In a galaxy not so far, far away, bacteria from the eastern redback salamander’s (Plethodon cinereus) microbiome inhibit Batrachochytrium dendrobatidis (Bd) by producing anti-fungal metabolites. Amphibians across the globe are at risk due to the fungal wildlife disease Bd, and chitinases are one group of bacterially-produced metabolites that likely play a key role in Bd-inhibition. Chitinases target the chitin polymer present in Bd fungal cell walls resulting in hydrolysis of its glycosidic bonds. Of interest now, is determining the diversity of chitinases produced by local bacteria and exploring how they may vary over space. For this study, we explored chitinase genomic diversity and function in the common soil bacteria Stenotrophomonas rhizophila which has been shown to protect both plants and amphibians from fungal diseases. To understand this microbe-pathogen interaction amongst different strains of S. rhizophila isolated at various locations in the New York City area, we developed primers to isolate the chitinase gene. Subsequently, we ligated, transformed, and expressed chitinase genes from distinct isolates of S. rhizophila and grew the transformants on solid media with ampicillin to induce expression with IPTG identifying successful clones. We sent the plasmids out for sequencing and analyzed the motifs of the chitinase genes.
Results/Conclusions
We found significant variation among the sequences of S. rhizophila chitinase genes. Despite this variation, preliminary analyses indicate that each strain codes for a protein with the chitin-binding domain, polycystic kidney disease domain, fibronectin-like domain, and catalytic domain. These results support that the chitinase genes of S. rhizophila strains, like others in the Stenotrophomonas genus, have conserved motifs despite slight variation in antifungal ability. Given that antifungal function is more important for conservation than sequence, we believe some strains may be better suited for conservation applications, such as genetically engineered microbiomes and probiotics. In the future, functional challenge assays will reveal if antifungal function is maximized by the unique properties of the sequences themselves. By delving into the genomic and chemical mechanisms of disease protection, we hope to add new solutions to the conservation of vulnerable taxa, such as amphibians, from impending extinction.