Individual-based modelling of adaptation in marine microbial populations using genetically defined physiological parameters

Ecological Modelling

Volumn 222, Issue 23-24, 2011, Pages 3823-3837

  Clark, James R ^a   Daines, Stuart J ^a   Lenton, Timothy M ^a   Watson, Andrew J ^b   Williams, Hywel T P ^a  

^a UNIVERSITY OF EXETER   (United Kingdom)

^b UNIVERSITY OF EAST ANGLIA   (United Kingdom)

Author keywords

Adaptation; Individual based modelling; Marine microorganisms; Resource competition; Storage strategies

Indexed keywords

ADAPTATION; CLONAL POPULATION; COMPETITION THEORY; DETAILED MODELS; ENVIRONMENTAL CONDITIONS; EVOLUTIONARY DYNAMICS; EVOLUTIONARY PROCESS; GENOMICS; GLOBAL MARINES; GROWTH STRATEGY; INDIVIDUAL-BASED; INDIVIDUAL-BASED MODELLING; INDIVIDUAL-BASED MODELS; MARINE ECOSYSTEM; MARINE MICROBIAL DIVERSITY; MARINE MICROORGANISM; MICROBIAL COMMUNITIES; MICROBIAL POPULATIONS; PHENOTYPIC TRAITS; PHYSIOLOGICAL PARAMETERS; PHYSIOLOGICAL TRAIT; PROCESS REPRESENTATION; RANDOM MUTATION; SPATIAL COMPLEXITY; VARIABLE ENVIRONMENT;

ECOSYSTEMS; MICROORGANISMS; PHYSIOLOGY;

PHYSIOLOGICAL MODELS;

ADAPTATION; ECOLOGICAL MODELING; ECOSYSTEM MODELING; ENVIRONMENTAL CONDITIONS; GENOMICS; MARINE ECOSYSTEM; MICROBIAL COMMUNITY; MUTATION; PHENOTYPE; PHYSIOLOGICAL RESPONSE; POPULATION MODELING; POPULATION STRUCTURE; REPRODUCTION; SPECIES DIVERSITY; TRADE-OFF;

EID: 80755159413     PISSN: 03043800     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ecolmodel.2011.10.001     Document Type: Article

References (65)

