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Background    Enterobacter aerogenes  is a facultative anaerobe and is one of the most widely studied bacterial strains because of its ability to use a variety of substrates, to produce hydrogen at a high rate, and its high growth rate during dark fermentation. However, the rate of hydrogen production has not been optimized. In this present study, three strategies to improve hydrogen production in  E. aerogenes , namely the disruption of  nuoCDE , overexpression of the small RNA RyhB and of NadE to regulate global anaerobic metabolism, and the redistribution of metabolic flux. The goal of this study was to clarify the effect of  nuoCDE , RyhB, and NadE on hydrogen production and how the perturbation of NADH influences the yield of hydrogen gas from  E. aerogenes .    Results  NADH dehydrogenase activity was impaired by knocking out  nuoCD  or  nuoCDE  in  E. aerogenes  IAM1183 using the CRISPR-Cas9 system to explore the consequent effect on hydrogen production. The hydrogen yields from IAM1183-CD( ∆nuoC / ∆nuoD ) and IAM1183-CDE ( ∆nuoC / ∆nuoD / ∆nuoE ) increased, respectively, by 24.5 and 45.6% in batch culture (100 mL serum bottles). The hydrogen produced via the NADH pathway increased significantly in IAM1183-CDE, suggesting that  nuoE  plays an important role in regulating NADH concentration in  E. aerogenes . Batch-cultivating experiments showed that by the overexpression of NadE (N), the hydrogen yields of IAM1183/N, IAM1183-CD/N, and IAM1183-CDE/N increased 1.06-, 1.35-, and 1.55-folds, respectively, compared with IAM1183. Particularly worth mentioning is that the strain IAM118-CDE/N reached 2.28 mol in H 2  yield, per mole of glucose consumed. IAN1183/R, IAM1183-CD/R, and IAM1183-CDE/R showed increasing H 2  yields in batch culture. Metabolic flux analysis indicated that increased expression of RyhB led to a significant shift in metabolic patterns. We further investigated IAM1183-CDE/N, which had the best hydrogen-producing traits, as a potential candidate for industry applications using a 5-L fermenter; hydrogen production reached up to 1.95 times greater than that measured for IAM1183.    Conclusions  Knockout of  nuoCD  or  nuoCDE  and the overexpression of  nadE  in  E. aerogenes  resulted in a redistribution of metabolic flux and improved the hydrogen yield. Overexpression of RyhB had an significant change on the hydrogen production via NADH pathway. A combination of strategies would be a novel approach for developing a more economic and efficient bioprocess for hydrogen production in  E. aerogenes . Finally, the latest CRISPR-Cas9 technology was successful for editing genes in  E. aerogenes  to develop our engineered strain for hydrogen production.    Electronic supplementary material  The online version of this article (doi:10.1186/s13068-017-0938-2) contains supplementary material, which is available to authorized users.

biotechnology for biofuels

Impairment of NADH dehydrogenase and regulation of anaerobic metabolism by the small RNA RyhB and NadE for improved biohydrogen production in Enterobacter aerogenes