http://lod.bco-dmo.org/id/dataset/885452
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2022-12-16
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
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
2022-12-16
publication
2022-12-16
revision
BCO-DMO Linked Data URI
2022-12-16
creation
http://lod.bco-dmo.org/id/dataset/885452
David L. Kimbro
Northeastern University
principalInvestigator
J. Wilson White
Oregon State University
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Kimbro, D. L., White, J., Breef-Pilz, A. (2022) 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. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-12-16 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/885452 [access date]
Methods and Sampling: <p>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.&nbsp;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.&nbsp;</p>
<p>To obtain site-specific information on seawater properties, a SeaBird HydroCAT-EP CTD instrument was deployed just seaward of the reefs. Measurements&nbsp;include temperature, conductivity, pressure, salinity, and oxygen.&nbsp;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&nbsp;4/2/2020 14:45) and Pellicer (8/19/2019 10:30 to&nbsp;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.</p>
<p>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.&nbsp;</p>
<p>Problem report:<br />
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.</p>
<p>&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1736943 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1736943
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1820540 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1820540
onGoing
David L. Kimbro
Northeastern University
617-373-2059
430 Nahant Rd.
Nahant
MA
01908
U.S.A.
d.kimbro@northeastern.edu
pointOfContact
J. Wilson White
Oregon State University
will.white@oregonstate.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Latitude
Longitude
Site
DateTime
Temp
Cond
Pressure
Oxygen
Salinity
SpCond
SeaBird HydroCAT-EP CTD
theme
None, User defined
latitude
longitude
site
Date and time
temperature of sample or a generic measurement (not in-situ water temp)
conductivity
water pressure
dissolved Oxygen
salinity
specific conductance
featureType
BCO-DMO Standard Parameters
CTD - fixed
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Collaborative research: Quantifying the influence of nonconsumptive predator effects on prey population dynamics
https://osprey.bco-dmo.org/project/709931
Collaborative research: Quantifying the influence of nonconsumptive predator effects on prey population dynamics
<p><em>NSF Award Abstract:</em><br />
Predators can affect populations of their prey in two ways: by consuming them ("consumptive effects" or "CE"s), or by causing the prey to change behavior to avoid contact with the predator. For example, prey often spend less time feeding and more time watching out for predators, which comes with the cost of lower food intake and thus slower growth. Such "non-consumptive effects" (NCEs) have been described for a wide range of terrestrial and marine prey species, from elk to clams, but mostly in short-term (< 1 month) experiments. These prior results suggest that in some cases, the behavioral changes (NCEs) have a bigger effect on prey populations than consumption by predators (CEs). However, those short-term, controlled experiments may artificially inflate the perceived importance of NCEs. Over longer time periods, prey may adapt or become acclimated to predation risk, and NCEs may become less important. Additionally, environmental variability (e.g., differences in the availability of the prey's food between study sites) may have a bigger effect on prey populations than NCEs do. This project will use a combination of short- (months) and long-term (years) field experiments and mathematical models to evaluate the role of NCEs on Florida oyster reefs. The prey species in this study is the eastern oyster, an important marine resource in the southeast US for harvesting and habitat creation; the main oyster predator is a mud crab. In this study, results from mathematical models of oyster populations will be compared to experimental data from the field to see whether including NCEs in the model leads to better model predictions. Better understanding of NCEs in oysters should improve management of that important marine resource. Furthermore, the mathematical model will be used to develop broader, generalizable conclusions about the importance of NCEs that could be applied to other important prey species. This project will provide data useful for oyster resource management, will support public education regarding the ecological importance of NCEs, and will enhance the scientific engagement of underrepresented groups in the study region. The project will support a partnership with the Guana Tolomato Matanzas National Estuarine Research Reserve in Florida, including data sharing, sponsoring an oyster management symposium, and funding the development of multimedia scientific outreach materials at the reserve that will be used by a large and diverse population of K-12 students in the surrounding community. The project will train a postdoctoral researcher, two graduate students, two undergraduate students, and research results will be disseminated by those students and the principal investigators at scientific conferences, in journal publications, and in online content through an ongoing partnership with a Florida public television station.</p>
