Collecting symbiotic bacteria and fungi
2011
Herrmann, Laetitia | Lesueur, Didier | Giamperi, F
Soil is the habitat of an array of microorganisms in all three taxonomic domains. Because many species of soil microorganisms are still unknown or non-described, the assessment of microbial diversity, especially the symbiotic bacteria and fungi is not feasible undertaking. In designing field sampling to collect symbiotic microorganisms, the challenge is to select a subset of the soil biota that adequately reflects the anticipated taxonomic spectrum, and which at the same time includes all the symbiotic microorganisms considered important. Designing a successful, practical sampling scheme is an art. In this chapter, we tried to provide a guideline to make it correctly ensuring the representative of all the indigenous symbiotic bacteria and fungi naturally present in the soils of sampled sites. As the majority of the microorganisms, including the symbiotic ones, are found in the upper 20cm of the soil profile, the main investigations have to be done on topsoil even if it doesn't mean that microorganisms are not naturally present in deeper layers. Once the samples have been harvested, it is important to be cautious and store them nicely for further microbial analysis. Otherwise the risk to lose them or to get only contaminants after streaking is pretty high. This chapter describes some protocols and methodologies with practical and simple recommendations easily repeatable by people who have interest to make such laboratory work. We tried to raise the main steps ensuring the success of the establishment of the collection of symbiotic bacteria and fungi coming from all around the world. (Résumé d'auteur)
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