Abstract
Oomycetes are a ubiquitous protistan lineage including devastating crop parasites. Although their ecology in agrosystems has been widely studied, little is known of their distribution in natural and semi-natural ecosystems and how they respond to edaphic and environmental factors. We provide here a baseline of the diversity and distribution of soil oomycetes, classified by lifestyles (biotrophy, hemibiotrophy and saprotrophy), at the landscape scale in temperate grassland and forest. From 600 soil samples, we obtained 1148 operational taxonomy units representing ~ 20 million Illumina reads (region V4, 18S rRNA gene). We found a majority of hemibiotrophic plant pathogens, which are parasites spending part of their life cycle as saprotrophs after the death of the host. Overall both grassland and forest constitute an important reservoir of plant pathogens. Distance-based RDA models identified soil type and mineral soil C/N ratio as the most influential factors in shaping oomycete communities in grassland and forest. Edaphic conditions and human-induced management intensification in forest triggered opposite responses in the relative abundances of obligate biotrophs and hemibiotrophs, suggesting different ecological requirements of these two lifestyles.
Highlights
Oomycetes are protists ubiquitous and widespread in terrestrial (Geisen et al 2015; Lara and Belbahri 2011; Singer et al 2016), freshwater (Duffy et al 2015) and marine ecosystems (Garvetto et al 2018)
We further investigated the effects of these selected environmental parameters on each of the oomycete lifestyles, by comparing their relative abundances in the two ecosystems
Based on the high sequencing depth (Fig. S2), we could detect detailed responses of each lifestyle to the ecological and edaphic factors involved in shaping oomycete distribution
Summary
Oomycetes are protists (phylum Stramenopiles or Heterokonta) ubiquitous and widespread in terrestrial (Geisen et al 2015; Lara and Belbahri 2011; Singer et al 2016), freshwater (Duffy et al 2015) and marine ecosystems (Garvetto et al 2018). Phytophthora, the “plant destroyer”, is responsible for the widespread rapid tree decline (Hayden et al 2013) and for damages to important crops like soybean, tomato, grapevine and tobacco (Lebeda et al 2008). Because of their negative economic impact, oomycetes are well-studied in silico and as many as 67 species have their genome available in public databases They affect forest ecosystems worldwide (Packer and Clay 2000) and are common pathogens in grasslands (Foley and Deacon 1985), their occurrence in natural habitats and their ecological role in maintaining plant species diversity (Bever et al 2015) is still poorly explored compared to agroecosystems
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