<p>Predators can alter prey population dynamics by causing fear-based shifts in prey traits (nonconsumptive effect, NCE). The importance of NCEs for prey populations - relative to direct consumption by predators (consumptive effects, CEs) - remains uncertain, particularly because short-term studies of NCEs cannot estimate their effect over multiple prey generations. This project addresses that knowledge gap by combining short- and long-term field experiments with population models to investigate the importance of NCEs on oyster population dynamics in a Florida estuary. The central question is whether accounting for NCEs improves the ability to predict long-term trends in oyster population abundance. Several types of NCEs are present in this system: exposure to water-containing predator odors reduces oyster larval recruitment and causes juvenile oysters to increase shell thickness, reducing their somatic growth. In addition to CEs and NCEs, environmental gradients in stress, food, and propagule delivery are also present in this system. Those environmental factors can have strong effects on post-settlement survivorship, growth, and recruitment of oysters, so the relative importance of predator CEs and NCEs may vary along those spatial gradients as well. This project will consist of four components. (1) A series of short-term field experiments to test how NCEs vary with predator density and environmental variables, and whether one of the NCEs (increased shell thickness) actually reduces vulnerability to predators. (2) A population model, parameterized using experimental results; model simulations will quantify how the relative importance of NCEs should vary over time, space, and environmental gradients. (3) A longer-term (3.5 year) field experiment; the results from this experiment will be compared to model predictions to test whether accounting for NCEs improves predictions of long-term variation in oyster population dynamics. (4) A general form of the model will be developed to broadly investigate the effect of NCEs on non-equilibrium, transient population dynamics. By combining models and field experiments, this project will bridge the gap between the theoretical understanding of how NCEs affect population dynamics and empirical tests of that theory, advancing the field towards the goal of predicting how multiple interacting factors structure communities.</p>
Predatory NCEs and Scale
largerWorkCitation
project
eng; USA
oceans
-81.2641
-81.2144
29.62923
29.77002
2019-07-23
2020-04-02
Sub-tropical estuarine waters (29.67,-81.21)
0
BCO-DMO catalogue of parameters from 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
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/885540.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of CTD deployment</p>
http://lod.bco-dmo.org/id/dataset-parameter/885541.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of CTD deployment</p>
http://lod.bco-dmo.org/id/dataset-parameter/885542.rdf
Name: Site
Units: unitless
Description: <p>Reef site (either Butler or Pellicer)</p>
http://lod.bco-dmo.org/id/dataset-parameter/885543.rdf
Name: DateTime
Units: unitless
Description: <p>DateTime of CTD measurement</p>
http://lod.bco-dmo.org/id/dataset-parameter/885544.rdf
Name: Temp
Units: degrees Celsius
Description: <p>Temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/885545.rdf
Name: Cond
Units: microSiemens per centimeter (uS/cm)
Description: <p>Conductivity</p>
http://lod.bco-dmo.org/id/dataset-parameter/885546.rdf
Name: Pressure
Units: decibar
Description: <p>Pressure</p>
http://lod.bco-dmo.org/id/dataset-parameter/885547.rdf
Name: Oxygen
Units: milligrams per liter (mg/L)
Description: <p>Dissolved oxygen from optical sensor</p>
http://lod.bco-dmo.org/id/dataset-parameter/885548.rdf
Name: Salinity
Units: practical salinity units (PSU)
Description: <p>Salinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/885549.rdf
Name: SpCond
Units: microSiemens per centimeter (uS/cm)
Description: <p>Specific conductivity</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
393204
https://datadocs.bco-dmo.org/docs/305/Predatory_NCEs_and_Scale/data_docs/885452_hydrocat/Butler_HydroCAT_CTD_raw.zip
HydroCAT CTD raw data for Butler site
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)
download
5228
https://datadocs.bco-dmo.org/docs/305/Predatory_NCEs_and_Scale/data_docs/885452_hydrocat/Hydrocat_RT.R
HydroCAT processing R script
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.
