The Interaction Between the Nematode Caenorhabditis elegans and Its Coexisting Fungal Microbiome Member Barnettozyma californica

The nematode Caenorhabditis elegans is known to feed on and interact with bacteria in its environment and has become a model organism for microbiome studies. However, whether and how C. elegans interacts with co-occurring fungi remains largely unknown, despite the presence of many fungal species in its natural habitat. Here, we isolate the yeast Barnettozyma californica from a mesocosm experiment with C. elegans and characterise its genome and interaction with the nematode. We find that, like bacterial microbiota, B. californica can colonise the intestine of C. elegans and can serve as a sole, albeit poor, food source for adult nematodes. Yet, when present together with Escherichia coli OP50, the fungus can lead to higher population growth and altered foraging behaviour, suggesting a context-dependent benefit. This effect varied between different natural C. elegans strains, suggesting a genomic basis for the nematode's interaction with B. californica. On the fungal side, we could not identify any obvious candidate genes for its interaction with C. elegans and/or E. coli OP50, despite obtaining a fully assembled and annotated genome of the isolated B. californica strain. Overall, our results provide an intriguing example of the complexity and multi-level relationship between naturally interacting fungi, bacteria and animals.