Dataset: Metabarcoding zooplankton at station ALOHA: OTU tables and fasta files

Name: Metabarcoding zooplankton at station ALOHA: Operational taxonomic unit (OTU) tables and fasta files for representative sequences from each OTU (Plankton Population Genetics project)
Published: 2017-05-25
Keywords: Metabarcoding, station ALOHA, mesopelagic and bathypelagic zooplankton, community composition, oceans

Cite This Dataset

DOI:10.1575/1912/bco-dmo.700279.1

Spatial Extent: N:22.75 E:-158 S:22.75 W:-158

Temporal Extent: 2014-06-13 - 2014-06-19

Project:

Basin-scale genetics of marine zooplankton (Plankton Population Genetics)

Principal Investigator:

Erica Goetze (University of Hawai'i, UH)

Contact:

Erica Goetze (University of Hawai'i, UH)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2017-05-25

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Metabarcoding zooplankton at station ALOHA: Operational taxonomic unit (OTU) tables and fasta files for representative sequences from each OTU (Plankton Population Genetics project)

Abstract:

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).

Expand/Collapse All

Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2017-05-25	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.1575/1912/bco-dmo.704664	2017-06-12
2017-05-25	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.1575/1912/bco-dmo.700279.1	2020-02-21

Description

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

Methods & Sampling

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/).

Data Processing Description

BCO-DMO processing notes:
* commas in the data were replaced with semicolons to support export as csv format.
* fasta files added to dataset

Data Files

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

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1338959
NSF Division of Ocean Sciences	OCE-1255697
NSF Division of Ocean Sciences	OCE-1029478

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
FK140613		2014-06-13	R/V Falkor	Erica Goetze (Chief Scientist)	data info

Instruments

Automated DNA Sequencer

Supplied Name: Illumina MiSeq

Supplied Description:

Illumina MiSeq using V3 chemistry (300-bp, paired-end)

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic 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.

Bioanalyzer

Supplied Name: Agilent 2100 Bioanalyzer

Supplied Description:

Instrument Type

Generic Name: Bioanalyzer

Generic 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.

Thermal Cycler

Supplied Name: quantitative PCR by the Evolutionary Genetics Core Facility (Hawaii Institute of Marine Biology)

Supplied Description:

Instrument Type

Generic Name: Thermal Cycler

Generic 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)

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
lat	Latitude of sample site (Station ALOHA)	decimal degrees	lat
lon	Longitude of sample site (Station ALOHA)	decimal degrees	lon
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
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	count
silva_tax_level13	Taxonomic classification level 13 for each OTU; assigned by mothur based on the Silva database	unitless	taxon
silva_tax_level14	Taxonomic classification level 14 for each OTU; assigned by mothur based on the Silva database	unitless	taxon
assigned_habitat	Assigned community/habitat, based on both mothur classification and NCBI top hit	unitless	sample_descrip
NCBI_query_sequence_id	Query sequence (BLAST qseqid); header description of representative sequence from fasta file	unitless	sequence
silva_tax_level1	Taxonomic classification level 1 for each OTU; assigned by mothur based on the Silva database	unitless	taxon
NCBI_top_hit	Subject sequence id (BLAST sseqid): sequence identifier for subject sequence from NCBI; Contains two NCBI accession numbers	unitless	accession_number
silva_tax_level2	Taxonomic classification level 2 for each OTU; assigned by mothur based on the Silva database	unitless	taxon
NCBI_percent_identity	Percent identity (BLAST pident): percentage of identical matches in the alignment	unitless	no_bcodmo_term
silva_tax_level3	Taxonomic classification level 3 for each OTU; assigned by mothur based on the Silva database	unitless	taxon
NCBI_percent_coverage	Percent coverage (BLAST qcovs): query coverage per sequence for all high-scoring segment pairs (HSPs)	unitless	no_bcodmo_term
silva_tax_level4	Taxonomic classification level 4 for each OTU; assigned by mothur based on the Silva database	unitless	taxon
NCBI_sequence_length	Alignment length (BLAST length)	unitless	no_bcodmo_term
silva_tax_level5	Taxonomic classification level 5 for each OTU; assigned by mothur based on the Silva database	unitless	taxon
NCBI_mismatch	Number of mismatches (BLAST mismatch)	unitless	no_bcodmo_term
silva_tax_level6	Taxonomic classification level 6 for each OTU; assigned by mothur based on the Silva database	unitless	taxon
NCBI_evalue	Expectation value of match (BLAST evalue)	unitless	no_bcodmo_term
silva_tax_level7	Taxonomic classification level 7 for each OTU; assigned by mothur based on the Silva database	unitless	taxon
NCBI_bitscore	Normalized alignment score for comparison across searches (BLAST bitscore)	unitless	no_bcodmo_term
analysis_name	Descriptive name of analysis including percent clustering and subsampling or no subsampling	unitless	sample_descrip
silva_tax_level8	Taxonomic classification level 8 for each OTU; assigned by mothur based on the Silva database	unitless	taxon
NCBI_percent_positive	Percentage of positive-scoring matches (BLAST ppos)	unitless	no_bcodmo_term
silva_tax_level9	Taxonomic classification level 9 for each OTU; assigned by mothur based on the Silva database	unitless	taxon
NCBI_top_hit_taxID	Taxonomic identifiers (BLAST staxids): unique subject taxonomy ID(s); multiple IDs are separated by a semicolon	unitless	no_bcodmo_term
silva_tax_level10	Taxonomic classification level 10 for each OTU; assigned by mothur based on the Silva database	unitless	taxon
NCBI_top_hit_title	Subject title from NCBI entry (BLAST stitle)	unitless	sample_descrip
OTU_ID	Operational taxonomic unit (OTU) identifier	unitless	sample
silva_tax_level11	Taxonomic classification level 11 for each OTU; assigned by mothur based on the Silva database	unitless	taxon
analysis_description	Analysis description	unitless	sample_descrip
silva_tax_level12	Taxonomic classification level 12 for each OTU; assigned by mothur based on the Silva database	unitless	taxon