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Are there any documented cases of extinction of a species of fungus?

Are there any documented cases of extinction of a species of fungus?


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Are there any documented cases of extinction of a species of fungus? I imagine it would be hard to detect something like this.

Edit: documented by humans when it happened and/or induced by humans.


According to the International Union for Conservation of Nature's Red List there are many endangered fungi, but none that are documented to have become extinct within the time frame of interest to you.

However, it seems likely that some fungi have gone extinct with their plant hosts - according to the IUCN there have been 133 documented extinctions of plant species. In particular, mycorrhizal1 (and other) associations between plants and fungi are prevalent and some of these associations appear to be specific (i.e. the fungus only associates with one plant species). For example, there are reported to be 28 species of fungi that only associate with the shrub Lantana camara.2

References:

1: Hoeksema, J. D., Bever, J. D., Chakraborty, S., Chaudhary, V. B., Gardes, M., Gehring, C. A.,… & Lajeunesse, M. J. (2018). Evolutionary history of plant hosts and fungal symbionts predicts the strength of mycorrhizal mutualism. Communications biology, 1(1), 116.

2: Hawksworth, D. L., & Rossman, A. Y. (1997). Where are all the undescribed fungi?. Phytopathology, 87(9), 888-891.


Yes. One example is of a fungus named Prototaxites. It was originally thought to be a tree, but it was a massive, tree-like fungus.


Phellinus

Robert A. Zabel , Jeffrey J. Morrell , in Wood Microbiology (Second Edition) , 2020

Major heart rots

Phellinus (Fomes) pini is reported to be the major cause of stem decays in conifers in the northern temperate zone. It is particularly severe on Douglas-fir in the northwest and white pine in the east. The common names for this decay are white-pocket rot, white spec, or red-ring rot since the small decayed pockets in some hosts are concentrated in the earlywood bands. The wood is a pink-reddish to purplish color in the incipient and early decay stages.

In the early stages of the decay, the hemicelluloses and lignin are attacked selectively and in the later decay stages cellulose remains in many, small-lenticular shaped pockets. Wood in the early stages of the red-ring rot is reported to be suitable for general construction uses until the decay pockets are visible (firm pocket stage). Wood in the firm-pocket stage is also acceptable for low-grade construction lumber and plywood. The fungus invades the living sapwood in the advanced stages of decay and sometimes forms cankers. Infected wood in the outer-sapwood zones is often resin infiltrated. The decay fungus dies out rapidly once the tree is cut and seasoned.

External evidences of red-ring rot in standing trees are the presence of swollen knots containing brownish punky masses of fungal material, extensive resin flow from the base of branch stubs, and the presence of characteristic brownish-shelving perennial basidiomata ( Fig. 12.2 ). Boyce (1961) reported that heart-rot columns extended a meter or more above the top basidioma or punk knot and about 1.3 m below the lowest. Haddow (1938) showed that small branches or buried weeviled tips were common infection courts on eastern white pine in the East. In studies of the infection process, DeGroot (1965) reported that the weeviled tip preference may reflect lower concentrations of pinosilvin in weeviled tips compared to recently dead branches. Pinosilvin levels decreased as branch stubs age and eventually basidiospores of Phellinus pini were able to germinate on these substrates however, heartrot infections were not obtained.

Figure 12.2 . Evidence of Phellinus pini decay in logs or lumber can include (A) a typical basidioma on red spruce, (B) an early stage (firm pocket decay) of decay in Douglas-fir showing decay concentrated in the earlywood, (C) a punk knot indicating extensive decay, (D) buried weeviled tips (arrows) are common infection courts for P. weirii in eastern white pine and a useful indicator of decay.

Photo (C) courtesy From Shigo, A. L. (1989). A New Tree Biology: Facts, Photos and Philosophies on Trees and Their Problems and Proper Care, second ed. Shigo and Trees, Associates, Durham, New Hampshire. www.ShigoandTrees.com .

