This Data Release makes available measurements of phytoplankton species composition, abundance and cell size made on samples collected in San Francisco Bay (CA) from January 2014 through December 2018. Whole water phytoplankton samples were collected at least monthly at fixed sampling stations along a 145-km transect where the variability of salinity, temperature, turbidity and nutrient concentrations reflected a broad range of environmental factors that regulate phytoplankton growth and abundance. A map and table of sampling locations are included in this Data Release. Immediately after samples were collected, they were preserved with acid Lugol’s solution. The samples were analyzed by BSA Environmental Services, Inc following the McNabb (1960) filter method. Following standard methods, at least 400 natural units (colonies, filaments, and unicells) were enumerated to the lowest possible taxonomic level from each sample. In 2014 and 2015, abundances were estimated by random field counts with at least 100 cells of the most numerous taxon counted. From 2016 onward, the 400 natural unit tally was met using two separate random field count efforts: (1) at least 100 natural units of organisms smaller than or equal to 5 μm were identified and enumerated; and (2) at least 300 natural units of organisms larger than 5 μm were identified and enumerated. The 2016 method was adopted to maximize detection of large but rare cells. For all data, cell volumes for each taxon were estimated with the formulas for solid geometric shapes that most closely matched the cell shape according to Hillebrand et al. (1999). Cell volume calculations were based on measurements of up to ten organisms for the most abundant taxa. The Biovolume (cubic microns per ml) of each taxon was computed as the product of abundance (cells per ml) and cell volume (cubic microns per cell). In order to assess replication of results, 10 duplicate samples were collected and analyzed in 2017 and are reported here. Hillebrand, H., Dürselen, C.-D., Kirschtel, D., Pollingher, U. and Zohary, T. 1999. Biovolume Calculation for Pelagic and Benthic Microalgae. Journal of Phycology, 35: 403–424. doi:10.1046/j.1529-8817.1999.3520403.x McNabb, C. D. 1960. Enumeration of freshwater phytoplankton concentrated on the membrane filter. Limnol. Oceanog., 5: 57-61.

This Data Release makes available measurements of phytoplankton species composition, abundance and cell size made on samples collected in San Francisco Bay (CA) from April 1992 through March 2014. Phytoplankton samples were collected at 31 stations along a 145-km transect where the variability of salinity, temperature, turbidity and nutrient concentrations reflected a broad range of environmental factors that regulate phytoplankton growth and abundance (station map on ScienceBase homepage). Whole water samples were preserved with acid Lugol’s solution, and 2 to 50 ml aliquots were settled in chambers for 6 to 24 hours (Utermöhl 1958). Phytoplankton cells were then counted and identified using a phase-contrast inverted microscope at 125x magnification, all cells greater than 30 μm diameter were enumerated. Cells smaller than 30 μm were counted at 1250x magnification; following the APHA (1989) strip count method, at least 100 cells of the most numerous taxon were counted. Cell volumes were estimated from measured linear dimensions and geometric formulas that varied with cell shapes. Phytoplankton samples representing 923 distinct date, station and depths were included. The 16,442 entries in this dataset include 609 different taxa within 11 functional groups. Diatoms dominated the total biovolume contributed by each functional group (77%) followed by dinoflagellates (14%) and cryptophytes (4.5%). The top 5 species contributing to the summed biovolume in all samples were: Thalassiosira punctigera, Chaetoceros socialis, Ditylum brightwellii, Thalassiosira rotula and Noctiluca scintillans. By frequency of occurrence, the top 5 species were: Teleaulax amphioxeia, Nannochloropsis spp., Plagioselmis prolonga var. nordica, Skeletonema costatum and Thalassiosira eccentrica. APHA. (1989). Standard methods for the examination of water and wastewater, 17th edn. American Public Health Association, Washington, DC Utermöhl H. (1958). Zur Vervollkommnung der quantitativen Phytoplankton-Methodik. Mitt Int Verh Theor Angew Limnol 9:1-38

