Fungal Community Profiling and Pathogen Detection in Conifer Seed Lots: Benchmarking Oxford Nanopore DNA Metabarcoding Against Conventional Methods
Bibliographic record
Abstract
Seedborne fungal pathogens, either native or exotic, spread through seed trade and pose serious risks to reforestation efforts. Traditional pathogen detection methods, such as seed plating assays, are limited in scope and sensitivity. We assessed the potential of DNA-metabarcoding with Oxford Nanopore Technologies (ONT) to detect and identify fungal pathogens in conifer seed lots. Using ONT-based sequencing of the internal transcribed spacer (ITS) and translation elongation factor 1-alpha (TEF1) loci, we analyzed 20 seed lots from Douglas fir ( Pseudotsuga menziesii) and interior spruce ( Picea engelmannii × glauca). Our results were benchmarked against culture-based and real-time PCR assays. The ITS ONT assay detected a broad range of fungal taxa, including conifer pathogens such as Fusarium spp., Sirococcus conigenus, and Caloscypha fulgens. Although the TEF1 ONT assay showed lower detection sensitivity, it increased the robustness of species complex resolution within the Fusarium genus. We observed a strong correlation between ITS ONT read counts and real-time PCR quantification cycle (Cq) values, indicating the potential for quantitative pathogen load assessment. Differences between detection methods highlighted the importance of optimizing seed sampling strategies to improve pathogen detection consistency. The portability, affordability, and ongoing improvements in ONT technology suggest a promising future for its application in forest seed diagnostics and biosecurity monitoring. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".