Contributors | Affiliation | Role |
---|---|---|
Cowen, Robert K. | Oregon State University (OSU) | Principal Investigator |
Sponaugle, Su | Oregon State University (OSU) | Co-Principal Investigator |
Sutherland, Kelly Rakow | University of Oregon | Co-Principal Investigator |
Corrales Ugalde, Marco | Princeton University | Scientist |
Conser, Elena | Oregon State University (OSU) | Student |
York, Amber D. | Woods Hole Oceanographic Institution (WHOI BCO-DMO) | BCO-DMO Data Manager |
This dataset will be updated to include additional data from deployments from the winter of 2022 and winter of 2023.
Location description: Six cross-shelf transects in the northern California Current, ranging from near the Oregon-California border (42.5°N) to southern Washington (47.1°N). Maximum depth of instrument is 100m or within 2-5m of the seafloor. A list of more detailed information about the individual transects is included (See Supplemental Files).
ISIIS-3 was deployed from the R/V Langseth, and towed the length of the transect in an undulating manner at 2.5 m/s, undulating between 1m and 100m depth, or within 2m of the seafloor in waters shallower than 100m depth. A total of six transects were sampled, with the longest transects split into inshore and offshore portions sampled over two nights. Each transect was sampled in the “tow-yo” fashion throughout the deployment of the instrument. ISIIS-3 was terminated to a fiber optic winch. Data were streamed to the shipboard ISIIS-3 computer in real time. A program manager written in JADE took the input data streams from both cameras, each sensor, and GPS data from the ship, and wrote into individual millisecond time-stamped files. Data were stored on the shipboard computers 16TB drives, then copied on to individual 6TB external drives in duplicate for each camera. Individual files were written for the CTD, GPS stream, voltage-based sensor readings (pH, dissolved oxygen, PAR), altimeter, and flowmeter, and files were written on the shipboard ISIIS-3 computer.
See Schmid et al. (2023, doi:10.3389/fmars.2023.1187771) for more information on ISIIS-3 imager and deployments on these research cruises.
Sensor data were written by individual publishers and millisecond time stamped. A Python script merge_environmental.py (Schmid et al., 2023, DOI: 10.5281/ZENODO.7739010) was used to merge these individual files into a final dataset based on the millisecond time stamps associated with each observation, creating a cohesive dataset over the time period sampled. Conversion factors and calibrations were applied to pH, oxygen, and irradiance voltage readings to yield final values, and chlorophyll-a was calculated using manufacturer conversions and calibration values. Conversion factors and calibrations were applied in R.
Histograms of sensor data values were used to determine extreme values to flag as potential outliers.
* Data tables from submitted files "s22_ISIIS3_enviro.csv" and "s23_ISIIS3_enviro.csv" were imported into the BCO-DMO data system for this dataset and concatenated. Values "NA" were imported as missing data values.
** In the BCO-DMO data system missing data identifiers are displayed according to the format of data you access. For example, in csv files it will be blank (null) values. In Matlab .mat files it will be NaN values. When viewing data online at BCO-DMO, the missing value will be shown as blank (null) values.
* ISO DateTime with timezone (UTC) column added in ISO 8601 format (converted from local "US/Pacific" timestamp in PDT/PDT time zone.
* Column "Cruise_ID" added.
* Lat,lon rounded to 5 decimal places as decided with data submitter. pH PAR and oxygen also rounded to 5 decimal places when over 5 places.
