Metal-AMR Co-selection Readiness

Tension

The Atlas can now formulate the co-selection question, but formulation is not proof. The current evidence says the test is high value, not that the result is already known.

Review Brief

What changed: new project evidence added metal type diversity, prophage density, soil metal-function associations, and T4SS/CAZy/metal co-enrichment to the co-selection question.

Why review matters: this conflict is the guardrail against turning a good DOE-site analysis into a premature claim. Reviewers should decide whether the resolving analysis has the right covariates and whether any side of the tension is missing.

Evidence to inspect:

• Metal tolerance and specificity evidence from metal_fitness_atlas and metal_specificity.
• AMR environment and fitness-cost evidence from the AMR project set.
• Mobile-context evidence from prophage_amr_comobilization and t4ss_cazy_environmental_hgt.
• Site and chemistry covariates from ENIGMA, NMDC, and soil metal projects.

Questions for reviewers:

• Are the proposed controls sufficient: taxonomy, habitat, sampling depth, metal co-contamination, mobile-element burden, and metadata quality?
• Should mobile-element burden be treated as a covariate, a mediator, or a separate mechanism?
• Which site or collection is ready enough for the first co-selection benchmark?
• What result would resolve the conflict rather than merely add another correlation?

Current Interpretation

Use this as a direction and hypothesis seed. Do not cite it as a resolved co-selection finding until site-level joins and controls are complete.

Resolving Analysis

The resolving analysis is a controlled contaminated-site benchmark that joins metal exposure, AMR profiles, metal tolerance scores, mobile-element context, and environmental covariates.