Data associated with the Hydrobiologia article titled "Spatial and temporal dynamics of a freshwater eukaryotic plankton community revealed via 18S rRNA gene metabarcoding." They include the number of reads and assigned taxonomies for each observational taxonomic unit (OTU) within each sampling date and location. This dataset is associated with the following publication: Banerji, A., M. Bagley, M. Elk, E. Pilgrim, J. Martinson, and J. Santodomingo. Spatial and temporal dynamics of a freshwater eukaryotic plankton community revealed via 18S rRNA gene metabarcoding. HYDROBIOLOGIA. Springer, New York, NY, USA, 818(1): 71-86, (2018).

18S OTU table with taxonomy, including metadata on sampled vessels. This dataset is associated with the following publication: Darling, J., J. Martinson, K. Pagenkopp-Lohan, K. Carney, E. Pilgrim, A. Banerji, K. Holzer, and G. Ruiz. Metabarcoding quantifies differences in accumulation of ballast water borne biodiversity among three port systems in the United States. SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM, NETHERLANDS, 749: 141456, (2020).

18S OTU table with taxonomy, including metadata on sampled vessels. This dataset is associated with the following publication: Darling, J., J. Martinson, K. Pagenkopp-Lohan, K. Carney, E. Pilgrim, A. Banerji, K. Holzer, and G. Ruiz. Metabarcoding quantifies differences in accumulation of ballast water borne biodiversity among three port systems in the United States. SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM, NETHERLANDS, 749: 141456, (2020).

To evaluate the ability of precipitation-based environmental DNA (eDNA) sample collection and mitochondrial 12S metabarcoding sequencing to reconstruct well-studied fish communities in lakes and rivers. Specific objectives were to 1) determine correlations between eDNA species detections and known community composition based on traditional field sampling, 2) compare efficiency of eDNA to detect fish biodiversity among systems with variable morphologies and trophic states, and 3) determine if species habitat preferences predicts eDNA detection. Fish community composition was estimated for seven lakes and two MIssissippi River navigation pools using sequence data from the mitochonrial 12S gene amplified from 10 to 50 water samples per waterbody collected in 50-mL centrifuge tubes at a single time point. Environmental DNA (eDNA) was concentrated without filtration by centrifuging samples to reduce per-sample handling time. Taxonomic detections from eDNA were compared to established community monitoring databases containing up to 40 years of sampling and a detailed habitat/substrate preference matrix to identify patterns of bias. Mitochondrial 12S gene metabarcoding detectec 15-47% of the known species at each waterbody and 30-76% of known genera. Non-metric multidimensional scaling (NMDS) assessment of the community structure indicated that eDNA detected communities grouped in a similar pattern as known communities. Discriminant analysis of principal components indicated that there was a high degree of overlap in habitat/substrate preference of eDNA detected and eDNA undetected species suggesting limited habitat bias for eDNA sampling. Large numbers of small volume samples sequenced at the mitochondrial 12S gene can describe the course community structure of freshwater systems. However, additional traditional sampling and environmental DNA sampling may be necessary for a complete diversity census.

This dataset records Cladophora and associated benthic algae, collectively Cladophora community or submerged aquatic vegetation (SAV), biomass collected during the growing season of 2020 at stations located along the U.S. shoreline of Lakes Michigan, Huron, and Erie. It also records a variety of supporting data collected at Cladophora measurement stations. These supporting data include: - measurements of Secchi disk depth and water chemistry; - water column profiles of temperature, specific conductivity, turbidity, pH, phycocyanin, chlorophyll, and dissolved oxygen; - diver observations of SAV, dreissenid mussels, round goby abundance, and substrate properties; - measurements of dreissenid mussel abundance and size class distribution coincident with SAV biomass; - nutrient content of SAV, dreissenid mussels, and sediments; - and information about sampling locations and operations. Similar data were collected at several of the same transects within four Great Lakes in 2018 and 2019 and are available at (2018) https://doi.org/10.5066/P9E570JS and (2019) https://doi.org/10.5066/P99O4QXB.

