Zooplankton was collected from 31\u00b0N to 29\u00b0N aboard the R/V Savannah at the 25m and 40m isobaths using a 1M (mouth opening) 5M length 200 \u00b5m mesh cone plankton net equipped with a filtering (202 \u00b5m mesh) cod-end.\u00a0 The mouth of the net was mounted in a swivel towing frame that allowed the opening of the net to track the water current. A mechanical flow meter (General Oceanics Part# 2030RC) was mounted in the center of the net. Flowmeter measurements for 2015 cruises (pdf) The net was deployed from a gently drifting ship and the entire water column was sampled by lowering the net to near the bottom and retrieving it (oblique tow).\u00a0 Net speed was maintained at approximately 15 meters per minute. Once retrieved the contents of the net were collected on a 200 \u00b5m sieve and preserved in 60% non-denatured ethanol.
\nSamples were split twice to create four subsamples using a Folsom plankton splitter.
\nOne of the subsamples was diluted to a known volume and stirred gently. Dilutions were adjusted depending on the density of zooplankton so that sufficient numbers of species were present in each sample to obtain a reliable estimate of the major taxonomic groups in each sample. Replicate aliquots from the subsample were counted under a dissecting microscope using a Bogorov counting chamber. The volume of sample counted was adjusted based on the density of zooplankton present but was generally 5 ml. A Stempel pipette was used to dispense the counted volume.
\nIn the case where the identity was uncertain, representative examples of the unidentified zooplankton were identified by DNA barcoding.\u00a0 DNA extractions were performed using the DNeasy Blood & Tissue Kit (Qiagen) according to manufacturer\u2019s protocol except that samples were macerated and homogenized with Kimble/Kontes Cordless Motor, the proteinase K incubation was extended to ~24 hours (overnight) and the volume of elution buffer AE varied depending on sample size (60ul for most). For DNA quantitation and quality testing, one (1) ul of DNA was used to measure the 260/280 ratio using the Thermo Scientific\u2122\u00a0 NanoDrop Lite Spectrophotometer.\u00a0 The presence of high molecular weight DNA in each extract was visually confirmed by agarose (1%) gel electrophoresis.\u00a0 Good quality DNA extractions, inferred by 260/280 ratio and electrophoresis, were selected for amplification by Polymerase Chain Reaction (PCR) of a fragment of the mitochondrial cytochrome oxidase subunit I (mtCOI) gene.\u00a0 A 708 base-pair mtCOI gene fragment was amplified using the consensus primer pairs LCO-1490 (5\u2019-GGTCAACAAATCATAAAGATATTGG-3\u2019) and HCO-2198 (5\u2019-TAAACTTCAGGGTGACCAAAAAATCA-3\u2019) (Folmer et al. 1994).\u00a0 Amplification was facilitated using a Bio-Rad T100Thermocycler with GoTaq Hot Start Green Master Mix. Cycling conditions were: 10 min at 95 \u00b0C; 35 cycles of 30 sec at 95 \u00b0C, 1 min at 47 \u00b0C and 1 min at 72 \u00b0C; and 10 min at 72 \u00b0C. PCR product quality and quantity was assessed by 2% agarose gel electrophoresis and subsequently sequenced by Eurofins Genomics. DNA sequences obtained were compared to a reference database library using the Basic Local Alignment Search Tool (BLAST) (Altschul et al. 1990) available at the National Center for Biotechnology Information (NCBI) and Bold Systems Identification engine for CO1 gene.\u00a0
This dataset includes zooplankton counts and abundances from meter net tows on multiple cruises on RV/Savannah in the South Atlantic Bight, Mid-Continental Shelf from August 2015 to December 2017.
\nLatitude and longitude data are\u00a0included in version 3.
The abundance of each zooplankton group was estimated accounting for all sample dilution and extrapolated based on the calculated initial net sampling volume.\u00a0 No further data processing was involved.\u00a0 All data was reviewed by at least one other expert.\u00a0 If outliers were identified all calculations were confirmed and in cases where errors were not obvious the sample was re-counted.
\nBCO-DMO Processing Notes:
\nVersion 1 [2017-04-28]: (2015 data)
\n- added\u00a0conventional\u00a0header with dataset name, PI name, version date
\n- modified parameter names to conform with BCO-DMO naming conventions
\n- blank values were replaced with no data value 'nd'
\n- added columns for cruise id, station, date, time, lat, lon, volume filtered, cast, replicate, splits, taxon_1
\nVersion 2 [2020-02-24] (2015-2017 data)
\n- added\u00a0conventional\u00a0header with dataset name, PI name, version date
\n- modified parameter names to conform with BCO-DMO naming conventions
\n- blank and\u00a0ND values were replaced with\u00a0'nd'
\n- date was converted to yyyy-mm-dd and ISO_DateTime_UTC was added
\n- \"Jekyll\u00a0 Is\" was replaced with \"Jekyll Is\" (one space between words)
\n- replaced blanks with zeroes in 'splits'\u00a0column
\nVersion 3 [2020-04-08] (2015-2017 data; includes lats/lons)
\n- added\u00a0conventional\u00a0header with dataset name, PI name, version date
\n- modified parameter names to conform with BCO-DMO naming conventions
\n- blanks, NO DATA, and\u00a0ND values were replaced with\u00a0'nd'
\n- date was converted to yyyy-mm-dd and ISO_DateTime_UTC was added
\n- latitude and longitude were converted from degrees, minutes, seconds to decimal degrees.
\n\u00a0