Skip to main content
SpringerLink
Log in

The metabolism of aquatic ecosystems: history, applications, and future challenges

  • Overview
  • Published:
Aquatic Sciences Aims and scope Submit manuscript

Abstract

Measurements of the production and consumption of organic material have been a focus of aquatic science for more than 80 years. Over the last century, a variety of approaches have been developed and employed for measuring rates of gross primary production (Pg), respiration (R), and net ecosystem production (Pn = Pg − R) within aquatic ecosystems. Here, we reconsider the range of approaches and applications for ecosystem metabolism measurements, and suggest ways by which such studies can continue to contribute to aquatic ecology. This paper reviews past and contemporary studies of aquatic ecosystem-level metabolism to identify their role in understanding and managing aquatic systems. We identify four broad research objectives that have motivated ecosystem metabolism studies: (1) quantifying magnitude and variability of metabolic rates for cross-system comparison, (2) estimating organic matter transfer between adjacent systems or subsystems, (3) measuring ecosystem-scale responses to perturbation, both natural and anthropogenic, and (4) quantifying and calibrating models of biogeochemical processes and trophic networks. The magnitudes of whole-system gross primary production, respiration and net ecosystem production rates vary among aquatic environments and are partly constrained by the chosen methodology. We argue that measurements of ecosystem metabolism should be a vital component of routine monitoring at larger scales in the aquatic environment using existing flexible, precise, and durable sensor technologies. Current and future aquatic ecosystem studies will benefit from application of new methods for metabolism measurements, which facilitate integration of process measurements and calibration of models for addressing fundamental questions involving ecosystem-scale processes.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Acuña V, Giorgi A, Muñoz I, Uehlinger U, Sabater S (2004) Flow extremes and benthic organic matter shape the metabolism of a headwater Mediterranean stream. Freshw Biol 49:960–971

    Google Scholar 

  • Algesten G, Sobek S, Bergstrom AK, Agren A, Tranvik LJ, Jansson M (2004) Role of lakes for organic carbon cycling in the boreal zone. Glob Change Biol 10:141–147

    Google Scholar 

  • Allen AP, Gillooly JF, Brown JH (2005) Linking the global carbon cycle to individual metabolism. Funct Ecol 19:202–213

    Google Scholar 

  • Aoki T, Hayami Y, Fujiwara T, Mukai H, Tanaka Y (1996) Nutrient dynamics in the north basin of Lake Biwa.1. Changes in the vertical distribution of nutrients due to an internal surge induced by a strong typhoon. J Great Lakes Res 22:331–340

    CAS  Google Scholar 

  • Aristegi L, Izagirre O, Elosegi A (2009) Comparison of several methods to calculate reaeration in streams, and their effects on estimation of metabolism. Hydrobiologia 635:113–124

    CAS  Google Scholar 

  • Arnell NW (1999) The effect of climate change on hydrological regimes in Europe: a continental perspective. Glob Environ Change 9:5–23

    Google Scholar 

  • Ask J, Karlsson J, Persson L, Ask P, Bystrom P, Jansson M (2009) Whole-lake estimates of carbon flux through algae and bacteria in benthic and pelagic habitats of clear-water lakes. Ecology 90:1923–1932

    PubMed  Google Scholar 

  • Barko JW, Murphy PG, Wetzel RL (1977) An investigation of primary production and ecosystem metabolism in a lake Michigan dune pond. Archiev für Hydrobiologie 2:155–187

    Google Scholar 

  • Barnes DJ (1983) Profiling coral reef productivity and calcification using pH and oxygen electrodes. J Exp Mar Biol Ecol 66:149–161

    CAS  Google Scholar 

  • Barth JA, Menge BA, Lubchenco J, Chan F, Bane JM, Kirincich AR, McManus MA, Nielsen KJ, Pierce SD, Washburn L (2007) Delayed upwelling alters nearshore coastal ocean ecosystems in the northern California current. Proc Natl Acad Sci USA 104:3719–3724

    PubMed  CAS  Google Scholar 

  • Bates NR, Mathis JT (2009) The Arctic Ocean marine carbon cycle: evaluation of air-sea CO2 exchanges, ocean acidification impacts and potential feedbacks. Biogeosciences 6:2433–2459

    CAS  Google Scholar 

  • Bender M, Grande K, Johnson K, Marra J, Williams PJB, Sieburth J, Pilson M, Langdon C, Hitchcock G, Orchardo J, Hunt C, Donaghay P (1987) A comparison of four methods for determining planktonic community production. Limnol Oceanogr 32:1085–1098

    Google Scholar 

  • Bender ML, Dickson M-L, Orchardo J (2000) Net and gross production in the Ross Sea as determined by incubation experiments and dissolved O2 studies. Deep-Sea Res II 47:3141–3158

    CAS  Google Scholar 

  • Benoy G, Cash K, McCauley E, Wrona F (2007) Carbon dynamics in lakes of the boreal forest under a changing climate. Environ Rev 15:175–189

    CAS  Google Scholar 

  • Beyers RJ, Odum HT (1959) The use of carbon dioxide to construct pH curves for the measurement of productivity. Limnol Oceanogr 4:499–502

    Google Scholar 

  • Blenckner T (2005) A conceptual model of climate-related effects on lake ecosystems. Hydrobiologia 533:1–14

    Google Scholar 

  • Borges AV, Delille B, Schiettecatte LS, Gazeau F, Abril G, Frankignoulle M (2004) Gas transfer velocities of CO2 in three European estuaries (Randers Fjord, Scheldt, and Thames). Limnol Oceanogr 49:1630–1641

    CAS  Google Scholar 

  • Borges AV, Delille B, Frankignoulle M (2005) Budgeting sinks and sources of CO2 in the coastal ocean: diversity of ecosystems counts. Geophys Res Lett 32:L14601. doi:10.1029/2005GL023053

