Genetics and Biotechnology

Edited by J. Philipp Benz and Kerstin Schipper. 2020. Third edition. [The Mycota. vol. 2.] Cham: Springer Nature. Pp. xxii + 452, illustr. 59 (42 col.). ISBN 978-3-030-49923-5 (hbk), 978-3-030-49924-2 (ebk). Price: £ 139.99 (hbk), £ 111.50 (ebk).

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Genetics and Biotechnology (2020)

This is the fifth of the 15 volumes of The Mycota to be issued as a third edition, and brings the total number of volumes in the series to 36. The first appeared in 1995 and the second in 2004. In such a rapidly moving area of mycology, it is not surprising that there is much new to report 16 years on. While badged as a third edition, it is more a collection of in-depth review articles, many on topics which have largely emerged in the years since the second. Of the 17 chapters presented here, none precisely cover what was included in the second. Indeed, only one of the 73 contributors to the third, Gerhard Braus, was also involved in the second.

The chapters are organized into two sections: Molecular Genetics and Biotechnology. In the first these cover an array of diverse topics including chromatin structure and function, accessory chromosomes, the circadian clock, small RNAs, self/non-self recognition systems, genomics of partner biology in AM fungi, secondary metabolism and development, and a particularly valuable synopsis of the current state of fungal genomics. The Biotechnology section reflects how advances in our understanding of fungal genetics are being exploited, or have the potential to be so: as hosts for heterologous production of proteins and secondary compounds, in developing new avenues for drug discovery and bio-blocks for ontogenetic systems, the use of yeasts to produce a staggering array of substances (primary and secondary compounds, recombinant proteins, and fatty acids), biodeterioration and bioconversion of lignocellulose substrates, biotechnological possibilities of marine fungi, and an especially exciting overview of the potential of anaerobic gut fungi.

As in previous releases of new editions of volumes in the series, while the text is presented to the highest standards, many of the illustrations leave something to be desired—especially some coloured figures which are excessively reduced and include text on coloured blocks.

The volume also includes an obituary of Karl Esser, who passed away in December 2019 at the age of 95 years (see also pp. 30–31), prepared by Ulrich Kück and seven other of his former students and colleagues. He launched The Mycota along with the late Paul Lemke in 1994, and was still working, and managing the present volume, just a few weeks before his death. The series has come to be an extraordinary resource for mycology as a whole with the diverse authoritative reviews included, but the issue of its future is not touched on here. As I have indicated before, my personal view is that the chapters would have been better presented in a special journal that would both make them more accessible, less expensive, and able to be issued in a timely manner than have to wait until a particular volume was being compiled. It will be interesting to see what happens to the series in the future….

Fungi and Trees: their complex relationships

By Lynne Boddy. 2021. Stonehouse, Gloucs: Arboricultural Association. Pp. xiv + 306, illustr. (mainly col.). ISBN 978-0-900978-70-8. Price: £ 45.

Fungi on Trees: a photographic reference

By David Humphries and Christopher Wright. 2021. Stonehouse, Gloucs: Arboricultural Association. Pp. xiii + 338, illustr. (full col.). ISBN 978-0-900978-71-5. Price: £ 45. Price (both volumes): £90.

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Fungi and Trees and Fungi on Trees (2021)

This splendidly produced large-format pair of complementary volumes has been published by the UK Arboricultural Association. They have been prepared to increase the knowledge of those working with trees about their importance to Earth surface processes and other organisms, and also to facilitate the correct identification of fungi, especially macromycetes growing directly on trees.

