Plankton identification and abundance

The diversity and abundances of (1) viruses; (2) non-pigmented planktonic cells < 1 µm, including archaea, heterotrophic bacteria, and chemosynthetic bacteria (hereafter called “bacteria”); (3) phytoplankton; (4) HFs; (5) aloricate ciliates and tintinnids; (6) large heterotrophic Dinophyceae; and (7) metazooplankton were determined. For each of these groups (except large heterotrophic Dinophyceae and metazooplankton), the methods of abundance estimation were described in Trombetta et al. (2020)²². Large heterotrophic Dinophyceae and metazooplankton were sampled using a plankton net (20 µm) towed at the sampling site over 424 L and then fixed with stabilised formaldehyde (4% final concentration) in 110 mL glass bottles and stored in the dark at 4 °C until analysis. Large zooplankton sampling took place in 2016 but not in 2015. Large heterotrophic Dinophyceae and metazooplankton taxon abundances were estimated using a binocular loop. Replicates of 2–5 mL were taken and placed into a Bogorov counting chamber. Zooplankton individuals were identified and counted under a stereo microscope (Olympus SZX7). Autotrophy, mixotrophy and heterotrophy of taxa was determined using previous evidence from the literature^74,75.

Supplementary Table ¹ summarises all data used in this manuscript, with the methods used and if already published elsewhere.