Dataset-specific Instrument Name | Altimeter (ImageNex 850) |
Generic Instrument Name | Altimeter |
Dataset-specific Description | Instrumentation associated with ISIIS-3. |
Generic Instrument Description | An instrument that measures height above a fixed surface. The data can be used to map ocean-surface topography and generate gridded surface height fields. |
Dataset-specific Instrument Name | Flowmeter (Valeport 803 ROV Current Meter) |
Generic Instrument Name | Flow Meter |
Dataset-specific Description | Instrumentation associated with ISIIS-3. |
Generic Instrument Description | General term for a sensor that quantifies the rate at which fluids (e.g. water or air) pass through sensor packages, instruments, or sampling devices. A flow meter may be mechanical, optical, electromagnetic, etc. |
Dataset-specific Instrument Name | Fluorescence (WetLabs ECO-FLRT, S/N FLRT-2611) |
Generic Instrument Name | Fluorometer |
Generic Instrument Description | A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. |
Dataset-specific Instrument Name | |
Generic Instrument Name | In Situ Ichtyoplankton Imaging System |
Dataset-specific Description | Instrumentation associated wth ISIIS-3 are listed in the "Instruments" section of this dataset page except:
Two linescan cameras (55 µm/pixel resolution, Bellamare ISIIS-DPI) **imagery data is not associated with this dataset "ISIIS Environmental Data" |
Generic Instrument Description | The In Situ Ichthyoplankton Imaging System (ISIIS) is an underwater imaging system aimed at capturing in situ, real time images of marine zooplankton of relatively low abundance such as fish larvae and fragile gelatinous organisms. The first prototype, delivered in 2007, was attached to a relatively simple vehicle towed by an oceanographic vessel at a speed of five knots. The vehicle, and associated imaging system and sensors, was moved up and down through the water column by paying cable in and out via an oceanographic winch. Subsequently, a new vehicle has been designed with the capacity of self undulation using motor actuated dive fins.
The ISIIS system utilizes a high-resolution line-scanning camera with a Light Emitting Diode (LED) light source, modified by plano-convex optics, to create a collimated light field to back-light a parcel of water.
ISIIS was developed in collaboration between the University of Miami's Rosenstiel School of Atmospheric and Marine Science (RSMAS) and the subsea engineering company, Bellamare, LLC, located in San Diego CA. See complete description from RSMAS.
Reference:
Cowen RK and Guigand CM. 2008. In situ Ichthyoplankton Imaging System (ISIIS): system design and preliminary results. Limnol. Oceanogr. Methods. 6:126-132. doi:10.4319/lom.2008.6.126 |
Dataset-specific Instrument Name | pH sensor (Seabird SBE 18) |
Generic Instrument Name | pH Sensor |
Dataset-specific Description | Instrumentation associated with ISIIS-3. |
Generic Instrument Description | An instrument that measures the hydrogen ion activity in solutions.
The overall concentration of hydrogen ions is inversely related to its pH. The pH scale ranges from 0 to 14 and indicates whether acidic (more H+) or basic (less H+). |
Dataset-specific Instrument Name | Photosynthetically active radiation/irradiance (Biospherical QCP-2300) |
Generic Instrument Name | Photosynthetically Available Radiation Sensor |
Dataset-specific Description | Instrumentation associated with ISIIS-3. |
Generic Instrument Description | A PAR sensor measures photosynthetically available (or active) radiation. The sensor measures photon flux density (photons per second per square meter) within the visible wavelength range (typically 400 to 700 nanometers). PAR gives an indication of the total energy available to plants for photosynthesis. This instrument name is used when specific type, make and model are not known. |
Dataset-specific Instrument Name | Dissolved oxygen (Sea-Bird 43) with pump (SBE M5) |
Generic Instrument Name | Sea-Bird SBE 43 Dissolved Oxygen Sensor |
Dataset-specific Description | Instrumentation associated with ISIIS-3. |
Generic Instrument Description | The Sea-Bird SBE 43 dissolved oxygen sensor is a redesign of the Clark polarographic membrane type of dissolved oxygen sensors. more information from Sea-Bird Electronics |
Dataset-specific Instrument Name | CTD (Sea-Bird SBE 49 FastCAT) |
Generic Instrument Name | Sea-Bird SBE 49 FastCAT CTD Sensor |
Dataset-specific Description | Instrumentation associated with ISIIS-3
|
Generic Instrument Description | The SBE 49 FastCAT is a CTD sensor for use in autonomous platforms. It contains a SBE 3P temperature sensor, a SBE 4C conductivity sensor and a strain-gauge pressure sensor as standard. It can operate in autonomus (16 Hz per sec) or polled mode (transmits each sample). The sensor is depth-rated to 350 m (plastic housing) or 7000 m (titanium housing). Accuracy: +/- 0.002 deg C (temperature), +/- 0.0003 S/m (conductivity), 0.1% of full scale range (pressure). |
