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Fungi are major decomposers in certain ecosystems and essential associates of many organisms. They provide enzymes and drugs and serve as experimental organisms. In 1991, a landmark paper estimated that there are 1.5 million fungi on the Earth. Because only 70000 fungi had been described at that time, the estimate has been the impetus to search for previously unknown fungi. Fungal habitats include soil, water, and organisms that may harbor large numbers of understudied fungi, estimated to outnumber plants by at least 6 to 1. More recent estimates based on high-throughput sequencing methods suggest that as many as 5.1 million fungal species exist. Technological advances make it possible to apply molecular methods to develop a stable classification and to discover and identify fungal taxa. Molecular methods have dramatically increased our knowledge of Fungi in less than 20 years, revealing a monophyletic kingdom and increased diversity among early-diverging lineages. Mycologists are making significant advances in species discovery, but many fungi remain to be discovered. Fungi are essential to the survival of many groups of organisms with which they form associations. They also attract attention as predators of invertebrate animals, pathogens of potatoes and rice and humans and bats, killers of frogs and crayfish, producers of secondary metabolites to lower cholesterol, and subjects of prize-winning research. Molecular tools in use and under development can be used to discover the world's unknown fungi in less than 1000 years predicted at current new species acquisition rates.
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American Journal of Botany 98(3): 426–438. 2011.
American Journal of Botany 98(3): 426–438, 2011; © 2011 Botanical Society of America
What are Fungi? Fungal biologists debated for more than
200 years about which organisms should be counted as Fungi.
In less than 5 years, DNA sequencing provided a multitude of
new characters for analysis and identifi ed about 10 phyla as
members of the monophyletic kingdom Fungi ( Fig. 1 ). Mycolo-
gists benefi ted from early developments applied directly to
fungi. The universal primers, so popular in the early 1990s
for the polymerase chain reaction (PCR), actually were de-
signed for fungi ( Innis et al., 1990 ; White et al., 1990 ). Use of
the PCR was a monumental advance for those who studied min-
ute, often unculturable, organisms. Problems of too few mor-
phological characters (e.g., yeasts), noncorresponding characters
among taxa (e.g., asexual and sexual states), and convergent
morphologies (e.g., long-necked perithecia producing sticky
ascospores selected for insect dispersal) were suddenly over-
come. Rather than producing totally new hypotheses of rela-
tionships, however, it is interesting to note that many of the new
ndings supported previous, competing hypotheses that had
been based on morphological evidence ( Alexopoulos et al.,
1996 ; Stajich et al., 2009 ). Sequences and phylogenetic analy-
ses were used not only to hypothesize relationships, but also to
identify taxa rapidly ( Kurtzman and Robnett, 1998 ; Brock
et al., 2009 ; Begerow et al., 2010 ).
Most fungi lack fl agella and have fi lamentous bodies with
distinctive cell wall carbohydrates and haploid thalli as a result
of zygotic meiosis. They interact with all major groups of or-
ganisms. By their descent from an ancestor shared with animals
about a billion years ago plus or minus 500 million years
( Berbee and Taylor, 2010 ), the Fungi constitute a major eukary-
otic lineage equal in numbers to animals and exceeding plants
( Figs. 2 10 ). The group includes molds, yeasts, mushrooms,
polypores, plant parasitic rusts and smuts, and Penicillium
chrysogenum , Neurospora crassa , Saccharomyces cerevisiae ,
and Schizosaccharomyces pombe , the important model organ-
isms studied by Nobel laureates.
Phylogenetic studies provided evidence that nucleriid pro-
tists are the sister group of Fungi ( Medina et al., 2003 ), nonpho-
tosynthetic heterokont fl agellates are placed among brown
algae and other stramenopiles, and slime mold groups are ex-
cluded from Fungi ( Alexopoulos et al., 1996 ). Current phyloge-
netic evidence suggests that the fl agellum may have been lost
several times among the early-diverging fungi and that there is
more diversity among early diverging zoosporic and zygosporic
lineages than previously realized ( Bowman et al., 1992 ; Blackwell
et al., 2006 ; Hibbett et al., 2007 ; Stajich et al., 2009 ).
Sequences of one or several genes are no longer evidence
enough in phylogenetic research. A much-cited example of the
kind of problem that may occur when single genes with differ-
ent rates of change are used in analyses involves Microsporidia.
These organisms were misinterpreted as early-diverging eu-
karyotes in the tree of life based on their apparent reduced mor-
phology ( Cavalier-Smith, 1983 ). Subsequently, phylogenetic
analyses using small subunit ribosomal RNA genes wrongly
supported a microsporidian divergence before the origin of mi-
tochondria in eukaryotic organisms ( Vossbrinck et al., 1987 ).
More recent morphological and physiological studies have not
upheld this placement, and analyses of additional sequences,
including those of protein-coding genes, support the view that
these obligate intracellular parasites of insect and vertebrate
1 Manuscript received 10 August 2010; revision accepted 19 January 2011.
The author thanks N. H. Nguyen, H. Raja, and J. A. Robertson for
permission to use their photographs, two anonymous reviewers who helped
to improve the manuscript, and David Hibbett, who graciously provided
an unpublished manuscript. She acknowledges funding from NSF DEB-
0417180 and NSF-0639214.
2 Author for correspondence (e-mail:
Meredith Blackwell 2
Department of Biological Sciences; Louisiana State University; Baton Rouge, Louisiana 70803 USA
Premise of the study: Fungi are major decomposers in certain ecosystems and essential associates of many organisms. They
provide enzymes and drugs and serve as experimental organisms. In 1991, a landmark paper estimated that there are 1.5 million
fungi on the Earth. Because only 70 000 fungi had been described at that time, the estimate has been the impetus to search for
previously unknown fungi. Fungal habitats include soil, water, and organisms that may harbor large numbers of understudied
fungi, estimated to outnumber plants by at least 6 to 1. More recent estimates based on high-throughput sequencing methods
suggest that as many as 5.1 million fungal species exist.
Methods: Technological advances make it possible to apply molecular methods to develop a stable classifi cation and to dis-
cover and identify fungal taxa.
Key results: Molecular methods have dramatically increased our knowledge of Fungi in less than 20 years, revealing a mono-
phyletic kingdom and increased diversity among early-diverging lineages. Mycologists are making signifi cant advances in
species discovery, but many fungi remain to be discovered.
Conclusions: Fungi are essential to the survival of many groups of organisms with which they form associations. They also
attract attention as predators of invertebrate animals, pathogens of potatoes and rice and humans and bats, killers of frogs and
crayfi sh, producers of secondary metabolites to lower cholesterol, and subjects of prize-winning research. Molecular tools in
use and under development can be used to discover the world s unknown fungi in less than 1000 years predicted at current new
species acquisition rates.
Key words: biodiversity; fungal habitats; fungal phylogeny; fungi; molecular methods; numbers of fungi.
March 2011] Blackwell — Fungal numbers
Fig. 1. Fungal phyla and approximate number of species in each group
( Kirk et al., 2008 ). Evidence from gene order conversion and multilocus
sequencing indicates that microsporidians are Fungi (see below; Lee et al.,
2010 ). Note also that zoosporic and zygosporic fungal groups are not sup-
ported as monophyletic. Tree based on Hibbett et al. (2007) , White et al.
(2006) , and James et al. (2006) .
hosts are members of the Fungi ( Keeling, 2009 ; Corradi and
Keeling, 2009 ). Additional evidence from genome structure as
well as phylogenetic analyses, supports the inclusion of mi-
crosporidians within the Fungi and indicates that comparison of
whole genomes contributes to the solution of challenging phy-
logenetic problems ( Lee et al., 2010 ).
The level of resolution and sophistication of systematics
studies made possible by molecular markers and phylogenetic
analyses put mycologists on equal footing with other biologists
for competitive funding, and they joined in several community-
wide efforts to organize fungal diversity within a phylogenetic
classifi cation. Three projects funded by the National Science
Foundation were initiated, including the Research Coordination
Network: A Phylogeny for Kingdom Fungi (Deep Hypha) and
successive Tree of Life projects, Assembling the Fungal Tree
of Life (AFTOL-1) and a second ongoing project (AFTOL-2)
( Blackwell et al., 2006 ). A major product of the Deep Hypha
project was the publication of 24 papers on fungal phylogeny in
a single journal issue ( Mycologia 98: 829 1103). The papers
included an introduction to progress in fungal phylogeny, a
paper on dating the origin of Fungi, one on the evolution of
morphological traits, and 21 articles with multilocus phyloge-
nies of most major groups. Participants included 156 authors
with some involved in more than one paper; only 72 of the au-
thors were originally from North America. The multi-investigator
AFTOL-1 publication ( Hibbett et al., 2007 ) included a widely
used and often cited phylogenetic classifi cation to the level of
order (e.g., Kirk et al., 2008 ; The NCBI Entrez Taxonomy Home-
page,; Science Watch,
The paper included 68 authors from more than 20 countries.
