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In less than 5 years, DNA sequencing provided a multitude of new characters for analysis and identified about 10 phyla as members of the monophyletic kingdom Fungi Fig. Mycologists benefited from early developments applied directly to fungi. Use of the PCR was a monumental advance for those who studied minute, often unculturable, organisms. Problems of too few morphological characters e. Rather than producing totally new hypotheses of relationships, however, it is interesting to note that many of the new findings supported previous, competing hypotheses that had been based on morphological evidence 4 ; Sequences and phylogenetic analyses were used not only to hypothesize relationships, but also to identify taxa rapidly 91 ; 30 ; Fungal phyla and approximate number of species in each group Evidence from gene order conversion and multilocus sequencing indicates that microsporidians are Fungi see below; Note also that zoosporic and zygosporic fungal groups are not supported as monophyletic.
Tree based on 68 , , and Most fungi lack flagella and have filamentous bodies with distinctive cell wall carbohydrates and haploid thalli as a result of zygotic meiosis. They interact with all major groups of organisms. By their descent from an ancestor shared with animals about a billion years ago plus or minus million years 21 , the Fungi constitute a major eukaryotic lineage equal in numbers to animals and exceeding plants Figs. 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 organisms studied by Nobel laureates.
Examples of fungal diversity. Lemonniera sp. This type of aquatic species, an Ingoldian ascomycete, is named for C. Ingold, who pioneered the study of these fungi, that are characterized by highly branched conidia. Photo courtesy of H. As the spore develops air is trapped in the coil and causes it to be buoyant.
The smut Testicularia sp. 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. 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. Perithecia of Pyxidiophora sp.
Laboulbeniomycetes developed in moist chamber on moose dung from Meredith Station, New Brunswick, Canada. 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 ca. Some collectors have referred to basidiomycetes that produce colorful basidiomata as charismatic megamycota of the fungus world. 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.
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.
Photo courtesy of N.
Erotylidae , was collected at Barro Colorado Island, Panama. More than novel yeasts have been isolated from the gut of ca. Photo courtesy of James A. Phylogenetic studies provided evidence that nucleriid protists are the sister group of Fungi , nonphotosynthetic heterokont flagellates are placed among brown algae and other stramenopiles, and slime mold groups are excluded from Fungi 4.
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Sequences of one or several genes are no longer evidence enough in phylogenetic research. Subsequently, phylogenetic analyses using small subunit ribosomal RNA genes wrongly supported a microsporidian divergence before the origin of mitochondria in eukaryotic organisms Additional evidence from genome structure as well as phylogenetic analyses, supports the inclusion of microsporidians within the Fungi and indicates that comparison of whole genomes contributes to the solution of challenging phylogenetic problems A major product of the Deep Hypha project was the publication of 24 papers on fungal phylogeny in a single journal issue Mycologia — 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 phylogenies of most major groups.
Participants included authors with some involved in more than one paper; only 72 of the authors were originally from North America. 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. The addition of microsporidians brings the total of all described fungi to about species Fig. Factors such as difficulty 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.
Numbers of known fungi from the Dictionary of the Fungi editions 1—10, — Authors state that the large increase in species numbers in the 10th edition may be inflated because asexual and sexual forms were counted separately and molecular techniques that distinguish close taxa have been used. A more recent estimate of the total number of fungi, , is also low compared to present estimates that include environmental samples.
Furthermore, the use of molecular methods had not yet been considered as a means of species discovery. For example, analysis of environmental DNA samples from a soil community revealed a high rate of new species accumulation at the site, and these data supported an estimate of 3. Using the present discovery rate of about fungal species per year based on the last 10 years, Hibbett and his colleagues in press estimated that it would take years to describe 1.
Using present higher estimates of land plant numbers as somewhat under species ; 78 fungal species numbers now are expected to outnumber land plants by as much as Taylor, University of Alaska, Fairbanks, personal communication, January The large gap between known and estimated species numbers has led to a series of papers and symposia e. 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, environmental 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 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 culture.
All taxa biological inventories ATBIs attempt to survey organisms within particular geographical regions by collection of specimens and culture of substrates. All fungal specimens have been identified, and the agarics have been studied to the extent that a culture, ITS barcode sequence, and genetic analysis are available for many species. DNA methodology makes it possible to use independent sampling methods to discover the presence of organisms without ever seeing a culture or a specimen. Several new methods significantly outperform previous automated sequencing methods e.
Although there may be certain limitations and biases for the different methods 6 ; , mycologists have been quick to embrace them in ecological and biodiversity studies. Fungi grow in almost all habitats on Earth, surpassed only by bacteria in their ability to withstand extremes in temperature, water activity, and carbon source Tropical regions of the world are considered to have the highest diversity for most groups of organisms ; 70 , and this is generally true for fungi as well A group of researchers are studying the diversity of the Guyana Shield.
Their current collections contain morphospecies, primarily basidiomycetes. Approximately species were collected repeatedly only in the Dicymbe plots. Thus far, two new genera and ca.
On the basis of groups already studied, Aime estimated that ca. Including novel saprobes as well as ectomycorrhizal fungi, ca. It is clear, however, that these are not simply high numbers of new taxa, but biologically interesting fungi as well 2. Aime, Louisiana State University, personal communication, August Many fungi have in fact come from temperate regions, and some studies report a high diversity of fungi. The authors also alluded to the possibility that previous studies of certain mycorrhizal fungi showed similar trends 7.
