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Assessment of the bacterial diversity in soils: Evolution of approaches and methods

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Abstract

This review analyzes the publications of Russian and foreign microbiologists presenting new approaches and methods for assessing the bacterial diversity of soils in the last twenty years. Using the example of peat soils, it is shown how the concepts of the diversity of the bacterial communities changed in conformity with the evolution of the analytical methods—from the traditional cultural to the molecular-biological ones. The data on the new phylotypes, genera, and species of bacteria adapted to growth in the acid medium and low temperatures characteristic of bog ecosystems are presented. Presently, one of the principal problems of soil microbiology is the necessity of the transfer from the databases on the microbial diversity constructed on the basis of molecular-biological methods to the analysis of the ecological functions of soil microorganisms. The prospects of the ecological evaluation of the bacterial diversity in soils based on the integration of different methods are discussed.

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References

  1. D. A. Begak, “Microbiological Study of the High-Moor Peatland: Quantitative Assessment of Bacteria in the High-Moor Peat,” Pochvovedenie, No. 2, 64–75 (1926).

  2. S. E. Belova, T. A. Pankratov, and S. N. Dedysh, “Bacteria of the Genus Burkholderia as a Typical Component of the Microbial Community of Sphagnum Peat Bogs,” Mikrobiologiya 75(1), 110–117 (2006) [Microbiology 75 (1), 90–96 (2006)].

    Google Scholar 

  3. F. P. Vavulo, “Soil Microflora in the Byelorussian Soviet Socialist Republic,” in Soil Microflora in the Northern and Central Parts of the Soviet Union (Nauka, Moscow, 1966), pp. 114–135 [in Russian].

    Google Scholar 

  4. L. V. Vasil’eva, “Oligotrophs as a Component of Biogeocenosis,” in Soil Organisms as Components of Biogeocenoses (Nauka, Moscow, 1984), pp. 232–241 [in Russian].

    Google Scholar 

  5. L. V. Vasil’eva, Extended Abstract of Doctoral Dissertation in Biology (Moscow, 1990).

  6. L. V. Vasil’eva, A. M. Semenov, and A. I. Giniyatullina, “New Species of Soil Bacteria from the Prosthecomicrobium Genus,” Mikrobiologiya 60(2), 350–359 (1991).

    Google Scholar 

  7. A. V. Golovchenko, L. M. Polyanskaya, T. G. Dobrovol’skaya, et al., “Specificity of the Spatial Distribution and Structure of Microbial Complexes in Forest Mire Ecosystems,” Pochvovedenie, No. 10, 78–89 (1993).

  8. A. V. Golovchenko, Yu. V. Sannikova, T. G. Dobrovol’skaya, and D. G. Zvyagintsev, “The Saprotrophic Bacterial Complex in the Raised Peat Bogs of Western Siberia,” Mikrobiologiya 74(4), 545–551 (2005) [Microbiology 74 (4), 471–476 (2005)].

    Google Scholar 

  9. A. V. Golovchenko, I. Yu. Chernov, and T. A. Semenova, “Saprotrophic Microbial Complex of Oligotrophic Peatlands in Western Siberia,” in Soils and Biodiversity. Transactions of the Institute of Soil Science, Moscow State University-Russian Academy of Sciences (Grif i K, Tula, 2004), issue 4, 144–159 [in Russian].

    Google Scholar 

  10. T. G. Dobrovol’skaya, Structure of Soil Bacterial Communities (IKTs “Akademkniga”, Moscow, 2002) [in Russian].

    Google Scholar 

  11. T. G. Dobrovol’skaya and A. V. Golovchenko, “Eco-Taxonomic Structure of Bacterial Communities in Hydromorphic Forest Soils,” Vestn. Mosk. Univ., Ser. 17: Pochvoved., No. 1, 55–58 (1999).

  12. T. G. Dobrovol’skaya, L. V. Lysak, G. M. Zenova, and D. G. Zvyagintsev, “Analysis of Soil Bacterial Diversity: Methods, Potentiality, and Prospects,” Mikrobiologiya 70(2), 149–167 (2001) [Microbiology 70 (2), 119–132 (2001)].

    Google Scholar 

  13. T. G. Dobrovol’skaya, I. N. Skvortsova, and L. V. Lysak, Methods of Isolation and Identification of Soil Bacteria (Izd-vo Mosk. Gos. Univ., Moscow, 1989) [in Russian].

    Google Scholar 

  14. E. N. Zhdannikova, “Microbiological Characterization of Peat Bog Soils in Tomsk Oblast,” in Boggy Forests and Mires of Western Siberia (Nauka, Moscow, 1963), pp. 170–182 [in Russian].

