Joseph J. Vallino, Ph.D.

Ecosystems Center Email:
Marine Biological Laboratory WWW:
7 MBL St. (508) 289-7648
Woods Hole, MA 02543 FAX: (508) 457-1548

Ph.D. Chemical Engineering, 1991 Massachusetts Institute of Technology,
M.S. Chemical Engineering, 1985 California Institute of Technology,
B.S. Chemical Engineering, 1983 University of California, Berkeley

2011 - Present Senior Scientist, The Ecosystems Center, Marine Biological Laboratory, Woods Hole, MA.
2018 - Present
Consortium for Advanced Science and Engineering Senior Scientist at-Large, University of Chicago, IL
2010-2013 Assistant Professor (MBL), Geological Sciences, Brown University.
2005-2011 Associate Scientist, The Ecosystems Center, Marine Biological Laboratory, Woods Hole, MA.
2004-2010 Adjunct Professor (MBL), Ecology and Evolutionary Biology, Brown University.
1997-2005 Assistant Scientist, The Ecosystems Center, Marine Biological Laboratory, Woods Hole, MA.
1997-1997 Research Associate, The Ecosystems Center
1994-1997 Postdoctoral Research Associate, The Ecosystems Center
1993-1994 Lakian Postdoctoral Scholar, The Ecosystems Center.
1991-1993 Mellon Postdoctoral Fellow, Scripps Institution of Oceanography, San Diego, CA.

  1. Tsakalakis, I., M. J. Follows, S. Dutkiewicz, C. L. Follett, and J. J. Vallino. 2022. Diel light cycles affect phytoplankton competition in the global ocean. Global Ecology and Biogeography, 00, 1– 12, doi: 10.1111/geb.13562

  2. Fortunato, C. S., D. A. Butterfield, B. Larson, N. Lawrence-Slavas, C. K. Algar, L. Zeigler Allen, J. F. Holden, G. Proskurowski, E. Reddington, L. C. Stewart, B. D. Topçuoğlu, J. J. Vallino, and J. A. Huber. 2021. Seafloor incubation experiment with deep-sea hydrothermal vent fluid reveals effect of pressure and lag time on autotrophic microbial communities. Applied and Environmental Microbiology:AEM.00078-00021, doi:10.1128/aem.00078-21.
  3. Vallino, J.J. and Tsakalakis, I. (2020) Phytoplankton temporal strategies increase entropy production in a marine food web model. Entropy, 22 (11), 1249, 25 pp., doi: 10.3390/e22111249. Code here:

  4. Stewart, L.C., Algar, C.K., Fortunato, C.S., Larson, L., Vallino, J.J., Huber, J.A., Butterfield, D.A. and Holden, J.F. (2019) Fluid geochemistry, local hydrology, and metabolic activity define methanogen community size and composition in deep-sea hydrothermal vents. ISME J, 13, 1711-1721, doi: 10.1038/s41396-019-0382-3.
  5. Vallino, J.J. and Huber, J.A. (2018) Using maximum entropy production to describe microbial biogeochemistry over time and space in a meromictic pond. Frontiers in Environmental Science 6, 100, 22pp., doi: 10.3389/fenvs.2018.00100. Code here:

  6. Fernandez-Gonzalez, N., Huber, J.A., Vallino, J.J. (2016) Microbial communities are well adapted to disturbances in energy input. mSystems 1 (5), 15 pp., doi: 10.1128/mSystems.00117-16.  Experimental data are here:
  7. Vallino, J.J. and Algar, C.K. (2016) Thermodynamics of Marine Biogeochemical Cycles: Lotka Revisited. Ann. Rev. Mar. Sci. 8, 333-356, doi: 10.1146/annurev-marine-010814-015843 (reprint here)

  8. Chapman, E.J., Childers, D.L. and Vallino, J.J. (2016) How The Second Law of Thermodynamics has informed ecosystem ecology through its history. BioScience 66 (1), 27-39, doi: 10.1093/biosci/biv166
  9. Rastetter, E.B. and Vallino, J.J. (2015) Ecosystem's 80th and the Reemergence of Emergence. Ecosystems 18 (5), 735-739, doi: 10.1007/s10021-015-9893-6.