Echinodontium tinctorium is the major cause of a serious heartrot in the true firs and western hemlock in the Pacific Northwest. The importance of this fungus varies with region and site, with losses as high as 30% of the gross merchantable volume on some poor sites. This fungus is a brown rot that causes a stringy or fibrous-textured decay. Wood in the incipient decay stage is a light-tan color and may extend 1–2 m longitudinally beyond the point of visible decay. In some cases, the decay may extend from the roots to the larger branches. Perennial, hoof-shaped basidiomata form beneath branch stubs ( Fig. 14.4 ) and are readily recognized by the toothed pore surface and the bright-red context that gives the fungus its common name “Indian paint fungus”. A single conk on a stem means essentially total stem cull. The earliest appearance of heart rot in stems has been estimated to range from 45 to 75 years. Infection is believed to originate some years earlier at the base of small branchlets on shade-killed lower branches. The fungus remains dormant for years as the branch tissues are slowly enveloped by stem growth. The fungus becomes activated later in response to surface wounds or loss of tree vigor ( Etheridge and Craig, 1976 ). Managerial controls appear to be limited to determining regional pathologic rotations and silvicultural treatments to limit suppression of tree growth.

Phaeolus (Polyporus) schweinitzii causes a serious brown-cubical rot in the roots and the butt log of all conifers species in the north temperate zone with the exception of cedars, junipers, and cypresses. This fungus is a particularly dangerous heart-rot pathogen, since the early decay stages are barely detectable in the wood, yet associated with sharp reductions in tensile strength and toughness ( Scheffer et al., 1941 ). There is a slight yellowing of the wood in vertical spires at the early stages of attack and incipient decay may project a meter or more above the zone of visible decay. The advanced decay stage is characterized by a brown cubical rot with near total tissue collapse. Decay develops in the roots and butt portions of logs and reaches a height of 2.4 m, although the decay column may extend 4.5–6.0 m above ground in some cases. Occasionally, young trees are killed by extensive decay in the roots and wind throw is common in severely diseased stands. The only external evidence of this heart rot is the occasional presence of the characteristic brown, velvety textured, stipitate basidiomata arising from the forest floor near the base of the infected tree or, rarely, sessile conks attached to basal wounds ( Fig. 14.4 ). Presumed entry points of the fungus are through broken roots or deep basal wounds. Conifer roots previously infected by Armillaria mellea may be predisposed to colonization by P. schweinitzii ( Barrett, 1970 ). Decayed trees often occur in clusters in pine stands, but the decay may not be detectable until felling. Managerial controls are not known other than following pathologic rotations and avoiding planting on sites where A. mellea is established. Heavy stand stocking to minimize root breakage during wind storms has been suggested as a potential method for decreasing infection.

Fomitopsis officinalis occurs on conifers in North America and Europe. It is important primarily on Douglas-fir, sugar pine, ponderosa pine and western hemlock in western North America and produces a brown cubical rot in the late stages that is often characterized by the presence of thick mycelial felts in the shrinkage cracks. Like P. schweinitzii, this fungus is dangerous in wood products since the early stage (a faint yellow to brown) is almost imperceptible and incipient decay may extend a meter or more longitudinally beyond the zone of visible decay. Infection pathways are uncertain but are presumed to occur through large broken branches in the upper bole and broken tops, but some infections are also associated with fire scars and logging wounds. Large chalky white, hoof-shaped perennial basidiomata are found in wound faces or knots ( Fig. 14.4 ) and the presence of a single basidioma indicates total cull.

Phellinus (Fornes) igniarius is an important major cause of heart rot in birches, maples, beech, and oaks in North America. Phellinus tremula, a closely related species, is the major cause of heart rot in aspens. This fungus causes a white-spongy rot in the heartwood, but can also invade and kill living sapwood. The rot, as seen on stem-cross sections, is characterized by a yellowish-green to brownish-black outer invasion zone that surrounds a core of irregularly mottled, white spongy wood. The advanced decay often contains fine, concentrically arranged zone lines. The decayed wood is still usable for pulping purposes. The fungus may continue to decay stored wood for some months, but eventually dies out in the finished product. Perennial hoof-shaped basidiomata commonly develop in late decay stages at wound margins or the base of branch stubs. The presence of a single conk generally indicates a cull tree with decay columns ranging from 3 to 5 m in length. Wounds are believed to be the principal infection sites. Minimizing stem injuries and following regional pathological rotations are the recommended management practices for limiting damage by this fungus.

