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Water Quality of San Francisco Bay
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A Glossary of Terms and Acronyms

Attenuation Coefficient: A measure of the rate at which light disappears with depth in Bay waters; large attenuation coefficients occur in turbid waters, and small attenuation coefficients occur in clear water
Biomass: The quantity of a living community or population, such as the phytoplankton; for example, phytoplankton biomass is often measured as chlorophyll concentration
Calibration: The process of converting electrical signals from instruments into measured quantities that describe water quality. For example, the relative concentration of dissolved oxygen can be measured with an electrode. These relative concentrations are then converted into real concentrations by making true measurements of oxygen concentration in a set of water samples, and then relating these to the concentrations estimated with the electrode
Chlorophyll: The green pigment of plants, including phytoplankton, which absorbs sunlight energy and converts it to chemical energy used in the process of photosynthesis. We report chlorophyll a in units of milligrams per cubic meter (i.e., the weight of chlorophyll contained in each cubic meter of water). Milligrams per cubic meter is equivalent to micrograms per liter.
Conductivity: A measure of the resistance of water to electrical flow; this resistance is a direct measure of the salinity of water, and it can be measured accurately with a conductivity sensor
CTD: An instrument package that measures Conductivity, Temperature, and Depth as the package is lowered through the water. Additional sensors for measuring oxygen concentration, chlorophyll, suspended solids, and light penetration are integrated with the CTD instrument-computer package.
Delta Outflow (Index): An estimate of the flow of freshwater from the Sacramento-San Joaquin River Delta into San Francisco Bay; units of measurement are cubic meters per second
Dissolved Oxygen: The concentration of oxygen dissolved in Bay waters; this is often measured in units of milligrams per liter, or as percent saturation (the measured concentration divided by the concentration that would occur if dissolved oxygen was determined only by exchanges with the atmosphere -- i.e., in the absence of biological processes of oxygen consumption and production)
DO: Dissolved Oxygen
Fluorometer: An instrument that measures the relative concentration of chlorophyll, by sending a beam of blue light into the water and measuring the production of red light (fluorescence) by the chlorophyll contained in phytoplankton cells; chlorophyll concentration is proportional to fluorescence
Hypersaline:A condition in which the salinity of the Bay becomes higher than the salinity of the ocean; this occurs during prolonged periods of drought (such as in 1977), when freshwater inputs are smaller than losses of water to evaporation
Inorganic:An inorganic compound refers to chemical compounds that do not contain carbon (C) e.g. nitrate (NO3-).
Light Penetration: A general term describing the absorbance of sunlight by Bay waters; usually, sunlight penetrates only a few meters below the water surface because waters of San Francisco Bay have high concentrations of suspended solids that absorb and reflect light (they are a source of turbidity). Low light penetration results in a high attenuation coefficient.
Limiting Factor: A parameter (e.g. light, temperature, nutrients) that controls the rate of a specific process. For example in SF Bay, light is frequently the limiting factor controlling phytoplankton production and growth.
Longitudinal Axis: The spatial dimension of an estuary, such as San Francisco Bay, that extends from the landward to the seaward domains; the USGS makes water quality measurements along the longitudinal axis of the Bay-Delta, from the Sacramento River, to the Central Bay, and into the South Bay
Longitudinal Profile: The distribution of a constituent, such as salinity or dissolved oxygen, along the longitudinal axis of the Bay-Delta
OBS: Optical Backscatter Sensor
Nitrogen: Nitrogen (N) is a critical nutrient for phytoplankton growth. In marine ecosystems the most abundant form of inorganic N available for organisms is typically nitrate, followed by ammonium. We measure nitrate plus nitrite (NO3- + NO2-) and ammonium (NH4+) in micromoles N per liter (molecular weight of N per liter of water). Typically, in marine ecosystems nitrogen is the limiting nutrient on phytoplankton production and growth. Consequently, nitrogen dynamics in the estuary are crucial to our understanding of phytoplankton dynamics.
