Dataset: HydroCAT data from oyster reciprocal transplant experiment

Name: Seawater properties at two locations in a northeast Florida estuary measured using HydroCAT CTD between July 2019 and April 2020 as part of an oyster reciprocal transplant experiment
Published: 2022-12-16
Keywords: CTD, physical gradient, estuarine water temperature, estuarine water salinity, oceans

View Data: Data not available yet

Cite This Dataset

Spatial Extent: N:29.77002 E:-81.2144 S:29.62923 W:-81.2641

Temporal Extent: 2019-07-23 - 2020-04-02

Project:

Collaborative research: Quantifying the influence of nonconsumptive predator effects on prey population dynamics (Predatory NCEs and Scale)

Principal Investigator:

David L. Kimbro (Northeastern University)

Co-Principal Investigator:

J. Wilson White (Oregon State University, OSU)

Technician:

Adrienne Breef-Pilz (Northeastern University)

BCO-DMO Data Manager:

Dana Stuart Gerlach (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2022-12-16

Restricted:

Validated:

Current State:

Data not available

Seawater properties at two locations in a northeast Florida estuary measured using HydroCAT CTD between July 2019 and April 2020 as part of an oyster reciprocal transplant experiment

Abstract:

The eastern oyster (Crassostrea virginica) is a foundation species in northeast Florida estuaries, including the Guana Tolomato Matanzas National Estuarine Research Reserve (GTMNERR), where intertidal reefs are extensive. Estuarine research to assess sustainability of oyster populations, plus various monitoring studies and oyster reef restoration projects have been undertaken, with an additional focus on testing theory regarding the effects of predation risk and local adaptation in the natural environment. To help quantify how environmental conditions (salinity, temperature, dissolved oxygen) varied over space and time between two sites in the GTM NERR, and therefore to provide physical context for the biological results of the project, a HydroCAT CTD was deployed approximately 3 meters seaward of the oyster reef at low tide for the duration of the experiment (July 2019 - April 2020). The instrument was deployed just seaward of the reef because the intertidal reefs were typically fully exposed at low tide.

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Methods & Sampling

A reciprocal transplant experiment was conducted at two sites in an estuary in NE Florida, USA that encompassed different environmental (salinity, aerial exposure) and biotic (predators) stressors. Juvenile oysters were reciprocally transplanted within and between the two locations within the Guana Tolomato Matanzas National Estuarine Research Reserve (GTMNERR)--the Butler site at 29.77002 N, -81.2641 W, and the Pellicer site at 29.62923 N, -81.2144 W.

To obtain site-specific information on seawater properties, a SeaBird HydroCAT-EP CTD instrument was deployed just seaward of the reefs. Measurements include temperature, conductivity, pressure, salinity, and oxygen. The HydroCAT ODO by Seabird was put in the water in front of the oyster reefs for the duration of the experiment, Butler (7/23/2019 8:00 to 4/2/2020 14:45) and Pellicer (8/19/2019 10:30 to 4/2/2020 14:45). The instrument was deployed in a PVC housing with the CTD in a 2 inch PVC pipe with drilled 1/2 inch holes to allow water flow. The frame of the housing was made up of 1 inch PVC pipe with the 2 inch PVC pipe resting on the edge of the housing at a 45 degree angle so the end with the sensors was lower in the water than the top of the instrument. The housing and sensor were deployed seaward at approximately three meters from the middle of the oyster reef.

In order to secure the CTD, the housing frame was pressed into sediment with the CTD being above the sediment. At each end of the housing frame, we also attached two pieces of rope and used rebar stakes to secure the rope into the ground. Samples were taken every 15 minutes but if the CTD was out of the water the observations were discarded; for Butler this was determined as salinity less than 25 and pressure less than 1 dbar, for Pellicer it was salinity less than 15 psu and pressure less than 0.008 dbar. Throughout the experiment, the CTDs were removed from the water to download data and cleaned prior to re-deployment.

Problem report:
No conductivity on 9/20/2019 through 4/2/2020 at Butler. Similarly, no conductivity beginning 11/15/2019 through 4/2/2020 at Pellicer, but specific conductivity was still measured at both sites at those times.

Data Processing Description

The data were uploaded using the UCI version 2.0.3 software by Seabird and saved as a .csv file. All data processing took place in RStudio under R version 4.2.1. using packages lubridate (v1.8.0; Grolemund & Wickham, 2011), tidyverse (v1.3.2; Wickham et al., 2019), oce (Kelley, 2018; Kelley & Richards, 2022). The script "Hydrocat_RT.R" processes the data to take out values when the CTD was out of the water and to label the sites. The salinity was not recorded during a few deployments, so the oce package was used to calculate the salinity.

