Despite the frequent presence of fungi in microbial communities, fungi-bacteria interactions are understudied and often ignored in microbiome studies. Investigating the cross-domain interactions between fungi and bacteria may reveal exciting new ecological process and novel bioactive metabolites.
When investigating these interactions its important that we identify community players to the strain level. We know that classifying microbes to species alone obscures crucial genetic differences between strains. Novel methodologies allow strain level identification, revealing finer scale dynamics between community members. My work integrates two fundamental questions in microbial ecology: how does strain variation impact ecological processes and what cross-domain roles do bacteria and fungi play in these processes?
Honey bee larval health
Honey bee populations are declining due to combinatory stressors (nutrition, pathogens, and pesticides). Fungal pathogens are the number one cause of insect disease and are predicted to increase in prevalence with climate change. In honey bees, late instar larvae harbor opportunistic fungal pathogens 81% of the time. When subjected to multiple stressors, these fungal pathogens, such as chalkbrood (Ascophaera apis) and stonebrood (Aspergillus flavus), can wipe out whole generations of brood.
To protect against fungal pathogens many insects have developed symbiotic relationships with bacteria that ward off fungal infection. These symbiotic bacteria can defend their host directly (by producing antifungals) or indirectly (by competing for nutrition or modulating the host environment to bar pathogen establishment).
In honey bees I discovered that a member of the larval microbiome, Bombella apis, can directly protect bee brood (larvae and pupae) from fungal infection with A. flavus. Over 66% of pupae exposed to A. flavus never develop infections when B. apis is present. Assays in the lab have revealed that an antifungal is responsible for this dramatic protection. Currently we are working towards identifying the antifungal B. apis produces.