  • Borum J, Sand-Jensen K (1996) Is total primary production in shallow coastal marine waters stimulated by nitrogen loading? Oikos 76:406–410

    Google Scholar 

  • Bozec Y, Thomas H, Schiettecatte LS, Borges AV, Elkalay K, de Baar HJW (2006) Assessment of the processes controlling the seasonal variations of dissolved inorganic carbon in the North Sea. Limnol Oceanogr 51:2746–2762

    CAS  Google Scholar 

  • Breed GA, Jackson GA, Richardson TL (2004) Sedimentation, carbon export and food web structure in the Mississippi River plume described by inverse analysis. Mar Ecol Progr Ser 278:35–51

    CAS  Google Scholar 

  • Broecker WS, Takahashi T, Simpson HJ, Peng TH (1979) Fate of fossil-fuel carbon-dioxide and the global carbon budget. Science 206:409–418

    PubMed  CAS  Google Scholar 

  • Brown JH, Gillooly JF, Allen AP, Savage VM, West GB (2004) Toward a metabolic theory of ecology. Ecology 85:1771–1789

    Google Scholar 

  • Caffrey JM (2003) Production respiration and net ecosystem metabolism in U.S. estuaries. Environ Monit Assess 81:207–219

    PubMed  Google Scholar 

  • Caffrey JM (2004) Factors controlling net ecosystem metabolism in U.S. estuaries. Estuaries 27:90–101

    CAS  Google Scholar 

  • Caffrey JM, Cloern JE, Grenz C (1998) Changes in production and respiration during a spring phytoplankton bloom in San Francisco Bay, California, USA: implications for net ecosystem metabolism. Mar Ecol Progr Ser 172:1–12

    Google Scholar 

  • Caraco NF, Cole JJ (2004) When terrestrial material is sent down the river: the importance of allochthonous carbon inputs to the metabolism of lakes and rivers. In: Polis GA, Power ME, Huxel GR (eds) Food webs at the landscape level. University of Chicago Press, Chicago, pp 301–316

    Google Scholar 

  • Chapin FS, Woodwell GM, Randerson JT, Rastetter EB, Lovett GM, Baldocchi DD, Clark DA, Harmon ME, Schimel DS, Valentini R, Wirth C, Aber JD, Cole JJ, Goulden ML, Harden JW, Heimann M, Howarth RW, Matson PA, McGuire AD, Melillo JM, Mooney HA, Neff JC, Houghton RA, Pace ML, Ryan MG, Running SW, Sala OE, Schlesinger WH, Schulze ED (2006) Reconciling carbon-cycle concepts, terminology, and methods. Ecosystems 9:1041–1050

    CAS  Google Scholar 

  • Chen CTA, Borges AV (2009) Reconciling opposing views on carbon cycling in the coastal ocean: Continental shelves as sinks and near-shore ecosystems as sources of atmospheric CO2. Deep-Sea Res Part II Topical Stud Oceanogr 56:578–590

    CAS  Google Scholar 

  • Christensen V, Walters CJ (2004) Ecopath with Ecosim: methods, capabilities and limitations. Ecol Modell 172:109–139

    Google Scholar 

  • Cole JJ, Fisher SG (1978) Annual metabolism of a temporary pond ecosystem. Am Midl Nat 100:15–22

    CAS  Google Scholar 

  • Cole JJ, Caraco NF, Kling GW, Kratz TK (1994) Carbon-dioxide supersaturation in the surface waters of lakes. Science 265:1568–1570

    PubMed  CAS  Google Scholar 

  • Cole JJ, Pace ML, Carpenter SR, Kitchell JF (2000) Persistence of net heterotrophy in lakes during nutrient addition and food web manipulations. Limnol Oceanogr 45:1718–1730

    Google Scholar 

  • Cole JJ, Carpenter SR, Pace ML, Van de Bogert MC, Kitchell JL, Hodgson JR (2006) Differential support of lake food webs by three types of terrestrial organic carbon. Ecol Lett 9:558–568

    PubMed  Google Scholar 

  • Cole JJ, Prairie YT, Caraco NF, McDowell WH, Tranvik LJ, Striegl RG, Duarte CM, Kortelainen P, Downing JA, Middelburg JJ, Melack J (2007) Plumbing the global carbon cycle: integrating inland waters into the terrestrial carbon budget. Ecosystems 10:171–184

    CAS  Google Scholar 

  • Coloso JJ, Cole JJ, Hanson PC, Pace ML (2008) Depth-integrated, continuous estimates of metabolism in a clear-water lake. Can J Fish Aquat Sci 65:712–722

    Google Scholar 

  • Crossland CJ, Kremer HH, Marshall Crossland JI, Le Tissier MDA (2005) Coastal fluxes in the anthropocene. The land–ocean interactions in the coastal zone project of the International Geosphere-Biosphere Programme. 1-232. Global Change, The IGBP Series

  • D’Avanzo C, Kremer JN, Wainright SC (1996) Ecosystem production and respiration in response to eutrophication in shallow temperate estuaries. Mar Ecol Progr Ser 141:263–274

    Google Scholar 

  • De Angelis DL (1992) Dynamics of nutrient cycling and food webs. Chapman & Hall, New York

    Google Scholar 

  • del Giorgio PA, Williams PJB (2005) Respiration in aquatic ecosystems, Oxford University Press. Inc., Oxford

  • del Giorgio PA, Cole JJ, Caraco NF, Peters RH (1999) Linking planktonic biomass and metabolism to net gas fluxes in northern temperate lakes. Ecology 80:1422–1431

    Google Scholar 

  • Diaz RJ, Rosenberg R (2008) Spreading dead zones and consequences for marine ecosystems. Science 321:926–929