The HydroCAT-EP CTD files for each site were compiled and run through the R code "Hydrocat_RT.R" (see Supplemental Files section)

Butler site HydroCAT raw data files:

HydroCAT-ODO-SDI12-03730256-Data-20200121T142941.csv, (time period: 2019-12-01 to 2020-01-08)
HydroCAT-ODO-SDI12-03730256-Data-20200417T232531.csv, (time period: 2020-01-21 to 2020-03-04)
HydroCAT-ODO-SDI12-03730258-Data-20190830T005058.csv, (time period: 2019-07-23 to 2019-08-29)
HydroCAT-ODO-SDI12-03730258-Data-20191112T233136.csv, (time period: 2019-09-20 to 2019-11-12)
HydroCAT-ODO-SDI12-03730258-Data-20200402T210143.csv, (time period: 2020-03-06 to 2020-04-02)

Pellicer site HydroCAT raw data files:

HydroCAT-ODO-SDI12-03730256-Data-20191120T131243.csv, (time period: 2019-11-15 to 2019-11-20)
HydroCAT-ODO-SDI12-03730256-Data-20191130T232934.csv, (time period: 2019-11-20 to 2019-11-30)
HydroCAT-ODO-SDI12-03730257-Data-20190830T004554.csv, (time period: 2019-08-19 to 2019-08-29)
HydroCAT-ODO-SDI12-03730257-Data-20191112T233512.csv, (time period: 2019-09-19 to 2019-11-12)
HydroCAT-ODO-SDI12-03730257-Data-20200402T210448.csv, (time period: 2020-02-19 to 2020-04-20)

BCO-DMO Processing description:
- Converted dates to format (YYYY-MM-DD)
- Adjusted field/parameter names to comply with BCO-DMO naming conventions
- Added columns for "Latitude" and "Longitude" based on geospatial bounds
- Added a conventional header with dataset name, PI names, version date
- Rounded Salinity values to 2 decimal places

Supplemental Files

File
HydroCAT CTD raw data for Butler site filename: Butler_HydroCAT_CTD_raw.zip (ZIP Archive (ZIP), 383.99 KB) MD5:de82fb225ef81e5b72483b3cd0739d76 Compressed folder of HydroCAT CTD raw data files for the Butler site. The files are inputs to the Hydrocat_RT.R processing script and are listed here with time periods of coverage: HydroCAT-ODO-SDI12-03730256-Data-20200121T142941.csv, (time period: 2019-12-01 to 2020-01-08) HydroCAT-ODO-SDI12-03730256-Data-20200417T232531.csv, (time period: 2020-01-21 to 2020-03-04) HydroCAT-ODO-SDI12-03730258-Data-20190830T005058.csv, (time period: 2019-07-23 to 2019-08-29) HydroCAT-ODO-SDI12-03730258-Data-20191112T233136.csv, (time period: 2019-09-20 to 2019-11-12) HydroCAT-ODO-SDI12-03730258-Data-20200402T210143.csv, (time period: 2020-03-06 to 2020-04-02) The headings are FrameSync, DateTime (UTC-4:00), Temperature (Celsius), Pressure (Decibar), Oxygen (mg/L), SpecConductivity (uS/cm), Date, Time (UTC-4:00)
HydroCAT CTD raw data for Pellicer site filename: Pellicer_HydroCAT_CTD_raw.zip (ZIP Archive (ZIP), 262.31 KB) MD5:01c9aa240b0dc2bd55df3bca706c0fe6 Compressed folder of HydroCAT CTD raw data files for the Butler site. The files are inputs to the Hydrocat_RT.R processing script and are listed here with time periods of coverage: HydroCAT-ODO-SDI12-03730256-Data-20191120T131243.csv, (time period: 2019-11-15 to 2019-11-20) HydroCAT-ODO-SDI12-03730256-Data-20191130T232934.csv, (time period: 2019-11-20 to 2019-11-30) HydroCAT-ODO-SDI12-03730257-Data-20190830T004554.csv, (time period: 2019-08-19 to 2019-08-29) HydroCAT-ODO-SDI12-03730257-Data-20191112T233512.csv, (time period: 2019-09-19 to 2019-11-12) HydroCAT-ODO-SDI12-03730257-Data-20200402T210448.csv, (time period: 2020-02-19 to 2020-04-20) The headings are FrameSync, DateTime (UTC-4:00), Temperature (Celsius), Pressure (Decibar), Oxygen (mg/L), SpecConductivity (uS/cm), Date, Time (UTC-4:00)
HydroCAT processing R script filename: Hydrocat_RT.R (Octet Stream, 5.11 KB) MD5:a94b77f3f36c20a1ec751afed9c15c28 This R script stitches together data from the Seabird HydroCat and then removes values for times when the logger was out of the water. Written by Adrienne Breef-Pilz (27-Oct-2022) and used for David Kimbro's reciprocal transplant experiment.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1736943
NSF Division of Ocean Sciences	OCE-1820540

Deployments

None available yet

Instruments

CTD - fixed

Supplied Name: SeaBird HydroCAT-EP CTD

Supplied Description:

Instrument Type

Generic Name: CTD - fixed

Generic Description:

A reusable instrument that always simultaneously measures conductivity and temperature (for salinity) and pressure (for depth).

This term applies to CTDs that are fixed and do not measure by profiling through the water column. For profiling CTDs, see https://www.bco-dmo.org/instrument/417.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Latitude	Latitude of CTD deployment	decimal degrees	lat
Longitude	Longitude of CTD deployment	decimal degrees	lon
Site	Reef site (either Butler or Pellicer)	unitless	site
DateTime	DateTime of CTD measurement Format: %Y-%m-%dT%H:%M:%SZ	unitless	DateTime
Temp	Temperature	degrees Celsius	temperature
Cond	Conductivity	microSiemens per centimeter (uS/cm)	cond
Pressure	Pressure	decibar	press
Oxygen	Dissolved oxygen from optical sensor	milligrams per liter (mg/L)	O2
Salinity	Salinity	practical salinity units (PSU)	sal
SpCond	Specific conductivity	microSiemens per centimeter (uS/cm)	specc

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Dataset: HydroCAT data from oyster reciprocal transplant experiment