Memorandum submitted by DEFRA
SUMMARY OF
DEFRA SUBMISSION
The Defra submission covers various aspects
of the Inquiry, and can be summarised as follows:
— Whilst Defra is a user of the outputs
of systematics and taxonomy, it is not a major utiliser of research
from these disciplines.
— Defra invests in systematics and
taxonomy mainly through its research agencies (CSL, Cefas and
VLA) and the RBG, Kew.
— Other Defra contributions are through
the Darwin Initiative, Convention on Biological Diversity, Global
Biodiversity Information Facility and the Convention on Trade
in Endangered Species.
— Defra's current and medium term research
priorities are described in our Evidence and Innovation Strategy
2005-08.
— We have not identified any specific
major impediments to delivering our priorities deriving from the
spheres of systematics and taxonomy.
— Defra investigated the options for
setting up a coordinating forum to address issues of the disciplines
but, considering the history of previous fora, had doubts about
the viability of a new body outside the professions themselves.
— Whilst recognising the role that
directly Defra funded organisations and other publicly funded
institutions play both nationally and internationally, we conclude
that the issue of funding itself is not straight forward.
INTRODUCTION
The Department of Environment, Food and Rural
Affairs submits evidence to the inquiry from two standpoints:
— as an investor in research and monitoring
activities which require the use of systematic or taxonomic science;
— as the owner of three laboratory
agencies—the Central Science laboratory (CSL—see annex
1); the Centre for Environment, Fisheries and Aquaculture Research
(CEFAS) and the Veterinary Laboratory agency (VLA)—which
supply systematic and taxonomic expertise among the other services
they deliver to the Department.
Defra also has an interest in this issue as
the provider of Grant in Aid to the Royal Botanic Gardens, Kew,
which is one of the major UK centres of systematic and taxonomic
science. As an independent body, RBG Kew has provided evidence
directly to the Enquiry.
From these viewpoints, Defra can answer some
of the questions into which the Committee is enquiring, but others
will be better placed to answer the questions about basic research
and development in these fields.
THE STATE
OF SYSTEMATICS
AND TAXONOMY
RESEARCH
Q1. What is the state of systematics research
and taxonomy in the UK?
1.1 Defra has limited direct involvement
in systematics research and taxonomy, but has contributed to the
discussions within the UK Biodiversity Research Advisory Group
(BRAG) and the Global Biodiversity Sub-Committee (GBSC) of the
Global Environment Change Committee on the state of these fields
in the UK and generally supports their submissions on this aspect
of the Inquiry.
Q2. What are the current research priorities?
2.1 Defra's current and medium term research
priorities are described in our Evidence and Innovation Strategy
2005-08. Systematics and taxonomy contribute in a number of
areas.
2.2 With regard to conservation and enhancement
of biodiversity, specific research needs included:
— Improve understanding of genetic
variation in wild populations, and of genetic diversity for species
of economic or conservation importance;
— Identify innovative control techniques,
develop and test methods for wildlife crime and regulating the
use of endangered species held in captivity.
2.3 Defra has recently funded a number of
projects to develop identification techniques to support implementation
of the Convention on International Trade in Endangered Species:
— Molecular Genetic Identity of Basking
Shark Population (CR0247)
— DNA Markers for Birds of Prey (WC05005)
— Forensic identification of CITES
listed Timber and Wood products (WC0702)
2.4 Defra also funds the Darwin Initiative
which aims to promote biodiversity conservation and sustainable
use of resources around the world. It uses UK expertise, working
with local partners, to help countries rich in biodiversity but
poor in resources to fulfil their commitments under the CBD. Since
it began in 1992, the Darwin Initiative has provided funding for
over 50 projects which have included taxonomy as their main focus.
Through these projects, the Darwin Initiative has contributed
to all key areas of the Global Taxonomy Initiative operational
objectives.
