Positions

Overview

  • My main focuses of research are: 1) ribotyping Escherichia coli to identify sources of fecal contamination in surface waters; 2) microbial cycling of mercury in estuarine and marine environments; 3) monitoring for toxic chemicals in the marine environment; 4) stormwater-related pollution of estuarine waters. I have many different projects that make up my research program, the majority of which are related to these 4 topic areas.

    • Selected Publications

    Academic Article

    Year Title
    2021 Cyanate is a low abundance but actively cycled nitrogen compound in soil.  COMMUNICATIONS EARTH & ENVIRONMENT.  2. 2021
    2021 The Seasonal Microbial Ecology of Plankton and Plankton-Associated Vibrio parahaemolyticus in the Northeast United States..  Applied and Environmental Microbiology.  87:e0297320. 2021
    2021 Compositional and geoenvironmental factors in microbially induced partial saturation.  Environmental Geotechnics.  8:282-294. 2021
    2020 Metagenome Sequences from Tidal Marsh and Marine Sediment from the Great Bay Estuary of New Hampshire..  Microbiol Resour Announc.  9. 2020
    2019 Forecasting Seasonal Vibrio parahaemolyticus Concentrations in New England Shellfish..  International Journal of Environmental Research and Public Health.  16:4341-4341. 2019
    2018 An assessment of the microbial community in an urban fringing tidal marsh with an emphasis on petroleum hydrocarbon degradative genes..  Marine Pollution Bulletin.  136:351-364. 2018
    2018 Varying Success of Relaying To Reduce Vibrio parahaemolyticus Levels in Oysters ( Crassostrea virginica)..  Journal of Food Protection.  81:659-669. 2018
    2018 Varying Success of Relaying To Reduce Vibrio parahaemolyticus Levels in Oysters (Crassostrea virginica).  Journal of Food Protection.  81:659-669. 2018
    2017 Parallel Evolution of Two Clades of an Atlantic-Endemic Pathogenic Lineage of Vibrio parahaemolyticus by Independent Acquisition of Related Pathogenicity Islands..  Applied and Environmental Microbiology.  83:e01168-e01117. 2017
    2017 Sequence Type 631 Vibrio parahaemolyticus, an Emerging Foodborne Pathogen in North America..  Journal of Clinical Microbiology.  55:645-648. 2017
    2016 Environmental Conditions Associated with Elevated Vibrio parahaemolyticus Concentrations in Great Bay Estuary, New Hampshire..  PLoS ONE.  11:e0155018. 2016
    2015 Use of Whole-Genome Phylogeny and Comparisons for Development of a Multiplex PCR Assay To Identify Sequence Type 36 Vibrio parahaemolyticus..  Journal of Clinical Microbiology.  53:1864-1872. 2015
    2015 Genetic characterization of clinical and environmental Vibrio parahaemolyticus from the Northeast USA reveals emerging resident and non-indigenous pathogen lineages..  Frontiers in Microbiology.  6:272. 2015
    2012 Mercury sources and fate in the Gulf of Maine..  Environmental Research.  119:27-41. 2012
