A method for amplifying a plurality of different nucleic acid populations in a single reaction mixture, comprising: a) providing a single reaction mixture including an emulsion that provides compartmentalization containing a first and a second population of nucleic acids, wherein the first population of nucleic acids contain a first common primer binding sequence and a first adaptor, and the second population of nucleic acids contain a second common primer binding sequence and a second adaptor, and wherein the first and second common primer binding sequences are different; a first plurality of beads having covalently attached a first capture primer that binds to the first common primer binding sequence; a second plurality of beads having covalently attached a second capture primer that binds to the second common primer binding sequence, wherein the first and the second capture primers are different; b) providing a first and a second soluble reverse primer, wherein the first soluble reverse primer is complementary or identical to the first adaptor or to the first and second adaptor, and wherein the second soluble reverse primer is complementary or identical to the second adaptor or to the first and second adaptor; c) amplifying, within the single reaction mixture compartments, one or more nucleic acids from the first population to form a first amplified population, and one or more nucleic acids from the second population to form a second amplified population, wherein the first amplified population is bound to one or more beads of the first type and the second amplified population is bound to one or more beads of the second type. a) providing a single reaction mixture including an emulsion that provides compartmentalization containing a first and a second population of nucleic acids, wherein the first population of nucleic acids contain a first common primer binding sequence and a first adaptor, and the second population of nucleic acids contain a second common primer binding sequence and a second adaptor, and wherein the first and second common primer binding sequences are different; a first plurality of beads having covalently attached a first capture primer that binds to the first common primer binding sequence; a second plurality of beads having covalently attached a second capture primer that binds to the second common primer binding sequence, wherein the first and the second capture primers are different; b) providing a first and a second soluble reverse primer, wherein the first soluble reverse primer is complementary or identical to the first adaptor or to the first and second adaptor, and wherein the second soluble reverse primer is complementary or identical to the second adaptor or to the first and second adaptor; c) amplifying, within the single reaction mixture compartments, one or more nucleic acids from the first population to form a first amplified population, and one or more nucleic acids from the second population to form a second amplified population, wherein the first amplified population is bound to one or more beads of the first type and the second amplified population is bound to one or more beads of the second type. <EOS>