Host genetics and geography influence microbiome composition in the sponge Ircinia campana

1.Marine spongesare host to large, diverse communities of microorganisms. These microbiomesare distinct among spongespecies and from seawater bacterial communities, indicating a key role of host identity in shaping its resident microbial community. However, the factors governing intraspecific microbiomevariability are underexplored, and may shed light on the evolutionary and ecological relationshipsbetween host and microbiome. 2.Here, we examined the influence of genetic variation and geographic location on the composition of the Irciniacampana microbiome. 3.We developed new microsatellite markers to genotype I. campana from two locations in the Florida Keys, USA, and characterised their microbiomesusing V4 16S rRNA amplicon sequencing. 4.We show that microbial community composition and diversity is influenced by host genotype, with more genetically similar spongeshosting more similar microbial communities. We also found that although I. campana was not genetically differentiated between sites, microbiomecomposition differed by location. 5.Our results demonstrate that both host genetics and geography influence the composition of the sponge microbiome. Host genotypic influence on microbiomecomposition may be due to stable vertical transmission of the microbial community from parent to offspring, making microbiomesmore similar by descent. Alternatively, spongegenotypic variation may reflect variation in functional traits that influence the acquisition of environmental microbes. This study reveals drivers of microbiomevariation within and among locations, and shows the importance of intraspecific variability in mediating eco‐ evolutionary dynamicsof host‐associated microbiomes.