MGRFA Report - UK Genetic Resources for Food and Agriculture

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Oct 23, 2013 (3 years and 10 months ago)

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CABI

Bioscience

A division of CAB International





The
establishment of an inventory for Genetic
Resources for Food and Agriculture and scope a
GRFA information system: Microbial domain
full report


Project code:

GC0134

Contract Reference
: CSA6461



2

The
establishment of an inventory for Genetic Resources for
Food and Agriculture and scope a GRFA information
system: Microbial domain full report


Project code:

GC0134

Contract Reference
: CSA6461

Representatives of the Parties

The Secretary of State’s r
epresentative
: Mr Tony Poole

DEFRA, Room 303, Cromwell House, Dean Stanley Street, Westminster, London SW1P 3JH

The Contractor’s representative
: Dr David Smith

CABI Bioscience UK Centre (Egham), Bakeham Lane, Egham, Surrey TW20 9TY

Partners

Nigel Maxted a
nd Brian Ford
-
Lloyd,
School of Biosciences,
University of Birmingham,
Edgbaston,

Birmingham B15 2TT

John Woolliams, Roslin Institute (Edinburgh), Roslin, Midlothian EH25 9PS

Date of Commencement:

01 October 2003

Date of Completion:

31 March 2004

Total proj
ect costs:

£65000

Additional costs for extra contracted work at CABI:

£15350

Scientific Objectives and Primary Milestones

Objectives common to all GRFA domains

1.

Consult with relevant UK, regional and international stakeholders in each GRFA domain to
establi
sh the extent to which inventory information is currently available, the mechanisms for
access and how best the inventory could best meet their and the broader user communities needs.

2.

Assess to what extent data are currently electronically available and wh
at requires digitisation.

3.

Assessment of the work currently being carried out through other initiatives on the co
-
ordination
and access to biodiversity inventories and associated information.

4.

Create a model inventory and define the extent of the associated
information needed to facilitate its
use.

5.

Undertake ‘gap analysis’ of and report on taxonomic and genetic diversity for each GRFA domain
as a means of ensuring its more effective conservation and use.

6.

Seek input from the GRFA organism domain stakeholders o
n the design of an information system
and its content that would add value to the inventory and information currently available and that
would provide the services needed.

7.

Design a model structure for the portal for the GFRA community.

8.

Report on the feasib
ility, provide recommendations for the next steps to realise the inventory and
information portal and provide, if applicable, an associated business plan.


Microorganisms Genetic Resources for Food and Agriculture (MGRFA) specific objectives

M1.

Defining

the scope of the microorganisms (strains, pathovars, serotypes) and their replicable parts
that should be included.

M2.

Determine how existing databases of strains can be mined through the GRFA portal for relevant
strains only

M3.

Determine how the Nati
onal Collection Network (UK National Culture Collection) can link to the
many specialist collections containing MGRFA giving access to their collection content.

M4.

Gap analysis for MGRFA in the UK


Primary Milestones

1.

Draft content of a UK GRFA inventory f
or consideration by DEFRA project officer

2.

Model inventory of UK GRFA

3.

Description of a UK GRFA Information System, its infrastructure and content

4.

Recommendation for the realisation of an inventory and information system for UK GRFA