It is important to note that there was broad participation and,
essentially, global involvement on these projects, emphasizing
that studies of biodiversity are indeed global endeavors. Addi-
tional pages were contributed to the Tree of Life web project
( to make information on
fungi more accessible to students and the general public. Two
objectives of the ongoing AFTOL-2 project include increased
taxon sampling of fungi for molecular data and the discovery of
correlated morphological and biochemical characters (AFTOL
Structural and Biochemical Database,;
Celio et al., 2006 ).
Known fungal species The Dictionary of Fungi ( Kirk
et al., 2008 ) reported 97 330 species of described fungi at the
numbers of fungi entry. The addition of 1300 microsporidi-
ans brings the total of all described fungi to about 99 000 spe-
cies ( Fig. 1 ). The Dictionary s estimate of known species has
almost tripled in the period between the fi rst edition in 1943
(38 000 described species) and now, amounting to an increase
of more than 60 000 described species over the 65-yr period
( Fig. 11 ). Factors such as diffi culty of isolation and failure to
apply molecular methods may contribute to lower numbers of
species in certain groups, but there cannot be any doubt that
ascomycetes and basidiomycetes comprise the vast majority of
fungal diversity ( Fig. 1 ).
Estimated total fungal numbers In 1991, a landmark
paper provided several qualifi ed estimates of the number of fungi
on the Earth based on ratios of known fungi to plant species
in regions where fungi were considered to be well-studied
( Hawksworth, 1991 ). Estimate G of 1.5 million species was
accepted as a reasonable working hypothesis based on a fungus
to plant ratio of 6 : 1, in contrast to the much lower 50 60-yr-old
estimates by Bisby and Ainsworth (1943) of 100 000 fungal
species and by Martin (1951) of 250 000 species based on one
fungus for every phanerogam known at the time. A more recent
estimate of the total number of fungi, 720 256 ( Schmit and
Mueller, 2007 ), is also low compared to present estimates that
include environmental samples.
Hawksworth s (1991) estimate now is considered to be con-
servative by many, including Hawksworth ( Hawksworth and
Rossman, 1997 ), because numerous potential fungal habitats
and localities remain understudied ( Hawksworth, 2001 ). Fur-
thermore, the use of molecular methods had not yet been con-
sidered as a means of species discovery. For example, analysis
of environmental DNA samples from a soil community re-
vealed a high rate of new species accumulation at the site, and
these data supported an estimate of 3.5 to 5.1 million species
( O Brien et al., 2005 ). Using the present discovery rate of about
1200 fungal species per year based on the last 10 years, Hibbett
and his colleagues (in press) estimated that it would take 1170
years to describe 1.4 million fungi (based on Estimate G of
Hawksworth [1991] ) and 2840 to 4170 yr to describe 3.5 to 5.1
million (based on O Brien et al., 2005 ).
Using present higher estimates of land plant numbers as
somewhat under 400 000 species ( Paton et al., 2008 ; Joppa
et al., 2010 ) fungal species numbers now are expected to outnum-
ber land plants by as much as 10.6 : 1 based on O Brien et al.
(2005) . Even higher ratios have been predicted using data from
high-throughput sequencing of clone libraries, although indi-
vidual ecosystems will vary (L. Taylor, University of Alaska,
Fairbanks, personal communication, January 2011). The large gap
between known and estimated species numbers has led to a series
428 American Journal of Botany [Vol. 98
March 2011] Blackwell — Fungal numbers
DNA methodology makes it possible to use independent
sampling methods to discover the presence of organisms with-
out ever seeing a culture or a specimen. Several new methods
signifi cantly outperform previous automated sequencing meth-
ods (e.g., Jumpponen and Jones, 2009 ; Metzker, 2010 ). Al-
though there may be certain limitations and biases for the
different methods ( Amend et al., 2010a ; Tedersoo et al., 2010 ),
mycologists have been quick to embrace them in ecological and
biodiversity studies. O Brien and colleagues (2005) pointed out
that collection and culture methods revealed numbers of fungi
similar to those acquired by sampling environmental DNA.
Hibbett et al. (in press) , however, used data from GenBank to
show that by 2008 and 2009 the number of environmental
samples, excluding overwhelming numbers of sequences dis-
covered by pyrosequencing, exceeded the accessions of speci-
men-based sequences. The rapid development of automated,
high-throughput methods also has made it possible to acquire
whole genome sequences for population level studies ( Liti
et al., 2009 ; Neafsey et al., 2010 ).
Which regions of the Earth harbor fungal diversity? Fungi
grow in almost all habitats on Earth, surpassed only by bacteria
in their ability to withstand extremes in temperature, water ac-
tivity, and carbon source ( Raspor and Zupan, 2006 ). Tropical
regions of the world are considered to have the highest diversity
for most groups of organisms ( Pianka, 1966 ; Hillebrand, 2004 ),
and this is generally true for fungi as well ( Arnold and Lutzoni,
2007 ).
A group of researchers are studying the diversity of the Guy-
ana Shield. For the last 11 years, Terry Henkel and Cathie Aime
and their colleagues have studied the fungi in six 1-km
2 plots —
three in a Dicymbe corymbosa -dominated forest and three in a
mixed tropical forest. Their current collections contain 1200
morphospecies, primarily basidiomycetes. Approximately 260
species were collected repeatedly only in the Dicymbe plots.
Thus far, two new genera and ca. 50 new species have been
of papers and symposia (e.g., Hawksworth and Rossman, 1997 ;
Hawksworth, 2001 ; Hyde, 2001 ; Mueller and Schmit, 2007 ) at-
tempting to answer the question Where are the missing fungi?
How to discover new fungi Collecting and culturing fungi
from the environment will remain important because of the
need to identify specimens, revise taxonomy, assess the roles in
the environment, and provide strains for biological control, en-
vironmental remediation, and industrial processes. A physical
specimen, including an inert culture, is still required as a type
specimen (but see Conclusions later), and vouchers of known
fungi are used for documenting DNA sequences deposited in
some databases ( Nilsson et al., 2006 ). For example, the current
AFTOL project has a requirement that each sequence deposited
as part of the project be linked to a specimen, including a
All taxa biological inventories (ATBIs) attempt to survey or-
ganisms within particular geographical regions by collection of
specimens and culture of substrates. One of these, Discover
Life in America, All Taxa Biological Inventory, seeks to survey
an estimated 50 000 to 100 000 species of organisms in the
Great Smoky Mountains National Park. Karen Hughes and
Ronald Petersen have been successful in collecting more
than 3000 species of fungi, mostly agarics housed in the Uni-
versity of Tennessee Fungal Herbarium (
out of about 17 000 species of all taxa that have been collected
by others in the park (Biodiversity Surveys and Inventories:
Agaric Diversity in the Great Smoky Mountains National Park,
NSF DEB 0338699). All fungal specimens have been identi-
ed, and the agarics have been studied to the extent that a cul-
ture, ITS barcode sequence, and genetic analysis are available
for many species. This successful project has required hours of
time over a number of years and costly resources for studying
the material, but it serves as an example of the commitment
needed to acquire specimen-based information on fungi.
Figs. 2 – 10. Examples of fungal diversity. 2. Lemonniera sp. Tetraradiate conidia developed on a submerged leaf in a well-aerated freshwater stream
surrounded by lush vegetation. This type of aquatic species, an Ingoldian ascomycete, is named for C. T. Ingold, who pioneered the study of these fungi,
that are characterized by highly branched conidia. Photo courtesy of H. Raja. 3. The aero-aquatic ascomycete Helicoon gigantisporum produces distinctive
tightly coiled conidia. As the spore develops air is trapped in the coil and causes it to be buoyant. This feature is an adaptation for the polyphyletic aero-
aquatic fungi that grow on leaves in slow-moving or stagnant freshwater. Photo courtesy of H. Raja. 4. The smut Testicularia sp. develops in the ovary of
grasses and (as shown here) sedges. The spores mature sequentially, with the dark spores being more mature. A plant taxonomy student once thought he
had discovered a new species of Leersia , distinguished by large ovaries of ca. 1 cm, only to be disappointed that the enlargement was caused by a fungus.
