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Bridging the gap between micro - and macro-scale perspectives on the role of microbial communities in global change ecology

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Abstract

In order to understand the role microbial communities play in mediating ecosystem response to disturbances it is essential to address the methodological and conceptual gap that exists between micro- and macro-scale perspectives in ecology. While there is little doubt microorganisms play a central role in ecosystem functioning and therefore in ecosystem response to global change-induced disturbance, our ability to investigate the exact nature of that role is limited by disciplinary and methodological differences among microbial and ecosystem ecologists. In this paper we present results from an interdisciplinary graduate-level seminar class focused on this topic. Through the medium of case studies in global change ecology (soil respiration, nitrogen cycling, plant species invasion and land use/cover change) we highlight differences in our respective approach to ecology and give examples where disciplinary perspective influences our interpretation of the system under study. Finally, we suggest a model for integrating perspectives that may lead to greater interdisciplinary collaboration and enhanced conceptual and mechanistic modeling of ecosystem response to disturbance.

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References

  • Balser TC (2000) Linking soil microbial communities and ecosystem functioning. Doctoral Dissertation, University of California, Berkeley

  • Balser TC, Firestone MK (2005) Linking microbial community composition and soil processes in a California annual grassland and mixed-conifer forest. Biogeochemistry 73:395–415

    Article  CAS  Google Scholar 

  • Balser TC, Kinzig AP, Firestone MK (2002) Linking soil microbial communities and ecosystem functioning. In: Kinzig A, Pacala S, Tilman D (eds) The functional consequences of biodiversity: empirical progress and theoretical extensions. Princeton University Press, Princeton, pp 265–293

    Google Scholar 

  • Bardgett RD, Bouman WD, Kaufmann R, Schmidt SK (2005) A temporal approach to linking aboveground and belowground ecology. Trends Ecol Evol 20:634–641

    Article  PubMed  Google Scholar 

  • Beare MH (1997) Fungal and bacterial pathways of organic matter decomposition and nitrogen mineralization in arable soils. In: Brussard L, Fererra-Cerrato R (eds) Soil ecology in sustainable agricultural systems. CRC Lewis Publishers, Boca Raton, pp 37–70

    Google Scholar 

  • Bernhardt ES, Likens GE (2002) Dissolved organic carbon enrichment alters nitrogen dynamics in a forest stream. Ecology 83:1689–1700

    Google Scholar 

  • Bever JD (2003) Soil community feedback and the coexistence of competitors: conceptual frameworks and empirical tests. New Phytol 157:465–473

    Article  Google Scholar 

  • Bond-Lamberty B, Wang C, Gower ST (2004a) A global relationship between the heterotrophic and autotrophic components of soil respiration? Glob Change Biol 10:1756–1766

    Google Scholar 

  • Bond-Lamberty B, Wang C, Gower ST (2004b) Contribution of root respiration to soil surface CO2 flux in a boreal black spruce chronosequence. Tree Physiol 24:1387–1395

    Google Scholar 

  • Bradford MA, Jones TH, Bardgett RD, Black HIJ, Boag B, Bonkowski M, Cook R, Eggers T, Gange AC, Grayston SJ, Kandeler E, McCaig AE, Newington JE, Prosser JI, Setala H, Staddon PL, Tordoff GM, Tscherko D, Lawton JH (2002) Impacts of soil faunal community composition on model grassland ecosystems. Science 298:615–618

    Article  PubMed  CAS  Google Scholar 

  • Braker G, Ayala-del-Rio HL, Devol AH, Fesefeldt A, Tiedje JM (2001) Community structure of denitrifiers, bacteria, and archaea along redox gradients in Pacific Northwest marine sediments by terminal Restriction Fragment Length Polymorphism analysis of amplified nitrate reductase (nirS) and 16S rRNA genes. Appl Environ Microbiol 67(4):1893–1901

    Article  PubMed  CAS  Google Scholar 

  • Carpenter SR, Caraco NF, Correll DL, Howarth RW, Sharpley AN, Smith VH (1998) Nonpoint pollution of surface waters with phosphorus and nitrogen. Ecol Appl 8:559–568

