To be economic and to be compatible with modern continuous bioconversion systems, it is imperative that the process organism exhibit an extremely high degree of stability. In the case of ethanol production from lignocellulosic biomass, functional stability of the potential process biocatalyst can be assessed in terms of the capacity to sustain high-performance fermentation during the continuous fermentation of biomass-derived sugars. This investigation employed glucose- or xylose-limited chemostat culture to examine the functional stability of two patented, genetically engineered E. coli-namely E. coli B (ATCC 11303) carrying the Zymomonas genes for pyruvate decarboxylase and alcohol dehydrogenase II on a multicopy plasmid pLOI297 and a chromosomal pet integrant of strain 11303, designated as strain KO11. Both recombinants carry markers for antibiotic resistance and have been reported to exhibit genetic stability in the absence of antibiotic selection. Chemostats were fed with Luria broth (LB) (with 25 g/L sugar) at a dilution rate of 0.14 and 0.07/h when the feed medium was glucose-LB and xylose-LB, respectively. The pH was controlled at 6.3. With glucose, both recombinants exhibited a rapid loss of ethanologenicity even when selection pressure was imposed. by the inclusion of antibiotics in the feed medium. With strain KO11, increasing the concentration of chloramphenicol from 40 to 300 mg/L, resulted in a retardation in the rate of loss of ethanologenicity, but it did not prevent it. Under xylose limitation, the plasmid-bearing recombinant appeared to be stabilized by antibiotics, but this did not reflect genetic stability, since the slower-growing revertant was washed out at a dilution rate of 0.07/h. With both recombinants, interpretation of functional stability with xylose was complicated by the inherent ethanologenicity associated with the host culture. Based on an average cost for large bulk quantities of antibiotics at $55/kg and an amendment level of 40 g/m(3), the estimated economic imp act regarding the potential requirement for operational stabilization by antibiotics in a plant operating in batch mode varied from a maximum of 29 cent/gal of E95 ethanol for antibiotic amendment of all fermentation media to a minimum of 0.45 cent/gal where antibiotics were used exclusively for the preparation of the inocula for every fourth batch fermentation cycle, The high degree of instability observed in these continuous fermentations does not auger well for the proposed potential industrial utility of these patented, genetically engineered constructs for the production of fuel ethanol from biomass and wastes.