Eukaryote diversity assessment of sediments of the Western English Channel (locations L4 and Plymouth Sound)

Sediments were collected at monthly intervals from the Western English Channel (site L4) and environmental DNA extracted. The effect of season on the community composition and diversity of eukaryotes was assessed using in depth sequencing of 18S rRNA genes. This data will be compared with traditional techniques used to identify benthic species to assess the efficacy of eDNA biomonitoring as a tool for measuring biodiversity. Also within this dataset are samples collected two inshore coastal areas in Plymouth Sound UK (one Zostera marina meadow and one non-vegetated). At station L4, sampling was undertaken as close as possible to slack water after high tide, to capture the fluff layer. On May, July, September, and November 2015, and on January, March and May 2016, four sediment cores (10.5 cm) were collected from separate deployments of a multi-corer, retrieving sediment cores (15 cm deep) and sealing the bottom water above them (70 cm column), thus preserving the structural integrity of the sediment water interface during retrieval to the deck. The water in each corer tube was gently syphoned off on deck and discarded, avoiding disturbance to the sediment water interface. A 2.5 mL sterile syringe which had the bottom cut off was then used to sample the top 1 cm of sediment. The sampled sediment was immediately transferred into a sterile microtube and frozen in liquid nitrogen. Once transported to Plymouth Marine Laboratory, samples were stored at -80 C until processing. Inshore sediment samples were collected by a scuba diver in April 2016. Triplicate core samples were collected from a shallower area (2 m depth below chart datum) dense with seagrass shoots (Zostera marina), and from a deeper unvegetated area (8 m depth below chart datum) in Firestone Bay, Plymouth, SW UK. Syringes were inserted vertically 8 cm into the sediment, capped, and returned to the laboratory at the Marine Biological Association of the UK where they were frozen at -20 C until later analysis. eDNA was extracted from all sediment samples using the MoBIO Powersoil DNA extraction kit following the manufacturer guidelines. The V9 region of the 18S rRNA gene was amplified using the primer pair Euk1391F (GTACACACCGCCCGTC) and EukBr (TGATCCTTCTGCAGGTTCACCTAC), and sequenced using MiSeq by commercial contract (Mr DNA, Molecular Research LP, USA).