  10. Algar, C.K. and Vallino, J.J. (2014) Predicting microbial nitrate reduction pathways in coastal sediments. Aquat.Microb.Ecol. 71 (3): 223-238, doi: 10.3354/ame01678
  11. Vallino, J.J., Algar, C.K., Fernandez Gonzalez, N., Huber, J.A.. (2014) Use of receding horizon optimal control to solve MaxEP-based biogeochemistry problems. In Beyond the Second Law: Entropy Production and Non-Equilibrium Systems, Dewar, R.C., Lineweaver, C., Niven, R. and Regenauer-Lieb, K.,  (eds), Springer, pp 337-359, doi: 10.1007/978-3-642-40154-1_18. (draft version)

  12. Bowden, W. B., B. J. Peterson, L. A. Deegan, A. D. Huryn, J. P. Benstead, H. Golden, M. Kendrick, S. M. Parker, E. Schuett, J. J. Vallino, and J. E. Hobbie. (2014) Ecology of Streams of the Toolik Region. Pages 173-237 in J. E. Hobbie and G. W. Kling, editors. Alaska's Changing Arctic: Ecological Consequences for Tundra, Streams, and Lakes. Oxford University Press, New York.
  13. Dunaj, Sara J. , Vallino, Joseph J. , Hines, Mark E. , Gay, Marcus , Kobyljanec, Christine, and Rooney-Varga, Juliette N. (2012) Relationships between soil organic matter, nutrients, bacterial community structure, and the performance of microbial fuel cells. Environmental Science & Technology 46 (3):1914-1922, doi: 10.1021/es2032532.

  14. Xia, Li C., Steele, Joshua A., Cram, Jacob A., Cardon, Zoe G., Simmons, Sheri L., Vallino, Joseph J., Fuhrman, Jed A., Sun, Fengzhu (2011) Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates. BMC Systems Biology, 5(Suppl 2):S15, 12 pp., doi: 10.1186/1752-0509-5-S2-S15

  15. Vallino,J.J. (2011) Differences and implications in biogeochemistry from maximizing entropy production locally versus globally. Earth Syst. Dynam. 2, 69-85, doi: 10.5194/esd-2-69-2011
  16. Zhao,L., Chen, C., Vallino, J., Hopkinson, C., Beardsley, R.C., Lin, H., and Lerczak, J. (2010) Wetland-estuarine-shelf interactions in the Plum Island Sound and Merrimack River in the Massachusetts Coast. JGR-Oceans, 115, C10039, 13 pp. doi:10.1029/2009JC006085.

  17. Vallino, J.J. (2010) Ecosystem biogeochemistry considered as a distributed metabolic network ordered by maximum entropy production. Phil. Trans. R. Soc. B, 365, 1417-1427, doi:10.1098/rstb.2009.0272

  18. Wan, Z., Vallino, J.J., and Peterson, B.J. (2008) Study of the inter-annual food web dynamics in the Kuparuk River with a first order approximation inverse model. Ecol. Model. 211 (1-2) 97-112, doi: 10.1016/j.ecolmodel.2007.08.022

  19. Lyons, M.M., Lau, Y.-T., Carden, W.E., Ward, J.E., Roberts, S.B., Smolowitz, R., Vallino, J., Allam, B. (2007) Characteristics of marine aggregates in shallow-water ecosystems: Implications for disease ecology. EcoHealth 4 (4) 406-420, doi: 10.1007/s10393-007-0134-0

  20. Deegan,L.A., Bowen,J.L., Drake,D., Fleeger,J.W., Friedrichs,C.T., Kari,A., Hobbie,J.E., Hopkinson,C., Johnson,D.S., Johnson,J.M., LeMay,L.E., Miller,E., Peterson,B.J., Picard,C., Sheldon,S., Sutherland,M., Vallino,J., and Warren,R.S. (2007) Susceptibility of salt marshes to nutrient enrichment and predator removal. Ecological Applications 17 (sp5) S42-S63, doi:10.1890/06-0452.1.

  21. Claessens, L., Hopkinson Jr, C.,Rastetter, E. and Vallino, J. (2006). Effect of historical changes in land-use and climate on the water budget of an urbanizing watershed. Water Resources Research, 42 (3), W03426, doi:10.1029/2005WR004131

  22. Wan, Z. and Vallino, J.J. (2005). An inverse ecosystem model of year-to-year variations with first order approximation to the annual mean fluxes. Ecol. Model., 187 (4), 369-388.

