Bibliographic record
Abstract
Jody W. Deming, School of Oceanography and Astrobiology Program, University of Washington, USA and Origins Institute, McMaster University, Canada (rec3141@mcmaster.ca) Although ‘follow the water’ has long been a mantra in astrobiology, the dominant state of water in our solar system is not as a liquid but as a solid. Water ice is present in abundance on the satellites of Saturn and Jupiter, including Titan and Europa, on Mars, on the Moon, and it may have played a prominent role in the evolution of life on Earth during putative ‘snowball Earth’ episodes. One form of solid water present on Earth today is sea ice, an extreme environment characterized by low temperature (−2 to −35◦C) and high salinity (35 to 270 parts per thousand) in its brine inclusions, where microbes have been observed to reside. The physical concentration of microorganisms and the subsequent imposition of physical, chemical, and biological stresses in autumn and winter sea ice brine may favor the occurrence of horizontal gene transfer there, which in turn is expected to aid in the adaptation of microorganisms to this seasonally and epochally dynamic environment. As part of the International Polar Year (IPY) Circumpolar Flaw Lead System Study (CFL) we found high concentrations of bacteria, viruses, and extracellular free DNA in sea ice brine relative to underlying seawater (Fig. 1), each a proxy for the raw materials required for horizontal gene transfer by conjugation, transduction, and transformation, respectively. Transduction is suggested as a prominent form of horizontal gene transfer in sea ice due to extremely high virus-to-bacteria contact rates predicted in sea ice brine (Fig. 2) and the presence of stressors, like rapid changes in temperature and salinity, that have been shown to promote the induction of prophage into the lytic cycle. Horizontally transferred genes with particular utility in sea ice may include those encoding for the production, degradation, or alteration of extracellular polymeric substances or compatible solutes, compounds thought to have utility as cryoprotectants and osmoprotectants. Complete genome comparisons using a sea ice affiliated psychrophilic gammaproteobacterium, Colwellia psychrerythraea, revealed evidence for the horizontal acquisition of genes necessary for the complete catabolism of glycine betaine (Fig. 3), a common compatible solute used for protection against salt stress by members of all three Domains of life. Growth experiments using a defined medium indicated that sarcosine (an intermediate in the catabolism of glycine betaine) was utilized by Colwellia psychrerythraea and several other isolates of Colwellia as a sole source of organic carbon and nitrogen, suggesting that the horizontally transferred operon was expressed in vitro.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 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".