Sterivex cartridge

Seawater samples were collected at multiple depths at the long-term stations and at the surface and DCM depths at the short-term stations using a CTD-rosette system equipped with 21 L × 12 L Niskin bottles. The water samples were successively filtered through 0.8 μm pore-size filters and then onto 0.2 μm pore-size Sterivex cartridges (Millipore, Billerica, NY, USA) or onto 47 mm, 0.2 μm pore-size Nuclepore polycarbonate filters (Whatman, Maidstone, UK) except for stations MAR and STB13 (successive filtration through 3.0 μm pore-size filters and then onto 0.2 μm Sterivex). Filtered volumes were noted and ranged between 4.5 and 8.1 L for the Sterivex collections and between 0.75 and 1.0 L for the polycarbonate filter collections. The filters and Sterivex cartridges were immediately stored in liquid nitrogen then at –80°C until nucleic acid extraction. DNA extractions were carried out on Sterivex cartridges from all stations except for HNL, STB8, STB11, and STB19 where only polycarbonate filters were available.

This research was conducted in the Heping Island fish market in Keelung City, the northeastern Taiwan from December 2020 to January 2021 (Figure 1A–C). Heping Island fish market is a small market (area: 200 m × 10 m), contains 20-30 traditional seafood stalls and restaurants (Figure 1D,E). The seafood here includes live fish, fresh fish, and processed products. It is mainly caught in the wild and comes from nearby fish harbors. Most seafood can be observed directly in the fish tank and at the food stall (Figure 1F–H). In order to reflect seafood diversity, two sampling sites were chosen near the drain of the fish market (100 m between two sites) (Figure 1A,D,E). We sampled twice in total, with an interval of about 1 month. We extracted the seawater near the drain with a bucket, and then 1 L seawater was filtered immediately through a Sterivex cartridge (0.45 μm, Millipore SVHV010RS, Merck Millipore, Billerica, MA, USA) with a syringe (500 mL) by hand. Each sampling was taken three times, and the interval was 10 min. Filtered samples were placed on ice until they were taken back to the laboratory.

Key ecosystem parameters have been sampled in the western English Channel for over a century [22] (link), [23] . The weekly phytoplankton samples (since 1992: see Table S1 for species list) were taken at a depth of 10 m using a 10 L Niskin bottle at station L4. A 200 mL subsample was then removed from the bottle and immediately fixed with 2% (final concentration) Lugol's iodine solution [24] . A second 200 mL sub-sample was also taken and preserved with neutral formaldehyde for the enumeration of coccolithophores. The samples were stored in cool, dark conditions until taxonomic analysis at the Plymouth Marine Laboratory (PML) using light microscopy [25] . Samples for zooplankton have been collected on a weekly basis since 1988 (see Table S2 for species list), using a vertical net haul from 50 m depth to the surface using a WP2 net with a mesh-size of 200 µm and mouth area of 0.25 m²[26] . Two hauls are taken and the samples preserved and stored in 5% formalin. These are then sub-sampled, counted and identified using light microscopy at PML [27] . Bacterial abundance data (2003–2008) were generated by extracting nucleic acids from 5 L seawater samples collected from the surface and filtered immediately through a 0.22 µm Sterivex cartridge (Millipore), which was stored at −80°C. DNA was isolated from each sample and then stored at −20°C prior to 454-pyrosequencing [28] (link).