3

Report on the Microbial
Genetic Resources Domain


Accronyms


ABCD

-

Access to Biological Collection Data

AGRFA

-

Animal Genetic Resources for Food and Agriculture

BCCM

-

Belgian Co
-
ordinated Culture Collections

BIOCASE

-

Biological Collection Access Service for Europe

BMS

-

B
ritish Mycological Society

BRC

-

Biological Resource Centre

CABI

-

CAB International

CABRI

-

Common Access to Biological Resources and Information

CBD

-

Convention on Biological Diversity

DAD
-
IS

-

Domestic Animal Database Information System

DEFRA

-

Department for Environment, Food and Rural Affairs

DDA

-

Disability Discrimination Act 1995

EBRCN

-

European Biological Resource Centre Network

ECAT

-

Electronic Catalogue of names

ECCO

-

European Culture Collection Organisation

ECP/GR

-

The European
Cooperative Programme for Crop Genetic Resources Networks

FAO

-

Food and Agriculture Organization

EUCARPIA

-

Genebank Committee of the European Association for Research on Plant Breeding

GBRCN

-

Global Biological Resource Centre Network

GRIN

-

Germpla
sm Resources Information Network

GSPC

-

Global Strategy for Plant Conservation

HRI

-

Horticulture Research International

IMI

-

Imperial Mycological Institute

MGRFA

-

Microorganism Genetic Resources for Food and Agriculture

PGRFA

-

Plant Genetic Resour
ces for Food and Agriculture

GBIF


Global Biodiversity Information Facility

GRFA

-

Genetic Resources for Food and Agriculture

IPGRI

-

International Plant Genetic Resources Institute

ISBER

-


International Society for Environmental and Biological Reposi
tories

NGRP


National Genetic Resources Program

OECD

-

Organisation for Economic Co
-
operation and Development

SfAM

-

Society for Applied Microbiology

SGM

-

Society for General Microbiology

TF

-

Task Force

UKFCC

-

United Kingdom Federation for Cult
ure Collections

UKNCC

-

United Kingdom National Culture Collection

UN

-

United Nations

UNDP

-

United Nations Development Programme

WDCM

-

World Data Centre for Microorganisms

WFCC

-

World Federation for Culture Collections



4

Executive Summary

Objecti
ves

The objectives were to develop an inventory, scope an information system and recommend the next
steps in providing support information in the conservation and utilisation of Genetic Resources for
Food and Agriculture.

Main findings

Analysis of the cata
logued data from the UK National Culture Collections (UKNCC), the UK
Federation for Culture Collections, microbial scientific societies and the survey of microbial collections
enabled the categorisation of over 640 species as microbial GRFA. Over 1600 stra
ins held in the UK
national collections are of direct relevance as GRFA. The 66 collections surveyed had over 525000
strains all told but only around 100000 of these were available electronically over the Internet. Several
collections did not wish to publ
icise their holdings.

The current GRFA inventory is not complete and the survey carried out is a snapshot of current
conservation activities. Most of the 643 microbial species have representatives that are cryopreserved.
However, the details of storage o
f the living material (<100000 strains) are not fully available. The UK
National Collections (UKNCC) use freeze
-
drying and cryopreservation for the long
-
term storage of
their biological materials. The Horticulture Research International collection of edi
ble mushrooms too
have their
c.
3000 strains cryopreserved in or above liquid nitrogen but this it not normally the case for
other collections. Although the majority of the microbial GRFA species are represented in
ex situ

collections there are still 79 sp
ecies to preserve and over 100 to cryopreserve.

As a result of the consultations with MGRFA stakeholders the following information portal
specifications were drawn together by CABI Publishing Division.

Core Content



the GRFA inventory, fully searchable, wit
h onward links



relevant news items



links to relevant full
-
text publications from the scientific literature and elsewhere



links to providers of relevant training and consultancy services



selected content from CABI Publishing's information products



links to
related CABI Bioscience databases, such as the Dictionary of the Fungi, Index
Fungorum and the Genetic Resource Collection

Background Information



objectives of the GRFA portal



details of the key stakeholders, with links to their websites



statements relatin
g to the inventory and how to contribute to it



legal statements, such as a privacy policy, copyright issues and contact information

Supporting Facilities and Services



e
-
mail newsletter and discussion group(s)



feedback section for visitors to suggest improv
ements or additions



simple site search facility (as opposed to the inventory search)



restricted access area for key stakeholders and contributors

Main implications of the findings for policy and future scientific research

Recommended actions to follow this

study



A mechanism should be established to update the inventory



An associated information portal/system should be established as specified



Cryopreservation research on Genetic Resources for Food and Agriculture should be drawn
together under the auspices
of DEFRA’s GRFA Framework. Research is needed to develop

5

protocols for preservation recalcitrant fungi and post preservation stability testing at the molecular
level.



A strategy to ensure GRFA is backed
-
up as cryopreserved germplasm in
ex situ

collections
is
needed. Again this could fall under DEFRA’s GRFA Framework.



Mechanisms for the transfer of cryopreservation technology between GRFA domains should be
established.