The first volume, by Lynne Boddy, whose career has been devoted to the study of fungi in and on trees, earned her an award from the Association this year. Following a basic introduction to fungi and how they feed, reproduce, and disperse, she then goes on to explain how leaves, roots and wood provide homes for fungi. The diagrams and photographs make this the most comprehensive treatment of fungal habitats in trees I have seen, and it also covers wood anatomy and explains how trees age and the fungi associate with different stages of their lives. A treatment of the beneficial relationships between fungi and trees follows, which covers the full range of mycorrhizal types, not only ectomycorrhizas, how to manage them, lichens, mycoheterotrophic plants, and endophytes. The major types of tree diseases are explained, leading to a superb overview of emerging diseases and how pathogens have invaded Europe—and flagging up the issue of biosecurity and the difficulty of ever being able to have meaningful checks on imported stock. I did not, however, note any mention of the carriage of spores into the country on birds, clothing, vehicles, or packaging; our trees will always be at risk from invasives, which may not even be known to science and so have no names. There is then a series of chapters focussing on interactions amongst tree-associated fungi and other organisms, including outcomes of inter-fungal wars (one of Lynne’s specialities), wood decay and fungal communities, heart-rot and hollowing, and sapwood decay in living trees. I was especially pleased to note the heads-up: “people often make the mistake of assuming that a fungus fruiting on a living tree is a pathogen, but if the fungus is feeding on dead central tissue it is acting saprotrophically not pathogenically” (p. 190). Tree-surgeons sadly are often too ready to recommend felling a tree just because some bracket fungus is present.

The final two sections deal in turn with environmental change and issues of conservation and management. She covers the different situations in which trees occur, traditional management practices, changes in basidome production patterns in relation to climate change, host switches, range changes, effects of nitrogen deposition and other pollutants, and introductions around the world of mycorrhizal fungi in particular. While I was pleased to see the effects of sulphur dioxide air pollution on lichens and how they could be used to estimate its severity covered, it would have been good to have drawn attention to how an upsurge of nitrogen and ammonia-loving lichens indicates when levels of those pollutants are a concern; abundant yellow-orange lichens on bark do not indicate the air is clean! The risk categories used in conservation status assessments for fungi are explained, and case studies provided of threatened fungi and of threatened habitats—not only dead wood and veteran trees, but further mycophagous and saproxylic organisms of all kinds. Finally, good practices are discussed, not only for forest management, with a flow chart for options of how best to deal with standing or fallen trees in urban settings (p. 278), veteranisation treatments (p. 280), and even translocation of fungi for conservation purposes. The work closes with a glossary, and I was pleased to see also a series of comprehensive indices. The layout, and standard of the colour photographs is truly superb although the quality of some of the drawings might have been improved, and each chapter has a summary of key points at the start and a carefully chosen further reading list at the end.

The whole is a real tour-de-force, with Lynne’s passion shining through every page, and I cannot recommend it too highly. One topic that she does not cover is identification, which is the province of the second volume of this pair, Fungi on Trees as opposed to Fungi and Trees. The authors’ names may not be familiar to many mycologists, but this has been prepared by two people intimately involved, and with a huge experience of, the management of trees: David Humphries as Trees Management Officer for the City of London Open Spaces and Christopher Wright, a Senior Arboricultural Consultant. They start by cautioning that this is primarily a work concerned with the British Isles, and that while much will apply to other northern temperate habitats in Europe, that will not be the case for the more southern Mediterranean regions. The first two rather brief chapters provide a short overview of tree-associated fungi and their determination; the section on microscopic methods is provided by Andy Overall, author of Fungi: mushrooms & toadstools of parks, gardens, heaths and woodlands (Overall 2017) and which would serve as a useful adjunct to this new volume.

The bulk of the book, roughly 80%, is devoted to what are delightfully termed “species biographies” of 100 selected species. These are divided into two categories, annuals and perennials, and within each subdivided pragmatically by coloured marginal tabs into brackets, crusts, cushions, clubs and balls, polypores, mushrooms, jellies, toothed, and slime moulds. Each species is allotted two, or in some cases three or even four, pages which include a dash-board like series of notes at the start with the scientific and common names, classification, seasonality, main host, decay type, frequency, and an innovative thumb-nail showing where they occur on a tree. Each has a box including a description, area affected, significance, additional hosts, similar species, and key synonyms. The descriptions are oriented to the field observer, and unfortunately the only actual measurements given are those of the sizes of basidiomes and there is no information on the spores apart from the colour. Many mycologists will find this frustrating, especially when microscopic techniques have been explained in the second part of the book, and these can be critical for the confirmation of the identity of some of the selected species. I appreciate, however, that some practising arboriculturalists might have found too much microscopical information off-putting. What is really valuable here, is that the bulk of the species pages are occupied by superb colour photographs selected from the staggering 25,000 David indicates he has so far (p. vii). These show different stages of development and variations in habit, undersides as well as views from above, and they are a real delight to see. At the end of the volume, in addition to an index, there is a tabulation of common fungi associated with particular trees that will be a helpful pointer to users. This volume is an incredible achievement and one which all tree surgeons should have to hand before pronouncing a tree as “diseased” and in need of felling. I do hope that it will get the circulation it really merits.

