Advertisement

Spatial Distribution Of Bacteria At The Microscale In Soil

  • Arnaud Deschesne
  • Céline Pallud
  • Geneviève L. Grundmann

After the discovery of the tremendous bacterial diversity in soil at all spatial scales, numerous studies have been motivated by the fact that soil represents a very large reservoir of various genes. Nevertheless, the organization of bacterial cells at the microscale in the soil fabric has been overlooked, although all functional interactions appearing at the ecosystem level initially intervene at the scale of the bacterial cells. Many microbiological processes are based on encounters between cells, and between cells and substrates, between cells and surfaces. This chapter provides insight into the microscale spatial distribution of bacteria in soil, with a special emphasis on the concepts of microcolonies and microhabitats as structuring elements for these patterns. Keywords: bacterial diversity, soil, spatial organization, microscale, microhabitat

Keywords

Bacterial Community Particulate Organic Carbon Bacterial Diversity Soil Column Soil Aggregate 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Arber, W., 1995, The generation of variation in bacterial genomes, J. Mol. Evol. 40:7-12.CrossRefGoogle Scholar
  2. Bent, S. J., C. L. Gucker, Y. Oda, and L. J. Forney, 2003, Spatial distribution of Rhodo-pseudomonas palustris ecotypes on a local scale, Appl. Environ. Microb. 69:5192-5197.CrossRefGoogle Scholar
  3. Bloemberg, G. V., A. H. Wijfjes, G. E. Lamers, N. Stuurman, and B. J. Lugtenberg, 2000, Simultaneous imaging of Pseudomonas fluorescens WCS365 populations expressing three different autofluorescent proteins in the rhizosphere: new perspectives for studying microbial communities, Mol. Plant Microbe Interact. 13:1170-1176.CrossRefPubMedGoogle Scholar
  4. Bundt, M., F. Widmer, M. Pesaro, J. Zeyer, and P. Blaser, 2001, Preferential flow paths: biological ‘hot spots’ in soils, Soil Biol. Biochem. 33:729-738.CrossRefGoogle Scholar
  5. Chalfie, M., Y. Tu, G. Euskirchen, W. W. Ward, and D. C. Prasher, 1994, Green fluorescent protein as a marker for gene expression, Science 263:802-805.CrossRefPubMedGoogle Scholar
  6. 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. Fert. Soils 34:349-356.CrossRefGoogle Scholar
  7. Cho, J. C., and J. M. Tiedje, 2000, Biogeography and degree of endemicity of fluorescentPseudomonas strains in soil, Appl. Environ. Microb. 66:5448-5456.CrossRefGoogle Scholar
  8. Daane, L. L., J. A. Molina, E. C. Berry, and M. J. Sadowsky, 1996, Influence of earthworm activity on gene transfer from Pseudomonas fluorescens to indigenous soil bacteria, Appl. Environ. Microb. 62:515-521.Google Scholar
  9. Daane, L. L., J. A. E. Molina, and M. J. Sadowsky, 1997, Plasmid transfer between spatially separated donor and recipient bacteria in earthworm-containing soil microcosms, Appl. Environ. Microb. 63:679-686.Google Scholar
  10. 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.CrossRefGoogle Scholar
  11. Dechesne, A., C. Pallud, F. Bertolla, and G. L. Grundmann, 2005, Impact of the microscale distribution of a Pseudomonas strain introduced into soil on potential contacts with indigenous bacteria, Appl. Environ. Microb. 71:8123-8131.CrossRefGoogle Scholar
  12. Dunbar, J., S. White, and L. Forney, 1997, Genetic diversity through the looking glass: effect of enrichment bias, Appl. Environ. Microb. 63:1326-1331.Google Scholar
