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Chapter 12 : Methods To Study Consortia and Mixed Cultures
Category: Genomics and Bioinformatics; Environmental Microbiology
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Nowadays many experimental approaches exist that one could not even imagine in Koch’s days. An alternative approach that focuses on dealing with undefined populations of microbes in the laboratory is the scope of this chapter. The approach consists of four steps. The first step is the definition of an ecological niche. In the second step, the complement of the niche is engineered in a laboratory bioreactor, which is to become an enrichment culture. In the third step, the culture is characterized in molecular detail. Finally, the detailed information is used to investigate the importance of the described processes and microbes in nature. In this approach, the target organism remains in continuous culture under chemo-spatio-temporal conditions that define its natural niche, in an open system that allows competition. With this approach and appropriate primers it is possible to specifically quantify a single organism or a clade of microorganisms. For example, the abundance of Crenarchaeota in soils can be shown by real-time PCR of ammonium monooxygenase genes from archaea and bacteria. Epifluorescence microscopy is of great value to visualize relative abundances determined with cloning or denaturing gradient gel electrophoresis (DGGE). The study of microorganisms in undefined mixed cultures could be applied more generally and has great potential for environmental microbiology.
Periodic system of a number of one-carbon microorganisms.
Experimental setups for enrichment in continuous culture. (A) Chemostat, (B) chemostat with an internal settler, (C) chemostat with a membrane unit, and (D) sequencing batch reactor.
Percoll purification of anammox bacterium K. stuttgartiensis from an enrichment culture. (A) FISH micrograph of an anammox cluster (light gray) from an enrichment culture with other microorganisms. (B) Anammox cell suspension on Percoll gradient before centrifugation. (C) “Anammox band” that forms after centrifugation. (D) FISH micrograph of Percoll-separated K. stuttgartiensis cells.
Phylogenetic tree showing cultivated and uncultivated anammox bacteria. Black, described species; dark gray with a dot, marine clone; light gray, reactor clone.