    Google Scholar 

  • Cavigelli MA, Robertson GP (2000) The functional significance of denitrifier community composition in a terrestrial ecosystem. Ecology 81:1404–1414

    Article  Google Scholar 

  • Cavigelli M, Robertson G (2001) Role of denitrifier diversity in rates of nitrous oxide coonsumption in a terrestrial ecosystem. Soil Biol Biochem 33:297–310

    Article  CAS  Google Scholar 

  • Cox PM, Betts RA, Jones CD, Spall SA, Totterdell IJ (2000) Acceleration of global warming due to feedbacks in a coupled climate model. Nature 408:184–187

    Article  PubMed  CAS  Google Scholar 

  • Davidson EA, Janssens IA (2006) Temperature sensitivity of soil carbon decomposition and feedbacks to climate change. Nature 440:165–173

    Article  PubMed  CAS  Google Scholar 

  • Davidson EA, Trumbore SE, Amundson R (2000) Soil warming and organic carbon content. Nature 408:789–790

    Article  PubMed  CAS  Google Scholar 

  • DeLucia EH, Hamilton JG, Naidu SL, Thomas RB, Andrews JA, Finzi A, Lavine M, Matamala R, Mohan JE, Hendrey GR, Schlesinger WH (1999) Net primary production of a forest ecosystem with experimental CO2 enrichment. Science 284:1177–1179

    Article  PubMed  CAS  Google Scholar 

  • Eliasson PE, McMurtrie RE, Pepper DA, Stromgren M, Linder S, Agren GI (2005) The response of heterotrophic CO2 flux to soil warming Glob. Change Biol 11:167–181

    Article  Google Scholar 

  • Ellert B, Bettany J (1992) Temperature dependence of net nitrogen and sulfur mineralization. Soil Sci Soc Am J 56:1133–1141

    Article  CAS  Google Scholar 

  • Ettema CH, Wardle DA (2002) Spatial soil ecology. Trends Ecol Evol 17:177–183

    Article  Google Scholar 

  • Fang C, Smith P, Moncrieff JB, Smith JU (2005) Similar response of labile and resistant soil organic matter pools to changes in temperature. Nature 433:57–59

    Article  PubMed  CAS  Google Scholar 

  • Fierer N, Craine J, McLauchlan K, Schimel J (2005) Litter quality and the temperature sensitivity of decomposition. Ecology 86:320–326

    Google Scholar 

  • Forney LJ, Zhou X, Brown CJ (2004) Molecular microbial ecology: land of the one-eyed king. Curr Opin Microbiol 7:210–220

    Article  PubMed  CAS  Google Scholar 

  • Forshay KJ, Stanley EH (2005) Rapid nitrate loss and denitrification in a temperate river floodplain. Biogeochemistry 75:43–64

    Article  CAS  Google Scholar 

  • Fraterrigo JM, Balser TC, Turner MG (2006) Microbial community variation and its relationship with nitrogen mineralization in historically altered forests. Ecology 87:570–579

    PubMed  Google Scholar 

  • Gholz HL (1982) Environmental limits on aboveground net primary productivity, leaf area index, and biomass in vegetation zones of the Pacific Northwest. Ecology 63:469–481

    Article  Google Scholar 

  • Giardina CP, Ryan MG (2000) Evidence that decomposition rates of organic carbon in mineral soil do not vary with temperature. Nature 404:858–861

    Article  PubMed  CAS  Google Scholar 

  • Golley FB (1993) A history of the ecosystem concept in ecology – more than the sum of the parts. Yale University Press, New Haven

    Google Scholar 

  • Gonzalez C (2001) Undergraduate research, graduate mentoring, and the University’s mission. Science 293:1624–1626

    Article  PubMed  CAS  Google Scholar 

  • Gray AN (2005) Eight nonnative plants in western Oregon forests: associations with environment and management. Environ Monit Assess 100:109–127

    Article  PubMed  Google Scholar 

  • Hooper DU, Chapin FS III, Ewel JJ, Hector A, Inchausti P, Lavorel S, Lawton JH, Lodge DM, Loreau M, Naeem S, Schmid B, Setälä H, Symstad AJ, Vandermeer J, Wardle DA (2005) Effects of biodiversity on ecosystem functioning: a consensus of current knowledge. Ecol Monogr 75:3–35