    PubMed  CAS  Google Scholar 

  • Dillon PJ, Molot LA (1997) Effect of landscape form on export of dissolved organic carbon, iron, and phosphorus from forested stream catchments. Water Resour Res 33:2591–2600

    CAS  Google Scholar 

  • Dineen CF (1953) An ecological study of a Minnesota pond. Am Midl Nat 50:349–376

    Google Scholar 

  • Dodds WK, Cole JJ (2007) Expanding the concept of trophic state in aquatic ecosystems: it’s not just the autotrophs. Aquat Sci 69:427–439

    CAS  Google Scholar 

  • Doney SC, Lima I, Feely RA, Glover DM, Lindsay K, Mahowald N, Moore JK, Wanninkhof R (2009) Mechanisms governing interannual variability in upper-ocean inorganic carbon system and air–sea CO2 fluxes: physical climate and atmospheric dust. Deep-Sea Res Part II Topical Stud in Oceanogr 56:640–655

    CAS  Google Scholar 

  • Duarte CM, Agusti S (1998) The CO2 balance of unproductive aquatic ecosystems. Science 281:234–236

    PubMed  CAS  Google Scholar 

  • Duarte CM, Prairie YT (2005) Prevalence of heterotrophy and atmospheric CO2 emissions from aquatic ecosystems. Ecosystems 8:862–870

    CAS  Google Scholar 

  • Duarte CM, Regaudie-de-Gioux A (2009) Thresholds of gross primary production for the metabolic balance of marine planktonic communities. Limnol Oceanogr 54:1015–1022

    CAS  Google Scholar 

  • Duarte CM, Agusti S, Vaque D, Agawin NSR, Felipe J, Casamayor EO, Gasol JM (2005) Experimental test of bacteria-phytoplankton coupling in the Southern Ocean. Limnol Oceanogr 50:1844–1854

    CAS  Google Scholar 

  • Fisher SG, Likens GE (1973) Energy flow in Bear Brook, New Hampshire: integrative approach to stream ecosystem metabolism. Ecol Monogr 43:421–439

    Google Scholar 

  • Flöder S, Sommer U (1999) Diversity in planktonic communities: an experimental test of the intermediate disturbance hypothesis. Limnol Oceanogr 44:1114–1119

    Google Scholar 

  • Frankignoulle M, Abril G, Borges A, Burge I, Canon C, Delille B, Libert E, Théate J-M (1998) Carbon dioxide emmision from European estuaries. Science 282:434–436

    PubMed  CAS  Google Scholar 

  • Gaarder T, Gran HH (1927) Investigations of the production of plankton in the Oslo Fjord. Rapp Et Proc Verg Cons Int Explor Mer 42:1–48

    Google Scholar 

  • Garnier J, Billen G (2007) Production vs. respiration in river systems: an indicator of an “ecological status”. Sci Total Environ 375:110–124

    PubMed  CAS  Google Scholar 

  • Gattuso J-P, Pichon M, Delesalle B, Frankignoulle M (1993) Community metabolism and air–sea CO2 fluxes in a coral reef ecosystem (Moorea, French Polynesia). Mar Ecol Progr Ser 96:259–267

    Google Scholar 

  • Gattuso JP, Frankignoulle M, Smith SV (1999) Measurement of community metabolism and significance in the coral reef CO2 source-sink debate. Proc Natl Acad Sci USA 96:13017–13022

    PubMed  CAS  Google Scholar 

  • Gazeau F, Borges AV, Barron C, Duarte CM, Iversen N, Middelburg JJ, Delille B, Pizay MD, Frankignoulle M, Gattuso JP (2005a) Net ecosystem metabolism in a micro-tidal estuary (Randers Fjord, Denmark): evaluation of methods. Mar Ecol Progr Ser 301:23–41

    CAS  Google Scholar 

  • Gazeau F, Duarte CM, Gattuso J-P, Barron C, Navarro N, Ruiz S, Prairie YT, Calleja M, Delille B, Frankignoulle M, Borges AV (2005b) Whole-system metabolism and CO2 fluxes in a Mediterranean Bay dominated by seagrass beds (Palma Bay, NW Mediterranean). Biogeosciences 2:43–60

    CAS  Google Scholar 

  • Gazeau F, Gattuso JP, Middelburg JJ, Brion N, Schiettecatte LS, Frankignoulle M, Borges AV (2005c) Planktonic and whole system metabolism in a nutrient-rich estuary (the Scheldt estuary). Estuaries 28:868–883

    CAS  Google Scholar 

  • Giddings J, Eddlemon GK (1978) Photosynthesis/respiration ratios in aquatic microcosms under arsenic stress. Water Air Soil Pollut 9:207–212

    CAS  Google Scholar 

  • Gordon DC, Boudreau Jr PR, Mann KH, Ong JE, Silvert WL, Smith SV, Wattayakorn G, Wulff F, Yanagi T (1996) LOICZ biogeochemical modeling guidelines, vol 5, LOICZ reports and studies, Texel, pp 1–96

  • Green RE, Bianchi TS, Dagg MJ, Walker ND, Breed GA (2006) An organic carbon budget for the Mississippi River turbidity plume and plume contributions to air–sea CO2 fluxes and bottom water hypoxia. Estuaries Coasts 29:579–597

    CAS  Google Scholar 

  • Guadayol O, Peters F, Marrase C, Gasol JM, Roldan C, Berdalet E, Massana R, Sabata A (2009) Episodic meteorological and nutrient-load events as drivers of coastal planktonic ecosystem dynamics: a time-series analysis. Mar Ecol Progr Ser 381:139–155

    CAS  Google Scholar 

  • Gucker B, Boechat IG, Giani A (2009) Impacts of agricultural land use on ecosystem structure and whole-stream metabolism of tropical Cerrado streams. Freshw Biol 54:2069–2085

