Microscopic characterisation of filamentous microbes: towards fully automated morphological quantification through image analysis

Mycelial morphology is a critically important process property in industrial fermentations of filamentous microorganisms, as particular phenotypes are associated with maximum productivity. The morphological form that develops in a given process results from the combination of various environmental factors, together with the genotype of the organism itself. The design of systems capable of rapidly and accurately characterising morphology within a given process represents a significant challenge to biotechnologists, as the complex phenotypes that are manifested are often not easily quantified. Over the last two decades, the proliferation of high-power personal computers and high-resolution digital cameras has enabled scientists to apply digital image analysis to this challenge. Although several fully automated systems have been designed for this purpose, manual analysis of images is still commonplace, together with qualitative, subjective descriptions of morphologies. This review describes the complex morphologies that can develop in fermentations of filamentous microbes and the application of microscopy and image analysis techniques to the quantification of such structures.