Dataset: Phytoflux_BATS

Name: BATS phytoplankton and cyanobacteria DGGE DNA data from R/V Atlantic Explorer, R/V Oceanus cruises in the Bermuda Atlantic Time Series Station (BATS) from 2008-2010 (Plankton particle flux project)
Published: 2013-04-15
Keywords: oceans

Cite This Dataset

Project:

Composition of the plankton community and its contribution to particle flux in the Sargasso Sea (Plankton particle flux)

Program:

Ocean Carbon and Biogeochemistry (OCB)

Principal Investigator:

Susanne Neuer (Arizona State University, ASU)

Co-Principal Investigator:

Michael W. Lomas (Bermuda Biological Station for Research, BBSR)

Student:

Jessica Amacher (Arizona State University, ASU)

BCO-DMO Data Manager:

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

Version:

2013-04-15

Version Date:

2013-04-15

Validated:

Yes

Current State:

Final no updates expected

BATS phytoplankton and cyanobacteria DGGE DNA data from R/V Atlantic Explorer, R/V Oceanus cruises in the Bermuda Atlantic Time Series Station (BATS) from 2008-2010 (Plankton particle flux project)

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Description

This dataset includes eukaryotic and cyanobacterial DNA sequence data obtained from the upper water column as well as from shallow drifting traps during regular BATS cruises from May 2008-April 2010. Specifically, it contains a complete list of denaturing gradient gel results and the closest sequence matches from the NCBI database for each excised band (phylotype) as well as original denaturing gradient gel images.

Methods & Sampling

Sampling and Analytical Methodology:
Sampling was conducted monthly from May 2008-April 2010 at the Bermuda Atlantic Time-Series (BATS). Samples were collected for DNA analysis from four depths in the upper water column and from 150 m particle traps. DNA was extracted from these samples and a region of the 18S ribosomal RNA gene for eukaryotes and 16S rRNA gene for cyanobacteria was amplified by PCR using eukaryotic and cyanobacterial primers. Each amplified sample was subjected to Denaturing Gradient Gel Electrophoresis in order to “fingerprint” the community. Individual bands were excised and identified by sequence matching using the NCBI database (http://blast.ncbi.nlm.nih.gov). Quantity One software package was used to determine similarity between samples. The efficiency of recovery was determined by qPCR in order to accurately calculate the DNA present in the water column and DNA flux into particle traps. For further detail please refer to:

Jessica Amacher, Susanne Neuer, Michael Lomas. 2013. DNA-based molecular fingerprinting of eukaryotic protists and cyanobacteria contributing to sinking particle flux at the Bermuda Atlantic time-series study. Deep Sea Research part II. 93: 71-83.

Data Processing Description

Data Processing:
Denaturing gradient gels were imaged and analyzed with the BioRad Fluor-S imager. Bands were selected and matched manually for band matrices included in these data.

BCO-DMO Note: Cruise 242 was on the RV/Oceanus, not the Atlantic Explorer. The cruise id was corrected 5/13/2013. (NJC)

Data Files

File
phytoflux_BATS.csv (Comma Separated Values (.csv), 575.38 KB) MD5:abc6217199a54ce325729dbf1481feb0 Primary data file for dataset ID 3818

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-0752592

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
AE0811	235 GF235	2008-05-28	R/V Atlantic Explorer	Anthony Knap (Chief Scientist)	data info
AE0813	236 GF236	2008-06-21	R/V Atlantic Explorer	Anthony Knap (Chief Scientist)	data info
AE0816	237 GF237	2008-07-15	R/V Atlantic Explorer	Anthony Knap (Chief Scientist)	data info
AE0820	238 GF238	2008-08-11	R/V Atlantic Explorer	Anthony Knap (Chief Scientist)	data info
AE0823	239 GF239	2008-09-09	R/V Atlantic Explorer	Anthony Knap (Chief Scientist)	data info
AE0826	240 GF240	2008-10-06	R/V Atlantic Explorer	Anthony Knap (Chief Scientist)	data info
AE0829	241 GF241	2008-11-08	R/V Atlantic Explorer	Anthony Knap (Chief Scientist)	data info
AE0901	243 GF243	2009-02-07	R/V Atlantic Explorer	Anthony Knap (Chief Scientist)	data info
AE0902	243A GF243A	2009-02-21	R/V Atlantic Explorer	Anthony Knap (Chief Scientist)	data info
AE0904	244	2009-03-16	R/V Atlantic Explorer	Anthony Knap (Chief Scientist)	data info
AE0907	245	2009-04-14	R/V Atlantic Explorer	Anthony Knap (Chief Scientist)	data info
AE0909	246	2009-05-14	R/V Atlantic Explorer	Anthony Knap (Chief Scientist)	data info
AE0911	247	2009-06-09	R/V Atlantic Explorer	Anthony Knap (Chief Scientist)	data info
AE0916	248	2009-07-13	R/V Atlantic Explorer	Anthony Knap (Chief Scientist)	data info
AE0919	249	2009-08-13	R/V Atlantic Explorer	Anthony Knap (Chief Scientist)	data info
AE0921	250	2009-09-09	R/V Atlantic Explorer	Anthony Knap (Chief Scientist)	data info
AE0924	251	2009-10-08	R/V Atlantic Explorer	Anthony Knap (Chief Scientist)	data info
AE0926	252	2009-11-06	R/V Atlantic Explorer	Anthony Knap (Chief Scientist)	data info
AE0928	253	2009-12-07	R/V Atlantic Explorer	Anthony Knap (Chief Scientist)	data info
AE1001	254 GF254	2010-02-02	R/V Atlantic Explorer	Anthony Knap (Chief Scientist)	data info
AE1003	255 GF255	2010-02-22	R/V Atlantic Explorer	Anthony Knap (Chief Scientist)	data info
AE1005	255A GF255A	2010-03-08	R/V Atlantic Explorer	Anthony Knap (Chief Scientist)	data info
AE1006	256 B256 GF256	2010-03-23	R/V Atlantic Explorer	Lilia Jackman (Chief Scientist)	data info
AE1009	257 GF257	2010-04-20	R/V Atlantic Explorer	Anthony Knap (Chief Scientist)	data info
OC449-10	242	2008-12-14	R/V Oceanus	Steven Bell (Chief Scientist)	data info

