Dale W. Griffin William M. Benzel Shawn C. Fisher Michael J. Focazio Luke R. Iwanowicz Daniel K. Jones Keith A. Loftin Timothy J. Reilly 20190425 Tabular Digital Data U.S. Geological Survey Data Release doi:10.5066/F7XS5SH2 Reston, VA U.S. Geological Survey https://doi.org/10.5066/F7XS5SH2 Timothy J. Reilly Daniel K. Jones Michael J. Focazio Kimberly C. Aquino Chelsea L. Carbo Erika E. Kaufhold Elizabeth K. Zinecker William M. Benzel Shawn C. Fisher Dale W. Griffin Luke R. Iwanowicz Keith A. Loftin William B. Schill 20150101 Publication (Other) Reston, VA U.S. Geological Survey https://pubs.usgs.gov/of/2015/1188/A/ofr20151188a.pdf Due to the recognized proliferation and spread of antibiotic resistance genes by anthropogenic use of antibiotics for human, agriculture and aquaculture purposes, antibiotic resistance genes have been defined as an emerging contaminant (Laxminarayan and others, 2013; Rodriguez-Rojas and others, 2013; Niu and others, 2016). The presence and spread of these genes in non-clinical and non-agricultural environments has created the need for background investigations to enhance our understanding of the magnitude and risks associated with this emerging field (Allen and others, 2010). The current global economic costs of antibiotic resistant microorganisms is about 5.8 trillion USD, which is approximately equivalent to the combined GDP of Germany and the United Kingdom (Taylor and others, 2014). In this study we screened soil and sediment samples for the presence of 15 antibiotic resistance gene targets and 5 species of Vibrio (a marker of marine inundation) to determine natural background concentrations. These data provide a foundation to address background prevalence of these genetic targets in the northeastern United States (U.S.) to address regional influences (sources of pollutants) and to contrast future influences due to sea-level rise and large scale storms. The purpose of these datasets was to define which samples contained antibiotic resistance genes (screened antibiotic resistance gene targets) and Vibrio species, the number of detectable targets per sample and the quantity of those respective gene targets per gram of soil. These data were determined from samples collected in the northeastern U.S. in support of Sediment-bound Contaminant Resiliency and Response (SCoRR) study. 20150803 20151112 ground condition Complete Not planned -79.303957 -66.983372 44.972041 33.352132 USGS Metadata Identifier USGS:356648ef-627a-40c0-8e13-d71276879f5b ISO 19115 Topic Category environment biota health USGS Thesaurus field sampling field monitoring stations contamination and pollution environmental health (human) microbiology genetic diversity soil resources unconsolidated deposits Geographic Names Information System Connecticut District of Columbia Delaware Massachusetts Maryland Maine New Hampshire New Jersey New York Pennsylvania Rhode Island South Carolina Virginia Oregon GEO Stratum Keywords Intertidal Estuarine Soil Surface Sediment Oregon GEO temporal Keywords Modern none Public domain data from the U.S. Government are freely redistributable with proper metadata and source attribution. The U.S. Geological Survey requests to be acknowledged as originator of these data in future products or derivative research. Dale W Griffin U.S. Geological Survey, Southeast Region Environmental and Public Health Microbiologist mailing address

