Comparing eDNA metabarcoding with morphological analyses: Fungal species richness and community composition of differently managed stages along a forest conversion of Norway spruce towards European beech in Germany

Heine, Peggy; Hausen, Jonas; Ottermanns, Richard; Roß-Nickoll, Martina

doi:10.1016/j.foreco.2021.119429

Cited by 6 publications

(3 citation statements)

References 81 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It is noticeable, however, that compared with this study the few studies that have compared the alpha diversity achieved by HTS approaches versus morphological studies have got a very small overlapping of taxa between approaches (Porter et al, 2008, Heine et al, 2021. Furthermore, the findings of this study align with previous assessments of the sensitivity of HTS workflows that employ mock community approaches (Pauvert et al, 2019), demonstrating consistent results in terms of the percentage of recovered sequences.…”

Section: Bioinformatic Pipelines Comparisonssupporting

confidence: 82%

Assessing fungal endophyte diversity: a comparative study of three automated metabarcoding pipelines

Molina,

Rajchenberg,

Aime

et al. 2023

Darwiniana, nueva serie

View full text Add to dashboard Cite

High-throughput sequencing approaches have become frequent in the study of endophyte communities allowing the cumulative description of fungal diversity in the last decade. However, they brought new challenges to researchers in terms of programming and developing of informatics tools. Currently, there is no consensus concerning the appropriate bioinformatics to process such sequence data. The aim of this study was to compare the performance of three pipelines of two cost-free toolkits designed to be friendly to non-programmer users, and specifically developed for fungal data: AMPtk and PIPITS. The sapwood-inhabiting fungal assemblages of two Nothofagus species from the Patagonian Forests were assessed through metabarcoding of the internal transcribed spacer (ITS) and compared with an extant sequence dataset obtained from culture prospection in the same study sites and trees. The AMPtk toolkit has performed better concerning community description in terms of precision of taxa clustering, mainly due to the DADA2 algorithm; PIPITS evidenced a higher sensitivity in detecting taxa known to be present, hence it is potentially useful for future specific taxa detection surveys. Because of a current lack of information of the reference databases, both bioinformatic toolkits performed poorly as to taxonomy assignment. It is imperative to continue studying these ecosystems to, concomitantly, improve databases and the explanatory potential of the new technologies.

show abstract

Section: Bioinformatic Pipelines Comparisonssupporting

confidence: 82%

Assessing fungal endophyte diversity: a comparative study of three automated metabarcoding pipelines

Molina,

Rajchenberg,

Aime

et al. 2023

Darwiniana, nueva serie

View full text Add to dashboard Cite

show abstract

“…In conclusion, the high specialization of HTS technologies and the statistic management of data should not be a bottleneck for their adoption for diagnosis in plant pathology, providing that expertise in each field will be positively shared among researchers in a holistic approach [ 185 , 186 ]. We show here that NGS methodologies are now a reality for diagnosis and fungal identification when several and unknown pathogens are involved, such as for complex diseases or where environmental surveillance is needed.…”

Section: Discussionmentioning

confidence: 99%

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

Aragona

Haegi

Valente

et al. 2022

JoF

View full text Add to dashboard Cite

The fast and continued progress of high-throughput sequencing (HTS) and the drastic reduction of its costs have boosted new and unpredictable developments in the field of plant pathology. The cost of whole-genome sequencing, which, until few years ago, was prohibitive for many projects, is now so affordable that a new branch, phylogenomics, is being developed. Fungal taxonomy is being deeply influenced by genome comparison, too. It is now easier to discover new genes as potential targets for an accurate diagnosis of new or emerging pathogens, notably those of quarantine concern. Similarly, with the development of metabarcoding and metagenomics techniques, it is now possible to unravel complex diseases or answer crucial questions, such as “What’s in my soil?”, to a good approximation, including fungi, bacteria, nematodes, etc. The new technologies allow to redraw the approach for disease control strategies considering the pathogens within their environment and deciphering the complex interactions between microorganisms and the cultivated crops. This kind of analysis usually generates big data that need sophisticated bioinformatic tools (machine learning, artificial intelligence) for their management. Herein, examples of the use of new technologies for research in fungal diversity and diagnosis of some fungal pathogens are reported.

show abstract

“…Fruiting body (mushroom) collections and sequencing of soil samples have been dominant methods for documenting the community (Mohatt et al, 2008;Trusty and Cripps, 2011). Fruiting body surveys can be poor proxies of the ECMF communities below ground (Gardes and Bruns, 1996;Durall et al, 2006;Lalli et al, 2015), though recent studies in fungal ecology (in particular in wood inhabiting fungi) demonstrate that fruiting body surveys can be comparable or complimentary to highthroughput sequencing and metabarcoding (Ovaskainen et al, 2013;Frøslev et al, 2019;Saine et al, 2020;Heine et al, 2021). ECMF composition can also follow successional patterns and change with tree age/life stage (Glassman et al, 2017b;Koizumi et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Characterizing the Ectomycorrhizal Fungal Community of Whitebark Pine in Interior British Columbia: Mature Trees, Natural Regeneration and Planted Seedlings

Southam¹,

Stafl²,

Guichon³

et al. 2022

Front. For. Glob. Change

View full text Add to dashboard Cite

Whitebark pine (Pinus albicaulis Engelm.; WBP) is an endangered subalpine tree species and requires associations with ectomycorrhizal fungi (ECMF) for survival and growth. Despite this obligate dependence, there are gaps in the identification of ECMF that associate with WBP. In addition, ECMF rarely feature in assessments of recovery actions and little is known about the relationship between ECMF and the insects and pathogens affecting WBP. We used next-generation sequencing to characterize ECMF occurring in soil and mycorrhizal root tip samples from naturally occurring mature WBP trees and seedlings as well as planted WBP seedlings in the Columbia Mountains of Interior British Columbia, Canada. ECMF data was paired with data on tree age, tree health and soil conditions. Thirty-three species and twenty-one genera of ECMF were identified with medium or high confidence from mycorrhizal root tip samples. Major groups were: generalist ascomycetes [Cenococcum, Meliniomyces (=Hyaloscypha)], Atheliales (Piloderma, Amphinema, Tylospora), non-ascomycetous generalists (e.g., Amphinema), associates of high-elevation conifers (species of Cortinarius, Russula) and Suilloids (Suillus, Rhizopogon). Differences in WBP ECMF with other, drier and southerly regions that have been studied previously, were consistent with a distinct forest type and an endemism hypothesis. Soil at the planting site and planted seedlings hosted a reduced ECMF community or were non-ectomycorrhizal, which can be explained by site factors and is expected to affect seedling survival. ECMF composition on mature trees was correlated with tree health, which may have implications for WBPs resistance to pathogens and signals that ECMF are affected by the decline of their host. Understanding the ecology of WBP ECMF and their relationship with tree performance is essential for WBP recovery efforts.

show abstract

Comparing eDNA metabarcoding with morphological analyses: Fungal species richness and community composition of differently managed stages along a forest conversion of Norway spruce towards European beech in Germany

Cited by 6 publications

References 81 publications

Assessing fungal endophyte diversity: a comparative study of three automated metabarcoding pipelines

Assessing fungal endophyte diversity: a comparative study of three automated metabarcoding pipelines

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

Characterizing the Ectomycorrhizal Fungal Community of Whitebark Pine in Interior British Columbia: Mature Trees, Natural Regeneration and Planted Seedlings

Contact Info

Product

Resources

About