- Open Access
IMA Fungus volume 3, pagesA10–A23(2012)
One Fungus = Which Name?
The special provisions that permitted asexual morphs of the same species of pleomorphic non-lichenized ascomycete and basidiomycete fungi to have separate names from that of the whole fungus, which was typified by a sexual morph, were ended at the International Botanical Congress in Melbourne in July 2011. These changes, that are embodied in the forthcoming International Code of Nomenclature for algae, fungi, and plants1, followed after extensive debates and consideration by different committees, and in particular The Amsterdam Declaration2. The Declaration resulted from the “One Fungus = One Name” symposium organized by the CBS-KNAW Fungal Biodiversity Centre (CBS) under the auspices of the International Commission on the Taxonomy of Fungi (ICTF) and held in Amsterdam on 19–20 April 2011 (see IMA Fungus 2: (7), 2011). Summaries of the changes which were introduced have been presented elsewhere3, 4 and are not repeated here, but it is important that the published version of the Code is consulted for the final wordings.
Mycologists now have the tasks of implementing the changes in their own publications, and also contributing to the production of Accepted and Rejected Lists of names. Recognizing the uncertainties some mycologists expressed as how to proceed, and also the need to progress work on the Lists, CBS organized a follow-up symposium on “One Fungus = Which Name ?” in the rooms of the Royal Netherlands Academy of Arts and Sciences in Amsterdam on Thursday and Friday 12–13 April 2012. The meeting was attended by 155 mycologists from 29 countries, almost all of whom were thrilled at the ending of the dual nomenclatural system and enthusiastic at the prospect of Accepted Lists which would place mycology at the cutting edge of biological nomenclature as a whole.
Each day of the symposium was organized in the form of a series of presentations in the morning, and discussion groups or debates in the afternoon. In a new venture aimed at making the presentations as widely available as possible, the talks were also videoed and made available via the Internet in real-time. Subsequently, a video-archive of the talks was compiled with a link to this through the CBS home-page to Youtube (https://doi.org/www.youtube.com/playlist?list=PLF8BF8F71D5A3AEDC). It was gratifying that 220 mycologists watched the proceedings via the videolink while they were in progress, and that since the meeting there had been hundreds of downloads of presentations at the time this issue went to press. This means that hundreds of individual mycologists have so far been able to benefit from the full talks of the symposium and others still can do so.
There were 12 presentations in total, all of which are freely available in the video-archive:
One fungus which name: how do we proceed?
(David L. Hawksworth, Spain/UK)5. Post-Melbourne fungal nomenclature: an overview (Lorelei Norvell,USA; Scott A. Redhead, Canada).
Why hyphomycete taxonomy is now more important than ever (Keith A. Seifert, Canada).
The nomenclature side of fungal databases, registration, etc (Joost A. Stalpers, The Netherlands; Paul M. Kirk, UK).
Single names in Hypocreales and Diaporthales (Amy Y. Rossman, USA).
Applications of old anamorph-typified names of genera and species (Uwe Braun)6.
A strategy for fungal names with teleomorph-anamorph connections (Xing-Zhang Liu, China).
The future of fungal biodiversity research (Pedro W. Crous, The Netherlands).
Naming environmental nucleic acid species (ENAS) (John W. Taylor, USA).
The value of epitypification (Kevin D. Hyde, China/Thailand).
An official DNA barcode for fungi (Conrad Schoch, USA).
1000 fungal genomes and beyond (Joey Spatafora, USA).
A series of break-out group discussions, primarily focused on different fungal taxa, was held on the Thursday afternoon, and those groups were charged with reporting at the end of the next day. Prior to the presentation of these reports, which are reproduced below, an open discussion was held to clarify aspects of the new provisions or other matters that some present had found unclear, and further to ascertain the views of those present on various issues that needed to be addressed by those developing Lists and the Nomenclature Committee for Fungi (NCF) or ICTF; those discussions are also summarized below.
In addition to the formal parts of the symposium, two new books were formally launched at a cocktail party on the first evening. John W. Taylor (IMA President) was presented with copies of the Taxonomic Manual of the Erysiphales (Powdery Mildews) by Uwe Braun and Roger A. Cook, and the Atlas of Soil Ascomycetes by Josep Guarro, Josepa Gené, Alberto M. Stchigel, and M. José Figueras. Further information about these works is presented in the Book News section of this issue (pp. (35)–(36)).
The One Fungus = Which Name? debate
Chair: David L Hawksworth
Rapporteur: John W. Taylor
Issues considered in this part of the meeting fell into two categories, a clarification of concepts and possibilities, and view on topics where the ICTF and NCF would appreciate guidance.
Clarification of concepts and possibilities
(1) Names on an Accepted List are NOT conserved, BUT treated as if conserved
Some speakers had used the term “conserved” for names that would be included on the Accepted Lists of names, but their status will not be identical to that of formally conserved names as, under the new Code, names included in the Lists of Conserved Names would have precedence over those on the Accepted Lists. Further, names that are formally conserved cannot be deleted, whereas there is no such restriction for names on the Accepted Lists. The meeting found this confusing, and felt that a different term should be found to replace “treated as if conserved.” One possibility could be refer to names as “White-“ or “Black-listed. It had also been suggested by Gams et al.7, that the terms “prioritization” and “suppression” were preferable to help minimize possibilities of confusion, and that option should be referred to the NCF for consideration.
(2) What names can be included in the Accepted and Rejected Lists?
There was uncertainty over the need to include names on Lists where there was no controversy or ambiguity. The Accepted Lists could include all names in use, including those where there was currently no dispute, as that would safeguard them from any earlier names that subsequently came to light. Alternatively, the Lists, could be restricted to cases where dual nomenclature had previously applied and which now had just one name.
It was felt that the Lists should be large enough to justify the time that would be spent on their preparation. The ideal would be a global checklist, though it was recognized that would not be realizable in the immediate future. However, there is no restriction on the ranks of names nor of taxonomic groupings. A List could be confined to all names in a particular rank, such as orders, families, genera or species, within a particular taxon. Alternatively, it could cover names at all ranks in use in a particular taxon. Thus, a List could deal with all accepted generic names of fungi, or just those in a particular order or family. It is really a matter for mycologists concerned with different groups of fungi to decide what protected Lists would be of most value to them and which should be prepared first. As there is evidently no obstacle to Lists being revised or replaced, unlike the situation with the already existing lists of conserved and rejected names, there could be some advantage in concentrating on generic names first, and adding species names at a later date.
