Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
  • BCO-DMO Processing Description
  • Problem Description
• Data Files
• Related Publications
• Related Datasets
• Parameters
• Instruments
• Deployments
• Project Information
• Funding

Data were collected on the Oregon-Washington continental shelf (between 44.5 N,124.2 W and 46.5 N, 124.6 W) and at water depths between 30-80 meters during the following cruises and dates:

R/V Oceanus OC1802B (dates: 2018-02-26 to 2018-03-01)
R/V Oceanus OC1805B (dates: 2018-05-07 to 2018-05-11)
R/V Oceanus OC1807A (dates: 2018-07-03 to 2018-07-05)
R/V Oceanus OC1810A (dates: 2018-10-04 to 2018-10-08)

R/V Oceanus OC1901A (dates: 2019-01-11 to 2019-01-15)
R/V Oceanus OC1904A (dates: 2019-04-22 to 2019-04-26)
R/V Oceanus OC1907A (dates: 2019-07-07 to 2019-07-11)

R/V Robert Gordon Sproul SP2215 (dates: 2022-07-22 to 2022-07-25)
R/V Robert Gordon Sproul SP2219 (dates: 2022-09-14 to 2022-09-19)

Sediment cores were collected from sites along the Newport Hydrographic Line on the Oregon shelf during the the February, May, July, and October 2018, January, April, and July 2019 cruises, and from 8 different sites, along the Oregon-Washington mid-shelf during the July and September 2022 cruises. Sediment cores were incubated using a unique method designed around the core tube itself. The method is described in Hughes et al. (2024). Briefly, sediment cores were collected in acrylic tubes with a radius of 5.3 centimeters (cm) and length of 94 cm using a hydraulically dampened Gravity Corer (Reimers et al., 2012). Once onboard, cores were immediately transported to a cold van, pre-set to the approximate in situ bottom water temperature. The core's overlying water was siphoned down to ~10 cm above the sediment surface and the core was sealed with a custom-made black Delrin puck. The pucks included two side grooves, two through-wells threaded at each end, two eye screws, and top and bottom axially aligned cavities. The two grooves each held an X-ring seal to ensure a seal with the core tube sides. One of the wells was fitted with a barbed connector joined to Tygon tubing (inner diameter of 3 millimeters (mm) and ranging in length from 0.66 meters (m) to 0.88 m) to enable overlying water sampling. The other well was plugged into the waterside. The top cavity was fitted with a 4-inch long threaded, clear PVC pipe (McMaster-Carr, part no. 4677T33) which contained an externally powered 6-volt DC mini electric motor. The output shaft of the motor ended in a small Delrin disk, fitted with four rare earth magnets (McMaster-Carr, part no. 5862K108). The bottom cavity held a second Delrin disk, with its top side fitted with four rare-earth magnets as well. The stir bar was set to rotate at 30 rpm at the top of the overlying water column. The resealed core was placed in a temperature-equilibrated, water-filled, incubation chamber with a lid to ensure the core remained at bottom water temperature and under low light conditions inside the cold van.

Incubations ran between 24 and 36 hours, with three to six time-point measurements conducted per core (about every 4 to 12 hours) before oxygen saturation dropped below 10%. For each measurement, the stirring motor of the core was stopped, and a custom device was used to slowly depress the black puck caps against the overlying water, expelling small, carefully measured volumes through the open sampling tube into a 10-milliliter (mL) gas-tight glass syringe with a luer-lock fitting. Following a flush of the sample tube, the sample water was directed to the flow-through cell of a PreSens Microx T3 micro-fiber optic oxygen sensor via a three-way valve at the end of the tubing, and its dissolved oxygen (DO) was recorded as percent air-saturation. The luer-lock fitting of the gas-tight glass syringe was attached to the exit side of the flow-through cell to collect timepoint water samples. These samples included 7 mL for shore-based dissolved inorganic carbon (DIC) analysis that were transferred to 8 mL borosilicate scintillation vials with polyethylene screw caps with poly-seal cone liners, pre-poisoned with 50 microliters (µL) of mercuric chloride to halt any biological activity. Another 10 mL was stored in a Nalgene™ HDPE bottle, and frozen (-20 degrees Celsius) for shore-based nutrient analysis. The second sample enabled a repeat oxygen measurement through the flow cell; however, the initial oxygen measurement was used for the flux calculation. After samples were collected, the stirring motor for the core was turned back on for the core to continue to incubate.

