| Contributors | Affiliation | Role |
|---|---|---|
| Goetze, Erica | University of Hawaii (UH) | Principal Investigator, Contact |
| York, Amber D. | Woods Hole Oceanographic Institution (WHOI BCO-DMO) | BCO-DMO Data Manager |
This data submission consists of metabarcoding data for the zooplankton community in the epipelagic, mesopelagic and upper bathypelagic zones (0-1500m) of the North Pacific Subtropical Gyre. The goal of this study was to assess the hidden diversity present in zooplankton assemblages in midwaters, and detect vertical gradients in species richness, depth distributions, and community composition of the full zooplankton assemblage. Samples were collected in June 2014 from Station ALOHA (22.75, -158) using a 1-meter square Multiple Opening and Closing Nets and Environmental Sampling System (MOCNESS, 200um mesh), on R/V Falkor cruise FK140613. Next generation sequence data (Illumina MiSeq, V3 chemistry, 300-bp paired-end) of the zooplankton assemblage derive from amplicons of the V1-V2 region of 18S rRNA (primers described in Fonseca et al. 2010). The data includes sequences and read count abundance information for molecular OTUs from both holoplanktonic and meroplanktonic taxa. All results derive from analyses in mothur v1.36.1 (Schloss et al. 2009, Kozich et al. 2013).
Tables from four analyses are included in this submission:
1) 97_OTUtable: read counts for each OTU (clustered at 97% similarity) across 54 samples (depth, size fractionated), with NCBI BLAST results for the top representative sequence from each OTU.
2) 97_OTU_subsampled: read counts for each OTU (clustered at 97% similarity), subsampled for even sequencing coverage across 54 samples (depth, size fractionated, with NCBI BLAST results for the top representative sequence from each OTU.
3) 99_OTU: read counts for each OTU (clustered at 99% similarity) across 54 samples (depth, size fractionated), with NCBI BLAST results for the top representative sequence from each OTU.
4) 99_OTU_subsampled: read counts for each OTU (clustered at 99% similarity), subsampled for even sequencing coverage across 54 samples (depth, size fractionated), with NCBI BLAST results for the top representative sequence from each OTU.
Related dataset containing NCBI accession numbers for sequence data:
Metabarcoding zooplankton at station ALOHA: NCBI SRA accession numbers www.bco-dmo.org/dataset/700961
Sample Codes:
Read count parameter names (e.g. FA3_N7_SF1) include the following three codes:
MOCNESS tow
FA3: Night sampling
FA4: Day sampling
Depth range:
N1: 1500-1000m
N2: 1000-700m
N3: 700-500m
N4: 500-300m
N5: 300-200m
N6: 200-150m
N7: 150-100m
N8: 100-50m
N9: 50m-0m
Wet-sieved zooplankton size fractions
SF1: 0.2-0.5 mm
SF2: 0.5-1.0 mm
SF3: 1.0-2.0 mm
Data parameters with the prefix (NCBI_) are from the National Center for Biotechnology Information (NCBI, https://www.ncbi.nlm.nih.gov/)
Data parameters with the prefix (silva_) are from the Silva database (https://www.arb-silva.de/).
BCO-DMO processing notes:
* commas in the data were replaced with semicolons to support export as csv format.
