Another

innovative technique mimicking natural conditions, this time used for the microcolony cultivation of uncultivated soil bacteria, is the soil substrate membrane system (Ferrari et al., 2005, 2008), which includes a polycarbonate membrane support and soil extract as a substrate. Although this system allowed the microcultivation of novel bacterial strains, the bacteria remained part of a mixed community on the membrane. A recent development of selleckchem the method has enabled the detection of live microcolonies on the membrane using viability staining, and the subsequent micromanipulation of such colonies for their isolation (Ferrari & Gillings, 2009). The study of bacteria with an obligate intracellular lifestyle presents a particular challenge and it can be difficult to determine and reproduce the environmental conditions required for metabolic Selleck CYC202 activity. For example, initial work investigating the metabolism of Coxiella burnetii used neutral pH buffers and concluded that there was negligible activity (Ormsbee & Peacock, 1964). When acidic buffers were

used, metabolism was markedly enhanced (Hackstadt & Williams, 1981). Further refinements of this approach including the use of a citrate buffer, provision of complex nutrients and high (140 mM) chloride have enabled metabolic activity to be maintained for over 24 h (Omsland et al., 2008), enabling the investigation of the physiology of this important species. Many of the methods described above use an open-ended approach with the aim of cultivating all bacteria present in a sample. As a result, they have led to the cultivation of numerous fastidious bacteria. However, the phylogenetic targeting of specific bacterial strains of interest requires alternative approaches. Advances in molecular biology have enabled the detection and sorting of specific target bacteria with a view to their selective enrichment or physical isolation.

Oligonucleotide probes can be designed to target phylotypes with no known cultivable representatives. Using methods such as FISH or catalysed reporter Calpain deposition (CARD)-FISH for added sensitivity, target-specific probes can detect cells of previously ‘unculturable’ taxa among mixed populations (Amann et al., 1995, 2001; Ferrari et al., 2006; Vartoukian et al., 2009), enabling the visualization of their cellular morphology. A limitation of these methods is that the cells detected within a sample are no longer viable after cell permeabilization and fixation procedures, and may not therefore be subsequently cultured in isolation. The colony hybridization method, on the other hand, is undertaken on membrane transfers from plate cultures that remain viable (Salama et al., 1993). Consequently, hybridization detections on membranes may be used to locate matched microcolonies within mixed cultures, from where they may be isolated. This method has been used in recent work (Vartoukian et al.