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The Mycological Society of Japan and the
Melbourne Code
The Mycological Society of Japan (MSJ)
held two meetings in 2012, related to the
Melbourne Code, the International Codeof Nomenclature for algae, fungi and plants(ICN). The Codee took effect from 30 July
2011, with some provisions operative fromeither 1 Januar y 2012 or 1 Januar y 2013.
These meetings were: (1) the “Symposiumon Nomenclatural Change” held during
the 56th annual meeting of the MSJ on 26
May in Gifu, Japan; and (2) the “Forum on
the Future of Microbial Databases” heldon 28 May in Tokyo, and organized by the
MSJ in collaboration with the Federationof Microbiological Societies of Japan anda number of other academic societies or
associations. The programmes and speakers
are shown in the accompanying two boxes.

Symposium on Nomenclatural Change
Mycologists have it easy.
y Paul M. Kirk, CABI Bioservices, UK .
The name that can be named is not the everlasting name - the new rules for the nomenclature of Asco- and Basidiomycota and theirimplications. Roland Kirschner, National Central University, Taiwan & Walter Gams, formerly CBS-KNAW Fungal Diversity
Centre, The Netherlands.
One Fungus Which Name: report of the Amsterdam symposium (12-13 April 2012). Robert A. Samson, CBS-KNAW Fungal
Diversity Centre, The Netherlands.
Impact of the current change of botanical nomenclature at the Melbourne Conference and a practical consideration on its application,
especially related to alteration of the Article 59. Takayuki Aoki, National Institute of Agrobiological Sciences, Japan.

Forum on the Future of Microbial Databases
Fungal diversity and systematics projects derived from the Tree of Life. Kentaro Hosaka, National Museum of Nature and Science,
Japan.
Transition of the use of microbial genome information and future perspective. Natsuko Ichikawa, National Institute of Technology and
Evaluation, Japan.
Moving from a web of information to a web of data. Paul M. Kirk, CABI Bioservices, UK.
WDCM databases and biological databases in China. Juncai Ma, Institute of Microbiolog y, Chinese Academy of Sciences, China.
MycoBank an on-line database as a service to the mycological and scientific society. Robert A. Samson, CBS-KNAW Fungal Diversity
Centre, The Netherlands.
MicrobeDB in National Bioscience Database Center project. Hideaki Sugawara, National Institute of Genetics, Japan.
Requirements for industrial microbial genome database. Tatsunari Nishi, Genaris, Inc., Japan.
As a leverage for research in industry; microbiological database and stock cultures. Hideharu Anazawa, Japan Bioindustry Association,
Japan.

Together with the two meetings above, wereport on the actions taken by the MSJ in
relation to the latest nomenclatural changes(Hawksworth 2011, 2012, Knapp et al.
2011, McNeill et al. 2011, 2012). These arepresented here as they may be found of value
by other mycological societies considering
actions they should take to comply with the
new Code.

(1) Actions in publication of the
MSJ official journals
The MSJ publishes two journals, Mycoscience(in English) and the Japanese Journal of
Mycolog y (in Japanese). Important actions
were taken by the Editorial Board for theeffective publication of fungal names in(48)

