Memorandum submitted by the Mycology sub-committee
of UK BRAG[30]
Fungi are critically important organisms as
symbionts of most plants, as recyclers of carbohydrates and minerals,
as pathogens of plant and animal disease, as food sources for
humans and other animals, as sources of valuable chemicals and
in food and beverage processing. Lichens are particularly important
in the formation of soils and as indicators of change within the
environment. The majority of the world's fungi (estimated at 1.5
million species, of which only 8-10 per cent have been described)
are as yet unknown to science, and even in the UK where native
biodiversity is relatively well documented dozens of species of
fungi new to science are discovered each year.
1. What is the state of systematic research
in the UK?
1.1 There has been considerable loss of
mycological expertise since 2002, particularly in UK universities;
research in fungal taxonomy no longer occurs at Reading or Exeter,
and the effort is much reduced at London, Sheffield and Newcastle.
Two taxonomic mycologists remain in Liverpool John Moores University
and Birkbeck College, London, but these posts are unlikely to
be replaced upon retirement of the individuals involved. Since
1996 there has been a > 50 per cent decline in the number of
PhD-level taxonomic mycologists in UK universities. The experts
that remain are, typically, in their 50s and, despite careful
succession planning in some instances, budget cuts have meant
that the majority of these are unlikely to be replaced upon their
retirement.
1.2 UK taxonomic expertise in mycology (including
the study of lichens) is therefore currently focused on five main
organisations: CABI, NHM, NMW, RBGE and RBGK. CABI and RBGK currently
share the brunt of the taxonomic mycology burden within the UK:
CABI concentrating on ascomycetes (often microscopic and containing
especially important groups economically) and its living culture
collection, RBGK on basidiomycetes (often macroscopic and containing
many important plant symbionts), and NMW, NHM and RBGE on lichens
and rusts. All five institutes hold extensive fungal reference
(herbarium) collections.
1.3 Specialist fungal culture collections
are also maintained by organisations such as the Scottish Crops
Research Institute and Forest Research, but also often under severe
threat through lack of funding. In the case of FR, of a worldwide
collection of 1500 Phytophthora cultures, about half died
in a warm weather episode in the 1990s as a result of inadequate
support resources. In addition, FR holds a culture collection
of 9,000 individual of Ophiostoma species (an ascomycete),
mainly those species which cause Dutch elm disease and at least
one of which is now close to extinction. These cultures have been
gathered over 40 years, mainly 1970-1990, come from all over the
world, and represent a huge and detailed resource (eg for reference
and genome sequencing), but which despite their significance receives
no financial support for maintenance.
1.4 It is important to acknowledge that
some specialist mycological expertise (in some cases considerable
taxonomic and phylogenetic expertise) is distributed among and
applied in certain government funded research institutes other
than those traditionally considered to be engaged in taxonomy
research. This is especially the case with fungal pathogens of
plants and animals. Examples include the Scottish Crops Research
Institute (SCRI), Forest Research (FR) and the Royal Horticultural
Society (RHS). FR currently has a PhD grade taxonomist funded
under the Defra Darwin Initiative to work on Phytophthora taxonomy,
specifically on species barriers in Phytophthora species.
Number of PhD-grade taxonomists
| Mycologists | Lichenologists
| | | |
|
| 1996 | 2002
| 2008 | 1996 |
2002 | 2008 |
CABI | 14 | 5
| 3 | 2 | 0 |
0 |
| Natural History Museum | |
| | 3 | 2
| 1 |
| National Museum of Wales | |
| | 1 | 1
| 1 |
| RBG Edinburgh | 2 | 1
| 1 | 1 | 1 |
1 |
| RBG, Kew | 5 | 4
| 4 | 0 | 0 |
0 |
| |
| | | |
|
1.5 In evidence submitted to the House of Lords Inquiry
on Systematic Biology and Conservation (2001/2), the NHM, RBGE
and RBGK, all reported that their grant-in-aid funding had decreased
in real-terms since 1992 with negative effects on research and
collections management and loss of professional taxonomist posts.
