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<p>Ciliates are a dominant group in the marine sediment microecosystem, and their interactions with symbiotic prokaryotes are important for understanding the adaptation mechanisms of marine benthic eukaryotes. However, the microbial communities (microbiome) associated with most benthic ciliates and the taxonomic attributes of the dominant symbiotic bacteria are unclear. In this study, we focused on <i>Paraspathidium apofuscum</i>, a ciliate prevalent in marine benthic environments, and comprehensively explored the diversity and cellular location of the microbiomes in two <i>P. apofuscum</i> isolates using single-cell-based full-length16S rRNA amplicon sequencing, phylogenetic analysis, and fluorescence <i>in situ</i> hybridization. The results showed that the <i>P. apofuscum</i> cell surface carried a highly diverse microbiome whose cellular localization was consistent with the positions of the ciliate’s somatic dikinetids. The dominant genera in the microbiome, <i>Pseudoalteromonas</i>, <i>Halobacteriovorax</i> and <i>Oceaniserpentilla</i>, were associated with unicellular eukaryotes. In particular, <i>Pseudoalteromonas</i> likely uses ciliate-secreted metabolites as nutrients and plays a role in host physical protection or pathogen resistance. <i>Halobacteriovorax</i> and <i>Oceaniserpentilla</i> are newly discovered or rare bacterial genera innovatively found to have ecological niches in symbiosis with benthic ciliates. Comparison analysis indicates that the microbiomes associated with benthic ciliates display species and population specificity, which are attributed to several factors such as environmental physicochemical properties, host physiological states, and interactions among associated bacteria. This study provides important insights into the environmental adaptation of eukaryotes through a symbiotic mechanism in the marine benthic environment.</p>

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Epibiotic Microbiomes Dominated by Pseudoalteromonas Were Associated with the Unicellular Ciliate Paraspathidium apofuscum from Marine Sediments

  • 期刊论文

  • 发表日期：

    2025年12月8日

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  • Ning Xu,
  • Xiaoxin Zhang,
  • Yunfeng Wang,
  • Qianqian Zhang

摘要

Ciliates are a dominant group in the marine sediment microecosystem, and their interactions with symbiotic prokaryotes are important for understanding the adaptation mechanisms of marine benthic eukaryotes. However, the microbial communities (microbiome) associated with most benthic ciliates and the taxonomic attributes of the dominant symbiotic bacteria are unclear. In this study, we focused on Paraspathidium apofuscum, a ciliate prevalent in marine benthic environments, and comprehensively explored the diversity and cellular location of the microbiomes in two P. apofuscum isolates using single-cell-based full-length16S rRNA amplicon sequencing, phylogenetic analysis, and fluorescence in situ hybridization. The results showed that the P. apofuscum cell surface carried a highly diverse microbiome whose cellular localization was consistent with the positions of the ciliate’s somatic dikinetids. The dominant genera in the microbiome, Pseudoalteromonas, Halobacteriovorax and Oceaniserpentilla, were associated with unicellular eukaryotes. In particular, Pseudoalteromonas likely uses ciliate-secreted metabolites as nutrients and plays a role in host physical protection or pathogen resistance. Halobacteriovorax and Oceaniserpentilla are newly discovered or rare bacterial genera innovatively found to have ecological niches in symbiosis with benthic ciliates. Comparison analysis indicates that the microbiomes associated with benthic ciliates display species and population specificity, which are attributed to several factors such as environmental physicochemical properties, host physiological states, and interactions among associated bacteria. This study provides important insights into the environmental adaptation of eukaryotes through a symbiotic mechanism in the marine benthic environment.