Periphyton is a complex community of detritus, bacteria, fungi, and algae that grows attached to submerged substrates. Assemblage structure data for algae and cyanobacteria from periphyton samples were collected on a monthly basis from 2017 to 2021. Compiled data were reported as absolute abundance (cells) and biovolume per volume as well as absolute abundance (cells) and biovolume per area at four locations increasing in distance East of the L-67 canal in Water Conservation Area 3 (WCA 3) of the Florida Everglades immediately north of Everglades National Park. The periphyton assemblages were analyzed for five sample types including periphyton plates (Plates), invertebrate inclusion and exclusion plates (Inverts), biological oxygen demand cores (BOD), vertical/sediment traps (VertSedTrap), and metaphyton cores (MetaCore).

These data include sample information and gene sequence reads for amplicon sequence variants from a study of freezing and storage duration effects on diatom-environment relationships. This dataset is associated with the following publication: Smucker, N., E. Pilgrim, C. Nietch, and C. Carpenter. Freezing periphyton samples and storage duration do not affect the use of diatom DNA metabarcoding to determine effects of stressors on streams. ENVIRONMENTAL MONITORING AND ASSESSMENT. Springer, New York, NY, USA, 197: 1360, (2025).

This dataset comprises in situ images of benthic algae collected by an autonomous underwater vehicle (AUV) in Lake Michigan during August and September 2020. The images were annotated, or labeled, to identify specific features for use in machine learning and algorithm development, specifically to train and validate an algorithm for the automated identification and assessment of submerged aquatic vegetation (SAV). The dataset is organized into individual zip files, each corresponding to different collection dates, with the date indicated in the file name. Each zip file contains original images, ground truth binary masks where benthic algae are represented by white pixels and the background by black pixels, and JSON files specifying the coordinates of polygons delineating the algae in each image. Additionally, the metadata associated with these images is accessible in the accompanying metadata spreadsheet. The AUV, a modified L3Harris-OceanServer Iver3, was equipped with a high-performance 9-megapixel CMOS sensor, specifically the Allied Vision Manta G-895C color camera. Advanced sensors and imaging systems onboard the AUV enabled precise navigation and image capture during the survey. In total, over 300 km of lakebed were surveyed by the AUV across thirty sites along the Lake Michigan shoreline. The 4096 x 2176-pixel color images were georeferenced using the AUV's inertial navigation system (INS), which relied on an iXBlue PHINS Compact C3 fiber-optic gyroscope for accurate positioning. Each image was accompanied by recorded parameters, including temperature, altitude, depth, and time. Collectively, these data provide a comprehensive dataset for analyzing and understanding the distribution and dynamics of submerged aquatic vegetation (SAV) in Lake Michigan.

Spatial reconnaissance of fluvial microcystins (MC) concentrations and select water-quality parameters, including nutrients and periphyton biomass, in 75 wadeable streams in the Piedmont region of the southeastern USA during 2014. Data set includes only those data specifically discussed in the associated journal article: Loftin, K.A., Clark, J.M., Journey, C.A., Kolpin, D.W., Van Metre, P.C., and Bradley, P.M., 2016, Spatial and temporal variation in microcystins occurrence in wadeable streams in the southeastern USA: Environmental Toxicology and Chemistry, http://dx.doi.org/10.1002/etc.3391.

Spatial reconnaissance of fluvial microcystins (MC) concentrations and select water-quality parameters, including nutrients and periphyton biomass, in 75 wadeable streams in the Piedmont region of the southeastern USA during 2014. Data set includes only those data specifically discussed in the associated journal article: Loftin, K.A., Clark, J.M., Journey, C.A., Kolpin, D.W., Van Metre, P.C., and Bradley, P.M., 2016, Spatial and temporal variation in microcystins occurrence in wadeable streams in the southeastern USA: Environmental Toxicology and Chemistry, http://dx.doi.org/10.1002/etc.3391.

This data release includes periphyton sample and taxonomic information collected within the Lower Grand River hydrologic unit code 10280103, Missouri and Iowa, 2011 through 2018. Sample information includes U.S. Geological Survey station name and identification number where the sample was collected, the sample date, if the sample was a replicate sample, and a unique sample identification code. Taxonomic information provided in each row includes the currently accepted taxa name, average cell density, average biovolume per cell, total taxa biovolume, relative biovolume, total sample biovolume, laboratory notes, and taxon name provided by the identifying laboratory.

This data release includes periphyton sample and taxonomic information collected within the Lower Grand River hydrologic unit code 10280103, Missouri and Iowa, 2011 through 2018. Sample information includes U.S. Geological Survey station name and identification number where the sample was collected, the sample date, if the sample was a replicate sample, and a unique sample identification code. Taxonomic information provided in each row includes the currently accepted taxa name, average cell density, average biovolume per cell, total taxa biovolume, relative biovolume, total sample biovolume, laboratory notes, and taxon name provided by the identifying laboratory.

This data release contains a 17-year record (2005-2022) of discrete chlorophyll data from inland waters, collected from across the nation and territories. These data are from discrete samples (collected in the field and analyzed in the laboratory) from plankton (suspended algae) and periphyton (benthic algae) from lakes, streams, rivers, reservoirs, canals, and other sites. These data are gathered to support process and remote sensing modeling and prediction of Harmful Algal Blooms (HABs). The chlorophyll data were compiled from the Water Quality Portal (WQP) and USGS National Water Quality Lab (NWQL).

