Biogeosciences www.biogeosciences.net 1726-4170 1726-4189 7 6 2010 10.5194/bg-7-1861-2010 http://www.biogeosciences.net/7/1861/2010/ http://www.biogeosciences.net/7/1861/2010/bg-7-1861-2010.html http://www.biogeosciences.net/7/1861/2010/bg-7-1861-2010.pdf 1861 1876 2010-06-04 Increased bacterial growth efficiency with environmental variability: results from DOC degradation by bacteria in pure culture experiments M. Eichinger R. Sempéré richard.sempere@univmed.fr G. Grégori B. Charrière J. C. Poggiale D. Lefèvre Université de la Méditerranée, Laboratoire de Microbiologie Géochimie et Ecologie Marines (LMGEM) CNRS/INSU, UMR 6117, Centre d'Océanologie de Marseille, Campus de Luminy, Case 901, 13288 Marseille Cedex 9, France This paper assesses how considering variation in DOC availability and cell maintenance in bacterial models affects Bacterial Growth Efficiency (BGE) estimations. For this purpose, we conducted two biodegradation experiments simultaneously. In experiment one, a given amount of substrate was added to the culture at the start of the experiment whilst in experiment two, the same amount of substrate was added, but using periodic pulses over the time course of the experiment. Three bacterial models, with different levels of complexity, (the Monod, Marr-Pirt and the dynamic energy budget – DEB – models), were used and calibrated using the above experiments. BGE has been estimated using the experimental values obtained from discrete samples and from model generated data. Cell maintenance was derived experimentally, from respiration rate measurements. The results showed that the Monod model did not reproduce the experimental data accurately, whereas the Marr-Pirt and DEB models demonstrated a good level of reproducibility, probably because cell maintenance was built into their formula. Whatever estimation method was used, the BGE value was always higher in experiment two (the periodically pulsed substrate) as compared to the initially one-pulsed-substrate experiment. Moreover, BGE values estimated without considering cell maintenance (Monod model and empirical formula) were always smaller than BGE values obtained from models taking cell maintenance into account. Since BGE is commonly estimated using constant experimental systems and ignore maintenance, we conclude that these typical methods underestimate BGE values. On a larger scale, and for biogeochemical cycles, this would lead to the conclusion that, for a given DOC supply rate and a given DOC consumption rate, these BGE estimation methods overestimate the role of bacterioplankton as CO₂ producers. Abboudi, M., Jeffrey, W. H., Ghiglione, J.-F., Oriol, L., Sempéré, R., Charrière, B., and Joux, F.: Effects of photochemical transformations of dissolved organic matter on bacterial metabolism and diversity in three contrasting coastal sites in the northwestern Mediterranean sea during summer, Microb. Ecol., 55(2), 344–357, doi:10.1007/s00248-007-9280-8, 2007. Amon, R. M. W. and Benner, R.: Bacterial utilization of different size classes of dissolved organic matter, Limnol. Oceanogr., 41(1), 41–51, 1996. Anderson, T. R. and Williams, P. J. L. B.: Modelling the seasonal cycle of dissolved organic carbon at station E-1 in the English Channel, Estuar. Coast. Shelf S., 46(1), 93-109, 1998. Anderson, T. R. and Williams, P. J. L. B.: A one-dimensional model of dissolved organic carbon cycling in the water column incorporating combined biological-photochemical