Posts Tagged ‘Coastal Endurance Array’
Observations of Cross-Shelf Nitrate Fluxes over the Oregon Continental Shelf
Extracted from OOI Quarterly Report, 2022.
The US Pacific Northwest coastal ecosystems are primarily limited in growth from nitrate supply. The nitrate supply that drives the highly productive marine growth in this region is primarily a result of wind driven coastal upwelling. This work seeks to investigate cross-shelf nitrate fluxes over the continental shelf off the coast of Oregon following the installation of new nitrate and Acoustic Doppler current profilers (ADCPs) in the Ocean Observatories Initiative Coastal Endurance Array.
[media-caption path="/wp-content/uploads/2022/02/Endurance.png" link="#"]Figure 24. A velocity and nitrate profile from the shelf site at the Newport line. Data used was from the 2019 summer, approximately mid-June to early October (deployments 13, 14, and 15). The net nitrate flux found at that site over this time period, found by vertically integrating the values above, is roughly 1.16 mmol Nitrate/second/meter coastline. [/media-caption]
The primary onshore flow of nitrate-rich water over the continental shelf is found to originate at the middle depths, consistent with previous research in the region. However, the upwelling and cross-shelf nitrate fluxes on the continental shelf are found to be in poor agreement with common upwelling indices, e.g., coastal upwelling transport index (CUTI) and biologically effective upwelling transport index (BEUTI). Several factors for this disagreement are proposed, including the focus of the indices on dynamics farther offshore of the continental shelf. Observed coastal wind stress, calculated on a weekly rolling average, is found to be a potential alternative for predicting nearshore nitrate concentrations. Farther offshore at the mid-shelf, only a weak correlation between observed wind stress and observed surface transport is found, suggesting the need for additional dynamics to fully explain the observed surface transport and nitrate fluxes. Correctly modelling the nitrate supply for coastal ecosystems is essential for predicting phytoplankton blooms that are vital to the production of fisheries on the coast. Thus, understanding these limitations is of great importance for ocean-driven coastal economies.
Written by Andrew Scherer, California State University, Monterey Bay and Cleveland State University and Thomas Connolly, Moss Landing Marine Laboratories, San José State University
Andrew Scherer is an undergraduate physics student at Cleveland State University. In summer 2021, he performed this research with Prof. Tom Connolly (MLML, SJSU) as part of a National Science Foundation Research Experience for Undergraduates program and presented it at the Eastern Pacific Ocean Conference Stanford Sierra Center, Fallen Leaf Lake, California 26-29 Sep 2021.
Read MoreR/V Oceanus Remembered as a Workhorse of the U.S. Academic Research Fleet
The long service of the R/V Oceanus (1976-2021) came to end on November 21, 2021 as the ship pulled into port after having successfully completed its last interdisciplinary cruise for Oregon State University (OSU). The Oceanus began its 45-year-run of scientific investigations at Woods Hole Oceanographic Institution (WHOI) in 1976. After a major mid-life refit, the ship was transferred to OSU in 2012, and contributed to the Ocean Observatories Initiative (OOI) off both coasts.
“The Oceanus proved to be a real workhorse for the Academic Research Fleet and also played a pivotal role for the OOI during its initial launch,” said Ed Dever, PI of OOI’s Coastal Endurance Array, who sailed on the ship many times. “While at WHOI, The Oceanus performed some of OOI’s at-sea-mooring test deployments and later the ship was used for the initial deployment of the Coastal Endurance Array off the Oregon coast.”
In spring and fall 2014, after moving to OSU, Oceanus performed the initial deployments of the Oregon and Washington inshore moorings and Washington profiler mooring. The real test for the Oceanus, however, came during 2015, when it was tasked with deploying the full scope of the Endurance Array, including the four large coastal surface moorings at the Oregon and Washington shelf and offshore sites.
