While mycorrhizal fungi are beneficial, there are a large number of formidable fungal pathogens that inhabit the world. Given their abundance it might seem a simple case of pathogenic fungus kills plant whenever the two meet. However, as is usual in the biological world, it is rarely quite this simple. Various examples could be used but perhaps one of the most widespread global fungal pathogens is the honey fungus, really a set of parasitic root and butt-rot fungal species that can live saprotrophically once its host is dead, using the dead stump as a base for further infection. There are numerous of these Armillaria species, geographically overlapping and varying greatly in their pathogenicity: A. mellea is often a virulent pathogen especially in lowlands, and is most dangerous in the absence of other fungi. Having killed a tree in a garden situation it may spread, devastating vulnerable trees and shrubs such as rhododendrons. It appears not to be so dangerous a parasite in forests where, in the opinion of a number of mycologists, the presence of other fungi diminish its effectiveness as a parasite. Armillaria ostoyae affects mostly conifers; A. gallica is normally a fairly innocuous saprotroph; and for many others little is known of their virulence. It has been suggested that no tree in the UK ever shows its full potential growth because of the stultifying effects of honey fungus even where it doesn't kill. This is undoubtedly a gross overstatement but demonstrates the legendary ability of some species to infect. But even here, the condition of the potential host can be of considerable importance in determining whether it will or will not become infected. Water stress, caused both by dry soils and waterlogging, has been shown to influence infection by honey fungus of susceptible woody species. Popoola and Fox (2003) used isolates of Armillaria mellea and A. gallica to infect healthy blackcurrant, strawberry, Lawson cypress and privet. Previous to this the host plants had been watered normally, subjected to drought or waterlogged for a period of 4 weeks. At the end of this period chemical analysis of the roots showed that levels of protein, lipids and carbohydrates were higher in both groups of stressed plants than they were in those watered normally. The increased nutrient levels found in both the droughted and waterlogged plants were sufficient to enhance the virulence of both A. mellea and A. gallica.
Pathogenic fungi are also known to affect hosts in different ways. A considerable number of mountain pines Pinus mugo in the Swiss Central Alps which had been killed by root fungi were investigated by Cherubini et al. (2002), in an attempt to evaluate the causes of the destabilization of the stands involved. In trees infected with honey fungus the decline in width of the annual rings after infection was relatively slow, whereas in c. 60% of cases involving Fomes root rot Heterobasidion annosum (an important circumboreal root pathogen) it was abrupt. It seems that honey fungus is, at least in this site, a secondary pathogen which tends to attack trees already weakened by competition, while H. annosum infects and kills trees relatively swiftly. Although tree rings can be used to indicate the history of decline they do not enable the date of infection to be determined. It should also be noted that in some trees, for a period prior to death, tree-ring growth occurred in only part of the trunk circumference.
A major difficulty in the investigation was that of determining the year of tree death. This has sometimes been taken as the year in which the tree no longer possesses any green needles; alternatively the year in which the outermost tree ring was formed may be taken as the last year of life. The problem is that green needles usually remain on a conifer for more than a year after the last annual ring is formed. The most striking discrepancy between the two criteria was in the case described above, where the variation was a remarkable 1-31 years.
Fungal attacks on seeds and young seedlings can play an important role in tree establishment. Evidence is building up that in tropical forests and more recently in temperate forests (O'Hanlon-Manners and Kotanen, 2004) the abundance of seedlings below canopy gaps is not just due to high light levels but also to temperature and moisture regimes less favourable to fungal pathogens. Below the canopy of trees loss of seeds and seedlings to pathogens is much higher than in warmer, drier gaps.
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