One-second TRIAXUS CTD profiles from R/V Point Sur cruises RISE2004, RISE2005a, RISE2006b in the Northeast Pacific coastal waters off states of Washington and Oregon from 2004 to 2006 (RISE project)

Website: https://www.bco-dmo.org/dataset/3579
Data Type: Cruise Results
Version: 2
Version Date: 2021-06-16

Project
» River Influences on Shelf Ecosystems (RISE)
ContributorsAffiliationRole
Zaron, Edward D.Portland State University (PSU)Principal Investigator
Jay, David A.Oregon Health and Science University (OGI/OHSU)Co-Principal Investigator
Gegg, Stephen R.Woods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager


Dataset Description

TRIAXUS towed Seabird CTD data from the RISE Project, NODC accession 49910.
Sea-bird SBE 9 pumped CTD attached to the Triaxus towed undulating platform.

The purpose of the data collection was to provide transects through the Columbia River plum
to understand the distribution of water mass properties and configuration of isopycnal surfaces.
The data were also used in an analysis of Thorpe overturning scales to quantify vertical mixing
along the 50m isobath near the mouth of the Columbia River.

Because of the amount of data, they are presented as the complete (24Hz) dataset and a decimated
to 1 second dataset.  Both are large datasets.  The 2005 24Hz data are broken into two parts to allow
retrieval without the system timing out.

Methods & Sampling

These CTD data were obtained during the NSF-sponsored RISE project during July 2004,
June 2005, and May-June 2006, on the continental shelf off Oregon and Washington, USA,
in the Northeast Pacific Ocean. The data were collected by a CTD mounted on the towed
Triaxus platform. The Triaxus was normally set to undulate between the ocean surface
and a depth of 40 to 60m. Transects obtained range from a few km to over 60km in length.

 


Data Processing Description

Netcdf files converted from a .cnv-format file created by Sea-Bird Electronics "Seasave Win32 V 5.30a".
Each Netcdf file contains global attributes taken verbatim from the ASCII header of the .cnv file.

BCO-DMO Edits
- Original data contributed as NetCDF files
- ARM Tools NetCDF Windows routine cdf2ascii.exe used to convert the data to ASCII format
- ARM Tools NetCDF Windows routine ncdump.exe used to extract header information (parameters and sensors)
- CTD dataset name, date, time, lat, lon imported from the header information in the converted files
- A common set of CTD parameters were generated for all three years worth of data.

BCO-DMO Data manager notes (2021-06-21):
Version 2 (2021-06-16) replaced dataset version 1 (2011-11-21). There were four lines in this dataset that had a single double quote character in them instead of data values and subsequent data values were misaligned in wrong columns.

These are the lines from the version 1 tsv file with the issues (before fixing in version 2):
        Line 179167: 2004        TRI30FACTM        20040720        061142        -124.26350        46.43017        50127        3.330633        46.379742        -124.264198        1.000000        "        202.282990        0.580174        34.810417        2088.625000        50128.000000        3.541456        15.473663        3.462942        -0.571200        -0.197648        24.537241        2.100122        13.634429        nd        nd        6.602526

        Line 184891: 2004        TRI31FACTM        20040720        081302        -124.25883        46.25000        13640        3.684268        46.235001        -124.258263        1.000000        "        202.349640        0.157870        9.472222        568.333313        13641.000000        8.410340        11.640263        8.307848        1.208022        -0.254203        8.019536        0.879121        14.061870        nd        nd        6.921542

        Line 825152: 2005        tr2038FACTM        20050602        141256        -125.19533        45.70683        135380        3.845251        45.846001        -125.332619        1.000000        13.219186        153.658356        1.566898        94.013885        5640.833496        135381.000000        "        nd        8.481271        -0.040919        nd        nd        nd        nd        1.137738        0.003443        0.000000

        Line 975451: 2005        tr2060FACTM        20050604        154734        -124.36850        46.23800        54035        3.767863        46.254101        "        -124.453644        13.858933        155.684845        0.625405        37.524307        2251.458252        54036.000000        1.000000        nd        3.970462        -0.049552        nd        nd        nd        nd        1.476200        0.033067        0.000000

The first two problem lines (Line 179167 and 184891) following two lines could be fixed by replacing the double quote character with a missing data identifier and adding the missing flag value at the end.