There was almost unanimous and enthusiastic support for first producing a List covering all accepted generic names (including those of lichen-forming fungi, see below), whether or not they exhibited pleomorphism.
There was a strong feeling at the meeting that provisional Lists should be open for consideration by the community as a whole before submission, in order to iron out any controversy. It was suggested that draft Lists be put on the IMA website, with options for comment so as to work towards a consensus.
(3) Typification of names in Lists
It is already possible to change the name-bearing type of a name by conservation, and there appears to be no obstacle to this in the new Lists. The new Lists can therefore include replacement types to deal with cases where well-known names have been misapplied, that bear both sexual and asexual morphs of the species when the previously designated type did not, or one has been sequenced and is widely available (for example as ex-type cultures).
(4) Terminology of specimens and cultures
There had been some confusion over the terminology used for specimens and cultures other than name-bearing types by different workers. General usage is as follows:
Authentic: One named by the author of the name, generally after it was published, or, if the name is a combination, the author of the basionym.
Voucher: One used in a particular study, either for experimentation or to support an identification, enabling the same material to be used by or verified by later researchers.
Representative: One or more from a large set or specimens or cultures considered to serve as vouchers where it is impractical to preserve all those used or cited in a particular study.
(5) Continued use of binomials in synonymized genera
There will be many cases in moving to one name per species in pleomorphic fungi, where it is uncertain whether all species currently under a particular name are congeneric with the type species of the generic name to be adopted. This situation is no different from that already occurring in non-pleomorphic genera where it has not been possible to ascertain the positions of all taxa previously referred to them. The Code does not rule on taxonomy, and, if there are no certain grounds to transfer a species from on genus to another, there is no nomenclatural obstacle to the continued use of the current name until the matter is resolved. This matter is discussed further elsewhere in this issue8. This situation is pragmatic not ideal, and one option used by some mycologists is to indicate in an informal way that a generic name is being retained in a wide sense, for example by the use of inverted commas, e.g. ‘Mycosphaerella’ where it is unclear if the fungus is truly a Cladosporium (syn. Davidiella) in the new system. Wholesale uncritical transfer of names is to be discouraged.
(6) Who can prepare and submit Lists?
There is no restriction on who can produce a draft List, and it could be an individual as well as formal or informal groups of mycologists. In view of the scale of the problem, the input of as many individuals as possible can only be welcomed. If you have information on particular families, genera, etc, prepare the first draft rather than wait and be angered by the content and quality of one someone else produces. However, be sure to inform the ICTF and NCF if you are willing to prepare a draft or contribute to a draft for a particular taxon so that duplication of effort can be avoided wherever possible. List preparation needs to be initiated quickly now to keep to the timetable necessary to achieve formal adoption at the 2017 congress9.
(7) Operational dates
There had been some confusion about when the one name for one fungus species system became effective, and in particular whether this was 30 July 2011 or 1 January 2013. The Preface to each edition of the Code now explains that all changes are immediately effective unless another date is indicated. This means that the special provisions ended on 30 July 2011, after which date all names of fungi compete on an equal footing, whether they are typified by material with the teleomorph or of the anamorph. The 1 January 2013 date in the new Code is there only to provide immunity to names published prior to that date that otherwise might be declared invalid or illegitimate. The use of a later date allows time for the change to be disseminated amongst researchers, and avoids works in press being contrary to the Code, i.e. introducing names that otherwise would be contrary to the Code and not available for use.
Issues requiring action or guidance
(1) Epitypes, teleotypes, and anatypes
Epitypes are specimens selected to supplement a name-bearing type where that types does exist, but does not show the characters necessary to determine the species. An epitype is a formal category recognized in the Code, and once selected an epitype cannot readily be displaced. An increasingly common practice amongst mycologists is to designated as epitypes material that has been sequenced when no DNA could be recovered from the name-bearing type.
Redhead10 had previously proposed the use of the term “teleotype” type as a special category of epitype selected to show the teleomorph when that was missing from the name-bearing type, but the proposal was withdrawn and not adopted at the Melbourne congress. Although Redhead did not propose it, logically the term “anatype” could also have been proposed for material selected to show the anamorph where that was not represented on the name-bearing type. As these two categories would not be epitypes, they could still be designated where there was already an epitype, and their existence would not preclude an epitype being selected subsequently where there was not.
The meeting rejected the idea of separate “teleotype” or “anatype” designations and considered that the type need not exhibit any particular morphology.
(2) The terms anamorph and teleomorph
The issue of whether it was desirable or useful, when describing fungi, to continue to use the terms anamorph and teleomorph was also raised. These had been introduced into the Code at the Sydney congress in 1981 specifically for fungi that exhibited pleomorphism. The meeting felt that these terms were an unnecessary complexity, especially in teaching, and that they would be better dropped in favour of the familiar terms asexual and sexual, respectively.
(3) Defining widely used
This issue was recognized as difficult, and the potential pitfalls in the use of the Google search engine in particular as an estimator of usage made it unreliable. Matches may not be exact for a variety of reasons. Google Scholar was considered probably better, if used critically. However, it was felt that experts in particular groups would have the best ideas of what was in the interests of mycologists as a whole. Those who disagreed, could make their own List for consideration, or comment on any posted. There was a strong view that applied usages and taxonomic usages were both important and neither should dictate.
(4) Evidence of holomorphy
This was a matter considered too complex to debate in the session, but one on which guidance would be welcome. It was suggested that the ICTF should consider providing guidance on this matter.
(5) Using the conserved/rejected mechanism while Lists are in preparation
The existing mechanisms for the conservation and rejection of names in the ranks of family, genus, and species would continue to operate while Lists were in preparation, revision, and proceeding towards formal adoption. There was therefore the possibility that decisions made on conservation or rejection might not be in accord with the Lists themselves. The NCF made clear that it would nevertheless still entertain conservation proposals, but that it would prefer to see lists with lots of names rather than proposals dealing with a single taxon.