1. Allen J.I., Aiken J., Anderson T.R., Buitenhuis E., Cornell S., Geider R.J., Haines K., Hirata T., Holt J., Le Quéré C., Hardman-Mountford N., Ross O.N., Sinha B., While J. Marine ecosystem models for earth systems applications: the marquest experience. Journal of Marine Systems 2010, 81:19-33.
2. Anderson T.R. Plankton functional type modelling: running before we can walk?. Journal of Plankton Research 2005, 27:1073-1081.
3. Anderson T.R. Progress in marine ecosystem modelling and the "unreasonable effectiveness of mathematics. Journal of Marine Systems 2010, 81:4-11.
4. Azam F., Malfatti F. Microbial structuring of marine ecosystems. Nature Reviews. Microbiology 2007, 5:782-791.
5. Barton A.D., Dutkiewicz S., Flierl G., Bragg J., Follows M.J. Patterns of diversity in marine phytoplankton. Science 2010, 327:1509-1511.
6. Bruggeman, J., 2009. Succession in plankton communities: a trait-based perspective. Ph.D. Thesis. de Vrije Universiteit, Amsterdam.
7. Bruggeman J., Kooijman S.A.L.M. A biodiversity-inspired approach to aquatic ecosystem modeling. Limnology and Oceanography 2007, 52:1533-1544.
8. Burmaster D.E. The unsteady continuous culture of phosphate-limited Monochrysis lutheri droop: experimental and theoretical analysis. Journal of Experimental Marine Biology and Ecology 1979, 39:167-186.
9. Burmaster D.E., Chisholm S.W. A comparison of two methods for measuring phosphate uptake by Monochrysis Lutheri Droop grown in continuous culture. Journal of Experimental Marine Biology and Ecology 1979, 39:187-202.
10. Camazine S., Deneubourg J.L., Franks N.R., Sneyd J., Theraulaz G., Bonabeau E. Self-organization in Biological Systems 2002, Princeton University Press.
11. Crowley P.H. Natural-selection and the Michaelis constant. Journal of Theoretical Biology 1975, 50:461-475.
12. Cuddington K., Leavitt P.R. An individual-based model of pigment flux in lakes: implications for organic biogeochemistry and paleoecology. Canadian Journal of Fisheries and Aquatic Sciences 1999, 56:1964-1977.
13. DeAngelis D.L., Gross L.J. Individual-based Models and Approaches in Ecology 1992, Chapman and Hall, New York, NY.
14. Denamur E., Matic I. Evolution of mutation rates in bacteria. Molecular Microbiology 2006, 60:820-827.
15. Dieckmann U. Coevolutionary Dynamics of Stochastic Replicator Systems 1994, Central Library of the Research Center Juelich, Juelich, Germany.
16. Doyle R.W. Upwelling, clone selection, and characteristic shape of nutrient uptake curves. Limnology and Oceanography 1975, 20:487-489.
17. 12 and marine ecology. IV. Kinetics of uptake growth and inhibition in Monochrysis lutheri. Journal of the Marine Biological Association of the United Kingdom 1968, 48:689-733.
18. Droop M.R. Vitamin B12 and marine ecology. Helgoland Marine Research 1970, 20:629-636.
19. Droop M.R. Some thoughts on nutrient limitation in algae. Journal of Phycology 1973, 9:264-272.
20. Droop M.R. Nutrient status of algal cells in continuous culture. Journal of the Marine Biological Association of the United Kingdom 1974, 54:825-855.
21. Ducobu H., Huisman J., Jonker R.R., Mur L.R. Competition between a prochlorophyte and a cyanobacterium under various phosphorous regimes: comparison with the Droop Model. Journal of Phycology 1998, 34:467-476.
22. Dutkiewicz S., Follows M.J., Bragg J.G. Modeling the coupling of ocean ecology and biogeochemistry. Global Biogeochemical Cycles 2009, 23.
23. Fasham M., Ducklow H., McKelvie S. A nitrogen-based model of plankton dynamics in the oceanic mixed layer. Journal of Marine Research 1990, 48:591-639.
24. Flynn K.J. Reply to Horizons article 'Plankton functional type modelling: running before we can walk' Anderson (2005): putting trophic functionality into plankton functional types. Journal of Plankton Research 2006, 28:873-875.
25. Flynn K.J. Use, abuse, misconceptions and insights from quota models: the Droop cell-quota model 40 years on. Oceanography and Marine Biology 2008, 46:1-23.
26. Follows M.J., Dutkiewicz S., Grant S., Chisholm S.W. Emergent biogeography of microbial communities in a model ocean. Science 2007, 315:1843-1846.
27. Follows M.J., Dutkiewicz S. Modeling diverse communities of marine microbes. Annual Review of Marine Science 2011, 3:427-451.
28. Friedrichs M.A.M., Dusenberry J.A., Anderson L.A., Armstrong R.A., Chai F., Christian J.R., Doney S.C., Dunne J., Fujii M., Hood R., McGillicuddy Dennis J.J., Moore J.K., Schartau M., Spitz Y.H., Wiggert J.D. Assessment of skill and portability in regional marine biogeochemical models: role of multiple planktonic groups. Journal of Geophysical Research 2007, 112.
29. Grimm V., Railsback S.F. Individual-based Modelling and Ecology 2005, Princeton University Press.
30. Grover J.P. Resource competition in a variable environment: phytoplankton growing according to the variable-internal-stores model. The American Naturalist 1991, 138:811-835.
31. Hellweger F.L. Spatially explicit individual-based modeling using a fixed super-individual density. Computational Geosciences 2008, 34:144-152.
32. Hellweger F.L. Carrying photosynthesis genes increases ecological fitness of cyanophage in silico. Environmental Microbiology 2009, 11:1386-1394.
33. Hellweger F.L., Bucci V. A bunch of tiny individuals-individual-based modeling for microbes. Ecological Modelling 2009, 220:8-22.
34. Hellweger F.L., Kianirad E. Accounting for intrapopulation variability in biogeochemical models using agent-based methods. Environmental Science & Technology 2007, 41:2855-2860.
35. Hellweger F.L., Kianirad E. Individual-based modeling of phytoplankton: evaluating approaches for applying the cell quota model. Journal of Theoretical Biology 2007, 249:554-565.