    Google Scholar 

  15. D. G. Zvyagintsev, Soil and Microorganisms (Izd-vo Mosk. Gos. Univ., Moscow, 1987) [in Russian].

    Google Scholar 

  16. D. G. Zvyagintsev, T. G. Dobrovol’skaya, I. P. Bab’eva, et al., “Role of Microorganisms in the Biogeocenotic Soil Functions,” in Structural-Functional Role of Soils and Soil Biota in the Biosphere (Nauka, Moscow, 2003) [in Russian].

    Google Scholar 

  17. G. M. Zenova, V. K. Orleanskii, and E. O. Omarova, “Soil Streptomycetes: The Components of Experimental Algo-Bacterial Cenoses,” Pochvovedenie, No. 10, 1251–1255 (2005) [Eur. Soil Sci. 38 (10), 1108–1111 (2005)].

  18. T. G. Zimenko, Microbial Cenoses of Peat Soils and Their Functioning (Nauka i Tekhnika, Minsk, 1983) [in Russian].

    Google Scholar 

  19. I. S. Kulichevskaya, S. E. Belova, V. V. Kevbrin, et al., “Analysis of the Bacterial Community Developing in the Course of Sphagnum Moss Decomposition,” Mikrobiologiya 76(5), 702–710 (2007) [Microbiology 76 (5), 621–629 (2007)].

    Google Scholar 

  20. I. S. Kulichevskaya, T. A. Pankratov, and S. N. Dedysh, “Detection of Representatives of the Planctomycetes in Sphagnum Peat Bogs by Molecular and Cultivation Approaches,” Mikrobiologiya 75(3), 389–396 (2006) [Microbiology 75 (3), 329–335 (2006)].

    Google Scholar 

  21. L. V. Lysak, T. G. Dobrovol’skaya, and I. N. Skvortsova, Methods of Evaluation of the Bacterial Diversity in Soils and Identification of Soil Bacteria (MAKS Press, Moscow, 2003) [in Russian].

    Google Scholar 

  22. M. V. Omel’chenko, L. V. Vasil’eva, G. A. Zavarzin, et al., “A Novel Psychrophilic Methanotroph of the Genus Methylobacter,” Mikrobiologiya 65(3), 384–389 (1996) [Microbiology 65 (3), 349–353 (1996)].

    Google Scholar 

  23. Bergey’s Manual of Determinative Bacteriology, J. A. Holt, N. R. Krieg, H. A. Peter, et al., (Eds.), (Williams and Wilkins, Baltimore, 1994).

    Google Scholar 

  24. N. S. Panikov, A. A. Titlyanova, M. V. Paleeva, et al., “Emission of Methane and carbon Dioxide from Mires in the South of Western Siberia: Spatial and Temporal Variability of Fluxes,” Zh. Ekol. Khim. 4, 13–23 (1995).

    Google Scholar 

  25. T. A. Pankratov, S. E. Belova, and S. N. Dedysh, “Evaluation of the Phylogenetic Diversity of Prokaryotic Microorganisms in Sphagnum Peat Bogs by Means of Fluorescence in situ Hybridization (FISH),” Mikrobiologiya 74(6), 831–837 (2005) [Microbiology 74 (6), 722–728 (2005)].

    Google Scholar 

  26. I. Aselman and P. J. Crutzen, “Global Distribution of Natural Fresh Water Wetlands and Rice Paddies, Their Net Primary Productivity, Seasonality and Possible Methane Emissions,” J. Atmos. Chemistry 8, 307–358 (1989).

    Article  Google Scholar 

  27. D. H. Buckley, V. Huangyutitham, T. A. Nelson, et al., “Diversity of Planctomycetes in Soil in Relation to Soil History and Environmental Heterogeneity,” Appl. Environ. Microbiol. 72, 4522–4531 (2006).

    Article  Google Scholar 

  28. E. K. Costello and S. K. Schmidt, “Alpine Tundra Soil at Spring Snow Melt Harboprs Novel and Abundant Groups of Chloroflexi Bacteria,” ASM General Meeting (2003).

  29. S. N. Dedysh, S. E. Belova, P. L. E. Bodelier, et al., “Methylocystis Heyeri sp. nov., a Novel Type II Methanotrophic Bacterium Possessing ’signature’ Fatty Acids of Type I Methanotrophs,” IJSEM 57, 472–479 (2007).

    Google Scholar 

  30. S. N. Dedysh, M. Derakshani, and W. Liesack, “Detection and Enumeration of Methanotrophs in Acidic Sphagnum Peat by 16S RRNA Fluorescence In Situ Hybridisation, Including the Use of Newly Developed Oligonucleotide Probes for Methylocella Palustris,” Appl. Environ. Microbiol. 67, 4850–4857 (2001).

