The data being released were part of a project funded by the Great Lakes Restoration Initiative (GLRI). This study sought to examine the influence of filter pore size (5.0 µm pre and 0.22 µm final filtration) on microbial communities and source-specific microbial source tracking (MST) markers at three locations along southern Lake Michigan: Racine, WI; Chicago, IL; and East Chicago, IN; between 2015 and 2017. In 2015, triplicate water samples were collected during three events, in 2016 individual water samples were collected during three events, and in 2017, individual water samples were collected one day a week for ten weeks between June and August. Samples were collected from twelve locations, two river, two river mouth, three offshore, one wetland outlet, and four shorelines. The upstream river locations are as follows: 1. Root River at the Root River Environmental Education Community Center (REC, 2015-2017), Racine, Wisconsin 2. Grand Calumet River at Columbus Drive (GC, 2015-2017), East Chicago, Indiana The river mouth locations are as follows: 1. Grand Calumet River Mouth (GCM, 2015 only), East Chicago, Indiana 2. Root River Mouth (RRM), Racine, Wisconsin The offshore locations are as follows: 1. Grand Calumet River (GCN, 2015 only), East Chicago, Indiana 2. Grand Calumet River (GCE, 2015 only), East Chicago, Indiana 3. Root River marina harbor wall (NBW, 2015 only), Racine, Wisconsin The shoreline locations are as follows: 1. North Beach (NB), Racine, Wisconsin 2. 63rd Street Beach (63rd), Chicago, Illinois 3. Jeorse Park (JP), East Chicago, Indiana 4. Whihala beach (WHW, 2015 only), Whiting, IN The wetland outlet location: 1. North Beach (IEB outlet, 2015 only), Racine, Wisconsin

The data being released were part of a project funded by the Great Lakes Restoration Initiative (GLRI). This study sought to examine the influence of filter pore size (5.0 µm pre and 0.22 µm final filtration) on microbial communities and source-specific microbial source tracking (MST) markers at three locations along southern Lake Michigan: Racine, WI; Chicago, IL; and East Chicago, IN; between 2015 and 2017. In 2015, triplicate water samples were collected during three events, in 2016 individual water samples were collected during three events, and in 2017, individual water samples were collected one day a week for ten weeks between June and August. Samples were collected from twelve locations, two river, two river mouth, three offshore, one wetland outlet, and four shorelines. The upstream river locations are as follows: 1. Root River at the Root River Environmental Education Community Center (REC, 2015-2017), Racine, Wisconsin 2. Grand Calumet River at Columbus Drive (GC, 2015-2017), East Chicago, Indiana The river mouth locations are as follows: 1. Grand Calumet River Mouth (GCM, 2015 only), East Chicago, Indiana 2. Root River Mouth (RRM), Racine, Wisconsin The offshore locations are as follows: 1. Grand Calumet River (GCN, 2015 only), East Chicago, Indiana 2. Grand Calumet River (GCE, 2015 only), East Chicago, Indiana 3. Root River marina harbor wall (NBW, 2015 only), Racine, Wisconsin The shoreline locations are as follows: 1. North Beach (NB), Racine, Wisconsin 2. 63rd Street Beach (63rd), Chicago, Illinois 3. Jeorse Park (JP), East Chicago, Indiana 4. Whihala beach (WHW, 2015 only), Whiting, IN The wetland outlet location: 1. North Beach (IEB outlet, 2015 only), Racine, Wisconsin

The data being released were part of a project funded by the United States Environmental Protection Agency (USEPA). This study sought to identify the planktonic communities (cyanobacteria, eukaryotic algae) potentially contributing to eutrophication within the Grand Calumet River Area of Concern (AOC) in northern Indiana along the southern shore of Lake Michigan. In 2021, triplicate water samples were collected from five locations during three events, 4/19/21 and 4/20/21, 7/7/21, and 9/15/21. Water samples were processed and planktonic communities were determined by a DNA-based technology (algal metabarcoding). Sampling locations: 1. Columbia Avenue, Hammond, IN 2. Lake George drainage ditch, Hammond, IN 3. Indiana Harbor Canal at Canal Street in East Chicago, IN 4. Airport Road in Gary, IN 5. Marquette Park Lagoon in Gary, IN

