differences in the composition and potential function profile of bacterial communities between water ecotypes were also observed, such as higher relative abundance in the taxonomic composition of Firmicutes and potential function of plastic degradation in water I than those in water II. Habitat filtering may play a more critical role in the assembly of bacterial communities in the river biofilm, while stochastic processes dominate the assembly process of bacterial communities in water and sediment. In water I, salinity and mean annual precipitation were the main drivers shaping the biogeography of taxonomic structure, while mean annual temperature, total organic carbon, and ammonium nitrogen were the main environmental factors influencing the taxonomic structure in water II. These results would provide conceptual frameworks about choosing habitat types or ecotypes for the research of microbial communities among different niches in the aquatic environment.

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Funding

This work was supported by the National Natural Science Foundation of China (grant number 41673127) and grants from the Youth Innovation Promotion Association of the Chinese Academy of Sciences (grant number Y201976 and 2017478).

All the raw data sets are publicly available in the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) under project accession no. PRJNA733708.

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W.S. and R.Q. conceived and designed the study; W.S., N.X., and R.Q. collected the samples and data; Y.Y. and W.S. performed the analysis; and W.S., X.Z., and L.Z. wrote and revised the manuscript.

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Correspondence to Wenjuan Song.

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Qi, R., Xue, N., Zhou, X. et al. Distinct Composition and Assembly Processes of Bacterial Communities in a River from the Arid Area: Ecotypes or Habitat Types?. Microb Ecol (2021). https://doi.org/10.1007/s00248-021-01902-9

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Keywords

  • Ili River
  • Community structure
  • Dirichlet multinomial mixture
  • Neutral community model
  • Stochastic process
  • Ecotypes