Dataset: HRR Metabarcoding

Name: Metabarcoding samples collected from surface and chlorophyll maximum depths from R/V Pt. Sur PS 18-09 Legs 01 and 03, Hurricane Harvey RAPID Response cruise (western Gulf of Mexico) September-October 2017.
Published: 2020-09-11
Keywords: biota, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.824599.1

Spatial Extent: N:29.0649 E:-94.9 S:27.2286 W:-97.268

Temporal Extent: 2017-09-23 - 2017-10-01

Project:

RAPID: Hurricane Impact on Phytoplankton Community Dynamics and Metabolic Response (HRR)

Principal Investigator:

Lisa Campbell (Texas A&M University, TAMU)

Co-Principal Investigator:

Darren W. Henrichs (Texas A&M University, TAMU)

Contact:

Chetan Gaonkar (Texas A&M University, TAMU)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2020-09-11

Restricted:

Validated:

Current State:

Final no updates expected

Metabarcoding samples collected from surface and chlorophyll maximum depths from R/V Pt. Sur PS 18-09 Legs 01 and 03, Hurricane Harvey RAPID Response cruise (western Gulf of Mexico) September-October 2017.

Abstract:

Metabarcode samples collected from surface and chlorophyll maximum depths from R/V Pt. Sur PS 18-09 Legs 01 and 03, Hurricane Harvey RAPID Response cruise (western Gulf of Mexico) September-October 2017.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2020-09-14	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.824599.1	2020-12-31

Description

Methods & Sampling

On each of 2 cruise legs 01 and 03, samples were collected at 7 stations (S01, S06, S11, S16, S21, SS and GI) from 2 depths [surface and chlorophyll maximum depth when possible; see HRR-bottle data] ) and triplicate 500-1000 ml samples were filtered and immediately fixed in RNALater. Triplicate samples from each station/depth were extracted with AllPrep DNA/RNA MiniKit (Qiagen, USA) following the manufacturer’s instructions. DNA concentration and quality were evaluated using a Nanodrop spectrophotometer (Thermo Fisher Scientific Inc, USA). All the samples extracted for DNA were normalized to 5ng/µl concentration for the amplicon library construction.

The V4 regions of the 18S rRNA genes were amplified using customized V4 primers (Bradley et al. 2016; Kozich et al. 2013). Library construction and amplicon sequencing was performed at Texas A&M University Agrilife’s Genomics and Bioinformatics Services (https://www.txgen.tamu.edu) using custom designed primers (Bradley et al. 2016; Kozich et al. 2013). Output of MiSeq results as fasta files were deposited in GenBank under the project number PRJNA592369.

Leg 01 Station 01 sample was not collected.

Sampling locations:

Sample ID	Station	Leg	Location Lat ^oN/Long ^oW
na		1	27.2286 -97.2686
L3_S01	S01	3	27.2286 -97.2686
L1_S06	S06	1	27.8358 -96.9874
L3_S06	S06	3	27.8358 -96.9874
L1_S11	S11	1	28.2614 -96.4129
L3_S11	S11	3	28.2614 -96.4129
L1_S16	S16	1	28.5366 -95.8656
L3_S16	S16	3	28.5366 -95.8656
L1_S21	S21	1	28.7644 -95.2978
L3_S21	S21	3	28.7644 -95.2978
L1_SS	SS	1	28.9600 -95.0946
L3_SS	SS	3	28.9600 -95.0946
L1_GI	GI	1	29.0649 -94.9000
L3_GI	GI	3	29.0649 -94.9000

Data Processing Description

Fastq files for all 13 station samples were quality checked using FastQC. Illumina paired end reads (2x300 bp) were processed in mothur v1.39.0 (Schloss et al. 2009). Contigs were assembled and pre-cleaned processed for homopolymers and ambiguities. These sequences were then screened for chimera using UCHIME in denovo mode (Edgar et al. 2011). Sequences were de-noised by pre-clustering at 1 bp per 100 bp and generate unique sequence for taxonomic annotation and characterization. Sequences less than three were eluted out in our study and rest OTUs were characterized using BLAST search using PR2 database v4.12.0. The BLAST analysis used a assignment approach with similarity was ≥ 90% and query coverage was ≥ 70% against the reference sequence. Any OTU that did not compile with this criterion was not used in this study. The following thresholds for identity with BLAST results were used for taxonomic assignment clustering: species (97%), genus (94%), family (93%), class (92%) and order (90%).

HTS-metabarcoding procedures were followed as mentioned in Gaonkar et al., (2020). Only HTS metabarcodes haplotypes (OTUs) with reads more than 3 allocated to Chaetocerotaceae (Chaetoceros and Bacteriastrum) were used with a selection criterion of ≥ 90% similarity and ≥ 70% similarity after BLAST analysis using the protistan PR2 dataset. A total of 206 (n=82881) OTUs annotated as Chaetocerotacean haplotypes were obtained from the HRR dataset. See figures 1 and 2 in the Supplemental Files section.