(6) Inclusion of lichen-forming fungi
Under the proposals adopted at the Melbourne congress, lichen-forming and allied fungi were excluded from the Lists. However, many considered this illogical, and the meeting voted unanimously for the deletion of this anomaly. It is clear that a formal proposal should be made to rectify this in the near future so that it can be considered by the NCF and approved by the General Committee in a timely manner so that lichenized taxa can be included where appropriate in the Lists.
(7) Use of subgeneric names
The issue of whether mycologists should use the rank of subgenus more frequently, especially in large monophyletic genera, proved very controversial. Some were completely against any subtaxa, whereas others saw good grounds for the use of subgenera in particular cases. The use of subgeneric names was a way of maintaining name stability as the generic and specific names would not be changed. On the other hand, some felt this meant that users might have to learn three names rather than two, were subgeneric names regularly to be inserted in parentheses between a generic name and a species epithet. No consensus emerged, and this may be a situation where the matter is best addressed on a case-by-case basis.
(8) Registration of typifications and First Revisers
There was a unanimous view that details of types designated after the original introduction of a new taxon should be deposited in the registering database at the time of typification. At present it was very difficult to locate later epi-, lecto-, or neotypifications. It was considered that this was an issue that the NCF should consider, with a view to requiring accredited repositories to record such information.
The Amsterdam Declaration had included the proposal that the first authors to make a choice of names when uniting anamorph- and teleomorph-typified genera should be registered and accepted, unless that was subsequently challenged — in which case it would have to be considered by the appropriate mandated body, i.e. the NCF. This concept is similar to the principle of the first-reviser in zoological nomenclature, but has not been used outside zoology. This provision was not part of the package adopted at the Melbourne Congress, but some of those present at the meeting did consider the matter nevertheless merited careful consideration, and perhaps could be discussed during IMC10 in Thailand in 2014.
There was also a lengthy discussion and interchanges between representatives of MycoBank and Index Fungorum on the issue of accreditation of repositories of nomenclatural data, which is required for the valid publication of new fungal taxa from 1 January 2013. In particular, there was a debate as to whether more than one repository should be recognized by the NCF. The meeting saw MycoBank as the logical immediate choice, but it also recognized the value of several centres, especially ones operating systems in different languages, such as Chinese. It also recognized the depth of nomenclatural detail in Index Fungorum and the key role that had in underpinning all fungal nomenclatural databases. If a distributed system were eventually developed, the meeting felt it was absolutely essential that there was data-sharing in a timely manner, and ideally in real-time, but at least on a daily basis.
(9) Proposal by Walter Gams
Gams and colleagues had recently published a proposal that when a binomial in a prioritized genus had a younger epithet than the corresponding name in the suppressed genus, priority should be granted to existing names in the prioritized genus11. This principle already applies in zoological nomenclature, and had been adopted by some botanists in the past where it became known as the “Kew Rule”12 — but this practice has not been permitted under the various editions of the botanical Code. Some of those present saw some advantages in this suggestion as a further means of minimizing name changes, but it was recognized that a formal proposal on this matter would have to be prepared for consideration by the NCF and a future congress. Gams indicated that he was encouraged by the comments and would explore this possibility further.
(10) Desirability of a joint NCF/ICTF/IMA dedicated Lists committee
The officers of the NCF, ICTF, and IMA present at the symposium did not see the need or value of establishing a dedicated Lists committee. There was a strong dialogue between the parties, and some mycologists were members of more than one of these bodies. It was recognized that the NCF was the body with mandatory responsibility for making recommendations on any Lists prepared, while the ICTF had a role in List preparation, through its various subcommissions.
(11) Environmental sequences
The increasingly urgent need to address the issue of the naming of fungal taxa only known from environmental DNA sequences had been considered at the One Fungus = One Name symposium in 2011, and some suggestions were made in the report of that meeting13. After some discussion, the ICTF agreed to establish a working group on naming environmental strains.
Working group reports
Rapporteurs: Scott A. Redhead and Dominik Bergerow
The group split into one dealing with heterobasidiomycetes, and the other with homobasidiomycetes (Agaricomycetes s.str.). For the heterobasidiomycetes, a web page in which it would be possible to comment on each name separately should be set up, if possible with a voting option. Most of the problems in these fungi were considered to be taxonomic rather than nomenclatural. The real need was for more people writing papers. For example, it is general knowledge that Cryptococcus is paraphyletic, but no one was resolving the problem, which in any case should be addressed together with the yeast commission and the group on medicinal fungi. In the rusts, the solution should be close to current practice. I.e. to maintain the use of Uredo for species only known from the uredinial stage and without any current possibility of assigning them to a monophyletic genus. If Uredo was to be restricted to it’s type species, there was a possibility that some would propose names that prove superfluous in an intermediate time-frame; this was not ideal, but an ad interim alternative.
In the case of the homobasidiomycetes (agaricomycetes), a working list could be generated shortly. When that was available, invitations to assist in the evaluation should be sent worldwide to all who had expressed interest in helping and an invitation will be sent to them to participate in the decision making process. Initial tables had been provided for the Amsterdam meeting by CBS, but it was recognized these were not complete. Further it was evident that while there were issues, many would be easy to decide on. Taking the first four generic names: one required research (Abortiporus vs. Fibrilklaria), one had an obvious solution (Abortiporus biennis vs. Sporotrichopsis terrestris), one no obvious solution (Aleurodiscus habgallae vs. Matula poroniforme), and one conservation (Armillaria vs. Rhizomorpha). As such cases could be resolved during the meeting, the group opted to start an online working group as soon as the logistics could be worked out. In each case the types for each of the generic or species names would need to be confirmed, and the links between the names needed to be questioned or confirmed. It was planned to have a first List available for comment by the end of 2012.