It is helpful to mycologists when plant taxonomists collect and accession fungal diversity by selecting some diseased plant specimens, an activity that
should be encouraged. 5. Perithecia of Pyxidiophora sp. (Laboulbeniomycetes) developed in moist chamber on moose dung from Meredith Station, New
Brunswick, Canada. The 150 µ m long ascospores are seen at the tip of the perithecium neck in the center. Spores adhere to phoretic mites that are carried
by dung beetles to fresh dung piles. Some fungi have complex animal dispersal systems. Pyxidiophora species are usually mycoparasites that grow on fungi
in dung or other substrates including wrack washed up on beaches. The genus is a missing link and provided clues to confi rm that Laboulbeniomycetes
are ascomycetes and not other kinds of fungi or fl oridian red algae. 6. The ca. 8 cm wide basidiomata of Pycnoporus sp., a wide-ranging, brightly colored,
wood-decaying polypore, photographed at Barro Colorado Island, Panama. Some collectors have referred to basidiomycetes that produce colorful basidi-
omata as charismatic megamycota of the fungus world. 7. Peniophorella baculorubrensis , a bark-decaying basidiomycete common on and restricted to
living live oak ( Quercus virginiana ), decays the bark and changes its water-holding capacity. The effect of decay on bryophyte communties by this fungus
was fi rst studied by ecologists ( Penfound and Mackaness, 1940 ) more than 70 yr ago but was not described until a specialist on wood-decaying fungi hap-
pened to notice it on the Louisiana State University campus, Baton Rouge ( Gilbertson and Blackwell, 1984 ). The inconspicuous basidiomata are shown
growing on the lower side of a 7 cm long bark segment aimed downward for basidiospore discharge in response to gravity. 8. Basidiomata of Perenniporia
phloiophila on the bark of living Quercus virginiana . Although the basidiomata are obvious against the darker bark, this species was not described until it
was discovered at the same time and often on the same trees as Peniophorella baculorubrensis . Although the fungus usually rots only the outer bark, it will
invade and decay wood whenever the vascular cambium is broached by a bird or insect. In addition to the two species on live oak, six other species have
been described from the campus, illustrating the need for specialists to study noncharismatic fungi. 9. A basidioma (8 cm diameter) of the wood-decaying
fungus, Favolus tenuiculus , a favorite food of several species of mushroom-feeding beetles (see Fig. 10 ). Photo courtesy of N. H. Nguyen. 10. The small
( > 10 mm long) brightly colored beetle, Mycotretus sp. (Erotylidae), was collected at Barro Colorado Island, Panama. Many erotylid beetles have special-
ized yeast-packed pouches at the anterior end of the midgut. More than 200 novel yeasts have been isolated from the gut of ca. 15 families of mushroom-
feeding beetles ( Suh et al., 2005 ). Photo courtesy of James A. Robertson.
430 American Journal of Botany [Vol. 98
In temperate deserts, mycorrhizal boletes, agarics, and rust
and smut fungi, are common. A surprising number of wood-
decaying basidiomycetes have been discovered on living and
dead desert plants, including cacti and are in the University of
Arizona, Robert L. Gilbertson Mycological Herbarium (http:// When a noted mycol-
ogist moved to Arizona early in his career, he became excited
about the new and unreported fungal diversity found in the des-
ert. His proposed study of the wood-decaying fungi of the
Sonoran Desert was poorly received with a comment that wood-
decaying fungi were not present in the desert (R. L. Gilbertson,
University of Arizona, personal communication, August 1979).
The Sonoran Desert, however, has many plants (e.g., cacti, oco-
tillo, and mesquite and other desert legumes) that are substrates
for polypores and resupinate basidiomycetes (e.g., Gilbertson
and Ryvarden, 1986 , 1987 ).
Fungi also grow at low temperatures. An example involves
fungal deterioration of historic huts built between 1901 and
1911 for use by Antarctic explorers including Robert Scott and
Ernest Shackleton, and although there are not large species
numbers, it is important not to overlook this fungal habitat in
diversity studies ( Held et al., 2005 ). Lichens have often been
reported to be common in Arctic and Antarctic regions ( Wirtz
et al., 2008 ), and yeasts are active under frozen conditions in
the Antarctic ( Vishniac, 2006 ; Amato et al., 2009 ). In some
cases, a yeast isolated from the Antarctic (based on 28S rDNA
barcoding) also has been reported from varied habitats, includ-
ing human infections, the gut of insects, deep seas, and hydro-
carbon seeps ( Kurtzman and Fell, 1998 ; Bass et al., 2007 ;
personal observation). Although some fungi are specialized for
cold regions, others simply occupy a wide variety of environ-
mental conditions.
Many regions and habitats of the world need to be included
in fungal discovery. In general, microscopic fungi and those
that cannot be cultured are very poorly known. Parts of Africa
remain to be collected for many, although not all, fungal groups
( Crous et al., 2006 ). Fungi are important as symbionts, and they
are associated with every major group of organisms, bacteria,
plants and green algae, and animals including insects. Because
certain under-studied symbiotic associations are known to in-
clude large numbers of fungi, these are a good place to search
for new taxa. The associated organisms also allow for resam-
pling, a quick way to obtain data about host specifi city. Target-
ing hosts also is a productive method for discovering fungal
fossils, such as those associated with plants of the Rhynie Chert
( Taylor et al., 2004 ). Examples of diversity in particular fungal
habitats are reviewed in the following sections.
Fungi and plant roots Mycorrhizal plants and their fungal
partners have been studied by a number of mycologists ( Trappe,
1987 ; Smith and Read, 2008 ). The fungi often are essential to
their plant hosts because they take up water, nitrogen, phospho-
rus, and other nutrients from the soil and transfer them to the
plant roots. Some of these fungi may not prosper or even grow
without the host. In addition to fl owering plants and conifers,
many bryophytes and ferns are mycorrhizal ( Pressel et al.,
2010 ). Certain mycorrhizal fungi specialize on orchids and eri-
coid plants, and some are known to have invaded new habitats
with successful invasive plants ( Pringle et al., 2009 ).
There are two main types of mycorrhizal fungi, arbuscular
mycorrhizae (AM) and ectomycorrhizae. AM associations are
more common and occur with up to 80% of all plant species and
92% of plant families. AM fungi are all members of the phylum
described. On the basis of groups already studied, Aime esti-
mated that ca. 120 new ectomycorrhizal taxa have been discov-
ered. Including novel saprobes as well as ectomycorrhizal
fungi, ca. 500 new species are expected among the 1200 taxa
collected. It is clear, however, that these are not simply high
numbers of new taxa, but biologically interesting fungi as well
( Aime et al., 2010 ). One species is so unusual, that a reviewer
of the original report called it the fi nd of the century ( Redhead,
2002 ). As Aime has quipped if one were to compare the ratio
of fungi to plants in the Dicymbe plots as did Hawksworth
(1991) , the ratio would be 260 to 1, obviously an overestimate
but also a cautionary exercise in basing any estimate on a single
ecotype (M. C. Aime, Louisiana State University, personal
communication, August 2010).
Many fungi have in fact come from temperate regions, and
some studies report a high diversity of fungi. For example, in a
study of indoor air from buildings using culture-independent
sampling methods, diversity was found to be signifi cantly
higher in temperate sites independent of building design or use.
The authors also alluded to the possibility that previous studies
of certain mycorrhizal fungi showed similar trends ( Amend
et al., 2010b ). More investigation in this area is needed, but it is
clear that many undescribed fungi are present in temperate re-
gions. Popular literature often rationalizes the need to save the
rainforests, not because of their intrinsic value, but because of
the potential drug-producing organisms that may be found
there. Many of the commercially most successful fungal drugs,
however, come from temperate fungi. Penicillium chrysoge-
num , producer of penicillin, was found in a northern temperate
city. Another remarkable fungus, Tolypocladium infl atum from
Norwegian soil, synthesizes cyclosporine, an immune-suppres-
sant drug that revolutionized organ transplants ( Borel, 2002 );
the sexual state of this fungus was collected in New York, USA
( Hodge et al., 1996 ). Today the drug is commonly used to treat
dry eye ( Perry et al., 2008 ), as well as many serious conditions.
Statins produced by fungi such as Aspergillus terreus from tem-
perate regions, combat high cholesterol levels, as well as pro-
viding other benefi ts ( Vaughan et al., 1996 ; Askenazi et al.,
2003 ; Baigent et al., 2005 ).
Fig. 11. Numbers of known fungi from the Dictionary of the Fungi
(editions 1 10, 1950 2008). Authors state that the large increase in species
numbers in the 10th edition may be infl ated because asexual and sexual
forms were counted separately and molecular techniques that distinguish
close taxa have been used.