  23. Vallino, J.J., Hopkinson, C.S., and Garritt, R.H. (2005). Estimating estuarine gross production, community respiration and net ecosystem production: A nonlinear inverse technique. Ecol. Model.,187 (2-3), 281-296.

  24. Williams, M., Hopkinson, C., Rastetter, E., Vallino, J. and Claessens, L. (2005). Relationships of land use and stream solute concentrations in the Ipswich River basin, Northeastern Massachusetts. Water, Air and Soil Pollution., 161 (1-4), 55-74.

  25. Hopkinson, C.S. and Vallino, J.J. (2005). Efficient export of carbon to the deep ocean through dissolved organic matter. Nature, 433, 142-145.

  26. Filoso, S., Vallino, J., Hopkinson, C., Rastetter, E. and Claessens, L. (2004). Modeling Nitrogen Transport in the Ipswich River Basin, Massachusetts, using HSPF. Journal of the American Water Resources Association, 40 (5), 1365-1384.

  27. Williams, M., Hopkinson, C., Rastetter, E., Vallino, J. (2004). N Budgets and Aquatic Uptake in the Ipswich River Basin, Northeastern Massachusetts. Water Resources Research, 40 (11), W11201, 12 pp.

  28. Tobias, C.R., Cieri, M., Peterson, B.J. Deegan, L.A., Vallino, J. and Hughes, J. (2003). Processing watershed-derived nitrogen in a well-flushed New England estuary. Limnol. Oceanogr., 48, 1766-1778.

  29. Vallino, J.J. (2003). Modeling microbial consortiums as distributed metabolic networks. Biol. Bull. 204, 174-179.

  30. Giblin, A.E., and Vallino, J.. (2003). The role of models in addressing coastal eutrophication problems. In: Canham, C. D., J. J. Cole, and W. K. Lauenroth (eds), The Role of Models in Ecosystem Science. Princeton University Press, 327-343.

  31. Hopkinson, C.S., Vallino, J.J. and Nolin, A. (2002). Decomposition of dissolved organic matter from the continental margin. Deep-Sea Res. II 49, 4461-4478.

  32. Vallino, J.J. (2000). Improving marine ecosystem models: use of data assimilation and mesocosm experiments. J. Mar. Res. 58, 117-164.

  33. Vallino, J.J. and Stephanopoulos, G. (2000). Metabolic Flux distributions in Corynebacterium glutamicum during growth and lysine overproduction. Biotechnol. Bioeng. 67, 872-885. (Republication of Vallino1993)

  34. Kirkby, R., L. Claessens, C. Hopkinson, E. Rastetter, J. Vallino (2000). Modeling the effects of land-use change on nitrogen biogeochemistry in the Ipswich watershed, Massachusetts. Biol. Bull. 199, 218-219.

  35. Perring, A., M. Williams, C. Hopkinson, Jr, E. Rastetter, and J. Vallino (2000). Solute dynamics in storm flow of the Ipswich River basin: effects of land use. Biol. Bull., 199, 219-221.

  36. Pease, K.M., L. Claessens, C. Hopkinson, E. Rastetter, J. Vallino, and N. Kilham (1999). Ipswich River nutrient dynamics: preliminary assessment of a simple nitrogen-processing model. Biol. Bull. 197, 289-290.

  37. Canfield,S., L. Claessens, C. Hopkinson, E. Rastetter and J. Vallino (1999). Long-term effect of municipal water use on the water budget of the Ipswich River basin. Biol. Bull. 197, 295-297.

  38. Vallino, J.J. and Hopkinson, C.S. (1998). Estimation of Dispersion and Characteristic Mixing Times in Plum Island Sound Estuary. Estuarine, Coastal and Shelf Science 46, 333-350.

  39. Hopkinson, C.S, Buffam, I., Hobbie, J., Vallino, J., Perdue, M., Eversmeyer, B., Prahl, F., Covert, J., Hodson, R., Moran, M.A., Smith, E., Baross, J., Crump, B., Findlay, S., and Foreman, D. (1998). Terrestrial inputs of organic matter to coastal ecosystems: an intercomparison of chemical characteristics and bioavailability. Biogeochemistry 43, 211-234.