Since then, each of the institutions has had modest increases
in grant-in-aid, but not sufficient to bring them back to the
1992 levels in real terms. Drafting Note: Suggest delete this
text on CABI because: 1.The 3 per cent figure is repeated in Para
8.2, with a more positive slant, 2. The 1989 change happened prior
to 1992.
1.6 Several policy areas are likely to require mycological
expertise such as the UK Plant Diversity Challenge (the UK's response
to the CBD's Global Strategy Plant Conservation), and meeting
the UK's international obligations under the Convention on Biological
Diversity as a major repository of the world's systematic mycological
resources.
1.7 It is important to note that the loss of taxonomic
expertise within fungal groups has been uneven. Much of the current
research is limited to the ascomycetes & basidiomycetes. Other
fungal organisms are no longer the focus of taxonomic study. In
particular, oomycetes (including Phytophthora spp.), a
relatively small group of major economic impact, are no longer
studied widely. Many within this group are serious pathogens of
horticultural crops and trees. The nature of these fungi means
that institutes such as SCRI, FR and RHS have developed their
own in-house expertise for taxonomic work on Phytophthora
spp. They have become active and successful in combining molecular
and traditional taxonomic approaches and made significant taxonomic
contributions, nationally and internationally. One topical example,
is the way work of FR with SCRI has highlighted the tendency of
Phytophthora spp to hybridise, and potentially generate
new species and species swarms which can have a major impact not
only on affected hosts but on entire ecosystems. Other groups,
such as the slime moulds, are significant components of many habitats
and are largely ignored, despite their importance in ecosystem
function/services.
What are the current research priorities?
1.8 There is no single national research strategy but
efforts are being made via UK-BRAG and GBSC to guide activities;
the 5 main non-university institutes have their own research priorities
and aim to ensure that "overlap" is minimised. Research
priorities in universities are largely driven by current funding
opportunities. Outlined below are some potential areas of growth:
1.9 The UK has the potential to lead the world in the
area of DNA barcoding for fungi, based on the unique collections
deposited in our natural history collections. The development
of barcoding technology (under-supported in the UK) presents an
unprecedented opportunity to tackle the taxonomic impediment in
mycology at a scale proportional to the magnitude of the task.
Of critical importance to the success of these techniques is a
reference dataset derived from reliably identified specimens using
morphological techniques, a resource that depends on ongoing input
by taxonomic mycologists.
1.10 The aquatic environment is especially rich in fungal
diversity; opportunities for investigating fungal biodiversity
within these habitats will be particularly driven by the need
to establish the impact of climate change and develop mitigation
and adaptation strategies, where practicable. In particular, the
ecological role (& response) of marine fungal organisms in
seas with changing acidity is a potential area of research of
international significance in which the UK could become a leader
in.
1.11 Fungi are of major importance, as symbionts, to
the health of wild and cultivated plants. It has been recognised
that continued seed banking (at the Millennium Seed Bank at the
Wakehurst Place site of RBGK) without concern for banking of the
fungal associates that many of these plants need to survive, is
only a partial strategy. Longer-term efforts to bank the seed
of 30 per cent of the world's plants have been proposed, but reintroduction
of the majority of these species would be difficult, if not impossible,
if their fungal associates are not studied and similarly conserved.
However, before such a fungal conservation initiative can be added
to the work of the seed bank, a great deal of taxonomic study
will also be required.
1.12 Lichens are especially diverse in the UK and are
extremely sensitive to environmental degradation, making them
particularly good indicators of climate change and the effects
of man-made disturbance and pollution in both the UK and overseas.
The UK's internationally significant collections have potential
to underpin research developing biomonitoring tools and for understanding
climate change. Succession planning at RBGE has capitalised on
the opportunity for collaboration between a lichen taxonomist
and lichen ecologist invigorating research in conservation biology
and climate impacts.
What are the barriers to developing these priorities?
1.13 All of the preceding opportunities are funding dependent.
There is a need for a renewed recognition of the importance of
mycological systematics to the UK science base.
2. What is the role of systematics and taxonomy and, in
particular, in what way do they contribute to research areas such
as biodiversity conservation, ecosystem services and climate change.
