Data & Analysis for: Soil microbiome sequencing reveals pathogen accumulation and nutrient cycle changes, but not mycorrhizal suppression in naturally occurring invasion of garlic mustard
Bibliographic record
Abstract
The disruption of soil microbial communities is thought to be an important contributor to range expansion of several invasive plants. Previous research has focused on identifying how invasive plants change soil microbial diversity and composition. However, it is also important to recognize the different functional roles of genetically distinct microbial taxa to understand the mechanism of plant invasion and its impact on nutrient cycling and other ecosystem services. We examine changes in soil microbial functional groups associated with the invasion of Alliaria petiolata. Laboratory experiments suggest that A. petiolata can suppress arbuscular mycorrhizal fungi (AMF) to disrupt native plant communities. Despite mounting evidence of AMF suppression under controlled laboratory and greenhouse experiments, it is less clear if allelochemicals persist under natural field conditions. To determine how A. petiolata invasion alters soil bacterial and fungal diversity and function in the field, we assigned taxonomic and functional classification to the 16S and ITS rRNA sequences present in edaphically matched soil samples inside and outside ten naturally occurring populations of A. petiolata. We also measured root health of plants co-occurring with A. petiolata to test the effect of soil microbial functional groups on plant health. In contrast to controlled experiments, we found no changes in mycorrhizal diversity, suggesting that mycorrhizal suppression is not a particularly strong mechanism of A. petiolata invasion. Instead, we recorded changes in pathogen community composition and an increase in root lesions for plants grown in A. petiolata invaded soils. These results support the ‘Enemy of my Enemy Hypothesis’ which predicts pathogen accumulation and spillover, decreasing native plant performance. Synthesis We did not find support for the suppression of AMF as a mechanism of invasion by A. petiolata in invaded field soils. However, changes in the community composition of pathogen and nutrient cycling microbes may be important forces underlying the invasion of A. petiolata and its impact on ecosystem function.
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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 | 0.002 | 0.004 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.003 | 0.002 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.002 | 0.003 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.176 | 0.059 |
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".