March 2011] Blackwell — Fungal numbers
phylloplane yeasts occupy leaf surfaces of many plants and
are increasingly recognized for their control of potential leaf
pathogens ( Fonseca and In á cio, 2006 ). In addition to the
thousands of native fungi that parasitize plants in the United
States, pathologists are constantly on the lookout for introduced
pathogens that often are undescribed when they arrive to deci-
mate na ï ve native plant populations. For example, invasive
fungi such as those grouped as Dutch elm disease fungi, chest-
nut blight fungus, dogwood anthracnose fungus, and redbay
wilt fungus, were all unknown until they were observed soon
after their introduction ( Alexopoulos et al., 1996 ; Zhang and
Blackwell, 2001 ; Harrington et al., 2008 ). Exotic localities will
need to be searched for undescribed fungi that probably go
largely unnoticed on their native hosts. It is important to note
that although fungi may cause only minor symptoms to hosts in
their native habitats, one of these may have the potential to be
the next destructive disease after introduction to a new region.
Molecular methods have helped to clarify limits of closely
related species and to establish host ranges (e.g., Crous et al.,
2008 ). In a study of 26 leaf spot fungi in Australia, three genera
of Myrtaceae, including Eucalyptus , were hosts for three new
genera and 20 new species ( Cheewangkoon et al., 2009 ). Al-
though the authors acknowledged the high level of new taxa
discovered, they pointed out that the potential for host shifts
within plantations might lower estimates of fungal species
numbers worldwide. Host or substrate specifi city is a concept
that can be applied to fungal groups that are closely associated
with hosts such as endophytes, pathogens, and mycorrhizal
fungi but not usually for saprobic species ( Zhou and Hyde,
2001 ). In the past species of plant pathogens often were based
on host identity, a practice that is not always effective because
some groups are host-specifi c while others are not.
Lichens and lichenicolus fungi About 20% of all fungi
and 40% of the ascomycetes (13 500 species) are lichen-forming
fungi ( Lutzoni and Miadlikowska, 2009 ). Lichenicolous fungi,
parasites, and other associates of lichens are not well col-
lected, but an estimate for the combined lichens and licheni-
colous fungi is about 20 000 species ( Feuerer and Hawksworth,
2007 ). Lichens and lichenicolous fungi are polyphyletic, and
several different groups of ascomycetes and a few species of
basidiomycetes have become associated with green algae and
cyanobacteria ( Lutzoni and Miadlikowska, 2009 ). Feuerer
(2010) can be consulted for information on lichen diversity
worldwide. This checklist also highlights the absence of collec-
tions in certain regions.
Deserts are rich in lichens. Of 1971 lichen species and asso-
ciated fungi reported from the Sonoran Desert, about 25% stud-
ied since 1990 are new. Three volumes on lichens of the greater
Sonoran Desert region have been published ( Nash et al., 2002 ,
2004 ). Other habitats of high lichen diversity are Arctic and
Antarctic regions ( Feuerer, 2010 ).
Fungi from arthropod and invertebrate animals There is
a need for more information on arthropod- and insect-associated
fungi. As was mentioned earlier, estimates of global fungal di-
versity usually omit insect-associated species because they are
so poorly known ( Hawksworth, 1991 ; Rossman, 1994 ; Mueller
and Schmit, 2007 ; Schmit and Mueller, 2007 ). Several post-
1991 estimates of insect-associated fungi suggested that 20 000
50 000 species exist ( Rossman, 1994 ; Weir and Hammond 1997a ,
b ; Schmit and Mueller, 2007 ). Some parasites are biotrophic,
associated with living insects, and many do not grow in culture.
Glomeromycota, a less diverse group than ectomycorrhizal
fungi with about 250 described species in a variety of taxa
( Gerdemann, 1968 ; Sch ü ß ler and Walker, 2011; Wang and Qiu,
2006 ). Evidence from recent molecular studies, however, indi-
cates that cryptic species with higher levels of host specifi city
than previously realized will increase the number of known AM
fungi ( Selosse et al., 2006 ; Smith and Read, 2008 ). More than
6000 species, mostly of mushroom-forming basidiomycetes,
form ectomycorrhizae with about 10% of all plant families.
Greater host specifi city usually occurs in the ectomycorrhizal
fungus plant associations than in AM associations ( Smith and
Read, 2008 ). Vast parts of the world remain to be sampled
( Mueller et al., 2007 ), and it is expected that barriers to inter-
breeding have led to high genetic diversity among these fungi
( Petersen and Hughes, 2007 ).
Inside plant leaves and stems Almost all plants on Earth
are infected with endophytes, fungi that do not cause disease
symptoms ( Saikkonen et al., 1998 ). Endophytes occur between
the cells, usually of above ground plant parts, and represent a
broad array of taxonomic groups ( Arnold, 2007 ; Rodriguez
et al., 2009 ). The earliest studies of endophytes were of those as-
sociated with grasses ( Diehl, 1950 ). Some grass endophytes are
specialized members of the Clavicipitaceae, relatives of insect
and fungal parasites in the Hypocreales, and many species pro-
duce alkaloid toxins effective against insects, other invertebrate
animals, and vertebrates ( Clay et al., 1993 ). Some grass endo-
phytes are transmitted to the host offspring in seeds, and others
inhibit sexual reproduction in the host and are dispersed within
plant parts such as leaf fragments. For grass endophytes that
reproduce sexually, fertilization may occur by insect dispersal.
Water intake is increased in infected hosts, and these plants
often grow taller than uninfected hosts.
A much more diverse group of endophytic fungi are associ-
ated with plants in addition to grasses, including a variety of
dicots and conifers ( Carroll, 1988 ; Rodriguez et al., 2009 ). In
some tropical forests considered to be diversity hotspots for en-
dophytes, there are extremely large numbers of the fungi, some-
times with hundreds reported from a single tree species, judged
by both cultural and molecular methods of discovery and iden-
tifi cation ( Arnold et al., 2001 ; Arnold and Lutzoni, 2007 ;
Pinruan et al., 2007 ; Rodriguez et al., 2009 ). In one study, more
than 400 unique morphotypes were isolated from 83 leaves of
two species of tropical trees. A subset of the fungi was distrib-
uted among at least seven orders of ascomycetes ( Arnold et al.,
2000 ). Leaves usually acquired multiple infections as they ma-
tured, and there was strong evidence that the endophytes pro-
tected leaves of plants, such as Theobroma cacao , from infection
when they were challenged with pathogens ( Arnold et al.,
2003 ). Vega and colleagues (2010) also found high diversity of
endophytes in cultivated coffee plants. Interestingly, some of
these were insect pathogens and experiments are being con-
ducted to develop endophytes as biological control agents of
insect pests.
Plant pathogens Plant pathogens differ from endophytes
in that they cause disease symptoms. Although some zoosporic
and zygosporic fungi are plant pathogens, most plant pathogens
are ascomycetes and basidiomycetes. A large number of asco-
mycetes and ca. 8000 species of basidiomycetes are plant patho-
gens. In addition to crop pathogens, it is important to remember
that many pathogens are numerous and important in natural
ecosystems ( Farr et al., 1989 ; Burdon, 1993 ). Nonpathogenic
432 American Journal of Botany [Vol. 98
Insects may be food for fungi, especially in low nitrogen en-
vironments. The mycelium of Pleurotus ostreatus , a favorite
edible species for humans, secretes toxic droplets that kill nem-
atodes. A study involving the mushroom-producing, ectomyc-
orrhizal basidiomycete, Laccaria bicolor , was designed to
determine the amount of predation by springtails on the fungal
mycelium. The study led to the surprise discovery that the fun-
gus was not insect food, but rather, it, and indirectly, the host
tree benefi ted by obtaining substantial amounts of nitrogen
from the insects ( Klironomos and Hart, 2001 ). The predatory
habit has arisen independently on several occasions in at least
four phyla of fungi and oomycetes. Predaceous fungi such as
species of Arthrobotrys and Dactylella lure, then trap, snare, or
grip nematodes and other small invertebrate animals in soils
and in wood ( Barron, 1977 ).
Ø degaard (2000) revised global estimates of arthropods
downward from 30 million to 5 10 million. Not all insects and
arthropods are tightly associated with fungi, but even the re-
vised species estimates indicate that the numbers of insect-
associated fungi will be very high.
Soil fungi Soil is a habitat of high fungal diversity ( W aksman ,
1922 ; Gilman, 1957 ; Kirk et al., 2004 ; Domsch et al., 2007 ).
