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J Ind Microbiol Biotechnol (2010) 37:12891297 DOI 10.1007/s10295-010-0866-7
REVIEW
Development of soil microbiology methods: from respirometry to molecular approaches
Jil Gabriel
Received: 25 June 2010 / Accepted: 26 August 2010 Society for Industrial Microbiology 2010
Abstract This review deals with techniques and methods used in the study of the function and development of micro-organisms occurring in soil with emphasis on the contributions of Czech Academician Ivan Mlek and his coworkers or fellows (Jil Macura, Frantinek Kunc) to the development of basic techniques used in soil microbiology. Early studies, including batch cultivation and respirometric techniques, as well as later developments of percolation and continuous-Xow methods of cultivation of soil microorganisms are discussed. Recent developments in the application of analytical chemistry (HPLC or GC) and of molecular biological techniques to ecological questions that have revolutionized concepts in soil microbiology and microbial ecology are also brieXy mentioned, including denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), phospholipid fatty acid analysis (PLFA) and others. The shift of soil microbiology from the study of individual microorganisms to entire microbial communities, including nonculturable species, is brieXy discussed.
Keywords Soil microbiology Continuous cultivation Microbial growth Enzymes Biomarkers
Introduction
Soil microbiology is a discipline that describes the numbers, activity, and interactions of microorganisms present in
soil, and how they are aVected by their environment or human activities. Understanding the function of soil ecosystems in relation to ever changing soil conditions is a key to understanding the basic mechanisms of soil productivity. Transformation of organic soil matter, and mineralization and immobilization of soil nutrients, are considered to be two of the most important factors inXuencing soil fertility. ScientiWc studies have focused attention on a variety of ways to enhance either soil fertility or plant nutrition [52, 168]. The presence of microorganisms in soil was observed in nineteenth century. Among others, G.G. Gustavson at the VIIIth Congress of Russian scientists and physicians in St. Petersburg said, that the soil is heavily colonized by invisible and inaudible inhabitants eagerly working to the beneWt of agriculture [58]. Stoklasa in 1911 [150] was one of the Wrst scientists who expressed the importance of considering soil as a complex and dynamic entirety. Vinogradsky in his lecture at the International Society of Soil Microbiology in Rome in...