Skip to main content
SpringerLink
Log in

Bacterial Interactions At The Microscale – Linking Habitat To Function In Soil

  • Chapter
The Spatial Distribution of Microbes in the Environment

There is a growing body of evidence that the spatial distribution of bacteria and their relationships with other soil features play a significant role in the macroscopic function of soil. In the past this has not been widely appreciated, possibly due to the difficulty of studying soils at scales that are relevant to bacterial communities. This paper reviews the evidence for the influence of microscale interactions on function at larger scales and describes recent methodological advances that allow the microscale spatial distribution of bacterial cells and bacterial activities to be quantified. Approaches for integrating the microscale into models of soil function are briefly discussed as are new techniques that have the potential to improve our understanding of microbial – habitat interactions and of how these are linked to soil function. Keywords: bacterial spatial distribution, microscale, microhabitat, scale, biological thin sections, microsampling

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Alexander, F. E. S., and R. M. Jackson, 1955, Preparation of sections for study of soil micro-organisms, in: Soil Zoology, D. K. M. Kevan, ed., Butterworth. London, pp. 433-440.

    Google Scholar 

  • Allison, S. D., 2005, Cheaters, diffusion and nutrients constrain decomposition by microbial enzymes in spatially structured environments, Ecol. Lett. 8:626-635.

    Google Scholar 

  • Almås, A. R., J. Mulder, and L. R. Bakken, 2005, Trace metal exposure of soil bacteria depends on their position in the soil matrix, Environ. Sci. Technol. 39:5927-5932.

    PubMed  Google Scholar 

  • Altemüller, H., and B. Vliet-Lanoe, 1988, Soil thin section fluorescence microscopy, Devel. Soil Sci. 19:565-579.

    Google Scholar 

  • Beijerink, M. W., 1913, De infusies en de ontdekking der backteriën. Jaarboek van de Koninklijke Akademie v. Wetenschappen, Müller, Berlin.

    Google Scholar 

  • Bergstrom, D. W., C. M. Monreal, J. A. Millette, and D. J. King, 1998, Spatial dependence of soil enzyme activities along a slope, Soil Sci. Soc. Am. J. 62:1302-1308.

    CAS  Google Scholar 

  • Bertrand, I., N. Grignon, P. Hinsinger, G. Souche, and B. Jaillard, 2001, The use of secondary ion mass spectrometry coupled with image analysis to identify and locate chemical elements in soil minerals: the example of phosphorus, Scanning 23:279-291.

    CAS  Google Scholar 

  • Bird, N. R. A., E. Perrier, and M. Rieu, 2000, The water retention function for a model of soil structure with pore and solid fractal distributions, Eur. J. Soil Sci. 51:55-63.

    Google Scholar 

  • Bloem, J., M. Veninga, and J. Shepherd, 1995, Fully-automatic determination of soil bacterium numbers, cell volumes, and frequencies of dividing cells by confocal laser-scanning microscopy and image-analysis, Appl. Environ. Microbiol. 61:926-936.

    PubMed  CAS  Google Scholar 

  • Bramley, R. G. V., and R. E. White, 1991a, An analysis of variability in the activity of nitrifiers in a soil under pasture. 1. Spatially dependent variability and optimum sampling strategy, Aust. J. Soil Res. 29:95-108.

    CAS  Google Scholar 

  • Bramley, R. G. V., and R. E. White, 1991b, An analysis of variability in the activity of nitrifiers in a soil under pasture. 2. Some problems in the geostatistical analysis of biological soil pro-perties, Aust. J. Soil Res. 29:109-122.

    Google Scholar 

  • Bruckner, A., E. Kandeler, and C. Kampichler, 1999, Plot-scale spatial patterns of soil water content, pH, substrate-induced respiration and N mineralization in a temperate coniferous forest, Geoderma 93:207-223.

    CAS  Google Scholar 

  • Bruneau, P. M. C., D. A. Davidson, I. C. Grieve, I. M. Young, and N. Nunan, 2005, The effects of soil horizons and faunal excrement on bacterial distribution in an upland grass-land soil, FEMS Microbiol. Ecol. 52:139-144.

