Detection of microorganisms in undisturbed soil by combining fluorescence in situ hybridization (FISH) and micropedological methods

• Published in: Soil biology & biochemistry 2008-06, Vol.40 (6), p.1284-1293
• Main Authors: Eickhorst, Thilo, Tippkötter, Rolf
• Format: Article
• Language: English
• Subjects: Agronomy. Soil science and plant productions; Biochemistry and biology; Biological and medical sciences; Chemical, physicochemical, biochemical and biological properties; Fish; Fluorescence in situ hybridization; Fluorescence microscopy; Fundamental and applied biological sciences. Psychology; methodology; microbial ecology; microbiology; Microorganisms; Micropedology; microscopy; oligonucleotide probes; Physics, chemistry, biochemistry and biology of agricultural and forest soils; provenance; ribosomal RNA; soil bacteria; soil microorganisms; Soil molecular microbiology; soil nutrients; Soil science; soil structure; soil water; spatial distribution; species diversity; Undisturbed soil
• ISSN: 0038-0717; 1879-3428
• DOI: 10.1016/j.soilbio.2007.06.019

In contrast to conventional approaches molecular microbiology leads to a deeper understanding of the biodiversity of soil microorganisms. Nevertheless, there is a lack of knowledge regarding the spatial distribution of microbiota in the complex soil matrix and the interaction between the soil structure and microorganisms. DNA analytical methods such as fluorescence in situ hybridization (FISH) are being utilized to improve the characterization of microbial biocoenosis. Micropedological procedures which preserve the soil structure by embedding it with resin, in combination with FISH, allow the localization and identification of soil microorganism diversity in relation to the specific properties of their microhabitats. In this study, FISH was used prior to resin embedding in undisturbed soil samples of four different soils. The polished sections provided visualization of the bound probes as well as the undisturbed soil matrix via fluorescence microscopy. Furthermore, cell counts of active bacteria, locating of hot spots and their relationship to microsites rich in nutrients and water, such as humus or clay minerals, are now easy to perform. This will lead to a better understanding of how soil structure can affect soil microorganisms and vice versa. Derived from the use of 16S rRNA targeted oligonucleotide probes, EUB338 and NON338, the cell counts of FISH-detected bacteria were in the same order of magnitude in the undisturbed and the suspended soil samples. Counterstaining with DAPI showed varying detection rates caused by differing activities of the soil microorganisms.