2.1 Currently, the role of extant mycology-based research
in these areas is rather limited; principally, this is due to
perceived (or real) funding barriers. However, NE has proposed
the establishment of a Fungus Conservation Unit. NE identified
RBGK as a base for this development. Such a Unit would be complementary
to and very much dependent on a functioning team of taxonomic
mycologists with the ability to identify and classify fungal material.
The proposed Unit would consist of three full-time equivalent
posts, providing support for the UKBAP, preparing conservation
assessments for non-lichenised fungi in the UK and within a European
context, and raising public awareness of the importance of fungal
conservation. The NMW has one lichenologist on the staff whose
contribution focuses on conservation work on UK lichens. The RBGE
contributes principally to the conservation of lichens within
the UK, under-pinning practical conservation initiatives (eg maintaining
the UK checklist and red data book, providing training in identification
skills) and undertaking novel research in lichen taxonomy, biodiversity
and climate change science.
2.2 Development of systematics and taxonomy-based research
that supports and underpins ecosystem services and climate change
research has significant opportunities. The potential opportunities
for the UK to lead in science and technology in DNA barcoding,
marine biology and climate science, terrestrial plant/fungal interactions
and biomonitoring are significant. The direct financial benefits
to the UK economy from technological innovation could be significant
and the indirect benefits from the possible development of adaptation
and mitigation strategies to climate change are of international
importance.
3. Does the way the in which systematic research is organised
and co-ordinated best meet the needs of the user community?
3.1 Please see paragraph 2.1. The proposed merger of
the RBGK and CABI collections presents an opportunity to build
on existing strengths and implement a concerted approach to succession
planning and the application of expertise to issues of economic
relevance;
3.2 An explicit and co-ordinated succession-planning
programme (focused on enhancing taxonomic research, maintaining
active databases, training future generations of experts in taxonomic
mycology and transferring the expertise of the generation about
to retire) that ensures products currently accessible to the broader
scientific community are not lost is urgently required.
3.3 In 2006, CABI separated its mycology activities into
a dedicated Bioservices Unit, focusing on using fungi for the
global good. Its taxonomy dependent activities include information
provision (particularly, the free-to-access Index Fungorum: www.indexfungorum.org,
in association with the Index Fungorum Partnership and publication
of key taxonomic reference works) as well as applied research
into fungi as biopesticides, conservation and sustainable use.
The Unit also runs diagnostic and analytical services operating
on a quality-managed commercial basis using morphological and
molecular methods (including barcoding approaches) and maintains
the internationally significant culture collection.
4. What level of funding would be needed to meet the need
for taxonomic information now and in the future?
4.1 Mycology and other similar disciplines where there
is a significant "taxonomic impediment" would benefit
from a scheme similar to that funded by the USA's National Science
Foundation's (NSF) Partnerships for Enhancing Expertise in Taxonomy
initiative (PEET). In partnership with academic institutions,
botanical gardens, freshwater and marine institutes, and natural
history museums, the NSF seeks to enhance taxonomic research and
help prepare future generations of experts.
4.2 The cost of establishing viable research programmes
in DNA barcoding, marine biology and climate science, terrestrial
plant/fungal interactions and biomonitoring (see paragraphs 1.2.1-1.2.4
and 2.1.1) is significant. Initial "set-up" costs would
be approximately £200-500,000 per project.
6. What impact have developments in DNA sequencing, genomics
and other technologies had on systematics research?
6.1 Molecular systematics (in conjunction with "traditional"
techniques) has revolutionised some aspects of systematic research;
this is particularly evident in the flowering plants where the
Angiosperm Phylogeny Group has made significant advances. Fungal
systematics has also embraced the molecular revolution; but, advances
have been less dramatic due to funding limitations (and a lack
of traditional taxonomic expertise in some groups). However, molecular
biology has considerably advanced our understanding of some groups
such as lichens and symbiotic basidiomycetes. Unfortunately, many
groups, such as the oomycetes, have received virtually no attention
and our knowledge is now decades old; the potential for molecular
systematics to make significant discoveries in these fields is
considerable.
8. What is the role of the major regional museums and collections?
How are taxonomic collections curated and funded?