decomposition, Global Biogeochem. Cy., 13(2), 337–349, 1999. Baretta-Bekker, J. G., Baretta, J. W., and Rasmussen, E. K.: The microbial food web in the European Regional Seas Ecosystem Model, Neth. J. Sea Res., 33(3/4), 363–379, 1995. Blackburn, N., Zweifel, U. L., and Hagstrom, A.: Cycling of marine dissolved organic matter, II A model analysis, Aquat. Microb. Ecol., 11(1), 79–90, 1996. Bratbak, G.: Bacterial biovolume and biomass estimations, Appl. Environ. Microb., 49(6), 1488–1493, 1985. Briand, E., Pringault, O., Jacquet, S., and Torréton, P.: The use of oxygen microprobes to measure bacterial respiration for determining bacterioplankton growth efficiency, Limnol. Oceanogr.-Meth., 2, 406–416, 2004. Cajal-Medrano, R. and Maske, H.: Growth efficiency, growth rate and the remineralization of organic substrate by bacterioplankton – revisiting the Pirt model, Aquat. Microb. Ecol., 19(2), 119–128, 1999. Cajal-Medrano, R. and Maske, H.: Growth efficiency and respiration at different growth rates in glucose-limited chemostats with natural marine bacteria populations, Aquat. Microb. Ecol., 38(2), 125–133, 2005. Carlson, C. A. and Ducklow, H. W.: Dissolved organic carbon in the upper ocean of the central equatorial Pacific Ocean, 1992: Daily and finescale vertical variations, Deep-Sea Res Pt II, 42, 639–656, 1995. Carlson, C. A. and Ducklow, H. W.: Growth of bacterioplankton and consumption of dissolved organic carbon in the Sargasso Sea, Aquat. Microb. Ecol., 10(1), 69–85, 1996. Carlson, C. A., Bates, N. R., Ducklow, H. W., and Hansell, D. A.: Estimation of bacterial respiration and growth efficiency in the Ross Sea, Antarctica, Aquat. Microb. Ecol., 19(3), 229–244, 1999. Carlson, C. A., Giovannoni, S. J., Hansell, D. A., Goldberg, S. J., Parsons, R., Otero, M. P., Vergin, K., and Wheeler, B. R.: Effect of nutrient amendments on bacterioplankton production, community structure, and DOC utilization in the northwestern Sargasso Sea, Aquat. Microb. Ecol., 30(1), 19–36, 2002. Carlson, C. A., Giovannoni, S. J., Hansell, D. A., Goldberg, S. J., Parsons, R., and Vergin, K.: Interactions among dissolved organic carbon, microbial processes, and community structure in the mesopelagic zone of the northwestern Sargasso Sea, Limnol. Oceanogr., 49(4), 1073–1083, 2004. Cherrier, J., Bauer, J. E., and Druffel, E. R. M.: Utilization and turnover of labile dissolved organic matter by bacterial heterotrophs in eastern north Pacific surface waters, Mar. Ecol.-Prog. Ser., 139(1–3), 267–279, 1996. Cherrier, J. and Bauer, J. E.: Bacterial utilization of transient plankton-derived dissolved organic carbon and nitrogen inputs in surface ocean waters, Aquat. Microb. Ecol., 35(3), 229–241, 2004. Coffin, R. B., Connolly, J. P., and Harris, P. S.: Availability of dissolved organic carbon to bacterioplankton examined by oxygen utilization, Mar. Ecol.-Prog. Ser., 101, 9–22, 1993. del Giorgio, P. A. and Cole, J. J.: Bacterial growth efficiency in natural aquatic systems, Annu. Rev. Ecol. Syst., 29, 503-541, 1998. Eichinger, M., Kooijman, S. A. L. M., Sempéré, R., Lefèvre, D., Grégori, G., Charrière, B., and Poggiale, J. C.: DOC consumption and release by marine bacteria in pulsed-substrate environment: from experiments to modelling, Aquat. Microb. Ecol., 56(1), 41–54, 2009. Eichinger, M., Poggiale, J. C., Van Wambeke, F., Lefèvre, D., and Sempéré, R.: Modelling DOC assimilation and bacterial growth efficiency in biodegradation experiments: a case study in the Northeast Atlantic Ocean, Aquat. Microb. Ecol., 43(2), 139–151, 2006. Goldman, J. C., Caron, D. A., and Dennett, M. R.: Regulation of gross growth efficiency and ammonium regeneration in bacteria by susbtrate C:N ratio, Limnol. Oceanogr., 32(6), 1239–1252, 1987. González, N., Anadón, R., and Marañón, E.: Large-scale variability of planktonic net community metabolism in the Atlantic Ocean: importance of temporal changes in oligotrophic subtropical waters, Mar. Ecol.