Data from: Compartment and seasonal stage structure endophytic microbiomes in an amphibious vernal pool plant

Amphibious plants inhabit environments that undergo seasonal transitions
between inundation and desiccation, yet little is known about how these
transitions shape their microbiomes. We examined bacterial endophytic
communities during such transitions in the amphibious plant Eryngium
castrense (Apiaceae) native to California's ephemeral wetlands
(vernal pools). Using 16S rRNA sequencing, we examined endophytic
communities in roots and shoots across aquatic and terrestrial
morphological stages, and compared these endophytic communities with
surrounding soil and water microbiomes. Community composition differed
most strongly between plant compartments (roots vs. shoots), with
additional but weaker differentiation between aquatic and terrestrial
stages.  Beta diversity analyses showed plant compartment as the
strongest variable in community differentiation, followed by morphological
state. Phylogenetically weighted distances explained more variation than
abundance-based distances.  In addition, endophytic communities
were clearly distinct from soil and water microbiomes within the vernal
pool ecosystem. Our results highlight the dynamic nature of microbial
communities in response to the seasonal transitions of their amphibious
plant hosts, suggesting a complex interplay in ephemeral wetlands that
warrants further exploration.