Scientific Research

In the spring of 2020, SacSewer staff studied how environmental conditions can affect phytoplankton living in Delta river channels. Many factors can influence the amount of phytoplankton occurring in Sacramento–San Joaquin River Delta, including nutrient concentrations, water clarity, water flow rates, and grazing by clams and zooplankton.

One method to investigate the relative importance of these factors is by measuring how phytoplankton respond to a dramatic change in environmental conditions, such as nutrient concentrations, water clarity, or flow rate. The United States Bureau of Reclamation owns and operates the Delta Cross Channel Gates, which allows water from the Sacramento River to flow through a large constructed channel into the Mokelumne River and South Delta.

SacSewer conducted an experiment measuring phytoplankton abundance and water quality parameters before, during, and after the Delta Cross Channel Gates were closed for four consecutive days. This experiment tested how reduced river flow rates (or increased water residence time) can affect phytoplankton living in Delta river channels.

We used a kayak to collect samples downstream of the Delta Cross Channel gates and at other selected locations in the northeast Delta for comparison, including the Sacramento River, Snodgrass Slough, Georgiana Slough, North Fork Mokelumne River, and South Fork Mokelumne River.

Our samples are currently being analyzed to determine if phytoplankton biomass, phytoplankton taxonomic composition, or nutrient concentrations changed during the experimental period. Findings from this study will inform water operations, shallow water habitat restorations, and nutrient management programs, by helping to identify the combination of environmental factors that regulate phytoplankton abundance in the Delta.

SacSewer staff and collaborators are studying the potential environmental effects of a change in nutrient loading to the Sacramento River in September 2019, which resulted from an effluent hold at the EchoWater Resource Recovery Facility.

This hold, which was planned as part of the EchoWater Project construction process, prevented treated effluent from entering the Sacramento River for 48 hours. Given the relatively high river flows in 2019, the hold created a zone of effluent river water over 20 miles long in the lower Sacramento River.

Scientists used a small fleet of four research boats to collect water samples in all these river regions before and during the effluent hold.

Sampling included

• Hydrodynamic (Water Flow) Modeling (Resource Management Associates)
• High Frequency Water Quality Boat Mapping (US Geological Survey)
• Water Quality Sampling and Laboratory Analysis (SacSewer)

Data and hydrodynamic modeling will be used to evaluate how phytoplankton (small aquatic plants) and zooplankton (tiny aquatic animals) responded to changes in physical and biological factors during the study. These factors include differences in nutrient loads and forms, water residence times, light levels, turbidity, and grazing by zooplankton and clams. It is important to understand the conditions regulating phytoplankton and zooplankton growth in the watershed because these organisms are a primary food source to the Delta’s ecosystem.

This study is jointly funded by the Delta Regional Monitoring Program, State Water Contractors, and US Bureau of Reclamation, with in-kind contributions from SacSewer and the US Geological Survey.

Resources

Sacramento River Nutrient Change Study. 2023. A report to the Delta Regional Monitoring Program, State Water Contractors, and Bureau of Reclamation. By Regional San – Lisa C. Thompson, Timothy D. Mussen, Michael Cook, Justin Nordin, James Noss, Ursula Bigler, Srividhya Ramamoorthy; Environmental Sciences Associates/Applied Marine Sciences, Inc. – Gry Mine Berg, Sara Driscoll, Clifton Herrmann; Estuary and Ocean Science Center, San Francisco State University – Wim Kimmerer, Toni Ignoffo; U.S. Geological Survey – Tamara Kraus, Joseph Fackrell, Brian Bergamaschi; Resource Management Associates – Marianne Guerin, Richard Rachiele

RMA Flow and Transport Model Files

Some previous research on the Sacramento River found declining phytoplankton concentrations at downstream locations. The cause for the observed phytoplankton decline is not easily discernible because the losses do not appear to be driven by effluent-derived nutrient concentrations.

While phytoplankton-consuming organisms, such as clams and zooplankton, are present in the river, they are not abundant enough to fully explain the declines. In 2016, SacSewer staff and consultants conducted scientific and hydraulic modeling studies to evaluate the factors that might potentially limit phytoplankton growth within the Sacramento River, both upstream and downstream of the EchoWater Resource Recovery Facility.

These studies consisted of the following:

• Surveyed the river between Knights Landing and Isleton to estimate the abundance and diversity of phytoplankton, zooplankton, and clams along the river; changes in phytoplankton growth rates; differences in water chemistry; and other environmental factors
• Modeled river flow to identify, for each survey location, the proportion of flow arising from different upstream sources
• Conducted a controlled mesocosm experiment to determine the relative importance of clam grazing, zooplankton grazing, river-water sources, and nutrient concentrations on phytoplankton growth
• RMA Technical Memorandum – Hydraulic Modeling to Estimate Proportional Water Sources to the Lower Sacramento River
• RMA Particle Tracking Modeling Report (please note that while this document is marked “draft”, it is the final version of the project deliverable)

Results

Our study found that phytoplankton biomass was regulated by multiple factors in the lower Sacramento River, including dilution, light limitation, respiration, and clam and zooplankton grazing, with the importance of individual factors differing by location.