The Arboricultural Association are to be congratulated on publishing these two volumes which will be of great benefit to mycologists as well as arboriculturalists, and at a reasonable price considering the lavish production.

Humongous Fungus

By Lynne Boddy. 2021. London: Dorling Kindersely. Pp. 64, illustr. ISBN 978-0-2414-6040-5. Price £ 12.00.

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This delightful little book is aimed at 7–9 year-olds and aims to introduce them to fungi and to appreciate their importance, from their role in the emergence of plants on land to the destruction of our crops (and the perhaps impending “bananageddon”) and applications such as plastic-eating “ecowarriors”. As one would expect from Lynne, there is much on their relationship with trees, but also their value in anaerobic digestion in animal guts. It includes pull-out tabs with fun fungal facts and is illustrated by photographs and also art work by experienced illustrator Wenjia Tang who now lives in New York. The book’s publicity claims this will “intrigue and amaze young readers, and open their eyes to the fungi thriving all around them” including a “magical tour of the forest floor”. I am sure that it will, and also enable them to surprise their teachers with fun “fungal facts”.

Healing Mushrooms: a practical guide to medicinal mushrooms

By Richard Bray. 2020. ISBN 9-798670-261661. Pp. x + 213, illustr. Hamburg: Monkey Publishing. Price: £ 10.74.

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This book, described on the back cover as by a “herbalist and bestselling author”, aims to introduce the “28 most powerful mushrooms you can add to your diet to maximise your health gains”. The two core sections of the book are an overview of these species and then a section organized by “ailments”.

In the overview, each is introduced with the scientific and selected common names, in most cases with half-tone illustrations and notes on reported main applications. The ailments section forms the largest part of the book, and 65 are considered from ageing to wounds and include numerous serious medical conditions. Information on dosage, the type of mushroom product, and published reports of their efficacy are compiled. The list of references is quite impressive with 337 entries, but the reason why some are duplicated is obscure; one appears in no less than 11 times.

There are cautionary notes on collecting and sourcing mushrooms, and a separate section addresses preparation methods including extracts and teas. I would, however, have wished to see more attention paid to the issue of misidentifications, which can be a particular hazard. Even commercial products may not be prepared with the species producers think they are using. Also, when considering preparations, the amounts of material required may vary depending on whether they come from mycelium, ground or sliced basidiomes, dry spores, or cracked spores.

In summary, an informative compilation, but one to be used only with considerable caution.

Life at rock surfaces: challenged by extreme light, temperature and hydration fluctuations

Edited by Burkhard Büdel and Thomas Friedl. 2021. Walter de Gruyter, Berlin.[Life in Extreme Environments vol. 9.] Pp. xiv + 244, illustr. (mostly col.). ISBN 978-3-11-064261-2 (hbk), 987-3-11-064646-7 (PDF), 987-3-11-0646264-3 (ebk). Price: 121.45 € (hbk).

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Life at Rock Surfaces (2021)

The complexity of the microbial communities inhabiting rock surfaces (“lithobionts”) has been increasingly recognized over recent decades, and so an overview by some of the foremost contributors to this explosion of knowledge is most welcome; 18 authors from various countries in Europe and South Africa have combined to produce nine chapters to produce this synthesis.