Inonotus (Poria) obliquus and I. (Polyporus) glomeratus cause a mottled white rot that is very similar to decays caused by Phellinus igniarius. Inonotus obliquus is a major cause of heart rot in birches in the northern hemisphere, while I. glomeratus is important primarily on maples and beech in eastern North America. Both decay fungi form large, black, coal or clinker-like abortive basidiomata that are sterile and perennial on living hosts. Both fungi also invade the living sapwood and may form stem cankers. The presence of a single sterile conk indicates extensive heart rot and a cull tree. Swollen knots or dead bark on canker faces in beech, may partially conceal the sterile conks of I. glomeratus. Wounds and cankers appear to be the principal infection courts for these fungi. Inonotus obliquus forms a brown resupinate basidioma in the decayed sapwood of dead hosts splitting off the outer sapwood and bark layers to expose the hymenial surface, while I. glomeratus forms large effused-reflexed basidiomas on the lower surface of logs ( Zabel, 1976 ). The basidioma of I. obliquus is also called “chaga” and is reputed to have medicinal properties. Neither fungus continues to decay wood in the product form.


White-Nose Syndrome

"Almost all North American bats rely on forests for survival," says Roger Perry, USDA Forest Service research wildlife biologist. Perry recently led the team that updated Forest Management and Bats, a booklet designed for private landowners and anyone managing forests. It was first published in 2006 by Bat Conservation International, and Daniel Taylor of BCI wrote the original version and contributed to the update. The updated publication is a 2020 product of the White-nose Syndrome National Plan.

White-nose syndrome has killed over 90% of northern long-eared, little brown and tri-colored bat populations in fewer than 10 years, according to a new study published in Conservation Biology. Researchers also noted declines in Indiana bat and big brown bat populations. The findings, detailed in "The scope and severity of white-nose syndrome on hibernating bats in North America," underscore the devastating impacts of the deadly fungal disease. The research tapped into the most comprehensive data set on North American bat populations to date, which includes data from over 200 locations in 27 states and two Canadian provinces.

The U.S. Fish and Wildlife Service (Service) announced today that a team of six researchers from Oregon State University and the University of California, Santa Cruz are the winners of a national prize challenge to combat white-nose syndrome (WNS), a lethal wildlife disease that has killed millions of bats in North America and pushed some native bat species to the brink of extinction. The Service's White-nose Syndrome Program launched the challenge last October as part of a multi-faceted funding strategy to develop management tools to fight the disease. A total of 47 proposed solutions were submitted for permanently eradicating, weakening or disarming Pseudogymnoascus destructans, the fungus that causes WNS , thereby improving survival in bat species affected by the disease. A panel of 18 experts from academic institutions, federal agencies and nongovernmental organizations evaluated the challenge entries based on readiness, deployment scale, species susceptibility, ease of use, cost efficiency, efficacy and risk to resources.

In the coming months, the Service will announce a second challenge to offer an additional $80,000, as we continue to pursue novel, innovative solutions that could help us permanently eradicate, weaken, or disarm the fungus that causes white-nose syndrome. The Service plans to hold additional idea prize challenges in the future to invite solvers with a diverse array of knowledge, skills, expertise and perspectives to help the agency tackle today’s toughest conservation issues.


Interspecific difference in pollinators (pollinator isolation) is important for reproductive isolation in flowering plants. Species-specific pollination by fungus gnats has been discovered in several plant taxa, suggesting that they can contribute to reproductive isolation. Nevertheless, their contribution has not been studied in detail, partly because they are too small for field observations during flower visitation. To quantify their flower visitation, we used the genus Arisaema (Araceae) because the pitcher-like spathe of Arisaema can trap all floral visitors.

We evaluated floral visitor assemblage in an altitudinal gradient including five Arisaema species. We also examined interspecific differences in altitudinal distribution (geographic isolation) and flowering phenology (phenological isolation). To exclude the effect of interspecific differences in altitudinal distribution on floral visitor assemblage, we established ten experimental plots including the five Arisaema species in high- and low-altitude areas and collected floral visitors. We also collected floral visitors in three additional sites. Finally, we estimated the strength and contribution of these three reproductive barriers using a unified formula for reproductive isolation.

