Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fourteen indigenous Saccharomyces cerevisiae strains isolated from the barks of three tree species located in the Atlantic Rain Forest and Cerrado biomes in Brazil were genetically and physiologically compared to laboratory strains and to strains from the Brazilian fuel ethanol industry. Although no clear correlation could be found either between phenotype and isolation spot or between phenotype and genomic lineage, a set of indigenous strains with superior industrially relevant traits over commonly known industrial and laboratory strains was identified: strain UFMG-CM-Y257 has a very high specific growth rate on sucrose (0.57 +/- 0.02 h(-1)), high ethanol yield (1.65 +/- 0.02 mol ethanol mol hexose equivalent(-1)), high ethanol productivity (0.19 +/- 0.00 mol L-1 h(-1)), high tolerance to acetic acid (10 g L-1) and to high temperature (40A degrees C). Strain UFMG-CM-Y260 displayed high ethanol yield (1.67 +/- 0.13 mol ethanol mol hexose equivalent(-1)), high tolerance to ethanol and to low pH, a trait which is important for non-aseptic industrial processes. Strain UFMG-CM-Y267 showed high tolerance to acetic acid and to high temperature (40A degrees C), which is of particular interest to second generation industrial processes.Indigenous strains of the yeast Saccharomyces cerevisiae, isolated from natural biomes, present suitable traits for biotechnological applications and illustrate microbial biodiversity in Brazil.Indigenous strains of the yeast Saccharomyces cerevisiae, isolated from natural biomes, present suitable traits for biotechnological applications and illustrate microbial biodiversity in Brazil.167FAPESPVALE through the PITE FAPESP/VALE grant [2010/51318-2]Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES, Brasilia, Brazil)Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP, Sao Paulo, Brazil) [2013/17859-4, 2014/10366-5]Novo Nordisk FoundationFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)