Assessment of functional and structural changes of soil fungal and oomycete communities in holm oak declined dehesas through metabarcoding analysis

Francisco J Ruiz Gómez,Andrea Vannini,Wolfgang Oβwald,Rafael M Navarro-Cerrillo,Carmen Morales-Rodríguez,Alejandro Pérez-De-Luque

doi:10.1038/s41598-019-41804-y

Abstract

Forest decline is nowadays a major challenge for ecosystem sustainability. Dehesas, which consists of savannah-like mediterranean ecosystems, are threatened by the holm oak decline in the south-west of Iberian Peninsula. Phytophthora cinnamomi is considered the main agent of holm oak root rot, but little is known about the relationship between diversity of soilborne microbial community and the decline syndrome of holm oak. It would be hypothesized that the changes in the structure and functionality of the soil microbiome might influence tree health status through changes in richness and diversity of beneficial organisms such as mycorrhizal species, or fungal plant pathogens such as Fusarium spp. or Alternaria spp. Total DNA of soil samples from declined oak dehesas was extracted and analyzed through metabarcoding techniques, to evaluate the specific composition and diversity of the fungal and oomycete communities and their relationship with the disease symptoms. The fungal community included a wide range of pathogens and abundance of ectomycorrhizal key taxa related with low defoliation degree. Phytophthora cinnamomi and Pythium spiculum did not appear among the most abundant oomycetes, nor were they related directly to defoliation levels. Moreover, a particular taxon belonging to the genus Trichoderma was strongly correlated with the scarcity of pathogenic Phytophthora spp. The diversity and composition of fungal and oomycete communities were related to the severity of the decline symptoms. The metabarcoding study of microbiome represents a powerful tool to develop biocontrol strategies for the management of the holm oak root rot.

Highlights

Alien-invasive species and global change are nowadays major threats for ecosystems sustainability around the world
After bioinformatic treatment of the raw data, 1789 fungal operational taxonomic units (OTUs) (Operational Taxonomic Units) and 178 oomycete OTUs were confidently assigned to the genus or species level
Our results revealed high levels of diversity in the fungal community and medium to low diversity of oomycetes, the presence of key taxa influencing holm oak health status and oomycete pathogenic abundance, and the dominance of plant pathogens and saprotrophs in the analysed soils

Summary

Introduction

Alien-invasive species and global change are nowadays major threats for ecosystems sustainability around the world. Among the most relevant diseases caused on European woody species by Phytophthora spp., root rot has been identified since the 1990’s affecting oaks[7]. Ilex in central Italy) and cork oak (Quercus suber L.) due to root rot were identified since the early 1980’s, affecting dehesa rangelands in Spain and Portugal, and wide forest areas in France and Italy[9,10,11]. Dehesa is a traditional land use in areas excluded from intensive agriculture, covering large extension of territory mostly characterized by a typical Mediterranean climate and soils usually shallow, acidic and deficient in nutrients[13] This agroecosystem is mainly composed by open woodlands of Quercus ilex and Q. suber, with an annual grassland understory, presenting canopy covers ranging from 5 to 60%14. The implication of other Phytophthora spp. in the decline of Q. ilex and other Quercus spp. in the Iberian Peninsula is recognized[28,29,30]

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