Collection
The CBS Collection of Fungi has more than 60.000 strains in its public
collection, making it the largest mycological culture collection in the world.
CBS is unchallenged as a reference collection for mycological research, as
practically all culturable groups of the Fungal Kingdom are represented.
Annually, thousands of CBS strains are delivered to some 50 countries. To
underpin its dedication to quality in materials and services, CBS set up a
quality management system, for which it obtained an ISO 9001:2000 certificate in
November 2007. CBS strains are also selected for DNA sequencing projects in the
framework of global initiatives, such as the Fungal Tree of Life and DNA
Barcoding. The CBS Bacterial Collection (NCCB) consists of another 10.000
strains, including a unique Plasmid and Phage Collection. The high quality of
CBS strains is ensured by the practice of having identities and typical features
authenticated by specialists of CBS and elsewhere. Scientific and other data
related to the strains are constantly added. Much attention is given to
expanding and improving CBS web-services, not only by digitising publications,
but also by allowing clients to use various types of collection data. CBS has
developed web-based polyphasic identification for specific groups such as
yeasts, and plans to also include additional economically important groups.
Moreover, CBS developed MycoBank, an on-line registration system for new fungal
taxonomic names now under the auspices of the International Mycological
Association (IMA).
Collection holdings
In the period of 2006 – 2007, CBS acquired 3500 strains, representing a
large number of species new to science or new to the public collection. CBS is
also an International Depository Authority (IDA) under the regulations of the
Budapest Treaty, holding now over 1000 Budapest Treaty deposits of fungi and
bacteria. Furthermore, CBS also holds almost 300 Safe deposits in the restricted
collection.
CBS preserves practically all cultures in metabolically inactive condition, so
that they remain as much as possible in the pristine original condition in which
they were received. The most important preservation methods are
cryo-preservation and freeze-drying (lyophilisation), for which cutting-edge
equipment is installed. Almost all strains are cryo-preserved and stored in
liquid nitrogen containers, where the samples are preserved in a dynamic gas
phase, at temperatures that are constantly below -180 °C anywhere in the
container. Most yeasts and bacterial strains, and about 60 % of the non-yeast
fungal strains are also preserved in a freeze-dried state. CBS uses
state-of-the-art freeze-drying equipment, such as Christ-Epsilon 2-80. All
crucial parameters are recorded during the freeze-drying process, and stored for
later reference. Some organisms that are recalcitrant to both cryospreservation
and freeze-drying need to be maintained in actively growing condition on agar.
However, over the past two years the number of fungal strains requiring
maintenance on agar was further reduced to about 2900.
The CBS collection currently contains over 5000 ex-type and authentic strains of
yeasts and filamentous fungi and many more reference strains. An ex-type strain
fixes the undisputed application of a fungal name, while reference strains,
which have been authenticated by a specialist or group of specialists, have a
similar function and can also serve as reference material for identification and
characterization of a fungal taxon. Moreover, type and reference strains are the
preferred material to generate DNA barcodes.
Rigorous identity control of strains is fundamental to good collection
management. The identity of new accessions is principally checked by curators or
specialist taxonomists based on morphological characters. Subsequent transfers
are checked by other qualified staff, who will consult the specialist in case of
doubt. Strains that are sterile on artificial media can be checked for obvious
infections, but a positive ID is difficult or impossible. In recent times,
however, the coverage by specialists of the various fungal groups in the
collection has decreased. Yet, most new accessions are already characterised at
the molecular level by the depositors. CBS performs standard ITS sequencing for
all new (ex-)type strains. A routine molecular check for all new acquisitions
requires considerable resources presently not available. However, due to the
RNAAS grant for barcoding, numerous strains will be sequenced and barcoded.
Generally, sequence data and barcodes can only be used to check the identity at
the species level, and are rarely strain specific. In collaboration with
industrial partners in Germany, the collection is currently investigating the
possibilities to use MALDI-Tof spectrophotometric analysis as a tool for
positive identity control of strains.
Fig. XX. Trends in the collections of filamentous fungi and yeasts according to
the preservation methods. LN = cryopreserved, LY = lyophilized, AG = agar.
ISO 9001:2000 Certificate for the CBS Collection
CBS Collections have a primary mission to preserve and supply strains of
microorganisms to researchers and other user groups world-wide. Thanks to the
constantly high quality of the material that is distributed and
customer-friendly services, CBS has built up a good reputation as a supplier of
cultures within the scientific community. In order to strengthen its position
particularly in the fields of applied science and technology, CBS decided to
implement a Quality management system according to the international standard of
ISO 9001:2000, and seek to obtain a certificate. In November 2007, Kema issued
an ISO 9001:2000 certificate to CBS for the following activities: “Accession,
preservation, storage and supply of micro-organisms (public deposits, safe
deposits and maintenance deposits) and related information”.
