Wood-decay fungus

A wood-decay or xylophagous fungus is any species of fungus that digests moist wood, causing it to rot. Some species of wood-decay fungi attack dead wood, such as Serpula lacrymans, and some, such as Armillaria, are parasitic and colonize living trees. Excessive moisture above the fibre saturation point in wood is required for fungal colonization and proliferation. In nature, this process causes the breakdown of complex molecules and leads to the return of nutrients to the soil. Wood-decay fungi consume wood in various ways; for example, some attack the carbohydrates in wood, and some others decay lignin. The rate of decay of wooden materials in various climates can be estimated by empirical models.
Wood-decay fungi can be classified according to the type of decay that they cause. The best-known types are brown rot, soft rot, and white rot. Each produce different enzymes, can degrade different plant materials, and can colonise different environmental niches. Brown rot and soft rot both digest a tree's cellulose and hemicellulose but not its lignin; white rot digests lignin as well. The residual products of decomposition from fungal action have variable pH, solubility and redox potentials. Over time this residue becomes incorporated in the soil and sediment so can have a noticeable effect on the environment of that area.
Wood decay fungi are considered key species in the forest ecosystems because the process of decomposing dead wood creates new habitats for other species, helps in the nutrient recycling, participate in the energy transportation and transformation and provides food to other species. They are also used as indicator species for conservation projects.
Wood decay fungi are dependent on wood. Due to forestry, cutting trees and removal of decaying wood, many species are classified as threatened.

Brown rot

Brown-rot fungi break down hemicellulose and cellulose that form the wood structure. Cellulose is broken down by hydrogen peroxide that is produced during the breakdown of hemicellulose. Because hydrogen peroxide is a small molecule, it can diffuse rapidly through the wood, leading to a decay that is not confined to the direct surroundings of the fungal hyphae. As a result of this type of decay, the wood shrinks, shows a brown discoloration, and cracks into roughly cubical pieces, a phenomenon termed cubical fracture. The fungi of certain types remove cellulose compounds from wood, and hence the wood turns brown.
Brown rot in a dry, crumbly condition is sometimes incorrectly referred to as dry rot in general. The term brown rot replaced the general use of the term dry rot, as wood must be damp to decay, although it may become dry later. Dry rot is a generic name for certain species of brown-rot fungi. Brown-rot fungi of particular economic importance include Serpula lacrymans, Fibroporia vaillantii, and Coniophora puteana, which may attack timber in buildings. Other brown-rot fungi include the sulfur shelf, Phaeolus schweinitzii, and Fomitopsis pinicola.
Brown-rot fungal decay is characterised by extensive demethylation of lignins whereas white-rot tends to produce low yields of molecules with demethylated functional groups. There are very few brown rot fungi in tropical climates or in southern temperate zones. Most brown rot fungi have a geographical range north of the Tropic of Cancer, and most of these are found north of the 35° latitude, corresponding to a roughly boreal distribution. Those brown rot fungi between latitudes 23.5° and 35° are typically found at high elevations in pine forest regions, or in coniferous forest regions such as the Rocky Mountains or the Himalayas.

Soft rot

Soft-rot fungi secrete cellulase from their hyphae, an enzyme that breaks down cellulose in wood. This leads to the formation of microscopic cavities inside the wood and, sometimes, to a discoloration and cracking-pattern, similar to brown rot. Soft-rot fungi need fixed nitrogen in order to synthesize enzymes, which they obtain either from the wood or from the environment. Examples of soft-rot-causing fungi are Chaetomium, Ceratocystis, and Kretzschmaria deusta.
Soft-rot fungi are able to colonise conditions that are normally too hot, cold or wet for brown- or white-rot to inhabit. They can also decompose woods containing high levels of protective from the compounds that are resistant to biological attack; the bark of many woody plants contains a high concentration of tannins, which are difficult for fungi to decompose, as well as suberin, which may act as a microbial barrier. The bark acts as a form of protection for the more vulnerable interior of the plant. Soft-rot fungi are, apparently, not able to decompose matter as effectively as white-rot fungi, as they are less aggressive decomposers.