Soil fungi and bacteria are important in biogeochemical cycles
( Vandenkoornhuyse et al., 2002 ), and the diversity of soil fungi
is highest near organic material such as roots and root exudates.
Per volume, large numbers of microscopic fungi occur in pure
soil, and these are largely asexual ascomycetes and some zygo-
mycetes, including animal-associated Zoopagales. Gams (2006)
estimated that 3150 species of soil fungi are known, and ca.
70% are available in culture. There presently is a high rate of new
species acquisition, and the group appears to be better known
than most ecologically defi ned groups. Molecular studies, how-
ever, are predicted to increase the total number ( Bills et al.,
2004 ). In fact a study of soil communities in several forest types at
the Bonanza Creek Long Term Ecological Research site, Fair-
banks, Alaska, United States, revealed not only seasonal changes
in community composition but also in dominance of fungi over
bacteria. The data acquired by several molecular methods in-
cluding high-throughput sequencing greatly increased the total
number of fungal sequences in GenBank at the time ( Taylor
et al., 2010 ). Taylor and his colleagues found more than 200
operational taxonomic units in a 0.25 g soil sample with only
14% overlap in a sample taken a meter away. This study is not
directly comparable with the soil fungi reported by Gams (2006)
because Gams ’ gures excluded fungi such as mycorrhizal
Another study of soil fungi based on environmental DNA
sequences showed an unexpected distribution of a group of
zoosporic fungi, Chytridiomycota. The chytrids, were found to
be the predominate group of fungi in nonvegetated, high-elevation
soils at sites in Nepal and in the United States in Colorado,
where more than 60% of the clone libraries obtained were from
chytrids. A phylogenetic analysis of the sequences compared
with those of a broad selection of known chytrids, indicated that
a diverse group of Chytridiomycota representing three orders
was present ( Freeman et al., 2009 ).
Most major fungal lineages are known from cultures and speci-
mens, but there have been a few surprises even in well-sampled
habitats such as soil. Soil clone group I (SCGI) represents a
major lineage of fungi that occurs in temperate and tropical soils
on three continents, but no one has ever seen or isolated any of
the species into culture ( Schadt et al., 2003 ; Porter et al., 2008 ).
These also usually require special methods for removal and
mounting, and few mycologists or entomologists have ever
seen members of the Laboulbeniomycetes or the fungal tricho-
mycetes, Asellariales and Harpellales ( Lichtwardt et al., 2001 ;
Cafaro, 2005 ). Laboulbeniomycetes are seta-sized, ectopara-
sitic ascomycetes of insects, mites, and millipedes ( Weir and
Blackwell, 2005 ). All 2000 known species have distinctive life
cycles with determinate thalli arising from two-celled as-
cospores. About 90% of the species have been found on adult
beetles (12 of 24 superfamilies) or on fl ies. New arthropod hosts
at the level of family are still being discovered ( Weir and
Hammond, 1997a , b ; Rossi and Weir, 2007 ), and there is
an indication that there is some degree of host specifi city ( De
Kesel, 1996 ). In the future, increased use of molecular meth-
ods will make it possible to determine the degree of species
level host specifi city, but the information is not available now.
Septobasidiales, relatives of the basidiomycete rust fungi are
associated with scale insects, and their felty basidiomata
presumably protect the insects from parasitoid wasps. Many
microsporidians also are parasites of a broad group of host
Necrotrophic parasites of insects include some members of
Chytridiomycota, Blastocladiales ( Coelomomyces ), Ento-
mophthorales, and Tubeufi aceae ( Podonectria ) ( Benjamin
et al., 2004 ). About 5000 members of three families of Hypoc-
reales are necrotrophic parasites of arthropods ( Spatafora et al.,
2007 , 2010). These species show an evolutionary pattern of
host shifting among plants, fungi, and insects in addition to dis-
playing a high level of host specifi city.
Fungi also occur in ancient, obligate gardening associations
with bark and ambrosia beetles, attine ants, and Old World ter-
mites, and new species are still being discovered in these groups
( Benjamin et al., 2004 ; Little and Currie, 2007 ; Harrington
et al., 2008 ; Aanen et al., 2009 ). Many yeasts are associated
with insects, particularly insects that feed on nectar ( Lachance,
2006 ; Robert et al., 2006 ).
Other insects contain gut yeasts, a habitat where few have
looked for them. Isolations from the gut of mushroom-feeding
beetles yielded up to 200 new species of yeasts ( Suh et al.,
2004 , 2005 ; see also Lachance et al., 2010 ). Because only about
1500 ascomycete yeasts (Saccharomycotina) have been de-
scribed, the gut yeasts represent a dramatic increase in diversity
from a limited geographical range ( Boekhout, 2005 ; C. Kurtzman,
USDA-ARS, personal communication, July 2010). In fact, the
estimated total number of yeast species worldwide could be in-
creased by as much as 50% by simply recollecting in previously
collected sites from the study ( Suh et al., 2005 ). As Lachance
(2006) pointed out, based on predictions of yeast numbers
using data from species in slime fl uxes and in associations with
ower-visiting insects, it is necessary to obtain more informa-
tion on specifi city and geographical ranges before better esti-
mates can be made. Although not all insects harbor large
numbers of yeasts in their guts, those with restricted diets in all
life history stages such as mushrooms or wood are often associ-
ated with yeasts. Host insects may acquire digestive enzymes or
vitamins from the yeasts. This contention is supported by the
fact that unrelated insects feeding on mushrooms (e.g., beetles
in different lineages, lepidopteran larvae) all have gut yeasts
with similar assimilative capabilities and vitamin production.
The high rate of discovery of yeasts in under-collected habitats
and localities suggests that far more taxa await discovery ( Suh
et al., 2005 ), and the gut habitat has been considered a yeast
diversity hotspot ( Boekhout, 2005 ).
March 2011] Blackwell — Fungal numbers
1991 ), and Hyde et al. (1998) estimated that more than 1500
species of marine fungi occur in a broad array of taxonomic
groups. Many of these fungi are distinct from freshwater aquatic
species, and they may be saprobic on aquatic plant substrates.
Some species have characters such as sticky spore appendages,
indicators of specialization for the marine habitat ( Kohlmeyer
et al., 2000 ).
It is interesting that few fungi from early-diverging lineages
have been reported from marine environments, perhaps in part
because mycologists studying these groups sampled more often
from fresh water habitats. More recently, an investigation of
deep-sea hydrothermal ecosystems revealed not only novel spe-
cies of ascomycetes and basidiomycetes, but also what may be
a previously unknown lineage of chytrids ( Le Calvez et al.,
2009 ).
Most marine fungi are ascomycetes and basidiomycetes, and
these include ascomycete and basidiomycete yeasts ( Nagahama,
2006 ). Some of the yeasts degrade hydrocarbon compounds
present in natural underwater seeps and spills ( Davies and
Westlake, 1979 ). Certain ascomycetes are specialists on calcar-
eous substrates including mollusk shells and cnidarian reefs.
Even a few mushroom-forming basidiomycetes are restricted to
marine waters ( Binder et al., 2006 ). Some fungi use other
marine invertebrates as hosts ( Kim and Harvell, 2004 ), includ-
ing antibiotic producers that live in sponges ( Bhadury et al.,
2006 ; Pivkin et al., 2006 ; Wang et al., 2008 ). A wide variety of
fungi considered to be terrestrial also are found in marine envi-
ronments. Basidiomycete (i.e., Lacazia loboi ) and ascomycete
yeasts, and other fungi including Basidiobolus ranarum , may
occur in marine waters where they infect porpoises and other
vertebrates ( Kurtzman and Fell, 1998 ; Murdoch et al., 2008 ;
Morris et al., 2010 ).
Fungal species Currently, molecular methods provide
large numbers of characters for use in phylogenetic species dis-
crimination (e.g., Kohn, 2005 ; Giraud et al., 2008 ). In the past,
biologists relied primarily on phenotype for species delimita-
tion, and most of the formally described species known today
were based on morphology. In addition, mating tests have been
used to distinguish so-called biological species, especially
among heterothallic basidiomycetes ( Anderson and Ullrich,
1979 ; Petersen, 1995 ). The ability to mate, however, may be an
ancestral character. For example, Turner et al. (2010) found
evidence that fungi have evolved strong barriers to mating when
they have sympatric rather than allopatric distributions. Distant
populations would not have had strong selective pressure
against hybridization, thereby avoiding production of progeny
less fi t than conspecifi c progeny (e.g., Garbelotto et al., 2007 ;
Stireman et al., 2010 ). This phenomenon, known as reinforce-
ment, helps to explain how fungi from different continents can
mate in the laboratory but never in nature and is an argument in
favor of recognizing species by phylogenetics. A number of re-
searchers have recognized species using phylogenetic species
recognition criteria ( Taylor et al., 2000 ). The operational phy-
logenetic method is based on a concordance of multiple gene
genealogies, and in addition to discriminating species, the
method indicates whether fungal populations actually exchange
genes in nature ( Taylor et al., 2000 ; Fisher et al., 2002 ; Dettman
et al., 2006 ; Jacobson et al., 2006 ).