Explained Dever, “Thanks to some excellent ship handling, care on the part of the deck crew and a huge assist from some very kind weather, we got the moorings safely in the water using the ship’s crane to deploy the 10,000-pound buoy off the starboard fantail and the heavy lift winch to deploy the 11,000-pound multifunction node (MFN, bottom lander) through the A-frame. The size of the buoys and MFNs meant that Oceanus could only carry one buoy out at a time and the cruise was completed in five legs with some very efficient port stops. By the end of the cruise, it was evident that we would need to move future operations to global and oceans class ships and after one more deployment in fall 2015 (with recoveries carried out on the R/V Thomas G. Thompson), we made that transition.”
[embed]https://youtu.be/pDRagMTDUTk[/embed]After the initial Endurance Array deployments, OOI transitioned to using larger global and oceans class ships needed to recover the bulky coastal surface moorings, with one exception. In spring 2019, with tight schedules on global class ships, UNOLS (University-National Oceanographic Laboratory System charged with ship scheduling) requested that OOI Endurance split the spring mooring recovery and deployment cruise between the R/V Sikuliaq and the R/V Oceanus. The Oceanus ably performed the profiler mooring deployment, anchor recoveries, coastal surface piercing profiler deployments, and glider deployments over five days in April and May 2019.
While not directly working with the OOI, the Oceanus continued to work off Oregon at and around the OOI arrays. Research and student cruises often sampled over the years near OOI’s Endurance and RCA Arrays at the Oregon inshore, shelf, offshore and Hydrate Ridge sites to compare shipboard measurements and OOI time series. This work included CTD profiles, net tows, coring, and sediment trap deployments.
The last Oceanus cruise, in fact, was one such interdisciplinary research cruise led by OSU researcher Clare Reimers, who also served as chief scientist. During its final official outing, the team aboard the Oceanus sampled the outer shelf at the northern end of Heceta Bank, Oregon to help scientists determine any changes that may have occurred to a swath of the margin that was reopened to commercial bottom trawling in 2020 after an 18-year closure. Reimers said, “The R/V Oceanus and crew performed flawlessly, and our science mission was fully completed.”
Added Dever, “What better way to end its long and illustrious career? We at OOI join many others in appreciation of the R/V Oceanus, and the dedication and skills of all who sailed on her and supported ocean science throughout her many years at sea.”
______________________________________________________________________________________
Special thanks to OOI Data Center Project Manager Craig Risien for sharing the GoPro time lapse of the loading of the Oregon Offshore mooring onto the R/V Oceanus in spring 2015.
Read MoreEndurance Array to Provide Hourly Meteorological Data
On 11 October 2021, the National Oceanic and Atmospheric Administration (NOAA)requested that OOI’s Coastal Endurance Array buoys provide hourly meteorological data to the National Data Buoy Center (NDBC) because a nearby NDBC buoy (46029, Columbia River bar) had gone offline. OOI buoy data are typically telemetered every two hours due to sampling schedule and bandwidth constraints (the actual sampling rate is higher).
Endurance Array team members examined sampling and telemetry schedules for the Endurance offshore coastal surface moorings to see if they could accommodate NOAA’s request. The team concluded that meteorological data from the moorings could be updated hourly while still meeting OOI sampling requirements.
“To help ensure continuity of data to the NDBC, we plan to distribute hourly meteorological data from the Endurance Array Oregon and Washington offshore sites for the duration of the outage at NBDC 46029,” said Edward Dever, lead of the Coastal Endurance Team. “We’re pleased to respond to NOAA’s request and hope these data prove useful to operational weather forecasts and marine safety.” The Oregon and Washington offshore sites have NDBC buoys designations of 46098 and 46100, respectively.
The Endurance Array team will continue to review the performance of the buoys and ensure the updated telemetry schedule does not impact OOI sampling. If data users do experience any impacts from this change in sampling frequency, please contact Jon Fram at Jonathan.Fram@oregonstate.edu.
Read MoreNew Underwater Camera with Off-the-Shelf Components
In September 2021, the Coastal Endurance Array began rolling out a much-needed upgrade to their underwater cameras. Endurance Array Innovator Chris Holm engineered a camera using off-the-shelf components to meet the specific needs of capturing environmental conditions and marine life in proximity to the Endurance Array moorings. The prototype was put in place on the inshore mooring (CE01) during the 15th turn of the Coastal Endurance Array.
