Microeukaryotes have unexpected importance in cold seep food webs through predation and parasitism

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Cold seeps are inhabited by a high abundance of chemosynthetic prokaryotes and invertebrates. However, a complete food web between invertebrates and prokaryotes cannot be established without the important link of microeukaryotes. Yet, question such as which microeukaryotes are at work in cold seeps is still mostly open. We, therefore, compared the biological communities in cold seeps and adjacent areas of the South China Sea by the metabarcoding and quantitative PCR (qPCR) of nuclear 18S and 16S rRNA genes, and estimated the potentially ecological roles of microeukaryotes by cross-domain microbial network analysis. The anaerobic methane oxidizing archaea (ANME), sulfate-reducing bacteria (SRB) and Radiolaria accounted for most variations between microbial communities from the cold seeps and adjacent areas. A significant correlation was detected between the copy numbers of 18S rRNA gene and communities of the ANME and SRB in cold seeps, indicating close links between microeukaryotes and chemosynthetic prokaryotes. After adding microeukaryotic nodes microbial network became more complex, and the negative correlation proportion and average path length increased, suggesting increased predation and parasitism. The ANME and SRB groups were mainly negatively correlated with and potentially preyed by Acantharea and Cercozoa, which were then negatively correlated with annelids and mollusks. Parasitic microeukaryotes of Syndiniales widely existed in cold seeps and had close relationships with Polycystinea. Parasitism might cause the death of Polycystinea and the release of Syndiniales spores, which may be an important carbon source for the cold seep biota. Using Mantel analyses, we also demonstrated that trophic relationships are closer in cold seeps than in the adjacently deep-sea sediments, and that microeukaryote-metazoans linkages in cold seeps are closer than those between prokaryotes and metazoans. Overall, our study outlines the main components of food webs in cold seeps and highlights that microeukaryotes have an unexpected importance in the carbon cycle.