Rapporteur: Kevin D. Hyde
It was agreed that a web page for Dothideomycetes should be set up within a few months, and all proposed committee members would be contacted by email or other social media (e.g. connect website). Of key importance was the type species of generic names, and it is with those than links should be substantiated; if correlations were with species other than the type, this needed to be made clear in a note on any List or in a supporting paper. Linkages should be based on sexuality/phylogeny, and if not the case needed to be well- argued. In general, the group considered that the oldest names should be given priority, regardless of the nature of their types. In cases where a younger name was prepared, the logic in support of the retention needed to be provided. The group considered that initial Lists could be published by September 2012, with a view to submission by January 2013.
Rapporteur: Robert A. Samson
The group recognized that many genera in the class were important for applied mycology, so the nomenclature should be simple, stable and not confusing. It was also noted that applied researchers are likely to ignore nomenclatorial changes. The phylogeny of Trichocomaceae was now well-established, and the IUMS International Commission on Penicillium and Aspergillus (ICPA) planned to tackle other genera in the family as well. However, in the case of Onygenaceae collaboration with medical mycologists would be sought. It was anticipated that ICPA would produce a list of accepted names in Penicillium within a short time, but it was recognized the case of Aspergillus would require more discussion with users. In Aspergillus, there were several options: retaining the name for all aspergillae, splitting the genus and re-naming the groupings according to their teleomorph names, changing the type of the genus to A. niger so that did not change in a splitting, or to use Aspergillus with an optional descriptor. It was also pointed out in open discussion that there was in addition the possibility of using subgeneric names, which could be those of the teleomorph-typified names if adopted in the Accepted List; it while names at the rank of subgenus or section could not be conserved under the Code, the Lists had no such rank restriction.sa noted that names in indicator. These matters would be discussed at a meeting of ICPA scheduled for the Saturday after the symposium, and open o all through the commission’s website (https://doi.org/www.aspergilluspenicillium.org).
Rapporteurs: Sybren de Hoog and Vishnu Chaturvedi
It was considered that the International Society for Human and Animal Mycology (ISHAM) should implement a democratic procedure to achieve a stable result, which would be adopted quickly by the entire community. There was a consensus for a practical approach, taking the needs of the user as the starting point. The community of medical mycologists must first decide which names we without doubt want to keep: for example, Candida albicans and Aspergillus fumigatus should be maintained, and Trichophyton used rather than Arthroderma. There could also be many other classical pathogens and opportunists that we wish to keep the current names for and which should be proposed for inclusion on an Accepted List. An important criterion over the choice of a name will be how frequently it has been used. However, “widely used” is an unclear criterion. How does one establish whether Scedosporium is more current than Pseudallescheria? For each name put forward, the reasons for the proposed retention should be specified. In cases where no single name was strongly favoured, the oldest name (whether anamorph- or teleomorph-typified) should have priority. For example: Aspergillus is older than Neosartorya, and therefore the Neosartorya species should be termed Aspergillus in the future.
Reclassifications can be phenotypic or molecular phylogenetic, but the key criterion of a group is the monophyly. The clade determines the group meriting a genus name, preferably the oldest available for that group is used, as for Aspergillus. Molecular taxonomy may reveal groups where all experts agree that they are clearly monophyletic, and also share essential characteristics such as pathogenicity or antifungal susceptibility, as in the yeasts. However, there are also groups where so many new data — often of environmental relatives — are being added, that the phylogeny is highly unstable, as in the rapidly developing black yeast taxonomy. The group felt it could be prudent to propose that for the time being we leave names as they are, even if some “genera” are polyphyletic. In the case of established but poorly differentiated genera, such as Acremonium, some may be highly polyphyletic and thus phylogenetically ambiguous. There was a proposal to abandon such generic names, but an alternative would be to redefine them in a modern sense on the basis of accessible type material.
The community of medical mycologists, including the ISHAM membership, is requested to propose Lists of preferred names on the basis of the above criteria. The names of many fungal pathogens have an ancient history and have become a source of confusion over the years. We therefore urge taxonomists, if necessary, to (re)define the groups of fungi they are working with by the deposition of (new) type material that can be protected in the Lists. As a first step, an ad hoc group has decided to provide a list of fungal names in current use based on the Atlas of Clinical Fungi14 for the ISHAM membership to comment on (comments to be sent to: email@example.com). The group hoped to have active involvement of as many medical mycologists as possible.
Rapporteur: Joey Spatafora
Participants: ca 30
In discussing the criteria to be used to choose between two generic name options, considerations should include: taxonomic clarity (i.e. the genus name should be well circumscribed), the morphology most commonly encountered, names used in plant pathology and industry (etc), quarantine issues, stability, and relevance. The credentials of a particular taxonomist needed to be made clear when making a decision on a particular group. The strength of an argument should consider the number of name changes, monophyly, that names represented clades not morphologies, distinguish taxonomic and nomenclatural issues, consilience, and historical uses, and the possibility of retaining genera but with a different type species. Should there be a preference for names that commemorated the history of a taxon (e.g. Cordyceps) or ones that were history (e.g. Tolpocladium). It was felt that several subgroups would be needed: Xylariales; Magnaporthales/Diaporthales; Fusarium; Hypocreales I (Bionectriaceae, Nectriaceae, Hypocreaceae, and Niessliaceae; Hypocreales II (Cordycipitaceae, Clavicipitaceae, and Ophiocordycipitaceae); Sordariales and allies; and Colletotrichum.
IMA Executive Committee Meeting
In mid-April 2012, The Netherlands again turned into an international centre for mycology and the IMA Executive Committee met on 14 April 2012 in Utrecht parallel to meetings of the International Commission on the Taxonomy of Fungi (ICTF) and the International Commission on Penicillium and Aspergillus (ICPA). This was the largest Executive Committee meeting ever held between IMC congresses, and illustrated the amount and importance of activities organized by the Association, under the presidency of John Taylor. The meeting covered all aspects of advancing mycology on a global scale, and here I just wish to highlight a few of the points, which were discussed and decided.
