Dataset Information

A metabarcoding protocol targeting two DNA regions to analyze root-associated fungal communities in ferns and lycophytes.

ABSTRACT:

Premise

Detailed studies of the fungi associated with lycophytes and ferns provide crucial insights into the early evolution of land plants. However, most investigations to date have assessed fern-fungus interactions based only on visual root inspection. In the present research, we establish and evaluate a metabarcoding protocol to analyze the fungal communities associated with fern and lycophyte roots.

Methods

We used two primer pairs focused on the ITS rRNA region to screen the general fungal communities, and the 18S rRNA to target Glomeromycota fungi (i.e., arbuscular mycorrhizal fungi). To test these approaches, we collected and processed roots from 12 phylogenetically distant fern and lycophyte species.

Results

We found marked compositional differences between the ITS and 18S data sets. While the ITS data set demonstrated the dominance of orders Glomerales (phylum Glomeromycota), Pleosporales, and Helotiales (both in phylum Ascomycota), the 18S data set revealed the greatest diversity of Glomeromycota. Non-metric multidimensional scaling (NMDS) ordination suggested an important geographical effect in sample similarities.

Discussion

The ITS-based approach is a reliable and effective method to analyze the fungal communities associated with fern and lycophyte roots. The 18S approach is more appropriate for studies focused on the detailed screening of arbuscular mycorrhizal fungi.

SUBMITTER: Guillen-Otero T

PROVIDER: S-EPMC10278937 | biostudies-literature | 2023 May-Jun

REPOSITORIES: biostudies-literature

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Publications

A metabarcoding protocol targeting two DNA regions to analyze root-associated fungal communities in ferns and lycophytes.

Guillen-Otero Thais T Lee Soon-Jae SJ Chen Cheng-Wei CW Szoevenyi Peter P Kessler Michael M

Applications in plant sciences 20230501 3

<h4>Premise</h4>Detailed studies of the fungi associated with lycophytes and ferns provide crucial insights into the early evolution of land plants. However, most investigations to date have assessed fern-fungus interactions based only on visual root inspection. In the present research, we establish and evaluate a metabarcoding protocol to analyze the fungal communities associated with fern and lycophyte roots.<h4>Methods</h4>We used two primer pairs focused on the ITS rRNA region to screen the ...[more]

PMID: 37342167

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Project description: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 Alnusglutinosa,Betula pendula,Pinus sylvestris, Piceaabies and Quercusrobur 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 Malasseziarestricta (6.7% of all of the high-quality sequences), Wilcoxinamikolae (5.0%), Pustularia sp. 3993_4 (4.6%), and Fusariumoxysporum (3.5%). The most common oomycetes were Pythiumultimum var. ultimum (0.6%), Pythiumheterothallicum (0.3%), Pythium spiculum (0.3%), and Pythiumsylvaticum (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.

Dataset Information

A metabarcoding protocol targeting two DNA regions to analyze root-associated fungal communities in ferns and lycophytes.

Premise

Methods

Results

Discussion

Publications

A metabarcoding protocol targeting two DNA regions to analyze root-associated fungal communities in ferns and lycophytes.

Similar Datasets

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