The microbiome of an amphibious plant shifts dramatically across the host life cycle

Abstract Interactions between plants and their associated microbiomes are thought to enhance the capacity of the host plant to overcome extreme conditions, yet the significance of microbially mediated stress tolerance in most plant species and ecosystems remains unknown. For the first time, we examined the microbiome of the amphibious plant Eryngium castrense (Apiaceae) inhabiting Mediterranean climate ephemeral wetlands in California. Eryngium castrense has the capacity to survive as both an aquatic and terrestrial plant, thereby living under contrasting extremes of water stress. Whether plant-associated microbial communities are also affected by such changes, and what ecological role they play while inhabiting amphibious plants, is an underexplored topic of plant-microbial interactions in natural and artificial systems. We amplified and sequenced 16S rRNA genes from bacteria and archaea to examine microbial communities associated with roots and shoots over the plants’ full life cycle. We observed that the microbiome changes from the aquatic stage to the terrestrial stage, and that roots and shoots represent distinct habitats within the plant host ecosystem. When compared with soil and water column samples, plant samples retained a unique, differentiated core microbiome. Taxa located in the roots during the terrestrial stage were linked with potential functions such as nitrogen acquisition, sulfur assimilation, and resistance to heavy metals, whereas aquatic roots held potential phythoparasites. Overall, our results provide new insights into symbiotic relationships in plants subject to stress-related to water saturation and deficiency.