Specific host-algae relationship, yet flexible bacterial microbiome, in diatom-bearing foraminifera

Whether the adaptive strategies of marine mixotrophs, organisms that combine heterotrophic and autotrophic nutrition, in response to global change are rooted in their symbiotic relationships is debated, especially for larger benthic foraminifera. Despite their importance in the ecosystem, there are controversial findings regarding the specificity of their algal endobionts, preventing a deeper understanding of their adaptive strategies. Using single-cell metabarcoding on 243 diatom-bearing foraminifera specimens from Indonesia, we found one highly dominant diatom strain in each foraminiferal host species bearing at least 90% of the reads in a majority of host species, whereas the bacterial community was very flexible, with only 25% of the variation explained by water depth, substrate type, location, and host species. Our results suggest that the adaptive strategy of the foraminiferal holobiont rather lies within its bacterial endobiome. Its dynamism likely facilitates the adaptive potential of foraminifera, supporting their proliferation across different environmental settings.