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9 - Measuring soil microbial parameters relevant for soil carbon fluxes

Published online by Cambridge University Press:  11 May 2010

By
Werner L. Kutsch ,
Joshua Schimel  and
Karolien Denef
Edited by
Werner L. Kutsch ,
Michael Bahn  and
Andreas Heinemeyer
Werner L. Kutsch
Affiliation:
Max-Planck-Institut für Biogeochemie, Jena
Michael Bahn
Affiliation:
Leopold-Franzens-Universität Innsbruck, Austria
Andreas Heinemeyer
Affiliation:
Stockholm Environmental Institute, University of York
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Summary

INTRODUCTION

The role of microbiota in soil carbon dynamics is a fitting example of the ‘borderland character’ mentioned in the introduction of this book. For years, the flux community largely followed the unspoken paradigm that ‘everything is everywhere’, which means that there is a universal potential of micro-organisms to decompose all kinds of organic matter, and that soil carbon dynamics, therefore, only depend on soil organic matter quality, soil properties and climate. A key distinction that controls whether the ‘everything is everywhere’ perspective is workable, however, is considering whether environmental conditions are in steady-state or non-steady-state conditions. Under steady-state conditions, microbial influences will be least apparent as they will have acclimatized to the existing physical, chemical or climatic constraints. Under non-steady-state conditions, however, extant microbial populations may reflect past, rather than present, conditions and their behaviour may be paramount and potentially counter-intuitive.

There is evidence that micro-organisms respond sensitively to changing environmental conditions by: (1) adjusting their intra- as well as extracellular enzymatic repertoire and, consequently, their physiological performance; (2) changes in the species composition and (3) growth or reduction of the microbial biomass.

There are several approaches to analyze the response of micro-organisms to changing environmental conditions.

  1. Microbial eco-physiology (Anderson, 1994) focuses on the microbial biomass and its performance. More recent approaches (Lynch et al., 2004; Zak et al., 2006) include community oriented approaches that allow linking metabolic pathways to species composition or, at least, functional groups.

  2. Microbial biochemistry analyses to determine the production and activity of microbial components, in particular enzymes. Since microbiota release a high portion of their enzymes, extracellular enzymes are included here (Sinsabaugh, 1994).

  3. […]

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Type
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Information
Soil Carbon Dynamics
An Integrated Methodology
 , pp. 169 - 186
Publisher: Cambridge University Press
Print publication year: 2010

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References

Alef, K. and Nannipieri, P. (1995) Methods in Applied Soil Microbiology and Biochemistry. San Diego, CA: Academic Press.Google Scholar
Allison, S. D. (2006) Soil minerals and humic acids alter enzyme stability: implications for ecosystem processes. Biogeochemistry, 81, 361–73.CrossRefGoogle Scholar
Allison, S. D. and Jastrow, J. D. (2006) Activities of extracellular enzymes in physically isolated fractions of restored grassland soils. Soil Biology and Biochemistry, 38, 3245–56.CrossRefGoogle Scholar
Anderson, T. H. (1994) Physiological analysis of microbial communities in soil: applications and limitations. In Beyond the Biomass, ed. Ritz, K., Dighton, J. and Giller, K. E.. Chichester: Wiley, pp. 67–76.Google Scholar
