Draft genome sequences of six Mycobacterium immunogenum strains isolated from a chloraminated drinking water distribution system simulator subjected to changes in operational parameters. This dataset is associated with the following publication: Gomez-Alvarez, V., and R. Revetta. Draft Genome Sequences of Six Mycobacterium immunogenum, Obtained from a Chloraminated Drinking Water Distribution System Simulator. Genome Announcements. American Society for Microbiology, Washington, DC, USA, 4(1): e01538-15, (2016).

The dataset includes the accession numbers to the RNA sequences and qPCR data for pathogens and validation of some important RNA sequences. This dataset is associated with the following publication: Lu, J., I. Struewing, and N. Ashbolt. Meta-Transcriptomic Response to Copper Corrosion in Drinking Water Biofilms. Microorganisms. MDPI, Basel, SWITZERLAND, 13(7): 1528, (2025).

These data describe microbiological analyses performed on groundwater samples from domestic drinking water supply collected from 42 groundwater wells in the Central Valley of California. Samples were collected between January 2014 and April 2014 for the Groundwater Ambient Monitoring and Assessment (GAMA) program priority basin assessment of the Madera, Chowchilla, and Kings (MACK) groundwater sub-basins’ shallow aquifers. A total of 75 wells were sampled for the MACK study unit between August 2013 and April 2014. Samples for this dataset were vacuum filtered and plated on MI and mEI agars prior to incubation to promote colony growth. Colonies were tallied by their species into columns for various fecal indicator bacteria (FIBs): total coliforms (TCs), Escherichia coli (E. coli), enterococci. Non-target growths were also counted and tallied. Six additional replicate samples were collected for quality assurance. Of the 579 total FIB colonies detected, 106 were selected for polymerase chain reaction (PCR) analysis with the goal of sequencing their DNA. Selected colonies consisted of both target and non-target growths and were taken from 14 samples collected at 13 different wells. DNA sequencing was successful for 34 of the sampled colonies out of a total of 59 submitted. Results for these analyses were reported in FASTA format with the number of bases and their starting position indicated for each batch.

These data describe microbiological analyses performed on groundwater samples from domestic drinking water supply collected from 42 groundwater wells in the Central Valley of California. Samples were collected between January 2014 and April 2014 for the Groundwater Ambient Monitoring and Assessment (GAMA) program priority basin assessment of the Madera, Chowchilla, and Kings (MACK) groundwater sub-basins’ shallow aquifers. A total of 75 wells were sampled for the MACK study unit between August 2013 and April 2014. Samples for this dataset were vacuum filtered and plated on MI and mEI agars prior to incubation to promote colony growth. Colonies were tallied by their species into columns for various fecal indicator bacteria (FIBs): total coliforms (TCs), Escherichia coli (E. coli), enterococci. Non-target growths were also counted and tallied. Six additional replicate samples were collected for quality assurance. Of the 579 total FIB colonies detected, 106 were selected for polymerase chain reaction (PCR) analysis with the goal of sequencing their DNA. Selected colonies consisted of both target and non-target growths and were taken from 14 samples collected at 13 different wells. DNA sequencing was successful for 34 of the sampled colonies out of a total of 59 submitted. Results for these analyses were reported in FASTA format with the number of bases and their starting position indicated for each batch.

The bacteria sequence data generated in this study is available in the Short Read Archive (SRA) of NCBI (https://www.ncbi.nlm.nih.gov/) under BioProject PRJNA509718. This dataset is associated with the following publication: Siponen, S., J. Ikonen, V. Gomez-Alvarez, A. Hokajärvi, M. Ruokolainen, B. Jayaprakash, M. Kolehmainen, I.T. Miettinen, T. Pitkänen, and E. Torvinen. Effect of Pipe Material and Disinfectant on Active Bacterial Communities in Drinking Water and Biofilms. JOURNAL OF APPLIED MICROBIOLOGY. Blackwell Publishing, Malden, MA, USA, 136(1): lxaf004, (2025).

These data include detailed sample description (sampling locations, sampling events, DNA concentrations in four separate spreadsheet in an Excel file) and DNA sequencing plate layout. This dataset is associated with the following publication: Li, L., D. Ning, Y. Jeon, H. Ryu, J. SantoDomingo, D. Kang, A. Kadudula, and Y. Seo. Ecological Insights into Assembly Processes and Network Structures of Bacterial Biofilms in Full-scale Biologically Active Carbon Filters under Ozone Implementation. SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM, NETHERLANDS, 751: 141409, (2021).

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 for sequence comparison of commamox genomes and genes identified. This dataset is associated with the following publication: Camejo, P., J. Santodomingo, K. McMahon, and D. Noguera. Genome-enabled insights into the ecophysiology of the comammox bacterium Ca. Nitrospira nitrosa. ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 2(5): 1-16, (2017).

The dataset contains the raw data used to produce the data in the following journal article: Evaluation of a Modified Rapid Viability-Polymerase Chain Reaction Method for Bacillus Spores in Water Matrices. This dataset is associated with the following publication: Bushon, R., A. Brady, C. Kephart, and V. Gallardo. Evaluation of a Modified Rapid Viability-Polymerase Chain Reaction Method for Bacillus atrophaeus Spores in Water Matrices. JOURNAL OF MICROBIOLOGICAL METHODS. Elsevier Science Ltd, New York, NY, USA, 188: 106293, (2021).

Acetylene (C2H2) is a molecule rarely found in nature, with few known natural sources, but acetylenotrophic microorganisms can use acetylene as their primary carbon and energy source. As of 2018 there were 15 known strains of aerobic and anaerobic acetylenotrophs, however we hypothesized that there may be yet unrecognized diversity of acetylenotrophs in nature. In this study, we expanded this diversity by isolating an aerobic acetylenotroph, Bradyrhizobium sp. strain I71, from trichloroethene (TCE)-contaminated soils undergoing bioremediation. TCE-contaminated soils from the NASA Ames Research Center in California were used to establish soil microcosms with acetylene as the primary carbon substrate and acetylene uptake was tracked over time and reported in T1_soil_microcosm_v2.0.csv. DNA was extracted from soil microcosm samples for microbial community analysis based on 16S rRNA gene sequencing; the resulting operational taxonomic units are presented in T2_soil_OTU_v2.0.csv. Bradyrhizobium sp. strain I71 was isolated from the soil microcosms and acetylene uptake and cell growth data for the isolate over time are shown in T3_soil_isolate_v2.0.csv. Nitrogen fixation assays for the pure culture of Bradyrhizobium sp. strain I71 are reported in T4_N2_fixation_v2.0.csv. Acetylene concentrations and cell densities from acetylenotrophic and heterotrophic growth assays for Bradyrhizobium sp. strain I71 are reported in T5_GrowthCurve_v2.0.csv