Studying the Bacterial Diversity of the Soil by Culture-Independent Approaches

Abstract

Studying bacterial diversity in soil is very complex because of the enormous macro-variety of soil habitats that exist, in addition to environmental conditions such as temperature, pH, water availability, salt concentration, anaerobic versus anoxic, etc. The micro-ecological aspects of a soil particle or aggregate, in which the O₂ concentration changes from almost complete saturation at the outer border to anoxic in the middle, affect the development of micro-organisms. Cultivation-based approaches therefore need a huge variety of incubation conditions, and there is a widespread opinion that only a small fraction of the bacterial population present in various ecosystems and niches is cultivable. Therefore, with the support of the molecular tools that became available during the last decennium, culture-independent approaches have attracted more and more attention in comparison with culture-dependent methods. However, molecular data alone are not sufficient to understand functionalities; we need to know Who is out there?, What are they doing? and What are they doing with whom?, so as to address the functionalities that are of increasing interest. It is now realized that mixed cultures and natural consortia may be the keys to our better understanding of microbial population ecology. Culture-independent studies have yielded an overwhelming amount of data concerning individual bacteria, specific bacterial taxa, and complex bacterial communities, and they have clearly improved our understanding of microbial ecology. This chapter reviews the methods for microscopic examination and for molecular approaches that explore the overall bacterial community or that reveal the functionality of the community.