    CAS  Google Scholar 

  • Hagy JD, Sanford LP, Boynton WR (2000) Estimation of net physical transport and hydraulic residence times for a coastal plain estuary using box models. Estuaries 23:328–340

    Google Scholar 

  • Hanson PC, Carpenter SR, Armstrong DE, Stanley EH (2006) Lake dissolved inorganic carbon and dissolved oxygen: Changing drivers from days to decades. Ecol Monogr 76:343–363

    Google Scholar 

  • Hanson PC, Carpenter SR, Kimura N, Wu C, Cornelius SP, Kratz TK (2008) Evaluation of metabolism models for free-water dissolved oxygen methods in lakes. Limnol Oceanogr Methods 6:454–465

    CAS  Google Scholar 

  • Harris LA, Duarte CM, Nixon SW (2006) Allornetric laws and prediction in estuarine and coastal ecology. Estuar Coasts 29:340–344

    Google Scholar 

  • Heath M (1995) An holistic analysis of the coupling between physical and biological processes in the coastal zone. Ophelia 42:95–125

    Google Scholar 

  • Heip CHR, Goosen NK, Herman PMJ, Kromkamp J, Middelburg JJ, Soetaert K (1995) Production and consumption of biological particles in temperate tidal estuaries. Oceanogr Mar Biol Annu Rev 33:1–149

    Google Scholar 

  • Hesslein RH, Broecker WS, Quay PD, Schindler DW (1980) Whole-lake radiocarbon experiment in an oligotrophic lake at the experimental lakes area, Northwestern Ontario. Can J Fish Aquat Sci 37:455–463

    Google Scholar 

  • Hoegh-Guldberg O, Mumby PJ, Hooten AJ, Steneck RS, Greenfield P, Gomez E, Harvell CD, Sale PF, Edwards AJ, Caldeira K, Knowlton N, Eakin CM, Iglesias-Prieto R, Muthiga N, Bradbury RH, Dubi A, Hatziolos ME (2007) Coral reefs under rapid climate change and ocean acidification. Science 318:1737–1742

    PubMed  CAS  Google Scholar 

  • Holtgrieve GW, Schindler DE, Branch TA, A’Mar ZT (2010) Simultaneous quantification of aquatic ecosystem metabolism and reaeration using a Bayesian statistical model of oxygen dynamics. Limnol Oceanogr 55:1047–1063

    CAS  Google Scholar 

  • Hopkinson CS, Giblin AE, Tucker J, Garritt RH (1999) Benthic metabolism and nutrient cycling along an estuarine salinity gradient. Estuaries 22:863–881

    CAS  Google Scholar 

  • Houghton RA (2007) Balancing the global carbon budget. Annu Rev Earth Planet Sci 35:313–347

    CAS  Google Scholar 

  • Howarth RW, Schneider R, Swaney DP (1996) Metabolism and organic carbon fluxes in the tidal freshwater Hudson river. Estuaries 19:848–865

    CAS  Google Scholar 

  • Howarth RW, Swaney DP, Butler TJ, Marino R (2000) Climatic control on eutrophication of the Hudson River estuary. Ecosystems 3:210–215

    Google Scholar 

  • Jenkins WJ (1977) Tritium–helium dating in Sargasso Sea: measurement of oxygen utilization rates. Science 196:291–292

    PubMed  CAS  Google Scholar 

  • Jin X, Gruber N, Dunne JP, Sarmiento JL, Armstrong RA (2006) Diagnosing the contribution of phytoplankton functional groups to the production and export of particulate organic carbon, CaCO3, and opal from global nutrient and alkalinity distributions. Global Biogeochem Cycles 20:1–17

    Google Scholar 

  • Jonsson A, Algesten G, Bergstrom AK, Bishop K, Sobek S, Tranvik LJ, Jansson M (2007) Integrating aquatic carbon fluxes in a boreal catchment carbon budget. J Hydrol 334:141–150

    Google Scholar 

  • Juday C (1940) The annual energy budget of an inland lake. Ecology 21:438–450

    Google Scholar 

  • Justic D, Rabalais NN, Turner RE (1996) Effects of climate change on hypoxia in coastal waters: a doubled CO2 scenario for the northern Gulf of Mexico. Limnol Oceanogr 41:992–1003

    CAS  Google Scholar 

  • Justic D, Turner RE, Rabalais NN (2003) Climatic influences on riverine nitrate flux: implications for coastal marine eutrophication and hypoxia. Estuaries 26:1–11

    CAS  Google Scholar 

  • Kaldy JE, Onuf CP, Eldridge PM, Cifuentes LA (2002) Carbon budget for a subtropical seagrass dominated coastal lagoon: How important are seagrasses to total ecosystem net primary production? Estuaries 25:528–539

    CAS  Google Scholar 

  • Karl DM, Laws EA, Morris P, le PJ, Williams B, Emerson S (2003) Metabolic balance of the open sea. Nature 426:32

    PubMed  CAS  Google Scholar 

  • Kelly MH, Fitzpatrick LC, Pearson WD (1978) Phytoplankton dynamics, primary productivity and community metabolism in a north-central Texas pond. Hydrobiologia 58:245–260

    CAS  Google Scholar 

  • Kemp WM, Boynton WR (1980) Influence of biological and physical processes on dissolved-oxygen dynamics in an estuarine system: implications for measurement of community metabolism. Estuar Coast Marine Sci 11:407–431

    Google Scholar 

  • Kemp WM, Testa JM (2011) Metabolic balance between ecosystem production and consumption. In: Wolansky E, McLusky D (eds), Treatise on estuarine and coastal science, vol 7, chap 6. Elsevier Ltd., Oxford (in press)

  • Kemp WM, Lewis MR, Jones TW (1986) Comparison of methods for measuring production by the submersed macrophyte, Potamogeton perfoliatus L. Limnol Oceanogr 31:1322–1334