2.5 At CSL, systematics research and taxonomy
are an integral part of the work of the Plant Health Group, which
uses a combination of morphology, molecular biology and bioinformatics
approaches, to meet research priorities identified by DEFRA customers.
In addition, in response to concerns highlighted by a National
Audit Office report about loss of taxonomic skills, DEFRA fund
an annual taxonomic fellowship, which may be a PhD studentship
or a defined R&D project to ensure appropriate investment
in taxonomic skills. Recent examples include:
— University of Nottingham/CSL: Plant
Health PhD studentship on "The taxonomy of phytoplasmas:
a molecular approach"
— University of Edinburgh/CSL: Plant
Health PhD studentship on nematode identification using DNA bar
coding "Aphelenchus and related taxa: molecular systematics
and molecular diagnostics"
— Imperial College/Forest Research:
Plant Health PhD studentship "Species boundaries in Phytophthora
pathogens of trees"
— CSL: Plant health Fellowship: Generic
imaging solutions to solve diverse taxonomic problems
2.6 At CEFAS, in the context of marine environmental
management, taxonomic science contributes to understanding the
impact of human activities in the sea, for example through assessment
of the vulnerability and resilience of benthic fauna, eg to fishing,
aggregate extraction, disposal of material to sea, oil and gas
activity and non-renewable energy exploitation or through the
assessment of changes in plankton populations and their impact
on fisheries.
2.7 Although not strictly systematics and
taxonomy research, VLA's interests in this area focus on understanding
the emergence of new and emerging diseases such as avian influenza
and the re-emergence of diseases like bovine tuberculosis. Changes
in pathogenicity, and ability to evade existing control measures
that could lead to important epidemiological variations are of
special interest
Q3. What are the barriers, if any, to delivering
these priorities?
3.1 We have not identified specific barriers
to delivering our requirements. Generically, as in all research
issues of finance, prioritisation and availability of suitable
staff, affect the progress of individual studies. In this sector,
access to appropriate taxonomic collections, often held in other
countries, is an important factor.
3.2 New DNA sequencing technology is advancing
and permitting rapid analysis. The block will be the overload
of data for which robust in silico analytical tools are
not fully available and providing sufficient capital investment
to exploit the rapid advances in technology.
Q4. 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?
Q5. How important is this contribution and
how is it recognised in the funding process?
Q6. How is systematics integrated in other
areas of research?
4.1 Systematics and Taxonomy underpin any
research on biological diversity, including, among those of importance
to Defra, that on conservation, ecosystem services, the biological
impacts of and adaptation to climate change, the exploitation
of natural and farmed resources and the management of pests weeds
and diseases.
4.2 Defra invests in research and field
data gathering (monitoring) to meet particular needs to develop
or implement policy. Where these require input of systematic or
taxonomic expertise, this will be factored into the contract.
Defra does not fund basic research in systematics or taxonomy.
In other words, these disciplines are not utilised on their own
but in integrated research with other disciplines such as ecology
and population dynamics.
4.3 See also the response to Q20 in relation
to Defra's provision of Grant in Aid to RBG Kew.
Q7. Does the way in which systematics research
is organised and co-ordinated best meet the needs of the user
community?
7.1 Systematics research is undertaken in
a diverse range of organisations, varying greatly in size, capability,
collections and significance, both in the UK and abroad. In general,
as users, we benefit from this diversity and, where needed, use
our own investment to ensure that different elements are coordinated
appropriately to meet our needs. In our experience, the systematics
and taxonomics community is one with a long history of cooperation
and interchange.
Q8. What progress has been made in setting
up a body to lead on this?
8.1 Following the previous report of the
Committee, Defra contacted a range of stakeholders to understand
more fully the then recent history surrounding previous attempts
to set up a forum to collate information and exchange views for
the profession.
8.2 In considering the options, particularly
in the light of the fate of an earlier forum, we developed doubts
both as to whether anything new could be achieved to justify the
effort and expenditure or that Defra itself would perhaps be best
positioned to lead an activity best driven by the community itself.
