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Unique bacterial assembly, composition, and interactions in a parasitic plant and its host

Citation

Fitzpatrick, Connor; Schneider, Adam (2020), Unique bacterial assembly, composition, and interactions in a parasitic plant and its host, Dryad, Dataset, https://doi.org/10.5061/dryad.7wm37pvnk

Abstract

How plant-associated microbiota are shaped by, and potentially contribute to the unique ecology and heterotrophic life history of parasitic plants is relatively unknown. Here, we investigate the leaf and root bacterial communities associated with the root holoparasite Orobanche hederae and its host plant Hedera spp. We sequenced the V4 region of the 16S rRNA gene from DNA extracted from leaf and root samples of naturally growing populations of Orobanche and infected and uninfected Hedera. Root bacteria inhabiting Orobanche were less diverse, had fewer co-associations, and displayed increased compositional similarity to leaf bacteria relative to Hedera. Overall, Orobanche bacteria exhibited significant congruency with Hedera root bacteria across sites, but not the surrounding soil. Infection had localized and systemic effects on Hedera bacteria, which included effects on the abundance of individual taxa and root network properties. Collectively, our results indicate that the parasitic plant microbiome is derived but distinct from host plant microbiota, exhibits increased homogenization between shoot and root tissues, and displays far fewer co-associations among individual bacterial members. Host plant infection is accompanied by modest changes of associated microbiota at both local and systemic scales compared with uninfected individuals. The results are a first step towards extending the growing insight into the assembly and function of the plant microbiome to include the ecologically unique but often overlooked guild of heterotrophic plants

Usage Notes

PPM_Analysis_Code_Dryad.R: R script used to process Illumina sequencing reads and perform all data formatting, statistical analyses, and figure generation. 

PPM_bac.tre: Phylogenetic tree of all bacterial ASVs generated from the R package 'DADA2'. We used the software PASTA to generate the bacterial tree. 

RDP_taxa.rds: R object that contains the taxonomy associated with each bacterial ASV generated from the R package 'DADA2'. We used the RDP classifer as implemented in DADA2 to assign taxonomy using the RDP training set 16. 

sample_yields.csv: DNA concentration of the original DNA extractions and final amplicon libraries. 

spe_table.rds: an ASV table which ennumerates the number of reads associated with each ASV in each sample. This data table was generated from the R package 'DADA2' and was used for all downstream analyses. 

Funding

NSF, Award: DEB-1601504