[media-caption path="https://oceanobservatories.org/wp-content/uploads/2021/10/camera.png" link="#"]The newly configured Endurance Array underwater camera is attached to the inshore mooring, ready for deployment. Photo: Chris Holm, OSU.[/media-caption]The innovation came in multiple steps. Holm first tried to salvage the camera’s hardware and reprogram the camera with new software. He hit a snag, however, in that the motherboard that controlled the camera was no longer supported.
Since it didn’t make sense to rebuild the camera using an out-of-date motherboard, Holm looked into finding a new camera on the market. It had to be suitable for use underwater, with the capability to go into a low-power mode. “What is really needed for low-light conditions underwater is a camera with a large physical sensor, but with fewer megapixels,” explained Holm.
“Since the moorings run on battery power, the cameras need to be able to go into a very low-power sleep state in between taking photos,” said Holm. “If the sleep current is high, the deployment life is low. So, we were trying to find an off-the-shelf solution for a way to go into low power.”
After some searching, Holm obtained a Raspberry Pi High Quality Camera. Although the Raspberry Pi doesn’t come with native power management capabilities, Holm found he could use Sleepy Pi, an add-on-board from Spell Foundry that can power the Raspberry Pi on and off.
For its launch, the camera is programmed to autonomously take a burst of three images every four hours. The system can also take photos when triggered by a Data Concentration Logger (DCL) and can be partially configured remotely. Future iterations will be fully configurable remotely via the DCL.
The final touch to this first iteration was figuring out how to turn the lights and lasers on and off. Holm used a relay board from Waveshare Electronics to power the original systems lights and lasers. The lights adjust their brightness depending on the voltage being sent through a signal line which is controlled by the GPIO pins of the Raspberry Pi.
Altogether, the system is very suitable for the Endurance Array’s needs and is an extremely cost-effective, off-the-shelf solution. The cameras also can be easily swapped out if the Endurance team decides to upgrade the cameras.
Since this newly configured camera was put in place in early September, Holm said, it has been performing flawlessly, with the auto-exposure working well. Since this mooring uses a cell modem to transmit data, the team has been able to see the photos the camera is taking in near real-time. Once the formal approval process for the camera’s integration and use across the OOI is completed, Holm will be building more camera systems for the Endurance Array to deploy on the offshore and shelf moorings during the spring.
Since the cameras and its settings can be upgraded and/or optimized for different use cases, depending on what an investigator is interested in (such as marine snow or benthic organisms), Holm would like to hear from scientists about what they’d like the camera to focus on. He created a survey for data users interested in the underwater cameras.
“It would be very helpful to know what kind of data would be most useful to scientists using the system,” he said.
For those interested in seeing underwater, please complete the survey here.
[media-caption path="https://oceanobservatories.org/wp-content/uploads/2021/10/camera-output.png" link="#"]The Endurance Array team has the capability to adjust the settings of the underwater cameras based on researchers’ interests. In addition, some post-processing tools could be developed to sort images or extract useful information from them. Photo: Chris Holm, OSU.[/media-caption]
Read More
Rocky Seas Didn’t Deter Endurance 15’s Success
In spite of rocking seas, a generator in need of repair, and a medical delay, the Coastal Endurance Array team successfully completed its mission to turn the array for the 15th time, achieving all of its science objectives.
Weather conditions in the northern Pacific were less-than-ideal for two of the three legs of the two-week expedition. At one point, winds speeds of 25-30 knots, with accompanying waves of up to 10 feet, caused a weather delay in operations and subsequent alterations in cruise plans.