    2012 Influence of seasonality on the genetic diversity of Vibrio parahaemolyticus in New Hampshire shellfish waters as determined by multilocus sequence analysis..  Applied and Environmental Microbiology.  78:3778-3782. 2012
    2011 Ecology and genetic structure of a northern temperate Vibrio cholerae population related to toxigenic isolates..  Applied and Environmental Microbiology.  77:7568-7575. 2011
    2010 Comparison of the pathogenic potentials of environmental and clinical vibrio parahaemolyticus strains indicates a role for temperature regulation in virulence..  Applied and Environmental Microbiology.  76:7459-7465. 2010
    2009 Detecting water quality patterns in New Hampshire's estuaries using National Coastal Assessment probability-based survey data..  Environmental Monitoring and Assessment.  150:129-142. 2009
    2009 BACTERIAL COMMUNITY PROFILING OF THE AMERICAN OYSTER (CRASSOSTREA VIRGINICA): COMPARISON OF CULTURE-DEPENDENT AND CULTURE-INDEPENDENT OUTCOMES.  Journal of Shellfish Research.  28. 2009
    2008 Integrated mercury monitoring program for temperate estuarine and marine ecosystems on the North American Atlantic coast..  Ecosystem Health EcoHealth.  5:426-441. 2008
    2008 Characterization of Escherichia coli populations from gulls, landfill trash, and wastewater using ribotyping..  Diseases of Aquatic Organisms.  81:53-63. 2008
    2005 Recovery of chlorine-exposed Escherichia coli in estuarine microcosms..  Environmental Science & Technology.  39:3083-3089. 2005
    2002 Microbiology of summer flounder Paralichthys dentatus fingerling production at a marine fish hatchery.  Aquaculture.  211:9-28. 2002
    2001 Monitoring for toxic contaminants in Mytilus edulis from New Hampshire and the Gulf of Maine.  Journal of Shellfish Research.  20:1203-1214. 2001
    2001 Gulfwatch: monitoring spatial and temporal patterns of trace metal and organic contaminants in the Gulf of Maine (1991-1997) with the blue mussel, Mytilus edulis L..  Marine Pollution Bulletin.  42:491-505. 2001
    1998 Incidence and detection of pathogenic Vibrio sp. in a northern New England Estuary, USA.  Journal of Shellfish Research.  17:1665-1669. 1998
    1998 Conversion of mercury(II) into mercury(O), monomethylmercury cation, and dimethylmercury in saltmarsh sediment slurries.  Chemosphere Chemosphere - Global Change Science.  36:1669-1687. 1998
    1995 INTERACTIONS OF TIN(IV) AND MONOMETHYLTIN CATION IN ESTUARINE WATER-SEDIMENT SLURRIES FROM THE GREAT-BAY-ESTUARY, NEW-HAMPSHIRE, USA.  Applied Organometallic Chemistry.  9:581-590. 1995
    1992 Seasonal incidence of Vibrio vulnificus in the Great Bay estuary of New Hampshire and Maine..  Applied and Environmental Microbiology.  58:3257-3262. 1992
    1990 INCIDENCE OF VIBRIO-VULNIFICUS IN NORTHERN NEW-ENGLAND WATER AND SHELLFISH.  FEMS Microbiology Letters.  72:163-168. 1990
    1990 Incidence of Vibrio vulnificus in northern New England water and shellfish..  FEMS Microbiology Letters.  60:163-167. 1990
    1987 A graphical presentation of three-dimensional joint mobility..  Clinical Biomechanics.  2:14-21. 1987

