Getting the "right" parameter values for models of the pelagic microbial food web

Limnology and Oceanography

Volumn 58, Issue 1, 2013, Pages 301-313

  Lignell, Risto ^a,b   Haario, Heikki ^c   Laine, Marko ^d   Thingstad, T Frede ^e  

^a FINNISH ENVIRONMENT INSTITUTE   (Finland)

^b UNIVERSITY OF HELSINKI   (Finland)

^c LAPPEENRANTA UNIVERSITY OF TECHNOLOGY   (Finland)

^d FINNISH METEOROLOGICAL INSTITUTE   (Finland)

^e UNIVERSITY OF BERGEN   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

ALLOMETRY; FOOD SELECTION; FOOD WEB; GRAZING; MESOCOSM; MICROBIAL COMMUNITY; NUTRIENT UPTAKE; PARAMETERIZATION; PARSIMONY ANALYSIS; PELAGIC ECOSYSTEM; PERTURBATION; QUANTITATIVE ANALYSIS;

EID: 84872509324     PISSN: 00243590     EISSN: None     Source Type: Journal    
DOI: 10.4319/lo.2013.58.1.0301     Document Type: Article

References (57)

1. Aksnes, D. L., and J. K. Egge. 1991. A theoretical model for nutrient uptake in phytoplankton. Mar. Ecol. Prog. Ser. 70: 65-72, doi:10.3354/meps070065
2. Anderson, T. R. 2005. Plankton functional type modeling: Running before we can walk? J. Plankton Res. 27: 1073-1081.
3. Arhonditsis, G. B., D. Papantou, W. Zhang, G. Perhar, E. Massos, and M. Shi. 2008. Bayesian calibration of mechanistic aquatic biogeochemical models and benefits for environmental management. J. Marine Syst. 73: 8-30, doi:10.1016/j.jmarsys.2007.07.004
4. Autio, R. M. 1992. Temperature regulation of brackish water bacterioplankton. Arch. Hydrobiol. Beih. Ergebn. Limnol. 37: 253-263.
5. Børsheim, K. Y., and G. Bratbak. 1987. Cell volume to cell carbon conversion factors for a bacterivorous Monas sp. enriched from seawater. Mar. Ecol. Prog. Ser. 36: 171-175, doi:10.3354/meps036171
6. Brooks, S. P., and G. O. Roberts. 1998. Assessing convergence of Markov chain Monte Carlo algorithms. Stat. Comp. 8: 319-335, doi:10.1023/A:1008820505350
7. Caperon, J., and J. Meyer. 1972. Nitrogen-limited growth of marine phytoplankton. I. Changes in population characteristics with steady-state growth rate. Deep-Sea Res. I 19: 601-618.
8. CLARK, J. S. 2005. Why environmental scientists are becoming Bayesians. Ecol. Lett. 8: 2-14, doi:10.1111/j.1461-0248. 2004.00702.x
9. Davis, P. G., and J. M. Sieburth. 1982. Differentiation of phototrophic and heterotrophic nanoplankton populations in marine waters by epifluorescence microscopy. Ann. Inst. Oceanogr. 58: 249-260.
10. Fagerbakke, K. M., M. Heldal, and S. Norland. 1996. Content of carbon, nitrogen, oxygen, sulfur and phosphorus in native aquatic and cultured bacteria. Aquat. Microb. Ecol. 10: 15-27, doi:10.3354/ame010015
11. Fenchel, T. 1982. Ecology of heterotrophic microflagellates. I. Some important forms and their functional morphology. Mar. Ecol. Prog. Ser. 8: 211-223, doi:10.3354/meps008211
12. Fenchel, T. 1986. Protozoan filter feeding. Prog. Protistol. I: 65-113.
13. Follows, M. J., S. Dutkiewicz, S. Grant, and S. W. Chisholm. 2007. Emergent biogeography of microbial communities in a model ocean. Science 315: 1843-1846, doi:10.1126/science. 1138544
