Dataset: Sciaenid egg identification

Name: Identity of sciaenid eggs collected from the Gulf of Mexico Estuary near Port Aransas, Texas from 2020 to 2022
Published: 2023-09-19
Keywords: fish eggs, ichthyoplankton, Sciaenidae, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.878631.2

Spatial Extent: N:27.9362 E:-97.0218 S:27.8396 W:-97.0727222

Temporal Extent: 2020-08-21 - 2022-03-08

Project:

Counter-gradient Flow of Fatty Acids in Marine Food Webs Through Egg Boons (Egg Boon Food Webs)

Principal Investigator:

Lee A. Fuiman (University of Texas - Marine Science Institute, UTMSI)

Co-Principal Investigator:

Parvathi Nair (University of Texas - Marine Science Institute, UTMSI)

Contact:

Lee A. Fuiman (University of Texas - Marine Science Institute, UTMSI)

BCO-DMO Data Manager:

Taylor Heyl (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

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

Version:

Version Date:

2023-09-19

Restricted:

Yes

Release Date:

2024-08-01

Validated:

Yes

Current State:

Final no updates expected

Identity of sciaenid eggs collected from the Gulf of Mexico Estuary near Port Aransas, Texas from 2020 to 2022

Abstract:

This dataset represents the identity (based on PCR results) of sciaenid eggs from the Gulf of Mexico Estuary near Port Aransas, Texas. Egg samples were collected from 20 August, 2020 through 8 March, 2022 from the research pier at UTMSI, located in the Aransas Pass inlet. Egg samples were collected bi-weekly during the Red Drum spawning season (August – December) and monthly outside the Red drum spawning season from two locations. Eggs were sorted by morphology to isolate sciaenid eggs and molecular PCR techniques were applied to subsamples of eggs to confirm the species identification.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2023-09-19	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.878631.2	2024-01-17

Methods & Sampling

Sampling and analytical procedures:
Egg samples were collected from 20 August, 2020 through 8 March, 2022 from the research pier at the University of Texas Marine Science Institute (UTMSI), located in the Aransas Pass inlet by deploying a 500-micron mesh plankton net. Egg samples were also collected by deploying a plankton net from a small boat from a location outside the extent of the Red drum egg boon in the Aransas Bay (Mud Island) from 20 August, 2020- December 2021. Egg samples were collected bi-weekly during the Red Drum spawning season (August – December) and monthly outside the Red drum spawning season from both locations. Eggs were sorted by morphology to isolate sciaenid eggs and molecular PCR techniques were applied to subsamples of eggs to confirm the species identification.

DNA was extracted from a single egg using a commercial kit (Thermo scientific Gene JET genomic DNA purification kit K0721). The following cycle conditions were used to run PCRs: an initial denaturing step of 94°C for 2 minutes followed by 30 cycles of 30 seconds at 94°C; 30 s at 60°C and 1 minute at 72°C, with a final extension of 5 min at 72°C. A species-specific primer set (NADH dehydrogenase 4 mtDNA gene) was used to identify wild caught sciaenid eggs (Carreon-Martinez et al., 2010). A set of universal primers (18S ribosomal RNA gene) was used as a positive control for the DNA extraction and PCR reaction. PCR products were size separated by gel electrophoresis (1.5% agarose) and visualized by 1% ethidium bromide solution (Fisher-Scientific). The species-specific primers identified southern king fish (550 bp), gulf kingfish(400 bp), black drum (350 bp), red drum (651 bp), Atlantic croaker (850 bp), and spotted seatrout (1201 bp) using DNA ladder.

** Note: Eggs were not tested for black drum if egg collection date was outside the spawning season of black drum and egg size was smaller than 1.00 millimeters

FAML: pier at in Corpus Christi Channel, Port Aransas, TX, United States, Fisheries and Mariculture Laboratory of the University of Texas Marine Science Institute (lat. 27.8396111, lon. -97.0727222);

MI: Mud Island in Aransas Bay, TX, United States (lat. 27.9362222, lon. -97.0217777)).

