National Research Program


Biogeochemistry of Carbon and Nitrogen in Aquatic Environments

Although it is clearly recognized that microorganisms play an important role in the transformation of carbon- and nitrogen-containing compounds in aquatic habitats, very little is known about the exact nature of these tranformations in either pristine or contaminated environments. Within the context of in situ environmental conditions, the mechanisms, pathways, rates, and factors controlling carbon cycling by microorganisms are poorly understood; however, these particular processes can significantly affect the entire range of biogeochemical and geochemical processes occurring within the aquatic environment. The objectives of this project are to study the mechanisms, pathways, and rates of transformation of carbon and nitrogen compounds (natural and contaminant) mediated by microorganisms in aquatic habitats; to identify some of the factors controlling these transformations; and to examine the effect that these transformations have upon other biogeochemical processes. For additional information, see project's home page.

REPORTS PUBLISHED 2003-2012

Barnes, R.T., Smith, R.L., and Aiken, G.R., 2012, Linkages between denitrification and dissolved organic matter quality, Boulder Creek watershed, Colorado: Journal of Geophysical Research, v 117, G01014, doi: 1029/2011JG001749 (on-line abstract of journal article).

Savoie, J.G., LeBlanc, D.R., Fairchild, G.M., Smith, R.L., Kent, D.B., Barber, L.B., Repert, D.A., Hart, C.P., Keefe, S.H., and Parsons, L.A., 2012, Groundwater-quality data for a treated-wastewater plume near the Massachusetts Military Reservation, Ashumet Valley, Cape Cod, Massachusetts, 2006–08: U.S. Geological Survey Data Series 648, 11 p. (on-line abstract or on-line report in pdf format, 1228 KB)

Underwood, J.C.,. Harvey, R.W., Metge, D.W., Repert, D.A., Baumgartner, L.K., Smith, R.L., Roane, T.M., and Barber, L.B., 2011, Effects of the antimicrobial sulfamethoxazole on groundwater bacterial enrichment: Environmental Science & Technology, v. 45, no. 7, p. 3096-3101. (on-line abstract of journal article)

Mueller, R.S., Denef, V.J., Kalnejais, L.H., Suttle, K.B., Thomas, B.C., Wilmes, P., Smith, R.L., Nordstrom, D.K., McCleskey, R.B., Shah, M.B., VerBerkmoes, N.C., Hettich, R.L., and Banfield, J.F., 2010, Ecological distribution and population physiology defined by proteomics in a natural microbial community: Molecular Systems Biology, Article Number 374, doi:10.1038/msb.2010.30. (on-line abstract or on-line journal article in pdf format, 2058 KB, Molecular Systems Biology is an on-line only, open-access journal)

Böhlke, J.K., Antweiler, R.C., Harvey, J.W., Laursen, A.E., Smith, L.K., Smith, R.L., and Voytek, M.A., 2009, Multi-scale measurements and modeling of denitrification in streams with varying flow and nitrate concentration in the upper Mississippi River basin, USA: Biogeochemistry, v. 93, p. 117–141. (on-line abstract or on-line paper in pdf format, 959 KB, published at Springerlink.com with open access)

Harris, S.H., and Smith, R.L., 2009, In situ measurements of microbially-catalyzed nitrification and nitrate reduction rates in an ephemeral drainage channel receiving water from coalbed natural gas discharge, Powder River Basin, Wyoming, USA: Chemical Geology, v. 267, no. 1-2, p. 77-84. (on-line abstract of journal article)

Miller, D.N., and Smith, R.L., 2009, Microbial characterization of nitrification in a shallow, nitrogen-contaminated aquifer, Cape Cod, Massachusetts and detection of a novel cluster associated with nitrifying Betaproteobacteria: Journal of Contaminant Hydrology, v. 103, no. 3-4, p. 182-193. (on-line abstract of journal article)

Smith, R.L., Böhlke, J.K., Repert, D.A., Hart, C.P., 2009, Nitrification and denitrification in a midwestern stream containing high nitrate: in situ assessment using tracers in dome-shaped incubation chambers: Biogeochemistry, v. 96, p. 189-208. (on-line abstract of journal article

