The nematode Caenorhabditis elegans can benefit from its coexisting fungal microbiome member Barnettozyma californica

Abstract

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 characterize its genome and interaction with the nematode. We find that B. californica is ingested by C. elegans and can serve as a sole, albeit poor, food source. Yet, when present together with Escherichia coli OP50, the fungus can lead to higher population growth and altered foraging behavior, suggesting that this fungi-bacteria mixture provides a better food source than bacteria alone. This effect varied between different natural C. elegans strains, suggesting a genomic basis for the nematodes interaction with B. californica. The fully assembled and annotated genome of the isolated B. californica strain does not indicate any obvious candidate genes for its interaction with C. elegans and/or E. coli OP50. Overall, our results provide an intriguing example of the complexity and multi-level relationship between naturally interacting fungi, bacteria, and animals. Graphical AbstractBarnettozyma californica is a member of the fungal microbiome of the model nematode Caenorhabditis elegans and can serve as food for worms. When combined with E. coli, this fungus can increase population growth and reduce foraging behaviour dependent on C. elegans genotype, revealing a genetic influence on host-fungus-bacterium interactions. O_FIG O_LINKSMALLFIG WIDTH=189 HEIGHT=200 SRC="FIGDIR/small/638710v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@184b29eorg.highwire.dtl.DTLVardef@eabb71org.highwire.dtl.DTLVardef@b810ceorg.highwire.dtl.DTLVardef@5745c7_HPS_FORMAT_FIGEXP M_FIG C_FIG