Each Arisaema species selectively attracted different fungus gnats in the altitudinal gradient, experimental plots and additional sites. Altitudinal distribution and flowering phenology differed among the five Arisaema species, whereas the strength of geographic and phenological isolations were distinctly weaker than those in pollinator isolation. Nevertheless, the absolute contribution of pollinator isolation to total reproductive isolation was weaker than geographic and phenological isolations, because pollinator isolation functions after the two early-acting barriers in plant life history.

Our results suggest that selective pollination by fungus gnats potentially contributes to reproductive isolation. Since geographic and phenological isolations can be disrupted by habitat disturbance and interannual climate change, the strong and stable pollinator isolation might compensate for the weakened early-acting barriers as an alternative reproductive isolation among the five Arisaema species.


Differences in Defensive Volatiles of the Forked Fungus Beetle, Bolitotherus cornutus, Living on Two Species of Fungus

Forked fungus beetles, Bolitotherus cornutus, feed, mate, and live on the brackets of several species of shelf fungus that grow on decaying logs. In response to the specific threat stimulus of mammalian breath, B. cornutus beetles produce a volatile defensive secretion. We tested beetles collected from different host fungi to determine whether defensive secretion blends varied with host type. Using solid phase microextraction and gas chromatography-mass spectrometry, we detected large amounts of the alkylated benzoquinones, methyl-p-benzoquinone (toluquinone) and ethyl-p-benzoquinone, and smaller quantities of p-benzoquinone, 3-methylphenol (m-cresol), 3-ethylphenol, 2-methylhydroquinone, and 2-ethylhydroquinone in secretions. Volatile composition did not differ between male and female beetles. Secretions did differ between beetles collected from two species of fungus, Ganoderma applanatum and Fomes fomentarius, with the relative amount of p-benzoquinone secreted being the most important factor. Other relationships among the volatile components are discussed.

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Discussion

In this study, as in numerous preceding works, pure culture synthesis techniques (axenic conditions) were used to establish if known fungal species could colonize fine roots of trees ( Riffle, 1973 Danielson, 1984 Egger & Paden, 1986, Buscot & Kottke, 1990 Yamada et al., 2001 ). In the cited works, the observed associations ranged from mycorrhizal symbiosis to pathogenicity, while many species did not show any affinity to roots. Yet, as axenic experimental design provides a method of testing plant–fungus interactions without interference from other soil organisms and under ecological conditions that differ from those in the field, care must be taken in extrapolating these results to natural conditions. Thus, the ability of a fungus to form mycorrhizas with a host in pure culture does not prove mycorrhizal formation in nature and vice versa ( Riffle, 1973 Egger & Paden, 1986 Buscot & Kottke, 1990 ).

Yet, in the present experiment, we have supporting evidence that the tested fungi are also able to colonize fine conifer seedling roots under xenic conditions in the field. In fact, the current results complement the findings of our earlier study, in which the colonization of healthy-looking conifer root tips by H. fasciculare, P. centrifuga and P. gigantea was observed in the bare root nursery ( Menkis et al., 2005 ).

Consequently, the results of this work provide more evidence for the ability of wood-decay fungi to live in the soil and to colonize healthy fine roots of conifer seedlings. The most evident pattern was exhibited by P. gigantea in P. abies roots, on the tips of which the fungus consistently formed mycelial mantle (Fig. 1b) and spread inside intercellularly between epidermal cells (Fig. 1c). Despite the fact that this was not explicitly demonstrated in the remaining microcosm systems, both the isolations and direct sequencing from root tips following their intensive external sterilization indicated clearly and consistently the presence of active mycelium of each tested fungus in the internal root tissue of healthy-looking seedlings of both tree species.

In the present study, no visible negative impacts on seedling vitality were observed in our microcosms during a half-year period (Fig. 1a). By contrast, a few similar attempts at microcosm syntheses of conifer seedling roots with saprotrophic soil-inhabiting basidiomycetes Leucopaxillus giganteus (Sow.Fr.) Sing. and Collybia dryophila (Bull.Fr.) Kummer have resulted in retarded growth ( Yamada et al., 2001 ) or death of a plant ( Riffle, 1973 ).