  13. El Balkhi, M., F. Mangenot, J. Proth, and G. Kilbertus, 1978, Influence de la percolation d’une solution de saccharose sur la composition qualitative et quantitative de la microflore bactérienne d’un sol, Soil Sci. Plant Nutr. 24:15-25.Google Scholar
  14. England, L. S., H. Lee, and J. T. Trevors, 1993, Bacterial survival in soil: effect of clays and protozoa, Soil Biol. Biochem. 25:525-531.CrossRefGoogle Scholar
  15. Errampalli, D., K. Leung, M. B. Cassidy, M. Kostrzynska, M. Blears, H. Lee, and J. T. Trevors, 1999, Applications of the green fluorescent protein as a molecular marker in environ-mental microorganisms, J. Microbiol. Methods 35:187-199.CrossRefPubMedGoogle Scholar
  16. Felske, A., and A. D. L. Akkermans, 1998, Spatial homogeneity of abundant bacterial 16S rRNA molecules in grassland soils, Microbial Ecol. 36:31-36.CrossRefGoogle Scholar
  17. Focht, D. D., 1992, Diffusional constraints on microbial processes in soil, Soil Sci. 154: 300-307.CrossRefGoogle Scholar
  18. Foster, R. C., 1988, Microenvironments of soil microorganisms, Biol. Fert. Soils 6:189-203.CrossRefGoogle Scholar
  19. Franklin, R. B., L. K. Blum, A. C. McComb, and A. L. Mills, 2002, A geostatistical analysis of small-scale spatial variability in bacterial abundance and community structure in salt marsh creek bank sediments, FEMS Microbiol. Ecol. 42:71-80.CrossRefPubMedGoogle Scholar
  20. Fulthorpe, R. R., A. N. Rhodes, and J. M. Tiedje, 1998, High levels of endemicity of 3-chlorobenzoate-degrading soil bacteria, Appl. Environ. Microb. 64:1620-1627.Google Scholar
  21. Gaillard, V., C. Chenu, S. Recous, and G. Richard, 1999, Carbon, nitrogen and microbial gradients induced by plant residues decomposing in soil, Eur. J. Soil Sci. 50:567-578.CrossRefGoogle Scholar
  22. Gammack, S. M., E. Paterson, J. S. Kemp, M. S. Cresser, and K. Killham, 1992, Factors affecting the movement of microorganisms in soils, in: Soil Biochemistry, Vol. 7, G. Stotzky and J. Bollag, eds., Marcel Dekker, New York, pp. 263-305.Google Scholar
  23. Gray, T. R. G., P. Baxby, I. R. Hill, and M. Goodfellow, 1968, Direct observation of bacteria in soil, in: The Ecology of Soil Bacteria, T. Gray and D. Parkinson, eds., Liverpool University Press, Liverpool, UK, pp. 171-192.Google Scholar
  24. Grundmann, G. L., and D. Debouzie, 2000, Geostatistical analysis of the distribution of NH4+ and NO2--oxidizing bacteria and serotypes at the millimeter scale along a soil transect, FEMS Microbiol. Ecol. 34:57-62.PubMedGoogle Scholar
  25. 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. Microb. 66:4543-4546.CrossRefGoogle Scholar
  26. 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.Google Scholar
  27. Harms, H., and A. J. Zehnder, 1994, Influence of substrate diffusion on degradation of dibenzo-furan and 3-chlorodibenzofuran by attached and suspended bacteria, Appl. Environ. Microb. 60:2736-2745.Google Scholar
  28. Harris, P. J., 1994, Consequences of the spatial distribution of microbial communities in soil, in: Beyond the Biomass, K. Ritz, et al., eds., Wiley, Chichester, UK, pp. 239-246.Google Scholar
  29. Hattori, T., 1967, Microorganisms and soil aggregates as their microhabitat, Bull. Inst. Agr. Res. Tohoku Univ. 18:159-193.Google Scholar
  30. Hattori, T., 1973, Microbial Life in the Soil, Marcel Dekker, New York. Google Scholar