First, the Executive Committee congratulates the winners of our young mycologist awards, which were finally completed with announcements on the two outstanding. The Elias Magnus Fries Medal was awarded to Cécile Gueidan (nominated by the European Regional Mycological Member Organization) and the Carlos Luis Spegazzini Medal to Luis Fernando Pascholati Gusmão (nominated by the Latin American Regional Mycological Member Organization; for further information see p. (25) in this issue. While the young mycologist awards are designated to the early years of a career and honours outstanding mycological research by young scientists from our regional member organizations, the Executive Committee also searches for ways of acknowledging substantial support of mycology by others. The introduction of a category of IMA Fellows as a midcareer award received great support from the Executive Committee, and guidelines will be available soon, so that a first round of mycologists can be recognized in this way during IMC10 in Bangkok.
Although the finances of the IMA are robust, we seek further external funding to increase our capabilities. While there is quite substantial support from external funding during our congresses, the IMA would like to attract companies and institutions to become patrons of the IMA for a yearly fee. The profits of several large international companies are based on fungi or fungal products, and the IMA supports the development of a closer link between research and economy. Mycology will become a big business in the future, and financial support to our work is highly appreciated.
To increase visibility and to provide better support for mycology worldwide, the Executive Committee agreed on the further development of our IMA Newsletter and the redesign of our webpage. IMA should reach all mycologists, worldwide, on a regular basis and information should be widely distributed in the age of the internet and free information exchange. Beside the issues of IMA Fungus volumes, the Executive wishes to enhance the Newsletter, and the option to subscribe will be highlighted much more often than has been the case before. In addition, we ask all members to contribute to the content of the IMA Newsletter and also to IMA Fungus to further increase the international visibility of global mycology.
Finally, the Executive Committee acknowledged the progress being made in the organization of IMC 10, which is to take place in Bangkok in 2014. Leka Manoch reported on progress made during the last year. Most exciting was the change of venue to the Queen Sirikrit National Convention Center, which will allows a great congress in Thai style. The Organizing Committee is already hard at work, with Leka Manoch and Morakot Tantichareon as co-chairs. The call for symposia will be made soon, and the Executive Committee suggested that there should be seven concurrent sessions per day, two for fungal diversity, and one for each of the following themes: fungal cells, fungal genomes, fungal ecology, fungal pathogenesis and fungal biological technology. In addition there would be nomenclature sessions held on three days, as at IMC9. The congress aims to reflect the best of international mycology, and the needs of our communities.
During the intensive discussions by the Executive Committee, a Skype conference was arranged to facilitate the participation of members who could not attend in person, so broadening the basis for discussions and decisions. Mycology is global, and the Executive Committee would like to get all of you who read this involved in discovering the future.
International Commission on the Taxonomy of Fungi (ICTF). 2012 General Meeting
The International Commission on the Taxonomy of Fungi (ICTF) held a general meeting at the CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands on Saturday, 14 April 2012 following the “One Fungus: Which Name?” symposium held in the Royal Dutch Academy of Arts and Sciences in Amsterdam. Eleven members of the Commission attended the meeting, an unusually high turnout for this group at a meeting outside an IMC. Approximately 20 observers also attended, some of them taking an active role. With an ambitious programme of work already in front of it, the added expectation that the ICTF and its subcommissions will play active roles in the nomenclatural exercises currently developing made this meeting particularly relevant.
The ICTF website (https://doi.org/www.fungaltaxonomy.org), has been hosted at the Technical University of Vienna by Irina Druzhinina and her colleagues since IMC7 in Oslo in 2002. Andrew Miller offered to host the website at the Illinois Natural History Survey (INHS) at the University of Illinois, and this transition is now complete. The ICTF plans to extend the contents of the website considerably, with a view to making it more attractive. The mandate of the ICTF is both to support fungal taxonomists and to provide information and tools that will be useful to those wishing to learn more about this subject. Until now, the website has primarily been a repository for the minutes of the Commission, links to the websites of subcommissions, and a small amount of other information. Plans are now being implemented to enhance the website with more visual information, to develop and make available information on good taxonomic practices (such as the article “How to describe a fungus”, IMA Fungus 1(2): 109–111, 2010), news items of general interest to fungal taxonomists, and other similar content.
The need to coordinate information on nomenclatural working groups addressing the changes in the International Code of Nomenclature (ICN) is discussed elsewhere in this issue of IMA Fungus. Some of these working groups will conduct their operations and post their draft lists of protected or rejected names on the ICTF website. Our intention is that links to all such working groups who develop their own websites, or those operating from the MycoBank website, will be listed on an ICTF webpage, allowing it to function as a starting point for taxonomists wishing to participate in these exercises.
The relationship between the ICTF, with its focus on promoting fungal taxonomy, and the Nomenclature Committee for Fungi (NCF), with its focus on nomenclature, was the topic of much discussion in Amsterdam and still seems to be a source of some confusion. For the nomenclatural exercises, the two bodies are cooperating as much as possible. While the ICTF envisions assisting in the coordination of the nomenclatural working groups in their preparation of lists, the NCF is the ultimate authority who will be making the final recommendations on the acceptance of these lists to the General Nomenclature Committee, a body appointed by the Melbourne International Botanical Congress in 2011. The existing subcommissions of the ICTF on Penicillium and Aspergillus, Fusarium, and Trichoderma and Hypocrea, are already actively leading the nomenclatural activities on these genera. We are particularly excited at the formation of new subcommissions on Colletotrichum (initiated by Cai Lei and Bevan Weir), and on rusts (initiated by Cathy Aime and José Dianese). Other nomenclatural working groups being formed will interact with the ICTF and the NCF as appropriate during their work.
One of the duties of the ICTF is to organize symposia and sessions at international meetings that will promote advances in fungal taxonomy to a broader scientific audience, as well as promote standards within the fungal community. For the 2014 IUMS congress in Montreal, Canada, we intend to organize a session addressing the changes to the names of economically important fungi resulting from the application of the new ICN. Further, we will propose a symposium on the interaction of genomics and taxonomy, which we hope will include presentations by bacteriologists, and virologists, as well as mycologists. The IMC10 in Bangkok, Thailand, will be held only a few days after the IUMS meeting, but will undoubtedly attract a larger but different crowd of mycologists. For IMC10, more detailed presentation and discussion of the nomenclatural lists will be organized by the ICTF, in collaboration with the NCF as appropriate. The ICTF will also offer a series of after lunch workshops on “Good Practice in Fungal Taxonomy”, presenting information on microscopy, culturing, molecular methods, data analysis and other aspects of fungal taxonomy that would lead to a useful set of publications or exercises on the ICTF website.