14. Franks, P. J. S. 2009. Planktonic ecosystem models: Perplexing parameterizations and a failure to fail. J. Plankton Res. 31: 1299-1306, doi:10.1093/plankt/fbp069
15. Fuhrman, J. A., AND F. Azam. 1982. Thymidine incorporation as a measure of heterotrophic bacterioplankton production in marine surface water: Evaluation and field results. Mar. Biol. 66: 109-120, doi:10.1007/BF00397184
16. Furnas, M. J. 1990. In situ growth rates of marine phytoplankton: Approaches to measurement, community and species growth rates. J. Plankton Res. 12: 1117-1151, doi:10.1093/plankt/12.6.1117
17. Gelman, A., J. B. Carlin, H. S. Stern, And D. B. Rubin. 2003. Bayesian data analysis, 2nd ed. Chapman & Hall.
18. Gismervik, I., T. Andersen, and O. Vadstein. 1996. Pelagic food webs and eutrophication of coastal waters: Impact of grazers on algal communities. Mar. Poll. Bull. 33: 22-35, doi:10.1016/ S0025-326X(96)00134-8
19. Grasshoff, K., M. Erhardt, and K. Kremling [EDS.], 1983. Methods of seawater analysis, 2nd ed. Verlag Chemie.
20. Haario, H., M. Laine, A. Mira, and E. Saksman. 2006. DRAM: Efficient adaptive MCMC. Stat. Comput. 16: 339-354, doi:10.1007/s11222-006-9438-0
21. Hansen, B. W., P. K. Bjørnsen, and P. J. Hansen. 1994. Prey size selection in planktonic zooplankton. Limnol. Oceanogr. 39: 395-403, doi:10.4319/lo.1994.39.2.0395
22. Hansen, P. J., P. K. Bjørnsen, and B. W. Hansen. 1997. Zooplankton grazing and growth: Scaling within the 2-2,000 mm body size range. Limnol. Oceanogr. 42: 687-704, doi:10.4319/lo.1997.42.4.0687
23. Jespersen, A.-M., and K. Christoffersen. 1987. Measurements of chlorophyll a from phytoplankton using ethanol as extraction solvent. Arch. Hydrobiol. 109: 445-454.
24. Jumars, P., J. Deming, P. Hill, L. Karp-Boss, and W. Dade. 1993. Physical constraints on marine osmotrophy in an optimal foraging context. Mar. Microb. Food Webs 7: 121-161.
25. Kiørboe, T., and E. Saiz. 1995. Planktivorous feeding in calm and turbulent environments, with emphasis on copepods. Mar. Ecol. Prog. Ser. 122: 135-145, doi:10.3354/meps122135
26. KUOSA, H. 1990. Protozoan grazing on pico-and nanophyto-plankton in the northern Baltic Sea: Direct evidence from epifluorescence microscopy. Arch. Hydrobiol. Beih. Ergebn. Limnol. 119: 257-265.
27. KUUPPO, P. 1994. Annual variation in the abundance and size of heterotrophic nanoflagellates on the SW coast of Finland, the Baltic Sea. J. Plankton Res. 16: 1525-1542, doi:10.1093/ plankt/16.11.1525
28. LIGNELL, R., L. HOIKKALA, and T. LAHTINEN. 2008. Effects of inorganic nutrients, glucose and solar radiation on bacterial growth and exploitation of dissolved organic carbon and nitrogen in the northern Baltic Sea. Aquat. Microb. Ecol. 51: 209-221, doi:10.3354/ame01202
29. LIGNELL, R., L. HOIKKALA, T. LAHTINEN, J. SEPPALA, P. KUUPPO, T. TAMMINEN, T. ANDERSEN, and I. GISMERVIK. 2003. Beyond bulk properties: Responses of coastal summer plankton communities to nutrient enrichment in the northern Baltic Sea. Limnol. Oceanogr. 48: 189-209, doi:10.4319/lo.2003.48.1.0189
30. LITCHMAN, E., and C. A. KLAUSMEIER. 2008. Trait-based community ecology of phytoplankton. Ann. Rev. Ecol. Evol. Syst. 39: 615-639, doi:10.1146/annurev.ecolsys.39.110707. 173549