    Conference Paper

    Year Title
    2015 GENETIC CHARACTERIZATION OF CLINICAL AND ENVIRONMENTAL VIBRIO PARAHAEMOLYTICUS FROM THE NORTHEASTERN US REVEALS EMERGING RESIDENT AND INVASIVE PATHOGEN LINEAGES.  Journal of Shellfish Research. 726-727. 2015
    2015 LONG-TERM TRENDS OF PATHOGENIC VIBRIO SPP. POPULATIONS IN NEW HAMPSHIRE OYSTERS.  Journal of Shellfish Research. 711-711. 2015
    2008 Enterococci populations in conventional, manufactured and LID stormwater treatment systems.  World Environmental and Water Resources Congress 2008: Ahupua'a - Proceedings of the World Environmental and Water Resources Congress 2008. 1-9. 2008

    Principal Investigator On

  • NERACOOS: A responsive ocean observing system for the changing Northeast region  awarded by NERACOOS 2021 - 2026
  • Tracking Bacterial Contamination in the Lamprey River Watershed 2022  awarded by Lamprey River Advisory Committees 2022
  • Optimizing Aquaponic Production Using and Integrated Systems Approach  awarded by US DA, Department of Agriculture 2018 - 2022
  • Tracking Bacterial Contamination in the Lamprey River Watershed  awarded by Lamprey River Advisory Committees 2021
  • Assessing Ocean Acidification as a Driver for Enhanced Metals uptake by Mussels (Mytilus edulis): Im  awarded by NERACOOS 2021
  • Lamprey River Water Quality Monitoring Program for the Town of Newmarket  awarded by Town of Newmarket 2019 - 2021
  • 2018 - 19 DES Shellfish Vibrio Analysis  awarded by NH Department of Environmental Services 2018 - 2019
  • Oyster Culture and Harvest Practices to Reduce Pathogenic Vibrio Parahaemolyticus Concentrations in the Northeast US  awarded by Interstate Shellfish Sanitation Conference 2018 - 2019
  • Pease Wastewater Treatment Facility Antidegradation Study  awarded by Underwood Engineers Inc 2018 - 2019
  • Cocheco River Water Quality Monitoring  awarded by Rochester, NH (City of) 2018 - 2019
  • Bellamy River Sonde Deployment-2017  awarded by City of Dover 2017 - 2019
  • Microbial Source Tracking in Maine Beaches  awarded by Maine Department of Environmental Protection 2018 - 2019
  • Cocheco River Sonde Deployment-2017  awarded by Rochester, NH (City of) 2017 - 2018
  • 2017 NH Shellfish Vibrio Analysis  awarded by NH Department of Environmental Services 2017
  • 2016 Annual Datasonde Deployment in the Cocheco River  awarded by City of Dover 2016 - 2017
  • 2016 NHDES Shellfish Vibrio Studies  awarded by NH Department of Environmental Services 2016
  • 2015 UNH Monitoring to Support the NCCA in 2015  awarded by NH Department of Environmental Services 2015 - 2016
  • Impact of the Dover NH Wastwater Treatment Facility on Water Quality in the Great Bay Estuary and Sonde Deployment in the Cocheco River  awarded by City of Dover 2015
  • 2015 NHDES Shellfish Program Vibrio Analysis  awarded by NH Department of Environmental Services 2015
  • Bacteria and Weather Based Beach Modeling for York Maine  awarded by Town of York ME 2014 - 2015
  • Dissolved Oxygen Study in NH Tidal Rivers  awarded by City of Dover 2014 - 2015
  • Vibrio Parahaemolyticus Testing of Little Bay Oysters  awarded by NH Department of Environmental Services 2014
  • Piscataqua River-Portsmouth Harbor Water Transparency Field Study  awarded by City of Dover 2013
  • Piloting Citizen Volunteer Participation in Monitoring Stormwater Discharges in NH Seacoast Municipalities  awarded by NH Department of Environmental Services 2011 - 2012
  • Ecoli Ribotyping and Water Quality Monitoring for the Colchester VT IWRMP  awarded by Forcier Aldrich & Assoc 2009 - 2012
  • Coordination of 2011-2012 Gulfwatch Project  awarded by Gulf of Maine Council 2011 - 2012
  • Dissolved Oxygen and Nutrients in the Squamscott River  awarded by Portsmouth, NH (City of) 2011
  • UNH Monitoring Activities that Support the National Coastal Condition Assessment in 2010  awarded by NH Department of Environmental Services 2010 - 2011
  • Gulfwatch Program  awarded by Gulf of Maine Council 2010 - 2011