Data for uncorrected chlorophyll a, corrected chlorophyll a, and pheophytin from EPA Methods 445 and 446 are included and reported, following the conventions of EPA section 445:

• 12.1 uncorrected chlorophyll a – based on the initial optical measurement of the sample, which includes both chlorophyll a and pheophytin
• 12.2 corrected chlorophyll a – based on optical measurement after acidification and calculation to estimate the amount of active chlorophyll in the original sample
• 12.3 pheophytin – based on calculations to estimate the amount of pheophytin in the original sample

These data were harmonized for reporting units (plankton as µg/L and periphyton as mg/m2), duplicate values, collection depth, site type, negative values, and some extreme values. HABs events are associated with high values of chlorophyll, as algae may be concentrated in dense surface scums. These data may include an indicator for hydrologic event code, which may be helpful in determining HABs events.

Acknowledgements

This work was completed as part of two projects in the USGS Water Mission Area (WMA) Water Quality Processes Program: (1) the Improved Understanding and Prediction of Prioritized Constituents Project, an effort to advance datasets and understanding of chlorophyll, nutrient, carbon, and sediment occurrence and transport, and (2) the Proxies Project, an effort to develop estimation methods for PFAS, harmful algal blooms, and metals, at multiple spatial and temporal scales.

Arar, E.J. and Collins, G.B. 1997. Method 445.0: In vitro determination of chlorophyll a and pheophytin a in marine and freshwater algae by fluorescence. EPA Office of Research and Development.

This data release contains a 17-year record (2005-2022) of discrete chlorophyll data from inland waters, collected from across the nation and territories. These data are from discrete samples (collected in the field and analyzed in the laboratory) from plankton (suspended algae) and periphyton (benthic algae) from lakes, streams, rivers, reservoirs, canals, and other sites. These data are gathered to support process and remote sensing modeling and prediction of Harmful Algal Blooms (HABs). The chlorophyll data were compiled from the Water Quality Portal (WQP) and USGS National Water Quality Lab (NWQL).

Data for uncorrected chlorophyll a, corrected chlorophyll a, and pheophytin from EPA Methods 445 and 446 are included and reported, following the conventions of EPA section 445:

• 12.1 uncorrected chlorophyll a – based on the initial optical measurement of the sample, which includes both chlorophyll a and pheophytin
• 12.2 corrected chlorophyll a – based on optical measurement after acidification and calculation to estimate the amount of active chlorophyll in the original sample
• 12.3 pheophytin – based on calculations to estimate the amount of pheophytin in the original sample

These data were harmonized for reporting units (plankton as µg/L and periphyton as mg/m2), duplicate values, collection depth, site type, negative values, and some extreme values. HABs events are associated with high values of chlorophyll, as algae may be concentrated in dense surface scums. These data may include an indicator for hydrologic event code, which may be helpful in determining HABs events.

Acknowledgements

This work was completed as part of two projects in the USGS Water Mission Area (WMA) Water Quality Processes Program: (1) the Improved Understanding and Prediction of Prioritized Constituents Project, an effort to advance datasets and understanding of chlorophyll, nutrient, carbon, and sediment occurrence and transport, and (2) the Proxies Project, an effort to develop estimation methods for PFAS, harmful algal blooms, and metals, at multiple spatial and temporal scales.

Arar, E.J. and Collins, G.B. 1997. Method 445.0: In vitro determination of chlorophyll a and pheophytin a in marine and freshwater algae by fluorescence. EPA Office of Research and Development.

A data package consisting of diatom, total phosphorus, and related data collected in Big Cypress National Preserve as part of the SFCN Periphyton Vital Signs protocol. Periphyton is a microbial mat community that forms the base of the aquatic food web in South Florida wetlands such as the marshes in Everglades National Park (EVER) and the Big Cypress National Preserve (BICY). It is a vital component of these wetlands, contributing to critical functions such as primary production, nutrient cycling, and soil production and stabilization. Periphyton is sensitive to changes in hydropattern (water quantity and duration) and water quality. Changes to these ecosystem processes can quickly alter periphyton community structure (species composition and relative abundance), which in turn can create cascading effects through higher trophic levels. Thus, periphyton is an early and integrative indicator of local and regional changes to hydrology. The South Florida/Caribbean Network has implemented the monitoring of periphyton communities in Big Cypress National Preserve to assess the impact of hydrologic and water quality changes on the diatom community structure and total phosphorous (TP) concentrations of the periphyton mats. The specific monitoring objectives are: 1) Identify any basins in the northwest section of Big Cypress National Preserve where periphyton community structure and periphyton TP content are different from an oligotrophic (low-nutrient) and unimpacted community signal. 2) Document any temporal and/or spatial changes in the periphyton community structure and periphyton TP content showing progression towards an oligotrophic, unimpacted condition or a eutrophic (high-nutrient), impacted condition. This dataset includes all data collected (both pilot and standard) between 2008 and 2025. 2025 sites are listed in this release alongside their field data, but lab results have yet to be received for these sites at this time.