Carbon and Electron Recovery in Integrated Biohydrogen Systems: A Critical Review of Dark Fermentation, Photo-Fermentation, and Microbial Electrolysis Cells

Hydrogen is increasingly recognized as a key energy carrier for decarbonizing hard-to-electrify sectors, yet more than 95% of current global production remains fossil-derived. Biological hydrogen (biohydrogen) produced by dark fermentation (DF), photo-fermentation (PF), or microbial electrolysis cells (MEC) offers the dual advantage of valorizing organic wastes while delivering low-carbon H2; however, none of these standalone technologies mobilizes more than 25–33% (DF), 40–70% (PF), or 40–60% (MEC) of feedstock organic carbon through H2-producing oxidation pathways. Most existing reviews compare these pathways on hydrogen yield alone, a metric that conceals where the majority of feedstock carbon and electrons are actually lost and obscures the quantitative rationale for system integration. This review reframes the comparison around carbon and electron flow, explicitly tracking how much input carbon is mobilized through H2-producing oxidation pathways, how much is retained in volatile fatty acids (VFAs), biomass, or unlinked CO2, and what happens to the associated electrons. Stoichiometric, mechanistic, and reactor-level evidence is synthesized to show that DF channels only 25–33% of input organic carbon through H2-yielding decarboxylation on real heterogeneous substrates, with 40–60% retained as residual VFAs and unhydrolyzed solids; PF can recover 60–80% of VFA carbon but is constrained by photon economics and nitrogenase sensitivity; and MEC achieves >85% COD removal only when coupled to an upstream acidogenic stage. Two-stage (DF–PF, DF–MEC) and three-stage (DF–PF–MEC, DF–MEC–AD) configurations are critically evaluated, with theoretical yields separated from experimentally demonstrated performance on real wastes and hidden energy inputs (pretreatment, inter-stage transfer, gas separation, and compression) explicitly accounted for. DF–MEC coupling is identified as the most near-term tractable configuration, achieving 55–70% H2-pathway carbon mobilization and 80–92% COD removal at an electrical input of 0.9–1.5 kWh/m3 H2, with levelized hydrogen costs of US$3–5.5/kg under favorable waste-tipping-fee conditions. Multi-stage systems push carbon recovery above 70% but carry unresolved capital, methanogenesis control, and scale-up penalties. This review closes by proposing a standardized ten-descriptor reporting framework including H2-pathway carbon mobilization (%), cathodic hydrogen recovery (rCAT), net energy recovery (NEB), and LCA carbon intensity under both attributional and consequential boundaries, and demonstrates its backward compatibility by retrospective application to seven studies already in the literature. Research priorities tractable on a 5–10 year horizon are identified, centered on methanogen suppression at pilot scale, real-waste MEC performance, and renewable-electricity coupling.