DOI: 10.5066/p97zbplh
title: Phytoplankton Species Composition and Abundance in the Sacramento-San Joaquin River Delta: Microscopic Enumeration of USGS Samples, beginning in 2016 (ver. 1.1, December 2023)

description: 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. Kirschtel, U. Pollingher, and T. Zohary. 1999. Biovolume calculation for pelagic and benthic microalgae. Journal of Phycology 35:403–424, https://doi.org/10.1046/j.1529-8817.1999.3520403.x. Jordahl, K. 2020. GeoPandas: Python tools for geographic data. https://doi.org/10.5281/zenodo.3946761. Lund, J.W.G., Kipling, C. & Le Cren, E.D. 1958. The inverted microscope method of estimating algal numbers and the statistical basis of estimations by counting. Hydrobiologia 11: 143–170. https://doi.org/10.1007/BF00007865. McNabb, C.D. 1960. Enumeration of Freshwater Phytoplankton Concentrated on the Membrane Filter. Limnology and Oceanography. 5(1): 57-61. https://doi.org/10.4319/lo.1960.5.1.0057. U.S. Geological Survey. 2023. USGS water data for the Nation: U.S. Geological Survey National Water Information System, [accessed 2023 August 28]. https://doi.org/10.5066/F7P55KJN.