This Data Release makes available measurements of phytoplankton species composition, abundance and cell size made on samples collected in San Francisco Bay (CA) from April 1992 through March 2014. Phytoplankton samples were collected at 31 stations along a 145-km transect where the variability of salinity, temperature, turbidity and nutrient concentrations reflected a broad range of environmental factors that regulate phytoplankton growth and abundance (station map on ScienceBase homepage). Whole water samples were preserved with acid Lugol’s solution, and 2 to 50 ml aliquots were settled in chambers for 6 to 24 hours (Utermöhl 1958). Phytoplankton cells were then counted and identified using a phase-contrast inverted microscope at 125x magnification, all cells greater than 30 μm diameter were enumerated. Cells smaller than 30 μm were counted at 1250x magnification; following the APHA (1989) strip count method, at least 100 cells of the most numerous taxon were counted. Cell volumes were estimated from measured linear dimensions and geometric formulas that varied with cell shapes. Phytoplankton samples representing 923 distinct date, station and depths were included. The 16,442 entries in this dataset include 609 different taxa within 11 functional groups. Diatoms dominated the total biovolume contributed by each functional group (77%) followed by dinoflagellates (14%) and cryptophytes (4.5%). The top 5 species contributing to the summed biovolume in all samples were: Thalassiosira punctigera, Chaetoceros socialis, Ditylum brightwellii, Thalassiosira rotula and Noctiluca scintillans. By frequency of occurrence, the top 5 species were: Teleaulax amphioxeia, Nannochloropsis spp., Plagioselmis prolonga var. nordica, Skeletonema costatum and Thalassiosira eccentrica. APHA. (1989). Standard methods for the examination of water and wastewater, 17th edn. American Public Health Association, Washington, DC Utermöhl H. (1958). Zur Vervollkommnung der quantitativen Phytoplankton-Methodik. Mitt Int Verh Theor Angew Limnol 9:1-38

This dataset contains taxonomy, density (cells/mL), and biovolume (μm3/mL) data for phytoplankton sampled across the Sacramento San Joaquin River Delta and San Francisco Bay (Bay-Delta) beginning in 2016. Whole water phytoplankton samples were collected intermittently during special projects and during routine visits to service continuous monitoring stations. Samples were preserved with Lugol’s iodine solution (2-5 %) immediately after collection and stored in a cool, dark environment until analysis. Preserved whole water samples are sent to BSA Environmental Services (BSA) in Beachwood, Ohio for microscopic identification and enumeration. A Leica DMLB compound microscope is used for enumerating filtered phytoplankton samples. The magnification used (100X, 200X, 400X, 630X, 1000X) depends upon the size of dominant taxa and presence of particulates. Samples are analyzed at multiple magnifications to ensure enumeration and identification of taxa which vary over several orders of magnitude in size. If a sample is dominated by cells or natural units below 10-20 µm, or when cells are fragile and difficult to identify, most counting is completed at 630X. For enumeration, phytoplankton cells are concentrated onto a filter (McNabb 1960, Standard Methods 2012) and then counted. The abundance of common taxa is estimated by random field counts (Lund 1958). At least 400 natural units (colonies, filaments, unicells) or a minimum of 50 fields are enumerated to the lowest possible taxonomic level from each sample. Additionally, an entire strip of the filter is counted at 630X and half of the filter is counted at 400X for any organisms missed during the random fields count to further ensure complete species detection. The density of cells per milliliter is calculated from the tally of cells counted, number of fields counted, and subsampling volumes. Note that density and biovolume calculations are both based on cell count, not natural unit count. Cell biovolumes of all identified phytoplankton taxa are also calculated. Biovolumes per cell are estimated using formulae for solid geometric shapes that most closely match the cell shape (Hillebrand et al., 1999). Biovolume calculations are based on measurements of 10 organisms per taxon for each sample where possible. The total biovolume of each taxa is reported as cubic micrometers per milliliter. Beginning in 2021, additional columns were added to the reports from BSA, including tally of natural units and measurements that are used in calculating biovolume (all formulas can be found in Hillebrand et al., 1999). These fields include: average length, width and depth of cells, and biovolume factor, and additionally average measurements e and f used to calculate the biovolume of gomphonemoid shaped organisms and average cymbelloid measurement used to calculate the biovolume for cymbelloid shaped organisms. In addition to phytoplankton data reported by BSA, spatial attributes are also included in this dataset. These attributes include spatial information describing the location of samples (collected at stations that can be found at the USGS water Natioansl Water Information System; U.S. Geological Survey, 2023) using across a range of nested descriptions from fine to broad resolution (e.g. Delta region, river, slough, etc.) and are intended to aid data aggregation and integration. For additional spatial analyses, the USGS has created a series of Bay-Delta shapefiles which have been split into multiple polygons defining 0.1, 1, and 5 river-mile segments. These Polygon IDs are assigned using the Python programming language’s ‘geopandas’ (Jordahl, 2020) package. Polygon IDs of each river-mile resolution corresponding to each sampling location are also included in these data to aid data aggregation efforts. American Public Health Association, 2012. Standard Methods For the Examination of Water and Wastewater, 22nd Edition. APHA, Washington, DC. ISBN 978-087553-013-0. Hillebrand, H., C.D. Durselen, D.