Anderson, T. H. (2003) Microbial eco-physiological indicators to assess soil quality. Agriculture, Ecosystems and Environment, 98, 285–93.CrossRefGoogle Scholar
Anderson, J. P. E. and Domsch, K. H. (1978) A physiological method for the quantitative measurement of microbial biomass in soils. Soil Biology and Biochemistry, 10, 215–21.CrossRefGoogle Scholar
Anderson, T. H. and Domsch, K. H. (1986) Carbon assimilation and microbial activity in soil. Zeitschrift Pflanzenernährung Bodenkunde, 149, 457–68.CrossRefGoogle Scholar
Anderson, T. H. and Domsch, K. H. (1990) Application of eco-physiological quotients (qCO2 and qD) on microbial biomasses from soils of different cropping histories. Soil Biology and Biochemistry, 22, 251–5.CrossRefGoogle Scholar
Bååth, E. and Anderson, T. H. (2003) Comparison of soil fungal/bacterial ratios in a pH gradient using physiological and PLFA-based techniques. Soil Biology and Biochemistry, 35, 955–63.CrossRefGoogle Scholar
Balota, E. L., Colozzi, A., Andrade, D. S. and Dick, R. P. (2003) Microbial biomass in soils under different tillage and crop rotation systems. Biology and Fertility of Soils, 38, 15–20.CrossRefGoogle Scholar
Balser, T. C. and Firestone, M. K. (2005) Linking microbial community composition and soil processes in a California annual grassland and mixed-conifer forest. Biogeochemistry, 73, 395–415.CrossRefGoogle Scholar
Balser, T. C., Kirchner, J. W. and Firestone, M. K. (2002) Methodological variability in microbial community level physiological profiles. Soil Science Society of America Journal, 66, 519–23.CrossRefGoogle Scholar
Bardgett, R. D. (2005) The Biology of Soil: A Community and Ecosystem Approach. Oxford: Oxford University Press.CrossRefGoogle Scholar
Bardgett, R. D. and McAlister, E. (1999) The measurement of soil fungal: bacterial biomass ratios as an indicator of ecosystem self-regulation in temperate meadow grasslands. Biology and Fertility of Soils, 29, 282–90.CrossRefGoogle Scholar
Bardgett, R. D., Hobbs, P. J. and Frostegård, A. (1996) Changes in the structure of soil microbial communities following reductions in the intensity of management of an upland grassland. Biology and Fertility of Soils, 22, 261–64.CrossRefGoogle Scholar
Beare, M. H., Neely, C. L., Coleman, D. C. and Hargrove, W. L. (1991) Characterization of a substrate-induced respiration method for measuring fungal, bacterial and total microbial biomass on plant residues. Agriculture, Ecosystems and Environment, 34, 65–73.CrossRefGoogle Scholar
Beck, T., Joergensen, R. G., Kandeler, E.et al. (1997) An inter-laboratory comparison of ten different ways of measuring soil microbial biomass C. Soil Biology and Biochemistry, 29, 1023–32.CrossRefGoogle Scholar
Berg, B. and Matzner, E. (1997) Effect of N deposition on decomposition of plant litter and soil organic matter in forest systems. Environmental Reviews, 5, 1–25.CrossRefGoogle Scholar
Berg, B. and McClaugherty, C. A. (2003) Plant Litter: Decomposition, Humus Formation, Carbon Sequestration. Berlin: Springer Verlag.CrossRefGoogle Scholar
Billings, S. A. and Ziegler, S. E. (2005) Linking microbial activity and soil organic matter transformations in forest soils under elevated CO2. Global Change Biology, 11, 203–12.CrossRefGoogle Scholar
Blagodatskaya, E. V. and Anderson, T. H. (1999) Adaptive responses of soil microbial communities under experimental acid stress in controlled laboratory studies. Applied Soil Ecology, 11, 207–16.CrossRefGoogle Scholar
Borneman, J. and Triplett, E. W. (1997) Rapid and direct method for extraction of RNA from soil. Soil Biology and Biochemistry, 29, 1621–4.CrossRefGoogle Scholar
Boschker, H. T. S., Nold, S. C., Wellsbury, P.et al. (1998) Direct linking of microbial populations to specific biogeochemical processes by 13C-labelling of biomarkers. Nature, 392, 801–5.CrossRefGoogle Scholar
