Imaging microorganisms and pollutants at the microscale

Fluorescence microscopy is a powerful tool for studying microorganisms in their natural environment without cultivation. The nucleic acids inside microbial cells can be stained with fluorescing dyes which specifically bind to targeted organisms. This technique can stain pollutant degrading microorganisms in natural samples for their identification, localisation and enumeration. Microbial degradation can break down and detoxify polycyclic aromatic hydrocarbons (PAHs). PAHs are carcinogenic pollutants present in organic liquids like crude oil or tar and also in numerous soils or sediments in the United Kingdom impacted by industrial activity. An interesting property of PAHs is their autofluorescence under ultraviolet light which means that they can be visualised with fluorescence microscopy. Fluorescence microscopy may thus be suitable for the simultaneous microscale imaging of PAH-rich patches in soils and sediments and their associated microbial communities. To this end criteria will be derived for the identification of PAH-rich patches in soil or sediment by fluorescence microscopy. Once the unambiguous distinction between the fluorescence of PAH-rich patches and other natural soil or sediment constituents has been achieved, a suitable methodology will be derived to stain and image the associated microorganisms using fluorescence in situ hybridisation (FISH), conventional epifluorescence microscopy and confocal laser scanning microscopy. The derived methodology could be used to study in detail and at the microscale the co-localisation of microorganisms and pollutants such as PAHs in the natural environment. A microscale investigation may shed light on the exact mechanisms controlling the microbial breakdown and attenuation of PAHs in polluted soils and sediments. Such insight is of fundamental importance for the design of bioremediation technologies and for the risk assessment for impacted ecosystems.