    CAS  Google Scholar 

  • Kemp WM, Sampou PA, Garber J, Tuttle J, Boynton WR (1992) Seasonal depletion of oxygen from bottom waters of Chesapeake Bay: roles of benthic and planktonic respiration and physical exchange processes. Mar Ecol Progr Ser 85:137–152

    CAS  Google Scholar 

  • Kemp PF, Falkowski PG, Flagg CN, Phoel WC, Smith SL, Wallace DWR, Wirick CD (1994) Modeling vertical oxygen and carbon flux during stratified spring and summer conditions on the continental-shelf, Middle Atlantic Bight, Eastern USA. Deep-Sea Res Part II Topical Stud Oceanogr 41:629–655

    CAS  Google Scholar 

  • Kemp WM, Smith EM, Marvin-Dipasquale M, Boynton WR (1997) Organic carbon balance and net ecosystem metabolism in Chesapeake Bay. Mar Ecol Prog Ser 150:229–248

    CAS  Google Scholar 

  • Kemp WM, Faganeli J, Puskaric S, Smith EM, Boynton WR (1999) Pelagic-benthic coupling and nutrient cycling. In: Malone TC, Maley A, Harding LW, Smodlaka N, Turner RE (eds) Coastal and estuarine studies, ecosystems at the land-sea margin: drainage basin to coastal sea. American Geophysical Union, Washington, DC, pp 295–339

    Google Scholar 

  • Kemp WM, Testa JM, Conley DJ, Gilbert D, Hagy JD (2009) Temporal responses of coastal hypoxia to nutrient loading and physical controls. Biogeosciences 6:2985–3008

    CAS  Google Scholar 

  • Kenney BE, Litaker W, Duke CS, Ramus J (1988) Community oxygen-metabolism in a shallow tidal estuary. Estuar Coast Shelf Sci 27:33–43

    CAS  Google Scholar 

  • Kettle H, Merchant CJ (2005) Systematic errors in global air–sea CO2 flux caused by temporal averaging of sea-level pressure. Atmos Chem Phys 5:1459–1466

    CAS  Google Scholar 

  • Kleypas J, Yates K (2009) Coral reefs and ocean acidification. Oceanography 22:108–117

    Google Scholar 

  • Kremer JN, Vaudrey JMP, Ullman DS, Bergondo DL, LaSota N, Kincaid C, Codiga DL, Brush MJ (2010) Simulating property exchange in estuarine ecosystem models at ecologically appropriate scales. Ecol Model 221:1080–1088

    Google Scholar 

  • Lamberti GA, Chaloner DT, Hershey AE (2010) Linkages among aquatic ecosystems. J North Am Benthol Soc 29:245–263

    Google Scholar 

  • Laursen AE, Seitzinger SP, Dekorsey R, Sanders JG, Breitburg DL, Osman RW (2002) Multiple stressors in an estuarine system: effects of nutrients, trace elements, and trophic complexity on benthic photosynthesis and respiration. Estuaries 25:57–69

    CAS  Google Scholar 

  • Laws EA, Falkowski PG, Smith WO, Ducklow H, McCarthy JJ (2000) Temperature effects on export production in the open ocean. Global Biogeochem Cycles 14:1231–1246

    CAS  Google Scholar 

  • Lee K (2001) Global net community production estimated from the annual cycle of surface water total dissolved inorganic carbon. Limnol Oceanogr 46:1287–1297

    CAS  Google Scholar 

  • Lehrter JC, Cebrian J (2010) Uncertainty propagation in an ecosystem nutrient budget. Ecol Appl 20:508–524

    PubMed  Google Scholar 

  • Lindeman RL (1942) The trophic-dynamic aspect of ecology. Ecology 23:399–417

    Google Scholar 

  • Lopez-Urrutia A, San Martin E, Harris RP, Irigoien X (2006) Scaling the metabolic balance of the oceans. Proc Natl Acad Sci USA 103:8739–8744

    PubMed  CAS  Google Scholar 

  • Lovett GM, Cole JJ, Pace ML (2006) Is net ecosystem production equal to ecosystem carbon accumulation? Ecosystems 9:1–14

    Google Scholar 

  • Luz B, Barkan E (2000) Assessment of oceanic productivity with the triple-isotope composition of dissolved oxygen. Science 288:2028–2031

    PubMed  CAS  Google Scholar 

  • Luz B, Barkan E, Bender ML, Thiemens MH, Boering KA (1999) Triple-isotope composition of atmospheric oxygen as a tracer of biosphere productivity. Nature 400:547–550

    CAS  Google Scholar 

  • Luz B, Barkan E, Sagi Y, Yacobi YZ (2002) Evaluation of community respiratory mechanisms with oxygen isotopes: a case study in Lake Kinneret. Limnol Oceanogr 47:33–42

    CAS  Google Scholar 

  • Martz TR, Johnson KS, Riser SC (2008) Ocean metabolism observed with oxygen sensors on profiling floats in the South Pacific. Limnol Oceanogr 53:2094–2111

    CAS  Google Scholar 

  • Matthews DA, Effler SW (2006) Long-term changes in the areal hypolimnetic oxygen deficit (AHOD) of Onondaga Lake: evidence of sediment feedback. Limnol Oceanogr 51:702–714

    CAS  Google Scholar 

  • McNiel CL, Katz DR, Ward B, McGillis WR, Johnson BD (2006) A method to estimate net community metabolism from profiles of dissolved O2 and N2. Hydrobiologia 571:181–190

    Google Scholar 

  • Moloney CL, Fields JG (1991) The size-based dynamics of plankton food webs 1. A simulation-model of carbon and nitrogen flows. J Plankton Res 13:1003–1038

    Google Scholar 

  • Najjar RG, Keeling RF (2000) Mean annual cycle of the air-sea oxygen flux: a global view. Global Biogeochem Cycles 14:573–584