    PubMed  CAS  Google Scholar 

  • Burmølle, M., L. H. Hansen, G. Oregaard, and S. J. Sørensen, 2003, Presence of N-acyl homoserine lactones in soil detected by a whole-cell biosensor and flow cytometry, Microb. Ecol. 45:226-236.

    PubMed  Google Scholar 

  • Callow, J. A., M. P. Osborne, M. E. Callow, F. Baker, and A. M. Donald, 2003, Use of environ-mental scanning electron microscopy to image the spore adhesive of the marine alga Enteromorpha in its natural hydrated state, Coll. Surf. B. 27:315-321.

    CAS  Google Scholar 

  • Chenu, C., J. Hassink, and J. Bloem, 2001, Short-term changes in the spatial distribution of microorganisms in soil aggregates as affected by glucose addition, Biol. Fertil. Soils 34:349-356.

    CAS  Google Scholar 

  • Chernin, L. S., M. K. Winson, J. M. Thompson, S. Haran, B. W. Bycroft, I. Chet, P. Williams, and G. S. A. B. Stewart, 1998, Chitinolytic activity in Chromobacterium violaceum: substrate analysis and regulation by quorum sensing, J. Bacteriol. 180:4435-4441.

    PubMed  CAS  Google Scholar 

  • Cliff, J. B., D. J. Gaspar, P. J. Bottomley, and D. D. Myrold, 2002, Exploration of inorganic C and N assimilation by soil microbes with time-of-flight secondary ion mass spectro-metry, Appl. Environ. Microbiol. 68:4067-4073.

    PubMed  CAS  Google Scholar 

  • Crawford, J. W., J. A. Harris, K. Ritz, and I. M. Young, 2005, Towards an evolutionary ecology of life in soil, Trends Ecol. Evol. 20:81-87.

    PubMed  Google Scholar 

  • Crecchio, C., P. Ruggiero, M. Curci, C. Colombo, G. Palumbo, and G. Stotzky, 2005, Binding of DNA from Bacillus subtilis on montmorillonite-humic acids-aluminum or iron hydroxylpolymers: Effects on transformation and protection against Dnase, Soil Sci. Soc. Am. J. 69:834-841.

    CAS  Google Scholar 

  • Darrah, P. R., R. E. White, and P. H. Nye, 1987, A theoretical consideration of the impli-cations of cell clustering for the prediction of nitrification in soil, Plant Soil. 99:387-400.

    CAS  Google Scholar 

  • Dechesne, A., C. Pallud, D. Debouzie, J. P. Flandrois, T. M. Vogel, J. P. Gaudet, and G. L. Grundmann, 2003, A novel method for characterizing the microscale 3D spatial distribution of bacteria in soil, Soil Biol. Biochem. 35:1537-1546.

    CAS  Google Scholar 

  • Dejonghe, W., J. Goris, S. El Fantroussi, M. Hofte, P. De Vos, W. Verstraete, and E. M. Top, 2000, Effect of dissemination of 2,4-dichlorophen-oxyacetic acid (2,4-D) degradation plasmids on 2,4-D degradation and on bacterial community structure in two different soil horizons, Appl. Environ. Microbiol. 66:3297-3304.

    PubMed  CAS  Google Scholar 

  • Dröge, M., A. Puhler, and W. Selbitschka, 1999, Horizontal gene transfer among bacteria in terrestrial and aquatic habitats as assessed by microcosm and field studies, Biol. Fertil. Soils 29:221-245.

    Google Scholar 

  • Durrett, R., and S. Levin, 1997, Allelopathy in spatially distributed populations, J. Theoret. Biol. 185:165-171.

    Google Scholar 

  • Ettema, C. H., and D. A. Wardle, 2002, Spatial soil ecology, Trends Ecol. Evol. 17:177-183.

    Google Scholar 

  • Feeney, D. S., J. C. Crawford, T. J. Daniell, P. D. Hallett, N. Nunan, K. Ritz, M. Rivers, and I. M. Young, 2006, 3D micro-organisation of the soil-root-microbe system. Microb. Ecol. 52:151-158.

    PubMed  Google Scholar 

  • Fierer, N., J. P. Schimel, and P. A. Holden, 2003, Variations in microbial community com-position through two soil depth profiles, Soil Biol. Biochem. 35:167-176.

