Spatio-temporal variation in zooplankton community composition in the southern Salish Sea: Changes during the 2015–2016 Pacific marine heatwave

Evaluating Metabarcoding Markers for Identifying Zooplankton and Ichthyoplankton Communities to Species in the Salish Sea: Morphological Comparisons and Rare, Threatened or Invasive Species

“…Plankton net tow sampling in the Salish Sea was conducted during Washington Ocean Acidification Center (WOAC) cruises using their protocols, procedures, and permits [16,[65][66][67]. We collected zooplankton (including ichthyoplankton) from seven long-term monitoring sites that span a breadth of oceanographic conditions (Figure 1, lettered A-G); here we present findings from spring and autumn 2018.…”

“…Water column physics and chemistry were characterized by WOAC scientists using CTD (conductivity, temperature, and pressure) casts conducted to 10 m above the seafloor. Niskin bottles collected water at 8-12 m depths for laboratory analyses of oxygen, nutrient concentrations (NO 3 , NO 2 , NH 3 , Si(OH) 4 , PO 4 ), and inorganic carbon chemistry (measurements of dissolved inorganic carbon and alkalinity, for calculation of pH and aragonite saturation state) using WOAC Best Practices [65,66]. Parameters at our net-tow sampling sites are in Table 1.…”

“…Parameters at our net-tow sampling sites are in Table 1. Vertical zooplankton tows were analyzed at every site, and oblique tows were additionally assessed for sites C and E. Morphological identifications of the zooplankton were conducted using traditional microscopy following [16,66,[68][69][70][71][72][73]. First, rare, larger organisms (usually >1 cm) were removed from the entire sample for identification and measurement.…”

“…All heterotrophic organisms in the subsamples were enumerated, identified, and differentiated by life history stage when possible using morphological characteristics. A minimum of 400 individuals were identified morphologically from each sample, using taxonomic keys and methodology that are standard to the JEK lab [16,66,[68][69][70][71][72][73][74][75][76]. All samples were taxonomically analyzed by two highly-trained taxonomists who have been working on Salish Sea zooplankton for more than a decade.…”

“…For small organisms, density was converted to carbon biomass using published values for average carbon per individual. For organisms that varied greatly in size within given life stages, up to 30 individuals were measured per stage and sampled to convert size to biomass using the length: carbon relationship [16,66]. Biomass was the primary morphological metric used for comparisons with the numbers (proportions) of sequence reads from metabarcoding; both numbers of individuals and biomass are reported here for morphology in our Figures and Supplementary Materials…”