  • Monitoring to Support the NH National Coastal Assessment Program  awarded by NH Department of Environmental Services 2009 - 2010
  • Management of the Gulfwatch Mussel Monitoring Program  awarded by Gulf of Maine Council 2009 - 2010
  • 2008 NH National Coastal Assessment Monitoring Program - NHEP  awarded by NH Department of Environmental Services 2008 - 2009
  • Management of the Gulfwatch Toxic Contaminant Monitoring Program  awarded by Gulf of Maine Council 2007 - 2009
  • Management of the 2008 GOMC Gulfwatch Program  awarded by Canadian Delegates to Gulf of ME 2008 - 2009
  • New Hampshire National Coastal Assessment 2006  awarded by NH Department of Environmental Services 2006 - 2007
  • Management of the Gulf of Maine Gulfwatch Program  awarded by Gulf of Maine Council 2006 - 2007
  • Beach Program Total Maximum Daily Load Microbial Source Tracking Project  awarded by NH Department of Environmental Services 2006 - 2007
  • Pollution Source Identification Study of Berry's Brook  awarded by NH Department of Environmental Services 2006
  • 2005 New Hampshire National Coastal Assessment  awarded by NH Department of Environmental Services 2005 - 2006
  • New Hampshire National Coastal Assessment (2004), Estuarine Survey of Coastal NH  awarded by NH Department of Environmental Services 2004 - 2006
  • Pollution Tracking in Bellamy River  awarded by NH Department of Environmental Services 2006
  • Gulfwatch Mussel Monitoring Project  awarded by Gulf of Maine Council 2005 - 2006
  • Beach Program Total Maximum Daily Load Microbial Source Tracking Project  awarded by NH Department of Environmental Services 2005 - 2006
  • Management Non Human Sources Bacteria Hampton Harbor  awarded by NH Department of Environmental Services 2004 - 2005
  • Gulfwatch Mussel Monitoring  awarded by Gulf of Maine Council 2004 - 2005
  • E Coli Ribotyping in Cains Brook, NH  awarded by NH Department of Environmental Services 2004 - 2005
  • Characterization & Recommended Monitoring Hodgson Brook  awarded by NH Department of Environmental Services 2002 - 2004
  • Ribotyping E Coli NH Shellfish Program  awarded by NH Office of the Governor, Office of Energy & Pla 2003 - 2004
  • Gulfwatch Monitoring Program  awarded by Gulf of Maine Council 2003 - 2004
  • 2003 National Coastal Assessment Estuarine Survey  awarded by State of New Hampshire Miscellaneous Sponsor 2002 - 2004
  • Stormwater Technology Verification  awarded by NH Department of Environmental Services 2001 - 2004
  • Identify Bacterial Sources Public Beaches Microbial Source  awarded by NH Department of Environmental Services 2003 - 2004
  • 2001-2002 Gulfwatch Project  awarded by Gulf of Maine Council 2002 - 2003
  • Ribotyping Capacity Building For Microbial Source Tracking  awarded by NH Department of Environmental Services 2002 - 2003
  • Ribotyping of E. Coli to ID Fecal Contamination in Maine  awarded by Maine Department of Environmental Protection 2002 - 2003
  • 2002 NH National Coastal Assessment  awarded by NH Department of Environmental Services 2001 - 2003
  • Microbial Source Tracking in Little Harbor & Atlantic Coast  awarded by NH Department of Environmental Services 2001 - 2003
  • Coastal 2001 Estuarine Survey of NH  awarded by NH Department of Environmental Services 2000 - 2002
  • Ribotyping for Tracking Sources of Bacteria in NH Waters  awarded by NH Office of the Governor, Office of Energy & Pla 2000 - 2002
  • Coastal 2000 Estuarine Survey of NH  awarded by NH Department of Environmental Services 1999 - 2001
  • Gulfwatch Monitoring Program  awarded by Gulf of Maine Council 1999 - 2001
  • Microbial Source Tracking in Vermont Using Ribotyping  awarded by Environmental Protection Agency (EPA) 1999 - 2001
  • NH Estuaries Project  awarded by NH Office of the Governor, Office of Energy & Pla 1998 - 2001
  • Ribotyping E Coli Isolates from Estuarine Waters  awarded by NH Department of Environmental Services 1998 - 2001
  • Great Bay NERR Monitoring Program  awarded by NH Department of Fish & Game 1999 - 2000
