Genomics of cellulolytic bacteria Daniela E Koeck 1,3 , Alexander Pechtl 1,3 , Vladimir V Zverlov 1,2 and Wolfgang H Schwarz 1 The heterogeneous plant biomass is efficiently decomposed by the interplay of a great number of different enzymes. The enzyme systems in cellulolytic bacteria have been investigated by sequencing and bioinformatic analysis of genomes from plant biomass degrading microorganisms with valuable insights into the variety of the involved enzymes. This broadened our understanding of the biochemical mechanisms of plant polymer degradation and made the enzymes applicable for modern biotechnology.A list of the truly cellulolytic bacteria described and the available genomic information was examined for proteins with cellulolytic and hemicellulolytic capability. The importance of the isolation, characterization and genomic sequencing of cellulolytic microorganisms and their usage for sustainable energy production from biomass and other residues, is emphasized. Addresses 1 Department of Microbiology, Technische Universita ¨t Mu ¨ nchen, Emil- Ramann-Str. 4, D-85350 Freising-Weihenstephan, Germany 2 Institute of Molecular Genetics, Russian Academy of Science, Kurchatov Sq. 2, 123182 Moscow, Russia Corresponding author: Schwarz, Wolfgang H (wschwarz@wzw.tum.de) 3 Equally contributing. Current Opinion in Biotechnology 2014, 29:171–183 This review comes from a themed issue on Cell and pathway engineering Edited by Tina Lu ¨ tke-Eversloh and Keith EJ Tyo http://dx.doi.org/10.1016/j.copbio.2014.07.002 1367-5931/Published by Elsevier Ltd. Introduction The major components of plant biomass, cellulose and hemicellulose, are the most prevalent organic compounds on earth and a tremendous resource of energy [1]. Microbes provide enzymes for the monomerization of the polysaccharides in biomass to sugars which are con- verted by the same or by other microbes in fermentative processes to the compounds needed. By contrast to fossil carbon sources, energy produced from biomass is CO 2 -neutral. Microbiology can contribute to the CO 2 -neutral energy production by supplying efficient polysaccharide hydrolyzing enzymes. In addition ethanol, organic chemicals such as solvents, plastics and core chemicals for generating a huge variety of products can be produced from the sugar derived from plant biomass by microbiological conversion thereby suspending our energy consuming life style. However, especially cellulose is extremely recalcitrant to enzymatic degradation due to its crystallinity. The ability to hydrolyze it is a rare trait in bacteria and archaea, and is very rarely found in other organisms except in saprophytic fungi. Fungal cellulolytic enzymes occur in the genus Trichoderma and Aspergillus. They have been extensively investigated and are predominant in applications in the industrial biotechnology [2  ]. Recently, there were also some reports about cellulolytic crenarchaeal species, such as Desulfurococcus fermentans and Thermogladius cellulolyti- cus [3,4]. However, the knowledge about cellulolytic species within the archaeal kingdom is still very limited. This review is focusing on the truly cellulolytic bacteria, which are able to utilize natural (=crystalline) cellulose. Besides the cellulolytic fungi these few truly cellulolytic bacteria are the efficient hydrolyzers of plant cell wall polysaccharides in nature, especially in thermophilic anaerobic ecosystems. These saprophytic bacteria are remarkably well adapted and secrete a plethora of enzymes with a distinct synergistic behavior. Their highly specialized, often intricate enzyme systems include cel- lulases, hemicellulases, pectinases and other related gly- coside hydrolases, as well as polysaccharide lyases and carbohydrate esterases [5  ]. They expose cellulose fibers and degrade them to a mixture of cellobiose, cellotetraose and other cellodextrins, which are taken up by the cells and further degraded by b-glucosidases/cellobiases, or cellobiose-phosphorylases and cellodextrin-phosphoryl- ases. Concomitantly the hemicelluloses and pectins are degraded as well. Cellulose degrading bacteria About half of the bacteria containing genes for cellulases, hemicellulases and pectinases are saprophytes, the bac- teria efficiently degrading dead plant biomass (data from March 2011) [6  ]. However, only a small number possess more than 3 genes for b-1,4-glucanases (cellulases), a prerequisite for the effective degradation of natural cel- lulose. In fact, up to date only relatively few bacterial species able to hydrolyze and to utilize natural (=crystal- line) cellulose was isolated and characterized [7]. A list of the bacterial species known to utilize cellulose as sole Available online at www.sciencedirect.com ScienceDirect www.sciencedirect.com Current Opinion in Biotechnology 2014, 29:171–183