8.1 The capacity to carry out major collections based
projects is diminishing in all institutions, but RBGK has made
major investments in terms of housing for the collections (purpose-built
herbarium for the 800,000 accessions, making RBGK one of the three
largest mycological collections in the world). CABI and RBGK have
agreed to merge their fungal reference collections at Kew (to
take place in June 2008). CABI are also particularly interested
in the banking of fungal cultures, and this would complement the
work of the Millennium Seed Bank. The merging of the RBGK and
CABI reference collections presents an opportunity to develop
more focused efforts on the study of fungi. These efforts have
significant cost implications, and larger impacts would be obtained
if there were increased financial support available.
8.2 CABI has intergovernmental status and is owned by
a consortium of 45 member countries (including the UK). Its headquarters
are in the UK, and it has played a major role in the support of
UK mycology for the whole of its existence. Unlike most intergovernmental
organisations, it is largely self-supporting financially, with
only 3 per cent of its annual budget contributed by member countries
as core funding. The remaining 97 per cent is earned through information
provision (CABI owns the largest agricultural science abstract
database in the world) and service provision (identifications,
consultancy, culture sales, project work etc.). CABI remains committed
to taxonomic mycology with a focus on economically important species.
It owns globally important collections of fungi, including a fully
databased dried fungal reference collection containing around
400,000 specimens and a living collection (incorporating the UK
National Collection of Fungus Cultures) of around 28,000 strains.
CABI receives no financial support from the UK Government to maintain
these collections, despite their significance as a UK scientific
resource.
8.3 NHM's core funding is derived from the Department
of Media Culture and Sport (DCMS). Curation of the Museum's collections
is primarily funded from this source. Although NHM is home to
the nation's largest and probably the world's most historically
significant collection of lichen specimens, taxonomic expertise
on British lichens at NHM has been significantly reduced in recent
years. The collections are also of global significance, with particularly
important collections from Southeast Asia. The expertise/ research
of the last three curators has focused on foreign, rather than
British, lichens. The collections are currently managed by an
experienced lichen curator with considerable research experience,
although his research activities are limited by other duties.
In addition, the last three curators have had non-overlapping
appointments, which has resulted in a lack of continuity of taxonomic
and curatorial knowledge. In addition to its lichen herbaria,
the NHM houses a historically important slime mould (myxomycete)
herbarium. As there is a rapidly increasing interest in this group
of organisms worldwide, NHM is ideally positioned to play a leading
role in researching these organisms.
8.4 RBGE receives core funding from the Scottish Government.
It holds historically important collections though is noted particularly
for its comprehensive, up-to-date collection of British lichens
which has contributed to modern developments in the taxonomy of
British lichens. Similarly, the collection of basidiomycetes directly
contributed to the base-line taxonomic treatise "Fungal Flora
of the British Isles", though this is no longer actively
researched by RBGE staff except for the rust-fungi.
9. What progress has been made in developing a web-based
taxonomy?
9.1 A "Fungal Portal" was proposed as a joint
venture between the BMS, CABI, RBGK and a private benefactor.
Its overall aim was to establish an integrated and comprehensive
digital fungal information and recording service. It would be
a web-based information network that could be used to exchange
data and disseminate information about fungi, initially within
the UK and potentially world-wide, as a public service. An aim
was to trigger a change in public understanding of fungi through
innovative linkages between non-specialists and the scientific
community. The Portal was to have linked a number of major existing
databases that contain information about British fungi and lichens
to provide a greatly enhanced and fully searchable facility, with
an extensive image library and other information resources for
identification and education.
9.2 A scoping exercise for the Portal was undertaken
by RBGK (with input from CABI) in response to a funded request
from Defra but the resulting proposal was not taken forward due
to high costs and lack of an identified funding consortium
11. How does the taxonomic community engage with the non-taxonomic
community? What role do field studies play?
11.1 It is important to define what the meaning of "non-taxonomic
community" is. The field-based mycologist has often been
defined (usually by others) as not being taxonomically skilled;
in many instances this is incorrect. Laboratory based mycological
research is often highly dependent upon the skills of field mycologists,
numerous discoveries of taxonomic significance have originated
in the field mycology community. Therefore, the role of field
studies has been, and should remain, a significant aspect of UK
taxonomic endeavour. New taxa are being described each year and
this is largely due to the efforts of the BMS, the BLS and more
than 30 Local Recording Groups.
