The experimental foundation of the research conducted in BioMatrix is a bacterial model community composed of four species originally isolated from soil: the Gram-negative Stenotrophomonas rhizophila and Xanthomonas retroflexus, and the Gram-positive Microbacterium oxydans and Paenibacillus amylolyticus. When combined, these four strains interact to produce more biofilm biomass, have higher tolerance to chemical inhibitors and predation, and gain new functionalities. BioMatrix explores the impact of the biofilm matrix components for facilitating these community intrinsic properties.
Initially, we characterized the biofilm matrix of single species and the community, using (i) specific fluorescent stains/compounds combined with microscopic and (ii) proteomic analysis of the matrix proteome. We have identified biofilm matrix structures uniquely present in either individual species or in the community, confirming the hypothesis that bacterial interactions shape biofilm matrix structure and composition. Based on this, and analysis of the bacterial genomes, we have identified genes potentially encoding matrix components. We are currently genetically engineering the strains, enabling the study of expression of these genes in mono vs multispecies biofilms, and over time. Moreover, we will delete selected genes from the genomes to assess the functional consequences imposed on the bacteria by lacking specific matrix components. To date, to such mutants have been constructed, one lacking the ability to express structural matrix proteins, amyloid fibres, and one that does not produce flagella.
For assessments of bacterial activities when forming biofilms individually, with partners and when lacking matrix components, several community intrinsic properties have been identified. We have shown that expression of some enzymes is strongly induced in the multispecies biofilm setting, including xylanase, catalysing degradation of the hemicellulose component xylan to the simple sugar xylose. We have also show that, in contrast to individual species, the community stimulates plant root development and moves on surfaces (also referred to as swarming). These and other community intrinsic properties will be assessed upon replacement of type strains with their matrix mutant counterparts.
We have developed methodology for 3D printing of artificial leaves, optimised for studies of biofilms in settings mimicking their natural environments and compatible with confocal microscopy.