The niche is more complicated than might at first be presumed, involving organisms that can be categorized by their positions: on the surface (epilithic), just below the surface under translucent crystals or pebbles (hypolithic), or inside rocks and soil crusts (endolithic). The endolithic organisms may be in fissures or cracks (chasmoendolithic), pre-existing cavities or pores (cryptoendolithic), actively penetrate into hard substrates (euendolithic), or on the underside of soil crusts (hypoendolithic). These categories are explained in the first chapter, with most helpful photomicrographs, and the wide range of evolving and increasingly sophisticated methods now used in their exploration are described. This first chapter also covers mineral interactions, especially bioweathering, while the second is devoted to the hypolithic habitat which is so important in desert soils and primarily composed of various bacterial organisms (including cyanobacteria).

A series of chapters then address the situation in different groups of organisms. Phylogenetically diverse black fungi, many described in recent years, melanins giving some protection from harmful sunlight, and which have been well-studied in Antarctica but are also of concern for their biodeterioration of stonework (especially of monuments of heritage importance. Cyanobacteria, including a novel and valuable key and notes on the characters of the 53 genera involved, which will also be of value to lichenologists. Lichens, self-sustaining ecosystems that are often the first colonizers of rock surfaces, either epilithic or endolithic depending on whether the rock is siliceous or calcareous. High alpine lichens where freezing and water availability are key issues. Complex lichen communities, on different rock types and interactions between them. Eukaryotic algae, including red algae and diatoms, with lists of genera. And finally desiccation-tolerant vascular plants.

The chapters are extensive referenced, well-edited, and many have great colour photographs or microphotographs. As stated on the back cover, this is a indeed a “unique overview of various organismal groups interacting with the rock surface”. This will now be THE go-to work for anyone contemplating research on these ecologicaly very specialized and so fascinating organisms. The editors are to be congratulated on pulling such a fascinating and informative synthesis together.

Atlas of Clinical Fungi: the ultimate benchtool for diagnostics

By G Sybren de Hoog, Josep Guarro, Josepa Gené, Sarah A Ahmed, Abdullah M S Al-Hatmi, Maria J Figueras and Roxana G Vitale. 2020. 4
th
edition. Hilversum: Foundation Atlas of Clinical Fungi. 2 vols. Pp. 1598, illustr. (many col.). ISBN 978-94-93226-12-8. Price: 275 €.

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Atlas of Clinical Fungi (2020)

This Atlas is now well-established as the keystone reference work, the vademecum, and “go to” source of clinical mycology, since it first appeared in 1995. The third edition of this was issued as a CD-ROM back in 2009, while the second edition was issued in hardback in 2000. The second edition was a comparatively modest single volume of 1126 pages, which has morphed here into two massive volumes, with 42% more pages in the fourth, and which together weigh 7 kg.

The first sections together amount to a textbook covering the range of diseases and kinds of mycoses, their histology, laboratory techniques, phenotypic and molecular methods of examination, media recipes, available antifungals (including side effects and interactions), and recommendations for treatment. There are keys to facilitate morphological identifications in tissue sections, the genera treated, a systematic arrangement, and a tabular comparison of names adopted in the first and second (but not the third) editions. Some 700 species are treated in depth, the “lower fungi”, basidiomycetes, yeasts, and filamentous ascomycetes A-B in the first volume (Part α), and filamentous ascomycetes C-Z in the second (Part β). The genera are arranged according to the systematic hierarchy, and then alphabetically within each family; personally, I would have preferred all to be in an alphabetical series, but arrangement in this way does have the advantage in enabling keys to genera and notes applicable at the family level to be brought together. In the case of larger genera, such as Aspergillus, keys to species are also provided. The individual species entries have information on colony characteristics, microscopic features, pathogenicity, growth characteristics, antifungal susceptibility, key references, nomenclature, line drawings, and generally first-rate colour photographs of both colonies on pertinent media and microscopic features. The second volume ends with a particularly comprehensive glossary of terms, an amazing 36-page compilation of doubtful names and unconfirmed clinical cases, and an index to the included species that will greatly facilitate users unfamiliar with systematic placements locating entries.

This is the first edition to be issue since the ending of the separate naming of different morphs of the same species in 2011, and it is pleasing to see this implemented throughout. As a result, this work will help ensure the adoption of single-name nomenclature in the medical mycology community.