  31. Hissett, R., and T. R. G. Gray, 1976, Microsites and time changes in soil microbe ecology, in: The Role of Terrestrial and Aquatic Organisms in Decomposition Process, J. Anderson, and A. MacFadyen, eds., Blackwell, Oxford, pp. 23-39.Google Scholar
  32. Holden, P. A., and M. K. Firestone, 1997, Soil microorganisms in soil cleanup: how can we improve our understanding? J. Environ. Qual. 26:32-40.Google Scholar
  33. Horner-Devine, M. C., K. M. Carney, and B. J. M. Bohannan, 2004, An ecological perspective on bacterial biodiversity, Proc. Roy. Soc. Lond. B Bio. 271:113-122.CrossRefGoogle Scholar
  34. Jocteur-Monrozier, L., J. N. Ladd, R. W. Fitzpatrick, R. C. Foster, and M. Rapauch, 1991, Physical properties, mineral and organic components and microbial biomass content of size fractions in soils of contrasting aggregation, Geoderma 50:37-62.CrossRefGoogle Scholar
  35. Jones, D., and E. Griffiths, 1964, The use of thin soil sections for the study of soil micro-organisms, Plant Soil 20:232-240.CrossRefGoogle Scholar
  36. Kilbertus, G., 1980, Etude des microhabitats contenus dans les agrégats du sol. Leur relation avec la biomasse bactérienne et la taille des procaryotes présents, Rev. Ecol. Biol. Sol 17:543-557.Google Scholar
  37. Lee, N., P. H. Nielsen, K. H. Andreasen, S. Juretschko, J. L. Nielsen, K. H. Schleifer, and M. Wagner, 1999, Combination of fluorescent in situ hybridization and microautoradiography - a new tool for structure-function analyses in microbial ecology, Appl. Environ. Microb. 65:1289-1297.Google Scholar
  38. Li, Y., W. A. Dick, and O. H. Tuovinen, 2003, Evaluation of fluorochromes for imaging bacteria in soil, Soil Biol. Biochem. 35:737-744.CrossRefGoogle Scholar
  39. Lünsdorf, H., R. W. Erb, W. R. Abraham, and K. N. Timmis, 2000, ‘Clay hutches’: a novel interaction between bacteria and clay minerals, Environ. Microbiol. 161-168.Google Scholar
  40. McArthur, J. V., D. A. Kovacic, and M. H. Smith, 1988, Genetic diversity in natural populations of a soil bacterium across a landscape gradient, Proc. Natl. Acad. Sci. USA 85:9621-9624.CrossRefPubMedGoogle Scholar
  41. Mendes, I. C., and P. J. Bottomley, 1998, Distribution of a population of Rhizobium legumino-sarum bv. trifolii among different size classes of soil aggregates, Appl. Environ. Microb. 64:970-975.Google Scholar
  42. Metting, F. B., 1992, Structure and physiological ecology of soil microbial communities, in: Soil Microbial Ecology: Application in Agricultural and Environmental Management, F. Metting, ed., Marcel Dekker, New York, pp. 3-25.Google Scholar
  43. Monier, J. M., and S. E. Lindow, 2003, Differential survival of solitary and aggregated bacterial cells promotes aggregate formation on leaf surfaces, Proc. Natl. Acad. Sci. USA 100:15977-15982.CrossRefPubMedGoogle Scholar
  44. Mummey, D. L., and P. D. Stahl, 2004, Analysis of soil whole- and inner-microaggregate bacterial communities, Microbial Ecol. 48:41-50.CrossRefGoogle Scholar
  45. Nikin, D. I., and F. Kunc, 1988, Structure of microbial soil associations and some mechanisms of their autoregulation, in: Soil Microbial Associations, V. Vancura and F. Kunc, eds., Elsevier, Amsterdam, pp. 157-190.Google Scholar
  46. Nishio, M., and C. Furusaka, 1970, The distribution of nitrifying bacteria in soil aggregates, Soil Sci. Plant Nutr (Tokyo) 16:24-29.Google Scholar