  40. Jay, D.A., Uncles, R.J., Largier, J., Geyer, W.R., Vallino, J., and Boynton, W.R. (1997). A Review of Recent Developments in Estuarine Scalar Flux Estimation. Estuaries 20, 262-280.

  41. Vallino, J.J., Hopkinson, C.S., and Hobbie, J.E. (1996). Modeling Bacterial Utilization of Dissolved Organic Matter: Optimization Replaces Monod Growth Kinetics. Limnology and Oceanography 41, 1591-1609.

  42. Carini, S., N. Weston, C. Hopkinson, J. Tucker, A. Giblin and J. Vallino. (1996). Gas exchange rates in the Parker River estuary, Massachusetts. Biol. Bull. 191, 333-334.

  43. Hopkinson, C.S. and Vallino, J.J. (1995). The Relationship Between Man's Activities in Watersheds and Rivers and Patterns of Estuarine Community Metabolism. Estuaries 18, 598-621.

  44. Alderman, D., B. Balsis, I. Buffam, R. Garritt, C. Hopkinson and J. Vallino. (1995). Pelagic metabolism in the Parker River/Plum Island Sound Estuarine System. Biol. Bull. 189, 250-251.

  45. Balsis, B., D. Alderman, I. Buffam, R. Garritt, C. Hopkinson and J. Vallino. (1995). Total system metabolism in the Plum Island Sound estuary. Biol. Bull. 189, 252-254.

  46. Uhlenhopp, A. G., J. Hobbie and J. Vallino. (1995). Effects of land use on the degradability of dissolved organic matter in three watersheds of the Plum Island Sound estuary. Biol. Bull. 189, 256-257.

  47. Hopkinson, C.S. and Vallino, J.J. (1994). Toward the Development of Generally Applicable Models of the Microbial Loop in Aquatic Ecosystems. Microb. Ecol. 28, 321-326.

  48. Vallino, J.J. and Stephanopoulos, G. (1994). Carbon Flux Distributions at the Pyruvate Branch Point in Corynebacterium glutamicum during Lysine Overproduction. Biotech. Prog. 10, 320-326.

  49. Vallino, J.J. and Stephanopoulos, G. (1994). Carbon Flux Distributions at the Glucose 6-Phosphate Branch Point in Corynebacterium glutamicum during Lysine Overproduction. Biotech. Prog. 10, 327-334.

  50. Ingram, K., C. S. Hopkinson, K. Bowman, H. Garritt and J. Vallino. (1994). From watershed to estuary: assessment of nutrient loading, retention and export from the Ipswich River Basin. Biol. Bull. 187, 277-278.

  51. Wikner, J., Vallino, J.J., Steward, G., Smith, D., and Azam, F. (1993). Nucleic acids from the host bacterium as a major source of nucleotides for three marine bacteriophages. FEMS Microbiol. Ecol. 12, 237-248.

  52. Vallino, J.J. and Stephanopoulos, G. (1993). Metabolic Flux distributions in Corynebacterium glutamicum during growth and lysine overproduction. Biotechnol. Bioeng. 41, 633-646.

  53. Stephanopoulos, G. and Vallino, J.J. (1991). Network rigidity and metabolic engineering in metabolite overproduction. Science 252, 1675-1681.

  54. Vallino, J.J. and Stephanopoulos, G. (1990). Intracellular flux analysis as means of identifying limiting nodes in amino acid fermentations. In: Proc. - Eur. Congr. Biotechnol., 5th, Vol. 2., Christiansen, C., Munck, L., Villadsen, J. (Eds.), Munksgaard, Copenhagen, Den. 1063-1066.

  55. Vallino, J.J. and Stephanopoulos, G. (1990). Flux determinations in cellular bioreaction networks: applications to lysine fermentations. In: Frontiers in Bioprocessing. Sikdar, S. K., Todd, P. W., and Bier, M. (Eds.), CRC Press, Florida, pp. 205-219.

  56. Vallino, J.J. and Stephanopoulos, G. (1987). Intelligent sensors in biotechnology: applications for the monitoring of fermentations and cellular metabolism. Ann. N.Y. Acad. Sci. 506, 415-430.