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Background  Hydrogen photoproduction from green microalgae is regarded as a promising alternative solution for energy problems. However, the simultaneous oxygen evolution from microalgae can prevent continuous hydrogen production due to the hypersensitivity of hydrogenases to oxygen. Sulfur deprivation can extend the duration of algal hydrogen production, but it is uneconomical to alternately culture algal cells in sulfur-sufficient and sulfur-deprived media.    Results  In this study, we developed a novel way to simulate sulfur-deprivation treatment while constantly maintaining microalgal cells in sulfur-sufficient culture medium by overexpressing an endogenous microRNA (miR1166.1). Based on our previous RNA-seq analysis in the model green alga  Chlamydomonas reinhardtii , three endogenous miRNAs responsive to sulfur deprivation (cre-miR1166.1, cre-miR1150.3, and cre-miR1158) were selected. Heat-inducible expression vectors containing the selected miRNAs were constructed and transformed into  C. reinhardtii . Comparison of H 2  production following heat induction in the three transgenic strains and untransformed control group identified miR1166.1 as the best candidate for H 2  production regulation. Moreover, enhanced photobio-H 2  production was observed with repeated induction of miR1166.1 expression.    Conclusions  This study is the first to identify a physiological function of endogenous miR1166.1 and to show that a natural miRNA can regulate hydrogen photoproduction in the unicellular model organism  C. reinhardtii .    Electronic supplementary material  The online version of this article (10.1186/s13068-018-1126-8) contains supplementary material, which is available to authorized users.

An endogenous microRNA (miRNA1166.1) can regulate photobio-H2 production in eukaryotic green alga Chlamydomonas reinhardtii