Group-Specific Carbon Fixation Activity Measurements Reveal Distinct Responses to Oxygen Among Hydrothermal vent <i>Campylobacteria</i>
Bibliographic record
Abstract
Abstract Molecular surveys of low temperature deep-sea hydrothermal vent fluids have shown that Campylobacteria (prev. Epsilonproteobacteria ) often dominate the microbial community and that three subgroups - Arcobacter , Sulfurimonas and Sulfurovum - frequently coexist. In this study, we used replicated radiocarbon incubations of deep-sea hydrothermal fluids to investigate the activities of each group under three distinct incubation conditions. In order to quantify group-specific radiocarbon incorporation, we used newly designed oligonucleotide probes for Arcobacter, Sulfurimonas, and Sulfurovum to quantify their activity using catalyzed-reporter deposition fluorescence in-situ hybridization (CARD-FISH) combined with fluorescence-activated cell sorting. All three groups actively fixed CO 2 in short-term (~ 20 h) incubations with either nitrate, oxygen, or no additions (control) at similar per-cell carbon fixation rates. Oxygen additions had the largest effect on community composition and overall cell numbers, and caused a pronounced shift in community composition at the amplicon sequence variant (ASV) level after only 20 h of incubation for all three groups. Interestingly, the effect of oxygen on carbon fixation rates appeared to depend on the initial starting community. Higher carbon fixation rates in oxygen-amended treatments were noted for all three taxa after an unintended disturbance to the sample site that may have selected for more oxygen-tolerant phylotypes. When viewed from a coarse taxonomic level, our data support assertions that these chemoautotrophic groups are functionally redundant in terms of their core metabolic capabilities since they were simultaneously active under all incubation conditions. In contrast, the higher resolution of amplicon sequencing allowed us to reveal finer-scale differences in growth that likely reflect adaptation of physiologically-distinct subtypes to varying oxygen concentrations in situ . Despite this progress, we still know remarkably little about the factors that maintain genomic diversity and allow for stable co-existence among these three campylobacterial groups. Moving forward, we suggest that more subtle biological factors such as enzyme substrate specificity, motility, cell morphology, and tolerance to environmental stress should be more thoroughly investigated to better understand ecological niche differentiation at deep-sea hydrothermal vents.
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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 | 0.000 |
| 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) | 0.001 | 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".