  • Urban Rivers: Storm Contaminat Ion  awarded by NH Office of the Governor, Office of Energy & Pla 1999 - 2000
  • Little Harbor/Back Channel Sanitary Survey Analyses  awarded by NH Department of Environmental Services 1998 - 2000
  • Strategy for Identifying Urban Contamination Sources  awarded by NH Office of the Governor, Office of Energy & Pla 1998 - 2000
  • Mercury Cycling in New England Estuaries  awarded by Environmental Protection Agency (EPA) 1996 - 2000
  • Bacterial Phase Partitioning in Stormwater  awarded by NH Office of the Governor, Office of Energy & Pla 1998 - 1999
  • Great Bay NERR Monitoring Program  awarded by NH Department of Fish & Game 1998 - 1999
  • NH Estuaries Project  awarded by NH Office of the Governor, Office of Energy & Pla 1998 - 1999
  • Urban Stormwater Contamination of New Hampshire Tidal Rivers  awarded by NH Office of the Governor, Office of Energy & Pla 1997 - 1999
  • A Monitoring Program for the Great Bay NERR  awarded by NH Department of Fish & Game 1997 - 1998
  • Continue Gulfwatch Monitoring Program  awarded by Gulf of Maine Council 1997 - 1998
  • Public Health Significance of Stormwater Microorganisms  awarded by NH Department of Environmental Services 1996 - 1998
  • Stormwater Contamination of Coastal Surface Waters  awarded by NH Office of the Governor, Office of Energy & Pla 1996 - 1998
  • Dryweather Bacterial Levels in Stormwater Systems  awarded by NH Office of the Governor, Office of Energy & Pla 1996 - 1997
  • Fieldwork Support for Gulfwatch  awarded by Gulf of Maine Council 1996 - 1997
  • Five-Year Analysis of Gulfwatch  awarded by Gulf of Maine Council 1996 - 1997
  • Continuation of Gomene Gulfwater Monitoring Program  awarded by Gulf of Maine Council 1995 - 1997
  • Septic Tank Disconnection Impacts on Coastal Water Quality  awarded by NH Office of the Governor, Office of Energy & Pla 1995 - 1997
  • Monitoring Plan for Great Bay Estuarine Research Reserve  awarded by NH Department of Fish & Game 1993 - 1997
  • Assessment of Nonpoint Source Pollution in GBE Tributaries  awarded by NH Office of the Governor, Office of Energy & Pla 1995 - 1996
  • IRC Company Match  awarded by Great Bay Aquafarms, Inc. 1995 - 1996
  • Assessment of Clam Resources & Sanitary Quality of Waters  awarded by NH Office of the Governor, Office of Energy & Pla 1994 - 1996
  • Effectiveness of Storm Water Control Measures  awarded by NH Office of the Governor, Office of Energy & Pla 1994 - 1996
  • Septic System Design & Effects on Coastal Habitat & Water  awarded by NH Office of the Governor, Office of Energy & Pla 1994 - 1996
  • Assessing Pollution Impacts on Coastal Watersheds  awarded by NH Office of the Governor, Office of Energy & Pla 1993 - 1995
  • Assessment of Nonpoint Source Pollution in Great Bay Estuary  awarded by NH Office of the Governor, Office of Energy & Pla 1993 - 1995
  • Bacteria and Nutrients from Subsurface Disposal Systems  awarded by NH Office of the Governor, Office of Energy & Pla 1993 - 1995
  • Pollution Sources & Environment Factors Affecting Water  awarded by NH Department of Health & Human Services 1993 - 1995
  • Mitigation of Contaminated Water Using Constructed Wetlands  awarded by NH Office of the Governor, Office of Energy & Pla 1993 - 1994
  • Contaminated Sediment Database for Gulf of Maine  awarded by Woods Hole Oceanographic Institution 1992 - 1994
  • Influence of Nonpoint Source Pollution on Estuarine Bacteria  awarded by US DOC, National Oceanic & Atmospheric Administration (NOAA) 1992 - 1994
  • Land Use and Nonpoint Source Pollution in Coastal Watersheds  awarded by NH Office of the Governor, Office of Energy & Pla 1992 - 1994
  • Monitoring Plan for the Great Bay Estuary  awarded by NH Department of Fish & Game 1991 - 1994
  • Agricultural Contamination of Estuarine Water  awarded by NH Office of the Governor, Office of Energy & Pla 1992 - 1993
  • Nonpoint Source Pollution in Oyster River Watershed  awarded by NH Office of the Governor, Office of Energy & Pla 1992 - 1993

