What Quality Suffices in Nanopore Metabarcoding? Reconsidering Methodology and Ectomycorrhizae in Decaying Fagus sylvatica Bark as a Case-Study DOI Open Access
Glen Dierickx, Lowie Tondeleir, Pieter Asselman

et al.

Published: Aug. 29, 2024

Nanopore raw read accuracy has improved to over 99%, making it a potential tool for metabarcoding. For broad adoption, guidelines on quality filtering are needed ensure reliable taxonomic unit recovery. This study aims provide those fungal metabarcoding context and apply them case-study of ectomycorrhizae in decaying bark Fagus sylvatica.We introduce the eNano pipeline test two standard approaches: (1) reference-based mapping leveraging UNITE’s species hypothesis system (SH-approach) (2) constructing 98% OTUs (OTU-approach). We evaluate these approaches using mock natural community. Our results demonstrate that both effective with data. When reference database, we recommend strict criteria rather than Phred-based filtering. OTUs, reads at ≥Q25 is recommended. reveals decay gradient primary determinant community composition, specific mycorrhizal fungi colonize bark. Complementing our root tip morphotypification, identify Laccaria amethystina Tomentella sublilacina as key saplings logs. These findings sequencing can valuable ecological insights support its broader use continues improve.

Language: Английский

Post-fire Quercus mycorrhizal associations are dominated by Russulaceae, Thelephoraceae, and Laccaria in the southern Appalachian Mountains DOI Creative Commons
Karen W. Hughes, Jennifer Franklin, Jennifer A. Schweitzer

et al.

Mycological Progress, Journal Year: 2025, Volume and Issue: 24(1)

Published: Feb. 19, 2025

Language: Английский

Citations

1
What Quality Suffices for Nanopore Metabarcoding? Reconsidering Methodology and Ectomycorrhizae in Decaying Fagus sylvatica Bark as Case Study DOI Creative Commons
Glen Dierickx, Lowie Tondeleir, Pieter Asselman

et al.

Journal of Fungi, Journal Year: 2024, Volume and Issue: 10(10), P. 708 - 708

Published: Oct. 10, 2024

Nanopore raw read accuracy has improved to over 99%, making it a potential tool for metabarcoding. For broad adoption, guidelines on quality filtering are needed ensure reliable taxonomic unit recovery. This study aims provide those fungal metabarcoding context and apply them case of ectomycorrhizae in the decaying bark

Language: Английский

Citations

1
Eschentriebsterben eindämmen durch Mikrobiom-Optimierung? DOI Creative Commons
Gitta Jutta Langer, Ewald Langer, Andreas Ulrich

et al.

BIOspektrum, Journal Year: 2024, Volume and Issue: 30(6), P. 634 - 636

Published: Oct. 1, 2024

Abstract ‘FraxForFuture’ was an interdisciplinary project to study the devastating effects of ash dieback on host, characterize associated microbiome, and develop non-chemical biological control strategies combat pathogen, Hymenoscyphus fraxineus . Bacteria fungi as well fungal secondary metabolites were identified, which have antagonistic effect against pathogen or can be used for microbiome optimisation. Results, conclusions, outlook are presented.

Language: Английский

Citations

0
What Quality Suffices in Nanopore Metabarcoding? Reconsidering Methodology and Ectomycorrhizae in Decaying Fagus sylvatica Bark as a Case-Study DOI Open Access
Glen Dierickx, Lowie Tondeleir, Pieter Asselman

et al.

Published: Aug. 29, 2024

Nanopore raw read accuracy has improved to over 99%, making it a potential tool for metabarcoding. For broad adoption, guidelines on quality filtering are needed ensure reliable taxonomic unit recovery. This study aims provide those fungal metabarcoding context and apply them case-study of ectomycorrhizae in decaying bark Fagus sylvatica.We introduce the eNano pipeline test two standard approaches: (1) reference-based mapping leveraging UNITE’s species hypothesis system (SH-approach) (2) constructing 98% OTUs (OTU-approach). We evaluate these approaches using mock natural community. Our results demonstrate that both effective with data. When reference database, we recommend strict criteria rather than Phred-based filtering. OTUs, reads at ≥Q25 is recommended. reveals decay gradient primary determinant community composition, specific mycorrhizal fungi colonize bark. Complementing our root tip morphotypification, identify Laccaria amethystina Tomentella sublilacina as key saplings logs. These findings sequencing can valuable ecological insights support its broader use continues improve.

Language: Английский

Citations

0