Data supporting the establishment of Syntrophotalea acetylenivorans SFB93 as a new microbial species. Data release includes growth curve and preferred growth conditions for the species.

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

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

Acetylene fermentation assays, nitrogen fixation assays, and growth studies were performed with Pelobacter sp. strain SFB93 and Pelobacter acetylenicus DSM3246. Data includes concentrations of acetylene and ethylene over time, and growth measured with OD680 and cell counts.

Acetylene fermentation assays, nitrogen fixation assays, and growth studies were performed with Pelobacter sp. strain SFB93 and Pelobacter acetylenicus DSM3246. Data includes concentrations of acetylene and ethylene over time, and growth measured with OD680 and cell counts.

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.

Bacteria were isolated from seeds of non-native Phragmites australis (haplotype M) then representatives were evaluated for their capacities to become intracellular in root cells, and their effects on: 1.) germination rates and seedling growth, 2.) susceptibility to damping-off disease, and 3.) mortality and growth of competitor plant seedlings (dandelion (Taraxacum officionale F. H. Wigg) and curly dock (Rumex crispus L.)). The experiments included the following assessments of Phragmites-associated bacteria (Pseudomonas spp, strains Sandy LB4 (Pseudomonas fluorescens) and West 9 (Pseudomonas sp.)): capacity for plant growth promotion (using Poa annua seeds), Poa annua and Phragmites australis seed germination and seedling root architecture, disease protection (co-culture experiments with soil fungi), damping off disease control (with pathogen Fusarium oxysporum), and multiple competitor inhibition experiments (with Taraxacum officionale and Rumex crispus L.). In total, 10 laboratory experiments were performed, data from eight of which are recorded in this data release.

Bacteria were isolated from seeds of non-native Phragmites australis (haplotype M) then representatives were evaluated for their capacities to become intracellular in root cells, and their effects on: 1.) germination rates and seedling growth, 2.) susceptibility to damping-off disease, and 3.) mortality and growth of competitor plant seedlings (dandelion (Taraxacum officionale F. H. Wigg) and curly dock (Rumex crispus L.)). The experiments included the following assessments of Phragmites-associated bacteria (Pseudomonas spp, strains Sandy LB4 (Pseudomonas fluorescens) and West 9 (Pseudomonas sp.)): capacity for plant growth promotion (using Poa annua seeds), Poa annua and Phragmites australis seed germination and seedling root architecture, disease protection (co-culture experiments with soil fungi), damping off disease control (with pathogen Fusarium oxysporum), and multiple competitor inhibition experiments (with Taraxacum officionale and Rumex crispus L.). In total, 10 laboratory experiments were performed, data from eight of which are recorded in this data release.

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 support the following publication: Burton, C.A., and Lawrence, C.J., 2021, Identification of bacteria in groundwater used for domestic supply in the southeast San Joaquin Valley, California, 2014: U.S. Geological Survey Scientific Investigations Report 2021–5030, 20 p., https://doi.org/ 10.3133/ sir20215030.