But the other two (lines 825152 and  975451) had other suspect values and misalignments and could not be salvaged.  Those lines were removed from the version 2 data.


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Data Files

File
TRIAXUS_CTD_1sec.csv
(Comma Separated Values (.csv), 460.37 MB)
MD5:0011d9d45f84ee18607b3c48d821ea5c
Primary data file for dataset ID 3579

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Parameters

ParameterDescriptionUnits
Year

Year of data

YYYY
Dataset

Dataset/Transect Id

text
Date

Date (GMT)

YYYYMMDD
Time

Start Time (GMT)

HHMM
Lon

Start longitude

decimal degrees (West is negative)
Lat

Start latitude

decimal degrees (South is negative)
Nrecord

Record number

integer
c0

Conductivity

S/m
latitude

Latitude

decimal degrees (South is negative)
longitude

Longitude

decimal degrees (West is negative)
pumps

Pump Status

integer
timeJ

Julian Days

decimal days
timeH

Time Elapsed hours

hours
timeM

Time Elapsed minutes

minutes
timeS

Time Elapsed seconds

seconds
scan

Scan count

integer
prDM

pressure Digiquartz

decibars
t090

temperatue ITS-90

degrees celsius
depSM

depth salt water

meters
dz_dt

Descent Rate

meters/second
acc

Acceleration

meters/second^2
flSCC

Fluorescence Turner Cor Chl

ug/L
obsscufa

OBS Turner SCUFA

NTU
n2sat

Nitrogen Saturation

mg/l
sbeox

Oxygen

SBE 43
wetstar

Fluorescence Wetlab Wetstar

mg/m^3
modError

Modulo Error Count

(na)
flag

Flag (0.000e+00)

0.00E+000


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Instruments

Dataset-specific Instrument Name
CTD TRIAXUS
Generic Instrument Name
CTD TRIAXUS
Generic Instrument Description
Sea-bird SBE 9 pumped CTD attached to the Triaxus towed undulating platform. The Triaxus towed undulating vehicle, designed and manufactured by MacArtney, achieves high resolution 3-dimensional surveys of the upper 180m of the water column. The standard sensor package includes a Seabird CTD (with optional secondary C and T sensors), transmissometer, dissolved oxygen, chlorophyll fluorometer, and PAR sensor. In addition to this basic configuration, Triaxus can accommodate up to 9 additional sensor packages / sensors. See http://www.macartney.com/systems/remote-technology/triaxus.


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Deployments

RISE2004

Website
Platform
R/V Point Sur
Report
Start Date
2004-07-08
End Date
2004-07-28
Description
One of the RISE project cruises carried out in 2004 with the R/V Wecoma (W0407A) in the coastal waters or Washington and Oregon. This cruise focused on mixing rates and large scale physical, nitrate, fluorescence surveys as well as frontal frontal processes, and data from remote sensing and model studies.  

Processing Description
Simple script RISE2004_TCTD_2_BCODMO.awk generated to reformat the converted NetCDF files to BCO-DMO

RISE2005a

Website
Platform
R/V Point Sur
Report
Start Date
2005-05-29
End Date
2005-06-21
Description
One of the RISE project cruises carried out in 2005 with the R/V Wecoma (W0505C) in the coastal waters or Washington and Oregon. This cruise focused on mixing rates and large scale physical, nitrate, fluorescence surveys as well as frontal frontal processes, and data from remote sensing and model studies.  

Processing Description
Simple script RISE2004_TCTD_2_BCODMO.awk generated to reformat the converted NetCDF files to BCO-DMO

RISE2006b

Website
Platform
R/V Point Sur
Report
Start Date
2006-06-02
End Date
2006-06-12
Description
One of the RISE project cruises carried out in 2005 with the R/V Wecoma (W0508) in the coastal waters or Washington and Oregon. This cruise focused on mixing rates and large scale physical, nitrate, fluorescence surveys as well as frontal frontal processes, and data from remote sensing and model studies.  