    CAS  Google Scholar 

  • Fisk, A. C., S. L. Murphy, and R. L. Tate, 1999, Microscopic observations of bacterial sorption in soil cores, Biol. Fertil. Soils 28:111-116.

    Google Scholar 

  • Foster, R., and J. Martin, 1981, In situ analysis of soil components of biological origin, Soil Biochem. 5:75-111.

    CAS  Google Scholar 

  • Foster, R., and A. Rovira, 1973, The rhizosphere of wheat roots studied by electron micro-scopy of ultra-thin sections. “Modern methods in the study of microbial ecology”, Bull. Ecol. Res. Comm. Sweden. 17:93-95.

    Google Scholar 

  • Foster, R., A. Rovira, and T. Cock, 1983, Ultrastructure of the Root-Soil Interface. American Phytopathological Society, St. Paul, Minnesota.

    Google Scholar 

  • Franklin, R. B., and A. L. Mills, 2003, Multi-scale variation in spatial heterogeneity for microbial community structure in an eastern Virginia agricultural field, FEMS Microbiol. Ecol. 44:335-346.

    PubMed  CAS  Google Scholar 

  • Franklin, R. B., J. L. Garland, C. H. Bolster, and A. L. Mills, 2001, Impact of dilution on microbial community structure and functional potential: comparison of numerical simula-tions and batch culture experiments, Appl. Environ. Microbiol. 67:702-712.

    PubMed  CAS  Google Scholar 

  • Fromm, H., K. Winter, J. Filser, R. Hantschel, and F. Beese, 1993, The influence of soil type and cultivation system on the spatial distributions of the soil fauna and microorganisms and their interactions, Geoderma 60:109-118.

    Google Scholar 

  • Ginovart, M., D. Lopez, and A. Gras, 2005, Individual-based modelling of microbial activity to study mineralization of C and N and nitrification process in soil, Nonlinear Anal. Real World Appl. 6:773-795.

    CAS  Google Scholar 

  • Gojon, A., N. Grignon, P. Tillard, P. Massiot, F. Lefebvre, M. Thellier, and C. Ripoll, 1996, Imaging and microanalysis of N-14 and N-15 by SIMS microscopy in yeast and plant samples, Cell. Mol. Biol. 42:351-360.

    PubMed  CAS  Google Scholar 

  • Gonzalez, O. J., and D. R. Zak, 1994, A geostatistical analysis of soil properties in a secondary tropical dry forest, St-Lucia, West-Indies, Plant Soil 163:45-54.

    Google Scholar 

  • Goovaerts, P., and C. N. Chiang, 1993, Temporal persistence of spatial patterns for mineralizable nitrogen and selected soil properties, Soil Sci. Soc. Am. J. 57:372-381.

    Article  CAS  Google Scholar 

  • Grundmann, G. L., and F. Gourbiere, 1999, A micro-sampling approach to improve the inventory of bacterial diversity in soil, Appl. Soil Ecol. 13:123-126.

    Google Scholar 

  • Grundmann, G. L., and P. Normand, 2000, Microscale diversity of the genus Nitrobacter in soil on the basis of analysis of genes encoding rRNA, Appl. Environ. Microbiol. 66:4543-4546.

    PubMed  CAS  Google Scholar 

  • Grundmann, G. L., A. Dechesne, F. Bartoli, J. P. Flandrois, J. L. Chasse, and R. Kizungu, 2001, Spatial modeling of nitrifier microhabitats in soil, Soil Sci. Soc. Am. J. 65:1709-1716.

    Article  CAS  Google Scholar 

  • Harris, P. J., 1994, Consequences of the spatial distribution of microbial communities in soil, in: Beyond the Biomass, K. Ritz, J. Dighton, and K. E. Giller, eds., British Society of Soil Science, Wiles-Sayce, London, pp. 239-246.

    Google Scholar 

  • Holden, P. A., M. G. LaMontagne, A. K. Bruce, W. G. Miller, and S. E. Lindow, 2002, Assess-ing the role of Pseudomonas aeruginosa surface-active gene expression in hexadecane biodegradation in sand, Appl. Environ. Microbiol. 68:2509-2518.

    PubMed  CAS  Google Scholar 

  • Jackson, R. B., and M. M. Caldwell, 1993, The scale of nutrient heterogeneity around individual plants and its quantification with geostatistics, Ecology 74:612-614.