BCO-DMO Processing Notes:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions

Data Files

File
metabarcode.csv (Comma Separated Values (.csv), 1.80 MB) MD5:ffd076a7f8f909d5d3eb308581830ac0 Primary data file for dataset ID 824599

Supplemental Files

File
Chaetocerotacean diversity filename: HRR_Chaetocerotacean_phylogeny.pdf (Portable Document Format (.pdf), 73.72 KB) MD5:9510b43f8eefaaa59cac95a51fe7ba71 Fig. 1. Chaetocerotacean diversity: Assessing the Chaetocerotacean diversity using the V4-hypervaiable region of 18S rDNA using HTS-metabarcoding. Maximum likelihood tree generated using raxmlGUI v2.0 (Edler et al. 2019) for the Chaetocerotacean species from the sample collected in the Gulf of Mexico, Texas coast. A total of 206 validated Chaetocerotacean metabarcode haplotypes along with 150 taxonomically validated Chaetocerotacean reference sequences and 26 outgroup sequences were used to generate the phylogenetic trees to assess species diversity. The OTU ID consists of the dataset name, unique identification number and number of reads at the end. Numbers on the internodes indicate bootstrap values if ≥50 (1000 replicates).
Karenia phylogeny filename: HRR_Karenia_phylogeny.pdf (Portable Document Format (.pdf), 1.22 MB) MD5:8dff398a441a5cdcebe6c8220edac9a9 Fig 2. Karenia phylogeny: Selection of appropriate metabarcoding marker for species detection and delineation. Maximum likelihood tree generated using raxmlGUI v2.0 (Edler et al. 2019) for the Karenia species. OTUs based on (a) V4-region and (b) V8-V9 regions of 18S rDNA gene yield different results. Numbers on the internodes indicate the bootstrap values if ≥50 (1000 replicates). Only those reference sequences which had full length 18S rDNA sequences were selected, and Karenia reference sequences are indicated with a colored dot. Only OTUs those with read abundance more than 100 were selected.
Station locations filename: locations_metatrans.csv (Comma Separated Values (.csv), 445 bytes) MD5:335177c22a60a318da8e433442c6a71a Table with locations for each of the station-leg collection sites.
Station map filename: station_locations.png (Portable Network Graphics (.png), 461.29 KB) MD5:7c598067f3efca47dec504ee13dc5121 Sampling locations and identification of the station abbreviations

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1760620

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
PS1809	HRR PS18-09	2017-09-22	R/V Point Sur	Lisa Campbell (Chief Scientist) Steven DiMarco (Chief Scientist)	data info

Instruments

Automated DNA Sequencer

Supplied Name: Illumina MiSeq

Supplied Description:

Used to obtain DNA sequences. See https://www.illumina.com/systems/sequencing-platforms/miseq.html

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.

Niskin bottle

Supplied Name:

Supplied Description:

Used to collect samples

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic Description:

A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.

Spectrophotometer

Supplied Name: Nanodrop spectrophotometer (Thermo Fisher Scientific Inc, USA)

Supplied Description:

Used for DNA concentration and quality evaluation.

Instrument Type

Generic Name: Spectrophotometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/

Generic Description:

An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Sequence_ID	OTU sequence generated from the HRR data	Unitless	sequence
Taxonomy	Taxonomic annotation of the OTU	Unitless	taxon
Similarity	percentage of identical matches	Unitless	no_bcodmo_term
Length	alignment length (sequence overlap)	Unitless	no_bcodmo_term
Mismatches	number of mismatches	Unitless	no_bcodmo_term
Gaps	number of gap openings	Unitless	no_bcodmo_term
Q_start	start of alignment in query	Unitless	no_bcodmo_term
Q_end	end of alignment in query	Unitless	no_bcodmo_term
R_start	start of alignment in reference sequence	Unitless	no_bcodmo_term
R_end	end of alignment in reference sequence	Unitless	no_bcodmo_term
e_value	number of expected hits of similar quality	Unitless	no_bcodmo_term
Score	Bit-score	Unitless	no_bcodmo_term
OTU	representative OTUs	Unitless	no_bcodmo_term
L1_S06	number of copies of the OTU at Leg 1 Station 06	Unitless	count
L1_S11	number of copies of the OTU at Leg 1 Station 11	Unitless	count
L1_S16	number of copies of the OTU at Leg 1 Station 16	Unitless	count
L1_S21	number of copies of the OTU at Leg 1 Station 21	Unitless	count
L1_SS	number of copies of the OTU at Leg 1 Surfside station SS	Unitless	count
L1_GI	number of copies of the OTU at Leg 1 Galveston Island station GI	Unitless	count
L3_S01	number of copies of the OTU at Leg 3 Station 01	Unitless	count
L3_S06	number of copies of the OTU at Leg 3 Station 06	Unitless	count
L3_S11	number of copies of the OTU at Leg 3 Station 11	Unitless	count
L3_S16	number of copies of the OTU at Leg 3 Station 16	Unitless	count
L3_S21	number of copies of the OTU at Leg 3 Station 21	Unitless	count
L3_SS	number of copies of the OTU at Leg 3 Surfside station SS	Unitless	count
L3_GI	number of copies of the OTU at Leg 3 Galveston Island station GI	Unitless	count

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Dataset: HRR Metabarcoding