Brookes, P. C., Powlson, D. S. and Jenkinson, D. S. (1982) Measurement of microbial biomass phosphorus in soil. Soil Biology and Biochemistry, 14, 319–29.CrossRefGoogle Scholar
Brookes, P. C., Landman, A., Pruden, G. and Jenkinson, D. S. (1985) Chloroform fumigation and the release of soil nitrogen: a rapid direct extraction method for measuring microbial biomass nitrogen in soil. Soil Biology and Biochemistry, 17, 837–42.CrossRefGoogle Scholar
Bull, I. D., Parekh, N. R., Hall, G. H., Ineson, P. and Evershed, R. P. (2000) Detection and classification of atmospheric methane oxidizing bacteria in soil. Nature, 405, 175–8.CrossRefGoogle ScholarPubMed
Carreiro, M. M., Sinsabaugh, R. L., Repert, D. A. and Parkhurst, D. F. (2000) Microbial enzyme shifts explain litter decay responses to simulated nitrogen deposition. Ecology, 81, 2359–65.CrossRefGoogle Scholar
Cho, J.-C. and Tiedje, J. M. (2002) Quantitative detection of microbial genes by using DNA microarray. Applied Environmental Microbiology, 68, 1425–30.CrossRefGoogle Scholar
Csonka, L. N. (1989) Physiological and genetic responses of bacteria to osmotic stress. Microbiological Reviews, 53, 121–47.Google ScholarPubMed
Davidson, E. A., Janssens, I. A. and Luo, Y. Q. (2006) On the variability of respiration in terrestrial ecosystems: moving beyond Q10. Global Change Biology, 12, 154–64.CrossRefGoogle Scholar
Vries, F. T., Hoffland, E., Eekeren, N., Brussaard, L. and Bloem, J. (2006) Fungal/bacterial ratios in grasslands with contrasting nitrogen management. Soil Biology and Biochemistry, 38, 2092–103.CrossRefGoogle Scholar
DeForest, J. L., Zak, D. R., Pregitzer, K. S. and Burton, A. J. (2004) Atmospheric nitrate deposition and the microbial degradation of cellobiose and vanillin in a northern hardwood forest. Soil Biology and Biochemistry, 36, 965–71.CrossRefGoogle Scholar
Dilly, O. (2005) Microbial energetics in soil. Microorganisms in Soils: Roles in Genesis and Functions, ed. Buscot, F. and Varma, A.. Berlin and Heidelberg: Springer-Verlag, pp. 123–38.CrossRefGoogle Scholar
Dilly, O. (2006) Ratios of microbial biomass estimates to evaluate microbial physiology in soil. Biology and Fertility of Soils, 42, 241–6.CrossRefGoogle Scholar
Dilly, O. and Munch, J. C. (1996) Microbial biomass content, basal respiration and enzyme activities during the course of decomposition of leaf litter in a Black Alder (Alnus Glutinosa (L.) Gaertn.) forest. Soil Biology and Biochemistry, 28, 1073–81.CrossRefGoogle Scholar
Dilly, O. and Munch, J. C. (1998) Ratios between estimates of microbial biomass content and microbial activity in soils. Biology and Fertility of Soils, 27, 374–9.CrossRefGoogle Scholar
Dilly, O., Blume, H. P., Sehy, U., Jimenez, M. and Munch, J. C. (2003) Variation of stabilised, microbial and biologically active carbon and nitrogen in soil under contrasting land use and agricultural management practices. Chemosphere, 52, 557–69.CrossRefGoogle ScholarPubMed
Eiland, F. (1983) A simple method for quantitative determination of ATP in soil. Soil Biology and Biochemistry, 15, 665–70.CrossRefGoogle Scholar
Evershed, R. P., Crossman, Z. M., Bull, I. D.et al. (2006) 13C-labelling of lipids to investigate microbial communities in the environment. Current Opinion in Biotechnology, 17, 72–82.CrossRefGoogle ScholarPubMed
Fang, C., Smith, P., Moncrieff, J. B. and Smith, J. U. (2005) Similar response of labile and resistant soil organic matter pools to changes in temperatured. Nature, 433, 57–9.CrossRefGoogle Scholar
Farrar, W. and Reboli, A. (1999) The genus Bacillus – medical. In The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community, ed. Dworkin, M.. New York: Springer.Google Scholar