600 4Th Street South

St. Petersburg FL 33701 USA 727-502-8075 727-502-8182 dgriffin@usgs.gov Environment as of Metadata Creation: Microsoft Windows 7 Version 6.1 (Build 7601) Service Pack 1; Esri ArcGIS 10.3.1 (Build 4959) Service Pack N/A (Build N/A) Griffin, D.W., Benzel, W.M., Fisher, S.C., Focazio, M.J., Iwanowicz, L.R., Loftin, K.A., Reilly, T.J., Jones, D.K. 2019 publication Environmental Monitoring and Assessment v.191, Issue 2, p.1573-2959 https://doi.org/10.1007/s10661-019-7426-z Laxminarayan, R., Duse, A., Wattal, C., Zaidi, A.K.M., Wertheim, H.F.L., Sumpradit, N., Vlieghe, E., Hara, G.L., Gould, I.M., Goossens, H., Greko, C., So, A.D., Bigdeli, M., Tomson, G., Woodhouse, W., Ombaka, E., Peralta, A.Q., Qamar, F.N., Mir, F., Kariuki, S., Bhutta, Z.A., Coates, A., Bergstrom, R., Wright, G.D., Brown, E.D., Cars, O. 2013 report Lancet Infectious Diseases v.13, no. 12, p.1057-1098 Rodriguez-Rojas, A., Rodriguez-Beltran, J., Couce, A., Blazquez, J. 2013 report International Journal of Medical Microbiology v.303, Issues 6-7, p.293-297 Niu, Z-G., Zhang, K., Zhang, Y. 2016 report Marine Pollution Bulletin v.107, Issue 1, p.245–250 https://doi.org/10.1016/j.marpolbul.2016.03.064 Allen, H.K., Donato, J., Wang, H.H., Cloud-Hansen, K.A., Davies, J., Handelsman, J. 2010 report Nature Reviews Microbiology v.8, p.251-259 Taylor, J., Hafner, M., Yerushalmi, E., Smith, R., Bellasio, J., Vardavas, R., Bienkowska-Gibbs, T., Rubin, J. 2014 report Santa Monica, CA RAND Corporation http://www.rand.org/pubs/research_reports/RR911.html Knapp C.W., Dolfing J., Ehlert P.A.I., Graham D.W. 2010 Environmental Science & Technology v.44, Issue 2, p.580-587 Bockelmann U., Dorries H.H., Ayuso-Gabella M.N., de Marcay M.S., Tandoi V., Levantesi C., Masciopinto C., Van Houtte E., Szewzyk U., Wintgens T., Grohmann E. 2009 Applied and Environmental Microbiology v.75, no.1, p.154-163 Singh P., Mustapha A. 2013 International Journal of Food Microbiology v.166, Issue 2, p.213-218 Panicker G., Bej A.K. 2005 Applied and Environmental Microbiology v.71, no.10, p.5702-5709 Plaon S., Longyant S., Sithigorngul P., Chaivisuthangkura P. 2015 Journal of Aquatic Animal Health v.27, Issue 3, p.156-163 Pollock F.J., Morris P.J., Willis B.L., Bourne D.G. 2010 Applied and Environmental Microbiology v.76, no.15, p.5282-5286 Lyon W.J. 2001 Applied and Environmental Microbiology v.67, no.10, p.4685-4693 Rizvi A.V., Panicker G., Myers M.L., Bej A.K. 2006 Fems Microbiology Letters v.262, Issue 2, p.185-192 No formal attribute accuracy tests were conducted. No formal logical accuracy tests were conducted. Dataset is considered complete for the information presented, as described in the abstract. Users are advised to read the rest of the metadata record carefully for additional details. A formal accuracy assessment of the horizontal positional information in the dataset has not been conducted. A formal accuracy assessment of the vertical positional information in the dataset has either not been conducted, or is not applicable. The SCoRR standard operating procedure (SOP) (https://pubs.usgs.gov/of/2015/1188/B/ofr20151188b.pdf) details the sample-collection methods used in this data release. The SOP provides step-by-step instructions for site preparation, sample collection and processing, quality assurance, and shipping of soil and surficial and bed sediment. 20151217 DNA extraction was performed by first calibrating the Mettler scale with a 50 gram certified weight and documented on the Mettler QA/QC sheet. Using sterile-techniques, approximately 0.25 g of soil from each sample weighted out and transferred to a PowerSoil bead beating tube. Sample weight was logged in the project electronic laboratory notebook (ELN). The MoBio PowerSoil kit protocol was used to elute DNA to a volume of 150 ul using Qiagens AE buffer recipe (10mM Tris-HCL, 0. 5mM EDTA, pH 9.0, filter sterilized and autoclaved). Eluted DNA was stored at -70 degrees C until use. 20160705 Digital PCR was run for all presence/absence qPCR positive samples using a QuantStudio 3D Digital PCR System and the following master mix recipe and amplification profile. Data was normalized and reported as gene copies per gram of soil. Master mix recipe (volumes per reaction): 2x digital master mix – 7.25ul, primer/probe mix – 1 ul, H2O – 4.25 ul, template - 2 ul. Amplification profile: 96 degrees C for 10 min – 1X, 60 degrees C for 2min and 98 degrees C for 0.5 min – 39X, 60 degrees C for 2min – 1X and hold at 10 degrees C. 20160705 Added keywords section with USGS persistent identifier as theme keyword. 20201013 U.S. Geological Survey VeeAnn A. Cross Marine Geologist Mailing and Physical

