NOVELTY - A recombinant microorganism having resistance to ionic liquids, comprising a heterologous gene encoding a major facilitator superfamily 1 (MFS1) polypeptide operably linked to a promoter, where the MFS1 polypeptide has at least 70% identity to fully defined 496 amino acids (SEQ ID NO. 2) given in the specification, is new.    USE - The recombinant microorganism and methods are useful for increasing yield of soluble sugar from biomass; and for increasing yield from reaction in which soluble sugars are source of carbon (all claimed).    ADVANTAGE - Method of genetically modifying microorganisms to enhance resistance to ionic liquids is provided.    DETAILED DESCRIPTION - INDEPENDENT CLAIMS are:    (1) a method of modifying a microorganism to have resistance to ionic liquids, comprising introducing an expression cassette into the microorganism, where the expression cassette comprises a gene encoding MFS1 polypeptide that has at least 70% identity to SEQ ID NO. 2;    (2) a method of increasing yield of soluble sugar from a biomass, comprising incubating biomass pretreated with the microorganism in an enzymatic hydrolysis reaction;    (3) a method of increasing yield from a reaction in which soluble sugars are source of carbon, comprising incubating biomass pretreated with ionic liquid with the microorganism;    (4) a composition comprising biomass pretreated with ionic liquid and the microorganism; and    (5) a method of identifying a gene that confers tolerance to an ionic liquid to an organism, comprising culturing a recombinant genomic expression library that comprises the genome of at least one microorganism that is resistant to ionic liquids under condition in a culture medium that comprises at least 0.1% ionic liquid in which genomic inserts from the genome of the at least one microorganism are expressed; and selecting at least one colony that grow faster in the presence of at least 0.1% ionic liquid in comparison to a control that does not comprises genomic sequences from the at least one microorganism.