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Most of the chemical and biochemical processes used for the de-polymerization of structural polymers of lignocellulosic biomass are environment unfriendly and costly. Here an efficient process based on xylanase, produced by Acinetobacter pittii MASK25 (MTCC 25132), hydrolysis of only physically treated rice straw and corn cob has been developed for the production of xylooligosaccharides. Bacterial strain isolated from soil was found to produce maximum xylanase at 30 °C and pH 7. While the optimum temperature and pH of xylanase were characterized as 40 °C and 5. Process was further improved by developing magnetic-xylanase CLEA. Crude xylanase and magnetic-xylanase CLEA could convert respectively more than 45percent and 60percent xylan of the powdered rice straw and corn cob into xylooligosaccharides. Interestingly, hydrolysis by both types of enzymatic forms was found to produce predominantly xylopentose and xylohexose. Hence, the process is environment friendly and the predominant production of xylopentose and xylohexose could find unique prebiotic applications.