* fasta files added to dataset
| File |
|---|
FASTA file - Representative sequences, 97% Clustering filename: RepSeqs97.fasta (FASTA, 2.05 MB) MD5:95c7b7787aaefcd69b78cf47a836bb3c FASTA file containing representative sequences for each OTU identified by abundance (top read) and with alignment gaps removed. Clustered at 97% similarity. |
FASTA file - Representative sequences, 99% Clustering filename: RepSeqs99.fasta (FASTA, 2.02 MB) MD5:4a20d1ca10aef9d64f724918982b3c5d FASTA file containing representative sequences for each OTU identified by abundance (top read) and with alignment gaps removed. Clustered at 99% similarity. |
OTU.csv (Comma Separated Values (.csv), 11.59 MB) MD5:63b6561afef4f0dea8f056305948289f Primary data file for dataset ID 700279 |
| Parameter | Description | Units |
| analysis_name | Descriptive name of analysis including percent clustering and subsampling or no subsampling | unitless |
| lat | Latitude of sample site (Station ALOHA) | decimal degrees |
| lon | Longitude of sample site (Station ALOHA) | decimal degrees |
| OTU_ID | Operational taxonomic unit (OTU) identifier | unitless |
| FA3_N1_SF1 | Read counts for each OTU within each sample; Sample collected during the day with net 1 (depth 1500-1000m) for zooplankton size fraction 1 (0.2 - 0.5mm) | per OTU |
| FA3_N1_SF2 | Read counts for each OTU within each sample; Sample collected during the day with net 1 (depth 1500-1000m) for zooplankton size fraction 2 (0.5 - 0.1mm) | per OTU |
| FA3_N1_SF3 | Read counts for each OTU within each sample; Sample collected during the day with net 1 (depth 1500-1000m) for zooplankton size fraction 3 (1.0 - 2.0 mm) | per OTU |
| FA3_N2_SF1 | Read counts for each OTU within each sample; Sample collected during the day with net 2 (depth 1000-700m) for zooplankton size fraction 1 (0.2 - 0.5mm) | per OTU |
| FA3_N2_SF2 | Read counts for each OTU within each sample; Sample collected during the day with net 2 (depth 1000-700m) for zooplankton size fraction 2 (0.5 - 0.1mm) | per OTU |
| FA3_N2_SF3 | Read counts for each OTU within each sample; Sample collected during the day with net 2 (depth 1000-700m) for zooplankton size fraction 3 (1.0 - 2.0 mm) | per OTU |
| FA3_N3_SF1 | Read counts for each OTU within each sample; Sample collected during the day with net 3 (depth 700-500m) for zooplankton size fraction 1 (0.2 - 0.5mm) | per OTU |
| FA3_N3_SF2 | Read counts for each OTU within each sample; Sample collected during the day with net 3 (depth 700-500m) for zooplankton size fraction 2 (0.5 - 0.1mm) | per OTU |
| FA3_N3_SF3 | Read counts for each OTU within each sample; Sample collected during the day with net 3 (depth 700-500m) for zooplankton size fraction 3 (1.0 - 2.0 mm) | per OTU |
| FA3_N4_SF1 | Read counts for each OTU within each sample; Sample collected during the day with net 4 (depth 500-300m) for zooplankton size fraction 1 (0.2 - 0.5mm) | per OTU |
| FA3_N4_SF2 | Read counts for each OTU within each sample; Sample collected during the day with net 4 (depth 500-300m) for zooplankton size fraction 2 (0.5 - 0.1mm) | per OTU |
| FA3_N4_SF3 | Read counts for each OTU within each sample; Sample collected during the day with net 4 (depth 500-300m) for zooplankton size fraction 3 (1.0 - 2.0 mm) | per OTU |
| FA3_N5_SF1 | Read counts for each OTU within each sample; Sample collected during the day with net 5 (depth 300-200m) for zooplankton size fraction 1 (0.2 - 0.5mm) | per OTU |
| FA3_N5_SF2 | Read counts for each OTU within each sample; Sample collected during the day with net 5 (depth 300-200m) for zooplankton size fraction 2 (0.5 - 0.1mm) | per OTU |
| FA3_N5_SF3 | Read counts for each OTU within each sample; Sample collected during the day with net 5 (depth 300-200m) for zooplankton size fraction 3 (1.0 - 2.0 mm) | per OTU |
| FA3_N6_SF1 | Read counts for each OTU within each sample; Sample collected during the day with net 6 (depth 200-150m) for zooplankton size fraction 1 (0.2 - 0.5mm) | per OTU |
| FA3_N6_SF2 | Read counts for each OTU within each sample; Sample collected during the day with net 6 (depth 200-150m) for zooplankton size fraction 2 (0.5 - 0.1mm) | per OTU |
| FA3_N6_SF3 | Read counts for each OTU within each sample; Sample collected during the day with net 6 (depth 200-150m) for zooplankton size fraction 3 (1.0 - 2.0 mm) | per OTU |