The use of phylogenetic species criteria results in recognition
of more species than those delimited by morphological charac-
ters. For example, work on Neurospora species resulted in the
discovery of 15 species within fi ve previously recognized species
The phylogenetic position of this lineage, perhaps a new phy-
lum, appeared as a sister group to the clade of Pezizomycotina
Saccharomycotina ( Porter et al., 2008 ). Other unexpected
higher taxonomic level fungal clades have been detected from
environmental DNA sequences ( Vandenkoornhuyse et al.,
2002 ; Jumpponen and Johnson, 2005 ; Porter et al., 2008 ). An-
other lineage detected by environmental sequences was sub-
jected to fl uorescent in situ hybridization (FISH). The outline of
a single-celled, fl agellated organism was detected ( Jones and
Richards, 2009 ), but apparently none of these fungi has been
cultured either. Higher-level bacterial taxa have been discov-
ered by environmental sampling, but this is a far less common
occurrence for fungi ( Porter et al., 2008 ).
Fungi form crusts that stabilize desert soils. Crusts usually
are made up of darkly pigmented ascomycetes, lichens, and
nitrogen-fi xing cyanobacteria ( States and Christensen, 2001 ).
Rock-inhabiting fungi occur in the surface and subsurface lay-
ers of desert rocks. These darkly pigmented ascomycetes are
members of the classes Dothideomycetes and Arthoniomycetes,
but basidiomycetes and bacteria may occur in the associations
( Kuhlman et al., 2006 ; Ruibal et al., 2009 ). Easily cultured
asexual ascomycetes and other fungi also occur in desert soils,
and these include an unusual zygomycete, Lobosporangium
transversale ( Ranzoni, 1968 ), known only from three isolations
including Sonoran Desert soil. Yeasts are well known from
American deserts in association with cacti and fl ies where they
detoxify plant metabolites ( Starmer et al., 2006 ).
Freshwater fungi Certain fungi are adapted for life in fresh
water. More than 3000 species of ascomycetes are specialized
for a saprobic life style in freshwater habitats where they have
enhanced growth and sporulation ( Shearer et al., 2007 ; Kirk
et al., 2008 ; Shearer and Raja, 2010 ). The asci are evanescent,
and ascospores have appendages and sticky spore sheaths, that
anchor the spores to potential substrates in the aquatic environ-
ment. Conidia have several dispersal strategies, and these
are designated as Ingoldian ( Fig. 2 ) and aero-aquatic ( Fig. 3 )
conidia. Ingoldian conidia are sigmoidal, branched, or tetraradi-
ate and attach to plants and other material in the water. The
conidia fl oat on foam that accumulates at the banks of streams,
especially during heavy runoff, and when the bubbles burst, the
spores may be dispersed for great distances from the water and
into trees, where they can be isolated from water-fi lled tree
holes ( Bandoni, 1981 ; Descals and Moralejo, 2001 ; G ö ncz ö l
and R é vay, 2003 ). Aero-aquatic fungi have multicellular, often
tightly helical conidia with air spaces to make them buoyant on
the surface of slower-moving waters ( Fisher, 1977 ).
Other, less obviously modifi ed fungi are present in water,
and some of these are active in degrading leaves in streams
after the heavy autumn leaf fall. A few specialized freshwater
basidiomycetes also are known, and several have branched
conidia similar to those of the Ingoldian ascomycetes. Flagel-
lated fungi occur in aquatic habitats, including Chytridiomy-
cota, Blastocladiomycota, and Monoblepharomycota ( James
et al., 2006 ). Batrachochytrium dendrobatidis , the recently
described amphibian killer, is an aquatic chytrid ( Longcore
et al., 1999 ). Members of Neocallimastigomycota also live in a
specialized largely aquatic environment, the gut of vertebrate
herbivores, where they are essential for digestion of cellulosic
Marine fungi Marine waters provide a habitat for certain
specialized fungi ( Kohlmeyer and Volkmann-Kohlmeyer,
434 American Journal of Botany [Vol. 98
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amount of overlap between species within a given region by
comparing soil samples a meter apart to fi nd only 14% species
overlap ( Taylor et al., 2010 ).
A better estimate of fungal numbers also can be speeded by
enlisting more biologists to accomplish the goal. When am-
phibian populations fi rst were observed to be dwindling and
some species were determined to have disappeared almost 20 yr
earlier, a number of causes, all nonfungal, were suggested as
the explanation. The revelation that a chytrid was involved
brought to mind that there were probably fewer than 10 my-
cologists in the world who could collect, isolate, culture, and
identify the novel fl agellated fungus, Batrachochytrium dend-
robatidis ( Longcore et al., 1999 ). Since that time interest in and
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cline also justifi ed other projects, including training new chy-
trid systematists in monographic work. This effort has resulted
in the discovery of many new chytrid species and the descrip-
tion of fi ve new orders between 2008 and 2010. The rise of
AIDS and the accompanying large number of fungal infections
brought about a similar interest in medical mycology several
decades ago.
In addition to any sudden infl ux of biologists to obtain better
estimates of fungal numbers, a new approach clearly is needed.
In a thoughtful paper, Hibbett and colleagues (in press) called
for obtaining clusters of similar sequences and assigning Latin
binomials to these molecular operational taxonomic units
(MOTUs). The names would allow the sequences to be inte-
grated into a specimen-based taxonomic data stream. They con-
sidered inclusion of the sequence-based taxa among all taxa to
be a better alternative than the candidate taxon status used by
bacteriologists. Changes in the International Code of Botanical
Nomenclature would be needed if sequence-based materials
were to be allowed as nomenclatorial types. This proposal
seems to be a practical approach to handling the overwhelming
fungal diversity being discovered.
Recent experience in working as a broadly inclusive group to
plan and produce a phylogenetic classifi cation, the develop-
ment of freely accessible databases, and the use of new tools to
survey fungi in ecological studies has prepared the mycological
community to accomplish a number of new goals, including the
discovery of millions of fungi.
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... Statistical design of experiments is a powerful approach for media optimization which offers a systematic way of simultaneously evaluating multiple parameters and analyzing the resulting process outputs. To achieve this purpose, central composite response surface design was used and this empirical technique enables to evaluate the relationship between independent variables to predict the response [57,58]. For Monascus spp., several experiments have been continuously made to find better carbon and nitrogen sources for the higher microbial production of pigments [59][60][61][62][63]. ...
... The occurrence of color change may be due to the production of other molecules or modifications of the parent compound in the media of increasing salt concentrations. Also, it could be explained that the increasing salt concentration might have altered the pH of the media and prevented diffusion of pigments or modified the metabolism.On the contrary, pigments were diffused into the media without containing any salts (0%) and hence the water soluble pigments gave a dark red hue compared to highly saline medium[57]. However, in highly saline medium, if pigments do not diffuse into the culture media, it might have been adhered to biomass either didn't produce pigments at all.Further study of this strain exposing to different pH ranges in saline medium as well as evaluation of intracellular pigments content may provide insight in the physiological behaviour and fungal growth. ...
