DNA-Metabarcoding of Belowground Fungal Communities in Bare-Root Forest Nurseries: Focus on Different Tree Species

Abstract

The production of tree seedlings in forest nurseries and their use in the replanting of clear-cut forest sites is a common practice in the temperate and boreal forests of Europe. Although conifers dominate on replanted sites, in recent years, deciduous tree species have received more attention due to their often-higher resilience to abiotic and biotic stress factors. The aim of the present study was to assess the belowground fungal communities of bare-root cultivated seedlings of Alnus glutinosa, Betula pendula, Pinus sylvestris, Picea abies and Quercus robur in order to gain a better understanding of the associated fungi and oomycetes, and their potential effects on the seedling performance in forest nurseries and after outplanting. The study sites were at the seven largest bare-root forest nurseries in Lithuania. The sampling included the roots and adjacent soil of 2–3 year old healthy-looking seedlings. Following the isolation of the DNA from the individual root and soil samples, these were amplified using ITS rRNA as a marker, and subjected to high-throughput PacBio sequencing. The results showed the presence of 161,302 high-quality sequences, representing 2003 fungal and oomycete taxa. The most common fungi were Malassezia restricta (6.7% of all of the high-quality sequences), Wilcoxina mikolae (5.0%), Pustularia sp. 3993_4 (4.6%), and Fusarium oxysporum (3.5%). The most common oomycetes were Pythium ultimum var. ultimum (0.6%), Pythium heterothallicum (0.3%), Pythium spiculum (0.3%), and Pythium sylvaticum (0.2%). The coniferous tree species (P. abies and P. sylvestris) generally showed a higher richness of fungal taxa and a rather distinct fungal community composition compared to the deciduous tree species (A. glutinosa, B. pendula, and Q. robur). The results demonstrated that the seedling roots and the rhizosphere soil in forest nurseries support a high richness of fungal taxa. The seedling roots were primarily inhabited by saprotrophic and mycorrhizal fungi, while fungal pathogens and oomycetes were less abundant, showing that the cultivation practices used in forest nurseries secured both the production of high-quality planting stock and disease control.

Effect of the Aqueous Extract of Neem Leaves (Azadirachta indica A. Juss.) on the Control of Costalimaita ferruginea (Fabricius, 1801)

“…The commercial expansion of the wood market reflected in the growth of the seedling market and, consequently, in enterprises suitable for the production and management of seedlings, characterized as forest nurseries [5].…”

The Functional Biogeography of eDNA Metacommunities in the Post-Fire Landscape of the Angeles National Forest

“…Some notable potential pathogens from the results were Pythium, Fusarium, Botryosphaeriaceae, Microbotrytomycetes, Xanthamonadales, and Hyphomonas. Pythium and Fusarium are common fungi in bare-root forest nurseries [67]. What was remarkable about the presence of these possible pathogens in the Gold Creek results was the way that the putative pathogens may be controlled by antibiotic-producers that were found in high abundance on the various Trails.…”

New-Generation Sequencing Technology in Diagnosis of Fungal Plant Pathogens: A Dream Comes True?

“…In fact, a gathering body of evidence is demonstrating the introduction and spread of invasive Phytophthora species in California wildlands as the result of restoration schemes involving planted native species raised in contaminated nurseries [ 81 ]. Based on this conclusion, different recent studies focus on the identification of Phytophthora species in forest nurseries plantings using metabarcoding to implement stringent biosecurity practices when raising stocks of native plants destined for planting onto ecologically sensitive sites [ 82 , 83 ].…”

“…Abad et al [ 90 ] reported that correct identification of Phytophthora to species levels in environmental DNA is possible targeting the full ITS rDNA via the miniaturized MinION portable device. Different studies on environmental fungal communities, that also includes Oomycetes , have been also performed with PacBio Sequencing [ 83 , 91 ], but no long-read sequencing method has been found to be applied specifically to Phytophthora genus.…”