Nutrient samples from sediment core incubation experiments were analyzed onshore using standard auto-analyzer colorimetric methods at Oregon State University (Gordon et al., 1993). For DIC samples collected during the 2018 and 2019 cruises, samples were analyzed using a UIC Coulometer with a 1 mL sample loop, however, the results were not found to be reliable and therefore these data are not reported. For the DIC samples collected during the 2022 core incubations, samples were processed for DIC with a Finnigan GasBench-II headspace sampler online with a Finnigan DELTAplusXL gas-source isotope-ratio mass spectrometer, with reported precision between 0.5 and 1%, using a procedure outlined in Torres et al. (2005). Additional details on core collection, incubations, and sample analyses can be found in Hughes et al. (2024).

The oxygen concentration of the overlying water at each timepoint of individual core incubations was calculated using oxygen solubility and percent air-saturation measured with the micro-fiber optic sensor. Oxygen solubility was calculated with inputs of sample temperature (obtained during each timepoint sampling), the latitude of the core collection, and bottom water salinity from the nearest CTD deployment using http://ocean.ices.dk/Tools/Calculator.aspx. Oxygen, nutrients, and DIC water sample concentration data were then used to calculate fluxes for each component using a linear fit to the time-varying inventory of the solute (in millimoles (mmol)) in the initial overlying water volume of the core, normalized to area. Inventory calculations were made by multiplying measured concentrations times volumes at each time point and adding back amounts contained in water volumes removed during preceding sample collections, over the time of the incubation. These results were also used to calculate stoichiometric ratios of component fluxes.

- Imported original file "AllBenthicFluxes_BCODMO.csv" into the BCO-DMO system.
- Renamed fields to comply with BCO-DMO naming conventions.
- Converted the "Date_UTC" column to ISO 8601 format and renamed "ISO_DateTime_UTC".
- Converted "Date_Local" column to ISO 8601 format and renamed "ISO_DateTime_Local".
- Submitter rounded fields and provided as file "940414_v1_benthic_do_and_nutrient_fluxes.xlsx".
- Imported file "940414_v1_benthic_do_and_nutrient_fluxes.xlsx" into the BCO-DMO system.
- Saved final file as "940414_v1_benthic_do_and_nutrient_fluxes.csv".

NSF Award Abstract:
The longstanding theory regarding the formation of low oxygen zones in coastal shelf regions at the eastern boundaries of the oceans has pointed to the upwelling of oxygen-depleted waters from off of the shelf. In other words, dense water from beyond the shelf break that is depleted in dissolved oxygen is drawn along the seafloor upwards onto the shelf, mixing with the oxygenated water there, and creating low oxygen (hypoxic) zones. This is a paradigm that the researcher in this project seeks to shift by analyzing the added effects of respiration in shelf sediments. The investigator hypothesizes that changes in the biological activity of sediments due to seasonal changes in organic matter input from overlying waters are a major factor in the changes in dissolved oxygen content of deep shelf water, perhaps being the leading variable in the creation of hypoxic zones. Though the field analysis will be confined to the Oregon margin, there is a great deal of applicability for this research in other coastal regions where hypoxic zones form. In addition to the potential for unraveling complex local feedbacks between physical and biogeochemical processes, the researcher plans to work with a small business called Analytical Instrument Systems to build a new oxygen sensor, called a rotating disc microelectrode (RDME), that does not intrude on the environment it is testing and that can be deployed for much longer periods of time than currently popular sensors, micro-optodes. Her RDME will be deployed with micro-optodes for comparison and to validate the necessity for the RDME in the study of coastal ecosystems. This project will provide a unique experience for a postdoctoral researcher as well as a graduate and three undergraduate students. A public database will be created which will greatly help with accessibility and archiving of data for anyone who is interested in similar research. The database will be connected with a variety of other ocean observing data products, which will allow the research community and the public to make connections outside of this particular field of study. This investigator has a strong track record of including Research Experiences for Undergraduates (REU) students in her research, and she will continue to do so in this project.

