Genomics of Ammonia-Oxidizing Bacteria and Insights into Their Evolution
Bibliographic record
Abstract
This chapter talks about ammonium-oxidizing bacteria (AOB), addresses the inventory involved in nitrification, attempts metabolic reconstruction of N transformation processes, and provides insights into their evolution. The AOB oxidizes ammonia aerobically as their sole source of energy and reductant belong taxonomically to two monophyletic groups in different proteobacterial classes. amoA-encoding archaea (AEA) is capable of being classified as obligate, ammonia-co-oxidizing mixotrophs, or chemoorganotrophs with nonfunctional amo genes in their genomes. While the anaerobic oxidation of methane by NC10 is coupled to denitrification, it is not yet clear whether the oxidation of ammonia is coupled to nitrite reduction. Ammonification, the production of ammonium from other nitrogen compounds, likely existed within early bacteria and archaea as a consequence of simple fermentations; however, these internal cycles did not likely increase net NH4 +/NH3 availability. The core hydroxylamine ubiquinone redox module (HURM) genes are encoded by a conserved gene cluster, hao-orf2-cycAB, in all AOB. Complete sequences of the genes encoding the HURM proteins had been published from several AOB prior to obtain genome sequences and the protein structures of HAO and c554 have since been resolved.
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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 | 0.001 | 0.001 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 0.001 |
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".