|BOTANICAL ELECTRONIC NEWS|
|No. 539 May 29, email@example.com||Victoria, B.C.|
Last BEN (BEN # 538) and this one (BEN # 539) are both dealing with mycological topics. BEN # 540 will return back to the "higher plants," ecology and environmental issues. I paid a debt to mycology that used to be a branch of botany, not such a long time ago. A.C.
Mushrooms of the Northwest: A Simple Guide to Common Mushrooms
by Teresa Marrone (Author), Drew Parker (Author)
Paperback: 288 pages
Publisher: Adventure Publications (March 22 2019)
Teresa Marrone is the lead author of three regional field identification guides for wild mushrooms (Mushrooms of the Upper Midwest, Mushrooms of the Northeast, and Mushrooms of the Northwest). She is also the sole author of more than a dozen outdoors-themed books, including the Wild Berries & Fruits Identification Guides series (currently available for four regions of the U.S.). She splits her time between her home in Minneapolis and her cabin in northern Minnesota, abutting the Boundary Waters Canoe Area Wilderness.
With a background in the visual arts, Drew Parker has always had a strong attraction to the natural sciences, as well. He found his focus in fungi after arriving in the Northwest in 1973 and innocently wandering into the mountains with a new mushroom book in hand. Drew is a longtime member of the North American Mycological Association and the Pacific Northwest Key Council, a group of amateur and professional mycologists that was formed to further the study of Northwest fungi. Over the years, he has served as foray mycologist for the Spokane Mushroom Club and has worked for several years conducting surveys of macrofungi for the U.S. Forest Service. As a photographer, Drew has supplied images for numerous mycological papers and books, as well as for MatchMaker, a digital mushroom identification program, of which he is a coauthor. He currently resides with his wife, Katie, at their home in the wild woods near Metaline Falls, Washington.
"Hundreds of full-color photographs with easy-to-understand text make this a perfect visual guide. Learn about more than 400 species of common wild mushrooms found in the Northwest states of Idaho, Oregon, and Washington. The species (from Morel Mushrooms to Shelf Mushrooms) are organized by shape, then by color, so you can identify them by their visual characteristics. Plus, with the Top Edibles and Top Toxics sections, you'll begin to learn which are the edible wild mushrooms. The information in the book, written by Teresa Marrone and Drew Parker, is accessible to beginners but useful for even experienced mushroom seekers."
A Field Guide to the Rare Fungi of California's National Forests Noah Siegel, Else C. Vellinga, Christian Schwarz, Michael A. Castellano & Diane Ikeda
The California Rare Fungi Working Group was assigned to produce a list of potentially rare fungi found in California's National Forests for the Region 5 Forest Plan Review with a focus on the "next four forests" (Stanislaus, Eldorado, Tahoe, and Plumas National Forests) for potential listing as "Forest Service Sensitive Species". Most of the species proposed were not currently in field guides and, for many species, data was lacking to determine rarity state-wide. The main purpose of this guide is to provide a reference for National Forest personnel to use for identifying the species of interest. Another goal is to publicize the need for data reporting on all macrofungi species through citizen-science portals like iNaturalist (www.inaturalist.org) to provide basic biological and ecological information such as species distributions and possible trends in abundance. Currently, the data needed to do this are lacking.
The Rare Fungi Working Group proposed a list of 112 macrofungi species, later increased to 128 species with 16 "placeholder" species profiles from the Survey and Manage species under the Northwest Forest Plan, which were considered too common to be included on a California rare species list. The Group included species that occur on other Sierra Nevada National Forests including the Inyo, Sequoia and Sierra National Forests. Given the lack of knowledge of fungal species ranges, it also considered species that occur in the southern Cascades and Siskiyou Mountains; thus we are confident that the existing profiles adequately represent the Northern Province forests. The profiles are based on accessible data existing as of June 2017, mostly from herbarium records included in MyCoPortal (www.mycoportal.org), the collection database for most of the North American fungal herbariums. A majority of the herbarium collections reside at SFSU, and most of these collections were examined as part of this project. Additional data came from the citizen science portals iNaturalist (www.inaturalist.org) and Mushroom Observer (www.mushroomobserver.org), as well as mycologist review for each species.
1) Phylogenetic research has revealed discordance between fungal evolution and lichen phenotype.
2) Single-celled microbes are emerging as ubiquitous components of lichens.
