Dataset: Microbial taxa (amplicon sequence variant or ASV) statistical analyses for two seagrass genotypes from wasting disease mesocosm experiments at Bodega Marine Laboratory in July-Sept of 2015

We used a substitutive design to test the effects of eelgrass (Zostera marina) genotypic identity (eight genotypes), diversity (monocultures of 1 genotype vs. polycultures of 4 genotypes), and temperature (ambient or + 3.2° C) on the prevalence and intensity of Labyrinthula over eight weeks in an array of flow-through 120-L mesocosms at the Bodega Marine Laboratory in Bodega Bay, CA. In July 2015, we created ten unique polyculture combinations of four genotypes (4 genotypes per experimental pot) randomly drawn from a pool of eight genotypes; all eight genotypes were also grown in monoculture (1 genotype per pot). We filled pots (8.9 x 8.9 cm) with coarsely sieved sediment collected from Bodega Harbor, and planted 4 shoots per pot, matching the lower range of average field densities reported for Bodega Harbor (Ha and Williams 2018) to allow for growth during the experiment. Plants were originally collected in Bodega Harbor, CA in 2012, confirmed to be unique genotypes using 11 DNA microsatellite loci developed specifically for Z. marina (Abbott et al. 2018), and propagated in separate flow through mesocosms at BML.

At the end of the experiment (10 weeks), we collected and preserved the top half of the focal leaf in individual plastic bags sealed with 30 ml of silica (Flower Drying Art Silica Gel; Activa) for subsequent DNA extraction and quantitative PCR to estimate Labyrinthula zosterae cells as a proxy for infection (Bergmann et al. 2011, Bockelmann et al. 2013, Groner et al. 2021).

We collected 2 cm of the focal leaf from directly below the midpoint and stored the tissue at -80˚C for later microbiome analyses to assess whether particular leaf microbial taxa changed in association with Labyrinthula presence on the focal leaf. From these samples, we selected a subset of 84 leaf microbial samples evenly distributed across temperature treatments and across genotypes in monoculture. We did not assess leaf microbiomes in genotypic polycultures. We extracted the surface community of these leaf segments with a modified protocol for the DNeasy Powersoil Kit (Qiagen) and sequenced the V4-V5 region of the 16S rRNA gene on an Illumina MiSeq to analyze differences in the leaf microbiome between treatments and among genotypes. Specifically, to extract the surface community of leaf segments we used a modified protocol for the DNeasy Powersoil Kit (Qiagen) where we first vortexed leaf samples in 500ul of MilliQ water, and then extracted the supernate of each sample. Extraction success was verified via Qubit dsDNA HS assay kit. We PCR-amplified the V4-V5 region of the 16S rRNA gene and then sequenced pooled barcoded fragments on an Illumina MiSeq through the Integrated Microbiome Resource at Dalhousie University (Halifax, NS; Comeau et al. 2017).

Life Science Identifiers (LSID) for taxonomic names:
Zostera marina (urn:lsid:marinespecies.org:taxname:145795)
Labyrinthula zosterae (urn:lsid:marinespecies.org:taxname:395093)
Labyrinthula (urn:lsid:marinespecies.org:taxname:119090)