    CAS  Google Scholar 

  • Nicholson D, Emerson S, Eriksen CC (2008) Net community production in the deep euphotic zone of the subtropical North Pacific gyre from glider surveys. Limnol Oceanogr 53:2226–2236

    CAS  Google Scholar 

  • O’Neill RV (1986) A hierarchical concept of ecosystems. Princeton University Press, New Jersey

    Google Scholar 

  • Odum HT (1956) Primary production in flowing waters. Limnol Oceanogr 1:102–117

    Google Scholar 

  • Odum HT (1957) Trophic structure and productivity of Silver Springs, Florida. Ecol Monogr 27:55–112

    Google Scholar 

  • Odum EP (1971) Fundamental of ecology. W.B. Saunders, Philadelphia

    Google Scholar 

  • Odum HT, Odum EP (1955) Trophic structure and productivity of a windward coral reef community on Eniwetok Atoll. Ecol Monogr 25:291–320

    Google Scholar 

  • Ostrom NE, Carrick HJ, Twiss MR, Piwinski L (2005) Evaluation of primary production in Lake Erie by multiple proxies. Oecologia 144:115–124

    PubMed  Google Scholar 

  • Oviatt CA, Keller AA, Sampou PA, Beatty LL (1986) Patterns of productivity during eutrophication: a mesocosm experiment. Mar Ecol Prog Ser 28:69–80

    Google Scholar 

  • Oviatt C, Doering PH, Nowicki BL, Zoppini A (1993) Net system production in coastal waters as a function of eutrophication, seasonality and benthic macrofaunal abundance. Estuaries 16:247–254

    Google Scholar 

  • Parry ML, Canziani OF, Palutikof JP, van der Linden PJ, Hanson CE (eds) (2007) Climate change 2007: impacts, adaptation and vulnerability: contribution of working group II to the fourth assessment report of the Intergovernmental Panel on Climate Change. Cambridge University Press, Cambridge

  • Peters RH (1983) The ecological implications of body size. Cambridge University Press, Cambridge

  • Prowe AEF, Thomas H, Patsch J, Kuhn W, Bozec Y, Schiettecatte LS, Borges AV, de Baar HJW (2009) Mechanisms controlling the air–sea CO2 flux in the North Sea. Cont Shelf Res 29:1801–1808

    Google Scholar 

  • Quay PD, Wilbur DO, Richey JE, Devol AH (1995) The 18O:16O of dissolved oxygen in rivers and lakes in the Amazon Basin: determining the ratio of respiration to photosynthesis rates in freshwaters. Limnol Oceanogr 40:718–729

    CAS  Google Scholar 

  • Quinones-Rivera ZJ, Wissel B, Justic D (2009) Development of productivity models for the Northern Gulf of Mexico based on oxygen concentrations and stable isotopes. Estuar Coasts 32:436–446

    CAS  Google Scholar 

  • Rabalais NN, Gilbert D (2009) Distribution and consequences of hypoxia. In: Urban E, Sundby B, Malanotte-Rizzoli P (eds) Watersheds, bays and bounded seas. Island Press, pp 209–226

  • Rabalais NN, Turner RE, Diaz RJ, Justic D (2009) Global change and eutrophication of coastal waters. ICES J Marine Sci 66:1528–1537

    Google Scholar 

  • Ram ASP, Nair S, Chandramohan D (2003) Seasonal shift in net ecosystem production in a tropical estuary. Limnol Oceanogr 48:1601–1607

    CAS  Google Scholar 

  • Reinthaler T, Van Aken HM, Herndl GJ (2010) Major contribution of autotrophy to microbial carbon cycling in the deep North Atlantic’s interior. Deep-Sea Res Part II Topical Stud Oceanogr 57:1572–1580

    CAS  Google Scholar 

  • Reuther R (1992) Arsenic introduced into a littoral freshwater model ecosystem. Sci Total Environ 115:219–237

    CAS  Google Scholar 

  • Roberts BJ, Mulholland PJ, Hill WR (2007) Multiple scales of temporal variability in ecosystem metabolism rates: results from 2 years of continuous monitoring in a forested headwater stream. Ecosystems 10:588–606

    CAS  Google Scholar 

  • Russ ME, Ostrom NE, Gandhi H, Ostrom PH (2004) Temporal and spatial variations in R:P ratios in Lake Superior, an oligotrophic freshwater environment. J Geophys Res 109:1–16

    Google Scholar 

  • Sanders IA, Heppell CM, Cotton JA, Wharton G, Hildrew AG, Flowers EJ, Trimmer M (2007) Emission of methane from chalk streams has potential implications for agricultural practices. Freshw Biol 52:1176–1186

    CAS  Google Scholar 

  • Sand-Jensen K, Staehr PA (2007) Scaling of pelagic metabolism to size, trophy and forest cover in small Danish lakes. Ecosystems 10:127–141

    Google Scholar 

  • Sand-Jensen K, Staehr PA (2011) CO2 dynamics along Danish lowland streams: water–air gradients, piston velocities and evasion rates. Biogeochemistry (in review)

  • Sargent MC, Austin TS (1949) Organic productivity of an atoll. Trans Am Geophys Union 30:245–249

    Google Scholar 

  • Sargent MC, Austin TS (1954) Biologic economy of coral reefs. Bikini and nearby atolls. US Geol Survey Protess 260E:293–300

  • Sarma VVSS, Abe O, Hashimoto S, Hinuma A, Saino T (2005) Seasonal variations in triple oxygen isotopes and gross oxygen production in the Sagami Bay, central Japan. Limnol Oceanogr 50:544–552

    CAS  Google Scholar 

  • Schindler DW (1998) Replication versus realism: the need for ecosystem-scale experiments. Ecosystems 1:323–334