CBS Course Medical Mycology — Chinese edition
Mycology” was organized in Nanjing, China, on 19–27 November 2011. The course was a joint effort of the Chinese Society for Microbiology (CSM), the Chinese Society of Dermatology, and the CBS-KNAW Fungal Biodiversity Centre. The Atlas of Clinical Fungi15 was used as the laboratory manual. This book is now also available in the Chinese language on a CD-ROM. A dedicated practical software was developed on fungal terminology, in order to assist Chinese participants in learning how to pronounce English and Latin names correctly. Eight specialist speakers from all over China were invited, while Sybren de Hoog gave presentations on biodiversity. The 70 participants that attended the course came from many parts of China, Taiwan, Hong Kong, and Indonesia. Their current positions were in hospital laboratories as clinicians, medical microbiologists, and medical technicians. The course was devoted to the identification of pathogenic and opportunistic moulds and yeasts. A large and representative set of organisms was offered for practical work and to introduce the participants to fungal diversity.
Hidden Danger, Bright Promise: 4th Meeting of the ISHAM Working Group on Black Yeasts
affiliated Working Group on Black Yeasts was held in Curitiba, Brazil, on 1–4 December 2011. Themes included new concepts on symbiotic interactions of black yeasts, bioremediation, extremophiles, and current overviews of diseases in humans and animals. There was much time for debate among scientists and clinicians, particularly on human diseases with significant impact such as chromoblastomycosis, a disease with impressive records in Brazil and China. Novel data on the lethargic crab disease in the Uca crab population at the northeastern Brazilian coast were also presented. A Brazilian Black Yeast Network was also introduced.
The presentations were organized in themes. The opening speech was by Sybren de Hoog with an overview of the latest achievements and future questions, followed by Flávio Queiroz-Telles who introduced the Brazilian Network. Sanjay Revankar reported on his recent experience on the MSG Phaeohyphomycoses Network, in cooperation with the ISHAM Working Group Fungiscope. Other themes, such as the biotechnological potential and biodiversity of melanized fungi, recent progress in melanin research, and the development of compounds with antifungal activity were debated. The workshop updated knowledge on treatment of diseases caused by black yeast infections.
A visit to the hospital of the Paraná State Federal University was part of the programme. Live patients with chromoblastomycosis and mycetoma were shown and discussed. On the last day a visit to a mangrove area was organized in order to draw the participants’ attention to the natural habitat of edible crabs where currently a black yeast epizootic is taking place.
The meeting had 73 full participants from 11 countries, and comprised 43 speeches and 18 posters, with a broad diversity of topics showing recent results in taxonomy, molecular techniques, identification and diagnosis of clinical and environmental agents, besides genome analysis data. Electronic abstracts and lectures in PDF format are available on the website (https://doi.org/www.blackyeast.org/Curitiba/report.html) and a film of the entire meeting can be viewed on YouTube.
From this event, new doors were opened for international and intercontinental cooperation involving both clinicians and scientists. At the end of the workshop a list was presented with all (about 20) full genomes that are currently being sequenced and annotated by different consortia, and plans were made for experimental reproduction and detection of agents of chromoblastomycosis in environmental sources.
The next meeting of the Black Yeast Working Group will be a symposium at the ISHAM Congress in Berlin on 12 June 2012, and a full meeting is planned in 2013 in Guangzhou, China.
International cooperation in zygomycete research
of the ECMM-ISHAM Working Group Zygomycoses in Athens, Greece, in May 2010, a Special Interest Group meeting was organized in conjunction with IMC9 in Edinburgh in August 2010. Kerstin Voigt and Sybren de Hoog were privileged to organize this pre-conference meeting that was attended by 20 mycologists from seven countries (Egypt, Germany, Japan, Poland, Taiwan, The Netherlands, and the United Kingdom). The aim of the meeting was to bring together mycologists working in various areas of the zygomycetes, to share recent discoveries, to establish an international network for discussion, and to exchange materials and sequences. The plan is to build up a database allowing rapid and reliable identification of species, leading to understanding of ecology, routes of infection, and food safety.
Five presentations demonstrated divergent themes in research on morphology, systematics, phylogeny, physiology, and etiology of zygomycetes, and underlined their growing importance as agents of disease. An alarming rise in the incidence of zygomycosis was noted worldwide, especially in Asia and South America. Tropical climates seem to favour the manifestation of mucoralean infections. The percentage of cases of zygomycoses increased over the past seven decades from 0 % to above 70 %, as documented by cultures (Roden et al. 2005). However, during the same period mortality decreased from almost 100 % to below 40 % due to improved diagnostics (Roden et al. 2005). Therefore, correct identification and reliable diagnostics were major themes in the SIG meeting. It became evident that the taxonomy and phylogenetic reconstruction of the zygomycetes is changing fundamentally with the application of molecular methods, particularly ones involving the ITS and the D1/D2 domain of the large subunit (LSU) nuclear ribosomal DNA as barcoding and phylogenetic markers. The ITS domain is the preferred region for species distinction.
In the first presentation, Sybren de Hoog (CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands) pointed out that ITS and LSU sequences do not fully determine the species level, because significant intraspecific variability is observed. Generic circumscription is also difficult, with ITS dissimilarities of up to 30 % observed between species of the same genus. Mucorales, the most prominent order of zygomycetes, was recently raised to the rank of subphylum, underlining the molecular divergence of these organisms. De Hoog advocated a multigene approach which also utilizes protein-coding genes and their diagnostic power hidden in the introns, supplemented with classical mating experiments. Members of Mucorales are ubiquitous in homes, bath- and bedrooms, as well as in refrigerators and pantries. They are known to have an ecological “hit-and-run-strategy”, which means that they arrive on virgin food sources prior to most other microbes, eat fast, grow fast, and get away before competing microorganisms arrive. This strategy leads to rapid spoilage of unattended food batches by abundant production of extracellular enzymes. Within hours, they form a disgusting hairy felt on fruits, vegetables, and cereal products alike. Humans have learnt to manipulate the decomposition process. Especially in Asia a wide variety of mucoralean fungi is applied for pre-digestion of fermented foods, such as soy sauce or Indonesian tempeh. However, de Hoog drew the attention to a possible downside to the use of Mucorales in food preparation, since the order also harbours confirmed causative agents of mycoses. Human infections tend to produce severely disfiguring and often fatal symptomatologies. These infections have been encountered particularly in patients with severe underlying disease, such as ketoacidotic diabetes or leukemia, but recently a species was found consistently causing chronic skin infections in otherwise healthy patients in East Asia. Inappropriate therapy of such lesions due to poor diagnostics of the causative agent of the infection may lead to fulminant growth and severe mutilation. Agents of these destructive infections in part belong to the same species that are used for food preparation. An example is Rhizopus microsporus, where the varieties classically maintained for food preparation and those responsible as agents of severe disease appear to be identical. Further research is needed to establish whether pathogens are consistently being used to prepare food.