Nutrients: Chemical elements or compounds necessary for or contributing to an organismís metabolism, growth or function. Nutrients provide energy and are used as molecular building blocks in the biosynthesis of cellular structures. Nitrogen (N) and phosphorous (P) are critical nutrients for phytoplankton, thus their growth can be limited by the availability of these nutrients when light and temperature are adequate.
Optical Backscatter Sensor: An instrument that measures the abundance of small particles suspended in water; it sends a beam of infrared light into the water, and measures the amount of light reflected off the particles - higher reflected light means higher concentrations of suspended solids. Used used to determine suspended sediment concentraion.
Organic Material: An organic compound refers to a large class of chemical compounds that contain carbon (C).
Oxygen Electrode: A sensor that produces an electrical current that is proportional to the amount of oxygen dissolved in water; used to measure dissolved oxygen
Phosphorous: Phosphorous (P) is an essential nutrient for all living organisms. Although it is not needed in as great abundances as oxygen, carbon, nitrogen or hydrogen, phosphorus is one of the major nutrients known to limit phytoplankton production in certain fresh and marine ecosystems. We measure phosphate (PO4-3) in micromoles P per liter (molecular weight of P per liter of water).
Photosynthesis: The set of reactions in plant cells (including phytoplankton) that use sunlight energy to convert carbon dioxide into food (carbohydrates) and oxygen
Phytoplankton: The diverse community of microscopic suspended algae (single-celled plants); in San Francisco Bay this community represents the largest component of living biomass; phytoplankton photosynthesis is a source of oxygen and phytoplankton biomass is an important food resource for the small animals that live in the Bay
Phytoplankton Bloom: Period of explosive population growth of the phytoplankton community; a recurrent event that occurs every spring in South San Francisco Bay
Primary Production: The process of producing organic compounds from carbon dioxide (CO2), principally through photosynthesis. The organisms responsible for this process are called primary producers and make up the base of most food chains e.g. phytoplankton are primary producers.
Quantum Sensor: A sensor that measures the instantaneous quantity of sunlight (number of light photons) hitting a surface, such as the surface of the Bay ; used to measure light penetration and the attenuation coefficient, by measuring the quantity of sunlight at different depths as it is lowered into the water
Respiration: Metabolic processes of organisms or communities that consume oxygen
Salinity: A measure of the salt content of water, which can be estimated accurately from measures of conductivity and temperature; salinity is measured in practical salinity units (psu), and the salinity of river water is often about 0.1 psu while the salinity of coastal Pacific Ocean water is about 33-34 psu; measures of salinity in the Bay tell the relative proportions of river water and ocean water at different locations
Salinity Stratification: Condition where the salinity of the surface waters is lower than the salinity of deeper waters; this condition acts to slow the rate of mixing between surface and bottom waters
Silica: Silica (Si) is an important nutrient particularly for diatoms. Diatoms are one of the most common types of phytoplankton and use silicate to cover their cells and form their cell wall called a frustule. Dissolved silica (DSi) is measured in micromoles Si per liter (molecular weight of Si per liter of water).
Suspended Sediments: the small mineral (mostly clay) particles suspended in Bay waters
Suspended Solids: The small suspended particles contained in a water sample; in San Francisco Bay, most suspended solids are sediment particles, so 'suspended solids' and 'suspended sediments' are nearly synonymous; the concentration of suspended solids is measured with an OBS, in units of milligrams per liter (i.e., the weight of all solids contained in each liter of water). On this website, the terms Total Suspended Solids (TSS) and Suspended Particulate Matter (SPM) are used interchangeably.
Temperature Gradient: A pattern in which water temperature varies spatially, such as along the longitudinal axis of the Bay-Delta or in a vertical profile
Trophic Level: Position that an organism occupies in a food chain, determined by the number of energy transfer steps to that level e.g. primary producer, primary consumer, secondary consumer, tertiary consumer.
TSS: Total suspended solids contained in a water sample
Turbidity: A general term describing the clarity of water; turbidity is caused by dissolved colored substances in water and by the suspended particles that absorb and reflect sunlight
Vertical Profile: The distribution of a constituent, such as salinity or dissolved oxygen, from the surface of the water to the seafloor

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