Development of a labeling system for microorganisms based on antimicrobial peptides

Complex biogeochemical processes are essential in various subsurface ecosystems (like in soils and rock formations), and are relevant for e.g. effective bioleaching of metals from various ores. For an improved mechanistic understanding of biogeochemical processes a non-invasive detection method of present microorganisms in a given geological sample is crucial. Ideally, microorganisms from all kingdoms should be determined in a single step (and may be later differentiated from DNA or cell degradation). Furthermore, microbial responses to changes of the physical or chemical conditions of the system such as flow regime, pH, and nutrient concentrations could be addressed non-invasively.
Our strategy for in-situ identification of microorganism in geological samples is to use labeled antimicrobial peptides (AMPs) as selectively binding agents. In the nuclear medical sciences, this strategy is successfully applied for the identification and visualization of bacterial infections in humans [1]. We aim at tagging the AMPs first with fluorescent dyes, in a later step with the radionuclide ¹⁸F for imaging with positron emission tomography (PET).
For our study, AMPs are selected based on their ability to bind to the cells of the tested bacterial strains in sub-lethal concentrations while their sorption to matrix compounds is minimal. We show that AMPs readily interact with microorganisms commonly found in soils such as Pseudomonas fluorescence and Lysinibacillus sphaericus. We aim at labeling the AMPs by means of established, commercial crosslinkers.
In combination with our GeoPET method [2-4] ¹⁸F-radiolabeled AMPs were an extremely useful agent for the in-situ visualization of microorganisms also in opaque geological environments. Radiolabeled AMPs could be used for the visualization of growth and dispersal of microbial communities in such environments.