Does host diversity beget microbiome diversity? Effects of zooplankton diversity and composition on environmental and host-associated microbes

Abstract

Microbiomes alter host health and are shaped by transmission within and among host taxa. Microbes can alter host communities, yet whether the diversity of hosts reciprocally shapes microbial communities remains poorly resolved. Diverse host communities may promote microbiome diversity through elevated cross-species microbial spillover or reduce it by diluting conspecific transmission. Here, we manipulated the composition and diversity of pond zooplankton communities to test how host diversity and density alter host-associated and environmental microbiomes. Host diversity had opposing effects on microbiome alpha diversity for different zooplankton host species, increasing microbiome diversity in calanoid copepods while reducing it in Daphnia, with no effect on environmental microbes. Host diversity amplified cross-species microbial spillover for subordinate competitors (calanoid copepods) and diluted conspecific transmission for the dominant competitor (Daphnia). These contrasting responses reflected shifts in indicator microbes associated with each host taxon. Increasing host turnover generated higher microbiome turnover, demonstrating that microbiome assembly depends on host community composition. Our results indicate that contact with both conspecifics and heterospecifics alters animal microbiomes, and that host diversity can either promote the spillover or dilute the transmission of microbes in different zooplankton with potential effects on host health and ecosystems.