| FA3_N7_SF1 | Read counts for each OTU within each sample; Sample collected during the day with net 7 (depth 150-100m) for zooplankton size fraction 1 (0.2 - 0.5mm) | per OTU |
| FA3_N7_SF2 | Read counts for each OTU within each sample; Sample collected during the day with net 7 (depth 150-100m) for zooplankton size fraction 2 (0.5 - 0.1mm) | per OTU |
| FA3_N7_SF3 | Read counts for each OTU within each sample; Sample collected during the day with net 7 (depth 150-100m) for zooplankton size fraction 3 (1.0 - 2.0 mm) | per OTU |
| FA3_N8_SF1 | Read counts for each OTU within each sample; Sample collected during the day with net 8 (depth 100-50m) for zooplankton size fraction 1 (0.2 - 0.5mm) | per OTU |
| FA3_N8_SF2 | Read counts for each OTU within each sample; Sample collected during the day with net 8 (depth 100-50m) for zooplankton size fraction 2 (0.5 - 0.1mm) | per OTU |
| FA3_N8_SF3 | Read counts for each OTU within each sample; Sample collected during the day with net 8 (depth 100-50m) for zooplankton size fraction 3 (1.0 - 2.0 mm) | per OTU |
| FA3_N9_SF1 | Read counts for each OTU within each sample; Sample collected during the day with net 9 (depth 50-0m) for zooplankton size fraction 1 (0.2 - 0.5mm) | per OTU |
| FA3_N9_SF2 | Read counts for each OTU within each sample; Sample collected during the day with net 9 (depth 50-0m) for zooplankton size fraction 2 (0.5 - 0.1mm) | per OTU |
| FA3_N9_SF3 | Read counts for each OTU within each sample; Sample collected during the day with net 9 (depth 50-0m) for zooplankton size fraction 3 (1.0 - 2.0 mm) | per OTU |
| FA4_N1_SF1 | Read counts for each OTU within each sample; Sample collected during the night with net 1 (depth 1500-1000m) for zooplankton size fraction 1 (0.2 - 0.5mm) | per OTU |
| FA4_N1_SF2 | Read counts for each OTU within each sample; Sample collected during the night with net 1 (depth 1500-1000m) for zooplankton size fraction 2 (0.5 - 0.1mm) | per OTU |
| FA4_N1_SF3 | Read counts for each OTU within each sample; Sample collected during the night with net 1 (depth 1500-1000m) for zooplankton size fraction 3 (1.0 - 2.0 mm) | per OTU |
| FA4_N2_SF1 | Read counts for each OTU within each sample; Sample collected during the night with net 2 (depth 1000-700m) for zooplankton size fraction 1 (0.2 - 0.5mm) | per OTU |
| FA4_N2_SF2 | Read counts for each OTU within each sample; Sample collected during the night with net 2 (depth 1000-700m) for zooplankton size fraction 2 (0.5 - 0.1mm) | per OTU |
| FA4_N2_SF3 | Read counts for each OTU within each sample; Sample collected during the night with net 2 (depth 1000-700m) for zooplankton size fraction 3 (1.0 - 2.0 mm) | per OTU |
| FA4_N3_SF1 | Read counts for each OTU within each sample; Sample collected during the night with net 3 (depth 700-500m) for zooplankton size fraction 1 (0.2 - 0.5mm) | per OTU |
| FA4_N3_SF2 | Read counts for each OTU within each sample; Sample collected during the night with net 3 (depth 700-500m) for zooplankton size fraction 2 (0.5 - 0.1mm) | per OTU |
| FA4_N3_SF3 | Read counts for each OTU within each sample; Sample collected during the night with net 3 (depth 700-500m) for zooplankton size fraction 3 (1.0 - 2.0 mm) | per OTU |
| FA4_N4_SF1 | Read counts for each OTU within each sample; Sample collected during the night with net 4 (depth 500-300m) for zooplankton size fraction 1 (0.2 - 0.5mm) | per OTU |
| FA4_N4_SF2 | Read counts for each OTU within each sample; Sample collected during the night with net 4 (depth 500-300m) for zooplankton size fraction 2 (0.5 - 0.1mm) | per OTU |
| FA4_N4_SF3 | Read counts for each OTU within each sample; Sample collected during the night with net 4 (depth 500-300m) for zooplankton size fraction 3 (1.0 - 2.0 mm) | per OTU |
| FA4_N5_SF1 | Read counts for each OTU within each sample; Sample collected during the night with net 5 (depth 300-200m) for zooplankton size fraction 1 (0.2 - 0.5mm) | per OTU |
| FA4_N5_SF2 | Read counts for each OTU within each sample; Sample collected during the night with net 5 (depth 300-200m) for zooplankton size fraction 2 (0.5 - 0.1mm) | per OTU |
| FA4_N5_SF3 | Read counts for each OTU within each sample; Sample collected during the night with net 5 (depth 300-200m) for zooplankton size fraction 3 (1.0 - 2.0 mm) | per OTU |