DNA-Barcoding the Collection
The term DNA barcoding was coined by Paul Hebert in 2003. The general idea was
to create, and create fast, a simple, unified species identification system
based on DNA sequence data. An international consortium (CBoL, Consortium for
the Barcode of Life) was formed to come up with binding suggestions as what
markers and protocols would be accepted for DNA barcoding and to act as mediator
between the DNA barcoding community and other parties, i.e. GenBank, potential
users, or technology developers. A coordinated approach in the DNA barcoding of
fungi (or any other group of organisms) requires the careful selection and
agreement upon a suitable marker region. ITS region of the ribosomal DNA has
been widely used as a marker in fungal studies, but additional marker regions
are needed for many groups of fungi, as the ITS region does not provide
sufficient resolution at the species level. Collections such as the CBS can play
a major role in the DNA barcoding effort. They are not only depositories for
specimens and vouchers, well studied collections are also summaries of the
current state of taxonomic knowledge. DNA barcoding of such specimens makes this
information accessible and usable for all kinds of molecular studies. Type
strains or specimens contained in collections are indispensable for the
taxonomic validation of DNA barcodes. It has become obvious in recent years,
that many presumed biological species in microfungi cannot be unambiguously
identified by morphological or physiological methods. Therefore, DNA barcoding
of the CBS collection will enhance the value of the collection enormously while
at the same time increasing the body of DNA barcoding reference data. This in
turn will put CBS in a position to be a sought-after partner for the development
of identification tools or to develop such tools itself. CBS aims at producing
at least an ITS sequence for all of its type strains within the coming two
years. Apart from this effort, many CBS strains are being sequenced in other
research projects providing state-of-the-art molecular identifications.
DNA Bank
The primary purpose of the DNA-Bank is to store genomic DNA extracts of CBS
strains selected for DNA-Barcoding or other research projects. Central storage
in the DNA-Bank is more economic, and can safe-guard genomic DNA for future use,
even after a strain loses viability. A secondary purpose of the DNA-Bank is to
keep DNA of fungi that cannot be cultivated, and DNA that has been isolated from
herbarium specimens.
Each DNA extract obtains a unique identifier (CBS D-XXXXX), independent of the
unique identifiers connected to the source. For long-term storage, a sample of
DNA in buffer is maintained for each accession in the dynamic gas-phase of a
liquid nitrogen container, at a temperature constantly below -180 °C. This is
relatively expensive compared to other DNA storage methods, but the advantage
for CBS is that it is compatible with the system already in place for
cryopreservation of strains. For most accessions, additional DNA samples are
also maintained in mechanical freezers at -80 °C. The latter samples will
normally be used first as stock for the distribution of DNA aliquots. A paid
service to distribute DNA extracts from CBS strains will be set up in the near
future. The RNAAS provided CBS with start-up funding for this DNA-Bank, and
additional funding is currently being actively sought in collaboration with
other partners in NL-TAF.
Research projects and collaboration
CBS co-organized a 2-day symposium on Fungal taxonomy in Goslar 2007. Moreover
Stalpers visited a microbial collection in Bogor in the framework of the
Committee for Endangered Collections. Current items which may have a
considerable impact on the functioning of Culture Collections concern
biosecurity; it is important to prevent that oncoming new regulations will make
the distribution of strains unnecessarily difficult. Also the problems around
the required risk analyses have to be formulated and solved.
CBS also played a major role in the development of a standard minimum Material
Transfer Agreement by ECCO, necessary to oblige the requirements of the CBD and
to safeguard Culture Collections’ interests. This proposal was discussed at the
ECCO meeting in Goslar (2007) and will be taken up by WFCC.
CBS represented the Dutch government in two working parties of the task force
Biological Resource Collections of the OECD, followed by that on the Global
Biological Resource Centres Network (GBRCN). This was concluded with a 2-day
workshop in Paris at OECD headquarters, where the German government offered to
host and support a pilot GBRCN for three years.
Ongoing concern about bioterrorism strongly increased the interest of
politicians in culture collections. Attention is being paid to the organisms
that are maintained and curated, and to the way the distribution of these
organisms is managed, with special focus on the security measurements instituted
to prevent undesired use. For these reasons CBS participates in the OECD Working
Party on Biotechnology, dealing with issues related to biosecurity
(bioterrorism) in the context of the development of a global Biological Resource
Centre. Especially the possible threats to agriculture and environment create
problems in risk assessment, which is a basic responsibility of BRC’s.