We believe that this scepticism is possibly shared by the profession—for
instance a view expressed at the Inquiry Seminar on Wednesday
6th February 2008.
8.3 However, we have in the meantime promoted
work in the relevant community as it operates in BRAG and GBSC
to identify issues and develop solutions. We have also participated
in a review of user needs through the UK Taxonomic Needs Assessment
(See in particular the answer to question 17).
Q9. What contribution do the leading systematics
research institutions make both nationally and internationally?
9.1 The major UK research establishments,
including the Royal Botanic Gardens at Kew, are widely recognised
as playing a globally significant role both in their research
and their collections.
9.2 Defra's own laboratory agencies such
as CSL and CEFAS have expertise and collections which are important
nationally and in some cases internationally (see Annex 1 with
respect to CSL's management of collections for example).
Q10. What level of funding would be needed
to meet the need for taxonomic information now and in the future?
Q11. Who should be providing this funding?
10.1 There is no simple answer to this question.
Basic research requirements are a matter for the Research Councils.
Defra will continue to invest to meet its own requirements for
information, but these will vary according to policy need. We
will also continue to provide Grant in Aid for RBG Kew.
Q13. Could there be more international collaboration?
Q14. If so, what form should this collaboration
take and how might it be achieved?
13.1 There are already many well-developed
mechanisms for international collaboration though there could
always be more. Defra encourages its contractors (including its
agencies) to work with national and international institutes and
other bodies through, for example, funded projects or mobility
grants, to improve R&D collaboration and technology transfer.
Among other benefits, this supports policy development at the
EU level. However, the recent policy changes by RCUK does potentially
limit national collaborations between PSREs and other research
organisations.
13.2 In the field of biodiversity research,
valuable international collaborations include the Global Taxonomy
Initiative under the Convention on Biological Diversity and the
Global Biodiversity Information Facility (both of which Defra
provides funding to). The European Platform for Biodiversity Research
Strategy provides a forum for the identification and prioritisation
of research needs across the European Union; a forthcoming meeting
is expected to address taxonomic needs.
13.3 In the marine environment, EU sponsored
networks of excellence such as MarBEF (www.marbef.org) provide
a forum for exchange of information and collaborative research
between 94 European organisations involved in systematics and
taxonomy, including CEFAS.
13.4 CSL is responsible for the administration
and management of EUPHRESCO, an FP6 ERA-NET involving the partnership
of 24 organisations funding phytosanitary research representing
17 European countries. A key achievement has been the confirmed
country funding commitment for eleven pilot projects. Various
leaflets, newsletters, press releases and articles to publicise
the Project have been produced.
13.5 CSL has also coordinated an EU 7th
Framework proposal "PRATIQUE" on the enhancement of
pest risk analysis techniques; participated since its formation
(1996) in the European Mycological Network to assist in Europe-wide
R&D projects in addition to development of EPPO Diagnostic
Protocols; worked with the Netherlands PRI/PD on diagnosis of
new viruses/viroids, with the USDA on techniques for the diagnosis
of fruit viruses, with AAFC, Canada on the diagnosis of Pepino
mosaic virus and with Plant Health Services in Estonia,
Lithuania, Poland, Hungary, Bulgaria, Russia, Croatia, USA, Mexico,
Chile among others, as well as in the international bodies EPPO
and IPPC.
Q15. What impact have developments in DNA
sequencing, genomics and other new technologies had on systematics
research?
Q16. In what way has systematics embraced
new technologies and how can these research areas interact successfully
and efficiently?
15.1 See reply to Q2. Defra has funded research
to apply DNA sequencing to identification of plants and animals
regulated in international trade, to the population dynamics of
endangered species (Basking Shark) and to the health of marine
organisms.
15.2 Defra agencies have made extensive
use of these new technologies (see Annex 2 for a detailed reply
from CSL). In the aquatic environment molecular techniques have
been well embedded in microbiological areas such as pathogen identification.
