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<p><i>Hucho bleekeri</i> is a Class I protected animal in China and is listed as Critically Endangered in the International Union for Conservation of Nature Red List. This study aimed to perform metagenomic (mainly for bacteria and aquatic organisms) and amplicon sequencing (12&#xa0;S rRNA for fish) of water samples collected from the upper reaches of the Dadu River, including 12 historical distribution areas of <i>H. bleekeri</i> and one breeding site. Metagenomic gene-catalog diversity in the breeding base was significantly lower than that observed in the other 12 wild habitats. The dominant phylum in water was Pseudomonadota, followed by Actinomycetota. Correlation analysis of environmental factors revealed that species belonging to 31 and 3 phyla were significantly correlated with dissolved oxygen and temperature, respectively. We also identified 115 species of algae, with some species uniquely present in either the wild or farmed environments. Linear discriminant analysis effect size was used to identify organisms with significant differences in samples from different environments. The species in the phyla Pseudomonadota, Bacteroidota, and Actinomycetota exhibited the greatest influence. Amplicon sequencing revealed that <i>H. bleekeri</i> was distributed at all sites examined, with higher abundance observed at its releasing sites. Furthermore, the distribution of some prey fish species of <i>H. bleekeri</i> had the trend to be positively correlated with <i>H. bleekeri</i> distribution, but the correlation was not statistically significant. This study represents the first application of environmental DNA to monitor the wild resources of <i>H. bleekeri</i> and provide critical insights for the conservation and management of this critically endangered species and other rare fish within their habitat.</p>

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Metagenomic and amplicon sequencing reveal the species distribution characteristics of the critically endangered Hucho bleekeri in wild and farmed environments

  • 期刊论文

  • 发表日期：

    2026年4月27日

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  • Yeyu Chen,
  • Hua Li,
  • Qinyao Wei,
  • Zhao Liu,
  • Yanling Chen,
  • Yi Yu,
  • Quanyu Tu,
  • Guiliang Liu,
  • Yan Liu,
  • Huanchao Yang

摘要

Hucho bleekeri is a Class I protected animal in China and is listed as Critically Endangered in the International Union for Conservation of Nature Red List. This study aimed to perform metagenomic (mainly for bacteria and aquatic organisms) and amplicon sequencing (12 S rRNA for fish) of water samples collected from the upper reaches of the Dadu River, including 12 historical distribution areas of H. bleekeri and one breeding site. Metagenomic gene-catalog diversity in the breeding base was significantly lower than that observed in the other 12 wild habitats. The dominant phylum in water was Pseudomonadota, followed by Actinomycetota. Correlation analysis of environmental factors revealed that species belonging to 31 and 3 phyla were significantly correlated with dissolved oxygen and temperature, respectively. We also identified 115 species of algae, with some species uniquely present in either the wild or farmed environments. Linear discriminant analysis effect size was used to identify organisms with significant differences in samples from different environments. The species in the phyla Pseudomonadota, Bacteroidota, and Actinomycetota exhibited the greatest influence. Amplicon sequencing revealed that H. bleekeri was distributed at all sites examined, with higher abundance observed at its releasing sites. Furthermore, the distribution of some prey fish species of H. bleekeri had the trend to be positively correlated with H. bleekeri distribution, but the correlation was not statistically significant. This study represents the first application of environmental DNA to monitor the wild resources of H. bleekeri and provide critical insights for the conservation and management of this critically endangered species and other rare fish within their habitat.