The rhizosphere environment has not been previously considered as a possible ecological niche for wood-decomposing fungi ( Rayner & Boddy, 1988 ). Therefore, to our knowledge these are the first reports on the presence of wood-decaying saprotrophs in fine, apparently healthy roots of trees and in the soil both in vitro and in vivo. This provides new insights into the ecology of wood-decay fungi, since, in the past, studies of their community ecology have been based on the occurrence of their fruitbodies on a given woody substrate, which was consequently regarded as the ultimate habitat of those fungi in nature ( Jahn, 1979 Eriksson et al., 1981 Breitenbach & Kränzlin, 1986 Hansen & Knudsen, 1992, 1997 Ryvarden & Gilbertson, 1993, 1994 Ryman & Holmasen, 1998 ). It is known, however, that such data can provide misleading information, since the fruitbody distribution does not necessarily fully reflect mycelial distribution and activity ( Rayner & Boddy, 1988 ). For example, our recent work has revealed a poor correspondence between fruitbody occurrence on woody debris and the relative abundance of fungal mycelia within the given substrate ( Allmer et al., 2006 ).

The currently reported results expand our knowledge of the habitat of wood-decay saprotrophs, demonstrating the ability of some of these fungi to live in the rhizosphere and colonize fine roots of trees, resembling closely the patterns characteristic for mycorrhizal fungi. Moreover, when exposed both to dead wood and to soil, mycelia of P. centrifuga exhibited more extensive growth in the soil (Fig. 1d). Consequently, two questions arise: do the observed colonization patterns result in a functional mycorrhizal relationship and are other species of wood-decay fungi also able to colonize fine roots of trees in a similar manner? Furthermore, P. gigantea is a large-scale biological control agent, its spore suspension being sprayed on cut stump surfaces in over 100 000 ha of forest in Europe annually ( Thor, 2003 ). As it was demonstrated that the fungus persist in sprayed stumps for up to 7 yr, and produces abundant sporocarps there which release viable basidiospores to the environment ( Vasiliauskas et al., 2005 ), it would be of interest to check if such an increased load of inoculum has any impact on mycorrhizal communities in treated forest stands.

The functional relationships of H. fasciculare, P. centrifuga and P. gigantea with P. abies and P. sylvestris are therefore being investigated in ongoing studies. Moreover, we are presently monitoring microcosms containing 200 species of wood-decay basidiomycetes with three species of trees (P. abies, P. sylvestris and Betula pendula Roth). Analysis of these systems will be carried out by investigating the potential for bidirectional transfer of nutrients and carbohydrates ( Finlay & Read, 1986 Lindahl et al., 1999, 2001 ), and should provide new information on how widespread the ability to colonize healthy roots is in fungal saprotrophs. For the future, it would be of utmost importance to study the functional relations of saprobic fungi and trees in situ, open to competition between fungi. The investigations of fungi on seedling roots that are established on Rotstop-treated stumps would be of particular interest.


The genus Phomopsis: biology, applications, species concepts and names of common phytopathogens

The genus Phomopsis (teleomorph Diaporthe) comprises phytopathologically important microfungi with diverse host associations and a worldwide distribution. Species concepts in Phomopsis have been based historically on morphology, cultural characteristics and host affiliation. This paper serves to provide an overview of the current status of the taxonomy in Phomopsis with special reference to biology, applications of various species, species concepts, future research perspectives and names of common pathogens, the latter being given taxonomic reappraisal. Accurate species identification is critical to understanding disease epidemiology and in developing effective control measures for plant diseases. Difficulties in accurate species identification using morphology have led to the application of alternative approaches to differentiate species, including virulence and pathogenicity, biochemistry, metabolites, physiology, antagonism, molecular phylogenetics and mating experiments. Redefinition of Phomopsis/Diaporthe species has been ongoing, and some species have been redefined based on a combination of molecular, morphological, cultural, phytopathological and mating type data. Rapid progress in molecular identification has in particular revolutionized taxonomic studies, providing persuasive genetic evidence to define the species boundaries. A backbone ITS based phylogenetic tree is here in generated using the sequences derived from 46 type, epitype cultures, and vouchers and is presented as a rough and quick identification guide for species of Phomopsis. The need for epitypification of taxonomic entities and the need to use multiple loci in phylogenies that better reflect species limits are suggested. The account of names of phytopathogens currently in use are listed alphabetically and annotated with a taxonomic entry, teleomorph, associated hosts and disease symptoms, including brief summaries of taxonomic and phylogenetic research. Available type culture information and details of gene sequences derived from type cultures are also summarized and tabulated.