These techniques are being migrated into environmental studies
such as research conducted at CEFAS on microbial ecology, the
identification of toxin producing harmful algal blooms and in
the area of fish stocks management by identification of fish eggs
and larvae that cannot be speciated by conventional means. In
the animal and zoonotic diseases area DNA sequencing, genomics
and bio informatics are having a huge impact on our understanding
of the spread of new and emerging diseases, as well as being an
integral component of the national response to the incursion of
exotic diseases such as FMD and avian influenza. At VLA, DNA sequencing
techniques are used for the rapid identification of diseases and
sequencing is used as an important disease tracing tool as well
as providing clues to the evolution of organisms during disease
outbreaks. As sequencing becomes more accessible with whole viral
and bacterial genomes being sequenced routinely, genomic databases
will provide detailed and important clues to the identity and
characteristics of new and emerging diseases.
DATA COLLECTION,
MANAGEMENT, MAINTENANCE
AND DISSEMINATION
Q17. Does the way in which taxonomic data
is collected, managed and maintained best meet the needs of the
user community?
17.1 The UK Taxonomic Needs Assessment,
undertaken as a contribution to the Global Taxonomy Initiative
of the Convention on Biological Diversity by the Natural History
Museum focussed on the needs of the biodiversity conservation
communities in the UK and its Overseas Territories for taxonomic
information and services, or information that is reliant on the
availability of taxonomic expertise. The Assessment was undertaken
by the Natural History Museum and was completed in 2006.
17.2 Defra accepts the findings, from the
consultation with users in the UK that the following types of
information, were identified as important for biodiversity conservation
but not sufficiently accessible (listed in order of priority):
1. Habitat requirements of animals/plants
2. Information on local species distributions
3. Information on regional species distributions
4. Geographic Information System (GIS) data
5. Information on name changes
6. Lists of invasive alien species
7. Specialised identification services (taxonomic)
17.3 The UK Taxonomic Needs Assessment suggested
that further action was needed by both the taxonomic and biodiversity
conservation sectors to:
— Facilitate the generation and delivery
of the taxonomic information needed for biodiversity conservation
in forms appropriate for users;
— Develop ways to translate the interests
of stakeholders, including conservationists, environmental managers,
statutory agencies and commerce, into the research priorities
of both taxonomic research institutions and funding bodies;
— Identify those urgent taxonomic information
needs that correspond with a genuine gap in UK taxonomic expertise,
as opposed to a failure in information management or dissemination;
— Foster best practice in the dissemination
of taxonomic information, and passing on of taxonomic skills to
stakeholders eg through online information services, field guides,
courses, qualifications.
17.4 Defra has contributed to addressing
these needs through support for the National Biodiversity Network
and Local Record Centres (see 18.1 and 21.5 below) and GBIF (see
13.2 above) and through engagement with BRAG and GBSC (see 8.3
above).
Q18. What is the state of local and national
recording schemes?
18.1 Biodiversity recording in the UK is
largely undertaken by National Schemes and Societies or by Local
Record Centres (LRCs). National Schemes and Societies usually
have a hierarchical structure, with identified experts for specific
taxa to ensure the accuracy of records. LRCs collate and manage
biodiversity data for a geographical area (usually a County or
Unitary Authority). A recent review of LRC activities[56]
identified four areas requiring development in order to sustain
local biodiversity recording:
— Financial security. This is the key
barrier preventing LRCs from making biological records widely
available because they rely on charges made for this service.
— Efficiency. A large proportion of
LRC data holdings are paper based and responding to data requests
is often a laborious, manual process. Data capture, management
and dissemination to end users needs to be streamlined, providing
access to existing and new species and habitat data via the NBN
Gateway as soon as possible after the data has been captured.
— Coverage. There are currently 35
record centres across England covering 83 per cent of counties.
Some counties have little or no coverage.