  47. Nishio, M., T. Hattori, and C. Furusaka, 1968, The growth of bacteria in sterilized soil aggregates, Rep. Inst. Agr. Res. Tohoku Univ. 19:37-43.Google Scholar
  48. Noguez, A. M., H. T. Arita, A. E. Escalante, L. J. Forney, F. Garcia-Oliva, and V. Souza, 2005, Microbial macroecology: highly structured prokaryotic soil assemblages in a tropical deciduous forest, Global Ecol. Biogeogr. 14:241-248.CrossRefGoogle Scholar
  49. 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.CrossRefGoogle Scholar
  50. 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, Microbial Ecol. 44:296-305.CrossRefGoogle Scholar
  51. 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.CrossRefPubMedGoogle Scholar
  52. Oda, Y., B. Star, L. A. Huisman, J. C. Gottschal, and L. J. Forney, 2003, Biogeography of the purple nonsulfur bacterium Rhodopseudomonas palustris, Appl. Environ. Microb. 69:5186-5191.CrossRefGoogle Scholar
  53. Or, D., B. F. Smets, J. M. Wraith, A. Dechesne, and S. P. Friedman, 2007, Physical constraints affecting bacterial habitats and activity in unsaturated porous media - A review, Adv. Water. Res. 30:1505-1527.CrossRefGoogle Scholar
  54. 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. Microb. 70:2709-2716.CrossRefGoogle Scholar
  55. Papke, R. T., and D. M. Ward, 2004, The importance of physical isolation to microbial diversification, FEMS Microbiol. Ecol. 48:293-303.CrossRefPubMedGoogle Scholar
  56. Parkin, T. B., 1987, Soil microsites as a source of denitrification variability, Soil Sci. Soc. Am. J. 51:1194-1199.CrossRefGoogle Scholar
  57. Parkin, T. B., 1993, Spatial variability of microbial processes in soil - a review, J. Environ. Qual. 22:409-417.CrossRefGoogle Scholar
  58. Pivetz, B. E., and T. S. Steenhuis, 1995, Soil matrix and macropore biodegradation of 2,4-D, J. Environ. Qual. 24:564-570.CrossRefGoogle Scholar
  59. Poly, F., L. Ranjard, S. Nazaret, F. Gourbiere, and L. J. Monrozier, 2001, Comparison of nifH gene pools in soils and soil microenvironments with contrasting properties, Appl. Environ. Microb. 67:2255-2262.CrossRefGoogle Scholar
  60. Postma, J., and J. A. Van Veen, 1990, Habitable pore space and survival of Rhizobium legumino-sarum biovar trifolii introduced into soil, Microbial Ecol. 19:149-161.CrossRefGoogle Scholar
  61. Rainey, P. B., A. Buckling, R. Kassen, and M. Travisano, 2000, The emergence and maintenance of diversity: insights from experimental bacterial populations, Trends Ecol. Evol. 15:243-247.CrossRefPubMedGoogle Scholar
  62. Ranjard, L., and A. S. Richaume, 2001, Quantitative and qualitative microscale distribution of bacteria in soil, Res. Microbiol. 152:707-716.CrossRefPubMedGoogle Scholar
  63. Ranjard, L., A. Richaume, L. Jocteur-monrozier, and S. Nazaret, 1997, Response of soil bacteria to Hg(II) in relation to soil characteristics and cell location, FEMS Microbiol. Ecol. 24:321-331.CrossRefGoogle Scholar
  64. Recorbet, G., A. Richaume, and L. Jocteur Monrozier, 1995, Distribution of a genetically-engineered Escherichia coli population introduced into soil, Lett. Appl. Microbiol. 21: 38-40.CrossRefPubMedGoogle Scholar
  65. Richardson, R. E., C. A. James, V. K. Bhupathiraju, and L. Alvarez Cohen, 2002, Microbial activity in soils following steam treatment, Biodegradation 13:285-295.CrossRefPubMedGoogle Scholar