| FA4_N6_SF1 | Read counts for each OTU within each sample; Sample collected during the night with net 6 (depth 200-150m) for zooplankton size fraction 1 (0.2 - 0.5mm) | per OTU |
| FA4_N6_SF2 | Read counts for each OTU within each sample; Sample collected during the night with net 6 (depth 200-150m) for zooplankton size fraction 2 (0.5 - 0.1mm) | per OTU |
| FA4_N6_SF3 | Read counts for each OTU within each sample; Sample collected during the night with net 6 (depth 200-150m) for zooplankton size fraction 3 (1.0 - 2.0 mm) | per OTU |
| FA4_N7_SF1 | Read counts for each OTU within each sample; Sample collected during the night with net 7 (depth 150-100m) for zooplankton size fraction 1 (0.2 - 0.5mm) | per OTU |
| FA4_N7_SF2 | Read counts for each OTU within each sample; Sample collected during the night with net 7 (depth 150-100m) for zooplankton size fraction 2 (0.5 - 0.1mm) | per OTU |
| FA4_N7_SF3 | Read counts for each OTU within each sample; Sample collected during the night with net 7 (depth 150-100m) for zooplankton size fraction 3 (1.0 - 2.0 mm) | per OTU |
| FA4_N8_SF1 | Read counts for each OTU within each sample; Sample collected during the night with net 8 (depth 100-50m) for zooplankton size fraction 1 (0.2 - 0.5mm) | per OTU |
| FA4_N8_SF2 | Read counts for each OTU within each sample; Sample collected during the night with net 8 (depth 100-50m) for zooplankton size fraction 2 (0.5 - 0.1mm) | per OTU |
| FA4_N8_SF3 | Read counts for each OTU within each sample; Sample collected during the night with net 8 (depth 100-50m) for zooplankton size fraction 3 (1.0 - 2.0 mm) | per OTU |
| FA4_N9_SF1 | Read counts for each OTU within each sample; Sample collected during the night with net 9 (depth 50-0m) for zooplankton size fraction 1 (0.2 - 0.5mm) | per OTU |
| FA4_N9_SF2 | Read counts for each OTU within each sample; Sample collected during the night with net 9 (depth 50-0m) for zooplankton size fraction 2 (0.5 - 0.1mm) | per OTU |
| FA4_N9_SF3 | Read counts for each OTU within each sample; Sample collected during the night with net 9 (depth 50-0m) for zooplankton size fraction 3 (1.0 - 2.0 mm) | per OTU |
| silva_tax_level1 | Taxonomic classification level 1 for each OTU; assigned by mothur based on the Silva database | unitless |
| silva_tax_level2 | Taxonomic classification level 2 for each OTU; assigned by mothur based on the Silva database | unitless |
| silva_tax_level3 | Taxonomic classification level 3 for each OTU; assigned by mothur based on the Silva database | unitless |
| silva_tax_level4 | Taxonomic classification level 4 for each OTU; assigned by mothur based on the Silva database | unitless |
| silva_tax_level5 | Taxonomic classification level 5 for each OTU; assigned by mothur based on the Silva database | unitless |
| silva_tax_level6 | Taxonomic classification level 6 for each OTU; assigned by mothur based on the Silva database | unitless |
| silva_tax_level7 | Taxonomic classification level 7 for each OTU; assigned by mothur based on the Silva database | unitless |
| silva_tax_level8 | Taxonomic classification level 8 for each OTU; assigned by mothur based on the Silva database | unitless |
| silva_tax_level9 | Taxonomic classification level 9 for each OTU; assigned by mothur based on the Silva database | unitless |
| silva_tax_level10 | Taxonomic classification level 10 for each OTU; assigned by mothur based on the Silva database | unitless |
| silva_tax_level11 | Taxonomic classification level 11 for each OTU; assigned by mothur based on the Silva database | unitless |
| silva_tax_level12 | Taxonomic classification level 12 for each OTU; assigned by mothur based on the Silva database | unitless |
| silva_tax_level13 | Taxonomic classification level 13 for each OTU; assigned by mothur based on the Silva database | unitless |
| silva_tax_level14 | Taxonomic classification level 14 for each OTU; assigned by mothur based on the Silva database | unitless |
| assigned_habitat | Assigned community/habitat, based on both mothur classification and NCBI top hit | unitless |
| NCBI_query_sequence_id | Query sequence (BLAST qseqid); header description of representative sequence from fasta file | unitless |