The collection participated in several EU projects. European Biological
Resources Centres Network (EBCRN), for the establishment of a framework to
maximize complementarities and minimize duplications among European Biological
Resource Centres (BRCs). CBS analyzed the amount of duplication between the
European collections and the reasons for duplication. It could be concluded that
most duplication was justified (e.g. ex-type strains and tester strains) and the
actual percentage of unnecessary duplication was below two percent.
CBS is also involved in the EDIT project (European Distributed Institute of
Taxonomy), an FP6 Network of Excellence, for which NL-TAF is coordinating
workpackage 3 on integration of the infrastructure basis for leading taxonomic
facilities in Europe. The main task of CBS in WP3 is the coordination of DNA
Barcoding. The National History Museum Naturalis, Leiden, is leading this
workpackage, and Gerard Verkley is the Team Leader for CBS. In October 2007, CBS
organized the DNA-Barcoding in Europe Meeting in collaboration with the other
Dutch partners in the EDIT consortium. Over 150 delegates attended this
successful meeting. CBS also maintains a website for the European Consorium for
the Barcode of Life (www.ecbol.org), which
is intended as a platform for European institutes involved in Barcoding of all
organism groups.
SYNTHESYS (www.synthesys.info) is
another FP6 programme, comprising 20 European natural history museums and
botanic gardens, aiming to create an integrated European infrastructure for
researchers in the natural sciences. SYNTHESYS is setting standards for
collection management and databases, and aims to raise scientists’ awareness of
best practice by offering improved training and workshop opportunities, and
guidelines for the care, storage and conservation of collections. The project
will also provide new policies on emerging technologies for storing collections,
such as DNA samples or tissue banks.
CBS also participated in EuroCat (European Catalogue of Life), a Species 2000
project, aiming at developing an interactive webbased catalogue.
In 2005-2007 the digitalisation project large-scale support from the
National Science Organisation (NWO), the Netherlands of the four major
Dutch taxonomic institutes [Naturalis, National Herbarium Netherlands (NHN),
Amsterdam University Zoological Museum (ZMA) and CBS] financed by NWO digitized
millions of herbarium specimens, and also produced species banks for
ecologically or economically important groups of organisms. The Database
Managers Committee controlling the process was chaired by CBS. The data for the
20.000 specimens present in the CBS herbarium have all been digitized. A concept
for a new service referred to as “species banks” with web-based curating
possibilities is being developed.
Fungal Identification Service
CBS offers a service for the identification of fungal, oomycetous and bacterial
isolates. In 2006-2007 a total of 1144 fungal and 106 bacterial cultures were
identified. The involvement of specialist taxonomists guarantees a
state-of-the-art identification of cultures. A correct identification is of the
utmost importance in scientific studies, phytopathology, industrial
contamination etc. Yeasts are identified mainly by means of DNA sequencing,
while filamentous fungal isolates are identified by morphology in culture on the
appropriate media and DNA sequencing. CBS has a significant unpublished database
of DNA sequences, based on ex-type and other well-characterised CBS strains, and
this information can be used by CBS experts for identification purposes. A
secondary effect of the revised procedures is that the identification service is
able to inform a significant minority of clients that the isolate they submitted
represents a new species. It is now far easier to fully confirm species as
undescribed than it was in the past, when only morphological characters were
available. In many cases, approval of the customers was obtained to add the
undescribed species and many other interesting isolates to the CBS collection.
Bioinformatics and databasing
Index Fungorum
Index Fungorum (IF) is a nomenclatural database, aiming to contain a complete
set of all nomenclatural data pertaining to fungi. Since 2003 IF is managed by
the Index Fungorum Partnership consisting of CABI Bioscience (P. Kirk), Landcare
New Zealand (J. Cooper) and CBS (J. Stalpers). At the moment the database
contains over 400.000 names and it is by far the most complete database in this
area. However, the quality of the data still has to be improved. For example,
many protologue data are missing, the status of many names is incorrectly
indicated, there is some discrepancy in dates of publication, etc. The recently
concluded NWO project allowed us to add and update many records, for example
with a list of verified pre-1832 names and the “Sydow lists” (lists published by
H.P. Sydow) representing all taxonomic novelties published in the years
1895–1918 and with additional data from the Petrak lists from 1918–1940. IF is
the base for the CBS initiative MycoBank, and an agreement has been reached to
maintain IF as a web-service, preventing unnecessary double checks.