Data were collected in August and September 2015 for analysis of bacteria communities of the Grand Calumet River and associated shorelines. Water samples were collected on three occasions corresponding to one rain-related (wet) events and two non-rain (dry) events. Water samples were collected in the Grand Calumet River, at the mouth of the river, at offshore locations around the peninsular impoundment and at shoreline locations: Jeorse Park (East Chicago, Indiana), Whihala (Whiting, Indiana), and 63rd Street (Chicago, Illinois) beaches. Samples were collected in triplicate, and water was filtered at the USGS Lake Michigan Ecological Research Station. After DNA extraction, samples were analyzed using 16S rRNA sequencing using Illumina sequencing. Taxonomic identification was assigned for communities in each sample, at multiple taxonomic levels (Kingdom, Phylum, Class, Order, Family, Genus). Water was also analyzed for E. coli bacteria and turbidity, at the USGS laboratory. Hydrological conditions corresponding to the days of sample collection were obtained from publicly available USGS information (NWIS-National Water Information System). The coordinate file includes information regarding sampling locations and their corresponding latitude and longitudes. The Data file include E. coli densities, laboratory turbidity measurements, and NWIS hydrological data. The raw metagenomic data can be accessed at the NCBI repository under the biproject accession PRJNA541325: https://www.ncbi.nlm.nih.gov/sra/PRJNA541325

Data were collected in August and September 2015 for analysis of bacteria communities of the Grand Calumet River and associated shorelines. Water samples were collected on three occasions corresponding to one rain-related (wet) events and two non-rain (dry) events. Water samples were collected in the Grand Calumet River, at the mouth of the river, at offshore locations around the peninsular impoundment and at shoreline locations: Jeorse Park (East Chicago, Indiana), Whihala (Whiting, Indiana), and 63rd Street (Chicago, Illinois) beaches. Samples were collected in triplicate, and water was filtered at the USGS Lake Michigan Ecological Research Station. After DNA extraction, samples were analyzed using 16S rRNA sequencing using Illumina sequencing. Taxonomic identification was assigned for communities in each sample, at multiple taxonomic levels (Kingdom, Phylum, Class, Order, Family, Genus). Water was also analyzed for E. coli bacteria and turbidity, at the USGS laboratory. Hydrological conditions corresponding to the days of sample collection were obtained from publicly available USGS information (NWIS-National Water Information System). The coordinate file includes information regarding sampling locations and their corresponding latitude and longitudes. The Data file include E. coli densities, laboratory turbidity measurements, and NWIS hydrological data. The raw metagenomic data can be accessed at the NCBI repository under the biproject accession PRJNA541325: https://www.ncbi.nlm.nih.gov/sra/PRJNA541325

To determine the differences in soil microbial community composition between native and non-native lineages of Phragmites, we sampled soils from eight sites in the Great Lakes basin where populations of native and non-native Phragmites co-occurred. In addition, we included samples of soils from 27 populations of Phragmites across the Gulf of Mexico and Atlantic Coasts of the US. Samples were collected between July 2015 and September 2017. At each site in the Great Lakes, we sampled rhizosphere and bulk soil surrounding one ramet of each lineage. Samples from Atlantic and Gulf coasts were collected by homogenizing rhizosphere soils from multiple ramets of one population within a single lineage. DNA was extracted from soils and fungal, bacterial, and oomycete DNA was amplified to identify the microbial constituents. Amplicons were sequenced using Illumina MiSeq. This dataset includes outputs of bioinformatic analysis of sequences including operational taxonomic unit (OTU) generation, OTU abundance, resolved taxonomy, and environmental metadata collected in our survey. Raw sequences were uploaded to the NCBI Sequence Read Archive under SRA accession number PRJNA601975. First posted: October 22, 2020 (available by request) Minor Revision: December, 2020 (version 1.1)

To determine the differences in soil microbial community composition between native and non-native lineages of Phragmites, we sampled soils from eight sites in the Great Lakes basin where populations of native and non-native Phragmites co-occurred. In addition, we included samples of soils from 27 populations of Phragmites across the Gulf of Mexico and Atlantic Coasts of the US. Samples were collected between July 2015 and September 2017. At each site in the Great Lakes, we sampled rhizosphere and bulk soil surrounding one ramet of each lineage. Samples from Atlantic and Gulf coasts were collected by homogenizing rhizosphere soils from multiple ramets of one population within a single lineage. DNA was extracted from soils and fungal, bacterial, and oomycete DNA was amplified to identify the microbial constituents. Amplicons were sequenced using Illumina MiSeq. This dataset includes outputs of bioinformatic analysis of sequences including operational taxonomic unit (OTU) generation, OTU abundance, resolved taxonomy, and environmental metadata collected in our survey. Raw sequences were uploaded to the NCBI Sequence Read Archive under SRA accession number PRJNA601975. First posted: October 22, 2020 (available by request) Minor Revision: December, 2020 (version 1.1)