  66. Rius, N., M. C. Fuste, C. Guasp, J. Lalucat, and J. G. Loren, 2001, Clonal population structure of Pseudomonas stutzeri, a species with exceptional genetic diversity, J. Bacteriol. 183:736-744.CrossRefPubMedGoogle Scholar
  67. Sessitsch, A., A. Weilharter, H. Gerzabek, H. Kirchmann, and E. Kandeler, 2001, Microbial population structures in soil particle size fractions of a long-term fertilizer field experiment, Appl. Environ. Microb. 67:4215-4224.CrossRefGoogle Scholar
  68. Skinner, F. A., 1976, Methods in soil examination, in: Microbiology in Agriculture, Fisheries and Food, F. A. Skinner and J. G. Carr, eds., Academic Press, London, pp. 19-35.Google Scholar
  69. 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.CrossRefPubMedGoogle Scholar
  70. Tombolini, R., D. J. Van Der Gaag, B. Gerhardson, and J. K. Jansson, 1999, Colonization pattern of the biocontrol strain Pseudomonas chlororaphis MA 342 on barley seeds visualized by using green fluorescent protein, Appl. Environ. Microb. 65:3674-3680.Google Scholar
  71. 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, Microbial Ecol. 45:20-28.CrossRefGoogle Scholar
  72. 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. Microb. 61:3415-3421.Google Scholar
  73. Vallaeys, T., F. Persello-carteaux, N. Rouard, C. Lors, G. Laguerre, and G. Soulas, 1997, PCR-RFLP analysis of 16S rRNA, tfdA and tfdB genes reveals a diversity of 2,4-D degraders in soil aggregates, FEMS Microbiol. Ecol. 24:269-278.CrossRefGoogle Scholar
  74. Vargas, R., and T. Hattori, 1990, The distribution of protozoa among soil aggregates, FEMS. Microbiol. Lett. 74:73-78.CrossRefGoogle Scholar
  75. Vilas Boas, G., V. Sanchis, D. Lereclus, M. V. Lemos, and D. Bourguet, 2002, Genetic differen-tiation between sympatric populations of Bacillus cereus and Bacillus thuringiensis, Appl. Environ. Microb. 68:1414-1424.CrossRefGoogle Scholar
  76. Vogel, J., P. Normand, J. Thioulouse, X. Nesme, and G. L. Grundmann, 2003, Relationship between spatial and genetic distance in Agrobacterium spp. in 1 cubic centimeter of soil, Appl. Environ. Microb. 69:1482-1487.CrossRefGoogle Scholar
  77. Vos, M., and G. J. Velicer, 2006, Genetic population structure of the soil bacterium Myxococcus xanthus at the centimeter scale, Appl. Environ. Microb. 72:3615-3625.CrossRefGoogle Scholar
  78. Wachinger, G., S. Fiedler, K. Zepp, A. Gattinger, M. Sommer, and K. Roth, 2000, Variability of soil methane production on the micro-scale: spatial association with hot spots of organic material and Archaeal populations, Soil Biol. Biochem. 32:1121-1130.CrossRefGoogle Scholar
  79. Yarwood, R. R., M. L. Rockhold, M. R. Niemet, J. S. Selker, and P. J. Bottomley, 2002, Noninvasive quantitative measurement of bacterial growth in porous media under unsaturated-flow conditions, Appl. Environ. Microb. 68:3597-3605.CrossRefGoogle Scholar
  80. Zvyagintsev, D. G., 1962, Adsorption of microorganisms to soil particles, Soviet Soil Sci. 140-144.Google Scholar

Copyright information

© Springer 2007

Authors and Affiliations

  • Arnaud Deschesne
    • 1
  • Céline Pallud
    • 2
  • Geneviève L. Grundmann
    • 3
  1. 1.Institute of Environment and ResourcesTechnical University of DenmarkDenmark
  2. 2.Department of Geological and Environmental SciencesStanford UniversityStanfordUSA
  3. 3.Laboratoire d'Ecologie MicrobienneUniversité de Lyon1France

Personalised recommendations