La grande majorité des colorants alimentaires naturels, utilisés dans la formulation des aliments et des boissons, proviennent des pigments extraits de matières premières végétales. Plusieurs couleurs dérivées de plantes peuvent entraîner des problèmes de formulation. Des facteurs, comme par exemple, la région, le climat, l'environnement, la variété cultivée, ont un effet de nuances de couleurs, de résistance et surtout de stabilité dans le produit final. Par ailleurs, les champignons filamenteux du genre Monascus, Penicillium et Talaromyces sont connus comme d'excellents producteurs de pigments rouges. Ces pigments intéressent de ce fait les industries car ils sont stables, non-toxiques et peuvent être utilisés comme colorants alimentaires.La recherche présentée dans le cadre de cette thèse de doctorat concerne la description des propriétés du pigment rouge que produit la souche de Talaromyces albobiverticillius isolée du milieu marin tropical autour de l'île de La Réunion. Les plans d’expérience (DOE) et la méthodologie des surfaces de réponses (RSM) ont été utilisés pour optimiser les conditions de culture et la formulation du milieu de fermentation, dans le but d'accroître les teneurs en polykétides colorés. Douze structures différentes ont été identifiées dans des extraits intracellulaires et extracellulaires des cultures fongiques, à l'aide de séparations et d'analyses spectroscopiques (HPLC-PDA-ESI/MS et RMN). Les pigments N-thréonine-monascorubramine, N-glutaryl-rubropunctamine et PP-O figurent ainsi parmi les 12 composants.Avec la demande croissante de composés colorés naturels dans le secteur industriel, les champignons isolés du milieu marin semblent présenter de nombreux intérêts. Des essais ont ainsi été menés afin d'étudier 1) l'amélioration des conditions de fermentation en fioles agitées ou en fermenteur de 2 litres; 2) les effets de la teneur en sel marin sur la synthèse des pigments; 3) des méthodes d'extraction respectueuses de l'environnement. Globalement, ces résultats font ressortir le grand potentiel des champignons marins produisant ce colorant rouge et la possibilité d'obtenir les colorants alimentaires adaptés.
... Multilocus GCPSR-based and detailed morphological analyses are crucial in biodiversity research and applied science, especially in Fusarium because it represents the most important genus of mycotoxigenic plant pathogens (Geiser et al. 2021). Fusarium is currently estimated to comprise at least 450 phylospecies , but this likely represents only a fraction of their global phylogenetic diversity based on estimates that fewer than 10% of fungi on planet Earth have been discovered (Blackwell 2011;Hawksworth and Lücking 2017). These estimates appear to be supported by our discovery and formal recognition of four novel fusaria among the culturable endophytes of healthy roots of agricultural and nonagricultural plants in Kazakhstan. ...
In this study, DNA sequence data were used to characterize 290 Fusarium strains isolated during a survey of root-colonizing endophytic fungi of agricultural and nonagricultural plants in northern Kazakhstan. The Fusarium collection was screened for species identity using partial translation elongation factor 1-α (TEF1) gene sequences. Altogether, 16 different Fusarium species were identified, including eight known and four novel species, as well as the discovery of the phylogen-etically divergent F. steppicola lineage. Isolates of the four putatively novel fusaria were further analyzed phylogenetically with a multilocus data set comprising partial sequences of TEF1, RNA polymerase II largest (RPB1) and second-largest (RPB2) subunits, and calmodulin (CaM) to assess their genealogical exclusivity. Based on the molecular phylogenetic and comprehensive morphological analyses, four new species are formally described herein: F. campestre, F. kazakhstanicum, F. rhizicola, and F. steppicola.
... This genetic diversity gives rise to an enormous variety of SMs, even not considering the numerous intermediate products that are being produced on the way (16). This makes fungi sheer endless reservoirs for novel bioactive substances, given that there are estimated to be more than 5 million fungal species worldwide (17). ...
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Background Fungi are important sources for bioactive compounds that find their applications in many important sectors like in the pharma-, food- or agricultural industries. In an environmental monitoring project for fungi involved in soil nitrogen cycling we also isolated Cephalotrichum gorgonifer (strain NG_p51). In the course of strain characterization work we found that this strain is able to naturally produce high amounts of rasfonin, a polyketide inducing autophagy, apoptosis, necroptosis in human cell lines and shows anti-tumor activity in RAS-dependent cancer cells. Results In order to elucidate the biosynthetic pathway of rasfonin, the strain was genome sequenced, annotated, submitted to transcriptome analysis and genetic transformation was established. Biosynthetic gene cluster (BGC) prediction revealed the existence of 22 BGCs of which the majority was not expressed under our experimental conditions. In silico prediction revealed two BGCs with a suite of enzymes possibly involved in rasfonin biosynthesis. Experimental verification by gene-knock out of the key enzyme genes showed that one of the predicted BGCs is indeed responsible for rasfonin biosynthesis. Conclusions The results of this study lay the ground for molecular biology focused research in Cephalotrichum gorgonifer. Furthermore, strain engineering and heterologous expression of the rasfonin BGC is now possible which allow both the construction of rasfonin high producing strains and biosynthesis of rasfonin derivates for diverse applications.
... Endophytic fungi are known to produce biologically active products, they are a rich source of functional secondary metabolites like flavonoids, terpenoids, steroids, phenols, phenyl propanoids, quinines, indole derivatives, amines, alkaloids, amides, pyrrolizidines, sesquiterpenes, diterpenes, lignans, isocoumarin derivatives, peptides, phenolic acids, chlorinated metabolites, aliphatic compounds, etc. Approximately one million endophytic fungi species are present on our planet (Blackwell, 2011), and produce bioactive compounds, with antioxidant, anticancer, immunomodulating, and antimicrobial properties (Ding et al., 2008). Endophytic fungi are of significant interest in applied microbiology and various studies have been done to evaluate their role in growth and development of plant and their survival strategy (Hiruma et al., 2018;Svenningsen et al., 2018;Toju et al., 2016). ...
... type sequencing revealed that Geodina guanacastensis is synonymous with, and has priority to G. salmonicolor (Pfister et al. 2020) The Dominican Republic includes a high diversity of ecosystems which correlates with a high mycological biodiversity. If we accept estimates in the literature (Bhunjun et al. 2022, Fernandez 2007, Blackwell 2001) then there would be 5 to 10 species of fungi for each species of plant. Of these, about 20% would be macrofungi (Senn-Irlet et al. 2007, Stamets et al. 2021, which suggests at least 5,000−8,000 species of macrofungi in the counry. ...
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Approximately 1,700 mushroom specimens were collected in the Dominican Republic from 2004 to 2021, comprising 450 species and 210 genera, as determined by morphological and/or molecular characteristics. The macrofungi belonging to Ascomycota include 28 species and 15 genera, while those in Basidiomycota include 432 species and 195 genera. Much taxonomic work is still ongoing, both for the identification of many collections and additional collecting for species not yet catalogued. It is estimated that this checklist represents 5−10% of the macrofungi present in the country. The webpage,, has been set up to document and illustrate the fungi of the Dominican Republic.
... The number of species in the kingdom Fungi has been debated for decades and different opinions continue to be expressed (e.g. Blackwell 2011;Tedersoo et al. 2014;Hawksworth and Lücking 2017;Wu et al. 2019;Hyde et al. 2020a). Different approaches for estimating the number of species, and the recent advent of high-throughput environmental sequencing, lead to the prediction of divergent numbers (Lücking et al. 2021a), and there is an ongoing debate among taxonomists on how taxa known Handling Editor: Kevin D. Hyde only from sequence data can be named (Hongsanan et al. 2018;Lücking and Hawksworth 2018;Thines et al. 2018;Wijayawardene et al. 2021b). ...
Background: The term mucormycosis refers to any fungal infection caused by fungi belonging to the Mucorales order. The disease often manifests in the skin and also affects the lungs and the brain. A large number of Mucormycosis cases were detected in Delhi, Maharashtra and Gujarat, and Madhya Pradesh. Objectives: (1) To describe the epidemiology, management, and outcome of individuals with mucormycosis. (2) To evaluate the risk factors associated with cases and control. Methodology: A case-control study, conducted in Hamidia Hospital, Bhopal, for 5 weeks. One hundred and sixty-eight patients diagnosed clinically with radiological or pathological findings was considered a case of Mucormycosis. Control was taken from March 2020 to May 28, 2021, the list of COVID-19-positive patients obtained from IDSP, MP. Results: Majority of the study participants were among the age group of 51-60 years and comprising 69.6% of males. Diabetes mellitus is the major comorbidity found in both cases (87.58%) and in controls (20.0%). Conclusion: There is a need to stress to control hyperglycemia, and monitor blood glucose levels after discharge following COVID-19 treatment.
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The purpose of this study was to explore the diversity and composition of endophytic fungal community in the root of three medicinal licorices, and learn more about its biological characteristics by analyzing its interaction with soil and root factors. A total of 2,118,633 effective sequences and 1,063 effective operational taxonomic units (OTUs) with 97% identity were obtained by high-throughput sequencing among 27 samples. In this study, a total of 8 phyla and 140 genera were annotated, among them, the phylum Ascomycota and Basidiomycota, and the genera Fusarium, Paraphoma and Helminthosporium were significantly dominant in the 27 samples. Wilcoxon rank sum test showed that the Shannon index was significantly different distribution between Glycyrrhiza uralensis and Glycyrrhiza inflata, especially 0-20cm at the root depth, the Chao1 index in Glycyrrhiza inflate was significantly affected by root depth, and there were significant differences in beta diversity between Glycyrrhiza uralensis and Glycyrrhiza inflata. Distance-based redundancy analysis (db-RDA) showed that soil physicochemical properties (available potassium and ammonium nitrogen), and the root factor (liquiritin and water content) were the main contributing factors to the variations in the overall structure of endophytic fungal community in this study. This study provides useful information for formulating strategies to improve the quantity and quality of medicinal licorices.