The status of zygomycete research in Taiwan outlined from historical and contemporary points of view was presented by Hsiao-Man Ho (National Taipei University of Education, Taiwan). Special emphasis was placed on thermotolerant species in Mucorales with a potential to cause human infections. The study of zygomycetous fungi in Taiwan started in the 1920s, and since that period a number of local mycologists recorded 38 genera with 123 species. The fungi comprise the following nine families, with their most prominent genera between parentheses: Chaetocladiaceae (Chaetocladium), Dimargaritaceae (Dispira), Kickxellaceae (Coemansia, Linderina, Ramicandelaber), Lichtheimiaceae (Lichtheimia), Mortierellaceae (Mortierella), Mucoraceae (Absidia, Gongronella, Cunninghamella), Pilobolaceae (Pilobolus, Utharomyces), Piptocephalidaceae (Piptocephalis, Syncephalis), and Thamnidiaceae (Thamnidium, Thamnostylum). The morphological beauty of the zygomycetes is demonstrated exemplarily for Syncephalis parvula (Fig. 1) and Zygorhynchus moelleri (Fig. 2). At present, most of the zygomycete research is carried out in the mycology laboratory of Hsiao-Man at the National Taipei University of Education. Species identification is based on morphological characters combined with ITS, LSU-D1/D2, SSU data for most of the taxa.
Kerstin Hoffmann (Jena Microbial Resource Collection, Department of Microbiology and Molecular Biology, Institute of Microbiology, Jena, Germany) gave an overview of the zygomycetes as emerging pathogens in recent years. Traditionally, the phylum Zygomycota has been divided into two classes, Zygomycetes and the Trichomycetes (Alexopolous et al. 1996). However, since the Zygomycota appeared to be polyphyletic, multigene based phylogenies suggested the elimination of the classical Zygomycota as a separate phylum and its subdivision into five distinct subphyla: Mucoromycotina, Entomophthoromycotina, Kickxellomycotina, Zoopagomycotina (Hibbett et al. 2007) and the newly described Mortierellomycotina (Hoffmann et al. 2010). Members of Entomophthoromycotina produce indolent subcutaneous and mucocutaneous infections in immunocompetent hosts, whereas the Mucoromycotina mostly cause rapidly progressing, fatal and often systemic infections in immunocompromised or severely debilitated hosts (Voigt et al. 1999, Ribes et al. 2000). Members of Mucorales are very significant in hospital settings. Of a total of 205 known species in the order, 25 species, belonging to the genera Apophysomyces, Cunninghamella, Lichtheimia, Mucor, Rhizomucor, Rhizopu, s and Saksenaea have been reported to be pathogenic, whereas only 4 four out of a total of 277 species described in Entomophthorales are reported as causing infection. Within Mortierellales, only a single species was found to be clinically relevant, Mortierella wolfii, causing abortion in cattle. Infection routes are variable, including inhalation, ingestion or direct inoculation into pre-damaged tissue. Ketoacidotic diabetes, burns, major surgery, severe trauma and immune disorders trigger the establishment of mucoralomycoses. Roden et al. (2005) listed malignancy, organ transplantation, desferoxamine therapy, injection drug use, bone marrow transplantation, renal failure, and malnutrition as additional risk factors, in order of decreasing significance. A relationship between predisposing factors and type of infection was reported, demonstrating that diabetes, malignancy, and desferoxamine therapy predispose for rhinocerebral, pulmonary, and disseminated infections, respectively. Differences between entomophthoromycoses and mucormycoses can be shown in virulence tests using a hen egg model (Fig. 3). While the mucoralean fungus Rhizopus oryzae produces a 40 % mortality at day six in hen egg embryos, infection with the entomophthoralean fungus Conidiobolus coronatus resulted in 60 % mortality of the embryos within one day, using comparable spore concentrations.
The hen egg model for testing virulence appears to be particularly suitable for large scale assessments of the pathogenic potential of zygomycetes. Ilse D. Jacobsen (Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology — Hans-Knöll-Institute, Jena, Germany) gave a summary of embryonated eggs as an alternative infection model to study virulence. She emphasized that zygomycetes are increasingly recognized as pathogens in both humans and animals. However, relatively little is known of their pathogenesis and virulence. Infection models for zygomycetes have only been described in a very few species. Based on her experience with embryonated eggs as alternative infection model for Candida albicans and Aspergillus fumigatus (Jacobsen et al. 2010, Olias et al. 2010), Jacobsen elucidated the suitability of this model for species of Lichtheimia (formerly Absidia; Hoffmann et al. 2009, Alastruey-Izquierdo et al. 2010), using L. corymbifera as the reference species. Eggs were infected on developmental day 10 on the chorioallantoic membrane (CAM) with 106 to 102 spores (n = 20 per dose and experiment). Survival was determined daily by candling, a standard method which allows visualization of embryonic structures and movement by applying a strong light source to the surface of eggs. Mortality upon infection with the reference strain was dose-dependent, with infectious doses of 106 to 104 spores per egg resulting in 95–100 % mortality within two days. 103 spores per egg killed 70–80 % of infected eggs, and the LD50 was found to be 102 spores per egg. These results were highly reproducible (2–4 experiments per infectious dose). Lichtheimia corymbifera could readily be re-isolated from the CAM of infected eggs, while the CAM of PBS-mock infected controls remained sterile. The three clinically relevant Lichtheimia species complexes, L. ramosa, L. corymbifera, and L. ornate, displayed a comparable virulence potential in embryonated eggs. In contrast, the L. sphaerocystis and L. hyalospora complexes were significantly attenuated in comparison to L. corymbifera. The embryonated egg model is reproducible, inexpensive, easy to handle and does not require specialized facilities. It could serve as alternative model to analyse the virulence potential of different zygomycetes and to directly compare the virulence potential between species, strains and isolates. As the model allows determination of fungal burden, histological analyses and measurement of the host’s cytokine response, it can also be used to assess potential pathogenicity mechanisms.