This research is now published in the scientific journals San Francisco Estuary and Watershed Science and Aquatic Biology. Both articles are available as “open source”:

Investigating Factors Contributing to Phytoplankton Biomass Declines in the Lower Sacramento River. 2023. Mussen, T.D., Driscoll, S., Cook, M.E., Nordin, J.D., Guerin, M., Rachiele, R., Smith, D.J., Berg, G.M., Thompson, L.C. San Francisco Estuary and Watershed Science, 21(1). http://dx.doi.org/10.15447/sfews.2023v21iss1art3 Retrieved from https://escholarship.org/uc/item/48×1287p

2024. Mussen, T.D., Berg, G.M., Driscoll. S., Nordin, J.D., Thompson, L.C. Clams on stilts: a phytoplankton bioassay investigating effects of wastewater effluent amendments and Corbicula fluminea grazing. Aquatic Biology 33:13-31. https://doi.org/10.3354/ab00764

We supported a large-scale research study by USGS and university scientists to investigate the effects of SacSewer discharge of treated wastewater on phytoplankton health in the Sacramento River, using a presence and absence study.

This study addressed concerns about reduced phytoplankton abundance and potential changes in relative phytoplankton species abundance reported in the Lower Sacramento River.

SacSewer temporarily diverted its discharge from the river into storage basins, creating a six-mile wastewater-free parcel of water in the river. Researchers traveled in boats along the river for five days, sampling water with and without wastewater.

Results

Results indicate that phytoplankton biomass declined in both the presence and absence of wastewater over time, suggesting that a factor other than wastewater is leading to the decline in phytoplankton biomass.

Diatoms, a preferred food source, comprised the bulk of phytoplankton in the presence and absence of diffused wastewater effluent. This suggests that wastewater effluent does not cause a rapid change in phytoplankton species composition in the Sacramento River, from preferred to non-preferred species.

This research is now published in the scientific journal Limnology and Oceanography and is available “open source”:

A river-scale Lagrangian experiment examining controls on phytoplankton dynamics in the presence and absence of treated wastewater effluent high in ammonium. 2017. Tamara E. C. Kraus, Kurt D. Carpenter, Brian A. Bergamaschi, Alexander E. Parker, Elizabeth B. Stumpner, Bryan D. Downing, Nicole M. Travis, Frances P. Wilkerson, Carol Kendall, Timothy D. Mussen. Limnology and Oceanography. Volume 62, Issue 3, Pages 1234–1253.

The nutrient ammonia in the Sacramento River is derived from multiple sources, including effluent from the EchoWater Resource Recovery Facility. Ammonia may be used by phytoplankton for growth, but some studies have suggested that excessive concentrations of it may inhibit phytoplankton growth.

We supported a field and laboratory study by UC Santa Cruz on the health and productivity of phytoplankton, the base of the Delta food web, related to environmental factors in the Sacramento River and Delta. The project is named the “Bad Suisun” study because previous field observations determined that there is reduced phytoplankton growth in Suisun Bay.

Results

Results of the field study indicate that phytoplankton are commonly stressed in Suisun Bay and occasionally stressed in other regions of the watershed, but this stress is largely related to factors other than ammonia. The laboratory results suggest that different phytoplankton species responded differently to the various treatments of nutrients and light levels.

However, at ammonia concentrations present in the environment, the growth rate of phytoplankton would not be inhibited.  Furthermore, while typical ammonia concentrations in Suisun Bay did not inhibit growth of two diatom phytoplankton species isolated from the Bay, their growth responded positively to increased light levels in the range likely to be present in the environment.

The laboratory research is now published in the scientific journals Journal of Phycology and Aquatic Biology and is available “open source”:

Variation in growth rate, carbon assimilation, and photosynthetic efficiency in response to nitrogen source and concentration in phytoplankton isolated from upper San Francisco Bay. 2017. Gry Mine Berg, Sara Driscoll, Kendra Hayashi, Melissa Ross, Raphael Kudela. Journal of Phycology. Volume 53, Issue 3, Pages 664-679.

Effects of nitrogen source, concentration, and irradiance on growth rates of two diatoms endemic to northern San Francisco Bay. 2019. Gry Mine Berg, Sara Driscoll, Kendra Hayashi, Raphael Kudela. Aquatic Biology. Volume 28, Pages 33-43.

We investigated the presence, distribution, and abundance of invasive clams in the Sacramento River between Sacramento and Isleton in 2013 and 2014.

Invasive clams graze on phytoplankton and compete for food with native Delta organisms. Clam and zooplankton grazing are known to limit phytoplankton abundance in the Low Salinity Zone (LSZ) of the Bay-Delta system (near Suisun Bay, between Martinez and Pittsburg). In the LSZ, clams and microzooplankton can consume phytoplankton faster than it is produced, and at some locations in the Sacramento River clams can filter approximately 50 percent of the river’s water per day.

Results

Results show that non-native clams (Corbicula fluminea) were present at all 11 stations. A total of approximately 18,000 clams were collected each year, with approximately 315 clams per 32-yard trawl. Lower clam abundance was observed downstream of the treatment plant’s discharge; this may be related to the lower phytoplankton biomass observed in that section of the river (see river survey).

This research is now published in the scientific journal Limnology and Oceanography and is available “open source”:

A river-scale Lagrangian experiment examining controls on phytoplankton dynamics in the presence and absence of treated wastewater effluent high in ammonium. 2017. Tamara E. C. Kraus, Kurt D. Carpenter, Brian A. Bergamaschi, Alexander E. Parker, Elizabeth B. Stumpner, Bryan D. Downing, Nicole M. Travis, Frances P. Wilkerson, Carol Kendall, Timothy D. Mussen. Limnology and Oceanography. Volume 62, Issue 3, Pages 1234–1253.