Instruments

Sediment Trap

Supplied Description:

Instrument Type

Generic Name: Sediment Trap

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/33/

Generic Description:

Sediment traps are specially designed containers deployed in the water column for periods of time to collect particles from the water column falling toward the sea floor. In general a sediment trap has a jar at the bottom to collect the sample and a broad funnel-shaped opening at the top with baffles to keep out very large objects and help prevent the funnel from clogging. This designation is used when the specific type of sediment trap was not specified by the contributing investigator.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
cell_type	eukaryotes or cyanobacteria	text	no_bcodmo_term
cruise_id1	official rvdata cruise name	alphanumeric	cruise_id
cruise_id2	original cruise number	alphanumeric	cruise_id
year	year of sampling	YYYY	year
month	month of sampling	0-12	month
day	day of sampling	0-31	day
yrday_gmt	year-day of sampling	1-365	yrday_gmt
lane	electrophoresis lane	integer	no_bcodmo_term
z10	10 meters sample flag; 1=yes; 0=no	0 or 1	flag
z20	20 meters sample flag; 1=yes; 0=no	0 or 1	flag
z25	25 meters sample flag; 1=yes; 0=no	0 or 1	flag
z30	30 meters sample flag; 1=yes; 0=no	0 or 1	flag
z40	40 meters sample flag; 1=yes; 0=no	0 or 1	flag
z60	60 meters sample flag; 1=yes; 0=no	0 or 1	flag
z70	70 meters sample flag; 1=yes; 0=no	0 or 1	flag
z75	75 meters sample flag; 1=yes; 0=no	0 or 1	flag
z80	80 meters sample flag; 1=yes; 0=no	0 or 1	flag
z85	85 meters sample flag; 1=yes; 0=no	0 or 1	flag
z90	90 meters sample flag; 1=yes; 0=no	0 or 1	flag
z100	100 meters sample flag; 1=yes; 0=no	0 or 1	flag
z110	110 meters sample flag; 1=yes; 0=no	0 or 1	flag
z120	120 meters sample flag; 1=yes; 0=no	0 or 1	flag
z130	130 meters sample flag; 1=yes; 0=no	0 or 1	flag
z138	138 meters sample flag; 1=yes; 0=no	0 or 1	flag
z140	140 meters sample flag; 1=yes; 0=no	0 or 1	flag
z150	150 meters sample flag; 1=yes; 0=no	0 or 1	flag
z180	180 meters sample flag; 1=yes; 0=no	0 or 1	flag
fixed_trap_150m	sample flag for 150 meter fixed trap	0 or 1	flag
unfixed_trap_150m	sample flag for 150 meter unfixed trap	0 or 1	flag
unfixed_trap_a_150m	sample flag for 150 meter unfixed trap a	0 or 1	flag
unfixed_trap_b_150m	sample flag for 150 meter unfixed trap b	0 or 1	flag
unfixed_trap_c_150m	sample flag for 150 meter unfixed trap c	0 or 1	flag
unfixed_trap_d_150m	sample flag for 150 meter unfixed trap d	0 or 1	flag
band_num	electrophoresis band number	integer	no_bcodmo_term
id_closest_match	species of closest dna match	text	species
accession_number_1	GenBank accession number of closest match	alphanumeric	accession_number
identity_pcent_1	percent similarity of sample with closest match	integer	no_bcodmo_term
id_closest_cultured_match	species of closest cultured match	text	species
accession_number_2	GenBank accession number of closest cultured match	alphanumeric	accession_number
identity_pcent_2	percent similarity of sample with closest cultured match	integer	no_bcodmo_term
taxon_1	coarse taxonomic identity	text	taxon
taxon_2	finer taxonomic identity	text	taxon

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Database

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Dataset: Phytoflux_BATS