ECOpuck Fluorometer data from 8 Wire Flyer deployments conducted on R/V Atlantis cruise AT42-03 in the Costa Rica Margin from October to November 2018

Website: https://www.bco-dmo.org/dataset/879330
Data Type: Cruise Results
Version: 1
Version Date: 2022-08-26

Project
» Collaborative research: Quantifying the biological, chemical, and physical linkages between chemosynthetic communities and the surrounding deep sea (Costa Rica Seeps)
ContributorsAffiliationRole
Roman, Christopher NeilUniversity of Rhode Island (URI)Principal Investigator
Rauch, ShannonWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager

Abstract
This dataset includes ECOpuck fluorometer data from 8 Wire Flyer deployments conducted on R/V Atlantis cruise AT42-03 in the Costa Rica Margin from October to November 2018.


Coverage

Spatial Extent: N:9.089473 E:-84.175318 S:8.538579 W:-85.144745
Temporal Extent: 2018-10-19 - 2018-11-03

Methods & Sampling

Data were collected from an ECOpuck fluorometer on Wire Flyer deployments R/V Atlantis cruise AT42-03 in the Costa Rica Margin from October to November 2018. The data have not been corrected for any time lags. The Chl and turbidity are from a Wet Labs Flbb-2k (470/695 nm Chl-a and 700nm turbidity). Refer to the Supplemental Files for more information on the Wire Flyer.

The Wire Flyer position was calculated using measurements of the clump weight depth and the wire payout. The layback distance is the Flyer's distance behind the ship. The raw count values were converted with the following coefficients:

self.turb_darkcount=50

self.turb_scalefactor=0.0747

self.chloro_darkcount=41.

self.chloro_scalefactor=0.0072

self.lcm_msg.turb = self.turb_scalefactor * (turb_data - self.turb_darkcount)

self.lcm_msg.chl = self.chloro_scalefactor * (chloro_data - self.chloro_darkcount)

Known Problems/Issues:
There is an asymmetry between the up and down directions, likely due to the flow over the sensor. We have not yet determined a correction for this.


Data Processing Description

BCO-DMO Processing:
- concatenated data from 8 separate files into one dataset;
- replaced "NaN" with "nd" (no data);
- created new column "deployment_id" (based on original file name);
- converted date/time field to ISO8601 format.


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Supplemental Files

File
AT42-03 Wire Flyer Summary Plots
filename: summary_plots.zip
(ZIP Archive (ZIP), 8.85 MB)
MD5:eb9054e1925496bf6f0522326dc96fa5
Summary plots of data from 8 Wire Flyer deployments conducted on R/V Atlantis cruise AT42-05. There is one PDF for each deployment. The file naming convention is YYYYMMDD_HHMMSS, set at the start of the deployment, e.g. 20170125_151748. The times are all in GMT, not local time.
Wire Flyer Launch and Recover Document
filename: flyer_launch_and_recover_document.pdf
(Portable Document Format (.pdf), 7.26 MB)
MD5:f9274b8c8b003b9a39083191e4f2c76b
Document describing the Wire Flyer launch and recovery procedures.
Wire Flyer Overview 2019
filename: Wire_flyer_overview_2019.pdf
(Portable Document Format (.pdf), 15.84 MB)
MD5:7c3c14f839142f115c5aa467894395d7
Slides from a presentation by Christopher Roman titled "The Wire Flyer vehicle system and
high resolution hydrographic sections".

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Related Publications

Roman, C., Ullman, D. S., Hebert, D., & Licht, S. (2019). The Wire Flyer Towed Profiling System. Journal of Atmospheric and Oceanic Technology, 36(2), 161–182. doi:10.1175/jtech-d-17-0180.1
Methods