— Consistency. Individual record centres
vary considerably in their adoption of standards relating to verification
and validation of records, data management and data exchange.
18.2 In August 2007 Defra announced a Fund
for Innovation in Local Biodiversity Recording. The overall aims
of the Fund are to build capacity in local record centres and
to increase the geographic scope, quantity and quality of biological
information available to the general public and key public sectors
through the National Biodiversity Network (NBN) Gateway. The Fund
is administered by Natural England and £181,000 is being
made available in 08/09.
18.3 Defra also provides ad-hoc funding
for specific national recording schemes, particularly where the
data provide a source of information for assessing status and
trends in biodiversity. Examples in the current year include the
development of the Butterfly Monitoring Scheme and the production
of trends from the various national bird surveys coordinated by
the British Trust for Ornithology. CSL participates in providing
identification services for statutory survey work for Defra eg
potato ring rot surveys.
18.4 In the marine environment, Defra fund
CEFAS annual trawl surveys and the UK Marine Monitoring and Assessment
Programmes that provide data on biodiversity trends in fish and
benthic invertebrates respectively, as well as contributing to
international assessments of biodiversity such as those coordinated
by the International Council for Exploration of the Sea (ICES).
Q19. What is the role of the major regional
museums and collections?
19.1 Taxonomic collections fulfil a number
of roles. They provide a resource to field workers, both for the
amateur and professional, for verification of identification;
research into systematics and evolutionary biology; environmental
change research and in the training of a new generation of taxonomists.
Defra does not use these collections directly, but has an interest
in ensuring that they continue to meet the needs of the taxonomic
user community.
Q20. How are taxonomic collections curated
and funded?
20.1 Curation of collections at the laboratory
agencies is done by specialists (see Q26) and funded principally
by DEFRA; for example Plant Health Division currently funds maintenance
of the plant pathogen collections at CSL. CSL add value to this
by bidding for external funding by EU and other projects. Cefas
holds national reference collections of fish viral, bacterial
and fungal pathogens of fish. Some phytoplankton, zooplankton
and fish reference materials are a retained at Cefas, but only
the benthic invertebrate collection would be regarded as a nationally
important reference in the museum sense of the word. Defra funds
the maintenance of these collections.
20.2 Defra currently contributes £17.6
million per annum as Grant in Aid to the Royal Botanic Gardens,
Kew, plus a sum for capital investment (£7.6 million in the
last year). Whilst Grant in Aid is not hypothecated for specific
purposes, this level of public funding recognises and directly
contributes to the important global role that Kew plays in taxonomy
and systematics. Recently, Defra capital allocations have made
a very significant contribution to the extension and refurbishment
of the Herbarium.
Q21 What progress has been made in developing
a web-based taxonomy?
Q22. How do such initiatives fit in with meeting
demand for systematics and taxonomy information?
Q23. How do UK-led initiatives fit in with
international initiatives and is there sufficient collaboration?
Q24. What needs to be done to ensure that
web-based taxonomy information is of high quality, reliable and
user-friendly? How does the taxonomic community engage with the
non-taxonomic community?
Q25. What role do field studies play?
21.1 Advances in computer technology, particularly
the ability for large numbers of people to access powerful databases
and the ability to display and cross reference data geographically
has greatly improved the way in which collection and management
meets the need of the user community.
21.2 The establishment of the Encyclopaedia
of Life (EOL) Project, is an important step towards ensuring consistent
identification and classification of taxa. EOL is an international
project but is supported by a number of UK institutions, including
the Natural History Museum and the Royal Botanic Gardens at Kew.
It aims to document all named species on Earth and to make these
data available to amateur and professional taxonomists alike.
There are a number of linked projects, notably the Barcode of
Life project which aims to integrate the use of DNA sequencing
as an international standard for the identification of species.
These initiatives are important for the user community, as in
the past it has not generally been possible to document global
biodiversity change precisely because of uncertainty about the
identification and classification of species.