download
268608
https://datadocs.bco-dmo.org/docs/305/Predatory_NCEs_and_Scale/data_docs/885452_hydrocat/Pellicer_HydroCAT_CTD_raw.zip
HydroCAT CTD raw data for Pellicer site
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)
download
https://osprey.bco-dmo.org/dataset/885452/data/download
download
onLine
dataset
<p>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.&nbsp;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.&nbsp;</p>
<p>To obtain site-specific information on seawater properties, a SeaBird HydroCAT-EP CTD instrument was deployed just seaward of the reefs. Measurements&nbsp;include temperature, conductivity, pressure, salinity, and oxygen.&nbsp;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&nbsp;4/2/2020 14:45) and Pellicer (8/19/2019 10:30 to&nbsp;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.</p>
<p>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.&nbsp;</p>
<p>Problem report:<br />
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.</p>
<p>&nbsp;</p>
Specified by the Principal Investigator(s)
<p>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;&nbsp;Grolemund &amp; Wickham, 2011), tidyverse (v1.3.2; Wickham et al., 2019), oce (Kelley, 2018; Kelley &amp; Richards, 2022).&nbsp; The script "Hydrocat_RT.R" processes the data to&nbsp;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&nbsp;oce package was used to calculate the salinity.&nbsp;</p>
<p>The HydroCAT-EP CTD files for each site were compiled and run through the R code "Hydrocat_RT.R" (see Supplemental Files section)</p>
<p><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">Butler site HydroCAT raw data files:&nbsp;</span></p>
<ul>
<li>HydroCAT-ODO-SDI12-03730256-Data-20200121T142941.csv, (time period: 2019-12-01 to 2020-01-08)</li>
<li>HydroCAT-ODO-SDI12-03730256-Data-20200417T232531.csv, (time period: 2020-01-21 to 2020-03-04)</li>
<li>HydroCAT-ODO-SDI12-03730258-Data-20190830T005058.csv, (time period:&nbsp;2019-07-23 to 2019-08-29)</li>
<li>HydroCAT-ODO-SDI12-03730258-Data-20191112T233136.csv, (time period: 2019-09-20 to 2019-11-12)</li>
<li>HydroCAT-ODO-SDI12-03730258-Data-20200402T210143.csv, (time period:&nbsp;2020-03-06 to 2020-04-02)</li>
</ul>
<p><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">Pellicer site HydroCAT raw data files:</span></p>
<ul>
<li>HydroCAT-ODO-SDI12-03730256-Data-20191120T131243.csv, (time period: 2019-11-15 to 2019-11-20)</li>
<li>HydroCAT-ODO-SDI12-03730256-Data-20191130T232934.csv, (time period: 2019-11-20 to 2019-11-30)</li>
<li>HydroCAT-ODO-SDI12-03730257-Data-20190830T004554.csv, (time period: 2019-08-19 to 2019-08-29)</li>
<li>HydroCAT-ODO-SDI12-03730257-Data-20191112T233512.csv, (time period: 2019-09-19 to 2019-11-12)</li>
<li>HydroCAT-ODO-SDI12-03730257-Data-20200402T210448.csv, (time period: 2020-02-19 to 2020-04-20)</li>
</ul>
<p><strong>BCO-DMO Processing description:</strong><br />
- Converted dates to format (YYYY-MM-DD)<br />
- Adjusted field/parameter names to comply with BCO-DMO naming conventions<br />
- Added columns for "Latitude" and "Longitude" based on geospatial bounds<br />
- Added a conventional header with dataset name, PI names, version date<br />
- Rounded Salinity values to 2 decimal places</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
SeaBird HydroCAT-EP CTD
SeaBird HydroCAT-EP CTD
PI Supplied Instrument Name: SeaBird HydroCAT-EP CTD Instrument Name: CTD - fixed Instrument Short Name: Instrument 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.