    Google Scholar 

  • Smith SV (1973) Carbon dioxide dynamics: a record of organic carbon production, respiration, and calcification in the Eniwetok reef flat community. Limnol Oceanogr 18:106–120

    CAS  Google Scholar 

  • Smith SV, Hollibaugh JT (1993) Coastal metabolism and the oceanic organic carbon balance. Rev Geophys 31:75–89

    Google Scholar 

  • Smith SV, Hollibaugh JT (1997) Annual cycle and interannual variability of ecosystem metabolism in a temperate climate embayment. Ecol Monogr 67:509–533

    Google Scholar 

  • Smith EM, Kemp WM (1995) Seasonal and regional variations in plankton community production and respiration for Chesapeake Bay. Mar Ecol Prog Ser 116:217–231

    Google Scholar 

  • Smith SV, Key GS (1975) Carbon dioxide and metabolism in marine environments. Limnol Oceanogr 20:493–495

    CAS  Google Scholar 

  • Smith SV, Marsh JA (1973) Organic carbon production on the windward reef flat of Eniwek Atol. Limnol Oceanogr 18:953–961

    CAS  Google Scholar 

  • Smith SV, Hollibaugh JT, Dollar SJ, Vink S (1991) Tomales Bay Metabolism: C–N–P stoichiometry and ecosystem heterotrophy at the land sea interface. Estuar Coast Shelf Sci 33:223–257

    CAS  Google Scholar 

  • Smith SV, Swaney DP, Buddemeier RW, Scarsbrook MR, Weatherhead MA, Humborg C, Eriksson H, Hannerz F (2005a) River nutrient loads and catchment size. Biogeochemistry 75:83–107

    CAS  Google Scholar 

  • Smith SV, Buddemeier RW, Wulff F, Swaney DP (2005b) C, N, P fluxes in the coastal zone. In: Crossland CJ, Kremer HH, Lindeboom HJ, Marshall-Crossland JI, Le Tissier MDA (eds) Coastal fluxes in the anthropocene. Springer, Berlin, pp 95–143

  • Sobek S, Tranvik LJ, Cole JJ (2005) Temperature independence of carbon dioxide supersaturation in global lakes. Global Biogeochem Cycles 19:1–10

    Google Scholar 

  • Squires MM, Lesack LFW, Hecky RE, Guildford SJ, Ramlal P, Higgins SN (2009) Primary production and carbon dioxide metabolic balance of a lake-rich arctic river floodplain: partitioning of phytoplankton, epipelon, macrophyte, and epiphyton production among lakes on the Mackenzie Delta. Ecosystems 12:853–872

    CAS  Google Scholar 

  • Staehr PA, Sand-Jensen K (2006) Seasonal changes in temperature and nutrient control of photosynthesis, respiration and growth of natural phytoplankton communities. Freshw Biol 51:249–262

    CAS  Google Scholar 

  • Staehr PA, Sand-Jensen K (2007) Temporal dynamics and regulation of lake metabolism. Limnol Oceanogr 52:108–120

    CAS  Google Scholar 

  • Staehr PA, Bade D, Van de Bogert MC, Koch GR, Williamson CE, Hanson PC, Cole JJ, Kratz T (2010a) Lake metabolism and the diel oxygen technique: state of the science. Limnol Oceanogr Methods 8:628–644

    CAS  Google Scholar 

  • Staehr PA, Sand-Jensen K, Raun AL, Nielsson B, Kidmose J (2010b) Drivers of metabolism and net heterotrophy in contrasting lakes. Limnol Oceanogr 55:817–830

    CAS  Google Scholar 

  • Staehr PA, Christensen JPA, Batt R, Read J (2011) Ecosystem metabolism in stratified lakes. Limnol Oceanogr (in review)

  • Swaney DP, Howarth RW, Butler TJ (1999) A novel approach for estimating ecosystem production and respiration in estuaries: application to the oligohaline and mesohaline Hudson river. Limnol Oceanogr 44:1509–1521

    CAS  Google Scholar 

  • Sweeney C, Hansell DA, Carlson CA, Codispoti LA, Gordon LI, Marra J, Millero FJ, Smith WO, Takahashi T (2000) Biogeochemical regimes, net community production and carbon export in the Ross Sea, Antarctica. Deep Sea Res Part II: Topical Stud Oceanogr 47:3369–3394

    CAS  Google Scholar 

  • Takahashi T, Sutherland SC, Sweeney C, Poisson A, Metzl N, Tilbrook B, Bates N, Wanninkhof R, Feely RA, Sabine C, Olafsson J, Nojiri Y (2002) Global sea–air CO2 flux based on climatological surface ocean pCO2, and seasonal biological and temperature effects. Deep-Sea Res Part II-Topical Stud Oceanogr 49:1601–1622

    CAS  Google Scholar 

  • Tank JL, Rosi-Marshall EJ, Griffiths NA, Entrekin SA, Stephen ML (2010) A review of allochthonous organic matter dynamics and metabolism in streams. J North Am Benthol Soc 29:118–146

    Google Scholar 

  • Testa JM, Kemp WM (2008) Variability of biogeochemical processes and physical transport in a partially stratified estuary: a box-modeling analysis. Mar Ecol Prog Ser 356:63–79

    CAS  Google Scholar 

  • Tobias CR, Bölke JK, Harvey W (2007) The oxygen-18 isotope approach for measuring aquatic metabolism in high-productive waters. Limnol Oceanogr 52:1439–1453

    CAS  Google Scholar 

  • Tobias CR, Bohlke JK, Harvey JW, Busenberg E (2009) A simple technique for continuous measurement of time-variable gas transfer in surface waters. Limnol Oceanogr Methods 7:185–195

