Glycoside linkage (cellobiose versus maltose) dramatically influenced bioenergetics to different extents and by different mechanisms in the hyperthermophilic archaeon Pyrococcus furiosus when it was grown in continuous culture at a dilution rate of 0.45 h(-1) at 90 degrees C. In the absence of S-0, cellobiose-grown cells generated twice as much protein and had 50%-higher specific H, generation rates than maltose-grown cultures. Addition of So to maltose-grown cultures boosted cell protein production fourfold and shifted gas production completely from H-2 to H2S. In contrast, the presence of S-0 in cellobiose-grown cells caused only a 1.3-fold increase in protein production and an incomplete shift from H-2 to H2S production, with 2.5 times more H-2 than H2S formed. Transcriptional response analysis revealed that many genes and operons known to be involved in alpha- or R-glucan uptake and processing were up-regulated in an S-0-independent manner. Most differentially transcribed open reading frames (ORFs) responding to S-0 in cellobiose-grown cells also responded to S-0 in maltose-grown cells; these ORFs included ORFs encoding a membrane-bound oxidoreductase complex (MBX) and two hypothetical proteins (PF2025 and PF2026). However, additional genes (242 genes; 108 genes were up-regulated and 134 genes were down-regulated) were differentially transcribed when S-0 was present in the medium of maltose-grown cells, indicating that there were different cellular responses to the two sugars. These results indicate that carbohydrate characteristics (e.g., glycoside linkage) have a major impact on So metabolism and hydrogen production in P.furiosus. Furthermore, such issues need to be considered in designing and implementing metabolic strategies for production of biofuel by fermentative anaerobes.