Bacterial assemblages in field-grown Arabidopsis thaliana from southeast Michigan

We surveyed bacterial colonists across the tissues of an annual plant throughout its life cycle to better understand spatial and temporal variation in natural plant bacterial assemblages. We planted surface-sterilized seeds of North American Arabidopsis thaliana accessions from a near isogenic haplogroup (HPG1) at two sites in southwest Michigan in two consecutive years. These accessions germinate in the fall, overwinter as small rosettes, flower in the spring, and senesce in the early summer. We harvested roots and rosette leaves throughout vegetative growth and also stems, cauline leaves, flowers, and siliques as they became available during flowering and senescence. To enrich for endophytes in the sampling, bacteria were washed from the surface of plant tissues by repeated vortexing in surfactant buffer. Soil at each site was also sampled at each timepoint during the second year of study for comparison with plant tissues. The V5, V6, and V7 regions of the 16S rRNA gene were amplified with primers 799F and 1193R in triplicate PCR and sequenced on the Illumina MiSeq (250 PE) with MiSeq V2 Reagent Kits. Study Authors: Matthew Perisin, Kathleen Beilsmith, & Joy Bergelson