Biotic and spatial effects structure the foliar microbiome of Douglas-fir (Pseudotsuga menziesii) across the Pacific Northwest, USA

Lilah Gonen, Posy E. Busby, F. Andrew Jones and Jared M. LeBoldus, Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, Jared M. LeBoldus, Department of Forest Engineering, Resources & Management, Oregon State University, Corvallis, OR

Background/Question/Methods
Host genetic and environmental drivers of fungal and bacterial community composition have been well documented in plant foliage using amplicon metabarcoding, yet little is understood about the factors structuring co-occurring oomycetes. Oomycetes are fungus-like eukaryotes in the kingdom Straminipila, and include among their ranks major plant pathogens. Many oomycetes, both endemic and exotic, have already been described in the temperate coastal forests of the Pacific Northwest, USA (PNW), making it a fitting location to examine their community dynamics alongside other microorganisms. We used fungal (ITS2) and oomycete (rps10) metabarcoding to characterize both domains of organisms in the foliage of coast Douglas-fir (Pseudotsuga menziesii var. menziesii), a dominant conifer in the PNW. Needles were collected from Douglas-fir trees as part of a long-term common garden experiment, whereby trees from naturally-occurring provenances (seed source regions) were reciprocally planted in corresponding common gardens throughout the tree’s endemic range in the PNW. We aimed to disentangle the effects of host genetic lineage and location on associated communities of fungi and oomycetes, as well as to investigate the ecological interactions between the two groups of organisms.
Results/Conclusions
We found evidence for both host genetic and spatial effects on fungal community composition. Fungal communities were structured most heavily among common gardens, and to a small extent among half-sibling tree families within common gardens. Large-scale seed source region had no impact on fungal community composition. Oomycete communities lacked diversity and were dominated by a single pervasive Phytophthora OTU (nearly 60% of oomycete reads) whose presence was not explained by host genetics or location. This oomycete was inversely correlated with overall fungal rarefied richness as well as with several individual fungi, including Nothophaeocryptopus gaeumannii, an important foliar pathogen of Douglas-fir. The oomycete’s putative negative relationship to fungi suggests that the two groups of organisms may occupy similar functional niches within needle tissue and could be competitors. Our results demonstrate that while oomycetes may be less diverse than fungi within conifer needles, their ecological roles within trees and across landscapes are far from being understood.