Genomic and physiological characterization of 'Candidatus Methylocystis sumavensis', a novel acid-tolerant methanotroph from peatland
Bibliographic record
Abstract
Abstract Methanotrophic bacteria in peatlands mitigate emissions of methane (CH 4 ), a potent greenhouse gas, yet the mechanisms enabling them to remain active under the acidic conditions typical of many peatlands remain poorly understood. Using enrichment cultivation and single-cell sorting, we isolated a novel peatland methanotroph from Czech soil, ‘ Methylocystis sumavensis ’. This species is moderately acidotolerant and active across broad pH and temperature ranges, with growth optima at pH 6.8 and 24–37 °C. The genome of ‘ M. sumavensis ’ encodes two particulate methane monooxygenase isozymes, a clade I nitrous oxide reductase, multiple terminal oxidases, and two [NiFe]-hydrogenases, including a complete complex of the previously uncharacterised membrane-bound hydrogenase group 4f, indicating substantial metabolic versatility. To link genomic potential with physiological function, we compared transcriptomes under acidic (pH 5.0) and alkaline (pH 9.0) conditions relative to the optimum pH (6.8). Under both stresses, ‘ M. sumavensis ’ increased transcription of genes involved in membrane remodelling, ion transport across both membranes, and stress response and repair, while reducing transcription of genes associated with methane oxidation and cell division. Alkaline stress additionally suppressed growth through reduced transcription of the carbon-assimilating Serine cycle. In contrast, acidic stress triggered a coordinated response requiring greater energetic investment. Among the most strongly upregulated genes were those encoding two formate dehydrogenases, the branched-chain alpha-keto-acid dehydrogenase complex, and all seven group 4f [NiFe]-hydrogenase-related genes, suggesting enhanced respiratory redox balancing under elevated external proton concentrations. These results reveal key mechanisms of pH-stress adaptation and highlight metabolic plasticity as a major determinant of methanotroph resilience in ecosystems.
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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 | 0.001 | 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) | 0.000 | 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".