    Google Scholar 

  • Johnson, A., I. M. Roy, G. P. Matthews, and D. Patel, 2003, An improved simulation of void structure, water retention and hydraulic conductivity in soil with the Pore-Cor three-dimensional network, Eur. J. Soil Sci. 54:477-489.

    Google Scholar 

  • Jones, D., and Griffiths, E., 1964, The use of thin sections for the study of soil micro-organisms, Plant Soil 20:232-240.

    Google Scholar 

  • Kampichler, C., and M. Hauser, 1993, Roughness of soil pore surface and its effect on available habitat space of microarthropods, Geoderma 56:223-232.

    Google Scholar 

  • Kerr, B., M. A. Riley, M. W. Feldman, and B. J. M. Bohannan, 2002, Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors, Nature 418:171-174.

    PubMed  CAS  Google Scholar 

  • Klironomos, J. N., M. C. Rillig, and M. F. Allen, 1999, Designing below-ground field experi-ments with the help of semi-variance and power analyses, Appl. Soil Ecol. 12:227-238.

    Google Scholar 

  • Knorr, W., I. C. Prentice, J. I. House, and E. A. Holland, 2005, Long-term sensitivity of soil carbon turnover to warming, Nature 433:298-301.

    PubMed  CAS  Google Scholar 

  • Lazof, D., R. W. Linton, R. J. Volk, and T. W. Rufty, 1992, The application of SIMS to nutrient tracer studies in plant physiology, Biol. Cell. 74:127-134.

    CAS  Google Scholar 

  • Levin, S. A., 1992, The problem of pattern and scale in ecology, Ecology 73:1943-1967.

    Google Scholar 

  • Levin, S. A., 1998, Ecosystems and the biosphere as complex adaptive systems, Ecosystems 1:431-436.

    Google Scholar 

  • Long, T., and D. Or, 2005, Aquatic habitats and diffusion constraints affecting microbial coexistence in unsaturated porous media, Water Resour. Res. 41:W08408.

    Google Scholar 

  • Macnaughton, S. J., T. Booth, T. M. Embley, and A. G. O’Donnell, 1996, Physical stabiliza-tion and confocal microscopy of bacteria on roots using 16S rRNA targeted, fluorescent-labeled oligonucleotide probes, J. Microbiol. Methods 26:279-285.

    CAS  Google Scholar 

  • Madden, L. V., and G. Hughes, 1999, An effective sample size for predicting plant disease incidence in a spatial hierarchy, Phytopathology 89:770-781.

    PubMed  CAS  Google Scholar 

  • Marx, M. C., E. Kandeler, M. Wood, N. Wermbter, and S. C. Jarvis, 2005, Exploring the enzymatic landscape: distribution and kinetics of hydrolytic enzymes in soil particle-size fractions, Soil Biol. Biochem. 37:35-48.

    CAS  Google Scholar 

  • Mummey, D. L., and P. D. Stahl, 2004, Analysis of soil whole- and inner-microaggregate bacterial communities, Microb. Ecol. 48:41-50.

    PubMed  CAS  Google Scholar 

  • Nunan, N., K. Ritz, D. Crabb, K. Harris, K. J. Wu, J. W. Crawford, and I. M. Young, 2001, Quantification of the in situ distribution of soil bacteria by large-scale imaging of thin sections of undisturbed soil, FEMS Microbiol. Ecol. 37:67-77.

    CAS  Google Scholar 

  • Nunan, N., K. Wu, I. M. Young, J. W. Crawford, and K. Ritz, 2002, In situ spatial patterns of soil bacterial populations, mapped at multiple scales, in an arable soil, Microb. Ecol. 44:296-305.

    PubMed  CAS  Google Scholar 

  • Nunan, N., K. J. Wu, I. M. Young, J. W. Crawford, and K. Ritz, 2003, Spatial distribution of bacterial communities and their relationships with the micro-architecture of soil, FEMS Microbiol. Ecol. 44:203-215.

    PubMed  CAS  Google Scholar 

  • Nunan, N., K. Ritz, M. Rivers, D. S. Feeney, and I. M. Young, 2006, Investigating microbial micro-habitat structure using x-ray computed tomography, Geoderma 133:398-407.