The structurally important lichen cortex may be a biofilm resulting from symbiont interplay. The term symbiosis was first used in biology to describe the 'living together' of fungi and algae in lichens. For much of the 20th century, the fungal partner was assumed to be invested with the ability to produce the lichen body plan in presence of a photosynthesizing partner. However, studies of fungal evolution have uncovered discordance between lichen symbiotic outcomes and genome evolution of the fungus. At the same time, evidence has emerged that the structurally important lichen cortex contains lichen-specific, single-celled microbes, suggesting it may function like a biofilm. Together, these observations suggest we may not have a complete overview of symbiotic interactions in lichens. Understanding phenotype development and evolution in lichens will require greater insight into fungal–fungal and fungal–bacterial interplay and the physical properties of the cortex.
[In this article, Toby describes the complexity of lichen symbioses and the problems which such complexity poses to the lichen study and lichen nomenclature. The article is a valuable annotated review of the current lichenological literature that deals with lichen fungi and their symbionts. AC]
Using the basic GenBank local alignment search tool program (BLAST) to identify fungi collected in a recently protected beech forest at Montricher (Switzerland), the number of ITS sequences associated to the wrong taxon name appears to be around 30%, even higher than previously estimated. Such results rely on the in-depth re-examination of BLAST results for the most interesting species that were collected, viz. first records for Switzerland, rare or patrimonial species and problematic species (when BLAST top scores were equally high for different species), all belonging to Agaricomycotina. This paper dissects for the first time a number of sequence-based identifications, thereby showing in every detail—particularly to the user community of taxonomic information—why sequence-based identification in the context of a fungal inventory can easily go wrong. Our first conclusion is that in-depth examination of BLAST results is too time consuming to be considered as a routine approach for future inventories: we spent two months on verification of approx. 20 identifications. Apart from the fact that poor taxon coverage in public depositories remains the principal impediment for successful species identification, it can be deplored that even very recent fungal sequence deposits in GenBank involve an uncomfortably high number of misidentifications or errors with associated metadata. While checking the original publications associated with top score sequences for the few examples that were here re-examined, a positive consequence is that we uncovered over 80 type sequences that were not annotated as types in GenBank. Advantages and pitfalls of sequence-based identification are discussed, particularly in the light of undertaking fungal inventories. Recommendations are made to avoid or reduce some of the major problems with sequence-based identification. Nevertheless, the prospects for a more reliable sequence-based identification of fungi remain quite dim, unless authors are ready to check and update the metadata associated with previously deposited sequences in their publications.
Limitations of morphology-based fungal identification (Box 1)
– Requires trained field mycologists to distinguish between different species in the field. Inexperienced collectors will either waste their time collecting the same species over and over again or they may overlook the most interesting species in the field being unable to make a difference between what is common or rare.
– Are selective in sampling as later identification may be impossible due to several factors. At moments when mushroom fruiting is peaking, morphology-based identification severely limits the number of samples that can be processed due to time needed to take photographs, necessary notes, labelling, drying and bagging. In such cases, time constraints will push sampling toward the collection of the more easily identified or 'favorite' groups of individual mycologists.
– Can be severely impacted by the poor state or development of fructifications such as too immature, too old or too scanty material, absence of particular developmental stages to observe essential features such as veils, too fast deterioration of fruiting bodies (as for example for genera such as Coprinopsis or Mycena) or the impossibility of obtaining spore prints needed for correct identification.
– Can be severely handicapped by the partial to complete absence of identification tools. In particular when doing inventories in poorly explored parts of the world, the absence of identification keys and the predominant presence of undescribed species renders an inventory quasi impossible.
Advantages and limitations of sequence-based fungal identification (Box 2)
– Are less dependent on expertise as long as mushroom fruiting is not overwhelming and thus as long as nearly everything can be collected. When fruiting is peaking, sampling will become dependent again on taxonomic expertise.
– Are not limited by the necessity of observing certain developmental stages.
– Are unbalanced by rapid deterioration typical of some fungal groups (fungal material can be stored for long term preservation in CTAB buffer).
– Are less impacted by time constraints for processing collections and are thus less selective in sampling. – Are less impacted by existence of morphological identification tools (keys, ?oras etc.)
