Microorganisms involved in the decay of plant biomass use an array of biochemical processes to mediate conversion. They can be categorized either genetically using molecular biology tools and/or biochemically, with emphasis on the types ofhydrolytic enzymes they produce. The biodegradation of complex polysaccharides is a multistep, hierarchical process. It is hierarchical in two senses. In general, removal of sugar modifications makes subsequent attack of main chain-degrading enzymes much more effective. Secondly, in nature there is a hierarchy of polymer degradation, from the least to the most recalcitrant compounds. During the early stages, the rate of decay is determined by the accessibility of the more easily decomposed carbohydrates. In general, pectins are degraded first, followed by hemicellulose, and then finally cellulose and lignin. This results in a succession of microorganisms that are able to assimilate specific substrates.

Hydrolytic enzymes capable ofbreaking down cellulose and hemicellulose (complex poly­mers of arabinose, mannose, glucose, and xylose) are widespread and are produced by a wide range of microorganism that include fungi, actinobacteria, Clostridiaceae, and mem­bers of the a-, (3-, and у -proteobacteria. The efficient conversion of plant polysaccharides is achieved by an array of enzymes with varying but synergistic specificities and activities. The diversity of these enzymes in nature is illustrated by the growing number of entries of hydrolytic enzymes in glycosyl hydrolase-specific databases such as the Carbohydrate-Active enzymes (CAZy) database (5). With the increasing number of sequenced genomes available it was recently estimated that over 12 000 glycosyltransferase and glycoside hydrolase open reading frames will have been added to the database during 2006 (6).

A second and more narrowly defined functional group includes the white rot Basidiomy — cota and xylariaceous Ascomycota, which are the primary agents of lignin degradation by secretion of nonspecific, extracellular enzymes that modify the lignin macromolecule. Lignin is a polyphenolic heteropolymer that is interconnected by stable ether and carbon-carbon bonds making it extremely resistant to microbial attack. Lignin degradation is carried out by the action of lignin modifying enzymes that are produced primarily by the white rot fungi. Lignin breakdown is an obligate aerobic reaction carried out by oxidative ligninolytic enzymes that remove various functional groups, side chains, and aromatic rings randomly from the lignin macromolecule. The initial steps often involve O2- or H2O2-dependent, lignin peroxidase, Mn peroxidase, or laccase. Frequently, flavin-dependent enzymes supply H2O2 to the lignin peroxidase or Mn peroxidase (7, 8). The lignin polymer is reduced to smaller, low molecular weight fragments that are then available for further decomposition by either fungi or bacteria.

Historically, microbiologists have defined decay communities based on individual isolated bacteria and on the basis of their physiologic and nutrition requirements. In general, classical isolation techniques require substantial knowledge of the organism’s habitat so that it can be reproduced and one population can be enriched over others. Within a small particle of biomass several different microenvironments can exist differing both chemically and physically. Physiochemical conditions, such as oxygen concentration change both temporally and spatially during decay. In many cases, individual bacteria cannot be isolated due to obligate interdependence upon other bacteria for growth that must be supplied using co­cultures of helper bacteria. Microorganisms may also be slow — growing, or obligate anaerobes requiring patience and tenacity to isolate and characterize. With the advent of new molecular tools for describing microbial communities, it has become clear that bacteria grown isolated in “pure culture” underrepresent the microbial diversity in most environments and are generally only a minor component.