Fungi can use many different carbon sources. There is however differences between different fungal species in how well they can use different carbon sources (Fig 7).
Fig 7. Substrates used by fungi. The is an approximation to the relative number of species that can use the different types of carbon sources. Most fungal species can use monosaccharides. Few fungi can use the single carbon compounds like methane and few fungi can break down the very large and recalcitrant polymer lignin.
One common substrate that is available to fungi and where bacterial degradation plays a very little role is wood. The succession of fungal species in wood is illustrated in Fig 8. First wood is colonised by week parasites and pathogens lready on the tree. When a branch or a tree die and fall off next comes pioneer saprotrophs. These first two groups live mainly on easily degradable compounds in the wood. The polymer degrading fungi that attacks the cellulose then follows. After this come the degraders of recalcitrant compounds. These last fungi also attack the lignin in the wood to get to the cellulose. Lignin is a very poor substrate but it protects the cellulose from breakdown. During most of the breakdown process secondary opportunistic fungi are also present. These grow on dead remains of the other fungi, parasitize other fungi or grow commensally with polymer-degraders.
Many different fungal species can grow on the same piece of wood. They often interact and try to poison each other by excreting phenolic compounds. The defence strategies used by the attacked fungus is to polymerise the phenolics. In wood these areas of "conflict" between adjacent mycelia can be seen as dark polyphenolic demarcation lines (Fig 8).
Fig 8. Part of a decaying tree stump showing polyphenolic demarcation lines between adjacent mycelia (top). Decorative bowl made from beech wood with dark zone lines
The decomposition of wood
Wood is a composite material made up of cellulose fibres embedded in a relatively hydrophobic lignin matrix (Fig 9). For a complete breakdown of wood the lignin matrix has to be removed ore at least made hydrophilic.
Fig 9. Wood is a composite material made up of cellulose fibres in a matrix of lignin.
Cellulose is a polymer that has to be broken down extracellularly. Two different kinds of extracellular enzymes are active, the cellobiohydrolases and the endoglucanases (Fig 10). The endoglucanases cuts randomly in the polymer crating many new ends. Then the cellobiohydrolases attaches to the ends of these shorter cellulose fragments and cuts of dimeric cellobiose units from the ends as they move along the polymer. The produced cellobiose is then taken up by active transport trough the membrane. Cellobiose is degraded to glucose intracellularly. There is a constitutive low production of the extracellular enzymes. Cellobiose is sensed and indicates the presence of cellulose. At low cellobiose concentrations cellulolytic enzymes are up-regulated and at high concentrations they are down-regulated to save production on extracellular enzymes.
cellulolytic enzymes are up-regulated and at high concentrations they are down-regulated to save production on extracellular enzymes.
Fig 10. Enzymatic processes involved in the degradation of cellulose
A problem for all wood decomposing fungi is to remove or change the lignin so that the cellulose can be attacked. Lignin is a complicated polymer built up of a complex mixture of compounds (a heteropolymer). It is a poor substrate and is not used to generate energy by fungi. On the other hand the fungi have to spend energy to either break it down like the so called white-rotting fungi do or chemically change it like the brown-rotting fungi do. The wood rotting fungi does not attack the lignin by normal enzymatic processes since:1. A normal enzyme can attack only one type of chemical bonds and there are too many different kinds of bonds in lignin. 2. Lignin is rather hydrophobic and this limits the access to enzymes. The fungi instead use enzyme systems that generate free radicals that attack the polymer and the breakdown becomes similar to a thermal combustion. These processes have consequently been called enzymatic combustions.
Fig 11. Chemical structure of lignin
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