The
establishment of an inventory for Genetic Resources for
Food and Agriculture and scop
e a GRFA information
system: The Microbial Domain


The inventory and assessment of the UK’s Genetic Resources for Food and
Agriculture (GRFA), funded by the Department of the Environment, Food and Rural
Affairs (DEFRA), was undertaken as partial fulfilment

of the UK’s commitment to
international biodiversity and genetic resources conservation agreements, including
the Convention on Biological Diversity (CBD), the Global Strategy for Plant
Conservation (GSPC) and the International Treaty on Plant Genetic Res
ources for
Food and Agriculture. DEFRA drew together a Framework for GRFA and as part of
the further development commissioned this study. Formally a strategic approach to
the conservation and sustainable use of the UK’s animal, plant and microbial genetic

resources for agriculture and food was being hampered by a lack of baseline
information on this important UK resource. Therefore, the general objective of the
UK National Inventory of Genetic Resources for Food and Agriculture was to:

Produce a common i
nventory for the UK’s animal, plant and
microbial genetic resources for agriculture and food, in consultation
with various stakeholders and which meets the needs of GR
stakeholders and the broader user communities. Further, it will
provide a GR review of
what data are currently available
electronically and permit preliminary gap
-
analysis and assessment of
taxonomic and genetic diversity.

This report encompasses the microbial genetic resources element of the UK GRFA
inventory and assessment, the inventory
and assessment of UK animal and plant
genetic resources will be reported on in complementary reports by Woolliams (2004)
and Maxted (2004).


1. Consult with relevant UK, regional and international stakeholders in each
GRFA domain to establish the extent
to which inventory information is currently
available, the mechanisms for access and how best the inventory could best meet
their and the broader user communities needs.


Internet searches and discussions with key players in microbial genetic resources
det
ermined what lists of UK GRFA were available. These actions were carried out
independently for the three domains (animal, plant and microorganisms) and drawn
together in a project meeting held in Birmingham on 19
th

January 2004. At this
meeting it was ag
reed to continue to establish the inventories as separate tasks for
them to be brought together on the DEFRA website. DEFRA had already compiled
information on Genetic Resources for Food and Agriculture (GRFA) available at
http://www.defra.gov.uk/farm/geneticresources/index.htm
. Reports available had
identified some relevant experts and their networks in the microbial domain. Using

6

this and domain specific information as background info
rmation was collated and
input and advice sought from microbiological networks. The information was
gathered through a combination of interviews, telephone consultations and attendance
of meetings. In addition, collection holders, information providers and

resource users
were also consulted.


The key organisations consulted were:

International


European Culture Collection Organisation (ECCO)

Global Biodiversity Information Facility (GBIF)

OECD Biological Resource Centre Initiative Task Force

World Federatio
n for Culture Collections (WFCC)

International Society for Environmental and Biological Repositories (ISBER)


UK

DEFRA

British Mycological Society (BMS)

Society for General Microbiology (SGM)

Society for Applied Microbiology (SfAM)

UK Federation for Cultur
e Collections (UKFCC)

UK National Culture Collection (UKNCC)


As a result of the consultations and searches an initial inventory was compiled from
the data sources identified.

UKNCC databases




10 collections

UKFCC Survey




45 Collections

BIOCASE UK Lis
t of Collections


672 collections

British Mycological Society (BMS)


c.
2000 members

Mycology Directory




167 Organisations

Society for General Microbiology


c.
5000 members

Society for Applied Microbiology (SfAM)

c.
2000 members


Of the above 66 Collections

were identified as relevant holding
525650
strains/specimens of which over 165000 were living specimens.


Information was very difficult to get from the collections. Initial contact was made
with the 66 collections of which 38 provided a small amount of
information and
agreed to receive a questionnaire. Few contacts wished to spend time on the telephone
complaining that they had gone through several exercises such as this e.g. organised
by European projects such as BioCASE and the UK Government, OST and D
EFRA
without much effect. In the first cycle of distribution and telephone contact only 4
from 66 questionnaires were returned. A second round of telephone contacts was
made and the remaining 34 were reminded, in all 10 responded with the full
information

requested, a 26.5% return (appendix 1). This information added to that
gathered from the UK Federation for Culture Collections (UKFCC) survey and that
directly held by CABI through the UK National Culture Collection (UKNCC)
secretariat.