“While it was comfortable to be aboard the R/V Thomas G. Thompson even in such conditions, sea conditions were borderline for entering or exiting Newport and deploying or recovering most platforms, “explained Chief Scientist Jonathan Fram, who led the 10-member science party. “Fortunately, we had good weather during the first leg of the cruise, which gave us some leeway to address weather-related downtime and other delays during latter legs of the cruise. We were able to switch the order of some activities, delay some deployments, and ultimately got most everything in and out of the water as planned during our time at sea.”[media-caption path=”https://oceanobservatories.org/wp-content/uploads/2021/09/Screen-Shot-2021-09-28-at-5.20.52-PM.png” link=”#”]When seas were calm, the team was able to deploy moorings like this one. After deployment, they headed back to port with a deck full of recovered equipment.[/media-caption]
The team successfully deployed and recovered six surface moorings, four gliders, and two profilers. They also recovered two additional profilers and an anchor from 2020. In addition, the team conducted CTD water sampling and also conducted sampling for researchers with instruments on Endurance Array moorings. The team succeeded in collecting fouling communities growing on buoy panels for researcher Linsey Haram of the Smithsonian Institution and organisms on devices attached to two multi-function nodes for Oklahoma State researcher Ashley Burkett.
While in the roaring sea, the team tested potential instrument replacements and new sampling strategies. They also assessed first-time implementation of technical improvements including a new solar panel frame to prevent sea lions from unplugging the panels, an underwater camera constructed with off-the-shelf replacement parts to ensure longevity and resilience, and a stretch hose from a new manufacturer with a slightly different design than previous versions.
“In spite of having to repeatedly change our plans,” adds Fram, “we were pleased to be able to meet all of the cruise objectives. The ocean in the Pacific Northwest is too harsh for scientists to go to sea often in fall and winter, so it is important to refresh this array of autonomous platforms that will keep recording and delivering data during rough times.”
Read MoreEndurance 15 Happening in Sept
On September 8th, a science team of ten and three students from Oregon State University will depart the dock at Newport, Oregon, aboard the R/V Thomas Thompson for the 15th turn of the Coastal Endurance Array. The team will recover and deploy seven moorings. Four of the moorings are located on the Washington Shelf, with the remaining three on the Oregon Shelf. It’s a busy expedition. The team also will be recovering four and deploying three Coastal Surface Profilers and recovering three gliders that are low on power. When not turning the arrays, they will be taking CTD (connectivity, temperature, and depth) casts to verify and calibrate instrumentation. Because of the quantity of the equipment to be recovered and deployed, the cruise will consist of three legs.
“As we head to sea for the fifteenth time to turn this array, it’s remarkable to consider that the Endurance Array has been generating data for researchers, teachers, and others interested in the ocean, every day, 24/7 for the past seven years, said Jonathan Fram, who is the chief scientist for Endurance 15. “Our data has helped identify everything from warm blobs to low-oxygen events, to even the impact of forest fire smoke miles from shore.”
[media-caption path=”https://oceanobservatories.org/wp-content/uploads/2021/09/Screen-Shot-2021-09-03-at-3.17.24-PM.png” link=”#”]Members of the Coastal Endurance Array 15 team prepare moorings for moving to pier for loading onto the R/V Thomas Thompson. Credit: Jon Fram, OSU.[/media-caption]To help advance science, the Endurance 15 team also will be sampling for researchers with instruments on the Endurance Array moorings. The team will collect fouling communities growing on panels attached to its deployed buoys for researcher Linsey Haram of the Smithsonian Institution. They will also collect settling organisms on devices attached to two multi-function nodes for Oklahoma State researcher Ashley Burkett.
The team also will be testing potential instrument replacements and new sampling strategies for coastal moorings. Additionally, they will be assessing technical improvements to the moorings and instrumentation that range from a new solar panel frame design to prevent sea lions from unplugging the panels to improvements to cameras deployed on the moorings with off-the-shelf replacement parts to ensure longevity and resilience.
Check back here often during September as the Endurance Array 15 team shares reports and photographs of their expedition.
Read MoreOregon Sea Grant Spotlights Partner OOI
In its August 2021 newsletter, Oregon Sea Grant highlights the work of OOI’s Endurance Array Team at Oregon State University. Sea Grant Scholar Charlotte Klein interviewed the Endurance Array Principal Investigator Ed Dever, who describes some of challenges in keeping arrays operational in a challenging offshore environment.
The article can be found here, on page four.
