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John B. Kirkpatrick
Postdoctoral Fellow
(401) 874-6220

Educational Background

Ph.D., Chemical Oceanography
A.B., History and Science
University of Washington
Harvard College

Areas of Specialization


I just earned my PhD investigating nutrient cycling in the redoxcline of the Black Sea. Specifically, my project involved working to understand the connections between geochemical processes, such as production and consumption of various N species, and the apparent activity of different bacterial groups. The former was inferred from nutrient profiles and stable isotope measurements, while the latter was based on the detection and amplification of various mRNA sequences. The Black Sea's suboxic zone is famous (or infamous) for being a model environment for anammox-driven N loss, but it's not as simple as it appears (is it ever?). Stay tuned for publications... Now I'm just getting started on this postdoc at URI! I'm working with Steve D'Hondt on a set of sediment cores from the Bay of Bengal (and other places, perhaps) that exhibit an apparent loss of NH4+ in the absence of typical oxidants (O2, NO2). Thermodynamically, it could simply be coupled to sulfate reduction (a la Schrum, H.N., A.J. Spivack, M. Kastner and S. D’Hondt, 2009. Sulfate-reducing denitrification: A thermodynamically feasible metabolic pathway in subseafloor sediments, Geology 37(10), 939-942) -- but who's involved? That's one of the questions we're trying to address. This is one project under the auspices of the Center for Dark Energy Biosphere Investigations, who have a lot of fascinating things going on... check it out! www.darkenergybiosphere.org


Here is one example of education and outreach skills I've been trying to work on at various workshops and meetings. These two videos are thanks to NASA Astrobiology! ............................................................................................................................................................. http://www.youtube.com/watch?v=jI9CiUcfM-0&feature=player_detailpage .................................................................. http://www.youtube.com/watch?v=zcwdJqlMzf4&feature=player_detailpage


Kirkpatrick, J. B., Fuchsman, C. A., Yakushev, E., Staley, J. T., and Murray, J. W. (2012) Concurrent activity of anammox and denitrifying bacteria in the suboxic zone of the Black Sea. Frontiers in Aquatic Microbiology 3: 256. doi: 10.3389/fmicb.2012.00256

Fuchsman, C. A., Staley, J. T., Oakley, B. B., Kirkpatrick, J. B., and Murray, J. W. (2012). Free-living and aggregate-associated Planctomycetes in the Black Sea. FEMS Microbiology Ecology 80, 402 - 416.

Fuchsman, C. A., Kirkpatrick, J. B., Brazelton, W. J., Murray, J. W., & Staley, J. T.  (2011) Metabolic strategies of free-living and aggregate associated bacterial communities inferred from biological and chemical profiles in the Black Sea suboxic zone.  FEMS Microbial Ecology: doi:10.1111/j.1574-6941.2011.01189.x

Stanley, R. H. R., Kirkpatrick, J. B., Cassar, N., Barnett, B. A., & Bender, M. L. (2010)  Net Community Production and Gross Primary Production Rates in the Western Equatorial Pacific. Global Biogeochemical Cycles 24: doi:10.1029/2009GB003651.

Kirkpatrick, J., Oakley, B., Fuchsman, C., Srinivasan, S., Staley, J. T., & Murray, J. W.  (2006)   Diversity and distribution of Planctomycetes and related bacteria in the suboxic zone of the Black Sea.  Applied and Environmental Microbiology 72: 3079-3083.

Murray, J. W., Fuchsman, C., Kirkpatrick, J., Paul, B., & Konovalov, S. K.  (2005)  Species and d15N signatures of nitrogen transformations in the suboxic zone of the Black Sea.  Oceanography 18: 36 – 47.

Kirkpatrick, J., Foreman, K., & Valiela, I. (1998)  Dissolved inorganic nitrogen flux and mineralization in Waquoit Bay as measured by core incubations.  Biological Bulletin 195 : 240 – 241.


Kirkpatrick, J. B., Fuchsman, C. A., Staley, J. T., & Murray, J. W.  (2010)  Nitrogen fixation in the Black Sea -- who, when, and why? AGU Ocean Sciences Meeting, 22-26 February: Portland, OR.

Fuchsman, C. A., Kirkpatrick, J. B., Brazelton, W. J. Staley, J. T., & Murray, J. W.  (2009)  Examining the free-living and particle-associated bacterial communities in the Black Sea's suboxic zone.  ICoMM Users Meeting, 5-9 April: Woods Hole, MA.

Kirkpatrick, J. B., Fuchsman, C. A., Murray, J. W., & Staley, J. T. (2009)  The more things change, the more they stay the same -- or do they?  N cycling in the Black Sea.  ASLO Aquatic Sciences Meeting, 25 - 30 January: Nice, France.  *Outstanding student presentation award*

Kirkpatrick, J. B., Fuchsman, C. A., Murray, J. W., & Staley, J. T. (2008)  Nitrogen Ins and Outs in the Black Sea: Changes and Balances of Denitrifying and Nitrogen Fixing Microbial Communities.  NSF Dissertation Symposium in Chemical Oceanography, 6 - 10 October: Honolulu, HI.

Kirkpatrick, J. B., Stanley, R. H., Cassar, N., Bender, M. L., Murray, J. W. (2008) Gross production and underway net community production measurements in the Equatorial Pacific. ASLO Ocean Sciences Meeting, 2 - 7 March; Orlando, FL. *Outstanding student poster award*

Kirkpatrick, J. B., Oakley, B., Fuchsman, C. A., Staley, J. T., Murray, J. W. (2006)  From bacterial “species” to biogeochemical cycles in the Black Sea.  National Astrobiology Institute Conference, 26 - 30 March; Washington, D.C.

Kirkpatrick, J. B., Oakley, B., Fuchsman, C. A., Staley, J. T., Murray, J. W. (2006)  Diversity and Biogeochemistry of Planctomycetes and Related Bacteria in the Suboxic Zone of the Black Sea.  Ocean Sciences Meeting, 20 - 24 February; Honolulu, HI.

Kirkpatrick, J. B., Oakley, B., Fuchsman, C. A., Staley, J. T., Murray, J. W. (2005)  The Black Sea DNA story: where to start?  Invited speaker at Bogacizi University, 25 March; Istanbul, Turkey.