36. Hickman A. Modelling the effects of chromatic adaptation on phytoplankton community structure in the oligotrophic environment. Marine Ecology Progress Series 2010, 2010:1-17.
37. Klausmeier C.A., Litchman E., Daufresne T., Levin S.A. Optimal nitrogen-to-phosphorus stoichiometry of phytoplankton. Nature 2004, 429:171-174.
38. Kooijman S.A.L.M. Dynamic Energy and Mass Budgets in Biological Systems 2000, Cambridge University Press. 2nd edition.
39. Le Quéré C., Harrison S.P., Prentice I.C., Buitenhuis E.T., Aumont O., Bopp L., Claustre H., Cunha L.C.D., Geider R., Giraud X., Klaas C., Kohfeld K.E., Legendre L., Manizza M., Platt T., Rivkin R.B., Sathyendranath S., Uitz J., Watson A.J., Wolf-Gladrow D. Ecosystem dynamics based on plankton functional types for global ocean biogeochemistry models. Global Change Biology 2005, 11:2016-2040.
40. Lenski R.E., Ofria C., Collier T.C., Adami C. Genome complexity, robustness and genetic interactions in digital organisms. Nature 1999, 400:661-664.
41. Levin S.A. Ecosystems and the biosphere as complex adaptive systems. Ecosystems 1998, 1:431-436.
42. Litchman E. Resource competition and the ecological success of phytoplankton. Evolution of Primary Producers in the Sea 2007, Elsevier Academic Press, chapter 16. P.G. Falkowski, A.H. Knoll (Eds.).
43. Litchman E., Klausmeier C.A., Yoshiyama K. Contrasting size evolution in marine and freshwater diatoms. Proceedings of the National Academy of Sciences 2009, 106:2665-2670.
44. Madigan M.T., Martinko J.M. Brock Biology of Microorganisms 2009, Pearson Prentice Hall, Upper Saddle River, NJ. 12th edition.
45. Marchetti A., Parker M.S., Moccia L.P., Lin E.O., Arrieta A.L., Ribalet F., Murphy M.E.P., Maldonado M.T., Armbrust E.V. Ferritin is used for iron storage in bloom-forming marine pennate diatoms. Nature 2009, 457:467-470.
46. McGillicuddy D.J., Anderson L.A., Bates N.R., Bibby T., Buesseler K.O., Carlson C.A., Davis C.S., Ewart C., Falkowski P.G., Goldthwait S.A., Hansell D.A., Jenkins W.J., Johnson R., Kosnyrev V.K., Ledwell J.R., Li Q.P., Siegel D.A., Steinberg D.K. Eddy/wind interactions stimulate extraordinary mid-ocean plankton blooms. Science 2007, 316:1021-1026.
47. Monod J. Recherches sur la croissance des cultures bacteriennes 1942, Hermann and Cie.
48. Morel F.M.M. Kinetics of nutrient-uptake and growth in phytoplankton. Journal Of Phycology 1987, 23:137-150.
49. Palmer J.R., Totterdell I.J. Production and export in a global ocean ecosystem model. Deep Sea Research Part I: Oceanographic Research Papers 2001, 48:1169-1198.
50. Rose K.A., Christensen S.W., DeAngelis D.L. Individual-based modeling of populations with high mortality: a new method based on following a fixed number of model individuals. Ecological Modelling 1993, 68:273-292.
51. Sakamoto C.M., Karl D.M., Jannasch H.W., Bidigare R.R., Letelier R.M., Walz P.M., Ryan J.P., Polito P.S., Johnson K.S. Influence of Rossby waves on nutrient dynamics and the plankton community structure in the North Pacific subtropical gyre. Journal Of Geophysical Research-Oceans 2004, 10:9.
52. Scheffer M., Baveco J.M., Deangelis D.L., Rose K.A., Vannes E.H. Super-individuals a simple solution for modeling large populations on an individual basis. Ecological Modelling 1995, 80:161-170.
53. Schuler A.J. Diversity matters: dynamic simulation of distributed bacterial states in suspended growth biological wastewater treatment systems. Biotechnology and Bioengineering 2005, 91:62-74.
54. Sommer U. The role of competition for resources in phytoplankton succession. Plankton Ecology: Succession in Plankton Communities 1989, Springer, Berlin.
55. Steele J.H. The Structure of Marine Ecosystems 1974, Harvard University Press, Cambridge, Massachusetts.
56. Thingstad T.F., Skjoldal E.F., Bohne R.A. Phosphorus cycling and algal-bacterial competition in Sandsfjord, Western Norway. Marine Ecology-Progress Series 1993, 99:239-259.
57. Tian R. Toward standard parameterizations in marine biological modeling. Ecological Modelling 2005, 193:363-386.
58. Tilman D. Resource Competition and Community Structure 1982, Princeton University Press.
59. Tozzi S., Schofield O., Falkowski P. Historical climate change and ocean turbulence as selective agents for two key phytoplankton functional groups. Marine Ecology-Progress Series 2004, 274:123-132.
60. Vaillancourt R.D., Marra J., Seki M.P., Parsons M.L., Bidigare R.R. Impact of a cyclonic eddy on phytoplankton community structure and photosynthetic competency in the subtropical North Pacific ocean. Deep-sea Research Part I: Oceanographic Research Papers 2003, 50:829-847.
61. Verdy A., Follows M., Flierl G. Optimal phytoplankton cell size in an allometric model. Marine Ecology-Progress Series 2009, 379:1-12.
62. Williams H.T.P., Lenton T.M. The flask model: emergence of nutrient-recycling microbial ecosystems and their disruption by environment-altering 'rebel' organisms. Oikos 2007, 116:1087-1105.
63. Williams R.G., Follows M.J. Physical transport of nutrients and the maintenance of biological production. Ocean Biogeochemistry: The role of the Ocean Carbon Cycle in Global Change 2003, Springer. M. Fasham (Ed.).
64. Woods J.D. The lagrangian ensemble metamodel for simulating plankton ecosystems. Progress in Oceanography 2005, 67:84-159.
65. Wroblewski J.S., Sarmiento J., Flierl G.R. An ocean-basin scale model of plankton dynamics in the North Atlantic. 1. Solutions for the climatological oceanographic conditions in May. Global Biogeochemical Cycles 1988, 2:199-218.