MycoBank
CBS launched MycoBank in 2004, with the purpose of on-line registration of the
mycological nomenclatural novelties and allowing authors to also deposit other
data associated with these novelties, for example descriptions, illustrations,
sequences, etc. It would allow users/depositors to check if their deposits are
unique, and the specialists of CBS check the names on correctness as ordained by
the International Code of Botanical Nomenclature. Each name is given a unique
MycoBank number that can be used in the publication, and also serves as its LSID
(Life Sciences Identifier) with the following structure:
urn:lsid:indexfungorum.org:names:nnnnnn.. The collaboration with Index Fungorum
prevents double issuance of LSID identifiers. Authors are notified of the
MycoBank accession number and of possible problems. In the last case they are
asked if they want to correct or adapt, but MycoBank will never apply
censorship; in all cases the depositor decides on the form of the deposited
name.
The main reason to start this service was that the Code hardly contains
restrictions where to publish nomenclatural novelties, resulting in a plethora
of possibilities that are far from covered by the average taxonomic library.
Although the Index of Fungi gives a relatively good coverage, it offers no
additional data, while on-line databases connected with MycoBank and Index
Fungorum can easily do that, and additionally allow sophisticated searches plus
links to other on-line sources of information.
Several important mycological journals have already agreed to make this
procedure obligatory for their authors, while others are currently considering
following suit.
At the moment MycoBank contains 23.000 descriptions and 8.700 illustrations.
Species banks
The number of taxonomists is rapidly dwindling, and no institute houses
up-to-date specialists for all fungal groups. CBS has, partly financed by NWO,
set up a number of dynamic species banks in various phases of completeness. A
species bank contains full obligate and facultative synonymy of the taxa
concerned, one or more descriptions, structured morphological, physiological,
ecological and/or molecular databases, references and links to both literature
and other web-based data, and allows polyphasic identification. The oldest and
most complete species bank is that of the yeasts, but there are also species
banks on for example Aspergillus/Penicillium, medical fungi,
Mycosphaerella and its anamorphs and resupinate Russulales.
Collaboration will be sought with international specialists or specialist groups
to adopt a group of fungi. They will be given full responsibility for the
taxonomy, have access to and full rights for the data of the group concerned and
will of course be recognized as such. It is hoped that in this way the most
adequate use can be made of the still available know-how.
Mycoheritage
Bioheritage is an initiative of SYNTHESYS to make important old works available
through the Internet. CBS supports this initiative through its new site
“Mycoheritage”, in which classic mycological works are displayed. A
priority has been given to works containing illustrations that give insight into
the historical taxonomic concepts devised by the great-grandfathers of Mycology
- for example Persoon, Fries and Saccardo.
Online publications
CBS continues to bring its publications online. Previously, this was done in
collaboration with the University of Utrecht and the Royal Netherlands Academy
of Sciences information institute NIWI, but in 2005 the management of CBS
information was moved in-house. New volumes of the journal Studies in
Mycology are now published simultaneously on the Web (HighWire Press) and
on paper, and all but one (copyright elsewhere) previously published volumes
have been placed on-line. The relevant data from these books have also been
transferred into the CBS descriptions database.
The CBS databases are definitely highly appreciated. A user analysis has
indicated that the numbers of visitors who actually perform a search (thus not
merely the number of hits, which average 10.000 per day!) in the Index Fungorum
is about 30.000 per month. The Aphyllophorales database processes about
1000 search requests per month. The yeast database, which provides both
information and also an interactive, polyphasic identification tool (via
BioloMICS software), is regularly used by more than 7000 researchers from 96
countries (see figure below). A new collaboration with a goal of creating
several databases related to fungal human pathogens was initiated in 2005 with
W. Meyer (University of Sydney, Westmead Hospital, Sydney, Australia). The goal
of this project (Australian grant #352303; Title: “Phylogeny as a basis for
molecular identification of pathogenic fungi”) is to allow Internet users to
perform online polyphasic identifications that include morphological,
physiological, electrophoretic and sequence data.
Data present in the CBS nomenclatural and taxonomic databases
|
Data
|
Number
|
|
Names
|
392.711
|
|
Protologue info
|
254.771
|
|
Basionymes (taxa)
|
272.212
|
|
Typeinfo
|
55.047
|
|
Citations
|
330.000
|
|
Descriptions
|
23.000
|
|
Images
|
8.700
|