7

Direct contact at

society and group meetings was restricted in the time
-
frame as it was
not always possible to attend annual or biannual meetings as they did not fall in the
period of the project. The meetings were often arranged months, if not years in
advance so it was
not possible to change agenda. However, direct contact was made
with representatives of several societies (listed above) getting feedback on collection
holdings, definition of microbial GRFA and the information system. The internet
searches enabled acces
s to a few databases (11 in all) and only a few collections were
willing to give up their data even on a confidential basis. Eight of the collections did
not publish catalogues. The key internet resources utilised in the survey are listed in
Appendix 4.


The 10 respondents indicated that they held over 30000 strains of which they made
just under half available to the public and identified 170 used directly as food, 3823 of
use in agriculture and a further 4122 used indirectly in food production or as provi
ders
of food ingredients (appendix 1). Thus the survey added significantly to information
we had obtained directly through the UKNCC secretariat and provided by the UKFCC
survey.


It was clear that all contacted through this exercise had their own interpr
etation of
which microorganisms should be included as GRFA (see microorganism domain
milestone M1 below). It was agreed at the project meeting in January 2004 that it was
all organisms used for food and agriculture and should exclude organisms that had
im
pact such as farm animal ruminant organisms and plant or crop pathogens. Those
included in the current inventory are those used directly as food, such as the edible
mushrooms, food starter cultures, meat substitutes, those used indirectly such as
cheese r
ipeners, fermented product producers, those providing food additives and
those used directly in agriculture such as in silage or biocontrol agents. This enabled
an initial focus, not one collection had attempted to list their holdings under the
category of

GRFA.


Database production and digitisation of data (project extension study)

CABI was additionally contracted to produce databases of microbial collection
information for those respondents that did not make their data available electronically
or over the

Internet. As a result CABI has created 5 catalogue databases in addition to
creating a strain database for the MGRFA content of the UKNCC collections.
Catalogue tables are presented in the GRFA database presented electronically with
this report. Collect
ion data from the Don Whittley bacteria collection; the bacteria and
yeasts of the Horticulture Plant Breeding Station; the wood biodegraders of the
National Collection of Wood Rotting Fungi, now absorbed into the CABI collection;
the species names of basi
diomycetes held at the Royal Botanical Gardens, Kew. This
will facilitate access to information and biological resources of these MGRFA
collections (total of 10538 strains).


International feedback

In addition to exploring these issues in the UK internati
onal organisations were
consulted. The European Culture Collection Organisation (ECCO) and the World
Federation for Culture Collections (WFCC) were directly approached and an Internet
search was conducted to gather information on initiatives in GRFA classi
fication and
provision globally. A number of relevant biodiversity initiatives were identified.



8

Japan: Ministry of Agriculture, Forestry and Fisheries Genebank

http://www.gene.affrc.go.jp/index.html


This initiative brings together collections of all agriculturally important organisms. A
single point of contact is provided for all GRFA held by the collections that fall under
the Japanese Ministry of Agriculture Fisheries and Food including all three
domains,
Plant, Animal, Microorganism and it includes access to a DNA bank. Requests for
access are co
-
ordinated to the different collections throughout Japan through this one
centre. However, little attempt had been made to separate GRFA from other
micr
oorganisms e.g. the plant and animal pathogens or the soil inhabiting organisms.


USA: National Genetic Resources Program (NGRP)

http://www.ars
-
grin.gov/


In 1990, the U.S. Congress authorised the establishment of

a National Genetic
Resources Program (NGRP). It is the NGRP's responsibility to acquire, characterise,
preserve, document and distribute to scientists, germplasm of all life forms important
for food and agricultural production.


The Germplasm Resources I
nformation Network (GRIN) web server provides
germplasm information about plants, animals, microbes and invertebrates. This
program is within the U.S. Department of Agriculture's Agricultural Research
Service. The web server provides links to individual cu
lture collections but again no
attempt is made to categorise the microorganisms into their utility and microbial
GRFA are not indicated.