Data Processing Description

Dataset version 1 (2022-12-01):
- File "Egg PCR Final Data 2020-2022.xlsx" (submitted 2022-07-08 by email ) was imported into the bco-dmo data system.
- Converted dates to format (YYYY-MM-DD)
- Adjusted field/parameter names to comply with BCO-DMO naming conventions
- Added columns for Latitude and Longitude
- Added a conventional header with dataset name, PI names, version date

Dataset version 2 (2023-09-19):
* Sheet 1 of file "Egg PCR Final Data 2020-2022.xlsx" (submitted by email Jun 22, 2023) was imported into the BCO-DMO data system.

Data Files

File
878631_v2_egg_pcr.csv (Comma Separated Values (.csv), 24.99 KB) MD5:8ebd64a43c53056c43df370dccf4c340 Primary data table for dataset 878631 version 2

Supplemental Files

File

Species List and Taxonomic Identifiers
filename: 878631_species_list.csv

(Comma Separated Values (.csv), 605 bytes)
MD5:7694dad49fa3f919cf0957c8437548bd

Species list for this dataset.  This table provides the scientific names for the common names provided as the dataset column names.  The scientific names were added from names provided in related BCO-DMO dataset  908171 "Stable Isotope measurements – field and lab samples".  Scientific names for Black Drum and Gulf Kingfish added using the names provided in the methods reference for this dataset Carreon-Martinez et al., (2010).

Column information:

Column_name_in_dataset, The column name in the data table for this dataset which is an organism common name
Scientific_name, Corresponding scientific name for the common name
AphiaID, Taxonomic identifier (AphiaID, see World Register of Marine Species)
LSID,  Lifescience identifier (LSID)

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-2023618

Deployments

None available yet

Instruments

Thermal Cycler

Supplied Name: Aria Mx Real-Time PCR System, Agilent Technologies

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
Egg_size	Size of the egg collected	millimeters	length
Collection_date	date of egg collection in format: YYYY-MM-DD Format: %Y-%m-%d	unitless	date
UIN	Unique identifiction number	unitless	sample
Site	location where sample was collected (FAML: pier at in Corpus Christi Channel, Port Aransas, TX, United States, Fisheries and Mariculture Laboratory of the University of Texas Marine Science Institute (lat. 27.8396111, lon. -97.0827222); MI: Mud Island in Aransas Bay, TX, United States (lat. 27.9362222, lon. -97.0217777))	unitless	site
Latitude	latitude North of sample collection	decimal degrees	lat
Longitude	longitude East (West is negative) of sample collection	decimal degrees	lon
DNA_extraction_date	Date DNA was extracted from egg in format YYYY-MM-DD Format: %Y-%m-%d	unitless	date
Date_analyzed	Date PCR was run in format YYYY-MM-DD Format: %Y-%m-%d	unitless	date
Red_Drum	Eggs positively (POS) or negatively (NEG) identified as red drum based on the presence of species specific NADH band on gel electrophoresis	unitless	sample_descrip
Gulf_Kingfish	Eggs positively (POS) or negatively (NEG) identified as Gulf kingfish based on the presence of species specific NADH band on gel electrophoresis	unitless	sample_descrip
Southern_Kingfish	Eggs positively (POS) or negatively (NEG) identified as southern kingfish based on the presence of species specific NADH band on gel electrophoresis	unitless	sample_descrip
Spotted_Seatrout	Eggs positively (POS) or negatively (NEG) identified as spotted seatrout based on the presence of species specific NADH band on gel electrophoresis	unitless	sample_descrip
Atlantic_Croaker	Eggs positively (POS) or negatively (NEG) identified as atlantic croaker based on the presence of species specific NADH band on gel electrophoresis	unitless	sample_descrip
Black_Drum	Eggs positively (POS) or negatively (NEG) identified as black drum based on the presence of species specific NADH band on gel electrophoresis	unitless	sample_descrip

Database

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Dataset: Sciaenid egg identification