– Are severely impacted by the coverage of existing species in public sequence databases for their barcode sequence, but offer the tremendous advantage that obtained sequences will allow for future identification once the fungal group becomes sufficiently covered in public databases.
– Are entirely dependent on correct identification of available sequences in public sequence databases.
– Are highly impacted by the quality of sequences and presence of chimeric sequences or heterozygotous sites.
– Are severely dependent on the capacity of correct interpretation of BLAST results, which is in our opinion a highly underestimated problem as it is directly related to sufficient taxonomic and molecular expertise.
– Are dependent on the chosen similarity cut-off for species recognition. The often applied 97% similarity cut-off is certainly too low for most mushrooms as suggested by several recent taxonomic revisions.
– Can be affected by contamination problems, e.g. for older tissues or when PCR favors shorter ITS than those of the mushroom to be identified (e.g. Cantharellus). Cloning may deal with such problems but is costly and time-consuming.
– Are dependent on whether the resolution or the variation of the ITS marker alone will allow for a precise identification of species. Indeed, in certain taxonomic groups of mushroom forming fungi, but particularly in the case of several important pathogen genera, the (often exaggerated) description of cryptic species that have identical ITS is based on genes such as beta-tubulin and calmodulin, which evolve more rapidly than ITS. An ITS sequence of such cryptic species may typically BLAST with a 100% similarity for a 100% coverage against a whole suite of different cryptic species.
Russula is a diverse genus of ectomycorrhizal fungi associated mainly with woody plants. Each continent has hundreds of endemic species (Looney et al. 2016). North America and Europe are continents with a long tradition of Russula taxonomy with hundreds of species described from each. In Europe, the majority of species are well defined and might be identified morphologically (Sarnari 1998, 2005). In North America, the original species concept has been lost for many species, and the efforts to re-introduce older Russula names have been successful only for a few species (Hesler 1961, Kibby & Fatto 1990).
Before 2007, the 419 Russula species reported from the USA include 332 species described from North America and 87 European species that were believed to occur in North America (Buyck 2007). Several more species have been described from the Pacific North West of North America. In the USA, the Russula diversity research was started by Charles Horton Peck (1833–1917), who described 47 species in various reports of local biota. Before 1950, William Alfonso Murrill (110 new Russula species), Gertrude Simmons Burlingham (58 spp.) and Calvin Henry Kauffman (12 spp.) made significant contributions to the Russula taxonomy in the USA. Later, from 1950 to 1971, the most active mycologists were Rolf Singer (32 spp.), Robert Lynn Schaffer (21 spp.), Raymond Fatto (11 new species) and Harry Delbert Thiers (8 new species). During the last 12 years, 14 species were described from the USA: 9 species Bazzicalupo & Miller in Hyde et al. (2017), and 5 species described each in different publication (Buyck et al. 2008; Adamcík et al. 2010, 2015; Arora and Nguyen 2014; Liu et al. 2015). Interesting is that except three species described by G. Burlingham from Canada, all other species were described from the USA.
North American knowledge of Russula diversity differs from the European situation in some positive and some negative ways. European Russula taxonomy started in early fungal research by Christian Hendrik Persoon who described the genus (Persoon 1796) and its type species, Russula emetic Pers. There are several Russula names described by C.H. Persoon and also by the second founding father of mycology, Elias Magnus Fries, giving them the advantage of priority. While older European species has no type herbarium specimens, almost all North American taxa have types, because the Russula research in North America started by C.H. Peck one hundred years later.
The relative stability in the taxonomic concept of species started after the monograph of Romagnesi (1967) introducing new microscopic standards. In Europe, the monograph was widely accepted, and similar monographs were also prepared later (e.g. Einhellinger 1985, Sarnari 1998, 2005, Marxmüller 2014). Several amateur mycologists further use these monographs, and some mycological societies have thousands of members.