White rot

White-rot fungi are a type of fungi comprising agaricomycetes, basidiomycetes, and some ascomycetes that are capable of decomposing many tree species. It is now recognized that saprotrophic interactions have profound effects on forest biomes. White-rot fungi are characterized by their ability to break down the lignin, cellulose, and hemicellulose of wood. As a result of this ability, white-rot fungi are considered a vital component of the carbon cycle, because of their ability to access carbon pools that would otherwise remain inaccessible. The name "white rot" derives from the white color and rotting texture of the remaining crystalline cellulose from wood degraded by these fungi. Most knowledge of white-rot fungi comes from Coriolus versicolor and Phanerochaete chrysosporium. White-rot fungi show strong participation in interspecific competition, culminating in the evolution of lignin catabolism specificity. The current and future applications of white-rot fungi as a potential component of mycoremediation merit greater study of these saprotrophs.

Biochemistry

Compared to other saprotrophs, white-rot fungi possess the specialized ability to cleave lignin into smaller, more processable molecules. Lignin is a biopolymer which combines with cellulose to form the lignocellulose complex, an important complex that confers strength and durability to plant cell walls. Lignin is a macromolecule formed from the combination of many phenolic aromatic groups via oxidative coupling. Because of its high stability, lignin is incapable of being broken down through simple decomposition. As a result, white-rot fungi employ a series of enzymes that break lignin down into smaller aromatic rings. The relative abundance of phenylpropane alkyl side chains of lignin characteristically decreases when decayed by white-rot fungi. Since lignin is the specialized food source of white-rot fungi, understanding the two different catabolic pathways is important.

Lignin metabolism through peroxidases

The first way white-rot fungi can break down lignin involves a high-redox-potential catalyzed peroxidase attack on the heme pocket, thus reducing the stability of lignin. The process starts with creation of extracellular hydrogen peroxide, a process completed via glyoxal oxidase. Extracellular hydrogen peroxide may be responsible for creation of hydroxyl radical via the Fenton reaction: Fe²⁺ + H₂O₂ → Fe³⁺ + ·OH + OH⁻ The peroxidases used to oxidize lignin are lignin peroxidase, manganese peroxidase, and versatile peroxidase. These peroxidases are commonly referred to as fungal class II peroxidases. Research suggests there may be another group of POD enzymes: basal peroxidases, including novel peroxidase. The NoP of Postia placenta is characterized by its inability to bind Mn²⁺ and its low redox potential. PODs developed in the common ancestor of white-rot, brown-rot and mycorrhizal fungi but these enzyme families have undergone secondary loss or contraction in the latter two groups. LiPs are oxidioreductases specific to lignin degradation. VPs are a class of peroxidase that combines elements of both LiPs and MnPs. LiPs and VPs are specific to heme product architecture allowing direct oxidation of benzene groups regardless of linkages. Direct oxidation of benzene groups results in the creation of an unstable radical aromatic. However, the hydrogen peroxide, bound to the heme group on the heme pocket, is unable to access the bulky lignin due to steric hindrance. As a result, LiP and VP enzymes create a tryptophan radical on their protein surface which allows long-range electron transfer from the aromatic substrate to the activated cofactor.

Lignin metabolism through laccase

The second mechanism for breaking down lignin involves laccase, a low-redox-potential oxidase incapable of direct attack. Laccase can be used both in breaking and forming lignin. It cleaves lignin by reducing oxygen, creating a free radical which allows a hydroxyl radical to attack the ring and deposit an alcohol group. Deprotonation follows, resulting in the breaking of C-C bond into two aromatic rings. These products enter the fungal hyphae to be further broken down via catabolic processes. After the lignin complex is broken down, other saprotrophs can enter and begin degrading the newly created products. The final products of these transformations are carbon dioxide and water. While it is known that brown-rot fungi can also target lignin, they are only capable of modifying and are not capable of completely recycling it with a few exceptions. The ability to degrade lignin, previously supposed to only occur in white-rot fungi which have PODs, was found in Botryobasidium botryosum and Jappia argillacea, two brown-rot fungi, lacking PODs. While the general pathway is currently unknown, research supports the existence of a continuum of features that separate the two fungal types rather than distinct categories.