EU: The European Cooperative Programme for Crop Genetic Resources Networks

http://www.ecpgr.cgiar.org/Introduction/AboutECPGR.htm


The European Cooperative Programme for Crop Genetic Resources Networks
(ECP/GR) was founded in 1980 on the basis of the recommendations of the United
Nations Development
Programme (UNDP), the Food and Agriculture Organization of
the United Nations (FAO) and the Genebank Committee of the European Association
for Research on Plant Breeding (EUCARPIA). ECP/GR is a collaborative
Programme among most European countries, aimed
at facilitating the long
-
term
conservation on a co
-
operative basis and the increased utilisation of plant genetic
resources in Europe. The Programme is co
-
ordinated by a Secretariat at the
International Plant Genetic Resources Institute (IPGRI).

This initi
ative
sponsors/provides access to databases on individual crops. However it refers
only
to
plant resources.


FAO (UN): Interdepartmental Working Group on Biological Diversity for Food
and Agriculture

http://www.fao.org/biodiversity/index.asp


Genetic resources section is divided intro Crops, Domestic animals, Aquatic and
Forests. The crops section is limited to FAO reports and links. Domestic animals
section has a searchable database, DAD
-
IS.
http://dad.fao.org/en/Home.htm



9

DAD
-
IS is the key communication and information tool for implementing the Global
Strategy for the Management of Farm Animal Genetic Resources. It is being
developed first to assist c
ountries and country networks, and also serves as the virtual
structure for the Strategy. It will increasingly provide extensive searchable databases,
tools, guidelines, a library, links and contacts. The service also provides
comprehensive list on documen
ts and papers on animal genetic resources.


Although there were many sources of microorganisms on the Internet it was rare that
the sites linked the microbial domain to plants and animals. In most cases the
information was provided on separate sites. Germa
ny and the Netherlands had sites
for GRFA but the microorganisms were not categorised i.e. the links were usually to
the national collection databases which did not distinguish GRFA from the other
organisms they hold. Overall, the need for better managem
ent, preservation and
cataloguing of GRFA seems to be increasingly recognised around the world, however
GRFA oriented activities, as opposed to general conservation and endangered species
work seems to be limited to the projects listed above. As a result n
o assistance in
determination of a definition of which microrganisms were GRFA and how data was
presented was evident.


Survey feedback indicated that the microorganism inventory should be kept simple.
Other projects were developing mechanisms to access d
ata across the Internet such as
the Global Biodiversity Information Facility and the Organisation for Economic Co
-
operation and Development (OECD) Biological Resource Centre (BRC) initiative and
the EU project, BioCASE. To create a high quality and authen
tic inventory, tools to
ensure data quality are needed and these projects are developing them. It was
considered inappropriate to duplicate the production of such tools but to take
advantage of them. For example the GBIF Electronic Catalogue of Names of
Known
Species (ECAT) which is being developed as the world standard for organism names.
Simply by keeping the inventory organism list up to date the names list can be used to
search GBIF or the OECD Global BRC Network (GBRCN) to provide the links to
sourc
es of information and biological resources through links between common
names, scientific names and synonyms. The inventory contains the current name by
which the organism is known, the collections and/or database URL where further
information can be found

and the use or relevance to GRFA. The Inventory includes
contact details under each entry to ensure users can obtain further information.


As part of the consultation process stakeholders were asked how they would use the
inventory and what associated i
nformation would be required to add value. The key
uses were considered to be:



To find out what microorganisms and strains of organisms were
available



Where to find these organisms



Description



Further information on uses and properties



How to identify micr
oorganisms



What services were available to help characterise strains and select
them for use



Interactions with other organisms



Conservation status



Image based and interactive identification keys


10


It was clearly a simple process to provide some of this info
rmation using the species
names as an entry point to the inventory. It also made the system less onerous to
maintain if links were made to original data and updates carried out by the database
owners and not at the inventory level. The inventory has been
constructed in
association with a list of synonyms and common names so that enquirers will find an
entry (indirectly) even if they use an old name or synonym.


The inventory and information resource will support several UK obligations and
initiatives.