    CAS  Google Scholar 

  • Tranvik LJ, Downing JA, Cotner JB, Loiselle SA, Striegl RG, Ballatore TJ, Dillon P, Finlay K, Fortino K, Knoll LB, Kortelainen PL, Kutser T, Larsen S, Laurion I, Leech DM, McCallister SL, McKnight DM, Melack JM, Overholt E, Porter JA, Prairie Y, Renwick WH, Roland F, Sherman BS, Schindler DW, Sobek S, Tremblay A, Vanni MJ, Verschoor AM, Von Wachenfeldt E, Weyhenmeyer GA (2009) Lakes and reservoirs as regulators of carbon cycling and climate. Limnol Oceanogr 54:2298–2314

    CAS  Google Scholar 

  • Tsai JW, Kratz TK, Hanson PC, Wu JT, Chang WYB, Arzberger PW, Lin BS, Lin FP, Chou HM, Chiu CY (2008) Seasonal dynamics, typhoons and the regulation of lake metabolism in a subtropical humic lake. Freshw Biol 53:1929–1941

    CAS  Google Scholar 

  • Twilley RR, Kemp WM, Staver KW, Stevenson JC, Boynton WR (1985) Nutrient enrichment of estuarine submersed vascular plant-communities.1. Algal growth and effects on production of plants and associated communities. Mar Ecol Prog Ser 23:179–191

    Google Scholar 

  • Uehlinger U (2006) Annual cycle and inter-annual variability of gross primary production and ecosystem respiration in a floodprone river during a 15-year period. Freshw Biol 51:950

    Google Scholar 

  • Uehlinger U, Kawecka B, Robinson CT (2003) Effects of experimental floods on periphyton and stream metabolism below a high dam in the Swiss Alps (River Spöl). Aquat Sci 65:199–209

    Google Scholar 

  • Vadeboncoeur Y, Lodge DM, Carpenter SR (2001) Whole-lake fertilization effects on distribution of primary production between benthic and pelagic habitats. Ecology 82:1065–1077

    Google Scholar 

  • Vadeboncoeur Y, Jeppesen E, Vander Zanden MJ, Schierup HH, Christoffersen K, Lodge DM (2003) From Greenland to green lakes: cultural eutrophication and the loss of benthic pathways in lakes. Limnol Oceanogr 48:1408–1418

    Google Scholar 

  • Van de Bogert MC, Carpenter SR, Cole JJ, Pace ML (2007) Assessing pelagic benthic metabolism using free water measurements. Limnol Oceanogr Methods 5:145–155

    Google Scholar 

  • Venkiteswaran JJ, Schiff SL, Wassenaar LI (2008) Aquatic metabolism and ecosystem health assessment using dissolved O2 stable isotope diel curves. Ecol Appl 18:965–982

    PubMed  Google Scholar 

  • Wiegner TN, Seitzinger SP, Breitburg DL, Sanders JG (2003) The effects of multiple stressors on the balance between autotrophic and heterotrophic processes in an estuarine system. Estuaries 26:352–364

    Google Scholar 

  • Williams PJL (1998) The balance of plankton respiration and photosynthesis in the open oceans. Nature 394:55–57

    CAS  Google Scholar 

  • Williamson CE, Dodds W, Kratz TK, Palmer MA (2008) Lakes and streams as sentinels of environmental change in terrestrial and atmospheric processes. Front Ecol Environ 6:247–254

    Google Scholar 

  • Woodwell GM, Whittaker RH (1968) Primary production in terrestrial ecosystems. Am Zool 8:19–30

    Google Scholar 

  • Yvon-Durocher G, Jones JI, Trimmer M, Woodward G, Montoya JM (2010) Warming alters the metabolic balance of ecosystems. Philos Trans R Soc B Biol Sci 365:2117–2126

    Google Scholar 

Download references

Acknowledgments

This paper was supported by (1-for P.A. Staehr) the Danish Natural Research Council, STENO grant no 272-05-0277, a Copenhagen faculty research grant no 10-08716, and the Danish Centre for lake restoration (CLEAR); (2-for J.M. Testa and W.M. Kemp) the United States National Oceanographic and Atmospheric Administration (NOAA) Coastal Hypoxia Research Program (CHRP; CHRP-NAO7NOS4780191), the United States National Science Foundation Chesapeake Bay Environmental Observatory (CBEO; CBEO-3 BERS-0618986), and by the State of Maryland Department of Natural Resources (K00B920002). We are thankful to Nathaniel E. Ostrom for comments on the methods section. This is contribution #4497 from the University of Maryland Center for Environmental Science.

Author information

Authors and Affiliations

  1. Department of Marine Ecology, National Environmental Research Institute, Aarhus University, Frederiksborgvej 399, PO Box 4000, Roskilde, Denmark

    Peter A. Staehr

  2. Horn Point Laboratory, Center for Environmental Science, University of Maryland, PO Box 775, Cambridge, MD, 21613, USA

    Jeremy M. Testa & W. Michael Kemp

  3. Cary Institute of Ecosystem Studies, Box AB, Millbrook, NY, 12545-0129, USA

    Jon J. Cole

  4. Freshwater Biological Laboratory, University of Copenhagen, Helsingørsgade 51, 3400, Hillerød, Denmark

    Kaj Sand-Jensen

  5. Departamento de Geología, Centro de Investigación Cientifica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico

    Stephen V. Smith

Authors
  1. Peter A. Staehr
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jeremy M. Testa
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. W. Michael Kemp
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jon J. Cole
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Kaj Sand-Jensen
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Stephen V. Smith
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Peter A. Staehr.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 103 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Staehr, P.A., Testa, J.M., Kemp, W.M. et al. The metabolism of aquatic ecosystems: history, applications, and future challenges. Aquat Sci 74, 15–29 (2012). https://doi.org/10.1007/s00027-011-0199-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00027-011-0199-2

Keywords

Search

Navigation