Table of Contents

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

Data were collected on several single-day cruises on small privateers out of the Virginia Institute of Marine Science, Gloucester Point, VA.

High-resolution sampling via Dataflow was performed along the lower York River estuary during two successive summers, 2020-21, before, during, and after intense blooms of Margalefidinium polykrikoides and Alexandrium monilatum for determinations of pCO2, temperature, salinity, pH, turbidity, chlorophyll-a, and dissolved oxygen (DO). High-resolution sampling was performed with a Dataflow system (Madden & Day, 1992) modified as described in Crosswell et al. (2017). The pCO2-Dataflow system is instrumented with a pCO2 analyzer, a multi-parameter datasonde (YSI 6600V2), Garmin global positioning system (GPS MAP 546S), and data acquisition system. The system continuously samples surface water (approximately every 30 meters (m) at an average speed of 20 knots) from a stern-mounted water intake located 0.5 m below the water surface with a pump, which delivers water in parallel to (1) a showerhead equilibrator and (2) a flow-through cell attached to the YSI which is configured to measure water temperature, salinity, pH, turbidity, chlorophyll-a fluorescence, and DO. pCO2 in the equilibration chamber is determined by recirculating a carrier gas at a flow of approximately 1.5 liters per minute (L/min) through the equilibrator chamber and a nondispersive infrared absorbance detection analyzer (LI-COR LI-840).

Concurrent with Dataflow sampling, grab sampling was performed at five stations within bloom patches (as determined by levels of chlorophyll-a) and at five stations outside of bloom patches for determinations of dissolved inorganic carbon (DIC), dissolved organic carbon (DOC), total dissolved nitrogen (TDN), nitrate (NO3), nitrite (NO2), ammonium (NH4), dissolved inorganic phosphorus (DIP), active chlorophyll-a (via extraction), and cell abundance of M. polykrikoides and A. monilatum. DIC samples were filtered through 0.2-micrometer (um) polycarbonate filters into 8-milliliter (mL) hungate tubes and refrigerated underwater until analysis on an Apollo SciTech AS-C3 analyzer coupled to a LI-COR LI-7000 infrared gas analyzer. DOC samples were filtered through 0.45 um polyethersulfone filters and frozen prior to analysis on a Shimadzu TOC-VCSN combustion analyzer. Nutrient samples were also filtered through 0.45 um polyethersulfone filters and frozen prior to analysis on a Lachat QuikChem 8000 automated ion analyzer (Lachat Instruments, Milwaukee, WI, USA); detection limits for NO3−, NH4+, and PO43- are 0.20, 0.36, and 0.16 micromolar (uM), respectively. Chlorophyll-a samples for extraction were filtered through 0.7 um glass fiber filters which were frozen prior to analysis following Arar and Collins (1997, EPA Method 445.0). Samples were extracted in the dark for 24 hours in 8 mL of a 45:45:10 dimethyl sulfoxide : acetone: distilled water solution with 1% diethylamine (Shoaf & Lium, 1976), and read on a 10 AU Turner Designs fluorometer before and after acidification to compute active chlorophyll-a.

Cell concentrations of M. polykrikoides (Marg) and A. monilatum (Alex) by qPCR were measured as described in Wolney et al. (2020). Briefly, 100 mL water samples were collected, and 25-100 mL were filtered onto 3 um Isopore membrane filters (Millipore Corp., Darmstadt, Germany), with the volume filtered for DNA extraction dependent on Dataflow-measured chlorophyll-a concentrations. Disposable filtration units were used to prevent cross contamination between samples. DNA was extracted from the filters using the Qiamp Fast Stool Mini Kit (QIAGEN Corp., Germantown, MD, USA) using the modified protocol as described in Wolney et al. (2020). DNA was amplified targeting Marg and Alex DNA using TaqMan qPCR assays designed in the Reece laboratory with York River Marg and Alex sequences included for assay design (Vandersea et al., 2017; Wolney et al., 2020). The cell concentrations of Marg and Alex cultures were determined by microscopy using a Sedgwick-Rafter counting cell chamber and DNA was extracted from a known number of cells. This material was used as positive control material and to generate standard curves by serially diluting the DNA to achieve a range of cell number equivalents.

Data represent means and standard errors (SE) at the five bloom and five non-bloom stations on each cruise. Dataflow values represent means and SE of all readings while sampling at each site; grab sample values represent the means and SE of three replicate samples.