Fierer, N. and Schimel, J. P. (2002) Effects of drying-rewetting frequency on soil carbon and nitrogen transformations. Soil Biology and Biochemistry, 34, 777–87.CrossRefGoogle Scholar
Fierer, N. and Schimel, J. P. (2003) A proposed mechanism for the pulse in carbon dioxide production commonly observed following the rapid rewetting of a dry soil. Soil Science Society of America Journal, 67, 798–805.CrossRefGoogle Scholar
Fierer, N., Schimel, J. P. and Holden, P. A. (2003) Influence of drying-rewetting frequency on soil bacterial community structure. Microbial Ecology, 45, 63–71.CrossRefGoogle ScholarPubMed
Fog, K. (1988) The effect of added nitrogen on the rate of decomposition of organic matter. Biological Reviews, 63, 433–62.CrossRefGoogle Scholar
Frey, S. D., Gupta, V., Elliott, E. T. and Paustian, K. (2001) Protozoan grazing affects estimates of carbon utilization efficiency of the soil microbial community. Soil Biology and Biochemistry, 33, 1759–68.CrossRefGoogle Scholar
Frostegård, A., Tunlid, A. and Bååth, E. (1993) Phospholipid fatty acid composition, biomass, and activity of microbial communities from 2 soil types experimentally exposed to different heavy metals. Applied and Environmental Microbiology, 59, 3605–17.Google Scholar
Gallo, M., Amonette, R., Lauber, C., Sinsabaugh, R. L. and Zak, D. R. (2004) Microbial community structure and oxidative enzyme activity in nitrogen-amended north temperate forest soils. Microbial Ecology, 48, 218–29.CrossRefGoogle ScholarPubMed
Garland, J. L. and Mills, A. L. (1991) Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization. Applied Environmental Microbiology, 57, 2351–9.Google ScholarPubMed
Gelsomino, A., Keijzer-Wolters, A. C., Cacco, G. and Elsas, J. D. (1999) Assessment of bacterial community structure in soil by polymerase chain reaction and denaturing gradient gel electrophoresis. Journal of Microbiological Methods, 38, 1–15.CrossRefGoogle ScholarPubMed
Gerson, U. and Chet, I. (1981) Are allochthonous and autochtonous soil microorganisms r- and K-selected?Revue d'Écologie et de Biologie du Sol, 18, 285–9.Google Scholar
Ginige, M. P., Hugenholtz, P., Daims, H.et al. (2004) Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community. Applied and Environmental Microbiology, 70, 588–96.CrossRefGoogle ScholarPubMed
Ginige, M. P., Keller, J. and Blackall, L. L. (2005) Investigation of an acetate-fed denitrifying microbial community by stable isotope probing, full-cycle rRNA analysis, and fluorescent in situ hybridization-microautoradiography. Applied and Environmental Microbiology, 71, 8683–91.CrossRefGoogle ScholarPubMed
Gregorich, E. G., Wen, G., Voroney, R. P. and Kachaniski, R. G. (1990) Calibration of a rapid direct chloroform extraction method for measuring soil microbial biomass C. Soil Biology and Biochemistry, 22, 1009–11.CrossRefGoogle Scholar
Hammel, K. E. (1997) Fungal degradation of lignin. In Driven by Nature: Plant Litter Quality and Decomposition, ed. Cadisch, G. and Giller, K. E.. Wallingford: CAB International, pp. 33–46.Google Scholar
Harris, R. F. (1981) Effect of water potential on microbial growth and activity. In Water Potential Relations in Soil Microbiology, ed. Parr, F., Gardner, W. R. and Elliott, L. F.. Madison, WI: American Society of Agronomy, pp. 23–95.Google Scholar
Hawkes, C. V., Wren, I. F., Herman, D. J. and Firestone, M. K. (2005) Plant invasion alters nitrogen cycling by modifying the soil nitrifying community. Ecology Letters, 8, 976–85.CrossRefGoogle Scholar
Herrmann, A. and Witter, E. (2002) Sources of C and N contributing to the flush in mineralization upon freeze–thaw cycles in soils. Soil Biology and Biochemistry, 34, 1495–505.CrossRefGoogle Scholar
