Comparison of sulfide‐oxidizing <i>Sulfurimonas</i> strains reveals a new mode of thiosulfate formation in subsurface environments
Bibliographic record
Abstract
Summary Sulfur‐oxidizing Sulfurimonas spp. are widespread in sediments, hydrothermal vent fields, aquifers and subsurface environments such as oil reservoirs where they play an important role in the sulfur cycle. We determined the genome sequence of the oil field isolate Sulfurimonas sp. strain CVO and compared its gene expression during nitrate‐dependent sulfide oxidation to the coastal sediment isolate Sulfurimonas denitrificans . Formation of elemental sulfur (S 0 ) and high expression of sulfide quinone oxidoreductase (SQR) genes indicates that sulfide oxidation in both strains is mediated by SQR. Subsequent oxidation of S 0 was achieved by the sulfur oxidation enzyme complex (SOX). In the coastal S. denitrificans , the genes are arranged and expressed as two clusters: soxXY 1 Z 1 AB and soxCDY 2 Z 2 H , and sulfate was the sole metabolic end product. By contrast, the oil field strain CVO has only the soxCDY 2 Z 2 H cluster and not soxXY 1 Z 1 AB . Despite the absence of the soxXY 1 Z 1 AB cluster, strain CVO oxidized S 0 to thiosulfate and sulfate, demonstrating that soxCDY 2 Z 2 H genes alone are sufficient for S 0 oxidation in Sulfurimonas spp. and that thiosulfate is an additional metabolic end product. Screening of publicly available metagenomes revealed that Sulfurimonas spp. with only the soxCDY 2 Z 2 H cluster are widespread suggesting this mechanism of thiosulfate formation is environmentally significant.
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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 | 0.001 |
| Bibliometrics | 0.001 | 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".