This dataset contains taxonomy, density (cells/mL), and biovolume (μm3/mL) data for phytoplankton sampled across the Sacramento San Joaquin River Delta and San Francisco Bay (Bay-Delta) beginning in 2016. Whole water phytoplankton samples were collected intermittently during special projects and during routine visits to service continuous monitoring stations. Samples were preserved with Lugol’s iodine solution (2-5 %) immediately after collection and stored in a cool, dark environment until analysis. Preserved whole water samples are sent to BSA Environmental Services (BSA) in Beachwood, Ohio for microscopic identification and enumeration. A Leica DMLB compound microscope is used for enumerating filtered phytoplankton samples. The magnification used (100X, 200X, 400X, 630X, 1000X) depends upon the size of dominant taxa and presence of particulates. Samples are analyzed at multiple magnifications to ensure enumeration and identification of taxa which vary over several orders of magnitude in size. If a sample is dominated by cells or natural units below 10-20 µm, or when cells are fragile and difficult to identify, most counting is completed at 630X. For enumeration, phytoplankton cells are concentrated onto a filter (McNabb 1960, Standard Methods 2012) and then counted. The abundance of common taxa is estimated by random field counts (Lund 1958). At least 400 natural units (colonies, filaments, unicells) or a minimum of 50 fields are enumerated to the lowest possible taxonomic level from each sample. Additionally, an entire strip of the filter is counted at 630X and half of the filter is counted at 400X for any organisms missed during the random fields count to further ensure complete species detection. The density of cells per milliliter is calculated from the tally of cells counted, number of fields counted, and subsampling volumes. Note that density and biovolume calculations are both based on cell count, not natural unit count. Cell biovolumes of all identified phytoplankton taxa are also calculated. Biovolumes per cell are estimated using formulae for solid geometric shapes that most closely match the cell shape (Hillebrand et al., 1999). Biovolume calculations are based on measurements of 10 organisms per taxon for each sample where possible. The total biovolume of each taxa is reported as cubic micrometers per milliliter. Beginning in 2021, additional columns were added to the reports from BSA, including tally of natural units and measurements that are used in calculating biovolume (all formulas can be found in Hillebrand et al., 1999). These fields include: average length, width and depth of cells, and biovolume factor, and additionally average measurements e and f used to calculate the biovolume of gomphonemoid shaped organisms and average cymbelloid measurement used to calculate the biovolume for cymbelloid shaped organisms. In addition to phytoplankton data reported by BSA, spatial attributes are also included in this dataset. These attributes include spatial information describing the location of samples (collected at stations that can be found at the USGS water Natioansl Water Information System; U.S. Geological Survey, 2023) using across a range of nested descriptions from fine to broad resolution (e.g. Delta region, river, slough, etc.) and are intended to aid data aggregation and integration. For additional spatial analyses, the USGS has created a series of Bay-Delta shapefiles which have been split into multiple polygons defining 0.1, 1, and 5 river-mile segments. These Polygon IDs are assigned using the Python programming language’s ‘geopandas’ (Jordahl, 2020) package. Polygon IDs of each river-mile resolution corresponding to each sampling location are also included in these data to aid data aggregation efforts. American Public Health Association, 2012. Standard Methods For the Examination of Water and Wastewater, 22nd Edition. APHA, Washington, DC. ISBN 978-087553-013-0. Hillebrand, H., C.D. Durselen, D.