Insam, H. and Domsch, K. H. (1988) Relationship between soil organic carbon and microbial biomass on chronosequences of reclamation sites. Microbial Ecology, 15, 177–88.CrossRefGoogle ScholarPubMed
Insam, H. and Haselwandter, K. (1989) Metabolic quotient of the soil microflora in relation to plant succession. Oecologia, 79, 174–8.CrossRefGoogle ScholarPubMed
Jenkinson, D. S. (1976) The effects of biocidal treatments on metabolism in soil. IV. The decomposition of fumigated organisms in soil. Soil Biology and Biochemistry, 8, 203–8.CrossRefGoogle Scholar
Jenkinson, D. S. and Powlson, D. S. (1976) The effects of biocidal treatments on metabolism in soil. V. A method for measuring soil biomass. Soil Biology and Biochemistry, 8, 209–13.CrossRefGoogle Scholar
Jenkinson, D. S., Brookes, P. C. and Powlson, D. S. (2004) Measuring soil microbial biomass. Soil Biology and Biochemistry, 36, 5–7.CrossRefGoogle Scholar
Joergensen, R. G. and Emmerling, C. (2006) Methods for evaluating human impact on soil microorganisms based on their activity, biomass, and diversity in agricultural soils. Journal of Plant Nutrition and Soil Science, 169, 295–309.CrossRefGoogle Scholar
Jones, D. L. and Kielland, K. (2002) Soil amino acid turnover dominates the nitrogen flux in permafrost-dominated taiga forest soils. Soil Biology and Biochemistry, 34, 209–19.CrossRefGoogle Scholar
Knorr, W., Prentice, I. C., House, J. I. and Holland, E. A. (2005) Long-term sensitivity of soil carbon turnover to warming. Nature, 433, 298–433.CrossRefGoogle ScholarPubMed
Kutsch, W. L. and Dilly, O. (1999) Ecophysiology of plant and microbial interactions in terrestrial ecosystems. In Ökophysiologie pflanzlicher Interaktionen, ed. Beyschlag, W. and Steinlein, T.. Vol. 14. Bielefelder Ökologischer Beiträge, pp. 74–84.Google Scholar
Kutsch, W. L., Eschenbach, C., Dilly, O.et al. (2001) The carbon cycle of contrasting landscape elements of the Bornhöved Lake district. In Ecosystem Properties and Landscape Function in Central Europe, ed. Lenz, R., Hantschel, R. and Tenhunen, J. D.. Vol. 147. Ecological Studies. Berlin: Springer, pp. 75–95.Google Scholar
Lennartsson, M. and Ogren, E. (2002) Causes of variation in cold hardiness among fast-growing willows (Salix spp.) with particular reference to their inherent rates of cold hardening. Plant Cell and Environment, 25, 1279–88.CrossRefGoogle Scholar
Lindstrom, J. E., Barry, R. P. and Braddock, J. F. (1999) Long-term effects on microbial communities after a subarctic oil spill. Soil Biology and Biochemistry, 31, 1677.CrossRefGoogle Scholar
Lueders, T., Wagner, B., Claus, P. and Friedrich, M. W. (2004a) Stable isotope probing of rRNA and DNA reveals a dynamic methylotroph community and trophic interactions with fungi and protozoa in oxic rice field soil. Environmental Microbiology, 6, 60–72.CrossRefGoogle ScholarPubMed
Lueders, T., Manefield, M. and Friedrich, M. W. (2004b) Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients. Environmental Microbiology, 6, 73–8.CrossRefGoogle ScholarPubMed
Lynch, J. M., Benedetti, A., Insam, H. (2004) Microbial diversity in soil: ecological theories, the contribution of molecular techniques and the impact of transgenic plants and transgenic microorganisms. Biology and Fertility of Soils, 40, 363–85.CrossRefGoogle Scholar
MacGregor, B. J., Bruchert, V., Fleischer, S. and Amann, R. (2002) Isolation of small-subunit rRNA for stable isotopic characterization. Environmental Microbiology, 4, 451–64.CrossRefGoogle ScholarPubMed
Manefield, M., Whiteley, A. S., Griffiths, R. I. and Bailey, M. J. (2002a) RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Applied Environmental Microbiology, 68, 5367–73.CrossRefGoogle Scholar
