Dynamic evolution of nitrogen cycle and pH homeostasis genes enabled the diversification of Pampinifervens gen. nov. (Aquificaceae)
Bibliographic record
Abstract
Abstract Background: Members of the phylum Aquificota were initially documented more than a century ago and play important roles in hydrogen, sulfur, and carbon cycles in geothermal systems as ubiquitous and abundant chemolithoautotrophs; however, their roles in the nitrogen cycle are not well defined. Results: Here, we show that a novel Aquificaceae isolate from Tengchong, China, fixes nitrogen in pure culture and that nitrogen fixation (nif) genes are transcribed in situ. We propose the name Pampinifervens diazotrophicum gen. et sp. nov. to accommodate this organism, with strain T-2T as the nomenclatural type. Analysis of metagenomes from physicochemically diverse springs in Tengchong showed that Pampinifervens dominates the Aquificota populations in most springs, consistent with a wide pH growth range for strain T-2T (pH 6.0-9.5) and another isolate, strain T-8T (pH 5.5-10.0). Despite the role of P. diazotrophicum in nitrogen fixation, strain T-8T does not fix nitrogen, but respires nitrate. Analysis of 104 metagenome-assembled genomes from 84 metagenomes globally, including at least 16 sympatric Pampinifervens species and other species from Canada, Japan, Malaysia, and Russia, revealed the variable presence of nif and denitrification genes. In contrast, genes for hydrogen chemolithotrophy, sulfur chemolithotrophy, and autotrophy were more conserved. Genes required for homeostasis were also present in the genus, with a proliferation of these genes in species recovered from Tengchong, China, that likely allowed them to diversify from neutral and alkaline bicarbonate-buffered springs into acidic sulfuric acid-buffered springs. Conclusions: Together, this work presents a widespread but overlooked genus of Aquificaceae and evolutionary patterns that suggest an important role for nitrogen metabolism and pH homeostasis in the local speciation of Pampinifervens in Southwest China. We suggest that Pampinifervens and possibly other Aquificaceae have underappreciated but diverse roles in nitrogen cycling.
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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 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.001 |
| 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".