A phylogenomic and metagenomic meta-analysis of bacterial diversity in the phyllosphere lifts a veil on Hyphomicrobiales dark matter
Bibliographic record
Abstract
Abstract The phyllosphere, or above-ground part of plants, hosts diverse bacterial communities that play critical ecological roles and provide beneficial functions for the plant. The Hyphomicrobiales (Alphaproteobacteria) are a highly diverse and ecologically important clade known to be key members of the plant microbiome, in particular in association with plant roots, but their diversity remain largely uncharacterized in the phyllosphere. Using a meta-analysis combining metabarcoding, metagenomics and phylogenomics, we explored the worldwide diversity of leaf-associated Hyphomicrobiales. We confirmed Methylobacterium was ubiquitous in the phyllosphere and revealed the dominance of two under-characterized Hyphomicrobiales taxa: Lichenibacterium , a lichen-associated genus previously identified as “1174-901-12” in taxonomic databases, and RH-AL1, an undescribed lineage of bacteria related to Beijerinckiaceae, previously isolated from coal slag. Despite their abundance in the phyllosphere, Lichenibacterium and RH_AL1 could not be properly detected by 16S rRNA gene barcoding, due in part to limitations of taxonomic resolution of the 16S rRNA gene and of representativeness in existing taxonomic databases, underlining limitations of this approach for their accurate identification in the phyllosphere. As for Methylobacterium, a significant proportion of Lichenibacterium and RH-AL1 were also detected in association with lichens and in environments with harsh conditions like exposed surfaces, air and snow, suggesting airborne or waterborne dispersal and high resilience in harsh environments. Overall, our study stresses the need to move toward metagenomics and culturomics to increase the representativeness of leaf-associated bacterial taxa in reference databases, and to improve our understanding of the evolutionary and functional mechanisms underpinning bacteria adaptations to living on plants. Graphical abstract Highlights Global meta-analysis reveals core Hyphomicrobiales in the phyllosphere Lichenibacterium and Methylobacterium dominate the phyllosphere and exposed surfaces Novel phyllosphere clades RH-AL1 and JAJXWB01 were identified by phylogenomics 16S rRNA gene limits taxonomic resolution in the phyllosphere; metagenomics refines taxonomy
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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 | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| 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".