Environment has a Stronger Effect than Host Plant Genotype in Shaping Spring <i>Brassica napus</i> Seed Microbiomes
Bibliographic record
Abstract
Seed are reproductive units that transfer genetic information to the next generation and harbor microbial communities that may interact with a host plant at all stages of its development. Here, we assessed the effect of the environment and plant genotype on the seed microbiome of eight spring Brassica napus lines harvested from four site years in Saskatchewan, Canada: one location each in 2016 and 2017 and two additional locations in 2017. Seed microbiomes were characterized using high-throughput amplicon sequencing of the bacterial 16S ribosomal RNA and fungal internal transcribed spacer regions. Our results revealed that microbial communities were predominantly shaped by the environment, with location explaining 34% of bacterial and 43% of fungal total variance. Meanwhile, genotype had a smaller effect, accounting for only 9% of bacterial and 13% of fungal variance. The seed microbiome of B. napus predominantly contained members of Enterobacteriales and Pseudomonadales bacterial orders as well as Pleosporales and Capnodiales fungal orders. Additionally, common taxa, including Enterobacteriales, Pseudomonadales, Micrococcales, Sphingomonadales, Pleosporales, Capnodiales, Tremellales, Filobasidiales, and Sporidiobolales, were detected across all site years. Our results demonstrate that the environment plays a dominant role in shaping spring B. napus seed microbiomes, with more subtle contributions related to host plant genotype. Information collected in this study may contribute to the development of novel and sustainable breeding and agricultural strategies that consider microorganisms carried by seed.
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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 | 0.000 | 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 | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 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".