T
he Convention on Biological Diversity
: The inventory provides a list of
microorganisms used in sustainable agriculture and food production and enables
links to made between
in situ

information and
ex situ

programmes, aiding their
conservation and improving

access for their sustainable use.



The International Treaty on Plant Genetic Resources for Food and Agriculture
: In
addition to the plant domain work the microbial inventory covers the fungi still
encompassed by the plant world and enables reference to be
made to conservation
and access to this genetic resource domain.



European Plant Conservation Strategy
: As above the inventory provides
information on the conservation of fungi.



European Cooperative Programme on Plant Genetic Resources
: as above



DEFRA objec
tives
: including protecting the rural environment, promoting
sustainable rural economies, promoting sustainable and adaptable farming,
promoting sustainable management of natural resources and ensuring high
standards of farm animal health and welfare. In p
articular the inventory enables
DEFRA to provide information on GRFA, their use and access. Additionally, an
information system would provide much more relevant information to support
DEFRA programmes and provide information to its many enquirers.


Recomm
endations:



A mechanism should be established to update the inventory on a regular basis



An associated information portal/system should be established to provide the
additional information requested by survey respondents


2. Assess to what extent data are
currently electronically available and what
requires digitisation

The survey confirmed that to a great extent information specifically on GRFA is not
available as electronic lists or as databases available across the Internet. Only data
from the public se
rvice collections, which hold some 100000 strains of
microorganisms was readily available. However, this data was not packaged in a way
that GRFA could be easily identified. Careful analysis of the catalogued data enabled
the categorisation of over 630 sp
ecies as microbial GRFA with over 1600 strains held
in the UK national collections (appendix 2), 3000 strains of edible mushrooms held by
Horticulture Research International (HRI) and this can be used to link to the available
databases. Over 525 000 speci
mens or strains are held leaving around 400000 items
to be digitised. In some instances such as at CABI and Kew Gardens initiatives are
being pursued to try and digitise a large proportion of this but as always this is subject
to funding being available.



11

As a result of the extension to this contract a further 10500 strains are now available
electronically. To support the 643 microbial species in the inventory there is data
provided on 12138 strains in an annexed electronic database in Microsoft Access.


Recommendations for future work

Work with the Global Biodiversity Information Facility (GBIF) to ensure mechanisms
are in place for data access and that co
-
ordinated programmes are in place to digitise
the UK’s biodiversity data inclusive of that consider
ed to be GRFA.


3.

Assessment of the work currently being carried out through other initiatives
on the co
-
ordination and access to biodiversity inventories and associated
information

There are a number of existing initiatives that have the intention to pr
ovide access to
biodiversity information on the Internet. The goals and activities of these initiatives
were examined. It was clear that there could be duplication of effort if the Defra
inventory and another information portal were to develop in paralle
l without
consultation. However, it was evident for the microorganisms that no effort had been
made to define what microbial GRFA were. The initiatives were addressing
biodiversity as a whole and split activities by domain, animals, plants and
microorgan
isms. It was evident that the initial work of the scoping study, to create an
inventory of GRFA did not overlap with other activities in the identified initiatives
but in terms of the information portal there were several areas of potential duplication
of

effort. The key conclusion from this analysis was that other initiatives would not
present GRFA separately therefore a distinct GRFA portal was needed. However, the
tools and data links being developed for example, by the Global Biodiversity
Information

Facility (GBIF) could be used. Almost all of the UK collections holding
microbial GRFA were identified by BIOCASE and the two key collections of fungi in
the UK, CABI and Kew Gardens were already linked through GBIF.

The overlapping initiatives examined
were:



Global Biodiversity Information Facility (GBIF) which is developing the tools to
access biodiversity data across the web. A meeting of the World Federation for
Culture Collections (WFCC) and GBIF was held in Brussels in November 2003.
This meeting e
nabled a collaboration to be established with GBIF through the
Belgian Co
-
ordinated Culture Collections (BCCM). The ability to access
microbial data using the GBIF data mapping schema, Access to Biological
Collection Data (ABCD) was explored. The schema
was developed to enable
enquiries on data to be channelled to the correct data fields in databases at multi
-
locations across the internet. As a result the CABI microbial data has been made
available via the GBIF Gateway. This can easily be achieved with a
ll microbial
collections that have a public database accessible on the web. The GBIF
requirements are for all holdings of collections so the GBIF gateway currently
does not highlight GRFA. However the same technologies could be used to
specifically targe
t GRFA.