Website | |
Platform | R/V Marcus G. Langseth |
Start Date | 2022-07-18 |
End Date | 2022-07-30 |
Website | |
Platform | R/V Sally Ride |
Start Date | 2023-08-09 |
End Date | 2023-08-21 |
NSF Award Abstract:
Marine plankton form the base of most ocean food webs that support valuable fisheries. This highly diverse and complex community is composed of organisms that drift with ocean currents. Planktonic organisms remain understudied: they are difficult to sample given that their sizes span more than six orders of magnitude from less than one micron to meters. Yet, understanding how these communities respond to climate change, and ultimately how these responses affect valuable fisheries, and therefore food security, is critical. Because many ecological and physiological processes are dictated by relative size, the theory of size spectra (i.e., the relationship between size and organism abundance as it drives ecosystem properties such as food webs) provides a valuable framework for forecasting climate change impacts on marine ecosystems. A deeper understanding of the scope and nature of variability in size spectra under contrasting environmental conditions is needed. The dynamic, highly productive northern California Current off Oregon and Washington, during the summer and winter seasons, produces a patchwork of oceanographic conditions including those associated with hypoxia and ocean acidification. This study is sampling the plankton communities in this region to investigate how gradients of temperature, nutrients, dissolved oxygen, and pH conditions impact size spectra. The broader impacts include the training of students, building scientific resources, and outreach to broader communities. Undergraduate and graduate students are being trained in oceanography, field research and new technologies. The automated image analysis pipeline developed as part of the project is openly accessible to the oceanographic community and the image data are available through the novel Global Plankton Imagery Library, an open-access repository for plankton imagery. Size spectra data from this study are shared directly with ecosystem modelers. The project’s flagship outreach activity is the collaboration with the Sitka Center for Art and Ecology and the hosting of an Artist-At-Sea Program. A professional artist is competitively selected to join the research cruises and to create artistic products that give a unique voice to oceanographic research and the organisms under study. The artwork is being assembled into a traveling public Art Exhibit with planned displays at the Sitka Center, Oregon State University’s Hatfield Marine Science Center, University of Oregon’s Charleston Marine Life Center and centers located in underserved coastal communities. Finally, imagery data from the project are being shared via the Plankton Portal, a public website developed in partnership with the Citizen Science Alliance’s Zooniverse, that invites citizen scientists to participate in classifying plankton images.
The coupling of in situ plankton imagery and morphometric data allows quantifying scales of variation in plankton size spectra as well as testing predictions of how changes in environmental conditions (notably, temperature, nutrients, oxygen, pH) correlate with shifts in size spectra to reveal functional consequences to the food web. Plankton size spectra are being compared across environmental conditions by sampling in a habitat with steep environmental gradients and during two contrasting seasons. Planktonic organisms spanning 10 orders of magnitude in biomass are sampled using two complementary high-resolution imaging systems: the In Situ Ichthyoplankton Imaging System (ISIIS) and the Laser In-Situ Scattering and Transmissometry (LISST) particle imager. High-throughput image analysis software is used to create size distributions together with taxonomic classification. Depth-discrete meso-zooplankton samples are collected in parallel to examine community shifts in carbon, obtain length-to-carbon conversions and calibrate image data. The normalized biomass size spectra computed from the image data are tested for deviations from expected patterns. The plankton collections are also being analyzed for diet and reproductive status of gelatinous zooplankton, and diet and daily growth rate of representative larval fishes. These two groups have been historically understudied yet play central roles in ecosystem function. The data are being used to examine how these organisms are impacted by environmental conditions, and how they affect plankton size spectra. This study is foundational to the understanding of marine ecosystems within the context of climate change.
This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
Funding Source | Award |
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NSF Division of Ocean Sciences (NSF OCE) | |
NSF Division of Ocean Sciences (NSF OCE) |