The interacting features of topography and hydrography around deep seamounts have strong influence on plankton biogeography. In addition, the intrinsic properties of various biological taxa inherently shape their distribution. Therefore, bacterial, protist and fungal diversity was investigated across the water column above and below the summit of a flat-topped seamount in the Western Pacific Ocean. We determined the distribution and connectivity patterns of bacteria, protists and fungi around the seamount, and explored the processes driving the observed distribution patterns. We found that the seamount enhanced the vertical connectivity of bacterial and protist communities, but significantly reduced the protist community connectivity along the horizontal dimension. Such effects provide ecological opportunities for eukaryotic adaption and diversification, resulting in a greater diversity on seamounts than in surrounding deep seas.

Thirty-eight water samples from five sampling stations were collected at the Kocebu Guyot in the Magellan Seamount chain located in the oligotrophic tropical Western Pacific Ocean. A total of 20 L seawater was collected from each water layer at all sampling stations with Niskin Bottles attached to a rosette equipped with a Seabird CTD probe. Samples were pre-filtered first through a 200 µm sieve, and subsequently filtered through a 0.22 µm polycarbonate filter. Filters were then flash frozen in liquid nitrogen and stored at −80°C until further processing. 

Environmental DNA was extracted from seawater samples using the All Prep DNA/RNA Mini Kit (Qiagen, Germany) following the manufacturer’s instructions. Specific primers and PCR protocols were utilized to amplify different target sequences. In order to amplify 16S gene sequences in bacteria, forward primer U341F  and reverse primer R685  were set. The hypervariable V4 region of protist 18S rRNA was amplified using a set of eukaryote-specific primers Reuk454FWD1 and TAReukREV3 . For the detection of fungi, the ITS2 (Internal transcribed spacer 2) gene was amplified using specific primers ITS3 and ITS4 . Each sample was analyzed in three PCR replicates for each primer pair to minimize PCR bias.