Smith, R.L., Repert, D.A., and Hart, C.P., 2009, Geochemistry of inorganic nitrogen in waters released from coal-bed natural gas production wells in the Powder River Basin, Wyoming: Environmental Science and Technology, v. 43, no. 7, p. 2348-2354. (on-line abstract or on-line article in pdf format, 1652 KB, published by the American Chemical Society, not subject to U.S. copyright)

Harris, S.H., Smith, R.L., and Barker, C.E., 2008, Microbial and chemical factors influencing methane production in laboratory incubations of low-rank subsurface coals: International Journal of Coal Geology, v. 76- no. 1-2, p. 46-51. (on-line abstract of journal article)

Sahl, J.W., Schmidt, R., Swanner, E.D., Mandernack, K.W., Templeton, A.S., Kieft, T.L., Smith, R.L., Sanford, W.E., Callaghan, R.L., Mitton, J.B., and Spear, J.R., 2008, Subsurface microbial diversity in deep-granitic-fracture water in Colorado: Applied and Environmental Microbiology, V. 74, no. 1, p. 143-152. (on-line abstract of journal article)

Smith, R.L., and Yoshinari, T., 2008, Occurrence and turnover of nitric oxide in a nitrogen-impacted sand and gravel aquifer : Environmental Science & Technology, v. 42 no. 22, p. 8245-8251. (on-line abstract of journal article)

Böhlke, J.K., Smith, R.L., and Hannon, J.E., 2007 Analysis of N and O isotopes in nitrite and nitrate by sequential selective bacterial reduction to N2O: Analytical Chemistry, v. 79, no. 15, p. 5888-5895. (on-line abstract or on-line article in pdf format, 149 KB, published by American Chemical Society; not subject to U.S. copyright)

Harris, S.H., Smith, R.L., and Suflita, J.M., 2007, In situ hydrogen consumption kinetics as an indicator of subsurface microbial activity: Federation of European Microbiological Societies Microbial Ecology, v. 60, p. 220-228. (on-line abstract of journal article)

Smith, R. L., and Harris, S. H., 2007, Determining the terminal electron-accepting reaction in the saturated subsurface, in C. J. Hurst, R. L. Crawford, J. L. Garland, D. A. Lipson, A. L. Mills, and L. D. Stetzenbach, eds., Manual of Environmental Microbiology, 3nd Edition, ASM Press, Washington, DC, p. 860-871.

Baeseman, J., Smith, R.L., and Silverstein, J., 2006, Denitrification in streams impacted by acid mine drainage - Effects os pH, various electron donors and iron: Microbial Ecology, v. 51, p. 232-241.

Böhlke, J.K., Smith, R.L., and Miller, D.N., 2006, Ammonium transport and reaction in contaminated groundwater - Application of isotope tracers and isotope fractionation studies: Water Resources Research, 42, W05411, doi:10.1029/2005WR004349. (on-line abstract or on-line journal article in pdf format, 1852 kb, published 2006 by American Geophysical Union, not subject to U.S. copyright)

Savoie, J.G., Smith, R.L., Kent, D.B., Hess, K.M., LeBlanc, D.R., and Barber, L.B., 2006, Ground-water-quality data for a treated-wastewater plume undergoing natural restoration, Ashumet Valley, Cape Cod, Massachusetts, 1994-2004: U.S. Geological Survey Data Series 198, 1 CD-ROM (on-line abstract and to download files)

Smith, R.L., Baumgartner, L.K., Miller, D.N., Repert, D.A., and Böhlke, J.K., 2006, Assessment of nitrification potential in ground water using short-term, single-well injection experiments: Microbial Ecology, v. 51, no. 1, p. 22-35. (on-line abstract of journal article)

Repert, D.A., Barber, L.B., Hess, K.M., Keefe, S.H., Kent, D.B., LeBlanc, D.R., and Smith, R.L., 2006, Long-term natural attenuation of carbon and nitrogen within a groundwater plume after removal of the treated wastewater source: Environmental Science and Technology, v. 40, p. 1,154-1,162. (on-line abstract or on-line report in pdf format, 474 kb, published by American Chemical Society; not subject to U.S. copyright)

Antweiler, R.C., Smith, R.L., Voytek, M.A., and Böhlke, J.K., 2005, Water-quality data from two agricultural drainage basins in northwestern Indiana and northeastern Illinois: II. Diel data, 1999-2001: U.S. Geological Survey Open-File Report 2005-1053, 114 p. (on-line abstract or on-line report in pdf format, 8.1 MB)

