Fluorescence in situ hybridization (FISH)

Microscopy picture of biofilm

Microorganisms are very small! In the microscopy picture above each tiny circle is a microbial cell, with a size of around one micrometre (0.001 milometers). It is a picture of a microbial biofilm with many species living together, where each colour represents a different population. The big cyan agglomerate in the lower left corner is one of my favourite bacteria: Anammox bacteria.

So, how was this picture made? To prepare the samples, I used a method known as fluorescence in situ hybridization (FISH), which can be used to detect specific microbial populations. All microorganisms have large RNA molecules known as ribosomes, and the sequences of these ribosomes differ between microbial species. In FISH these ribosomes are targeted using specific DNA probes, which have attached a dye (a fluorophore). The FISH probe will only bind to the population we want to target (for example anammox bacteria). Then using a confocal laser microscope or an epifluorescence microscope, we illuminate the sample, and the cells with bound FISH probes will become fluorescent.

Another interesting thing that can be done with FISH is to study the physical location of microbial populations, and to identify the populations they co-exist with. One way to achieve this is with cryosections, where the biofilm sample is frozen using liquid nitrogen, and then using a cryotome, ultra-thin slices are made.

Microscopy picture of biofilm
FISH cryosectioning. From Suarez et al 2015 (https://doi.org/10.1093/femsec/fiv124)

Years ago, I wondered if anammox bacteria living in biofilms could be eaten by other microscopic predators. This was thought to be unlikely as anammox bacteria live in the deeper layers of biofilms, which would likely protect them against predation. Using FISH we targeted both anammox bacteria and protozoa living in the biofilm. We could show that protozoa could go deep in the biofilm, even in the layers where anammox bacteria live. We also observed anammox bacteria inside the food vacuoles of protozoa, showing that these protozoa were eating anammox bacteria.

Microscopy picture of biofilm
FISH picture of amoeba grazing anammox bacteria in a biofilm. Green: Anammox bacteria. Red: Protozoa

You can read more predation of anammox bacteria here:

Carolina Suarez, Frank Persson, Malte Hermansson. Predation of nitritation–anammox biofilms used for nitrogen removal from wastewater. FEMS Microbiology Ecology, Volume 91, Issue 11, November 2015, fiv124, https://doi.org/10.1093/femsec/fiv124.

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