The Mooring Report  •   February 2016
Snapshots of San Francisco Bay’s ecosystem nutrition

Hot off the Press

The Mooring Report is the new monthly e-newsletter from San Francisco Estuary Institute’s Nutrients Team. It directly links to a web article containing interactive versions of the graphics you receive in the email and preliminary analyses of some of our favorite discoveries. We wish to take this opportunity to update you on our progress and solicit your feedback. Please sign up to receive future editions of The Mooring Report.

The Nutrients Team at SFEI is striving to unravel the effects of human-caused nutrient increases on the complex ecosystem health of San Francisco Bay. We’re monitoring the heartbeat of the bay–and we want to share our discoveries with you. Along with our many collaborators, we have been very busy expanding our Lower South Bay moored sensor network, analyzing San Francisco Bay-wide water quality data, building a 3-D hydrodynamic water quality model, collecting discrete samples for algal toxins, and much more! Nutrient concentrations are a big deal in estuaries, especially urbanized estuaries. Nutrients help control life across all links of the food chain: too little nutrition and nothing grows, too much and there can be large algae blooms, concomitant dissolved oxygen decreases when the algae decay, and even fish die-offs.

Emily Novick and Rusty Holleman prep sensors for vertical profiling of Alviso Slough

El Niño has arrived!
Can we see it in our data? (Hint: we can!)

In this first issue, we’d like to show off the extent of our Lower South Bay (LSB) moored sensor network and highlight some of the most salient effects of El Niño on LSB water quality. Water quality is affected by quite a few things in estuaries, from semidiurnal tides to anthropogenic inputs and exports to decadal cycles. Teasing apart the various influences, investigating their effects, and communicating this information to various stakeholders is what drives the Nutrients Team.

Where are our sensors?

Each monitoring location in our sensor network was carefully selected in order to capture a unique influence or set of influences. Our sensors lie along the deep channel of the bay as well as in multiple shallower creeks and sloughs. SFEI’s Lower South Bay sensors are situated at the following sites:
Click on image above to view interactive map

El Niño has arrived!

We are already observing interesting phenomena in Lower South Bay. However, the full effects of El Niño won’t be apparent until after the Spring at the earliest (when higher-than-normal freshwater inputs from snowmelt will drive additional changes to the bay’s biogeochemistry) and must be compared to decades of data for precise attribution. Take a look at the following image of salinity at a subset of our moored sensor sites. The sites are arranged in this figure along a gradient of freshwater influence, from least (top) to greatest (bottom). The more frequent vertical striations represent tidal influences: at low tide, the ocean has less influence on each site, so they all become somewhat fresher (that is, lower salinity or bluer on this scale); at high tide, the ocean has the greatest influence, resulting in saltier water. Notice how much fresher each site gets as the Winter rains continue to deliver more and more freshwater throughout December and January.
SMB = San Mateo Bridge; DMB = Dumbarton Bridge; NWK = Newark Slough; COY= Coyote Creek
Click on the graph to view interactive version.
Of course, we’re interested in much more than just the mixing of fresh and salty water. At our Dumbarton Bridge near-surface sensor, we see that the large, sporadic freshening due to rain events (for example, examine the salinity record circa Dec 23) brings about other changes in water quality. It appears that the dips in salinity bring about temporary increases in both fluorescent dissolved inorganic matter (FDOM, reported in relative fluorescence units) and chlorophyll-a fluorescence (also relative fluorescence units).
Salinity, fluorescent dissolved organic matter (in relative fluorescence units), chlorophyll-a pigment fluorescence (also relative fluorescence units), and depth at Dumbarton Bridge. Note the dips in salinity and contemporaneous peaks in FDOM and chlorophyll fluorescence, corresponding to rain events on Dec 21-24, Jan 5-6, and Jan 17-19. Click on the graph to view interactive version.
Note that twice-daily (or semidiurnal) fluctuations occur in all parameters, mirroring the tides (see the depth record). We’ll discuss tidal variability much more in future editions of The Mooring Report. FDOM and chlorophyll are important because they represent the abundance of living (or once-living) material flowing past our sensors. We’ll keep a close eye on these signals and many others to see how they change as El Niño progresses and the (likely) Spring phytoplankton bloom arrives.

EnViz: SFEI’s latest tool for visualizing water quality sensor data

Lastly, we’re continually updating our high frequency water quality data visualization tool, EnViz, both with the latest data and with new features to make it more user friendly. Visit EnViz in order to examine the above time-series and datasets including many water quality parameters, from temperature and conductivity to chlorophyll fluorescence and dissolved oxygen, across the Bay-Delta region.

Let us know if you find any interesting features in the data; we’d love to hear from you. What other types of figures would you like to see? What other analyses should we consider? What interesting features do you see in the dataset? Contact info is at the bottom of this email as is a link to additional San Francisco Bay water quality datasets.
Thanks for reading!

The Nutrients Team
San Francisco Estuary Institute

*Note: data have gone through a preliminary QC process but should not be published in their current format. 
Email The Mooring Report’s editor, Phil Bresnahan, with any questions and comments.
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