Mycoscience, but none are proposed for theJapanese Journal of Mycolog y as it is notexpected to have nomenclatural novelties(though this cannot be ruled out). However,use of earlier sexual (teleomorphic) andasexual (anamorphic) names in the Japanese
Journal of Mycology is also expected because
the corresponding names are now treatedas synonyms, irrespective of the morphs
represented.
For Mycoscience, changes torequirements for effective publication relateto: (1) online publication, i.e. electronic
distribution of articles in PDF format via
the worldwide web (Arts 29–31, Recs
29A, 30A, and 31A); (2) deposition of key
nomenclatural information in a recognizedrepository (Art. 37); and (3) acceptance ofa Latin or English diagnosis or description(Art. 36).
Online publication: For this to beconsidered effective, Art. 29 requires
electronic distribution of papers in
Portable Document Format (PDF) withan International Standard Serial Number(ISSN). Rec. 29A.1 recommends that the
PDF complies with the PDF/A archival
standard (ISO 19005). The PDF format
for papers in Mycosciencee volume 53 isavailable at the website (http ://www.
springer.com/life+sciences/microbiolog y/journal/10267; until 31 December 2012),
and those of volume 54 at a new site(http ://www.sciencedirect.com/science/
journal/13403540; from 20 July 2012);
these meet the PDF/A archival standard
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VOLUME 3 · NO. 2& Redhead 2012). The latter is built in
Chinese, and the former two were createdoriginally in English, but are now translated
into several lang uages. The deposition of
key nomenclatural information in MB andcitation of that number is already requiredfor papers in Mycoscience. This practice willcontinue, and the MSJ supports a Japanesetranslation of the interface.
Acceptance of either a Latin or an
English diagnosis or description: An
amended Art. 36 permitted the use ofeither English or Latin for the diagnosis or
description on all new scientific names from
1 Januar y 2012. Mycosciencee recommends
that authors write both an English diagnosis
and a detailed English description for new
fungal taxa, although the use of a Latin
diagnosis is not rejected.
If a Latin or English diagnosis isprovided, the description could thencontinue to be in any language of theauthor’s choice. However, Mycoscience
requires authors to use only English
except for Latin diagnoses and citationsof original writings (in quotation marks).
In the Japanese Journal of Mycolog y, ataxonomic novelty with a Latin or English
diagnosis and then a Japanese description
would be possible, but that practice is notrecommended to authors.
Practices at the MSJ Editorial Office:All submitted taxonomic papers arechecked against the major changes made in
the new Code. In particular, the amended
Art. 59 does not allow the proposal of
two or more names simultaneously for asingle taxon. Since 1 May 2012, taxonomic
papers proposing two or more names fordifferent morphs of a new fungus havebeen sent back to authors, notif ying themof the changes in the Code. In such cases,
however, the Editorial Office neither judges
nor suggests which of two or more names
is correct or appropriate for a fung us underconsideration.
A notice of the major changes in the
new ICN is provided for authors at thefollowing site: http ://www.elsevier.com/
framework_products/promis_misc/myc_
Fungal_Nomenclature.pdf.f(2) Recent meetings in Japan witha focus on the Code
Based on the symposium held at the56th MSJ meeting, together with the
publication of Okada (2011), the MSJ
has endeavoured to distribute the mostrecent information related to the current

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(ISO 19005). Currently, the ISSN number
does not appear in the PDF and the Board
has requested the publisher (Elsevier Japan),to prominently show this on each PDF.
Parallel to the PDF version, a Hypertext
Markup Lang uage (HTML) version is alsoavailable at the same site which has theonline-publication date. Mycoscience is being
published by Elsevier Japan from volume 54(2013). All papers published in the printed
version of volume 53 (2012) by Springer
Japan were already becoming available on
the MSJ/Springer Japan site from the end of
May 2012.
Art. 29.4 does not permit any alterationin the content of a particular electronic
publication after it is released, which isthe date of effective publication. To meetthis requirement, Mycosciencee is to publish
papers in the electronic version with thefinal volume number and pagination so thatthe electronically published PDF and thehard-copy version are exactly the same; i.e.
adopting “Article Based Publication”.
Rec. 29A.2 recommends the depositionof the online published materials in
multiple trusted online digital repositories.
Both Springer and Elsevier, as most major
publishers, participate in CLOCKSS(Controlled Lot of Copies Save Stuff ), atrusted community-governed archive, inwhich Mycosciencee is now placed.
Art. 30.2 requires evidence associatedwith or within the publication that the
publisher considers a particular version
final; and Rec. 30A.1 recommends a clear
indication that an electronically publishedversion is final. “Article Based Publication”
fulfills this requirement.
Deposition of key nomenclatural
information: Under Art. 37, the depositionof key nomenclatural information in arecognized online repository becomesmandatory for valid publication of all newscientific names of fungi. The requirement
to cite the protologue of an identifier
issued from the repository where thenomenclatural information has been
deposited becomes effective on 1 Januar y
2013. The following repositories are
currently operating , although at the timeof writing none has been “recognized” by
the Nomenclature Committee for Fungi(NCF) appointed by the Melbourne
Congress: MycoBank (MB; http ://www.mycobank.org), Index Fungorum(http://www.indexfungorum.org/names/
IndexFungorumRegister.htm), and Fungal
Name (http://www.fungalinfo.net/
fungalname/fungalname.html ) (Norvell