Data represent means and standard errors (SE) at the five bloom and five non-bloom stations on each cruise. Dataflow values represent means and SE of all readings while sampling at each site; grab sample values represent the means and SE of three replicate samples.

Version History:

Version 1:
Date: 2021-06-22
Dataset contained only 2020 data.
BCO-DMO Processing:
- changed date format to YYYY-MM-DD;
- renamed fields.

Version 2:
Date: 2025-04-01
Dataset contains 2020-2021 data, including corrections/additions to the 2020 data.
BCO-DMO Processing:
- Imported original file "water_column_2020_2021.xlsx" into the BCO-DMO system.
- Marked "n.d." as a missing data value (missing data are empty/blank in the final CSV file).
- Converted Date column to YYYY-MM-DD format.
- Saved final file as "854194_v2_water_column.csv".

NSF Award Abstract:
Estuaries, coastal water bodies where rivers mix with ocean water, are hotspots for the processing of carbon and nutrients moving from land to the coastal ocean. Within estuaries land-based nutrient inputs can cause intense blooms of single-celled algae called phytoplankton, which can have significant impacts on the ecosystem. As blooms move down-estuary some of the phytoplankton material is buried on the bottom, and some is decomposed, resulting in low oxygen conditions (hypoxia), harmful to marine life, and production of carbon dioxide (CO2), the major greenhouse gas, which can exchange with the atmosphere. The remaining phytoplankton material can be exported to the ocean. The type and amount of carbon exported from the estuary depend both on its biological activity and physical factors such as fresh water discharge, temperature, and light availability. If phytoplankton production is greater than decomposition, the estuary will take up atmospheric CO2 and export phytoplankton carbon to the coastal ocean. On the other hand, if decomposition is greater than production the estuary will be a source of CO2 to the atmosphere and dissolved CO2 to the coastal ocean. The investigators expect that intense phytoplankton blooms will greatly amplify carbon exchanges with the atmosphere, coastal ocean, and bottom sediments. As intense phytoplankton blooms increase in the future due to increased nutrient inputs and temperature, low oxygen events may become more frequent with potential negative impacts on fisheries and increased export of carbon to the coastal ocean and atmosphere. This study will fill critical gaps identified by the Coastal Carbon Synthesis Program in knowledge of how microtidal estuaries transform and export C to the atmosphere, benthos, and coastal ocean. In addition, there will be a strong teaching and training component to this project, with support for graduate and undergraduate students. The graduate student will be partnered with secondary teachers to gain teaching experience and enrich the middle school educational programs. Summer undergraduate interns will be recruited for a summer program from Hampton University, a historically Black college. There will be public outreach through participation in existing programs at VIMS.

Estuaries serve as critical hotspots for the processing of carbon (C) as it transits from land to the coastal ocean. Recent attempts to synthesize what is known about sources and fates of C in estuaries have noted large data gaps; thus, the role of estuaries, especially those that are microtidal, as important sources of carbon dioxide (CO2) to the atmosphere and total organic carbon (TOC) and dissolved inorganic carbon (DIC) to the coastal ocean, or as a C sink in bottom sediments, remains uncertain. Intensive phytoplankton blooms are becoming increasingly frequent in many estuaries and are likely to have important and yet unknown impacts on the C cycle. The trophic status of an estuary will determine in large part the species of C exported to the atmosphere, bottom sediments, and coastal ocean. The overarching objective of this project is to identify the impacts of intense phytoplankton blooms on C speciation, net C fluxes and exchanges in the Lower York River Estuary (LYRE), a representative mesotrophic, microtidal mid-Atlantic estuary. Metabolic processes are hypothesized to be spatially and temporally dynamic, driving the speciation, abundance, and fates of C in the LYRE. High spatiotemporal resolution sampling in the LYRE will capture rates of C cycling under both baseline conditions throughout most of the year, and during periods when the estuary is perturbed by widespread and intense, but patchy, late summer phytoplankton blooms. The short-term effects of physical drivers (wind, temperature, salinity, fresh water discharge, nutrient and organic carbon loads) and biological drivers (metabolic rates, bacterial and phytoplankton abundances and composition) on C transformations, speciation, and exchanges will be assessed. Expected longer term variations in the C cycle due to anthropogenic and natural disturbances will be predicted through use of modeling. In addition, laboratory manipulations will examine the impacts of specific organisms dominating intensive phytoplankton blooms on benthic metabolism, processing of organic C by the microbial community, and C fluxes to the water column.