The establishment of a not-for-profit Foundation to enable this Atlas to be published and have a continuing future is a wonderful and magnanimous initiative of the authors. This has meant that the hardback volumes, of which I understand only a rather limited number were printed, could be offered at a very reasonable cost for such a complex and well-produced work. Furthermore, this was made available at a modest online-only cost during 2021, and from 1 January 2022 it is scheduled to become available online (www.atlasclinicalfungi.org) entirely free of charge – an immense service to medical mycology which will surely aid the diagnosis and treatment of numerous cases to an extent not previously possible. The authors deserve our thanks for not only producing such a scholarly fundamental reference work, but for their generosity.

Emerging Plant Diseases and Global Food Security

Edited by Jean B. Ristaino and Angela Records. 2020. ISBN 978-0-89054-637-6 (hbk), 978-0-89054-639-0 (ebk). St Paul, MN: American Phytopathological Society Press. Pp. vi + 305, illustr. (most col.). Price: US$ 249 (hbk).

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Emerging Plant Diseases and Global Food Security (2020)

It is not always appreciated how vulnerable some of the key crops we depend on for food are to fungal pathogens. In the first section of this book, chapters focus on the vulnerability of supplies and the farmers in the poorest regions of the world, the current and worrying extent of global losses from pests and diseases, and the difficulty of adapting disease management systems in a period of global climate change—the challenge of developing climate-smart agriculture integrating disease resistance, control, and forecasting.

In-depth explorations of the situation in selected species are provided for the cases of wheat rust, maize leaf necrosis, late blight, cassava viruses, Panama disease of bananas, and coffee rust. The spread of the Ug99 race of wheat stem rust (Puccinia graminis f.sp. tritici) is a particular and increasing concern with a race between evolving fungal genotypes and resistance genes in the host. The situation with late blight (Phytophthora infestans) is complex with the genotype frequencies changing year by year on potatoes (and to a lesser extent on tomatoes) and even in different parts of even a small country such as the UK. Panama disease (Fusarium oxysporum f.sp. cubense) is now threatening the long-resistant Cavandish banana cultivar due to a newly emerged race TR4; breeding for resistance is a particular challenge as this not always correlates with taste and resistance to bruising during transport. Resistance has also broken down against coffee rust (Hemileia vastastrix) in Central America, with the climate favouring particular races of the rust and also adversely affecting the most commonly grown Lempira cultivar; technical solutions may be the way ahead but may mean production becomes unprofitable.

The final group of chapters focuses on approaches to addressing and limiting the prospect of major disease episodes. These include “Plantwise”, an international initiative led by CAB International to promote “plant health systems” and plant clinics, collecting data and providing an advisory service to help monitor outbreaks. An overview of geospatial analysis to monitor disease spread, a review of models to predict epidemics and optimize detection and management. And finally an examination of the situation in blast diseases caused by Magnaporthe oryzae pathotypes on diverse grass species, including rice, wheat, millet, perennial rye-grass, and tall fescue; this masterly overview shows the host specificity of the different pathotypes and discusses how resistance may be managed and outbreaks contained, but also highlights the prospect of spread to crops such as barley and oats should it become adapted to cooler climates.

All the chapters are by teams of specialists, well-edited, fully referenced, and superbly laid-out and illustrated to the high standards we have come to expect from APS Press. I cannot commend this work too highly, and trust that it helps increase political awareness of just how vulnerable are some of our staple foods, and how fragile is this element of the global food supply. Funding for basic research and field experiments should surely be increased to a level commensurate with the risk these diseases pose to global food security.

Hidden Kingdom: the surprising story of fungi in our forests, homes, and bodies

By Keith A. Seifert. 2022. Vancouver: Greystone Books. Pp. xiv + 288. ISBN 978-1-77164-662-8 (hbk), 978-1-77100-663-5 (ebk). Price: CAN $ 34.95 (hbk).

