In this study, we evaluated how well DNA metabarcoding of environmental samples captures changes in marine mesozooplankton community composition to optimize the use of sequencing data for studying seasonal dynamics. Although DNA metabarcoding is increasingly used to monitor the distribution of marine communities, there is a lack of standardized methods, and it remains uncertain to what extent the DNA data reflects patterns of community dynamics observed by other methods.
To capture seasonal changes in the mesozooplankton community dynamics, samples were collected from small research vessels every 2 weeks before noon (8 a.m.–12 p.m.) during 2017 from a deep-water temperate coastal station (QU39) in the northern Salish Sea, British Columbia (in the Sutil Channel between Marina Island and Quadra Island, lat: 50.0307, long: −125.0992; bottom depth of 260 m). To evaluate the differences between sampling and analysis methods, three different kinds of samples were collected. Zooplankton net samples were collected according to the standard method for zooplankton monitoring in the Strait of Georgia using a bongo ring net with weighted cod ends (0.5 m diameter, 250 µm mesh size; Aquatic Research Instruments, Hope, BC, Canada). In brief, the net was towed vertically from a stationary position, from ∼10 m above the bottom (in our case ∼230 m depth) to the surface, retrieved at 1 meter per second, and with a calibrated flow meter attached to record the sampled volume. One net was preserved in a 4% formaldehyde seawater solution for microscopic analysis. A second net was preserved in 95% ethanol for DNA metabarcoding. Two-liter water samples were collected weekly with Niskin bottles from near the surface at 5, 30, 100, and 260 m depths. The water was filtered onto separate 0.22 µm polycarbonate Sterivex filters and preserved at −80°C after the addition of a sucrose lysis buffer until further molecular analysis. During this sampling campaign, a total of 24 zooplankton nets were collected for microscopic analysis, 26 zooplankton nets for DNA analysis, and 218 filtered water samples from 43 different dates were collected for DNA analysis
To assess if taxa specific trends are sensitive to the selection of genetic marker, we sequenced both short fragment of the COI gene, with primers optimized to capture marine invertebrate community and the 18S gene, with universal primers optimized for marine microbial eukaryotes on an Illumina MiSeq in the Hakai Genome Lab. In doing so, we provide both new insights into the reliability of DNA metabarcoding analysis and guidelines for future studies that aim to use environmental DNA to study marine community dynamics. Further, through analysis of discreet water column DNA samples, we demonstrate the potential of the DNA approach in resolving differences in vertical zooplankton distributions.
10.21966/6b20-7r76