    Article  Google Scholar 

  31. S. N. Dedysh, T. A. Pankratov, S. E. Belova, et al., “Phylogenetic Analysis and in situ Identification of Bacteria Community Composition in an Acidic Sphagnum Peat Bog,” Appl. Environ. Microbiol. 72(3), 2110–2117 (2006).

    Article  Google Scholar 

  32. N. Fierer, M. A. Braddford, and R. B. Jackson, “Toward an Ecological Classification of Soil Bacteria,” Ecology 88(6), 1354–1364 (2007).

    Article  Google Scholar 

  33. N. Fierer and R. B. Jackson, “The Diversity and Biogeography of Soil Bacterial Communities,” Proc. Natl. Acad. Sci. 103, 626–631 (2006).

    Article  Google Scholar 

  34. P. H. Given and C. H. Dickinson, “Biochemistry, Microbiology of Peats,” Soil Biochemistry 3, 123–212 (1975).

    Google Scholar 

  35. E. Hackl, S. Zechmeister-Boltenrstern, L. Bodrossy, and A. Sessitsch, “Comparative Diversity and Composition of Bacterial Communities Inhabiting Natural Forest Soils,” Geophysical Research Abstracts 7, 02765 (2005).

    Google Scholar 

  36. M. W. Hahn, H. Lunddorf, Q. Wu, et al., “Isolation of Novel Ultramicrobacteria Classified as Actinobacteria from Five Freshwater Habitats in Europe and Asia,” Appl. Environ. Microbiol. 69, 1442–1451 (2003).

    Article  Google Scholar 

  37. M. C. Horner-Devine, K. M. Carney, and J. M. Bohannan, “An Ecological Perspective on Bacterial Biodiversity,” Proc. R. Soc. Lond. 271, 113–122 (2004).

    Article  Google Scholar 

  38. T. Kauri, “Rapid Multipoint Method for Quantification of Various Physiological Groups of Bacteria in Soil,” Soil Biol. Biochem. 12, 125–130 (1980).

    Article  Google Scholar 

  39. O. R. Kotsyurbenko, M. W. Friedrich, M. V. Simankova, et al., “Shift from Acetoclastic to H2-Dependent Methanogenesis in a West Siberian Peat Bog at Low pH and Isolation of an Acidophilic Methanobacterium Strain,” Appl. Environ. Microbiol. (2007).

  40. I. S. Kulichevskaya, A. O. Ivanova, O. I. Baulina, et al., “Singulisphaera Acidiphila gen. nov., sp. nov., a Non-Filamentous, Isosphaera-Like Planctomycete from Acidic Northern Wetlands,” int. J. Syst. Evol. Microbiol 58, 1186–1193 (2008).

    Article  Google Scholar 

  41. I. S. Kulichevskaya, A. O. Ivanova, S. E. Belova, et al., “Schlesneria Palidicola gen. nov., sp. nov., the First Acidophilic Member of the Order Planctomycetales, from Sphagnum-Dominated Boreal Wetlands,” Int. J. Syst. Evol. Microbiol 57, 2680–2687 (2007).

    Article  Google Scholar 

  42. W. Liesack and E. Stackebrandt, “Occurrence of Novel Groups of the Domain Bacteria as Revealed by Analysis of Genetic Material Isolated from an Australian Terrestrial Environment,” J. Bacteriol. 174, 5072–5078 (1992).

    Google Scholar 

  43. D. A. Lipson and S. K. Schmidt, “Seasonal Changes in an Alpine Soil Bacterial Community in the Colorado Rocky Mountains,” Appl. and Environ. Microbiol 70(5), 2867–2879 (2004).

    Article  Google Scholar 

  44. B. L. Maidak, J. R. Cole, C. T. Parker, et al., “A New Version of the RDP (Ribosomal Database Project),” Nucleic Acids Research 27(1), 171–173 (1999).

    Article  Google Scholar 

  45. M. K. Mannisto and M. M. Haggblom, “Characterization of Psychrotolerant Heterotrophic Bacteria from Finnish Lapland,” Syst. Appl. Microbiol. 29, 229–243 (2006).

    Article  Google Scholar 

  46. H. P. McVeigh, J. Munro, and T. M. Embley, “Molecular Evidence for the Presence of Novel Actinomycete Lineages in a Temperate Forest Soil,” J. Industrial Microbiol. 17, 197–204 (1996).

    Article  Google Scholar 

  47. S. E. Morales, P. J. Mouser, N. Ward, et al., “Comparison of Bacterial Communities in New England Sphagnum Bogs Using Terminal Restriction Fragment Length Polymorphism (T-RFLP),” Microb. Ecol. 52, 34–44 (2006).