Antweiler, R.C., Smith, R.L., Voytek, M.A., Böhlke, J.K., and Dupre, D.H., 2005, Water-quality data from two agricultural drainage basins in northwestern Indiana and northeastern Illinois: III. Biweekly data, 2000-2002: U.S. Geological Survey Open-File Report 2005-1197, 66 p. (on-line abstract or on-line report in pdf format, 18.1 MB)

Antweiler, R.C., Smith, R.L., Voytek, M.A., Böhlke, J.K., and Richards, K.D., 2005, Water-quality data from two agricultural drainage basins in Northwestern Indiana and Northeastern Illinois: I. lagrangian and synoptic Data, 1999-2002: U.S. Geological Survey Open-File Report 2004-1317, 216 p. (on-line abstract or on-line report in pdf format, 4.9 MB)

Holloway, J.M., and Smith, R.L., 2005, Nitrogen and carbon flow from rock to water: Regulation through soil biogeochemical processes, Mokelumne River watershed, California, and Grand Valley, Colorado: Journal of Geophysical Research, v. 110, no. F1, F01010, doi:10.1029/2004JF000124. (on-line abstract of journal article)

Smith, R.L., Buckwalter, S.P., Repert, D.A., and Miller, D.N., 2005, Small-scale, hydrogen-oxidizing-denitrifying bioreactor for treatment of nitrate-contaminated drinking water: Water Research, v. 39, no. 10, p. 2014-2023. (on-line abstract of journal article)

Smith, R.L., 2005, Small-scale, hydrogen-oxidizing denitrifying bioreactor: U.S. Patent Office, no. 6,863,815 (on-line patent).

Baeseman, 2004, Denitrification in acid-impacted mountain stream sediments: Ph.D., Dissertation, Department of Civil, Environmental and Architectural Engineering, University of Colorado, 200 p.

Holloway, J.M., Smith, R.L., and Nordstrom, D.K., 2004, Nitrogen transformations in hot spring runoff, Yellowstone National Park, USA, in Wanty, R.B., and Seal, R.R., II, eds., Water-Rock Interaction, Proceedings of the Eleventh International Symposium on Water - Rock Interaction, Saratoga Springs, New York, July 2004: New York, A.A. Balkema, p. 145-148.

Savoie, J.G., Kent, D.B., Smith, R.L., Leblanc, D.R., and Hubble, D.W., 2004, Changes in ground-water quality near two granular-iron permeable reactive barriers in a sand and gravel aquifer, Cape Cod, Massachusetts, 1997-2000: U.S. Geological Survey Water-Resources Investigations Report 03-4309, 77 p. (on-line abstract or report in pdf format - 3MB)

Smith, R.L., Böhlke, J.K., Garabedian, S.P., Revesz, K.M., and Yoshinari, T., 2004, Assessing denitrification in groundwater using natural gradient tracer tests with 15N: In situ measurement of a sequential multistep reaction: Water Resources Research, v. 40, No. 7, W07101, doi:10.1029/2003WR002919. (on-line abstract)

Hatzinger, P.B., Palmer, P., Smith, R.L., Penarrieta, C.T., and Yoshinari, T., 2003, Applicability of tetrazolium salts for the measurement of respiratory activity and viability of groundwater bacteria: Journal of Microbiological Methods, v. 52, p. 47-58. (on-line abstract)

McCobb, T.D., Leblanc, D.R., Walter, D.A., Hess, K.M., Kent, D.B., Smith, R.L., 2003, Phosphorus in a ground-water contaminant plume discharging to Ashumet Pond, Cape Cod, Massachusetts, 1999, U.S. Geological Survey Water-Resources Investigations Report 02-4306, 69 p. (on-line abstract or report in pdf format - 9MB)


FOR ADDITIONAL INFORMATION ON THIS PROJECT, CONTACT:
Richard L. Smith
U.S. Geological Survey, 3215 Marine St., Boulder, CO 80303
Email: rlsmith@usgs.gov
Telephone: 303-541-3032

 For information on additional projects in the National Research Program, see Indexes to NRP projects and bibliographies.

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