Endophytes are defined as organisms that grow within a living host plant but not strictly within living cells, thereby deriving nutrition without detrimental symptoms for the host. It is believed that the living stems, twigs, and leaves of most woody plants contain symptomless endophytes, but because of their clandestine nature their prevalence is ambiguous, and identification of their presence relies on arduous techniques such as careful isolation from surface sterilized tissues and histological studies (Petrini 1991). Numerous endophytic species may be potentially allied with an individual host (e.g., 85 different fungal taxa have been isolated from root and stem tissues of Alnus). Moreover, host specificity varies, with some endophytes displaying little host specificity (e.g., Phomopsis has been isolated from Buxus, Ilex, Hedera, Ruscus, Ulex, Pinus, Fagus, Juniperus, Fraxinus, and Quercus; and anamorphs of Xylaria isolated from Fagus, Fraxinus, and Quercus) whereas others, such as Peniophora and Vuilleminia comedens tend to be more stringent (Griffith and Boddy 1990; Fisher and Petrini 1990). Although resident endophytes may not produce disease symptoms as such, their occupation is not without effect on the host.

The leaves or needles of many if not most plants contain fungal endophytes, estimated at a supporting cost of up to 0.5% of annual needle production in the case of conifer needle endophytes (Carroll 1992). However, the presence of some endophytes, such as Phomposis oblonga in elm stems (Carroll 1991), may confer a selective advantage on the plant host, either due to secondary metabolite production or conceivably due to competitive exclusion, thereby protecting against pathogen invasion particularly insect attack or larvae development. Some may even be potential pathogens of other competitor plants, with obvious consequences for the plant community, and have therefore been investigated as a potential biological control system (Leuchtmann and Clay 1988).

Endophytes may also be involved with initiation of decay following stress or death of host tree tissues. Many endophytes, such as the Xylariaceae and their anamorphs, Daldinia and Hypoxylon spp. and Nodulisporium, are known wood-decay species. Some are observed to fruit extensively on very recently dead fallen logs, or form extensive primary decay columns or strip cankers (e.g., by Eutypa spinosa in European beech) very rapidly following host tree stress, particularly after drought (Hendry et al. 1998). Observation of such rapid and massive decay column formation has identified the role of endophytic morphs or latent invaders, distributed as somatically compatible or clonal latent propagules, dispersed within functional sapwood of standing trees. Such propagules may then be rapidly activated due to host stress such as declining wood water content and the growing spatial domains of individual genets may then converge and merge, thereby securing early and spatially extensive infection of dead wood (Boddy 1992; 1994). Latent presence of propagules in living bark tissues allows rapid and extensive invasion of dead attached twigs or recently felled logs (Griffith and Boddy 1990). However, detection of propagules does not necessarily implicate that species in initiating decay, as some endophytes have been isolated from host species known infrequently to support decay columns of these latent colonizers (Boddy 1994; Petrini 1991). This seemingly destructive activity within stressed and functionally redundant tissues may also be of ecological advantage to the tree, resulting in natural pruning of expensive nutrient sinks and the subsequent mobilization of nutrient resource.

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