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Parameters

ParameterDescriptionUnits
deployment_id

identifier for the deployment; indicates the start date and time of deployment in format: YYYYMMDD_hhmmss (time zone is GMT)

unitless
temp_counts

raw temperature data

unitless
timestamp

time stamp in microunix seconds

microunix seconds
lcmlog_timestamp

time stamp in deployment 20181028_235258 only

?
chl

chlorophyll

micrograms per liter (ug/L)
turb_counts

raw turbidity reading

unitless
chl_counts

raw chl-a reading

unitless
turb

turbidity; calculated from the raw count value

NTU
datestring

date-time string (GMT) in format where xxx represent milliseconds: YYYY-MM-DD hh:mm:ss.xxx

unitless
ISO_DateTime_UTC

date-time string converted to ISO8601 format: YYYY-MM-DDThh:mm:ss.xxxxxxZ. Note that data are accurate to milliseconds (not microseconds)

unitless
lat

Latitude. This is either the ship or the flyer position, but it is the best position available. If the Flyer position was known, accounting for the tow cable, this is the value used here. If the flyer position was not known (e.g. maybe the winch cable counter failed), the ship position was recorded

degrees North
lon

Longitude. This is either the ship or the flyer position, but it is the best position available. If the Flyer position was known, accounting for the tow cable, this is the value used here. If the flyer position was not known (e.g. maybe the winch cable counter failed), the ship position was recorded

degrees East


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Instruments

Dataset-specific Instrument Name
ECOpuck fluorometer
Generic Instrument Name
Wet Labs ECO Puck
Generic Instrument Description
The Puck is a miniature version of the ECO series of sensors, specifically designed for use in AUVs, profiling floats, and Slocum gliders with a dry science bay. This compact optical sensor is available in combinations of backscattering and fluorescence measurements. Manufacturer's website: https://www.seabird.com/auv-rov-sensors/eco-puck/family?productCategoryI...

Dataset-specific Instrument Name
Wet Labs Flbb-2k
Generic Instrument Name
WETLabs ECO FLBB scattering fluorescence sensor
Dataset-specific Description
The Chl and turbidity are from a Wet Labs Flbb-2k, 470/695 nm Chl-a and 700nm turbidity.
Generic Instrument Description
A dual-optical-sensor that carries a single-wavelength chlorophyll fluorometer (470nm ex/695nm em) and backscattering sensor (700 nm) that measures phytoplankton and particle concentration. It operates by using blue (470nm) and red (700 nm) LEDs that alternately flash. The blue LED stimulates chlorophyll fluorescence in plants while the red light illuminates the total particle field. The backscattering sensor has an in-water centroid angle of 142 degrees and can be calibrated to measure turbidity. The fluorometer can typically measure phytoplankton concentrations in the range 0-30 ug/l, with a sensitivity of 0.015 ug/l. The backscattering sensor can measure within the range 0-3 m-1, with a sensitivity of 0.0015 m-1. The instrument output in the standard version is digital and uses a low power mode and stores data. Other variants are used. The instrument is rated to a depth of 600m as standard, with the options of deeper instruments rated up to 6000m and instruments with bio-wipers, rated to 300 m. This instrument comes in the following optional models: FLbb(RT), FLbb(RT)D, FLbbB, FLbbS, FLbbBS, FLbb2k. Refer to the datasheet from the manufacturer: https://www.seabird.com/asset-get.download.jsa?id=55460873804

Dataset-specific Instrument Name
Wire Flyer
Generic Instrument Name
Wire Flyer Towed Profiling System
Generic Instrument Description
Description from Roman et al. (2019): The Wire Flyer towed vehicle is a platform able to collect high-resolution water column sections. The vehicle is motivated by a desire to effectively capture spatial structures at the submesoscale. The Wire Flyer profiles up and down along a ship-towed cable autonomously using controllable wings for propulsion. At ship speeds between 2 and 5 kt (1.02–2.55 m s−1), the vehicle is able to profile over prescribed depth bands down to 1000 m. The vehicle carries sensors for conductivity, temperature, depth, oxygen, turbidity, chlorophyll, pH, and oxidation reduction potential. During normal operations, the vehicle is typically commanded to cover vertical regions between 300 and 400 m in height with profiles that repeat at kilometer spacing. The vertical profiling speed can be user-specified up to 150 m min−1. During operations, an acoustic modem is used to communicate with the vehicle to provide status information, data samples, and the ability to modify the sampling pattern.   Detailed information can be found in the following publication: Roman, C., Ullman, D. S., Hebert, D., & Licht, S. (2019). The Wire Flyer Towed Profiling System. Journal of Atmospheric and Oceanic Technology, 36(2), 161–182. doi:10.1175/jtech-d-17-0180.1


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Deployments

AT42-03

Website
Platform
R/V Atlantis
Start Date
2018-10-17
End Date
2018-11-06
Description
More cruise information is available from Rolling Deck to Repository (R2R):  * https://www.rvdata.us/search/cruise/AT42-03 * https://doi.org/10.7284/908473


