Culture Based and Direct Methods

Bacterial and fungal abundances have traditionally been estimated as colony forming units (CFU) using the plate count technique (Baath 1989). For example, Oliveira and Pampulha (2006) found that the total number of CFU of bacteria, fungi and actino-mycetes was significantly reduced after heavy metal contamination. In this study, fungi and actinomycetes were less sensitive than culturable heterotrophic bacteria or even nonsymbiotic nitrogen fixers. However, this is now a very controversial method as far as fungi are concerned, since the plate count technique mainly determines the number of spores, and actively growing hyphae have little chance of forming a colony. It is also a doubtful method in the case of bacteria, especially when nutrient-enriched media are used, since only a fraction of the total bacterial population will be able to grow on such media (Ritz 2007; Nichols 2007).

Direct counts or biovolume estimations using conversion factors can also be used to directly estimate microbial biomass. Different soil preparation methods and staining techniques in combination with epifluorescence microscopy and automated image analysis can be used routinely in monitoring programs (Bloem and Breure 2003), as they clearly discriminate between polluted and unpolluted soils (Ellis et al. 2002).

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