Guido Fischer (Arbeitsmedizin, Umweltbezogener Gesundheitsschutz, Landesgesundheitsamt Baden-Württemberg, Stuttgart, Germany) introduced “Fungiscope — a Global Rare Fungal Infection Registry” and its services for the scientific community. The registry is supported by the pharmaceutical industry as well as by scientific communities (as an ISHAM working group) and is hosted at the University of Cologne (https://doi.org/www.fungiscope.net). While the registry focuses on the detailed documentation of cases of rare infectious fungi from different taxa, a number of zygomycete infections have been included. Of 41 recently published cases of zygomycote infections (Rüping et al. 2009), 63.4 % occurred in patients with malignancies, 17.1 % in patients with diabetes mellitus, and 9.8 % in patients having undergone transplantation. Diagnosis of zygomycete infection was made by culture in 68.3 % and/or histology in 63.4 % of the cases. The sites of infection were: lung (58.5 %), soft tissue (19.5 %), rhino-sinuorbital region (19.5 %), and brain (14.6 %). In 82.9 %, a targeted treatment against zygomycetes was applied and the overall survival rate of patients was 51.2 % (Riiping et al. 2009). All strains collected within Fungiscope are stored in the collection of the mycology laboratory of the State Health Office Baden-Württemberg (LGA-BW Germany) and were re-identified by morphology-based methods to cross-check the initial identification in the hospital. In addition, all strains were sequenced at CBS. 29 % (4 of 14) of the identifications carried out in the respective centers were incorrect at the genus level; 50 % of the strains had only been identified to that level. Lichtheimia corymbifera was the most frequent infectious agent (6 of 14) with a preference for lung infection, followed by Rhizopus microsporus and R. oryzae (each 3 of 14), and two single isolates of Mucor racemosus and M. circinelloides. From these findings, two questions could be raised: (1) how reliable is the statistics on clinical cases reported in the literature for different fungal taxa?; and (2) does the correct identification have any implication for therapy? For the cases reported here, application of liposomal amphothercin B was associated with a higher survival rate (cfr Rüping et al. 2009). For Rhizopus microsporus/oryzae infections, the ratio of fatal outcomes tended to be higher than that of Lichtheimia corymbifera infections. In general, antimycotic therapy of zygomycetes is difficult because: (a) clinical and microbiological diagnosis of zygomycete infections is difficult in practice, while species may have different susceptibility profiles; (b) zygomycetes grow very quickly causing fulminant infections; and (c) zygomycetes are resistant to some azoles, except posaconazole, and may show reduced susceptibility to amphotericin-B. Exposure prophylaxis may be relevant to high-risk patients, as infectious zygomycetes occur ubiquitously in the environment. Effective risk assessment is based on knowledge of fungal concentrations in the environment and of possible sources of infection. Quantitative data were presented at the SIG meeting from Fischer’s preliminary studies. The concentration of Rhizopus species lies below 1 cfu m−3 air in natural environments, and is thus one order of magnitude lower compared to Aspergillus fumigatus. Concentrations can be higher due to human activities, such as waste-handling. Lichtheimia species are associated with composting facilities (up to 4 × 102 cfu m−3), and are rarely encountered in air in natural habitats. A study in a suburban area showed that R. pusillus was the most frequently encountered species, followed by R. oryzae and R. microsporus; L. corymbifera was encountered infrequently. It was concluded that knowledge on distribution and habitats of potentially infectious zygomycetes may help to improve risk assessment and infection prophylaxis for immuno-compromised patients.
All participants came to the conclusion that networking of scientists with research interests in zygomycetes on a global basis is necessary to exchange and calibrate materials and data. A platform for future collaboration was created with an expansion of the clinically oriented ECMM-ISHAM Working Group of Zygomycetes by a section on biodiversity and ecology. A follow-up meeting, on “The dynamics of zygomycete research in a changing world”, was held at the CBS-KNAW Fungal Biodiversity Centre in Utrecht, The Netherlands, on 3–5 March, 2011. That workshop was organized by Kerstin Voigt (Jena, Germany), Anna Skiada (Athens, Greece), and Sybren de Hoog (Utrecht, The Netherlands). The keynote speakers were Mary Berbee (University of British Columbia, Canada), Hsiao-man Ho (National University of Taipei, Taiwan), Ashraf Ibrahim (Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance and David Geffen School of Medicine at UCLA, Los Angeles, USA), Ilse D. Jacobsen (HKI, Jena, Germany), and Paul M. Kirk (CAB International, Egham, UK). Topics covered all areas of zygomycete biodiversity, including genomic, phylogenetic, morphological, physiological and ecological aspects. Participants were able to present their latest research data on the many beautiful and bizarre members of these fungi. The meeting will culminate soon in a special issue on zygomycete phylogeny in the journal Persoonia, scheduled for publication in December 2012.
Mycologists, food and nutrition scientists, medical microbiologists, infection and immune biologists, molecular biologists, and bioinformaticians, are welcome to join the Working Group in any of its upcoming initiatives. For more information please consult the Group’s web page (https://doi.org/www.zygomycota.eu).
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We appreciate financial support from the IUMS Executive Board, which enabled Andrew Miller to attend the 2012 meetings in The Netherlands.
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Begerow, D., Seifert, K.A., Miller, A.N. et al. Reports. IMA Fungus 3, A10–A23 (2012). https://doi.org/10.1007/BF03449328