21.3 The problem of inconsistent identification
and classification is seen as less serious in the UK, largely
because of our longer history of well organised taxonomy. However,
classification and nomenclature have changed over time and many
species have been recorded under different synonyms. The Natural
History Museum, on behalf of the National Biodiversity Network
(NBN) Trust, has established a species dictionary which lists
all synonyms for species in the UK. This has been central in the
process of collating data on species abundance and distribution
as it allows data from all sources to be displayed together. In
turn, this has allowed for the data to be used to assess biodiversity
change. Defra have contributed to this process through their funding
of the NBN-Trust.
21.4 On-line identification guides are growing
in number, and Defra has funded some development in this area.
For example, Defra funding helped to provide on line keys to coral
identification (project code WP01024, see www.arkive.org/coral/Coral/coral.html)
and identification of CITES listed plants (project code WC01005,
see: http://www.kew.org/conservation/cites-profile.html£cap).
21.5 In the UK, the development of the National
Biodiversity Network to collate and manage biological records
and display them via the web-based NBN Gateway has significantly
improved the value of the data to the users. The main barrier
to fully meeting the needs of the user community is that not all
schemes and societies are willing to pass all of their data to
the NBN, either because they rely on it for income or because
they are older schemes that have developed their own systems to
handle the data.
21.6 Defra is the major UK funder of the
Global Biodiversity Information Facility (GBIF), which provides
a similar service to the NBN Gateway at a global scale. GBIF also
funds work to improve accuracy and availability of taxonomic and
biological data.
21.7 CSL are exploring advances in imaging
technology, in order to enhance our existing taxonomic expertise
and thus underpin the UK's Plant Health diagnostic capabilities.
We are building on our reference collection of indigenous and
non-indigenous pest and disease symptoms, by adding to our photographic
collection already made available through our web-based Plant
Health Information Warehouse. Plans to use this resource as an
e-teaching aid are in hand and should generate an international
exchange of experts in diagnosis and identification. CSL's web-based
information warehouse is accessible to the UK Plant Health Service
(PHD, PHSI, CSL), and plant health officials in Scotland (SASA).
CSL collaborate with other UK and International collections. Evidence
of this is the current EU FP7 call, where CSL is a lead partner,
bidding for over £300,000 of funding to DNA bar-coding statutory
plant health pests & diseases.
21.8 Cefas collections are routinely exchanged
with other expert laboratories around the world. There are a number
of initiatives to provide wider access to this material including
working with industry to provide diagnostic kits for pathogens.
Access benthic invertebrate material is via the National Biology
Analytical Quality Control scheme which forms part of the UK Marine
Monitoring and Assessment Strategy.
21.9 Generally, because of high levels of
user engagement the initiatives mentioned in Q21 provide a good
fit with requirements for conservation management. UK-led initiatives
are closely aligned with international work. For example the National
Biodiversity Network provides the UK node of the Global Biodiversity
Information Facility.
SKILLS BASE
Q26. What are the numbers and ages of trained
taxonomists working in UK universities and other organisations?
What is the state of training and education in systematics and
taxonomy?
Q27. Are there any gaps in capacity
Q28. Is the number of taxonomists in post,
and those that are being trained, sufficient to meet current and
future needs across all taxonomic subject areas?
26.1 Defra can reply only with respect to
its own laboratories. CSL has a team with a range of expertise
and depth of knowledge on pests and diseases, which is unsurpassed
in the United Kingdom using morphology and taxonomy to state of
the art molecular techniques. This is also drawn upon to provide
advice to plant health consultants and researchers within Plant
Health Group and other Groups at CSL in addition to technical
advice directly to Defra. As recognised experts, diagnosticians
at all levels provide the key parts of the many PHSI training
courses organised throughout the year. In this team there are
approximately 12 trained taxonomists as follows:
— Nematology—2 specialists aged
50's and 20's
— Virology/phytoplasmas—2 specialists
aged 30's
— Mycology—3 specialists aged
30's
— Bacteriology—2 specialists
aged 40's
— Entomology—3 specialists aged
30's and 40's
26.2 At Cefas there are a large number of
taxonomic experts engaged for a small or large part of their time
in species identification as part of research and monitoring programmes.
