Sel’skokhozyaistvennaya Biologiya [Agricultural Biology], 2016, Vol. 51, № 1, p. 46-59.

UDC 631.461:57.083

doi: 10.15389/agrobiology.2016.1.46eng

Acknowledgements:
Supported by Russian Science Foundation (grant number 14-26-00094)

MICROBIAL COMMUNITY OF SOIL: PHYSIOLOGICAL DIVERSITY
PATTERNS AND ASSESSMENT (review)

Yu.V. Kruglov

All-Russian Research Institute for Agricultural Microbiology, Federal Agency of Scientific Organizations,
3, sh. Podbel’skogo, St. Petersburg, 196608 Russia,
e-mail yuvkruglov@yandex.ru

Received August 6, 2015

Study of the taxonomic and functional diversity of soil microorganisms association is of  great theoretical significance for understanding the structure of the soil microbial community, the nature of the interaction of individual species of microorganisms belonging to this community, as well as their participation in the processes of soil formation and circulation of substances. This article summarises a brief history of ideas about the functioning of soil microbial complex, providing transformation and mineralization of organic matter in soil formation processes. Soil as habitat for microorganisms is heterogeneous that defines microzonal character of the distribution and activity of microorganisms that live in it. The structure of the association of microorganisms and its physiological profiles vary in time and space (D.G. Zvyagintsev, 1987). This defines methodological difficulties and the significant variability of the results of the evaluation of soil microflora by various authors. This review discusses the methodological approaches in determining the physiological diversity of soil microorganisms association. Traditional methods of elective culture media in over a century allowed to reveal numerous physiological groups of microorganisms and developed an idea about their role in the cycle of matter, processes of soil formation and plant nutrition. However, such work is almost not given anything new in principle, both in environmental studies, as well as in agronomy over the past 20 years. At the end of the 1990s a method of analysis of the carbon source utilization profiles (SUP) of natural microorganisms association by BIOLOG system used previously only in medical and general microbiology was proposed  to study the physiological diversity for the test strain (J.L. Garland, A.L. Mills, 1991). This approach was further developed by H. Insam (1997), M.V. Gorlenko and P.A. Kozhevin (2005) and others. A number of modifications of this method (Eso-Plates, ECOLOGY and others) characterized by a set of organic substrates, which, as the authors suggest, is most likely present in natural environments were worked out. Instrumentation of ECOLOG (M.V. Gorlenko, P.A. Kozhevin, 2005) allows to determine not only the range of organic substrates used by microorganisms, but also to quantify the consumption of each substrate. For the processing and interpretation of a significant amount of information obtained in the course of the analysis of soil samples there are an apparatus of multidimensional mathematical statistics, cluster analysis, rank distribution, and ecological indexes of Shannon and Pielou. SUP method (multisubstrat test) possesses a high performance, good resolution (104), a satisfactory reproducibility and is a high-tech and effective tool to assess the physiological diversity. The article deals with the positive and negative aspects of the method. SUP reflects to some extent the potential of aerobic soil microorganisms using low molecular weight organic compounds in the catabolism. However, because of availability of several modifications, as well as some technical problem it is difficult to compare the results obtained by different authors, there is no unified SUP analysis protocol that is required for the comparative environmental studies and the establishment of relevant national and international databases. Thus, analysis of the carbon source utilization profiles (SUP) in BIOLOG system now is under development and testing, and with the accumulation of experimental data and critical analysis, it has good prospects in soil ecology, in research of the relationship between microorganisms and plants, and in assessment of the impact of anthropogenic factors.

Кeywords: association, physiological groups, physiological diversity of bacteria, range of consumed substrates, multisubstrate test, system BIOLOG, ECOLOG, EcoPlates.

 

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