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Conclusions

In conclusion, nail and skin infections due to Chaetomium spp. occur predominantly in immunocompetent patients, typically presenting with secondary to traumatic implantation, or in elderly people. The infection may manifest as phaeohyphomycosis, chromoblastomycosis or onychomycosis with brown discoloration. The infection progresses slowly and patients usually present several years after it first appears. For the first time ever, we report a case of infection caused by C. brasiliense, involving otitis externa in a cancer patient that manifested histologically as phaeohyphomycosis. The second report deals with a case of onychomycosis due to C. globosum which included such typical signs of nail infection due to Chaetomium, as history of nail trauma and brown discoloration of the affected nail. Therapy strategy is not established due to the small number of cases. The infection has been most effectively eradicated when treatment included terbinafine or itraconazole. Chaetomium species have a specific antifungal susceptibility pattern that includes primary resistance to 5-fluorocytosine and fluconazole. Important interspecies differences in antifungal susceptibility were observed particularly with amphotericin B.


Plant collecting and Documentation

Living Collections

A very valuable type of plant collection is a live specimen removed from the wild. This may be either a whole plant, a vegetative propagule , or a seed. Living plant collections are typically grown in a greenhouse or botanic garden, where they can be accessible to a researcher. Growing them and keeping them alive requires some horticultural experience and may involve trial and error under different regimes of potting or soil mixture, moisture, and photoperiod. As with liquid-preserved collections, they should be properly labeled with permanent metal or plastic tags, with collection information corresponding to a voucher specimen deposited in an herbarium.


Cellular Constitution, Water and Nutritional Needs, and Secondary Metabolites

Sclerotia

Compact aggregations of hyphae differentiated into an outer, pigmented rind and an inner mass of hyaline cells, called a medulla, are called sclerotia. Such fungal structures contain food reserves and are a type of survival propagule produced by a number of fungi in the Ascomycetes and Basidiomycetes. Sclerotia are mostly neglected as important fungal structures, because they are not distinctly present in most fungal isolations.

Sclerotial development has a role in dormancy and is also considered an important condition for sexual development. 26 Asci and ascospores can be found in sclerotia in species in the Aspergillus sections Flavi 27–29 and Circumdati, 30,31 showing that these structures are important for propagation. In these fungi, ripe asci can be obtained by mating or are produced after an extended time of incubation.

Sclerotia are also regarded as important in view of the production of specific compounds. Metabolites from the sclerotia of a non-aflatoxigenic strain of Aspergillus flavus showed substantial antifeedant activity against insects. 32 Arthropod predation is recognized as a selective force that has shaped the chemical defense systems of A. flavus and other sclerotium-producing fungi.

Wicklow and Shotwell 33 examined the distribution of aflatoxins among the conidia and sclerotia of toxigenic strains of A. flavus and Aspergillus parasiticus and found that the substantial aflatoxin levels in conidia could place agricultural workers exposed to dust containing large numbers of A. flavus conidia at risk. Cellular ratios of aflatoxin B1 to aflatoxin G1 were nearly identical in conidia and sclerotia even though levels of total aflatoxins in these propagule types may have differed greatly. Aflatoxin G1 was detected in the sclerotia of all A. flavus strains but in the conidia of only one strain. Each of the A. parasiticus strains examined accumulated aflatoxin G1 in both sclerotia and conidia.

Frisvad et al. 34 could induce the production of sclerotia by certain strains of Aspergillus niger when grown on Czapek yeast agar with raisins, on other fruits, or on rice. In strains in which sclerotia were found, up to 11 apolar indoloterpenes of the aflavinine type were detected, which had not been reported before for strains of A. niger. The induction of sclerotium formation can thus be a way of inducing the production of new secondary metabolites from previously silent gene clusters.