Rare-earth-element bio-recovery from low-grade secondary waste

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=None target=None mode=produce. Report id b5cf82fb2c88 (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: NOT-EXPRESSIBLE

GAP TYPE = vocabulary absence (the target metabolite has no exchange in the corpus at all). No rare-earth-element species in the corpus vocab: la/ce/nd/dy/y and every lanthanide are absent by BiGG symbol AND by name (no lanthanum/cerium/neodymium/dysprosium/yttrium/samarium etc.). The biogenic lixiviants biology would make ARE present (gluconate glcn=6992, citrate cit=11153, oxalate oxa=6747), but the recovered-REE product itself has no corpus representation, so there is no target metabolite to rank a recovery on. MARKET DEMAND: Payer is DOE/DOD funded programs (US$154M coal-to-REE demonstration portfolio, DOE CMEI FOA 3105) plus magnet/catalyst recyclers, driven by supply-security/de-risk-from-China; biology is specifically favored because solvent extraction is uneconomic on dilute low-grade waste. Per the 2024 J. Environ. Manage. review, REE bioleaching is still pre-commercial with economics the main barrier.

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.