    • Investigator On

  • Assessing Microbial Safety Issues Associated with Emerging Shellfish Aquaculture Practices to Increase Productivity in the Northeast US  awarded by US DOC, National Oceanic & Atmospheric Administration (NOAA) 2018 - 2022
  • 2020-2021 Data Collection in the Great Bay Estuary  awarded by NH Department of Environmental Services 2020 - 2021
  • 2014-2017 NH Sea Grant Omnibus  awarded by US DOC, National Oceanic & Atmospheric Administration (NOAA) 2014 - 2019
  • Vibrio Detection With Phage  awarded by Cornell University 2017 - 2019
  • Piscataqua Region Estuaries Partnership - Year 20 Workplan (2015)  awarded by Environmental Protection Agency (EPA) 2015 - 2017
  • PREP Year 19  awarded by Environmental Protection Agency (EPA) 2014 - 2017
  • Piscataqua Region Estuaries Partnership's  awarded by Environmental Protection Agency (EPA) 2012 - 2016
  • Piscataqua Region Estuaries Partnership Year 15 Workplan to Implement the Management Plan for the Region's Estuaries in 2011  awarded by Environmental Protection Agency (EPA) 2010 - 2016
  • Sustaining Coastal Systems: Linking Science and Decision-Making to Reduce Pollution-Related Impairment  awarded by National Science Foundation (NSF) 2013 - 2016
  • PREP Year 18  awarded by Environmental Protection Agency (EPA) 2013 - 2015
  • Piscataqua Region Estuaries Partnership Year 16 Workplan to Implement the Management Plan for the Region's Estuaries in 2012  awarded by Environmental Protection Agency (EPA) 2011 - 2014
  • Piscataqua Region Estuaries Partnership Year 14 Work Plan to Implement the Management Plan for the Region's Estuaries in 2010  awarded by Environmental Protection Agency (EPA) 2009 - 2012
  • 2006-08 Sea Grant Program  awarded by US DOC, National Oceanic & Atmospheric Administration (NOAA) 2006 - 2012
  • New Hampshire Estuaries Project Year 13 Work Plan to Implement the Management Plan for NH's Estuaries in 2009  awarded by Environmental Protection Agency (EPA) 2008 - 2011
  • New Hampshire Estuaries Project Year 12 Work Plan to Implement the Management Plan for NH's Estuaries in 2008  awarded by Environmental Protection Agency (EPA) 2007 - 2011
  • Work Plan of New Hampshire Estuaries Project  awarded by Environmental Protection Agency (EPA) 2005 - 2008
  • UNH Monitoring Activities that Support the National Coastal Assessment in 2007  awarded by NH Department of Environmental Services 2007 - 2008
  • CICEET 2001-2003  awarded by US DOC, National Oceanic & Atmospheric Administration (NOAA) 2001 - 2004

    • Teaching Activities

  • Senior Honors Thesis Taught course 2022
  • Senior Honors Thesis Taught course 2021
  • Doctoral Thesis Taught course 2019
  • Doctoral Thesis Taught course 2019
  • Doctoral Thesis Taught course 2018
  • Doctoral Research Taught course 2018
  • Doctoral Research Taught course 2017
  • Doctoral Research Taught course 2017
  • Doctoral Research Taught course 2017
  • Environmental Eng Microbiology Taught course 2017
  • Environmental Eng Microbiology Taught course 2017
  • Environmental Eng Microbiology Taught course 2017
  • Doctoral Research Taught course 2016
  • Doctoral Research Taught course 2016
  • Environmental Eng Microbiology Taught course 2016
  • Environmental Eng Microbiology Taught course 2016
  • Environmental Eng Microbiology Taught course 2016
  • Doctoral Research Taught course 2015
  • Investigations Taught course 2015
  • Doctoral Research Taught course 2015
  • Environmental Eng Microbiology Taught course 2015
  • Environmental Eng Microbiology Taught course 2015
  • Environmental Eng Microbiology Taught course 2015
  • Doctoral Research Taught course 2014
  • Investigations Taught course 2014
  • Doctoral Research Taught course 2014

    • Education And Training

  • B.S. Soil Science, University of Maine
  • M.S. Soil Science, University of Wisconsin
  • Ph.D. Bacteriology, University of Wisconsin

    • Full Name

  • Stephen Jones