Surface water quality, water isotope, and phytoplankton enumeration data were collected to evaluate the impact of an Emergency Drought Barrier (EDB) in False River in the Sacramento-San Joaquin Delta. Data were collected on six days during 2022 and 2023 (June 7, June 21, July 27, August 9, October 12, November 30, 2022, and February 21, 2023). Sampling occurred in Franks Tract, Mildred Island, the San Joaquin River, and various sloughs and cuts connecting these water bodies. High-resolution boat-based mapping data and discrete water samples were collected and analyzed for: nitrate, nitrite, ammonium, soluble reactive phosphorus (orthophosphate), total dissolved nitrogen, total dissolved phosphorus, total phosphorus, total particulate carbon and nitrogen, water isotopes (2H and 18O), dissolved organic carbon, chlorophyll a, and phytoplankton enumeration (microscopy).

Surface water quality, water isotope, and phytoplankton enumeration data were collected to evaluate the impact of an Emergency Drought Barrier (EDB) in False River in the Sacramento-San Joaquin Delta. Data were collected on six days during 2022 and 2023 (June 7, June 21, July 27, August 9, October 12, November 30, 2022, and February 21, 2023). Sampling occurred in Franks Tract, Mildred Island, the San Joaquin River, and various sloughs and cuts connecting these water bodies. High-resolution boat-based mapping data and discrete water samples were collected and analyzed for: nitrate, nitrite, ammonium, soluble reactive phosphorus (orthophosphate), total dissolved nitrogen, total dissolved phosphorus, total phosphorus, total particulate carbon and nitrogen, water isotopes (2H and 18O), dissolved organic carbon, chlorophyll a, and phytoplankton enumeration (microscopy).

The dataset documents the spatial and temporal variability of nutrients and related water quality parameters at high spatial resolution in the San Francisco Bay of California, USA in 2021 and 2022. The dataset includes nitrate, temperature, conductivity, dissolved oxygen, and chlorophyll as well as information about phytoplankton community composition. Data-collection cruises were conducted under different environmental/flow conditions. Version history: On 3/15/24, the provisional data files hosted on this webpage were removed, and replaced with updated finalized files.

The dataset documents the spatial and temporal variability of nutrients and related water quality parameters at high spatial resolution in the San Francisco Bay of California, USA in 2021 and 2022. The dataset includes nitrate, temperature, conductivity, dissolved oxygen, and chlorophyll as well as information about phytoplankton community composition. Data-collection cruises were conducted under different environmental/flow conditions. Version history: On 3/15/24, the provisional data files hosted on this webpage were removed, and replaced with updated finalized files.

Changes in ocean conditions such as chemical and thermal shifts are habitat pressures on marine organisms. As the basis of the marine food web, microorganisms such as bacteria and phytoplankton are responsible for important biogeochemical processes, such as nutrient cycling, and the primary production. They are also part of the environment surrounding aquatic organisms such as marine mammals, and serve as a source of both beneficial and harmful microbes associated with larger organisms. Due to their small size and direct physiological interactions with seawater, these microorganisms can rapidly respond to environmental changes, resulting in shifts in community composition and in relative abundances of community members. Shifts at these trophic levels can cause a ripple effect in the structure and function of the ecosystem for coastal and offshore species. Most assessments of biological responses to ocean acidification (OA) have been performed by controlled conditions, and there have been few opportunities to evaluate real-world relationships between biology and OA. This project leverages the sampling and chemical analyses conducted during the northern leg of the 2016 West Coast Ocean Acidification Cruise led by the Pacific Marine Environmental Laboratory (PMEL) to document ocean chemistry in the California Current during a period of likely coastal upwelling and greater ocean acidification. During that cruise, water from the same water samples that were used for chemical measurements by PMEL were preserved & analyzed for cellular abundances of bacterioplankton and eukaryotic picoplankton.