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Marine multicellular organisms host a diverse collection of bacteria, archaea, microbial eukaryotes, and viruses that form their microbiome. Such host-associated microbes can significantly influence the host’s physiological capacities; however, the identity and functional role(s) of key members of the microbiome (“core microbiome”) in most marine hosts coexisting in natural settings remain obscure. Also unclear is how dynamic interactions between hosts and the immense standing pool of microbial genetic variation will affect marine ecosystems’ capacity to adjust to environmental changes. Here, we argue that significantly advancing our understanding of how host-associated microbes shape marine hosts’ plastic and adaptive responses to environmental change requires (i) recognizing that individual host–microbe systems do not exist in an ecological or evolutionary vacuum and (ii) expanding the field toward long-term, multidisciplinary research on entire communities of hosts and microbes. Natural experiments, such as time-calibrated geological events associated with well-characterized environmental gradients, provide unique ecological and evolutionary contexts to address this challenge. We focus here particularly on mutualistic interactions between hosts and microbes, but note that many of the same lessons and approaches would apply to other types of interactions. 

Migration is an integral feature of modern mysticete whale ecology, and the demands of migration may have played a key role in shaping mysticete evolutionary history. Constraining when migration became established and assessing how it has changed through time may yield valuable insight into the evolution of mysticete whales and the oceans in which they lived. However, there are currently few data which directly assess prehistoric mysticete migrations. Here we show that calcite δ¹⁸O profiles of two species of modern whale barnacles (coronulids) accurately reflect the known migration routes of their host whales. We then analyze well-preserved fossil coronulids from three different locations along the eastern Pacific coast, finding that δ¹⁸O profiles from these fossils exhibit trends and ranges similar to modern specimens. Our results demonstrate that migration is an ancient behavior within the humpback and gray whale lineages and that multiple Pleistocene populations were undertaking migrations of an extent similar to those of the present day.

 

To examine N-isotope ratios (¹⁵N/¹⁴N) in tissues and shell organic matrix of bivalves as a proxy for natural and anthropogenic nutrient fluxes in coastal environments,Pinctada imbricata,Isognomon alatus, andBrachidontes exustusbivalves were live-collected and analyzed from eight sites in Bocas del Toro, Panama. Sites represent a variety of coastal environments, including more urbanized, uninhabited, riverine, and oceanic sites. Growth under differing environmental conditions is confirmed byδ¹⁸O values, with open ocean Escudo de Veraguas shells yielding the highest averageδ¹⁸O (−1.0‰) value and freshwater endmember Rio Guarumo the lowest (−1.7‰). At all sites there is no single dominant source of organic matter contributing to bivalveδ¹⁵N andδ¹³C values. Bivalveδ¹⁵N andδ¹³C values likely represent a mixture of mangrove and seagrass N and C, although terrestrial sources cannot be ruled out. Despite hydrographic differences between end-members, we see minimalδ¹⁵N andδ¹³C difference between bivalves from the river-influenced Rio Guarumo site and those from the oceanic Escudo de Veraguas site, with no evidence for N from open-ocean phytoplankton in the latter. Populated sites yield relative¹⁵N enrichments suggestive of anthropogenic nutrient input, but lowδ¹⁵N values overall make this interpretation equivocal. Lastly,δ¹⁵N values of tissue and shell organic matrix correlate significantly for pterioideansP. imbricataandI. alatus. Thus for these species, N isotope studies of historical and fossil shells should provide records of ecology of past environments.