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The chemical composition and use of fungi as has been done in relation to the use and content of the chemical composition. The specific nutritional properties of mushroom fruiting bodies, along with their texture and flavor, are one reason why they are consumed and considered a delicacy. In this review, we collected data from several scientific studies that focused on the chemical composition and various uses of wild edible mushrooms. Other uses are briefly described.
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Target 1 of the Global Strategy for Plant Conservation (GSPC) is, "a widely accessible working list of all known plant species, as a step towards a complete world Flora". This paper discusses the importance of the Target to the GSPC itself, to many sectors of science and society, and to decision makers. It then examines the progress made to date and prospects for the Target's completion. Good progress has been made in bryophytes, ferns and gymnosperms with widely accessible working lists either complete or almost so for these groups. Online working lists are available for around 50% of flowering plants. In all, Target 1 is around 53% complete. It is estimated that there are around 352,000 flowering plants and that the current gap in online coverage is around 177,000 species. The major families constituting the gap are identified, the four largest being Apocynaceae, Malvaceae, Ericaceae and Apiaceae. The large majority of families for which there is no working list available are either cosmopolitan or pantropical in distribution. However, progress to date suggests that neither broad distribution nor large numbers of species in a family are insurmountable problems in compiling working lists. The major barrier to completion of Target 1 remains the availability of taxonomists to contribute to the target. Completion of Target 1 by 2010 is possible if botanical institutions recognise the importance of the Target and collaborate, lever funding and prioritise activities appropriately.
Coccidioides posadasii sp. nov., formerly known as non-California (non-CA) Coccidioides immitis, is described. Phylogenetic analyses using single nucleotide polymorphisms, genes, and microsatellites show that C. posadasii represents a divergent, genetically recombining monophyletic clade. Coccidioides posadasii can be distinguished from C. immitis by numerous DNA polymorphisms, and we show how either of two microsatellite loci may be used as diagnostic markers for this species. Growth experiments show that C. posadasii has significantly slower growth rates on high-salt media when compared with C. immitis, suggesting that other phenotypic characters may exist.
Research in fungal phylogenetics and systematics progressed rapidly in the past decade due to advances in DNA sequencing technologies and analytical methods. A newfound wealth of sequence data acquired through community-wide initiatives has advanced the process of acquiring a stable phylogenetic classification of many fungal taxa. Financial support from the National Science Foundation Research Coordination Networks: a phylogeny for kingdom Fungi (Deep Hypha) for 5 y enabled more than 100 fungal systematists to assess the taxon sampling, molecular markers and analytical methods necessary to facilitate such a project. Later a second NSF program provided financial support for the Assembling the Fungal Tree of Life (AFTOL) project to accomplish much of the research. Deep Hypha may be viewed as an involved parent of AFTOL with a continuing role as coordinator of likeminded workers. Many questions posed at the beginning of the Deep Hypha project have been addressed, at least in part, although some details remain to be clarified. Many of the main branches of the fungal tree are stable and well supported, often as a result of multigene analyses that involved collaboration of many laboratories. More work is necessary, however, to resolve certain branching events near the base of the tree, as well as to reconstruct relationships in some terminal groups. The phylogenetic classification in this issue of Mycologia is a product of the AFTOL project and many other independent research initiatives, and it is an initial synthesis of a working classification designed to be used for all majorPUBLICations that require a phylogenetic classification of fungi.
We tested whether fungal communities are impacted by nitrogen deposition or increased precipitation by PCR-amplifying partial fungal rRNA genes from 24 soil and 24 root samples from a nitrogen enrichment and irrigation experiment in a tallgrass prairie at Konza Prairie Biological Station in northeastern Kansas, U.S.A. Obtained fungal sequences represented great fungal diversity that was distributed mainly in ascomycetes and basiodiomycetes; only a few zygomycetes and glomeromycetes were detected. Conservative extrapolated estimates of the fungal species richness suggest that the true richness may be at least twice as high as observed. The effects of nitrogen enrichment or irrigation on fungal community composition, diversity or clone richness could not be unambiguously assessed because of the overwhelming diversity. However, soil communities differed from root communities in diversity, richness and composition. The compositional differences were largely attributable to an abundant, soil-inhabiting group placed as a well-supported sister group to other ascomycetes. This group likely represents a novel group of fungi. We conclude that the great fungal richness in this ecosystem precluded a reliable assessment of anthropogenic impacts on soil or rhizosphere communities using the applied sampling scheme, and that detection of novel fungi in soil may be more a rule than an exception.
Samples were taken from the top 2 inches, including the surface, of virgin soils from 24 localities in the Sonoran Desert. There were 107 genera and 229 species isolated in addition to some unidentified Phoma spp., mycelia with clamp connections, and large numbers of other sterile mycelia. No thermophiles were isolated. There does not seem to be a fungus flora that is characteristic of desert soils. The melanic Fungi Imperfecti occurred in large numbers, though not necessarily in greater numbers of species than non-melanic forms. Many of the isolated species are pan-world. The soil contained many species more commonly associated with dung, others known to be plant or animal pathogens and others as laboratory contaminants. Many of the species may not be true soil fungi and their presence in the soil simply fortuitous.
Armillaria mellea consists of at least ten reproductively isolated groups, the equivalent of “biological species.” Each biological species possesses bifactorial heterothallism with compatibility discernible by the gross mycelial morphology of paired monosporous isolates rather than the presence or absence of clamp connections and dikaryotic cells. Monosporous testers were obtained from 97 fruiting bodies in North America. Pairings of testers from different fruiting bodies indicated that each isolate belongs to one and only one intersterile group, i.e., intersterility between groups is complete. Nutritional selection applied to confronted auxotrophic strains from two of the biological species revealed no prototrophy (genetic complementation) between the strains of these groups, whereas prototrophy was revealed by the same method within groups. Members of several of the biological species are distributed widely in North America. Isolates may be collected from a broad range of host species or also as saprophytes. The 10 biological species are not clearly distinguishable by unique geographical ranges or substrate specificities. Armillaria mellea is considered to be a complex of morphologically distinct species. This study shows that the taxon is divided into genetically isolated distinct biological species.
A collection of Cordyceps subsessilis is documented. Axenic cultures of single part ascospores produced an anamorph attributable to the common soil hyphomycete Tolypocladium inflatum (= T. niveum). Efrapeptins were identified in culture filtrates of the anamorph. The efrapeptin profile of the C. subsessilis anamorph was found to be similar to that of other isolates of T. inflatum. This is the first report of a teleomorph for this important anamorph genus.
The roots of most plants are colonized by symbiotic fungi to form mycorrhiza, which play a critical role in the capture of nutrients from the soil and therefore in plant nutrition. Mycorrhizal Symbiosis is recognized as the definitive work in this area. Since the last edition was published there have been major advances in the field, particularly in the area of molecular biology, and the new edition has been fully revised and updated to incorporate these exciting new developments. . Over 50% new material . Includes expanded color plate section . Covers all aspects of mycorrhiza . Presents new taxonomy . Discusses the impact of proteomics and genomics on research in this area.
Previous observations of morphological, reproductive and genetic variation have suggested that Neurospora discreta, as presently circumscribed, might represent a diverse complex of multiple species. To investigate this hypothesis we examined the phylogenetic relationships among 73 fungal strains traditionally identified as N. discreta. Strains were chosen from across the morphological, ecological and geographical ranges of the species. Sequence data were obtained from three unlinked nuclear loci, and phylogenetic species recognition was applied to the dataset using protocols that have been shown to be reliable for identifying independent lineages and delineating species of Neurospora. The results demonstrate that the present circumscription of N. discreta includes at least eight separate phylogenetic species. This research also reveals an abundance of previously unrecognized genetic diversity within the genus, characterizes the interspecific evolutionary relationships and contributes to a fuller understanding of species diversity in Neurospora.
Three new species of Corethromyces (Ascomycetes, Laboulbeniales, Stigmatomycetinae) parasitic on South American Staphylinidae (Insecta Coleoptera) are described. These are C. aequatorialis, parasitic on Gnathymenus sp. from Ecuador, C. otongaensis, parasitic on Biocrypta sp. from Ecuador, and C. thayerae, parasitic on Medon obscuriventer from Chile.