This includes:
— 12 Viral, bacterial and parasite
experts
— 5 phytoplankton and 4 zooplankton
experts
— 2 meiofaunal, 8 benthic and 10 epifaunal
species experts
— 3 highly specialised experts and
a further 20 scientists involved in fish identification
26.3 Specialists at CSL and Cefas are also
engaged in policy advice and diagnostic service provision as well
as providing taxonomic services.
Annex 1
THE CENTRAL
SCIENCE LABORATORY
The Central Science Laboratory (CSL) is an executive
Agency established within the Department of Food and Rural Affairs
(Defra), formed from the amalgamation of 5 scientific laboratories
and completed in 1999.
The primary responsibilities of CSL are the
provision of quality scientific development, research and technical
support to public sector departments and agencies, and private
customers. The main focus for the scientific work is food safety,
agriculture, agrochemical safety, product development, safeguarding
the food supply, and environmental management, protection and
conservation.
The Plant Health Group of the CSL provides scientific
support to the Plant Health Division of Defra facilitating international
trade in plants and planting material and protecting the UK industry
and environment. The strong research base with international expertise
in diagnostics and quarantine pest and disease biology engenders
vital links with other organisations and academia both within
UK and internationally. The CSL is also the depository for the
national plant health reference collections; a unique and internationally
important collection of plant pests and pathogens.
CSL is the curator of several unique and internationally
important taxonomic collections which underpins systematic biology
and pest and disease identification services for Defra and other
customers. The core invertebrate collection contains over 135,000
specimens. In addition to the existing collections of plant and
food pests, including both insects, nematodes and mites, CSL is
also acquiring The Rothamsted Collection, consisting of over 14,000
plant-parasitic nematode specimens. This is one of the most extensive
and renowned collections of its type in the world. Combined, these
form one of the most comprehensive reference collections of plant
pests, found anywhere in Europe. CSL also holds internationally
significant collections of fungi, viruses, phytoplasmas and bacteria.
CSL is also the curator of the national Collection of Plant Pathogenic
bacteria (NCPPB)
As the UK's premier plant health laboratory,
this combined reference collection is indispensable; underpinning
the disease and invertebrate identification work at CSL and thus
providing vital support to the identification & diagnostic
work of Defra's Plant Health Division. This work underpins Defra's
policy for plant and bee heath. The collections are vital for
CSL to maintain its status as one of Europe's leading Plant Health
Laboratories and thus enabling it to remain as a prime candidate
for European reference Laboratory status in the future should
EU policy develop in this direction.
Specialists at CSL develop international status
as diagnosticians, with unique experience in the identification
of pests of worldwide origin. They are required to distinguish
pests from non-pests and to recognise those of quarantine significance.
We have experience in well-established taxonomic methods, such
as microscopical examination or culturing, but have also been
in the forefront of adapting and using new and innovative methods
and techniques to improve the comprehensive identification service.
Techniques must be robust and rapid as well as accurate, sensitive
and inexpensive.
Annex 2
CSL DETAILED RESPONSES
TO QS
15 & 16
Q15. What impact have developments in DNA
sequencing, genomics and other new technologies had on systematics
research?
DNA SEQUENCING:
Taxonomic collections are vital to existing
and future DNA sequencing R&D projects. For example, molecular
studies (such as DNA bar coding) rely on the accurate identification
of voucher specimens and their storage in properly curated collections,
such as those held at CSL. Hence in order for this new technology
to develop and be successful, strength must be maintained in traditional
taxonomic/morphological areas, running in parallel to the DNA-based
technologies. So indeed the organisations based placed to take
bar-coding forward are not simply those with molecular expertise,
but probably more importantly those with morphological expertise.