Paul Kirk at MSJ.

rule changes, especially on Art. 59, withmembers who may work with pleomorphic
fungi. At the symposium, the now unified
fungal nomenclature system was explained
by Paul Kirk and Roland Kirschner,
respectively, from their own standpoints.
Nomenclatural discussion from the One
Fung us = Which Name? (1F=WN)
symposium in Amsterdam was also reported
on by Rob Samson, together with theproposals of the International Commission
on Penicillium and Aspergillus (ICPA).
Possible practical examples of procedures
towards unification of sexual and asexualstates were provided by Takayuki Aoki,
with examples from Fusarium and related
ascomycetes. In moving to the unificationof names of pleomorphic fungi, priority ofgeneric names and species epithets should
be considered independently. When an
asexually typified (anamorphic) genericname has priority by date over a sexually
typified (teleomorphic) one, and thesexually typified epithet has priority by dateover an asexually typified one, or vice versa,
a recombination of the priorable specificepithet to the priorable generic name will
be necessary. This process could result inmany unfamiliar recombinations of genericand specific names. In order to minimize
disruption, a democratic process is being
initiated, in which active participation by
all mycologists, whether users or generatorsof names, is encouraged. In due course,
it is envisaged that lists of protected andsuppressed names will be internationally(49)

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agreed. In the interim, enquiries should
be made to the NCF or the International
Commission on the Taxonomy of Fungi(ICTF) on doubtful or ambig uous cases andprocesses being put in place. The symposium
participants saw this as a complicatedsituation which would be laborious andtime-consuming , and a lively discussion
on how to reach a unified nomenclature
followed (see the below box).
At the Forum on the Future of
Microbial Databases, Kentaro Hosaka
overviewed projects since Deep Hypha, andmentioned some DNA barcode projects inwhich he was involved. Natsuko Ichikawa
introduced a new function of genome
database created by NITE; information
on secondary metabolite genes was being
accumulated, which will be attractive to
many working in applied areas. Paul Kirk
stressed the importance of developing a
Global Names Architecture in order toassemble all the mycological data in theworld. Juncai Ma announced the transfer
of WDCM/WFCC to Beijing. He intends
to develop a user friendly catalog ue offungi and microbes that member biologicalresource centers can distribute, so that onestop ordering of strains will be possible.
Rob Samson introduced a variety of usefulfunctions being implemented in MycoBank,and Hideaki Sugawara a new project,
MicrobialDB.Jp, for the virtual integrationof microbial databases in Japan. A physicalintegration of heterogeneous databases
is a considerable challenge, but Semantic
Web Technologies will facilitate virtual
integration and will be one of the future
directions for numerous kinds of databases.

Major questions or comments on the procedures in the new Code from the two meetings
For the registration of new names, three different databases are expected to be recognized: Index Fungorum, MycoBank, and Fungal
Name. Although each database is different in structure, the registration of names and their data release are planned to besynchronized in a minute (Norvell & Redhead 2012).
If an author describes a morph of a new taxon, a separate name of another morph of the same taxon cannot be adopted in thatpublication. Some saw this as a problem, but there was no obstacle to the use of informal names (e.g. acremonium-morph).
The 1F=1N process has just beg un implementation, and will take a considerable time to work through all fungal organisms affected by
1F=WN. Anybody can participate in the particular working groups or committees now being established, or propose to start a
new group.
A user, a geneticist who does not know much about taxonomy or nomenclature, wondered why the dual naming system had beenabandoned.
Many scientists confuse taxonomic changes and nomenclatural changes. Nomenclatural change is one based on the requirements of therules in the Code. It is, however, a major challenge to avoid the misapplication of names and to reach taxonomic consensus. All
taxonomists need to cooperate closely in this.
Microbial genome datasets will be accelerated to increase; probably more than 1,000 per year. If metagenome data is counted, an
enormous increase in the information available is expected.