Read MoreJupyter Notebook Produces Quality Flags for pH Data
OOI uses the SAMI2-pH sensor from Sunburst Sensors, LLC to measure seawater pH throughout the different arrays. Assessing the data quality from this instrument is an involved process as there are multiple parameters produced by the instrument that are then used to calculate the seawater pH. These measurements are subject to different sources of error, and those errors can propagate through the calculations to create an erroneous seawater pH value. Based upon the vendor documentation and MATLAB code Sunburst provides to convert the raw measurements, OOI data team members have created a set of rules from those different measurements to flag the pH data as either pass, suspect or fail.
The resulting flags can be used to remove failed data from further analysis. They can also be used to help generate annotations for further Human in the Loop (HITL) QC checks of the data to help refine quality metrics for the data. OOI team member, Chris Wingard (OSU), has written up the QC process as a Python Jupyter notebook. This notebook and other example notebooks are freely available to the scientific community via the OOI GitHub site (within the OOI Data Team Python toolbox accessed from https://oceanobservatories.org/community-tools/ ).
In this notebook, Wingard shows how the quality rules can be used to remove bad pH data from a time series, and how they can be used to then create annotations. The impact of using these flags is shown with a set of before and after plots of the seawater pH as a function of temperature. The quality controlled data can then be used to estimate the seasonal cycle of pH to set climatological quality control flags.
Here an example is shown using data from a pH sensor on the Oregon Inshore Surface Mooring (CE01ISSM) near surface instrument frame (NSIF), deployed at 7 m depth (site depth is 25 m).
[media-caption path="https://oceanobservatories.org/wp-content/uploads/2021/07/EA-Highlight.png" link="#"]Figure 25: pH data from the Oregon Inshore Surface Mooring (CE01ISSM) near surface instrument frame (NSIF). Good data are shown in black, failed data in red. Note that simple range tests on the final calculated pH are often not enough to distinguish good from failed data. The automated QC processing examines intermediate measurements and fails data if intermediate measurements are outside acceptable ranges and propagated to final measurements.[/media-caption] [media-caption path="https://oceanobservatories.org/wp-content/uploads/2021/07/EA-highlight-2.png" link="#"]Figure 26: Good data together with annual cycles (red) constructed with available good data from initial deployment through 2021. Data which falls outside three standard deviations of the climatology is flagged as suspect. The climatological tests are used to flag suspect data. Simple range tests for suspect (cyan) and failed (magenta) data are also shown. The annual cycle at this site is strongly influenced by annual summer upwelling and winter storms and river plumes. The summer decrease in pH is consistent with cold, relatively acidic upwelled water high in CO2 (see e.g., Evans et al., 2011)[/media-caption]
Evans, W., B. Hales, and P. G. Strutton (2011), Seasonal cycle of surface ocean pCO2on the Oregon shelf,J. Geophys. Res., 116, C05012, doi:10.1029/2010JC006625.
Read MoreOOI Community Members Guide Pioneer Relocation
From 21-25 June, 37 members of the Ocean Observatories Initiative (OOI) community are participating in the National Science Foundation-sponsored Phase 2 Innovations Lab to identify the best location within the recently designated geographic region of the Mid-Atlantic Bight (MAB) between Cape Hatteras and Norfolk Canyon for the Pioneer Array relocation.
During the week, participants will work to identify the observatory opportunities that can be offered by the new Pioneer Array location. They will explore how the Pioneer Array sensors and platforms can be optimized to achieve science and education goals at a new site, based on environmental, logistical, and infrastructural considerations. The group will also evaluate challenges presented by deployment of Array infrastructure at a new location, and discuss the potential for partnerships and collaborations at a new site.
The MAB region offers opportunities to collect data on a wide variety of cross-disciplinary science topics including cross-shelf exchange, land-sea interactions associated with large estuarine systems, a highly productive ecosystem with major fisheries, and carbon cycle processes. This geographic region also offers opportunities to improve understanding of hurricane development, tracking and prediction, and offshore wind partnerships. The relocation of the Pioneer Array will take place in 2024.