An excellent example of this is the current EU FP7 call, where
CSL is a lead partner, bidding for over £300,000 of funding
to DNA bar-coding statutory plant health pests & diseases.
This project will be underpinned by access to validated specimens,
deposited and maintained within the CSL invertebrate collections.
Again reiterating the importance of the collections.
DIGITAL REFERENCE
COLLECTIONS:
The use of morphological characteristics still
underpins the identification of many organisms of plant health
significance, including both the fungi and the invertebrates;
insects, mites and nematodes. However many species are extremely
hard to distinguish, as diagnostic morphological differences are
often small and/or hard to visualise. Even when such features
can be readily seen, it is important to be able to capture images
of these, for a variety of reasons. For example to provide a permanent
record associated with a particular identification for quality
assurance and legal purposes. Such reference images are also extremely
useful for training, data sharing with overseas collaborators
and also the cataloguing of information for reference purposes.
This latter area is becoming increasingly important
with the development of new molecular techniques, such as DNA
barcoding. This technology offers the potential for enhancing
phylogenetic and taxonomic investigation, through the production
of comprehensive, validated sequence databases. However, in order
to ensure the robustness of such DNA databases, the information
held in them must be correctly assigned to the taxonomic framework.
The best way to achieve this is to relate sequence information
to specific, individual specimens. Ideally, this should be a real
"voucher" specimen, but increased capability to archive
the specimen digitally, through both image analysis software linked
to either light- or electron microscopes, will contribute to both
the permanent record of the molecular sequence and the ability
of researchers at varying locations to access that information.
In this way "virtual" or "digital" reference
collections, containing high-quality images are an excellent complementary
resource to "real" reference collections, containing
actual preserved specimens.
Q16. In what way has systematics embraced
new technologies and how can these research areas interact successfully
and efficiently?
Our reference collections serve as routine "tools
of trade". However, as a result of our increasingly unique
responsibility in diagnosis and identification of alien organisms,
they are assuming a national and international importance. We
must continue to invest in curation of these to maintain and build
on this reputation. Traditional reference collection methodology
will be supplemented by more "portable" technologies
(digital images and molecular sequences etc.) to enable the international
use of these unique reference standards.
ADDITIONAL ISSUES
In addition to laboratories, which are the basic
requirement for taxonomic work, CSL has a scanning and transmission
electron microscopy suite, essential for examination of pest and
fungi characteristics and virus diagnosis respectively.
The quarantine glasshouse, laboratory, growth
rooms, cabinet facilities and quarantine pest facilities enable
contained longer-term examination and identification of both alien
and indigenous pests and diseases. State-of-the-art microscopy
laboratories, incorporating the latest developments in computer
enhancement, are used to improve the study of pests.
Our reference collections of alien pests and
disease organisms are an increasingly important national and international
resource and are managed by the pest and disease identification
team. Improved curation of our important Arthropod sub-collection
has led to the invitation to participate in the Insect Collections
Managers Group which represents the main entomological collections
in the UK (NHM, National Museums of Scotland and Wales). The National
Collection of Plant Pathogenic Bacteria maintained within the
Group is part of the UK National Culture Collection.
CSL has invested in unique molecular (DNA/RNA)
diagnostic and analytical facilities (Molecular Technology Unit
(MTU)), including real-time and conventional PCR[57],
genetic fingerprinting, sequencing and microarrays. This unique
facility is in the forefront of providing molecular diagnostic
and analytical services for both statutory and non-statutory samples
including those related to plant and bee health and participates
in R&D activities including method development, ring testing
and validation. Seedcorn funding has been used to develop an integrated
equipment booking system and other electronic management systems
to make efficiency improvements (eg electronic information systems).
February 2008
56 Review of Local Record Centres (2007), Natural England. Back
57
Polymerase Chain Reaction. Back
| 