Unfortunately, there was not similar Russula monograph in North America and only a few species were included in popular field guides. Majority of Russula types published in the 19th and 20th centuries were studied by Hesler (1961) and Singer (e.g. Singer 1938, 1943, 1947). However, these studies did not lead to the more frequent use of names; one of the possible reason is an insufficient quality or a lack of microscopic illustrations and field photos. It is worth to mention a good tradition established in Michigan by C.H. Kauffman; his Russula names remain in use not only in America but also in Europe (e.g. Russula borealis Kauffm.). Kauffman's follower, R.L. Shaffer, published good quality of Russula descriptions and studied morphologically similar species within defined groups (e.g. Shaffer 1964, 1970). Since 2008, S. Adamcík & B. Buyck started to publish type studies provided by the modern description of the microscopic structure and updated classification of species. They published 77 type studies and the most important is publication summarising their type studies of Russula species described by C.H. Peck (Adamcík et al. 2018). Based on their microscopic descriptions, they proposed a change of subgenus for 19% of studied species, suggesting the urgent need of taxonomic revision of older North American Russula species. Only a few of North American Russula species have been re-described and illustrated based on the type, and recent collection, successful re-introduction of species name also needs a photo of basidiomata, such as presented in Russula levyana (Adamcík and Buyck 2010) and Russula hixonii (Buyck et al. 2011).
Distribution of North American Russula
Because of initial hesitations, whether or not European species might occur in North America, the use of European names in the continent have become marginal. Most North American mycologists soon believed that American Russula diversity is different or only slightly overlapping with the European conditions. This question is not resolved sufficiently to present, Looney et al. (2016) reported 9% overlap of Russula diversity between continents based on analysis of ITS sequences deposited in public databases. Geml et al. (2012) suggested a wide distribution of hemiboreal species. Bazzicalupo et al. (2017) taxon concluded that 28 of 72 Russula species from North West America would match barcodes of European species. However, Adamcík et al. (2016) demonstrated a much lower threshold for species delimitation of Russula subsect. Xerampelinae, using only ITS region. The barcode threshold, in combination with insufficient sampling, might contribute to failing to recognize species in some lineages of closely related taxa. Cabon et al. (2019) demonstrated that relative homogeneity of boreal and arctic environments across the northern hemisphere and its geographical continuity is the possible reason of wide distribution of Russula species in these habitats, but climate and geographical discontinuity probably caused divergence and endemism of Russula species of temperate and subtropical areas in America, Europe and Asia.
Another unresolved question is a divergence of Russula diversity between various adjacent areas of North and Latin America. Russula diversity on the Pacific coast of the US is considered to be different from the Atlantic coast (Theirs 1994, 1997, Bazzicalupo et al. 2017). Little is known about the divergence of Russula diversity among North and Latin America and Caribbean islands. There is no doubt that most taxa from Latin America are different, but there are still doubts about southern distribution limits of some subtropical species described from the southern USA. Buyck et al. (2003) reported two look-alike Russula taxa from Costa Rica and treated them as form and subspecies of species described from North America: Russula burlinghamiae f. claricolor and Russula polyphylla subsp. guanacastae.
Start of molecular techniques
DNA sequences are a powerful tool for taxonomy. The use of molecular techniques for Russula taxonomy is only starting in North America. Looney (2015) was able to obtain ITS sequence data from 16 types described by W.A. Murrill (66% of type collections that he analyzed). That suggests that not all type specimens might be successfully sequenced due to contamination of other fungi or low quality of DNA. The morphology remains the only tool when to re-define species concept of some old names. The use of next-generation sequencing applied on type of Russula pectinatoides revealed a problem with multiple mixed species within one type collection (Melera et al. 2016), this suggests again the importance of morphology to sort out concept of older names. Bazzicalupo et al. (2017) published so far largest sequence dataset of North American Russula. They successfully sequence ITS2 region of Benjamin Woo's samples collected between 1974–2007, and among 72 candidate species, they recognized several unknown species. Later, they published 9 of them as new (Hyde et al. 2017).
Conclusion and future perspectives
The studies of Russula in North America will, first of all, require an understanding of the correct concepts of already described species. The types need to be sequenced when possible, and their microscopic structure has to be described in detail, applying modern standards. We need to look for a combined morphological and molecular match with recent collections. However, this is not good enough; there might be still other closely related species differing in a few positions in the barcode sequence and almost cryptic in the morphology. Moreover, questions about the geographical distribution and the host range are also challenging., sampling of species within a lineage of closely related taxa from various areas and habitats is needed to resolve these questions. There is too much work for one person's lifetime and, unfortunately, no specific funding for the research is available. The excellent solution might be an alliance of mycologists working on North American Russula and implementation of citizen science and environmental DNA to support sampling effectively.
[This contribution was supported by the national grant APVV 15-0210. For more on this project see: http://ibot.sav.sk/dipofungi-en/project-team/events/ .]
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