http://lod.bco-dmo.org/id/dataset/882674
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
2022-10-16
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Water flow data from oyster reciprocal transplant experiment conducted at two sites in an estuary in NE Florida between July 2019 and April 2020
2022-10-16
publication
2022-10-16
revision
BCO-DMO Linked Data URI
2022-10-16
creation
http://lod.bco-dmo.org/id/dataset/882674
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. (2022) Water flow data from oyster reciprocal transplant experiment conducted at two sites in an estuary in NE Florida between July 2019 and April 2020. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-10-16 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/882674 [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. At each location, the home and away oyster ‘demes’ were randomly assigned between a predator exclosure and a control treatment.&nbsp;</p>
<p>To obtain site-specific information of water flow, a Nortek current profiler (Aquadopp Profiler 2MHz)&nbsp;was placed in a PVC stand and deployed in the water in front of the oyster reefs during the monthly oyster checks. The instrument was set with a blanking distance of 0.2m. The bin sizes were set 0.1m and 15 cells. The instrument recorded every minute except for two days (9/2/2018 and 9/4/2018) when the sampling interval was set to 30 seconds. The data was offloaded using AquaPro V1.37.08 and then converted to a Profile CSV. The .csv was uploaded into R and reorganized (see Processing Description).&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
Nortek current profiler (Aquadopp Profiler 2MHz)
theme
None, User defined
Nortek Aquadopp Doppler current profiler
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
biota
oceans
-81.2641
-81.2144
29.62923
29.77002
2019-08-19
2020-04-02
Sub-tropical estuarine waters (29.67,-81.21)
0
BCO-DMO catalogue of parameters from Water flow data from oyster reciprocal transplant experiment conducted at two sites in an estuary in NE Florida between July 2019 and April 2020
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
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
436126
https://datadocs.bco-dmo.org/docs/305/Predatory_NCEs_and_Scale/data_docs/882674_water_flow/Butler_AquaDopp_flowmeter_raw.zip
Flowmeter raw data for Butler site
Compressed folder of AquaDopp flowmeter raw data for the Butler site. The files are inputs to the Flowmeter_Processing_R_Script and are listed here with time periods of coverage:
RR.B0202.csv (time period: 2019-09-20 to 2019-11-12)
RR.BU01.csv (time period: 2019-12-01 to 2020-01-07)
Risk.B01.csv (time period: 2020-01-21 to 2020-01-31)
RiskB01.csv (time period: 2020-02-08 to 2020-03-04)
RR.301.csv (time period: 2020-03-06 to 2020-03-30)
The headings are DateTime, Battery, Heading, Pitch, Roll, Pressure, Temperature, AnalogIn1, AnalogIn2, Speed, and Direction. These last two parameters are repeated as needed for sampling.
download
4161
https://datadocs.bco-dmo.org/docs/305/Predatory_NCEs_and_Scale/data_docs/882674_water_flow/Flowmeter_Processing.R
Flowmeter processing R script
This Flowmeter processing script stitches together data from the AquaDopp instrument and compiles information into a long format with usable depths. Written by Adrienne Breef-Pilz (26 Oct 2022) and used for David Kimbro's reciprocal transplant experiment.
download
476905
https://datadocs.bco-dmo.org/docs/305/Predatory_NCEs_and_Scale/data_docs/882674_water_flow/Pellicer_AquaDopp_flowmeter_raw.zip
Flowmeter raw data for Pellicer site
Compressed folder of AquaDopp flowmeter raw data for the Pellicer site. The files are inputs to the Flowmeter_Processing_R_Script and are listed here with time periods of coverage:
RT.Pel01.csv (time period: 2019-08-19 to 2019-08-29)
RT.Pel03.csv (time period: 2019-10-02 to 2019-10-22)
RT.P201.csv (time period: 2019-11-06 to 2020-02-19)
RT.pel04.csv (time period: 2020-03-04 to 2020-04-02)
The headings are DateTime, Battery, Heading, Pitch, Roll, Pressure, Temperature, AnalogIn1, AnalogIn2, Speed, and Direction. These last two parameters are repeated as needed for sampling.
download
265735
https://datadocs.bco-dmo.org/docs/305/Predatory_NCEs_and_Scale/data_docs/882674_water_flow/rt_flow.csv
Summary of water flow data from reciprocal transplant experiment
Water flow data from reciprocal transplant oyster experiment. Current meter summary data with date, site, speed, and number of readings collected per deployment.