    Google Scholar 

  • Horner-Devine MC, Carney KM, Bohannan BJM (2004a) An ecological perspective on bacterial biodiversity. Proc R Soc London Ser B-Biol Sci 271:113–122

    Article  Google Scholar 

  • Horner-Devine MC, Lage M, Hughes JB, Bohannan BJM (2004b) A taxa–area relationship for bacteria. Nature 432:750–753

    Article  CAS  Google Scholar 

  • Horz HP, Barbrook A, Field CB, Bohannan BJM (2004) Ammonia-oxidizing bacteria respond to multifactorial global change. Proc Nat Acad Sci USA 101:15136–15141

    Article  PubMed  CAS  Google Scholar 

  • Intergovernmental Panel on Climate Change (2001) [Houghton JT, Ding Y, Griggs DJ, Noguer M, van der Linden PJ, Dai X, Maskell K, Johnson CA (eds)]. Cambridge University Press, Cambridge, United Kingdom and New York, NY, USA, p 881

  • IPCC (2001) Climate change 2001: the scientific basis. Contribution of Working Group I to the Third Assessment Report

  • Jessup CM, Kassen R, Forde SE, Kerr B, Buckling A, Rainey PB, Bohannan BJM (2004) Big questions, small worlds: microbial model systems in ecology. Trends Ecol Evol 19:189–197

    Article  PubMed  Google Scholar 

  • Jiang L, Morin PJ (2004) Productivity gradients cause positive diversity-invasibility relationships in microbial communities. Ecol Lett 7:1047–1057

    Article  Google Scholar 

  • Kercher S, Zedler J (2004) Flood tolerance in wetland angiosperms: a comparison of invasive and noninvasive species. Aquat Bot 80:89–102

    Article  Google Scholar 

  • Kirschbaum MUF (1995) The temperature dependence of soil organic matter decomposition and the effect of global warming on soil organic C storage. Soil Biol Biochem 27(6):753–760

    Article  CAS  Google Scholar 

  • Knorr W, Prentice IC, House JI, Holland EA (2005) Long-term sensitivity of soil carbon turnover to warming. Nature 433:298–301

    Article  PubMed  CAS  Google Scholar 

  • Kuijper LDJ, Berg MP, Morrien E, Kooi BW, Verhoef HA (2005) Global change effects on a mechanistic decomposer food web model. Glob Change Biol 11:249–265

    Article  Google Scholar 

  • Lattuca LR, Voigt LJ, Fath KQ (2004) Does interdisciplinarity promote learning? Theoretical support and researchable questions. Rev High Educ 28:23–48

    Google Scholar 

  • Luo Y, Wan S, Hui D, Wallace LL (2001) Acclimatization of soil respiration to warming in a tall grass prairie. Nature 413:622–625

    Article  PubMed  CAS  Google Scholar 

  • Mack R, Simberloff D, Lonsdale WM, Evans H, Clout M, Bazzaz FA (2000) Biotic invasions: causes, epidemiology, global consequences, and control. Ecol Appl 10:689–710

    Google Scholar 

  • Myrold DD (1998) Transformations of Nitrogen. In: DM Sylvia et al. (eds) Principles and Applications of Soil Microbiology. Prentice Hall, pp 259–294

  • NRC, N.R.C. (2003) BIO 2010: transforming undergraduate education for future research biologists. National Academy of Sciences, Washington DC, p 191

  • Ogilvie BG, Rutter M, Nedwell DB (1997) Selection by temperature of nitrate-reducing bacteria from estuarine sediments: species composition and competition for nitrate. FEMS Microbiol Ecol 23(1):11–22

    Article  CAS  Google Scholar 

  • Pellmar TC, Eisenberg L (eds) (2000) Bridging disciplines in the brain, behavioral, and clinical sciences. National Academy Press, pp 1–130

  • Pennanen T, Liski J, Bååth E, Kitunen V, Uotila J, Westman CJ, Fritze H (1999) Structure of the microbial communities in coniferous forest soils in relation to site fertility and stand development age. Microbial Ecol 38:168–179

