In-situ uranium bioimmobilization in groundwater (Geobacter, acetate-stimulated)

Provenanced sample report (Syntropa discovery, role-aware Stage-1). Corpus v0.2.2 (15,664 models, fingerprint 58a8f20e2aba) · tools v0.1.1 (git 44a8422, code a412618fd214) · env py3.13.13 win32 swiglpk5.0.13+osqp1.1.3+highspy1.15.1+pyscipopt6.2.1+optlang1.9.1 (deps 7f138ead8863). Feed={'acetate': 10, 'u6': 10} target=u6 mode=destroy. Report id d8b84aed3f79 (content-addressed to config + EXACT corpus + EXACT tools -> auditable; git-reproducibility is PENDING a committed + tagged tool release). Every claim here is computed; every drop reason and known limit is listed below.

Verdict: PENDING

not yet run in this discovery pass (the run is still in progress): NOT a negative finding.

Destroy-mode caveat. The metric here is the target's uptake / consumption flux under FBA: an uptake-exchange capability, not a demonstrated degradation pathway. The downstream CATABOLIC reactions that actually break the compound down may not be fully modeled, so read a 'degradation' result as an UPTAKE CANDIDATE to verify against the literature, not a proven catabolic route.

Single-organism result (no emergence)

• A single organism does the chemistry (best single 0.000); no cross-feeding emergence was found, so no multi-member consortium is required.
• The 0 feedstock-dependent candidates are COMBINATIONS over a diverse front-end core and largely SHARE the finisher(s) []: they are variations on a small number of core relays, NOT 0 independent discoveries. The biological finding is the finisher + its best partners, not the raw count.

Ranked feedstock-dependent candidates (top 0 of 0)

The production column = the target's community UPTAKE / CONSUMPTION flux (destroy mode) (FBA objective, mmol/gDW/h) on an OPEN medium: an UPPER BOUND, not a measured rate. It can EXCEED the feed-limited stoichiometric ceiling (an open-medium artifact); any value above the ceiling is NOT an achievable closed-medium yield. See caveats.

Attribution

Every model above is credited by id + source. Model authors: your reconstruction appears in this result. (Impact-ledger stamping = flywheel, pending.)

Caveats (disclosed up front)

• PRODUCTION IS AN OPEN-MEDIUM UPPER BOUND, NOT A YIELD. The production flux is FBA on an OPEN medium: carbon and reductant may enter from the background medium, not only the named feed: so a value CAN EXCEED the feed-limited stoichiometric ceiling (e.g. CO2+H2->acetate <=~5 at 4 H2/acetate; glucose->CH4 <=~1 per glucose by the hydrogenotrophic route). Read every production number as an unconstrained UPPER BOUND; a value above the ceiling is an open-medium artifact, not an achievable closed-medium yield. Closed-medium re-runs are Phase-2.
• FBA proves a route is stoichiometrically POSSIBLE, not that a living cell will do it.
• Every consortium here is a HYPOTHESIS until cultured; nothing is wet-lab validated.
• MEMBER IDENTITY IS A LEAD, NOT A CLAIM. Named members are FBA-feasible only in AUTOMATED, GAP-FILLED DRAFT reconstructions: gap-filling can add transporters/reactions an organism does not actually have, so a named member may CONTRADICT established physiology (a strain the literature does not know to perform this chemistry). Check each named organism against the literature before treating it as a real candidate; the value here is the metabolic PATTERN, not the specific strain.
• Feedstock-dependence is the anti-medium-artifact control: withdraw the feed and the product must collapse (a NOT-feedstock-dependent result is flagged SUSPECT, not a discovery).
• The ranking score is a documented heuristic for human review, not a truth or biology claim.
• Stage-1 selects finisher x diverse front-ends; multi-finisher relays are out of scope. Stage-2 expansion of winners is pending: these are PRELIMINARY until it runs.