Development of soil microbiology methods: from respirometry to molecular approaches

Abstract

This review deals with techniques and methods used in the study of the function and development of microorganisms occurring in soil with emphasis on the contributions of Czech Academician Ivan Málek and his coworkers or fellows (Jiří Macura, František 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-flow 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 briefly 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 briefly discussed.

Exploring the diversity of Acinetobacter populations in river water with genus-specific primers and probes

“…Culture-independent molecular methods, such as cloning and sequencing of rRNA genes, denaturing gradient gel electrophoresis (DGGE), fluorescent in situ hybridization (FISH) and recently, high-throughput pyrosequencing analysis, are increasingly and widely used in environmental microbiology (Gabriel, 2010;Muhling et al, 2008). Fluorescent in situ hybridization using a genus-specific rRNA-targeted oligonucleotide probe has been used for the analysis of Acinetobacter populations in activated sludge (Wagner et al, 1994).…”

Ivan Málek [1909-1994]: a tribute

“…During my student days at the University of Nottingham and my first academic post, at Bedford College (University of London), I was exposed to many aspects of soil microbiology. The paper by Jirí Gabriel10 speaks to Málek's very evident influence on this field—ecosystems are open as opposed to closed, ipso facto continuous flow apparatus is likely to be a very promising laboratory analogue in the study of microbial ecology. These investigations were spear headed by Jirí Macura and one of the inspirations for the cultivation equipment came from the soil percolation unit designed about 15 years earlier by Leslie Audus my head of department at Bedford College.…”

Effects of Soil Quality on the Microbial Community Structure of Poorly Evolved Mediterranean Soils

“…The analysis by DGGE allows to discriminate, through electrophoresis using polyacrylamide gels, differences of one nucleotide between amplicons, which is very useful in diversity studies, so this is still a useful technique to explore community patterns when multiple microbial groups are considered, as in our study [26]. Many studies into microbial soil diversity focus on a single taxonomic kingdom, either Bacteria, Archaea or Fungi [24,27,28], all of which may play different ecological roles. It is much less common, however, to find studies where a more integrative analysis, as we performed here, has been carried out: Here, the diversity patterns of all these microbial groups have been jointly studied by comparing them in soils showing different production potentials along a degradation gradient.…”