The Ocean Observatories Initiative Facilities Board (OOIFB), in partnership with KnowInnovations, is facilitating the Phase 2 Innovations Lab. “We selected a diverse mix of Lab participants to achieve a broad range of disciplines and professional expertise, career stage (from early to senior), gender, cultural background, and life experience. By involving such a wide range of people in the conversations this week, it is our hope that the innovative quality, outputs, and outcomes of the Lab will be enriched,” said Kendra Daly, chair of the OOIFB. “And, throughout the year, we will continue to work with the community on the exciting optimization process via scientific meetings, seminars, and other means to ensure we receive broad input.”
Read MoreTackling Sea Surface Sampling Issues
The sea surface is the hardest place to work, according to Jonathan Fram, Project Manager of the Coastal Endurance Array. That’s because at the surface, waves are constantly sloshing around. At any time, a large wave can tug on mooring winch lines, creating sudden tension, which can wear down cables and even cause them to break.
Scuba divers know that surface waters are rough, but below a certain depth—about one wave orbital below the surface—the waters calm significantly. Unfortunately, a lot of great science takes place at the surface, so it’s important for sampling instruments like the Coastal Surface Piercing Profiler (CSPP) to be able to withstand the waves at and near the surface. Fortunately, OOI engineers have found ways to meet the many challenges of working in this rough environment.
“The Coastal Endurance Array Team has made changes to the CSPP to make it more robust, so that we can get the kind of continuous time series that are so valuable to scientists,” said Fram.
A CSPP spends most of its time near the sea floor, but either two or four times a day, the profiler winches itself up to the surface, taking samples as it ascends. Once it reaches the surface, the profiler sends its data back to shore and then quickly returns to the safety of the seafloor. Profilers are important ocean observatory tools because they can help capture what is happening at certain depths where stationary instruments aren’t present. “We’ve had times where you get a persistent chlorophyll bloom at a certain depth where there is zero mooring data,” explained Fram. “So the CSPP sampling is needed to make sense of what’s happening. It’s impossible to have all the instruments at all depths. The CSPP fills in this gap.”
Last year, the Coastal Endurance Array team reviewed their activities looking for ways to reduce lost time at sea. One thing they discovered was that the anchor systems of the CSPPs were unreliable. To deal with this problem, the team created a new kind of anchor. The old profiler anchors had a chain between the profiler and anchor that helped dampen the waves so that the device was not tugged on when resting in between profiles. The chain, however, made it difficult to deploy the anchor in an upright position. Anchors need to be deployed upright so their recovery floats can be acoustically released. The team redesigned the anchors so they now behave like a weeble wobble toy that is weighted so it always rights itself. This new design makes it hard to deploy an anchor upside down, making the anchors more reliable.
The team also made updates to the modems that send data to shore. When the CSPP is at the surface, the winch must stay on because it keeps the antenna vertical. This time-on takes up about a quarter of the battery power. To reduce the power demand, the team switched out some of the iridium modems for cellular modems, which has allowed the CSPPs to send data more quickly. A faster modem means that the profiler spends less time at the surface, not only saving power, but reducing the risk of being damaged by a large wave. The team is currently working on upgrading to faster cellular modems that can connect further from shore.
“At the same time we are making these updates on the Oregon Shelf Mooring, we’re also implementing them on the Washington Shelf Mooring,” said Fram. “So an improvement on one platform is also leading to an improvement on another platform.”
A third innovation involves improvements to the batteries.
“When waves tug on the winch, it goes from being a power sink to a power source. That sometimes creates power spikes that can fry the connectors. So we’ve rewired the batteries to make them more robust,” explained Fram. The rewiring is expected to reduce the number of power failures and keep the CSPPs running continuously. “Since April when we first started using the rewiring scheme, we’ve had four profilers in the water with no problems for six weeks,” said Fram.
The team also is in the process of replacing batteries that power the profiler with their own design of rechargeable batteries. While OOI engineers prefer to use commercially available parts for easier repair and replacement, when parts on the market don’t fit their needs, they design their own. The new batteries will be more reliable than those they are replacing. The newly designed batteries will also be deployed on the wire-following profilers on the Coastal Pioneer Array.
“My focus is on making all of the Coastal Endurance instrumentation work,” said Fram. “When we’re able to get a full three months’ deployment through the winter, through super rough seas, that makes my day. Making improvements is what I look forward to the most.”
Read More