2.3. Confocal laser scanning microscopy (CLSM)
The labelled samples were analysed with a Leica TCS SP confocal
laser-scanning microscope (Leica Microsystem, Heidelberg,
Germany) equipped with argon and helium/neon laser. Photomultipliers
parameters were adjusted to achieve the maximum signal
from each fluorochrome, but at the same time trying to keep the
noise signal generated by the soil particles and by the algal cells
as low as possible. Up to three FISH probes were applied in parallel
on the samples and signals were measured simultaneously.
The ranges of wavelength set to detect the emission signal of the
fluorochromes labelling the FISH probes were the following: Cy3
at 560–610 nm, Cy5 at 660–700 nm, 6-FAM and FITC at 470–530.
Stacks of 0.5 m slices were scanned through the 30 m thick
section and their maximum projections were converted into 2D
pictures. The 3D-reconstructions of 2D stacks and the different section
levels to characterize the size and the position of the bacteria
colonies were performed with the software AMIRA v. 5.2 (Visage
Imaging GmbH). No image artifacts were present or needed to be
corrected.