Manefield, M., Whiteley, A. S., Ostle, N., Ineson, P. and Bailey, M. J. (2002b) Technical considerations for RNA-based stable isotope probing: an approach to associating microbial diversity with microbial community function. Rapid Communications in Mass Spectrometry, 16, 2179–83.CrossRefGoogle ScholarPubMed
Martens, R. (1995) Current methods for measuring microbial biomass C in soil: potentials and limitations. Biology and Fertility of Soils, 19, 87–99.CrossRefGoogle Scholar
Marx, M. C., Kandeler, E., Wood, M., Wermbter, N. and Jarvis, S. C. (2005) Exploring the enzymatic landscape: distribution and kinetics of hydrolytic enzymes in soil particle-size fractions. Soil Biology and Biochemistry, 37, 35–48.CrossRefGoogle Scholar
McDonald, I. R., Radajewski, S. and Murrell, J. C. (2005) Stable isotope probing of nucleic acids in methanotrophs and methylotrophs: a review. Organic Geochemistry, 36, 779–87.CrossRefGoogle Scholar
Methe, B. A., Nelson, K. E., Deming, J. W.et al. (2005) The psychrophilic lifestyle as revealed by the genome sequence of Colwellia psychrerythraea34H through genomic and proteomic analyses. Proceedings of the National Academy of Sciences of the United States of America, 102, 10913–18.CrossRefGoogle ScholarPubMed
Michel, K. and Matzner, E. (2003) Response of enzyme activities to nitrogen addition in forest floors of different C-to-N ratios. Biology and Fertility of Soils, 38, 102–9.CrossRefGoogle Scholar
Mikan, C. J., Schimel, J. P. and Doyle, A. P. (2002) Temperature controls of microbial respiration in arctic tundra soils above and below freezing. Soil Biology and Biochemistry, 34, 1785–95.CrossRefGoogle Scholar
Mills, D. K., Entry, J. A., Gillevet, P. M. and Mathee, K. (2007) Assessing microbial community diversity using amplicon length heterogeneity polymerase chain reaction. Soil Science Society of America Journal, 71, 572–8.CrossRefGoogle Scholar
Moorhead, D. L. and Sinsabaugh, R. L. (2006) A theoretical model of litter decay and microbial interaction. Ecological Monographs, 76, 151–74.CrossRefGoogle Scholar
Morris, S. A., Radajewski, S., Willison, T. W. and Murrell, J. C. (2002) Identification of the functionally active methanotroph population in a peat soil microcosm by stable-isotope probing. Applied and Environmental Microbiology, 68, 1446–53.CrossRefGoogle Scholar
Murase, J., Matsui, Y., Katoh, M., Sugimoto, A. and Kimura, M. (2006) Incorporation of 13C-labeled rice-straw-derived carbon into microbial communities in submerged rice field soil and percolating water. Soil Biology and Biochemistry, 38, 3483–91.CrossRefGoogle Scholar
Nannipieri, P., Greco, S. and Ceccanti, B. (1990) Ecological significance of the biological activity in soil. In Soil Biochemistry, ed. Bollag, J. M. and Stotzky, G.. Vol. 6. New York: Marcel Dekker, pp. 293–355.Google Scholar
Neufeld, J. D., Wagner, M. and Murrell, J. C. (2007a) Who eats what, where and when? Isotope-labelling experiments are coming of age. The Isme Journal, 1, 103–10.CrossRefGoogle ScholarPubMed
Neufeld, J. D., Dumont, M. G., Vohra, J. and Murrell, J. C. (2007b) Methodological considerations for the use of stable isotope probing in microbial ecology. Microbial Ecology, 53, 435–42.CrossRefGoogle ScholarPubMed
Odum, E. P. (1969) The strategy of ecosystem development. Science, 164, 262–70.CrossRefGoogle ScholarPubMed
Parton, W. J., Schimel, D. S., Cole, C. V. and Ojima, D. S. (1987) Analysis of factors controlling soil organic matter levels in Great Plains grasslands. Soil Science Society of America Journal, 51, 1173–9.CrossRefGoogle Scholar
Paul, E. A. (2007) Soil Microbiology, Ecology and Biochemistry, 3rd edn. San Diego, CA: Academic Press.Google Scholar