BIOCASE


UK node of a European Project to provide access to biological
collections. This is a metadatabase and gives descriptions of collections and their
content. The extent to which data is segregated depends upon how each
individual collectio
n categorises its data. Although this database is extremely
helpful in locating collections it does not specifically help target GRFA.



OECD Biological Resource Centre (BRC) Initiative which aims to set up a Global
System for BRCs. This initiative is in
its early stages but will be piloting a virtual

12

BRC over the next two years. It will eventually link biological databases world
wide and it is currently investigating, amongst other options, using GBIF
technology. Again there was not an immediate overlap

hjere but certainly in the
future it would be worth looking at a GRFA gateway to this potentially vast
source of
ex situ

collection data.



4.

Create the inventory

The inventories for each domain were created using the information gathered from
objectives

1 to 3 above. The domain specific inventories were established
independently but it is recommended that they are to be placed together on one web
page on the DEFRA web site. The inventories from the 3 domains (based upon the
data available at this time) w
ith their defined structures are provided as the’ central
deliverable of the project. The inventory is presented in two forms as a Microsoft
Access database on CD and as web pages with URL linkages to the original data
sources. The inventory is ready for

loading onto the DEFRA web site and is being
tested on the UKNCC server to test updating and operating mechanisms. It is also
provide as appendix 2 to this report.


5. Undertake ‘gap analysis’ of and report on taxonomic and genetic diversity for
each GRFA

domain as a means of ensuring its more effective conservation and
use.


It was evident that not all UK GRFA is adequately backed up by
ex situ

conservation
and it is recommended that a programme to cryogenically preserve material to bridge
the gaps. The c
urrent GRFA inventory is not complete and the survey carried out is a
snapshot of current conservation activities. Most of the 643 species have
representatives that are cryopreserved. However, the details of storage of the living
material (<100000 strain
s) are not fully available. All UK National Collections of
microorganisms use freeze
-
drying and/or cryopreservation for the long
-
term storage
of their biological materials. HRI too have their edible fungi
c.
3000 strains
cryopreserved in or above liquid n
itrogen but this it not normally the case for other
collections.


Additionally one representative of a species is inadequate. The intra
-
specific
variation necessitates large numbers of examples for some species that are more
variable. It is apparent tha
t some examples of a species will have a property when
others don’t. It is therefore essential that more than one example of a species be
maintained. On average 71 strains are held for every species of microorgansim by the
collections of the World Data C
entre for Microorganisms. This may be excessive for
some species and is more a factor of the utility of the organisms where samples are
duplicated in different countries to make them more readily accessible. It is
recommended that at least 10 representat
ives must be stored to reflect variation within
a species and to date this is far from the case in excess of 50% of species are
represented by one isolate only.


The taxonomic relatives of the identified MGRFA must also be taken into account as
these may a
lso be harnessed for use. Including a taxonomic hierarchy
-
interrogating
tool that could be used via the information portal to give access to these resources
could provide this additional information. The number of edible fungi relatives
reflects this. Al
though there are 29 species regularly cultivated commercially only 6

13

are produced on an industrial scale. Members of the British Mycological Society
indicate 59 species that they would eat. In total there are approximately 95 species
commonly eaten belon
ging to 57 genera. However, there are 4009 known species in
these genera, 3952 related species that are not cultivated to eat.


Recommendation

Link the inventory to a taxonomic hierarchy that enables the user to trace taxonomic
relatives of those organism
s already used as GRFA.


6.

Seek input from the GRFA organism domain stakeholders on the design of an
information system and its content that would add value to the inventory and
information currently available and that would provide the services needed


F
eedback from those consulted indicated that access to current and validated
information was of prime importance. Initially what was required was a simple list of
what was of relevance to GRFA, where it was, what it was being used for, access to
informatio
n on properties, use and availability. The inventory would provide this. It
was considered that the creation of an information system must provide defined
benefits. To be of value it should be up to date and maintained. It should provide easy
access to a
vailable information and provide a means to answer specific enquiries.
There was some interest in getting access to information generated from new
technologies, genomics, proteomics and metabolomics. It must also be authoritative,
operate to high standards
, offering validated information.