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The Hidden Kingdom of Fungi (2022)

This new public-oriented book is due to be published on 22 May 2022, but I have been privileged to see an uncorrected proof copy so can draw it your attention now. It is a roller-coaster authoritative and gripping exposé of fungi, and how we and our environments interact with them daily in multifarious, but often unseen and unappreciated, ways. It reflects Keith’s wide interests in aspects of pure and applied mycology in its breadth, and this sets it apart from other texts of the genre. The style is engaging, with personal insights, and his enthusiasm and fascination for fungi emerges from every page. Topically, he also provides an exciting vision of how fungi might contribute to a more sustainable Earth. There are inevitably a few quibbles other mycologists will have as he strays out of his comfort zone, but it would be invidious to highlight any here as those I found were all rather minor. This book has the potential to heighten public awareness and respect for fungi, and merits a wide circulation in bookstores around the world.

Trends in the Systematics of Bacteria and Fungi

Edited by Paul Bridge, David Smith and Erko Stackebrandt. 2021. Wallingford: CAB International. Pp. xviii + 346. ISBN 978-1-789-24498-4 (hbk), 978-1-77100-663-5 (ebk). Price: £ 115 (hbk).

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Trends in the systematics of Bacteria and Fungi (2021)

I have always been keen to learn from approaches and methodologies being used by systematists working on organisms other than fungi, something that goes back to my student days at Leicester University in the 1960s. There I learnt of novel methods being used by several of the leading systematists of the day working on bacteria, fossils, and plants—and adopted several in my PhD on a lichen-forming genus. The first editor started his reach on bacteria and yeasts before turning to filamentous fungi, so was well-placed to take the lead on such a volume; the second is one of the foremost specialists on culture preservation procedures; and the last, one of the best-known names in prokaryote nomenclature and systematics.

The editors have marshalled a further 49 contributors from diverse countries to put together a volume of 18 chapters in what they refer to as “a pivotal time for microbial systematics” (p. xvii). The reliance of prokaryote nomenclature on type cultures is flagged up in the first chapter as a key problem due to the demand for names from those working with environmental samples which are not known in culture; the issue is coming to a head as the International Commission on Systematics of Prokaryotes (ICSP) voted against making any much provision last year—it is now a case of “reconciliation or divorce” (p. 13), with a separate “UnCode” for unculturable organisms now being debated. This same topic is highlighted at the end of an overview of fungal identification by Tom May, where he notes that discussion is currently polarized (p. 27) and the issue of these so-called “dark taxa” is returned to again in Chapter 12 (pp. 204–205). The following chapters deal with data sources on names; the issue of preservation of reference strains, their management, and quality control procedures; the value of older molecular sequences; and the role and services of culture collections. Two chapters examine the use of MALDI-TOF and similar approaches in bacteria and fungi, respectively, which remain constrained in fungi by issues surrounding standardization and a lack of reference databases. A contribution on chemotaxonomy focusses on biomarkers in bacteria, especially fatty acids, lipids, polyamines and sugars, but surprisingly there is no equivalent contribution on fungi where compounds such as polyketides have proved especially valuable markers.

Whole-genome sequencing is becoming increasingly recognized as the way for the near future, and this is addressed in four contributions, but is clearly much more advanced in the case of bacteria than fungi; mycologists considering such approaches could benefit from contemplating the experience in bacteriology. The always thorny issue of what is a “species” is considered in separate chapters on bacteria and fungi, but while these are far too short to adequately address various definitions and approaches, extensive reference lists are provided. The “species question” is one of those returned to in the final reflections of the editors on the future direction of bacterial and fungal systematics, where they also discuss the problems in obtaining sequence data from historic collections, curation of names, global networking of strain information, and difficulties in working with and exchanging living material as a consequence of international treaties (especially the Nagoya Protocol)—and the work-arounds some countries have developed.

There are inevitably aspects which might have been addressed more fully, for example improvement in the stability of fungal names through protected lists, and initiatives being taken to promote good practice by the International Commission on the Taxonomy of Fungi (ICTF), a body that most surprisingly I could not see mentioned at all. The book does, however, provide much for mycologists to reflect on and learn from their bacteriologist counterparts, and in that it clearly succeeds here, and the editors are to be congratulated in pulling such a work together.

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