(3) Expectations of concerned
mycologists in JapanAs Rob Samson stated at the symposium,the 1F=1N process has just started andrequires a great deal of collaborative work.
The MSJ therefore encourages concerned
mycologists in Japan to participate inthis important mission. Anyone who isinterested in a particular taxon is requested
to contact Keith Seifert (Chair, ICTF)
to either join an existing working groupor committee, or initiate a new group(see the ICTF website; http://www.
fungaltaxonomy.org/subcommissions).
Hawksworth DL (2011) A new dawn for thenaming of fungi: impacts of decisions madein Melbourne in July 2011 on the future(50)

publication and regulation of fungal names.

MycoKeys 1: 7–20; IMA Fungus 2: 155–162.
Hawksworth DL (2012) Managing and copingwith names of pleomorphic fungi in a period oftransition. IMA Fungus 3: 15–24.
Knapp S, McNeil, J, Turland NJ (2011) Changes topublication requirements made at the XVIIIInternational Botanical Congress in Melbourne— what does e-publication mean for you?
Taxon 60: 1498–1501.
McNeill J, Barrie FR. Buck WR, Demoulin V,
Greuter W, Hawksworth DL, Herendeen PS,
Knapp S, Marhold K, Prado J, Prud’homme
van Reine WF, Smith GF, Wiersema JH,
Turland NJ (eds) (2012) International Codeof Nomenclature for algae, fungi, and plants(Melbourne Code) adopted by the EighteenthInternational Botanical Congress Melbourne,
Australia, July 2011. [Regnum Vegetabile no.

154.] Ruggell: A.R.G. Ganter Verlag.
McNeill J, Turland NJ, Monro A, Lepschi BJ (2011)
XVIII International Botanical Congress:
preliminary mail vote and report of Congressaction on nomenclature proposals. Taxon 60:
1507–1520.
Norvell LL, Redhead SA (2012) Registries of names
and the new Code. IMA Fungus 3: (2).
Okada G (2011) Unified nomenclature foranamorphic fungi or fungi with a pleomorphic
life cycle adopted at the 18th International
Botanical Congress (IBC2011, Melbourne).
Japanese Journal of Mycolog y 52: 82–97. [inJapanese]

Toru Okuda, Yoshitaka Ono, Takayuki
Aoki, and Gen Okada(torula@lab.tamagawa.ac.jp)

IMA FUNGUS

As announced in IMA Fungus 3 (1): (7)( June 2012), this European Cooperationin Science and Technology (COST)
programme aims to promote research into
the exploitation of endophytic fungi andbacteria in biotechnolog y and agriculture.
In large funding schemes related to “White
Biotechnolog y” and “Bioeconomy”, theseorganisms are now being exploited not
only as biocontrol agents, but as producersof fine chemicals, industrial enzymes, andeven biofuel from plant waste (Stadler& Schulz 2009). However, there are stillbottlenecks limiting the full exploitation of
their potential, and insufficient knowledgeof their ecology.
COST Action FA1103, “Endophytesin Biotechnology and Agriculture”1,
is now getting underway. The Action
has so far been joined by 20 countries,
and around 150 scientists from over 50
institutions are actively involved. Most
have already contributed to the scientificprogramme, and the number of interested
scientists is steadily increasing. The ratiosof bacteriologists vs. mycologists, andapplied vs. basic scientists, involved areabout balanced. Indeed, several scientists
and companies involved are dealing withboth bacteria and fungi, and numerous
active European research groups in basic
and applied mycology and microbiology are
represented.
The Action is divided into fourthematic working groups (WG), whichdo, however, closely interact with one
another: WG1 (Ecolog y of endophytes),
WG2 (Identification of new competentendophytes), WG3 (Development of
new microbial inocula), and WG4 (Newindustrial products in life sciences). One
important goal will be to bring expertise in,for example, molecular ecolog y, taxonomy,
and other fields of basic research, together
with applied aspects, such as bioprospecting
and biocontrol.
Even though the COST Action cannot
provide direct funding for joint research
activities, several joint projects, based on

1

For more information see: www.endophytes.eu(Action website), and http://www.cost.eu/domains_actions/fa/Actions/FA1103?parties (corresponding
COST website).

