In nature, diverse microbial consortia degrade recalcitrant lignocellulosic substrates efficiently through poorly defined mechanisms. Their study can help to design a microbial consortium that performs a consolidated bioprocess for biofuel production. Microbial consortia from anaerobic sludge, epiphytic microorganisms, ruminal fluids, and soil were examined with regard to H-2 production from untreated wheat straw. Cell wall degradation in short cells and the stomata was analyzed by confocal laser scanning microscopy. On day 7, the highest rate and H-2 production were reached by native microflora. For all inocula, sugars from the hemicellulosic matrix were preferably consumed. The microscopic images showed that the cell wall in stomatal areas was degraded more extensively than in short cells. Also, fungal populations were detected in consortia with better H-2 production. Of the consortia that we tested, the epiphytic microorganisms were notable, because they delignified the lignocellulosic substrate and converted the hemicellulosic sugars into H-2 efficiently. Copyright (C) 2014, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.