    Article  Google Scholar 

  • Perry L, Galatowitsch S (2003) A test of two annual cover crops for controlling Phalaris arundinacea invasion in restored sedge-meadow wetlands. Restor Ecol 11:297–307

    Article  Google Scholar 

  • Peterson BJ, Wolheim W, Mulholland PJ, Webster JR, Meyer JL, Tank JL, Marti E, Bowden WB, Valett HM, Hershey AE, McDowell WH, Dodds WK, Hamilton SK, Gregory S, Morrall DD (2001) Control of nitrogen export from watersheds by headwater streams. Science 292:86–90

    Article  PubMed  CAS  Google Scholar 

  • Rabalais NN, Turner RE, Justic D, Dortch Q, Wiseman WJ Jr, Gupta BKS (1996) Nutrient changes in the Mississippi river and system response on the adjacent continental shelf. Estuaries 19:386–407

    Article  CAS  Google Scholar 

  • Raich JW, Schlesinger WH (1992) The global carbon dioxide flux in a soil respiration and its relationship to vegetation and climate. Tellus B 44B:81–99

    Google Scholar 

  • Real LA, Brown JH (eds) (1991) Foundations of ecology – classic papers with commentaries. University of Chicago Press, Chicago, pp 1–905

  • Rustad LE, Huntington TG, Boone RD (2000) Controls on soil respiration: implications for climate change. Biogeochemistry 48:1–6

    Article  Google Scholar 

  • Rustad LE, Campbell JL, Marion GM, Norby RJ, Mitchell MJ, Hartley AE, Cornelissen JHC, Gurevitch J (2001) A meta-analysis of the response of soil respiration, net nitrogen mineralization, and aboveground plant growth to experimental ecosystem warming. Oecologia 126:543–562

    Article  Google Scholar 

  • Sakai AK, Allendorf FW, Holt JS, Lodge DM, Molofsky J, With KA, Baughman S, Cabin RJ, Cohen JE, Ellstrand NC, McCauley DE, O’Neil P, Parker IM, Thompson JN, Weller SG (2001) The population biology of invasive species. Annu Rev Ecol Syst 32:305–332

    Article  Google Scholar 

  • Schimel J (2004) Playing scales in the methane cycle: from microbial ecology to the globe. Proc Nat Acad Sci USA 101:12400–12401

    Article  PubMed  CAS  Google Scholar 

  • Schimel JP, Gulledge J (1998) Microbial community structure and global trace gases. Glob Change Biol 4:745–758

    Article  Google Scholar 

  • Schimel J, Balser TC, Wallenstein M Microbial stress-response physiology and its implications for ecosystem functioning. Ecology (in press)

  • Sinsabaugh RL, Saiya-Corka K, Long T, Osgood MP, Neher DA, Zak DR, Norby RJ (2003) Soil microbial activity in a Liquidambar plantation unresponsive to CO2-driven increases in primary production. Appl Soil Ecol 24:263–271

    Article  Google Scholar 

  • Steenwerth KL, Jackson LE, Calderon FJ, Stromberg MR, Scow KM (2002) Soil microbial community composition and land use history in cultivated and grassland ecosystems of coastal California. Soil Biol Biochem 34:1599–1611

    Article  CAS  Google Scholar 

  • Stuedler PA, Jones RD, Castro MS, Melillo JM, Lewis DL (1996) Microbial controls of methane oxidation in temperate forest and agricultural soils. In: Murrell JC, Kelly DP (eds) Microbiology of atmospheric trace gases. Springer, Berlin, pp 69–81

    Google Scholar 

  • Sung NS, Gordon JI, Rose GD, Getzoff ED, Kron SJ, Mumford D, Onuchic JN, Scherer NF, Sumners DL, Kopell NJ (2003) Educating future scientists. Science 301:1485

    Article  PubMed  CAS  Google Scholar 

  • USGS (1999) The quality of our nation’s waters – nutrients and pesticides. U.S. Geological Survey Circular 1225, Reston, Virginia

  • Valentine DW, Holland EA, Schimel DS (1994) Ecosystem and physiological controls over methane production in northern wetlands. J Geophys Res Atmos 99:1563–1571

    Article  CAS  Google Scholar 

  • Vitousek PM, Mooney HA, Lubchenco J, Milillo JM (1997) Human domination of Earth’s ecosystems. Science 277:494–499

