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Biologically compatible quantum dot (QD) nanoparticles are hybrid inorganic-organic materials with increasing
popularity as fluorescent probes for studying biological specimens. QDs have several advantageous optical features
compared to fluorescent dyes and they are electron-dense, allowing for correlated fluorescence and electron microscopic
imaging. Despite these features, widespread use of QDs as biological probes has generally been limited by the complex
chemistry required for their synthesis and the conjugation. In this work, we show that easily prepared quantum dot (QD)
probes provide excellent contrast for fluorescent confocal and environmental scanning electron microscopy (ESEM)
analysis of pure microbial cultures and microbial communities. Two conjugation strategies were employed in order to
specifically target the QDs to bacterial cell surfaces. The first was biotinylation of the bacteria followed by labeling with
commercially available QDs incorporating the high-affinity partner for biotin (QD-streptavidin). Second, we designed a
novel QD probe for Gram negative bacteria: QD-polymyxin B (PMB), which binds to lipopolysaccharide (LPS) in the
Gram negative cell wall. Pure cultures of Gram positive and Gram negative strains were used to illustrate that QDs
impart electron density and irradiation stability to the cells, and so no other preparation apart from QD labeling is
required. The techniques were then extended to a set of recently characterized microbial communities of perennial cold
springs in the Canadian High Arctic, which live in close association with unusual sulfur crystals. Using correlated
confocal and and ESEM, we were able to image these organisms in living samples and illustrate their relationship to the
minerals.
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