    Google Scholar 

  • Okabe, H., and M. J. Blunt, 2004, Prediction of permeability for porous media reconstructed using multiple-point statistics, Phys. Rev. E 70:066135.

    Google Scholar 

  • Pallud, C., A. Dechesne, J. P. Gaudet, D. Debouzie, and G. L. Grundmann, 2004, Modification of spatial distribution of 2,4-dichloro-phenoxyacetic acid degrader microhabitats during growth in soil columns, Appl. Environ. Microbiol. 70:2709-2716.

    PubMed  CAS  Google Scholar 

  • Parkin, T. B., 1993, Spatial variability of microbial processes in soil - a review, J. Environ. Qual. 22:409-417.

    Article  Google Scholar 

  • Parkin, T. B., and D. R. Shelton, 1992, Spatial and temporal variability of carbofuran degradation in soil, J. Environ. Qual. 21:672-678.

    Article  CAS  Google Scholar 

  • Peat, D. M. W., G. P. Matthews, P. J. Worsfold, and S. C. Jarvis, 2000, Simulation of water retention and hydraulic conductivity in soil using a three-dimensional network, Eur. J. Soil Sci. 51:65-79.

    Google Scholar 

  • Pierson, E. A., D. W. Wood, J. A. Cannon, F. M. Blachere, and L. S. Pierson, 1998, Inter-population signaling via N-acyl-homoserine lactones among bacteria in the wheat rhizo-sphere, Mol. Plant Microbe Interact. 11:1078-1084.

    CAS  Google Scholar 

  • Postma, J., and H. J. Altemüller, 1990, Bacteria in thin soil sections stained with the fluorescent brightener Calcofluor White M2R, Soil Biol. Biochem. 22:89-96.

    CAS  Google Scholar 

  • Protz, R., S. J. Sweeney, and C. A. Fox, 1992, An application of spectral image-analysis to soil micromorphology. 1. Methods of analysis, Geoderma 53:275-287.

    Google Scholar 

  • Ranjard, L., S. Nazaret, F. Gourbiere, J. Thioulouse, P. Linet, and A. Richaume, 2000a, A soil microscale study to reveal the heterogeneity of Hg(II) impact on indigenous bacteria by quantification of adapted phenotypes and analysis of community DNA fingerprints, FEMS Microbiol. Ecol. 31:107-115.

    CAS  Google Scholar 

  • Ranjard, L., F. Poly, J. Combrisson, A. Richaume, F. Gourbiere, J. Thioulouse, and S. Nazaret, 2000b, Heterogeneous cell density and genetic structure of bacterial pools associated with various soil microenvironments as determined by enumeration and DNA fingerprinting approach (RISA), Microb. Ecol. 39:263-272.

    CAS  Google Scholar 

  • Rappoldt, C., and J. W. Crawford, 1999, The distribution of anoxic volume in a fractal model of soil, Geoderma 88:329-347.

    Google Scholar 

  • Ritz, K., W. McNicol, N. Nunan, S. Grayston, P. Millard, D. Atkinson, A. Gollotte, D. Habeshaw, B. Boag, C. D. Clegg, B. S. Griffiths, R. E. Wheatley, L. A. Glover, A. E. McCaig, and J. I. Prosser, 2004, Spatial structure in soil chemical and microbiological properties in an upland grassland, FEMS Microbiol. Ecol. 49:191-205.

    PubMed  CAS  Google Scholar 

  • Robertson, G. P., and K. L. Gross, 1994, Assessing the heterogeneity of belowground resources: quantifying pattern and scale, in: Exploitation of Environmental Heterogeneity by Plants: Ecophysiological Processes Above- and Belowground, M. M. Caldwell, and R. W. Pearcy (eds.), Academic Press, New York, pp. 237-253.

    Google Scholar 

  • Robertson, G. P., K. Klingensmith, M. Klug, E. Paul, J. Crum, and B. Ellis, 1997, Soil resources, microbial activity, and primary production across an agricultural ecosystem, Ecol. Appl. 7:158-170.

    Google Scholar 

  • Ronn, R., B. S. Griffiths, F. Ekelund, and S. Christensen, 1996, Spatial distribution and succes-sional pattern of microbial activity and micro-faunal populations on decomposing barley roots, J. Appl. Ecol. 33:662-672.