    Article  Google Scholar 

  48. M. L. Nagy, A. Perez, and F. Garcia-Pichel, “The Prokaryotic Diversity of Biological Soil Crusts in the Sonoran Desert (Organ Pipe Cactus National Monument, AZ),” FEMS Microbiol. Ecology 54, 233–245 (2005).

    Article  Google Scholar 

  49. P. Nannipieri, J. Aschner, M. T. Ceccherini, et al., “Microbial Diversity and Soil Functions,” Eur. J. Soil Science 54, 655–670 (2003).

    Article  Google Scholar 

  50. T. A. Pankratov, Y. M. Serkebaeva, E. S. Kulichevskaya, et al., “Substrate-Induced Growth and Isolation of Acidobacteria from Acidic Sphagnum Peat,” The ISME Journal 2, 551–560 (2008).

    Article  Google Scholar 

  51. T. A. Pankratov, B. J. Tindall, W. Liesack, and S. N. Dedysh, “Mucilaginibacter Paludis gen. nov., sp. nov. and Mucilaginibacter Gracilis sp. nov., Pectin-, Xylan- and Laminarin-Degrading Members of the Family Sphingobacteriaceae from Acidic Sphagnum Peat Bog,” int. J. Syst. Evol. Microbiol 57, 2349–2354 (2007).

    Article  Google Scholar 

  52. H. Rheims, C. Sprör, F. A. Rainey, and E. Stackebrandt, “Molecular Biological Evidence for the Occurrence of Uncultured Members of the Actinomycete Line of Descent in Different Environments and Geographical Locations,” Microbiology 142, 2863–2870 (1996).

    Article  Google Scholar 

  53. M. R. Rondon, R. M. Goodman, and J. Handelsman, “The Earth’s Bounty: Assessing and Accessing Soil Microbial Diversity,” Trends Biotech. 17, 403–409 (1999).

    Article  Google Scholar 

  54. M. V. Sizova, N. S. Panikov, T. P. Tourova, and P. W. Flanagan, “Isolation and Characterization of Oligotrophic Acido-Tolerant Methanogenic Consortia from a Sphagnum Peat Bog,” FEMS Microbiol. Ecol. 45, 301–315 (2003).

    Article  Google Scholar 

  55. S. Tarleral, K. Jangid, A. H. Ivester, et al., “Microbial Community Succession and Bacterial Diversity in Soils during 77000 Years of Ecosystem Development,” FEMS Microbiol. Ecol. 64(1), 129–140 (2008).

    Article  Google Scholar 

  56. The Procaryotes, H. P. Starr, et al., (Eds.) (Springer, Berlin, 1981).

    Google Scholar 

  57. V. Torsvik, L. Øvreås, “Microbial Diversity and Function in Soil: from Genes to Ecosystems,” Current Opinion in Microbiology, No. 5, 240–245 (2002).

  58. V. Torsvik, R. Sorheim, and J. Goksoyr, “Total Bacterial Diversity in Soil and Sediment Communities: A Review,” J. Indust. Microbiol. 17, 170–178 (1996).

    Article  Google Scholar 

  59. M. Upton, B. Hill, C. Edwards, et al., “Combined Molecular Ecological and Confocal Laser Scanning Microscopic Analysis of Peat Bog Methanogen Populations,” FEMS Microbiol. Lett. 193, 275–281 (2000).

    Article  Google Scholar 

  60. S. A. Waksman and E. R. Purvis, “The Microbiological Population of Peat,” Soil Sci. 34, 95–109 (1932).

    Article  Google Scholar 

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Authors and Affiliations

  1. Faculty of Soil Science, Moscow State University, Moscow, 119991, Russia

    T. G. Dobrovol’skaya, A. V. Golovchenko, L. V. Lysak & D. G. Zvyagintsev

  2. Vinogradsky Institute of Microbiology, pr. 60 letiya Oktyabrya 7/2, Moscow, 117312, Russia

    T. A. Pankratov

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  1. T. G. Dobrovol’skaya
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  2. A. V. Golovchenko
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  3. T. A. Pankratov
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  4. L. V. Lysak
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  5. D. G. Zvyagintsev
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Original Russian Text © T.G. Dobrovol’skaya, A.V. Golovchenko, T.A. Pankratov, L.V. Lysak, D.G. Zvyagintsev, 2009, published in Pochvovedenie, 2009, No. 10, pp. 1222–1232.

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Dobrovol’skaya, T.G., Golovchenko, A.V., Pankratov, T.A. et al. Assessment of the bacterial diversity in soils: Evolution of approaches and methods. Eurasian Soil Sc. 42, 1138–1147 (2009). https://doi.org/10.1134/S1064229309100081

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