Pirt, S. J. (1975) The Principles of Microbe and Cell Cultivation. Oxford: Blackwell Scientific Publications.Google Scholar
Porazinska, D. L., Bardgett, R. D., Blaauw, M. B.et al. (2003) Relationships at the aboveground–belowground interface: plants, soil biota, and soil processes. Ecological Monographs, 73, 377–95.CrossRefGoogle Scholar
Powlson, D. S. (1994) The soil microbial biomass: before, beyond, back. In Beyond the Biomass, ed. Ritz, K., Dighton, J. and Giller, K.. Chichester: Wiley.Google Scholar
Radajewski, S. and Murrell, J. C. (2001) Stable isotope probing for detection of methanotrophs after enrichment with 13CH4. Methods in Molecular Biology, 179, 149–57.Google Scholar
Radajewski, S., Ineson, P., Parekh, N. R. and Murrell, J. C. (2000) Stable-isotope probing as a tool in microbial ecology. Nature, 403, 646–9.CrossRefGoogle ScholarPubMed
Rangel-Castro, J. I., Killham, K., Ostle, N.et al. (2005) Stable isotope probing analysis of the influence of liming on root exudate utilization by soil microorganisms. Environmental Microbiology, 7, 828–38.CrossRefGoogle Scholar
Ritchie, N. J., Schutter, M. E., Dick, R. P. and Myrold, D. D. (2000) Use of length heterogeneity PCR and fatty acid methyl ester profiles to characterize microbial communities in soil. Applied and Environmental Microbiology, 66, 1668–75.CrossRefGoogle ScholarPubMed
Ritz, K., Dighton, J. and Giller, K. (1994) Beyond the Biomass. Chichester: Wiley.Google Scholar
Saiya-Cork, K. R., Sinsabaugh, R. L. and Zak, D. R. (2002) The effects of long term nitrogen deposition on extracellular enzyme activity in an Acer saccharum forest soil. Soil Biology and Biochemistry, 34, 1309–15.CrossRefGoogle Scholar
Schimel, J. P. and Weintraub, M. N. (2003) The implications of exoenzyme activity on microbial carbon and nitrogen limitation in soil: a theoretical model. Soil Biology and Biochemistry, 35, 549–63.CrossRefGoogle Scholar
Schimel, J., Balser, T. C. and Wallenstein, M. D. (2007) Microbial stress-response physiology and its implications for ecosystem function. Ecology, 88, 1386–94.CrossRefGoogle ScholarPubMed
Sinsabaugh, R. L. (1994) Enzymic analysis of microbial pattern and process. Biology and Fertility of Soils, 17, 69–74.CrossRefGoogle Scholar
Sinsabaugh, R. L. and Liptak, M. (1997) Enzymatic conversion of plant biomass. In The Mycota: Environmental and Microbial Relationships, ed. Soderstrom, B. and Wicklow, D. T.. Berlin: Springer-Verlag, pp. 347–57.Google Scholar
Sinsabaugh, R. L., Carreiro, M. M. and Repert, D. A. (2002) Allocation of extracellular enzymatic activity in relation to litter composition, N deposition, and mass loss. Biogeochemistry, 60, 1–24.CrossRefGoogle Scholar
Skogland, T., Lomeland, S. and Goksoyr, J. (1988) Respiratory burst after freezing and thawing of soil: experiments with soil bacteria. Soil Biology and Biochemistry, 20, 851–66.CrossRefGoogle Scholar
Slater, J. H. (1979) Microbial population and community dynamics. In Microbial Ecology. A Conceptual Approach, ed. Lynch, J. M. and Poole, N. J.. Oxford: Blackwell Scientific Publications, pp. 45–63.Google Scholar
Sparling, G. P. and West, A. W. (1988) A direct extraction method to estimate soil microbial C: calibration in situ using micribial respiration and 14C labelled cells. Soil Biology and Biochemistry, 20, 337–43.CrossRefGoogle Scholar
Stark, J. and Firestone, M. K. (1995) Mechanisms for soil moisture effects on activity of nitrifying bacteria. Applied and Environmental Microbiology, 61, 218–21.Google ScholarPubMed
Suzina, N. E., Mulyukin, , A. L., Kozlova, A. N.et al. (2004) Ultrastructure of resting cells of some non-spore-forming bacteria. Microbiology, 73, 435–47.CrossRefGoogle ScholarPubMed
