Culturing and direct DNA extraction find different fungi from the same ericoid mycorrhizal roots
Bibliographic record
Abstract
• This study compares DNA and culture-based detection of fungi from 15 ericoid mycorrhizal roots of salal (Gaultheria shallon), from Vancouver Island, BC Canada. • From the 15 roots, we PCR amplified fungal DNAs and analyzed 156 clones that included the internal transcribed spacer two (ITS2). From 150 different subsections of the same roots, we cultured fungi and analyzed their ITS2 DNAs by RFLP patterns or sequencing. We mapped the original position of each root section and recorded fungi detected in each. • Phylogenetically, most cloned DNAs clustered among Sebacina spp. (Sebacinaceae, Basidiomycota). Capronia sp. and Hymenoscyphus erica (Ascomycota) predominated among the cultured fungi and formed intracellular hyphal coils in resynthesis experiments with salal. • We illustrate patterns of fungal diversity at the scale of individual roots and compare cloned and cultured fungi from each root. Indicating a systematic culturing detection bias, Sebacina DNAs predominated in 10 of the 15 roots yet Sebacina spp. never grew from cultures from the same roots or from among the > 200 ericoid mycorrhizal fungi previously cultured from different roots from the same site.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.003 | 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 teacher head, 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".