384 Woods Hole Road

Woods Hole MA 02543-1598 508-548-8700 x2251 508-457-2310 vatnipp@usgs.gov dPCRdata_SCoRR2015.csv Table containing attribute information associated with the dataset. Digital polymerase chain reaction (dPCR) data are provided in comma separated values format. U.S. Geological Survey Sample Sample bottle identifier U.S. Geological Survey Sample bottle identifier SCoRR_ID Sediment-bound Contaminant Resiliency and Response (SCoRR) site identifier U.S. Geological Survey SCoRR site identifier NA SCoRR ID not applicable. U.S. Geological Survey Sample_Date Date sample was collected U.S. Geological Survey 20150803 20151112 Date (YYYYMMDD) NA Sample date not applicable. U.S. Geological Survey Sample_Mode Samples collected under Resiliency (baseline) or Response (event) Mode U.S. Geological Survey NA Sampling mode not applicable. U.S. Geological Survey resiliency Samples collected under Resiliency (baseline) mode U.S. Geological Survey response Samples collected under Response (event) mode U.S. Geological Survey tetB Tetracycline resistance genetic target U.S. Geological Survey 313.2 2305.5 Number of copies of genetic target per gram of soil {Null Value / Empty Field Entry} Not analyzed as the presence/absence PCR reactions were both negative U.S. Geological Survey tetL Tetracycline resistance genetic target U.S. Geological Survey 3023.3 10122.5 Number of copies of genetic target per gram of soil {Null Value / Empty Field Entry} Not analyzed as the presence/absence PCR reactions were both negative U.S. Geological Survey tetM Tetracycline resistance genetic target U.S. Geological Survey 1518.2 4990320 Number of copies of genetic target per gram of soil {Null Value / Empty Field Entry} Not analyzed as the presence/absence PCR reactions were both negative U.S. Geological Survey tetO Tetracycline resistance genetic target U.S. Geological Survey 308.9 15636945 Number of copies of genetic target per gram of soil {Null Value / Empty Field Entry} Not analyzed as the presence/absence PCR reactions were both negative U.S. Geological Survey tetW Tetracycline resistance genetic target U.S. Geological Survey 278.4 458707.5 Number of copies of genetic target per gram of soil {Null Value / Empty Field Entry} Not analyzed as the presence/absence PCR reactions were both negative U.S. Geological Survey ampC Cephalosporin (ampicillin, pcn, etc.) resistance genetic target U.S. Geological Survey 4393.8 5387475 Number of copies of genetic target per gram of soil {Null Value / Empty Field Entry} Not analyzed as the presence/absence PCR reactions were both negative U.S. Geological Survey vanA Vancomyucin resistance genetic target U.S. Geological Survey 41116.2 41116.2 Number of copies of genetic target per gram of soil {Null Value / Empty Field Entry} Not analyzed as the presence/absence PCR reactions were both negative U.S. Geological Survey ermB Erythromycin resistance genetic target U.S. Geological Survey 269.7 9428614 Number of copies of genetic target per gram of soil {Null Value / Empty Field Entry} Not analyzed as the presence/absence PCR reactions were both negative U.S. Geological Survey mecA Methicillin resistance genetic target U.S. Geological Survey {Null Value / Empty Field Entry} Not analyzed as the presence/absence PCR reactions were both negative U.S. Geological Survey blaSHV Cephalosporin (ampicillin, pcn, etc.) resistance genetic target U.S. Geological Survey 295.8 9572175 Number of copies of genetic target per gram of soil {Null Value / Empty Field Entry} Not analyzed as the presence/absence PCR reactions were both negative U.S. Geological Survey blaPSE Cephalosporin (ampicillin, pcn, etc.) resistance genetic target U.S. Geological Survey 295.8 195119.3 Number of copies of genetic target per gram of soil {Null Value / Empty Field Entry} Not analyzed as the presence/absence PCR reactions were both negative U.S. Geological Survey floR Chloramphenenicol resistance genetic target U.S. Geological Survey 2818.8 126063 Number of copies of genetic target