Processing Description
Simple script RISE2004_TCTD_2_BCODMO.awk generated to reformat the converted NetCDF files to BCO-DMO


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Project Information

River Influences on Shelf Ecosystems (RISE)


Coverage: Northeast Pacific, coastal waters off states of Washington and Oregon


River Influences on Shelf Ecosystems (RISE) - A Study of the Columbia River Plume
A Multi-Institutional Collaborative Project Sponsored by the National Science Foundation

In 2004 an interdisciplinary study "River Influences on Shelf Ecosystems" (RISE) was initiated to determine the extent to which alongshore gradients in ecosystem productivity might be related to the existence of the massive freshwater plume from the Columbia River. RISE was designed to test three hypotheses: - During upwelling the growth rate of phytoplankton within the Columbia plume exceeds that in nearby areas outside the plume being fueled by the same upwelling nitrate.
- The plume enhances cross-margin transport of plankton and nutrients.
- Plume-specific nutrients (Fe and Si) alter and enhance productivity on adjacent shelves.

Within those constraints, RISE provides the first comprehensive interdisciplinary study of the rates and dynamics governing the mixing of river and coastal waters in an eastern boundary system, as well as the effects of the plume formed by the mixing processes on rates, standing stocks and community structure of plankton in the local ecosystem. The RISE project, includes 4 field and two different numerical model applications. We collected simultaneous measurements of water chemistry, phytoplankton growth and grazing rates, zooplankton populations, water currents, and turbulent mixing. These are being combined with data from satellites, radar, and moorings, as well as detailed numerical simulations, to develop a deeper understanding of this important ecosystem.

The overall RISE sampling strategy was to compare mixing rates, nutrient supply, and phytoplankton production, grazing and community structure within the plume and outside the plume; i.e. on the shelf to the north of the river mouth, presumed more productive, and on the shelf to the south of the river mouth, presumed less productive, as well as in the important "plume lift off" area (the region where the plume loses contact with the bottom) near the river mouth and the plume "near field". The backbone for this project consists of data collected during four cruises that took place in the seasonally high-flow period (May-June) in each of three years (2004-06) and in a low-flow period in the second year (August, 2005). The sampling was spread over three years to attempt to include interannual differences in processes related to wind and river flow variability. The 21-day length of the cruises ensured that a variety of circulation and growth regimes, including upwelling and relaxation/downwelling and neap/spring tides, were observed.

The field studies used two vessels operating simultaneously. The R/V Wecoma obtained primarily biological and chemical rate data: a) at individual stations on cardinal lines north and south of the river mouth (off Grays Harbor, WA and Cape Meares, OR) and near the river mouth; b) at selected process study stations; and c) at fixed stations near the river mouth during strong neap and spring tides (time series). A towed sensor package was used to obtain micronutrient samples near the sea surface on cardinal lines and other selected transects. Underway measurements included macronutrients (N, P, Si), dissolved trace metals (Fe, Mn), supplemented with discrete samples from the underway system (microscopy, FlowCAM and particulate trace metals). At CTD stations vertical profiles (0-200 m where possible; and 500 m at selected stations) of T, S, vertical shear and currents, dissolved O2, in vivo fluorescence, PAR, chlorophyll a, dissolved macronutrients (NO3, NH4, urea, PO4, SiO4), dissolved trace metals, and heterotrophic and autotrophic plankton composition were obtained. Surface drifters were used to follow the mixing of individual plumes and to provide information on surface currents.

On the R/V Pt. Sur, synoptic mesoscale and fine-scale features were sampled with underway measurements of near-surface T, S, velocity, particle size and concentration, PAR, transmissivity and fluorescence and nitrate+nitrite. The Pt. Sur's Triaxus tow fish provided high-resolution sections of T, S, zooplankton (Laser-OPC), PAR and transmissivity, fluorescence, particle size and concentration (LISST-FLOC25X), UV absorption and nitrate (Satlantic ISUS) and radiance/irradiance (7 channels) through the upper water column to 50 m. Rapidly-executed transects of turbulence and fine-structure were also carried out using the Chameleon profiler; these provide full-depth profiles of T, S, optics (880 nm backscatter and fluorescence), turbulence dissipation rates and turbulent fluxes every 1-3 minutes. During selected periods, transects were repeated hourly to capture the high-frequency evolution in the plume's nearfield and river estuary. Acoustics (surface-deployed 1200 kHz ADCP and 120 kHz echosounder) were used to image fine-scale features of the velocity and backscatter fields, resolving fronts, nonlinear internal waves, and turbulent billows.