    Google Scholar 

  • Saetre, P., and E. Bååth, 2000, Spatial variation and patterns of soil microbial community structure in a mixed spruce-birch stand, Soil Biol. Biochem. 32:909-917.

    CAS  Google Scholar 

  • Sexstone, A., N. Revsbech, T. Parkin, and J. Tiedje, 1985, Direct measurement of oxygen profiles and denitrification rates in soil aggregates, Soil Sci. Soc. Am. J. 49:645-651.

    Article  CAS  Google Scholar 

  • Stoyan, H., H. De Polli, S. Bohm, G. P. Robertson, and E. A. Paul, 2000, Spatial hetero-geneity of soil respiration and related properties at the plant scale, Plant Soil 222:203-214.

    CAS  Google Scholar 

  • Strong, D. T., P. W. G. Sale, and K. R. Helyar, 1997, Initial soil pH affects the pH at which nitrification ceases due to self-induced acidification of microbial microsites, Aus. J. Soil Res. 35:565-570.

    Google Scholar 

  • Thieme, J., G. Schneider, and C. Knochel, 2003, X-ray tomography of a microhabitat of bacteria and other soil colloids with sub-100 nm resolution, Micron. 34:339-344.

    PubMed  Google Scholar 

  • Tippkötter, R., 1990, Staining of soil microorganisms and related materials with fluoro-chromes, in: Soil Micromorphology: A Basic and Applied Science, L. A. Douglas (ed.), Elsevier, Amsterdam, pp. 605-611.

    Google Scholar 

  • Tippkötter, R., and K. Ritz, 1996, Evaluation of polyester, epoxy and acrylic resins for suitability in preparation of soil thin sections for in situ biological studies, Geoderma 69:31-57.

    Google Scholar 

  • Tippkötter, R., K. Ritz, and J. F. Darbyshire, 1986, The preparation of soil thin sections for biological studies, J. Soil Sci. 77:681-690.

    Google Scholar 

  • Top, E. M., and D. Springael, 2003, The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds, Curr. Opin. Biotechnol. 14:262-269.

    PubMed  CAS  Google Scholar 

  • Top, E. M., P. Van Daele, N. De Saeyer, and L. J. Forney, 1998, Enhancement of 2,4-dichlorophenoxyacetic acid (2,4-D) degradation in soil by dissemination of catabolic plasmids, Antonie Van Leeuwenhoek Int. J. Gen. Mol. Microbiol. 73:87-94.

    CAS  Google Scholar 

  • Treves, D. S., B. Xia, J. Zhou, and J. M. Tiedje, 2003, A two-species test of the hypothesis that spatial isolation influences microbial diversity in soil, Microb. Ecol. 45:20-28.

    PubMed  CAS  Google Scholar 

  • Tsuji, T., Y. Kawasaki, S. Takeshima, T. Sekiya, and S. Tanaka, 1995, A new fluorescence staining assay for visualizing living microorganisms in soil, Appl. Environ. Microbiol. 61:3415-3421.

    PubMed  CAS  Google Scholar 

  • Velthof, G. L., S. C. Jarvis, A. Stein, A. G. Allen, and O. Oenema, 1996, Spatial variability of nitrous oxide fluxes in mown and grazed grasslands on a poorly drained clay soil, Soil Biol. Biochem. 28:1215-1225.

    CAS  Google Scholar 

  • Vieublé-Gonod, L., J. Chadoeuf, and C. Chenu, 2006, Spatial distribution of microbial 2,4-Dichlorophenoxy acetic acid mineralization from field to microhabitat scales, Soil Sci. Soc. Am. J. 70:64-71.

    Google Scholar 

  • Vogel, H. J., and K. Roth, 1998, A new approach for determining effective soil hydraulic functions, Eur. J. Soil Sci. 49:547-556.

    Google Scholar 

  • Vogel, H. J., and K. Roth, 2001, Quantitative morphology and network representation of soil pore structure, Adv. Water Resour. 24:233-242.

    Google Scholar 

  • Warrick, A. W., and D. E. Myers, 1987, Optimization of sampling locations for variogram calculations, Water Resour. Res. 23:496-500.