This dataset records Cladophora and associated benthic algae, collectively Cladophora community or submerged aquatic vegetation (SAV), biomass collected during the growing season of 2021 at stations located along the U.S. shoreline of Lakes Michigan, Huron, Erie, and Ontario. It also records a variety of supporting data collected at Cladophora measurement stations. These supporting data include: - seasonal time series of light, currents, wave action, temperature, specific conductivity, turbidity, pH, phycocyanin, chlorophyll, and dissolved oxygen from moored sensors at a subset of stations; - measurements of Secchi disk depth and water chemistry; - water column profiles of PAR, temperature, specific conductivity, turbidity, pH, phycocyanin, chlorophyll, and dissolved oxygen; - diver observations of SAV, dreissenid mussels, round goby abundance, and substrate properties; - measurements of dreissenid mussel abundance and size class distribution coincident with SAV biomass; - nutrient content of SAV, dreissenid mussels, and sediments; - and information about sampling locations and operations. Similar data were collected at several of the same transects within four Great Lakes in 2018, 2019, and 2020 are available at (2018) https://doi.org/10.5066/P9E570JS, (2019) https://doi.org/10.5066/P99O4QXB, and (2020) https://doi.org/10.5066/P9O9FSTT.

This dataset records Cladophora and associated benthic algae, collectively Cladophora community or submerged aquatic vegetation (SAV), biomass collected during the growing season of 2022 at stations located along the U.S. shoreline of Lakes Michigan, Huron, Erie, and Ontario. It also records a variety of supporting data collected at Cladophora measurement stations. These supporting data include: - seasonal time series of light, currents, wave action, temperature, specific conductivity, turbidity, pH, phycocyanin, chlorophyll, and dissolved oxygen from moored sensors at a subset of stations; - measurements of Secchi disk depth and water chemistry; - water column profiles of PAR, temperature, specific conductivity, turbidity, pH, phycocyanin, chlorophyll, and dissolved oxygen; - diver observations of SAV, dreissenid mussels, round goby abundance, and substrate properties; - measurements of dreissenid mussel abundance and size class distribution coincident with SAV biomass; - nutrient content of SAV, dreissenid mussels, and sediments; - and information about sampling locations and operations. Similar data were collected at several of the same transects within four Great Lakes in 2018, 2019, 2020, and 2021 are available at (2018) https://doi.org/10.5066/P9E570JS, (2019) https://doi.org/10.5066/P99O4QXB, (2020) https://doi.org/10.5066/P9O9FSTT, and (2021) https://doi.org/10.5066/P9449EUF.

This dataset records Cladophora and associated benthic algae, collectively the Cladophora community or submerged aquatic vegetation (SAV), biomass collected during the growing season of 2023 at stations located along the U.S. shoreline of Lakes Michigan, Huron, Erie, and Ontario. It also records a variety of supporting data collected at Cladophora measurement stations. These supporting data include: - seasonal time series of photosynthetically available radiation (PAR), currents, wave action, temperature, specific conductivity, turbidity, pH, phycocyanin, chlorophyll, and dissolved oxygen from moored sensors at a subset of stations; - measurements of Secchi disk depth and water chemistry; - water column profiles of PAR, temperature, specific conductivity, turbidity, pH, phycocyanin, chlorophyll, and dissolved oxygen; - diver observations of SAV, dreissenid mussels, round goby abundance, and substrate properties; - measurements of dreissenid mussel abundance and size class distribution coincident with SAV biomass; - nutrient content of SAV, dreissenid mussels, and sediments; - and information about sampling locations and operations. Similar data were collected at several of the same transects within four Great Lakes in 2018- 2022 are available at (2018) https://doi.org/10.5066/P9E570JS, (2019) https://doi.org/10.5066/P99O4QXB, (2020) https://doi.org/10.5066/P9O9FSTT, (2021) https://doi:10.5066/P9449EUF, and (2022) https://doi.org/10.5066/P9449EUF. This is a revised version of data release; all changes are described in the Release History for Cladophora_v2_2023.txt First posted: March 4, 2025 Revised: April 2025.