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A simple surface-enhanced Raman spectroscopy (SERS) microflow cell was developed to investigate distributions of scytonemin pigment within cyanobacteria, from samples of rock collected from an arctic desert that contained endolithic cyanobacteria. The assay, which has future potential use in a variety of applications, including astrobiology and analysis of microorganisms in remote environments, involved studying SERS spectra of bacteria from within geological samples. By using a dispersed colloidal substrate in the microfluidic device, surface enhancement of the order > 10(5) was obtained for the determination of the pigment in the microorganisms when compared to the native Raman spectra. The SERS assay, which had a nM sensitivity for scytonemin, showed that the concentration of pigment was highest in samples that had experienced the highest stress environments, as a result of high doses of UV irradiation.