31. MALVE, O., M. LAINE, H. HAARIO, T. KIRKKALA, and J. SARVALA. 2007. Bayesian modelling of algal mass occurrences-using adaptive MCMC methods with a lake water quality model. Environ. Model. Software 22: 966-977, doi:10.1016/j. envsoft.2006.06.016
32. MULLIN, M. M. 1969. Production of zooplankton in the ocean: The present status and problems. Oceanogr. Mar. Biol. 7: 293-314.
33. NORLAND, S. 1993. The relationship between biomass and volume of bacteria, p. 303-306. In P. F. Kemp, B. F. Sherr, E. B. Sherr, and J. J. Cole [eds.], Handbook of methods in aquatic microbial ecology. CRC Press.
34. OLLI, K., and J. SEPPALA. 2001. Vertical niche separation of phytoplankton: Large-scale mesocosm experiments. Mar. Ecol. Prog. Ser. 217: 219-233, doi:10.3354/meps217219
35. PUTT, M., and D. K. STOECKER. 1989. An experimentally determined carbon: volume ratio for marine "oligotrichous" ciliates from estuarine and coastal waters. Limnol. Oceanogr. 34: 1097-1103, doi:10.4319/lo.1989.34.6.1097
36. REDFIELD, A. C. 1958. The biological control of chemical factors in the environment. Am. Sci. 6: 205-221.
37. SHELDON, R. W., A. PRAKASH, and W. H. SUTCLIFFE. 1972. The size distribution of particles in the ocean. Limnol. Oceanogr. 17: 327-340, doi:10.4319/lo.1972.17.3.0327
38. SHERR, E. B., and B. F. SHERR. 2007. Heterotrophic dinoflagellates: A significant component of microzooplankton biomass and major grazers of diatoms in the sea. Mar. Ecol. Prog. Ser. 352: 187-197, doi:10.3354/meps07161
39. SHERR, E. B., B. F. SHERR, and C. T. SIGMON. 1999. Activity of marine bacteria under incubated and in situ conditions. Aquat. Microb. Ecol. 20: 213-223, doi:10.3354/ame020213
40. SIEBURTH, J. M., V. SMETACEK, and J. LENZ. 1978. Pelagic ecosystem structure: Heterotrophic compartments of the plankton and their relationship to plankton size fractions. Limnol. Oceanogr. 23: 1256-1263, doi:10.4319/lo.1978.23.6.1256
41. Šimek K., and OTHERS. 2006. Maximum growth rates and possible life strategies of different bacterioplankton groups in relation to phosphorus availability in a freshwater reservoir. Environ. Microbiol. 8: 1613-1624, doi:10.1111/j.1462-2920.2006.01053.x
42. TAMBI, H., G. A. FONNES FLATEN, J. K. EGGE, G. Bødtker, A. JACOBSEN, and T. F. THINGSTAD. 2009. Relationship between phosphate affinities and cell size and shape in various bacteria and phytoplankton. Aquat. Microb. Ecol. 57: 311-320, doi:10.3354/ame01369
43. TANAKA, T., P. HENRIKSEN, R. LIGNELL, K. OLLI, J. SEPPALA, T. TAMMINEN, and T. F. THINGSTAD. 2006. Specific affinity for phosphate uptake and specific alkaline phosphatase activity as diagnostic tools for detecting phosphorus-limited phytoplankton and bacteria. Estuar. Coasts 29: 1226-1241.
44. THINGSTAD, T. F. 1998. A theoretical approach to structuring mechanisms in the pelagic food web. Hydrobiologia 363: 59-72, doi:10.1023/A:1003146310365
45. THINGSTAD, T. F. 2000. Control of bacterial growth in idealized food webs, p. 229-259. In D. L. Kirchman [ed.], Microbial ecology of the ocean. John Wiley & Sons. p. 229-259.