    Article  CAS  Google Scholar 

  • Wardle DA, Verhoef HA, Clarholm M (1998) Trophic relationships in the soil microfood-web: predicting the responses to a changing global environment. Glob Change Biol 4:713–727

    Article  Google Scholar 

  • Wardle DA, Yeates GW, Nicholson KS, Bonner KI, Watson RN (1999) Response of soil microbial biomass dynamics, activity and plant litter decomposition to agricultural intensification over a seven-year period. Soil Biol Biochem 31:1707–1720

    Article  CAS  Google Scholar 

  • Wardle DA, Bardgett RD, Klironomos JN, Setälä H, van der Putten WH, Wall DH (2004) Ecological linkages between aboveground and belowground biota. Science 304:1629–1633

    Article  PubMed  CAS  Google Scholar 

  • Whitaker RJ, Grogan DW, Taylor JW (2003) Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301:976–978

    Article  PubMed  CAS  Google Scholar 

  • Whitham TG, Young WP, Martinsen GD, Gehring CA, Schweitzer JA, Shuster SM, Wimp GM, Fischer DG, Bailey JK, Lindroth RL, Woolbright S, Kuske CR (2003) Community and ecosystem genetics: a consequence of the extended phenotype. Ecology 84:559–573

    Google Scholar 

  • Wolters V, Silver WL, Bignell DE, Coleman DC, Lavelle P, Van der Putten WH, De Ruiter P, Rusek J, Wall DH, Wardle DA, Brussaard L, Dangerfield JM, Brown VK, Giller KE, Hooper DU, Sala O, Tiedje J, Van Veen JA (2000) Effects of global changes on above- and belowground biodiversity in terrestrial ecosystems: implications for ecosystem functioning. Bioscience 50:1089–1098

    Article  Google Scholar 

  • Zhang W, Parker KM, Luo Y, Wan S, Wallace LL, Hu S (2005) Soil microbial responses to experimental warming and clipping in a tallgrass prairie. Glob Change Biol 11:266–277

    Article  CAS  Google Scholar 

  • Zogg GP, Zak DR, Ringelberg DB, MacDonald NW, Pregitzer KS, White DC (1997) Compositional and functional shifts in microbial communities due to soil warming. Soil Sci Soc Am J 61:475–481

    Article  CAS  Google Scholar 

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Acknowledgements

We thank the Andrew W. Mellon Foundation, and the US National Science Foundation and Departments of Energy and Agriculture for support of the Ecosystem Microbiology group at UW-Madison and the Balser laboratory. Two anonymous reviewers provided excellent feedback leading to substantial improvements in the manuscript.

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Authors and Affiliations

  1. Department of Soil Science, University of Wisconsin, Madison, WI, 53706, USA

    T. C. Balser, D. Bart & M. L. Flores-Mangual

  2. Gaylord Nelson Institute for Environmental Studies, University of Wisconsin, Madison, WI, 53706, USA

    T. C. Balser & N. Craig

  3. Department of Civil and Environmental Engineering, University of Wisconsin, Madison, WI, 53706, USA

    K. D. McMahon, S. E. Jones, A. E. Kent & A. L. Shade

  4. Department of Forest Ecology and Management, University of Wisconsin, Madison, WI, 53706, USA

    D. Bronson

  5. Department of Entomology, University of Wisconsin, Madison, WI, 53706, USA

    D. R. Coyle

  6. Department of Zoology, University of Wisconsin, Madison, WI, 53706, USA

    K. Forshay

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  1. T. C. Balser
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  2. K. D. McMahon
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  3. D. Bart
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  4. D. Bronson
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  5. D. R. Coyle
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  6. N. Craig
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  7. M. L. Flores-Mangual
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  8. K. Forshay
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  9. S. E. Jones
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  10. A. E. Kent
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  11. A. L. Shade
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Correspondence to T. C. Balser.

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Balser, T.C., McMahon, K.D., Bart, D. et al. Bridging the gap between micro - and macro-scale perspectives on the role of microbial communities in global change ecology. Plant Soil 289, 59–70 (2006). https://doi.org/10.1007/s11104-006-9104-5

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