-Prog. Ser., 233, 21–30, 2002. Hanegraaf, P. P. F. and Kooi, B. W.: The dynamics of a tri-trophic food chain with two-component populations from a biochemical perspective, Ecol. Model., 152(1), 47–64, 2002. Hansell, D. A., Bates, N. R., and Gundersen, K.: Mineralization of dissolved organic carbon in the Sargasso Sea, Mar. Chem., 51(3), 201–212, 1995. Hedges, J. I.: Global biogeochemical cycles: Progress and problems, Mar. Chem., 39, 67–93, 1992. Jahnke, R. A. and Craven, D. B.: Quantifying the role of heterotrophic bacteria in the carbon cycle – a need for respiration rate measurements, Limnol. Oceanogr., 40(2), 436–441, 1995. Jiménez-Mercado, A., Cajal-Medrano, R., and Maske, H.: Marine heterotrophic bacteria in continuous culture, the bacterial carbon growth efficiency, and mineralization at excess substrate and different temperatures, Microb. Ecol., 54, 56–64, doi:10.1007/s00248-006-9171-4, 2007. Konopka, A.: Theoretical analysis of the starvation response under substrate pulses, Microb. Ecol., 38(4), 321–329, 1999. Konopka, A.: Microbial physiological state at low growth rate in natural and engineered ecosystems, Curr. Opin. Microbiol., 3, 244–247, 2000. Kooi, B. W. and Kooijman, S. A. L. M.: The transient-behaviour of food-chains in chemostats, J. Theor. Biol., 170(1), 87–94, 1994. Kooijman, S. A. L. M.: Dynamic energy and mass budgets in biological systems, 2nd~edition, Cambridge University Press, Cambridge, 424~pp., 2000. La Ferla, R., Azzaro, F., Azzaro, M., Caruso, G., Decembrini, F., Leonardi, M., Maimone, G., Monticelli, L. S., Raffa, F., Santinelli, C., Zaccone, R., and Ribera d'Alcalá, M.: Microbial contribution to carbon biogeochemistry in the Central Mediterranean Sea: Variability of activities and biomass, J. Mar. Syst., 57, 146–166, 2005. Lancelot, C., Staneva, J., Van Eeckhout, D., Beckers, J. M., and Stanev, E.: Modelling the Danube-influenced north-western continental shelf of the Black Sea, II:~Ecosystem response to changes in nutrient delivery by the Danube River after its damming in 1972, Estuar. Coast. Shelf S., 54(3), 473–499, 2002. Lee, C. W., Bong, C. W., and Hii, Y. S.: Temporal variation of bacterial respiration and growth efficiency in tropical coastal waters, Appl. Environ. Microb., 75, 7594–7601, doi:10.1128/AEM.01227-09, 2009. Lee, S. and Fuhrman, J. A.: Relationships between biovolume and biomass of naturally derived marine bacterioplankton, Appl. Environ. Microb., 53(6), 1298–1303, 1987. Lemée, R., Rochelle-Newall, E., van Wambeke, F., Pizay, M. D., Rinaldi, P., and Gattuso, J.