The researcher aims to challenge the paradigm that hypoxic zones on the Oregon shelf are created by upwelling of offshelf oxygen-depleted water and that most of the local primary productivity is exported off the shelf during downwelling periods. Preliminary data suggests the possibility that seasonal benthic respiration may be a major factor in hypoxic water formation on the shelf. With the use of eddy covariance measurements, sediment core incubations, and near seabed particulate organic matter (POM) collections, the biogeochemical fluxes of the Oregon margin will be characterized for every season. This work is ambitious on its own, but the investigator also plans to incorporate the development of a new oxygen sensor called a rotating disc microelectrode (RDME) that will be compared to currently popular micro-optodes when making eddy covariance measurements. The RDME will be small enough as not to interfere with the physical properties being measured in situ; it will be insensitive to flow and deployable for longer periods of time. Not only does this project contain the possibility of completely overturning the current best theory of hypoxic zone formation on shelf margins, but the use of eddy covariance is new to the study of dynamic coastal ecosystems and will yield great insights into the biogeochemical processes of shelf benthos.

This project is affiliated with the Coastal Endurance Array of the Ocean Observatories Initiative (OOI): https://www.bco-dmo.org/program/661079

NSF Award Abstract:
Highly productive US West Coast fishery species and marine mammals rely on benthic invertebrate communities for food. However, these communities are changing. This project addresses the potential ecological consequences of a new member to these benthic communities, the ghost shrimp Neotrypaea. In estuaries, Neotrypaea continuously rework the sediment via their burrowing activities. The combination of high shrimp abundances and the effects of burrowing mitigate the impacts of nutrient run-off (natural and human-induced) that can exacerbate low oxygen conditions. However, Neotrypaea are also considered threats to the oyster industry because of their sediment-excavating activities. An expansion of their distribution beyond estuaries may have additional unforeseen consequences for the Dungeness crab fishery (regionally valued at $33-74M/y) as Neotrypaea are both competitors with juveniles and prey for larger Dungeness crab. Thus, new data are needed to determine how offshore benthic communities are being altered by the recruitment of Neotrypaea into new habitats. This study is comparing communities with high and low shrimp abundances to understand their impact on offshore benthic communities. The shrimp’s contributions to oxygen and carbon cycling are being estimated through field measurements. Benthic community assessments are quantifying changes to food resources on the seafloor caused by the presence of these relatively large shrimp. The coastal waters along the Oregon-Washington shelf are commercially valuable, yet they are also subject to growing human-related impacts. Sustainable management requires optimizing extractive, cultural, and recreational activities. The broader impacts of this research include key data for managers, commercial fisheries’ stakeholders and oyster growers that inform decisions regarding ocean-use planning and management of burrowing shrimp. This project is providing research training for three graduate students and two summer undergraduate students. Curriculum development for elementary school students is focused on the ecology of soft-bottom benthos. The ocean sandy/muddy benthos are often unknown to K-12 students on the West Coast who are usually more familiar with intertidal and kelp forest systems.

Changing environmental conditions in shelf waters along the Oregon and Washington coasts and elsewhere have included increasingly frequent and severe hypoxia events, ocean acidification, and warming. These changes have affected biological communities and altered species distributions. An abundant mid-shelf population of the burrowing ghost shrimp, Neotrypaea sp. was documented in shelf waters following the Marine Heat Wave of 2015. Neotrypaea are ecosystem engineers that were previously known to be abundant in intertidal estuary mudflats with an insignificant presence in the open ocean. In estuaries Neotrypaea continuously rework the sediment via their burrowing activities. The shrimp can increase oxygen cycling due to burrow irrigation and reduce impacts of nutrient loading such as low-oxygen conditions. However, enhanced benthic oxygen consumption linked to Neotrypaea sp. beds could have the opposite effect on the shelf by intensifying regional hypoxia. This study is characterizing the environmental conditions associated with the expanded distribution of Neotrypaea using a habitat-suitability modeling approach. Model predictions are being validated through extensive field sampling via box coring and video lander observations. In addition, the benthic samples are documenting changes in the benthic invertebrate communities within the Neotrypaea beds and how this is potentially affecting biological interactions. Analyses of aquatic eddy covariance and of core incubations in shelf areas with and without abundant shrimp are providing estimates of the shrimp’s contribution to benthic oxygen fluxes and organic carbon cycling. These data are being used to quantify the shrimp’s and their burrows’ effects on the overall productivity of the mid-shelf benthos relative to reference areas. How Neotrypaea alter seafloor structure and biogeochemistry need to be characterized to predict the impact of these ecosystem engineers on the food supply for higher trophic levels and fisheries.

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.