Resurrecting host–microbiome interactions: combining resurrection ecology and microbiome transplants to test temporal local adaptation

Sam Paplauskas , Dagmar Frisch 

Host-associated microbiomes can influence fitness, respond rapidly to environmental change, and potentially contribute to host adaptation. Yet, determining whether host–microbiome associations evolve adaptively over ecological timescales remains challenging because historical host genotypes and their associated microbial communities are rarely available for experimental comparison. Resurrection ecology offers a means of recovering historical host genotypes from dormant propagules, while microbiome transplantation provides an experimental approach for testing the effects of microbial communities on host performance. Combining these approaches could enable direct tests of temporal local adaptation in host–microbiome associations. Freshwater Daphnia provide a promising model because their dormant eggs can persist in lake sediments, allowing historical host genotypes to be resurrected. However, the microbiota associated with dormant eggs may originate from multiple sources, including ancestral hosts, lake water, and surrounding sediment, complicating the recovery of historically associated microbial communities. We outline a framework combining sediment archives, host resurrection, microbiome characterisation, and reciprocal transplantation experiments to test whether historical and contemporary hosts perform better with microbiomes from their respective time periods. We discuss the conceptual predictions, methodological challenges, and experimental controls required to distinguish temporal local adaptation from microbial environmental effects, host-genotype specificity, and changes in community composition. This framework could extend resurrection ecology beyond host evolution to experimentally investigate the historical evolution of host–microbiome interactions.