Methylomicrobium alcaliphilumis an alkaliphilic and halotolerant methanotroph. The physiological responses ofM. alcaliphilumto high NaCl concentrations, were studied using RNA sequencing and metabolic modeling. This study revealed thatM. alcaliphilumpossesses an unusual respiratory chain, in which complex I is replaced by a Na(+)extruding NQR complex (highly upregulated under high salinity conditions) and a Na(+)driven adenosine triphosphate (ATP) synthase coexists with a conventional H(+)driven ATP synthase. A thermodynamic and metabolic model showing the interplay between these different components is presented. Ectoine is the main osmoprotector used by the cells. Ectoine synthesis is activated by the transcription of anectoperon that contains five genes, including the ectoine hydroxylase codingectDgene. Enzymatic tests revealed that the product ofectDdoes not have catalytic activity. A new Genome Scale Metabolic Model forM. alcaliphilumrevealed a higher flux in the oxidative branch of the pentose phosphate pathway leading to NADPH production and contributing to resistance to oxidative stress.