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.&nbsp..., , # Data from: Compartment and seasonal stage structure endophytic microbiomes in an amphibious vernal pool plant Paper: JA Mandussí Montiel-Molina, Jason P Sexton, J Michael Beman, A Carolin Frank. Compartment and seasonal stage structure endophytic microbiomes in an amphibious vernal pool plant. *Ecological microbiomes.* Dataset DOI: [10.5061/dryad.8sf7m0d45](https://doi.org/10.5061/dryad.8sf7m0d45) ## Description of the data and file structure: Sequence data in this project was processed with Qiime2, following the next workflow: [link](https://docs.qiime2.org/2024.10/tutorials/moving-pictures/) Files list: * Metadata_16s_Mercedendophytes_-_96samples.tsv * paired-end-demultiplexed_plantmicrobiome.zip Code/software: The Qiime files (.qza) were imported into R, via the package Qiime2R, to be analyzed using phyloseq package and to produce figures.  , ,