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More investigation in this area is needed, but it is clear that many undescribed fungi are present in temperate regions. Many of the commercially most successful fungal drugs, however, come from temperate fungi. Penicillium chrysogenum , producer of penicillin, was found in a northern temperate city.
Today the drug is commonly used to treat dry eye , as well as many serious conditions. Statins produced by fungi such as Aspergillus terreus from temperate regions, combat high cholesterol levels, as well as providing other benefits ; 14 ; In temperate deserts, mycorrhizal boletes, agarics, and rust and smut fungi, are common.
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When a noted mycologist moved to Arizona early in his career, he became excited about the new and unreported fungal diversity found in the desert. Gilbertson, University of Arizona, personal communication, August The Sonoran Desert, however, has many plants e. Fungi also grow at low temperatures. An example involves fungal deterioration of historic huts built between and 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 Lichens have often been reported to be common in Arctic and Antarctic regions , and yeasts are active under frozen conditions in the Antarctic ; 5.
In some cases, a yeast isolated from the Antarctic based on 28S rDNA barcoding also has been reported from varied habitats, including human infections, the gut of insects, deep seas, and hydrocarbon seeps 90 ; 18 ; personal observation. Although some fungi are specialized for cold regions, others simply occupy a wide variety of environmental 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 Fungi are important as symbionts, and they are associated with every major group of organisms, bacteria, plants and green algae, and animals including insects. The associated organisms also allow for resampling, a quick way to obtain data about host specificity.
Targeting hosts also is a productive method for discovering fungal fossils, such as those associated with plants of the Rhynie Chert Examples of diversity in particular fungal habitats are reviewed in the following sections. Mycorrhizal plants and their fungal partners have been studied by a number of mycologists ; The fungi often are essential to their plant hosts because they take up water, nitrogen, phosphorus, 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 flowering plants and conifers, many bryophytes and ferns are mycorrhizal Certain mycorrhizal fungi specialize on orchids and ericoid plants, and some are known to have invaded new habitats with successful invasive plants There are two main types of mycorrhizal fungi, arbuscular mycorrhizae AM and ectomycorrhizae. Evidence from recent molecular studies, however, indicates that cryptic species with higher levels of host specificity than previously realized will increase the number of known AM fungi ; Greater host specificity usually occurs in the ectomycorrhizal fungus—plant associations than in AM associations Vast parts of the world remain to be sampled , and it is expected that barriers to interbreeding have led to high genetic diversity among these fungi Almost all plants on Earth are infected with endophytes, fungi that do not cause disease symptoms Endophytes occur between the cells, usually of above ground plant parts, and represent a broad array of taxonomic groups 9 ; The earliest studies of endophytes were of those associated with grasses Some grass endophytes are specialized members of the Clavicipitaceae, relatives of insect and fungal parasites in the Hypocreales, and many species produce alkaloid toxins effective against insects, other invertebrate animals, and vertebrates Some grass endophytes 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 associated with plants in addition to grasses, including a variety of dicots and conifers 33 ; In some tropical forests considered to be diversity hotspots for endophytes, there are extremely large numbers of the fungi, sometimes with hundreds reported from a single tree species, judged by both cultural and molecular methods of discovery and identification 11 ; 10 ; ; In one study, more than unique morphotypes were isolated from 83 leaves of two species of tropical trees.
A subset of the fungi was distributed among at least seven orders of ascomycetes Leaves usually acquired multiple infections as they matured, and there was strong evidence that the endophytes protected leaves of plants, such as Theobroma cacao , from infection when they were challenged with pathogens Interestingly, some of these were insect pathogens and experiments are being conducted to develop endophytes as biological control agents of insect pests.
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 ascomycetes and ca. In addition to crop pathogens, it is important to remember that many pathogens are numerous and important in natural ecosystems 47 ; Nonpathogenic phylloplane yeasts occupy leaf surfaces of many plants and are increasingly recognized for their control of potential leaf pathogens For example, invasive fungi such as those grouped as Dutch elm disease fungi, chestnut blight fungus, dogwood anthracnose fungus, and redbay wilt fungus, were all unknown until they were observed soon after their introduction 4 ; ; 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. 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 Although 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 specificity 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 Lichenicolous fungi, parasites, and other associates of lichens are not well collected, but an estimate for the combined lichens and lichenicolous fungi is about species 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 This checklist also highlights the absence of collections in certain regions.
Brandon Blackwell works on domestic and international patent issues for clients in academia and industry. He helps clients build and maintain patent portfolios, and implement patent strategies that help them achieve their business goals. Brandon has handled intellectual property matters dealing with a number of technologies, including chemical processing and manufacturing, energy storage devices, environmental technologies including carbon emissions mitigation and water desalination, optical devices, semiconductor device processing and packaging, metallurgical compositions, and composite materials.
He attended the David H. Prior to graduate school, Brandon also designed a unique emissions capture system for a Fortune 50 pharmaceutical company. While in law school, Brandon received the following awards: Daniel J. Fern Award for graduating first in his class, Lindsay R.