    Google Scholar 

  • Wheatley, R. E., 2002, The consequences of volatile organic compound mediated bacterial and fungal interactions, Antonie van Leeuwenhoek Int. J. Gen. Mol. Microbiol. 81:357-364.

    CAS  Google Scholar 

  • White, D., E. A. Fitzpatrick, and K. Killham, 1994, Use of stained bacterial inocula to assess spatial-distribution after introduction into soil, Geoderma 63:245-254.

    Google Scholar 

  • Whitehead, N. A., A. M. L. Barnard, H. Slater, N. J. L. Simpson, and G. P. C. Salmond, 2001, Quorum-sensing in gram-negative bacteria, FEMS Microbiol. Rev. 25:365-404.

    PubMed  CAS  Google Scholar 

  • Williamson, K. E., M. Radosevich, and K. E. Wommack, 2005, Abundance and diversity of viruses in six Delaware soils, Appl. Environ. Microbiol. 71:3119-3125.

    PubMed  CAS  Google Scholar 

  • Wright, D. A., K. Killham, L. A. Glover, and J. I. Prosser, 1995, Role of pore-size location in determining bacterial-activity during predation by protozoa in soil, Appl. Environ. Microbiol. 61:3537-3543.

    PubMed  CAS  Google Scholar 

  • Wu, K. J., N. Nunan, J. W. Crawford, I. M. Young, and K. Ritz, 2004, An efficient Markov chain model for the simulation of heterogeneous soil structure, Soil Sci. Soc. Am. J. 68:346-351.

    Article  CAS  Google Scholar 

  • Young, I. M., and J. W. Crawford, 2001, Protozoan life in a fractal world, Protist 152:123-126.

    PubMed  CAS  Google Scholar 

  • Young, I. M., and J. W. Crawford, 2004, Interactions and self-organization in the soil-microbe complex, Science 304:1634-1637.

    PubMed  CAS  Google Scholar 

  • Young, I. M., and K. Ritz, 1998, Can there be a contemporary ecological dimension to soil biology without a habitat? Soil Biol. Biochem. 30:1229-1232.

    CAS  Google Scholar 

  • Young, I. M., and K. Ritz, 2000, Tillage, habitat space and function of soil microbes, Soil Till. Res. 53:201-213.

    Google Scholar 

  • Young, I. M., and K. Ritz, 2005, The habitat of soil microbes, in: Biological Diversity and Function in Soils, R. D. Bardgett, M. B. Usher, and D. W. Hopkins eds., Cambridge University Press, Cambridge, pp. 31-43.

    Google Scholar 

  • Young, I. M., J. W. Crawford, and C. Rappoldt, 2001, New methods and models for characterising structural heterogeneity of soil, Soil Till. Res. 61:33-45.

    Google Scholar 

  • Zhou, J. Z., B. C. Xia, D. S. Treves, L. Y. Wu, T. L. Marsh, R. V. O’Neill, A. V. Palumbo, and J. M. Tiedje, 2002, Spatial and resource factors influencing high microbial diversity in soil, Appl. Environ. Microbiol. 68:326-334.

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. CNRS, BioEMCo, Bât. EGER, Centre INRA-INAPG, 78850, Thiverval-Grignon, France

    Naoise Nunan

  2. SIMBIOS Center, University of Abertay Dundee, Bell Street, DD1 1HG, Dundee, UK

    Iain M. Young & John W. Crawford

  3. National Soil Resources Institute, Cranfield University, MK45 4DT, Silsoe, UK

    Karl Ritz

Authors
  1. Naoise Nunan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Iain M. Young
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. John W. Crawford
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Karl Ritz
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Virginia Commonwealth University, 23284, Richmond, VA, USA

    Rima B. Franklin

  2. University of Virginia, 22904-4123, Charlottesville, VA, USA

    Aaron L. Mills

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Springer

About this chapter

Cite this chapter

Nunan, N., Young, I.M., Crawford, J.W., Ritz, K. (2007). Bacterial Interactions At The Microscale – Linking Habitat To Function In Soil. In: Franklin, R.B., Mills, A.L. (eds) The Spatial Distribution of Microbes in the Environment. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-6216-2_3

Download citation

Publish with us

Policies and ethics

Search

Navigation