11.2 The very substantial data resources compiled by
the BMS cannot be accessed as efficiently as required by all those
interested and there is little strategic direction on a nation-wide
scale; the Fungal Portal proposal was developed as a strategy
for addressing these concerns (see paragraph 9.2). In contrast,
the BLS has had a strategy for the collation of high quality geo-located
data since the 1960s, and the Scottish dataset (funded by SNH)
is now available through the NBN with full access to all. This
knowledge-base is developed by taxonomists over decades, project
is in the planning stage for England and Wales.
11.3 CABI, NHM, RBGE and RBGK have substantial expertise
in the production of information resources for fungal taxonomy.
RBGE has had a long-running programme to publish an account of
the UK basidiomycetes, and it and the NHM have collaborated with
a number of other groups to produce an account of British lichen-forming
fungi (a second edition is currently in preparation). RBGE maintains
the British checklist for lichens and lichenicolous-fungi, the
lichen red-data book, the lichen synonym list, a biannual account
of literature pertaining to British lichens. RBGK and CABI have
worked for some years on an account of the UK ascomycetes. CABI
produced the first modern checklist of the British Ascomycota
(including lichen-forming ascomycotes) in the 1980s and provided
IT support for the production of the recent Checklist of the British
and Irish Basidiomycota (2005, published by RBGK). Both products
were linked into and augmented CABI's "Species Fungorum—towards
a global checklist of the fungi" contribution to the Catalogue
of Life (Species 2000 and ITIS) and also the Fungal Records Database
of Britain and Ireland (hosted by CABI). CABI also produces database-driven
publications such as the Index of Fungi (the mycology equivalent
of the International Plant Names Index, incorporating Index Kewensis),
the Bibliography of Systematic Mycology (the mycology equivalent
of Kew Record) and the Dictionary of the Fungi, the key reference
work for fungal taxonomy worldwide.
12. What are the numbers and ages of trained taxonomists
working in the UK universities and other organisations?
12.1 See paragraphs 1.1, 1.2 and 1.5.
13. What is the state of training and education in systematics
and taxonomy?
13.1 Currently, no UK University has a teaching programme
in fungal taxonomy. Fungal and lichen taxonomy forms part of the
curriculum of the joint University of Edinburgh/RBGE MSc course
on biodiversity and taxonomy, and the joint Scottish Agricultural
College/RBGE BSc Horticulture course. Most training delivered
in the UK is by either the BMS, BLS or one of the Local Recording
Groups.
13.2 In 2002, the BLS presented a paper on the key role
of the RBGE lichen taxonomist in supporting conservation initiatives.
In 2003 SNH provided funding to the BLS to support the training
of "lichen apprentices". Over three years training was
provided through a series of field-based and reference collection
workshops and formal training in site monitoring for lichens.
There is now an active group of lichen trainees, drawn from Scotland
and the wider UK, who are contributing to conservation projects
and scientific research on lichens.
13.3 RBGE developed plans to recruit a "trainee"
lichenologist on external funding, to work alongside the lichen
taxonomist; this post has been supported for three years by the
Esmée Fairbairn Foundation and a benefactor and is now
funded directly by RBGE. The post has provided training in lichen
identification and taxonomy for a PhD-grade ecologist employed
to work on the biodiversity and conservation of lichens.
13.4 CABI has a long track record of capacity building
in mycology through training courses, PhD placements etc. and
has been granted no less than ten awards from Defra's Darwin Initiative
with a substantial taxonomic mycology component.
13.5 In 1996 NHM hired a lichen taxonomist, who trained
a number of young, foreign lichenologists in molecular systematics
before leaving in 2000. Unfortunately, his post was not replaced,
and the resources for funding this position have subsequently
been lost. NHM continues to train foreign lichenologists through
various programmes such as a number of SYNTHESYS and Marie Curie
fellowship visitors. The NHM lichen curator post also contains
a strong element of taxonomic research.
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