download
https://osprey.bco-dmo.org/dataset/882674/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. At each location, the home and away oyster ‘demes’ were randomly assigned between a predator exclosure and a control treatment.&nbsp;</p>
<p>To obtain site-specific information of water flow, a Nortek current profiler (Aquadopp Profiler 2MHz)&nbsp;was placed in a PVC stand and deployed in the water in front of the oyster reefs during the monthly oyster checks. The instrument was set with a blanking distance of 0.2m. The bin sizes were set 0.1m and 15 cells. The instrument recorded every minute except for two days (9/2/2018 and 9/4/2018) when the sampling interval was set to 30 seconds. The data was offloaded using AquaPro V1.37.08 and then converted to a Profile CSV. The .csv was uploaded into R and reorganized (see Processing Description).&nbsp;</p>
Specified by the Principal Investigator(s)
<p><strong>Data processing</strong><br />
The data was offloaded using AquaPro V1.37.08 and then converted to a Profile CSV.&nbsp;The .csv file was uploaded into R and reorganized using the R code titled "Flowmeter_Processing.R", which is accessible&nbsp;from the Supplemental Files section below, along with the data files used for input.&nbsp;&nbsp;</p>
<p>Butler site Aquadopp raw data files:&nbsp;</p>
<ul>
<li>RR.B0202.csv (time period: 2019-09-20 to 2019-11-12)</li>
<li>RR.BU01.csv (time period: 2019-12-01 to 2020-01-07)</li>
<li>Risk.B01.csv (time period: 2020-01-21 to 2020-01-31)&nbsp;</li>
<li>RiskB01.csv (time period: 2020-02-08 to&nbsp;2020-03-04)</li>
<li>RR.301.csv (time period: 2020-03-06 to 2020-03-30)</li>
</ul>
<p>Pellicer site Aquadopp raw data files:&nbsp;</p>
<ul>
<li>RT.Pel01.csv (time period: 2019-08-19 to 2019-08-29)</li>
<li>RT.Pel03.csv (time period: 2019-10-02 to 2019-10-22)</li>
<li>RT.P201.csv (time period: 2019-11-06 to 2020-02-19)</li>
<li>RT.pel04.csv (time period: 2020-03-04 to 2020-04-02)</li>
</ul>
<p>Both sites (Butler and Pellicer) have&nbsp;multiple raw data files because each logger deployment (time period) had specific processing steps that needed to be performed.&nbsp;</p>
<p>Readings that were underwater or included the surface of the water were used while the rest of the readings were not. This was done by adding 0.1 to the pressure sensor readings and then only including values less than the position of the cell. For example, if the&nbsp;pressure was 0.54m then the sort value would be 0.64. Cells with measured values of&nbsp;0.5&nbsp;and 0.6 would be included, but 0.7 would not.&nbsp;</p>
<p>Attitude sensor data (i.e. pitch, roll, and bearing) were used to correct for any motion or change in the instrument's position.&nbsp; Additional summary and statistics information can be found in the "rt_flow.csv" file, which includes the Date, Site, Speed&nbsp;(meters/second), and N&nbsp;(number of readings collected per deployment).&nbsp;<br />
<br />
<strong>Problems/Issues</strong><br />
Aquadopp data was missing from:</p>
<ul>
<li>Butler: June 2019;</li>
<li>Butler 3: November 2019;&nbsp;</li>
<li>Pellicer 1: January 2020 and Febuary 2020</li>
<li>Pellicer 3: January 2020 and February 2020;&nbsp;</li>
</ul>
<p>Note: Pellicer 1 and Pellicer 3 are the same from September 2019 onward.&nbsp;</p>
<p><strong>BCO-DMO Processing description:</strong><br />
- Converted dates to format (YYYY-MM-DD)<br />
- Sorted by Site and DateTime<br />
- Added columns for "Latitude" and "Longitude" based on geospatial bounds<br />
- Added a conventional header with dataset name, PI names, version date</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
Nortek current profiler (Aquadopp Profiler 2MHz)
Nortek current profiler (Aquadopp Profiler 2MHz)
PI Supplied Instrument Name: Nortek current profiler (Aquadopp Profiler 2MHz) PI Supplied Instrument Description:To obtain site-specific information of water flow, a Nortek current profiler (Aquadopp Profiler 2MHz) was placed in a PVC stand and deployed in the water in front of the oyster reefs Instrument Name: Nortek Aquadopp Doppler current profiler Instrument Short Name:Aquadopp Instrument Description: A family of self-contained Doppler current profilers, Nortek Aquadopp Profilers are often referred to as AquaPro instruments. They are designed for deployment on the seabed, moorings, buoys or fixed structures. They can feature a range of transducers - 400 kHz (60-90m range: 2-8m cell size), 600 kHz (30-40m range: 1-4m cell size), Z-cell 600 kHz, 1 MHz (12-25m range: 0.3-4m cell size), Z-cell 1MHz, 2 MHz (4-10m range:0.1-2m cell size) and side-looking. Each transducer has 3 beams and the instrument has a maximum of 128 cells. Current speeds up to 10 m/s may be measured at an accuracy of 1% of measured value ±0.5cm/s. The standard depth rating is 300 m with 3000 m or 600m versions available. Temperature (embedded thermistor with 0.1C accuracy and 0.01C resolution), compass (magnetometer with 2 degrees accuracy and 0.1 degree resolution providing tilt