| NCBI_top_hit | Subject sequence id (BLAST sseqid): sequence identifier for subject sequence from NCBI; Contains two NCBI accession numbers | unitless |
| NCBI_percent_identity | Percent identity (BLAST pident): percentage of identical matches in the alignment | unitless |
| NCBI_percent_coverage | Percent coverage (BLAST qcovs): query coverage per sequence for all high-scoring segment pairs (HSPs) | unitless |
| NCBI_sequence_length | Alignment length (BLAST length) | unitless |
| NCBI_mismatch | Number of mismatches (BLAST mismatch) | unitless |
| NCBI_evalue | Expectation value of match (BLAST evalue) | unitless |
| NCBI_bitscore | Normalized alignment score for comparison across searches (BLAST bitscore) | unitless |
| NCBI_percent_positive | Percentage of positive-scoring matches (BLAST ppos) | unitless |
| NCBI_top_hit_taxID | Taxonomic identifiers (BLAST staxids): unique subject taxonomy ID(s); multiple IDs are separated by a semicolon | unitless |
| NCBI_top_hit_title | Subject title from NCBI entry (BLAST stitle) | unitless |
| analysis_description | Analysis description | unitless |
| Dataset-specific Instrument Name | Illumina MiSeq |
| Generic Instrument Name | Automated DNA Sequencer |
| Dataset-specific Description | Illumina MiSeq using V3 chemistry (300-bp, paired-end) |
| Generic Instrument Description | General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. |
| Dataset-specific Instrument Name | quantitative PCR by the Evolutionary Genetics Core Facility (Hawaii Institute of Marine Biology) |
| Generic Instrument Name | Thermal Cycler |
| Generic Instrument Description | A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html) |
| Dataset-specific Instrument Name | Agilent 2100 Bioanalyzer |
| Generic Instrument Name | Bioanalyzer |
| Generic Instrument Description | A Bioanalyzer is a laboratory instrument that provides the sizing and quantification of DNA, RNA, and proteins. One example is the Agilent Bioanalyzer 2100. |
| Website | |
| Platform | R/V Falkor |
| Start Date | 2014-06-13 |
| End Date | 2014-06-19 |
| Description | Student Cruise #3
More about this cruise from the Schmidt Ocean Institute page:https://schmidtocean.org/cruise/net-gains-at-station-aloha/ |
Description from NSF award abstract:
Marine zooplankton show strong ecological responses to climate change, but little is known about their capacity for evolutionary response. Many authors have assumed that the evolutionary potential of zooplankton is limited. However, recent studies provide circumstantial evidence for the idea that selection is a dominant evolutionary force acting on these species, and that genetic isolation can be achieved at regional spatial scales in pelagic habitats. This RAPID project will take advantage of a unique opportunity for basin-scale transect sampling through participation in the Atlantic Meridional Transect (AMT) cruise in 2014. The cruise will traverse more than 90 degrees of latitude in the Atlantic Ocean and include boreal-temperate, subtropical and tropical waters. Zooplankton samples will be collected along the transect, and mitochondrial and microsatellite markers will be used to identify the geographic location of strong genetic breaks within three copepod species. Bayesian and coalescent analytical techniques will test if these regions act as dispersal barriers. The physiological condition of animals collected in distinct ocean habitats will be assessed by measurements of egg production (at sea) as well as body size (condition index), dry weight, and carbon and nitrogen content. The PI will test the prediction that ocean regions that serve as dispersal barriers for marine holoplankton are areas of poor-quality habitat for the target species, and that this is a dominant mechanism driving population genetic structure in oceanic zooplankton.
Note: This project is funded by an NSF RAPID award. This RAPID grant supported the shiptime costs, and all the sampling reported in the AMT24 zooplankton ecology cruise report (PDF).
Online science outreach blog at: https://atlanticplankton.wordpress.com
| Funding Source | Award |
|---|---|
| NSF Division of Ocean Sciences (NSF OCE) | |
| NSF Division of Ocean Sciences (NSF OCE) | |
| NSF Division of Ocean Sciences (NSF OCE) |