Data were collected as part of a study to identify sources of E. coli contamination at several beaches located in the Grand Calumet River Areas of Concern, located in northern Indiana on Lake Michigan. The study was funded by the Great Lakes Restoration Initiative. Water samples were collected at each site (Jeorse Park 1, Jeorse Park 2, Hammond East, Hammond West, Whihala West, Whihala East, Whihala west breakwater, Hammond Marina, Whihala offshore locations, and the Grand Calumet River) one day a week or three times a week between 2015 and 2018. While the 2015 data were included in analysis, these data were previously publicly released https://doi.org/10.5066/F7H70F3D. Samples (water, sand, sediment) were analyzed for E. coli bacteria (an indicator bacterium for fecal contamination) and species-specific molecular markers (microbial source tracking, MST), including human (HF183, Mnif), gull (Gull2), and dog (DogBact). Presence of MST markers indicates a fecal source associated with the target animal at that location. Bird counts were recorded during each site visit. Water samples were analyzed in the laboratory for E. coli using defined substrate technology, for MST markers using quantitative polymerase chain reaction (qPCR) methods, and turbidity, conductivity, and pH. Additionally in 2015, samples were collected during two dry and one wet event and subjected to metagenomics analysis for determining bacterial communities. The additional samples were collected at Whihala, Jeorse Park, Grand Calumet River, as well as three offshore locations associated with the Grand Calumet River: mouth to the lake at a peninsular structure and north and east of the structure. Lat_long file includes information regarding sampling locations and their corresponding latitude and longitudes. The EcoliWaterChem data include E. coli densities and water chemistry (turbidity, conductivity, pH) measurements. Data from the MST file includes results from quantitative polymerase chain reaction (qPCR) method for detection of host-specific microbial source tracking markers as follows: Gulls (Gull2), Dogs (DogBact), and human (HF183, Mnif). Data from Birds included number of birds (gulls, geese, ducks, cormorants, etc.) counted on the beach and in the water. The metagenomics file includes taxonomic information and corresponding percent abundance of each organism for each sample. The metagenomics file includes taxonomic information and corresponding organisms' percent abundance for each sample. The metagenomicsKey file includes information pertinent to individual samples.

Data were collected as part of a study to identify sources of E. coli contamination at several beaches located in the Grand Calumet River Areas of Concern, located in northern Indiana on Lake Michigan. The study was funded by the Great Lakes Restoration Initiative. Water samples were collected at each site (Jeorse Park 1, Jeorse Park 2, Hammond East, Hammond West, Whihala West, Whihala East, Whihala west breakwater, Hammond Marina, Whihala offshore locations, and the Grand Calumet River) one day a week or three times a week between 2015 and 2018. While the 2015 data were included in analysis, these data were previously publicly released https://doi.org/10.5066/F7H70F3D. Samples (water, sand, sediment) were analyzed for E. coli bacteria (an indicator bacterium for fecal contamination) and species-specific molecular markers (microbial source tracking, MST), including human (HF183, Mnif), gull (Gull2), and dog (DogBact). Presence of MST markers indicates a fecal source associated with the target animal at that location. Bird counts were recorded during each site visit. Water samples were analyzed in the laboratory for E. coli using defined substrate technology, for MST markers using quantitative polymerase chain reaction (qPCR) methods, and turbidity, conductivity, and pH. Additionally in 2015, samples were collected during two dry and one wet event and subjected to metagenomics analysis for determining bacterial communities. The additional samples were collected at Whihala, Jeorse Park, Grand Calumet River, as well as three offshore locations associated with the Grand Calumet River: mouth to the lake at a peninsular structure and north and east of the structure. Lat_long file includes information regarding sampling locations and their corresponding latitude and longitudes. The EcoliWaterChem data include E. coli densities and water chemistry (turbidity, conductivity, pH) measurements. Data from the MST file includes results from quantitative polymerase chain reaction (qPCR) method for detection of host-specific microbial source tracking markers as follows: Gulls (Gull2), Dogs (DogBact), and human (HF183, Mnif). Data from Birds included number of birds (gulls, geese, ducks, cormorants, etc.) counted on the beach and in the water. The metagenomics file includes taxonomic information and corresponding percent abundance of each organism for each sample. The metagenomics file includes taxonomic information and corresponding organisms' percent abundance for each sample. The metagenomicsKey file includes information pertinent to individual samples.

A large spill of wastewater from oil and gas operations was discovered adjacent to Blacktail Creek near Williston, North Dakota in January 2015. To determine the effects of this spill on streambed microbial communities over time, bed sediment samples were taken from Blacktail Creek upstream, adjacent to, and at several locations downstream from the spill site. Blacktail Creek is a tributary of the Little Muddy River, and additional samples were taken upstream and downstream from the confluence of Blacktail Creek and the Little Muddy River. Samples were collected in February 2015, June 2015, June 2016, and June 2017. DNA was extracted from these sediments, and sequencing of the 16S ribosomal RNA gene was performed to enable analysis of the microbial community structure. Raw sequence data was processed, and taxonomy was assigned based on the Silva 132 database (Yilmaz et al, 2014) using the MOTHUR software package (Schloss et al, 2009). Raw sequence data are available from GenBank at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA666160.