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Project Information

Collaborative research: Quantifying the biological, chemical, and physical linkages between chemosynthetic communities and the surrounding deep sea (Costa Rica Seeps)

Coverage: Costa Rica Pacific Margin


NSF abstract:
If life were to disappear from the deep sea, would we notice? We only have a cursory understanding of this vast region and the connectivity among its communities and the rest of the oceans, and yet the ecosystems of the deep sea have been implicated in the larger function of the global marine ecosystems. We now rely on the deep ocean for food, energy, novel drugs and materials, and for its role in the global cycling of carbon, as well as for supporting services such as habitat creation, nutrient replenishment for shallow waters, and the maintenance of biodiversity. Cold seeps, active areas of the seafloor where methane and other chemicals are released, are key features along the continental margins worldwide. To characterize how methane seep communities interact with the surrounding ecosystems and vice versa, we will study methane seeps off the Pacific coast of Costa Rica in 2017 and 2018. It is the sphere of influence around the seep, both along the seafloor and up into the water column, that we seek to better understand. We will map the structure and the chemistry surrounding these habitats using a novel 3-dimensional framework, combining typical transects with vertical characterizations of the water column just above the seafloor. This will include measurements of methane flux into the water column and changes in the overlying carbonate chemistry and oxygen levels that are critical to our understanding of the effect of warming, oxygen loss and ocean acidification in this region. Within this framework, we will collect seep organisms in sediments and on rocks (including all sizes from microbes to large animals), and transplant some of these from within the area of seep influence to the background deep sea, and vice-versa. Together, these studies will help us to measure the size of the seep sphere of influence, and also demonstrate the role of these seeps within the deep sea and the greater, global, marine ecosystem. We will share this information with a group of teachers during a series of workshops in the San Diego area, at an exhibit at the Birch Aquarium, and through the work of an artist who has worked extensively with marine organisms in extreme environments.

Chemosynthetic ecosystems are inextricably linked to the broader world-ocean biome and global biogeochemical cycles in ways that we are just beginning to understand. This research will identify the form, extent, and nature of the physical, chemical, and biological linkages between methane seeps and the surrounding deep-sea ecosystem. The proposed research builds critical understanding of the structural and functional processes that underpin the ecosystem services provided by chemosynthetic ecosystems. We target a critical continental margin, Costa Rica, where methane fates and dynamics loom large and play out in an setting that reflects many oceanographic stressors. We will use quantitative sampling and manipulative studies within a 3-dimensional oceanographic framework. We will ask what are the shapes of the diversity and density functions for organisms of different size classes and trophic position over the transition from the seep habitat through the ecotone to the background deep sea? Further, we will ask how do depth, dissolved oxygen concentrations, pH and carbonate ion availability, relative rates of fluid flux, and substrate (biogenic, authigenic carbonate, sediments) alter these linkages and interactions with the surrounding deep sea? Evidence for distinct transitional communities and biotic patterns in density and alpha and beta diversity will be quantified and placed in a global biogeographic context. All of these investigations will occur across biological size spectra: for microorganisms (archaea, bacteria, microeukaryotes), the macrofauna, and the megafauna that form biogenic habitats. Our research results will be interpreted in the context of potential effects of global ocean change in the equatorial Pacific to determine how the linkages with the surrounding deep sea will be altered as anthropogenic impacts proceed in the future. 

Related publications:
Levin, L.A., V.J. Orphan, G.W. Rouse, W. Ussler, A. E. Rathburn, G. S. Cook, S. Goffredi, E. Perez, A. Waren, B. Grupe, G. Chadwick, B. Strickrott. (2012). A hydrothermal seep on the Costa Rica margin: Middle ground in a continuum of reducing ecosystems. Proc. Royal Soc. B. 279: 2580-88 doi: 10.1098/rspb.2012.0205

Sahling, H., Masson, D. G., Ranero, C. R., Hühnerbach, V., Weinrebe, W., Klaucke, I., & Suess, E. (2008). Fluid seepage at the continental margin offshore Costa Rica and southern Nicaragua. Geochemistry, Geophysics, Geosystems 9: doi: 10.1029/2008GC001978



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Funding

Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)

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