The temporal context for observed variability was provided by an array of moored sensors deployed in the plume near field as well as on the shelf north and south of the plume (complemented by the pre-existing long-term estuarine and plume stations of the CORIE/SATURN network. To better resolve regional differences, moorings were moved farther north and south to the cardinal sampling lines after the first year of the program. Surface currents were mapped hourly from shore using HF radar with two simultaneously operating arrays, one with a 40 km range and a 2 km range resolution, the other with a 150 km range and a 6 km range resolution. Satellite ocean color, sea surface temperature, turbidity and synthetic aperture radar (SAR) were also obtained when available.

Two modeling systems were developed or enhanced during RISE. The system developed specifically for RISE employed a structured grid model (ROMS) and was used in hindcast mode (MacCready et al., 2008). The CORIE/SATURN modeling system (Baptista, 2006)- based on two unstructured-grid models (SELFE, Zhang and Baptista, 2008; and ELCIRC, Zhang et al., 2004)- was used in both near real-time prognostic mode and multi-year hindcast mode. Both modeling systems incorporated the estuary in the simulation domain (although at different resolutions) and used realistic river, ocean and atmospheric forcing conditions, tidal forcing, and Columbia River estuary forcing. Wind/heat flux model forcing for ROMS was derived from the 4 km MM5 regional wind/heat flux model. SELFE and LCIRC were also forced by MM5. Conditions on open boundaries were provided by ~9 km resolution models from the Navy Research Laboratory (NRL) (NCOM); ROMS used the smaller domain NCOM-CCS NRL model, SELFE and ELCIRC used the larger domain Global-NCOM model. The biological model is a four-box ("NPZD") nitrogen-budget model that tracks nutrients, phytoplankton, zooplankton, and detritus in every cell of the ROMS grid. The rich RISE biological dataset allowed model validation against not just stocks (chlorophyll, microzooplankton, nutrients) but rates (phytoplankton growth and grazing) directly, a level of validation that is seldom possible. These rate observations also allowed the setting of key model parameters (e.g., zooplankton ingestion rate and mortality) empirically (Banas, et al., 2008).

References:
Banas, N. S., P. MacCready, and B. M. Hickey (2008), The Columbia River plume as cross-shelf
exporter and along-coast barrier, doi:10.1016 Cont. Shelf Res., 2008.03.011

Baptista, A. M. (2006), CORIE: the first decade of a coastal-margin collaborative observatory,
Oceans'06, MTS/ IEEE, Boston, MA.

Hickey, B.M., and the RISE PIs. River Influences on Shelf Ecosystems: Introduction to the RISE
Volume, Cont. Shelf Res., in press.

MacCready, P., N. S. Banas, B. H. Hickey, E. P. Dever, and Y. Liu (2008), A model study of
tide- and wind-induced mixing in the Columbia River Estuary and Plume, ,doi:10.1016/j.
Cont. Shelf Res. 2008.03.015.

RISE Cruise Reports and Figures:
2004 RISE-1
RISE04W1=R/V Wecoma, W0407A, July 8-28, 2004
Cruise Report
Cruise Track
Stations and Moorings
Wind Events

RISE2004=R/V Point Sur, (tbd), July 8-28, 2004
Cruise Report

2005 RISE-2
RISE05W2=R/V Wecoma, W0505C, May 29-June 21, 2005
Cruise Report
Cruise Track
Stations and Moorings
Wind Events

RISE2005a=R/V Point Sur, (tbd), May 29-June 21, 2005
Cruise Report

2005 RISE-3
RISE05W3=R/V Wecoma, W0508, August 4-August 26, 2005
Daily Cruise Report
Lessard Cruise Report
Peterson/Shaw Zooplankton Report
Cruise Track
Stations and Moorings
Wind Events

RISE2005b=R/V Point Sur, (tbd), August 2-August 27, 2005
Cruise Report
Cruise Log

2006 RISE-4
RISE06W4=R/V Wecoma, W0605B, May 21-June 13, 2006
Cruise Report 1
Cruise Report 2
Cruise Track
Stations and Moorings
Wind Events

RISE2006a=Leg 1, R/V Point Sur, (tbd), May 21-May 31, 2006
Cruise Report Leg 1
RISE2006b=Leg 2, R/V Point Sur, (tbd), June 2-June 12, 2006
Cruise Report Leg 2



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Funding

Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)

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