Suzuki, M., Rappe, M. S. and Giovannoni, S. J. (1998) Kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity. Applied and Environmental Microbiology, 64, 4522–9.Google ScholarPubMed
Swift, M. J., Heal, O. W. and Anderson, J. M. (1979) Decomposition in Terrestrial Ecosystems. Studies in Ecology, Vol. 5. Los Angeles, CA: University of California Press.Google Scholar
Tate, K. R. and Jenkinson, D. S. (1982) Adenosine triphosphate measurement in soil: an improved method. Soil Biology and Biochemistry, 14, 331–5.CrossRefGoogle Scholar
Tate, R. L. I. (2000) Soil Microbiology. Chichester: Wiley & Sons.Google Scholar
Thiet, R. K., Frey, S. D. and Six, J. (2006) Do growth yield efficiencies differ between soil microbial communities differing in fungal: bacterial ratios? Reality check and methodological issues. Soil Biology and Biochemistry, 38, 837–44.CrossRefGoogle Scholar
Tiedje, J. M., Asuming-Brempong, S., Nusslein, K., Marsh, T. L. and Flynn, S. J. (1999) Opening the black box of soil microbial diversity. Applied Soil Ecology, 13, 109–22.CrossRefGoogle Scholar
Torsvik, V., Daae, F. L., Sandaa, R. A. and Ovreas, L. (1998) Novel techniques for analysing microbial diversity in natural and perturbed environments. Journal of Biotechnology, 64, 53–62.CrossRefGoogle ScholarPubMed
Treonis, A. M., Ostle, N. J., Stott, A. W.et al. (2004) Identification of groups of metabolically-active rhizosphere microorganisms by stable isotope probing of PLFAs. Soil Biology and Biochemistry, 36, 533–7.CrossRefGoogle Scholar
Vance, E. D., Brookes, P. C. and Jenkinson, D. S. (1987) An extraction method for measuring soil microbial biomass C. Soil Biology and Biochemistry, 19, 703–7.CrossRefGoogle Scholar
Vedder, B., Kampichler, C., Bachmann, G., Bruckner, A. and Kandeler, E. (1996) Impact of faunal complexity on microbial biomass and N turnover in field mesocosms from a spruce forest soil. Biology and Fertility of Soils, 22, 22–30.CrossRefGoogle Scholar
Vestal, J. R. and White, D. C. (1989) Lipid analysis in microbial ecology: quantitative approaches to the study of microbial communities. BioScience, 29, 535–41.CrossRefGoogle Scholar
Waksman, S. A. (1932) Principles of Soil Microbiology. Baltimore, MD: Williams and Wilkins.Google Scholar
Waldrop, M. P., Zak, D. R., Sinsabaugh, R. L., Gallo, M. and Lauber, C. (2004) Nitrogen deposition modifies soil carbon storage through changes in microbial enzymatic activity. Ecological Applications, 14, 1172–7.CrossRefGoogle Scholar
Wardle, D. A. (2002) Communities and Ecosystems: Linking the Aboveground and Belowground Components. Monographs in population biology, Vol. 34. Princeton, NJ: Princeton University Press.Google Scholar
Whitby, C. B., Hall, G., Pickup, R.et al. (2001) 13C incorporation into DNA as a means of identifying the active components of ammonia-oxidizer populations. Letters in Applied Microbiology, 32, 398–401.CrossRefGoogle ScholarPubMed
Williams, M. A., Myrold, D. D. and Bottomley, P. J. (2006) Carbon flow from 13C-labeled straw and root residues into the phospholipid fatty acids of a soil microbial community under field conditions. Soil Biology and Biochemistry, 38, 759–68.CrossRefGoogle Scholar
Winogradsky, S. (1924) Sur la microflora autochtone da la terre arable. Comtes rendus ebdomadaire des séances de Academie des Sciences (Paris) D, 178, 1236–9.Google Scholar
Witteveen, C. F. B. and Visser, J. (1995) Polyol pools in Aspergillus niger. FEMS Microbiology Ecology, 134, 57–62.CrossRefGoogle ScholarPubMed
Zak, D. R., Blackwood, C. B. and Waldrop, M. P. (2006) A molecular dawn for biogeochemistry. Trends in Ecology and Evolution, 21, 288–95.CrossRefGoogle ScholarPubMed

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