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COST Action FA1103: European scientists
investigating endophytic microrganisms and fungiParticipants in the Reims COST workshop (March 2012).

Participants in the San Michele dell’Adige COST workshop (November 2012).

synergies and institutional budgets of theparticipating institutes and companies, havealready been initiated. The meetings of the
Action provide a fruitful atmosphere fordiscussions about future international grantapplications on interdisciplinary themesthat could eventually result in successful
applications for calls by the European
Commission.
Two well-attended workshops havealready been held; in Reims (France) in
March 2012) and San Michele dell’ Adige
near Trento (Italy) in November 2012.
Members of the Action presented theirscientific results in symposia and poster
sessions at these workshops. International
experts were invited to deliver keynoe
lectures, for example Linda Johnson (New
Zealand) and T. S. Sur yanarayanan (India)
addressed the Trento meeting.
It is envisaged that members of the
Action will co-organise some symposia
at the conference “Endophytes for plant
protection: the state of the art” in Berlinin May 2013. The German Society for
Plant Protection and Plant Health (DPG)
is to sponsor this meeting, which is also
being promoted by IUBS (International
Union of Biological Sciences). The topics
the Working Group sessions will coverinclude one on the construction and designof a European database on endophytes.
Furthermore, training schools are alsoplanned, for instance on analyses of natural

products and statistical computing andgraphics. A special issue of Fungal Diversity,
covering the mycological parts of the
Action is planned for publication during
2013. Complementary publications are alsoplanned by participating bacteriologists,and participation in several important
European and international conferences
will follow. Outreach activities include aninterview recently reported in International
Innovation Reports.
Aside from networking , the Action
particularly supports early stage researchers(ESR). Further, the programme also
provides for “Short Term Scientific
Missions” (STMS), during which ESR
and other scientists will receive funding
from COST to visit different European
laboratories for up to three months fortraining in complementary disciplines or to
conduct joint research; 8-10 such postings
can be funded each year. The Action canalso provide travel grants to enable highly
qualified ESR to attend international
scientific meetings.
An example of the kind of results tobe expected from the joint investigationsof bioprospectors and biodiversity experts
is that of Bills et al.l (2012). That study
emphasised that culturing of apparently new
phylogenetic lineages will be imperative not
only to make them available for sustainablebiotechnological exploitation, but also
to elucidate life-cycles and ecological(51)

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(52)

interactions. In this respect, pure in silico
mycolog y and microbial ecolog y, merely
relying on PCR-based methods, should be
discouraged.
In summary, this new COST Action
provides a forum for the identification ofbottlenecks limiting the use of endophytes
in biotechnolog y and agriculture. It is
anticipated that it will ultimately provide
solutions for economically and ecologicallycompatible exploitation of these organisms
within Europe and beyond. Non-European
participants and European researchers
from non-COST countries are invited

to participate in the Action, but will
not be eligible for direct reimbursementfrom the Action budget. I trust that thisreport will alert mycologists to these newopportunities to fund networking activities
and international collaborations. After all,the scope of the COST Actions may also be
attractive for other interdisciplinary research
fields involving mycological expertise.
Indeed some actions targeting plant
pathogenic fungi and chemical biology
approaches are already under way. The next
deadline for proposals will be in March2013.

Bills GF, González-Menéndez V, Martín J,
Platas G, Fournier J, Peršoh D, Stadler
M (2012) Hypoxylon pulicicidum sp. nov.
(
(Ascomycota, Xylariales), a pantropicalinsecticide-producing endophyte. PLoS
ONE 7(10): e46687; DOI:10.1371/
journal.pone.0046687.
Stadler M, Schulz B (2009) High energ ybiofuel from endophytic fungi? Trends in
Plant Science 14: 353-355

Marc Stadler(marc.stadler@helmholtz--hzi.de)

IMA FUNGUS