Separate switchgrass enzyme profiles from demonstrated causal mechanisms #1498

Finding

High_Solids_Switchgrass_Methanogenic_Microbiome (000194), PMID:35790765: fraction-associated CAZyme profiles are currently labeled NICHE_PARTITIONING and linked causally to maintained solubilization. Hydrogenotrophic enzyme profiles and bulk methane are not a route-resolved flux measurement.

Repair

Preserve positive carbohydrate-solubilization and gas-production observations, distinguish LC-MS protein abundance from catalytic activity, and qualify both existing arrows. Remove unqualified niche-partitioning labels and source/target pairs from community profile nodes; use existing canonical participants without changing taxonomy. Centrifugation fractions are enriched fractions, not pure organism niches. Bound the single sequential reactor design: vitamins, medium, mixing and adaptation can covary with solids loading. Treat hydrogenotrophic dominance as pathway inference, not a measured fraction of methane flux.

Record the authors' AA6/Fenton accessibility hypothesis and missing selective mechanism tests in an anchored gap, not a newly demonstrated oxidative branch. Existing structure is reviewed, not every conceivable mechanism.

Evidence and gates

Whole record and complete cached primary main body, Methods and embedded figure captions inspected; no original images, supplements, source data or analysis code audited. Add ledger, append-only history, regression and canonical-participant coverage; run focused validation and publication gates. Existing cache says abstract-only but includes appended primary full text; do not misstate read scope.

Deduplication checked 806 all-state issue titles/bodies and 25 ignored/hidden-inclusive local matches. Closed #401/#366 address taxonomy tooling, which remains unchanged. Keep open until protected main merge; non-graph fields remain outside certification.