46. THINGSTAD, T. F, and E. SAKSHAUG. 1990. Control of phytoplankton growth in nutrient recycling ecosystems. Theory and terminology. Mar. Ecol. Prog. Ser. 63: 261-272, doi:10.3354/ meps063261
47. THINGSTAD, T. F, M. PEREZ, S. PELEGRI, J. DOLAN, and F. Rassoulzade-gan. 1999. Trophic control of bacterial growth in microcosms containing a natural community from northwest Mediterranean surface waters. Aquat. Microb. Ecol. 18: 145-156, doi:10.3354/ame018145
48. THINGSTAD, T. F, M. PEREZ, S. PELEGRI, J. DOLAN, F. Rassoulzade-gan, and R. LIGNELL. 1997. Theoretical models for the control of bacterial growth rate, abundance, diversity and carbon demand. Aquat. Microb. Ecol. 13: 19-27, doi:10.3354/ame013019
49. THINGSTAD, T. F, M. PEREZ, S. PELEGRI, J. DOLAN, F. Rassoulzade-gan, R. LIGNELL, L. øvreås, J.K. EGGE, T. Løvdal, and M. HELDAL. 2005. Use of non-limiting substrates to increase size; a generic strategy to simultaneously optimize uptake and minimize predation in pelagic osmotrophs? Ecol. Lett. 8: 675-682, doi:10.1111/j.1461-0248.2005.00768.x
50. THINGSTAD, T. F, M. PEREZ, S. PELEGRI, J. DOLAN, F. Rassoulzade-gan, R. LIGNELL, L. øvreås, J.K. EGGE, T. Løvdal, M. Heldal, and F. RASSOULZADEGAN. 1999. Conceptual models for the biogeochemical role of the photic zone food web, with particular reference to the Mediterranean Sea. Prog. Oceanogr. 44: 271-286, doi:10.1016/S0079-6611(99)00029-4
51. THINGSTAD, T. F, M. PEREZ, S. PELEGRI, J. DOLAN, F. Rassoulzade-gan, R. Lignell, L. øvre as, J. K. EGGE, T. Løvdal, M. HELDAL, F. RASSOULZADEGAN, E. STRAND, andA. LARSEN. 2010. Stepwise building of plankton functional type (PFT) models: A feasible route to complex models? Prog. Oceanogr. 84: 6-15, doi:10.1016/ j.pocean.2009.09.001
52. THINGSTAD, T. F, M. PEREZ, S. PELEGRI, J. DOLAN, F. Rassoulzade-gan, R. LIGNELL, L. ØVREAS, J.K. EGGE, T. Løvdal, M. HELDAL, F. RASSOULZADEGAN, E. STRAND, A. LARSEN, and OTHERS. 2007. Ability of a "minimum" microbial food web model to reproduce response patterns observed in mesocosms manipulated with N and P, glucose, and Si. J. Mar. Syst. 64: 15-34, doi:10.1016/j.jmarsys.2006.02.009
53. Timmermans, K. R., B. van der Wagt, M. J. W. Veldhuis, A. Maatman, and H. J. W. DE Baar. 2005. Physiological responses of three species of marine pico-phytoplankton to ammonium, phosphate, iron and light limitation. J. Sea Res. 53: 109-120, doi:10.1016/j.seares.2004.05.003
54. Utermohl, H. 1958. Zur Vervollkommung der Quantitativen Phytoplanktonmethodik. Mitt. Internat. Verein. Theor. Angew. Limnol. 9: 1-38. [Perfecting the quantitative phytoplankton method.]
55. Vichi, M., N. Pinardi, and S. Masina. 2007. A generalized model of pelagic biogeochemistry for the global ocean ecosystem.Part I: Theory. J. Mar. Syst. 64: 89-109, doi:10.1016/ j.jmarsys.2006.03.006
56. Yooseph, S., and OTHERS. 2010. Genomic and functional adaptation in surface ocean planktonic prokaryotes. Nature 468: 60-67, doi:10.1038/nature09530
57. Zhang, W. T., and G. B. Arhonditsis. 2008. Predicting the frequency of water quality standard violations using Bayesian calibration of eutrophication models. J. Great Lakes Res. 34: 698-720.