-P.: Seasonal variation of bacterial production, respiration and growth efficiency in the open NW~Mediterranean Sea, Aquat. Microb. Ecol., 29, 227–237, 2002. Lyman, J. and Fleming, R.: Composition of sea water, J. Mar. Res., 3, 134–146, 1940. Maier, U. and Büchs, J.: Characterisation of the gas–liquid mass transfer in shaking bioreactors, Biochem. Eng. J., 7, 99–106, 2001. Marr, A. G., Nilson, E. H., and Clark, D. J.: The maintenance requirement of Escherishia coli, Ann. NY. Acad. Sci., 102, 536–548, 1963. Monod, J.: Recherches sur la croissance des cultures bactériennes, Ph.D thesis, University of Paris, Paris, France, 1942. Morita, R. Y.: Bacteria in oligotrophic environment: starvation – survival lifestyle, Chapman~&~Hall, New York, 529~pp., 1997. Nagata, T.: Production mechanisms of dissolved organic matter, in: Microbial ecology of the oceans, edited by: Kirchman, D. L., Wiley-Liss, New York, 121–152, 2000. Pirt, S. J.: The maintenance energy of bacteria in growing cultures, P. Roy. Soc. Lond. B~Bio., 163, 224–231, 1965. Pomeroy, L. R.: The ocean's food web, a changing paradigm, Bioscience, 24, 499–504, 1974. Price, P. B. and Sowers, T.: Temperature dependence of metabolic rates for microbial growth, maintenance, and survival, P. Natl. Acad. Sci. USA, 101(13), 4631–4636, 2004. Raguénès, G. H. C., Peres, A., Ruimy, R., Pignet, P., Christen, R., Loaec, M., Rougeaux, H., Barbier, G., and Guezennec, J. G.: \textitAlteromonas infernus sp nov., a new polysaccharide-producing bacterium isolated from a deep-sea hydrothermal vent, J. App. Microbiol., 82, 422–430, 1997. Raymond, P. A. and Bauer, J. E.: Bacterial consumption of DOC during transport through a temperate estuary, Aquat. Microb. Ecol., 22, 1–12, 2000. Reinthaler, T. and Herndl, G. J.: Seasonal dynamics of bacterial growth efficiencies in relation to phytoplankton in the southern North Sea, Aquat. Microb. Ecol., 39(1), 7–16, 2005. Reinthaler, T., Winter, C., and Herndl, G. J.: Relationship between bacterioplankton richness, respiration, and production in the southern North Sea, Appl. Environ. Microb., 71(5), 2260–2266, doi:10.1128/AEM.71.5.2260-2266.2005, 2005. Rivkin, R. B. and Legendre, L.: Biogenic carbon cycling in the upper ocean: Effects of microbial respiration, Science, 291(5512), 2398–2400, 2001. Sempéré, R., Dafner, E., Van Wambeke, F., Lefèvre, D., Magen, C., Allegre, S., Bruyant, F., Bianchi, M., and Prieur, L.: Distribution and cycling of total organic carbon across the Almeria-Oran Front in the Mediterranean Sea: Implications for carbon cycling in the western basin, J. Geophys. Res.-Oceans, 108(C11), 3361, doi: 3310.1029/2002JC001475, 2003. Sempéré, R., Yoro, S. C., Van Wambeke, F., and Charrière, B.: Microbial decomposition of large organic particles in the northwestern Mediterranean Sea: an experimental approach, Mar. Ecol.-Prog. Ser., 198, 61–72, 2000. Sohrin, R. and Sempéré, R.: Seasonal variation in total organic carbon in the northeast Atlantic in 2000–2001, J. Geophys. Res.-Oceans, 110, C10S90, doi:10.1029/2004JC002731, 2005. Tolla, C., Kooijman, S. A. L. M., and Poggiale, J. C.: A kinetic inhibition mechanism for maintenance, J. Theor. Biol., 244(4), 576–587, 2007. van Bodegom, P.: Microbial Maintenance: A critical review on its quantification, Microb. Ecol., 53, 513–523, doi:10.1007/s00248-006-9049-5, 2007. Vrede, K., Heldal, M., Norland, S., and Bratbak, G.: Elemental composition~(C, N, P) and cell volume of exponentially growing and nutrient-limited bacterioplankton, Appl. Environ. Microb., 68(6), 2965–2971, 2002. Williams, P. J. L. B.: Heterotrophic bacteria and the dynamics of dissolved organic material, in: Microbial ecology of the oceans, edited by: Kirchman, D. L., Wiley-Liss, New York, 153–199, 2000. Williams, P. M. and Druffel, E. R. M.: Radiocarbon in dissolved organic-matter in the central north Pacific-Ocean, Nature, 330(6145), 246–248, 1987.