per gram of soil {Null Value / Empty Field Entry} Not analyzed as the presence/absence PCR reactions were both negative U.S. Geological Survey aadA2 Streptomycin resistance genetic target U.S. Geological Survey 261 169815.3 Number of copies of genetic target per gram of soil {Null Value / Empty Field Entry} Not analyzed as the presence/absence PCR reactions were both negative U.S. Geological Survey tetG Tetracycline resistance genetic target U.S. Geological Survey 561.2 193562 Number of copies of genetic target per gram of soil {Null Value / Empty Field Entry} Not analyzed as the presence/absence PCR reactions were both negative U.S. Geological Survey tetQ Tetracycline resistance genetic target U.S. Geological Survey 304.5 169989.3 Number of copies of genetic target per gram of soil {Null Value / Empty Field Entry} Not analyzed as the presence/absence PCR reactions were both negative U.S. Geological Survey Vibrio_cholerae Bacterial pathogen and marine inundation marker for Vibrio cholerae U.S. Geological Survey 8151.9 8151.9 Number of copies of genetic target per gram of soil {Null Value / Empty Field Entry} Not analyzed as the presence/absence PCR reactions were both negative U.S. Geological Survey NA Not screened U.S. Geological Survey V_parahaemolyticus Bacterial pathogen and marine inundation marker for V. parahaemolyticus U.S. Geological Survey {Null Value / Empty Field Entry} Not analyzed as the presence/absence PCR reactions were both negative U.S. Geological Survey NA Not screened U.S. Geological Survey V_vulnificus Bacterial pathogen and marine inundation marker for V. vulnificus U.S. Geological Survey {Null Value / Empty Field Entry} Not analyzed as the presence/absence PCR reactions were both negative U.S. Geological Survey NA Not screened U.S. Geological Survey V_alginolyticus Bacterial pathogen and marine inundation marker for V. alginolyticus U.S. Geological Survey {Null Value / Empty Field Entry} Not analyzed as the presence/absence PCR reactions were both negative U.S. Geological Survey NA Not screened U.S. Geological Survey V_coralliilyticus Bacterial pathogen and marine inundation marker for V. coralliilyticus U.S. Geological Survey {Null Value / Empty Field Entry} Not analyzed as the presence/absence PCR reactions were both negative U.S. Geological Survey NA Not screened U.S. Geological Survey Note Sample notes U.S. Geological Survey Samples identified with complete inhibition of the assay as stated for each. IPC normal reaction was set at an Rn (normalized reporter value) of 0.1 with a CT (threshold cycle) of 29 plus or minus 1. Target reactions were judged positive if they breached Rn of 0.1 with an exponential type signal. {Null Value / Empty Field Entry} No notes recorded U.S. Geological Survey The entity and attribute information provided here describes the tabular data associated with the dataset. Please review the detailed descriptions that are provided (the individual attribute descriptions) for information on the values that appear as fields/table entries of the dataset. The entity and attribute information was generated by the individual and/or agency identified as the originator of the dataset. Please review the rest of the metadata record for additional details and information. U.S. Geological Survey Physical and Mailing

600 4th Street South

St. Petersburg FL 33701 USA 727-502-8000 dgriffin@usgs.gov Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey (USGS), no warranty expressed or implied is made regarding the display or utility of the data on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government. CSV (Comma Separated Values) none https://coastal.er.usgs.gov/data-release/doi-F7XS5SH2/data/dPCRdata_SCoRR2015.zip None 20201013 Dale W Griffin U.S. Geological Survey, Southeast Region Environmental and Public Health Microbiologist mailing address

600 4Th Street South

St. Petersburg FL 33701 USA 727-502-8075 727-502-8182 dgriffin@usgs.gov Content Standard for Digital Geospatial Metadata FGDC-STD-001-1998