Utilising the information gathered under objective 4 and 6 CABI Publishing designed
a specification that would provide support to the GRFA community. This is presented
in appendix 3. The information system would provide
support for the users of GRFA
in the following areas:




Thesaurus


definitions of terminology used in the field



Related publications



Identification, consultancy and germplasm provision



Training opportunities



Legislative requirements



Collaborative opportuni
ties



Discussion groups



A solution provider


7. Design a model structure for the portal for the GFRA community

Based upon the information gathered under objectives 4 and 6 a specification for a
portal infrastructure with appropriate content and links is des
cribed, taking into
account state
-
of
-
the
-
art search technology, metadata standards, interoperability and
user friendly presentation, including the need for compliance with the Disability
Discrimination Act 1995 (DDA). See appendix 3


Recommendation

Call f
or bids to establish the prescribed information system on the DEFRA web site to
support the GRFA community



14

8.

Report on the feasibility, provide recommendations for the next steps to realise
the inventory and information portal and provide, if applicable,

an associated
business plan


The GRFA inventory has been an output of this project and needs to be made
available via the DEFRA web site. It will require regular update and some further
research to add to it. Much of this can be done via the Web pages t
hemselves inviting
visitors to contribute further to the list or to provide updates on where the information
can be found. It is not recommended that this data be directly added to the inventory
but a small editing board should review the supplied informa
tion and be responsible
for adding the data.


A specification for an associated GRFA information system has been provided. It is
recommended that such a system is adopted to add value to the inventory and to
provide the GRFA community with the informatio
n they require. This will also enable
DEFRA to put together a strategy to protect and conserve the UK GRFA within its
publish framework in this area.


Recommendation

Place the three inventories on the DEFRA web site for access via a single page.


Microorga
nisms Genetic Resources for Food and Agriculture (MGRFA) specific
objectives


M1.

Defining the scope of the microorganisms (strains, pathovars, serotypes)
and their replicable parts that should be included

There are many microorganisms that have direct im
pact on food production and
agriculture and cannot be ignored by an information system on GRFA. However, the
inventory must only include those microorganisms that are utilised directly as food, in
food manufacturing processes and in agriculture, for exampl
e those necessary for
plant growth and health. The organisms that have impact on GRFA and that are
therefore relevant to the study should be indicated via the GRFA information system.
The following categories were considered relevant:


Direct use as food

E
dible mushrooms (cultivated and those collected for consumption from the
wild) (3000 HRI)


Starter cultures


Nutriceuticals


Single cell protein


meat substitutes




Use in Agriculture


Biocontrol agents

Fixation of atmospheric nitrogen Decomposition of
organic wastes and
residues

Suppression of soil
-
borne pathogens (Competitors)

Recycling and increased availability of plant nutrients

Degradation of toxicants including pesticides

Production of antibiotics and other bioactive compounds

Production of si
mple organic molecules for plant uptake


15

Complexation of heavy metals to limit plant uptake

Solubilization of insoluble nutrient sources

Production of polysaccharides to improve soil aggregation


Indirect use as food i.e. food production or ingredients
in food products


e.g Cheese ripeners


Brewers


Fermentation products



Soy sauce; Bread beverages; Yeast extract


Algae in larva bread

Organic acids and enzymes for food processing or as ingredients; food
colourings

UKNCC collections hold 140 food strains


The following organisms and information concerning them were considered best
suited to be associated information for the GRFA information portal


Pathogens of animal, plant and microbial GRFA (1587 strains in the
UKNCC)


Soil health


microbial consorti
a (325 biodeteriorgens in the UKNCC; 637
Biodegraders)


Food safety


pathogens and poisoners of man associated with AGRFA,
PGRFA and MGRFA

Food spoilage (184 in the UKNCC)


Animal feeds (direct or upgrading agricultural wastes)


silage (637
Biodegraders
in UKNCC)


Animal Health
-

Ruminant organisms (150 UKFCC)


Plant health (nitrogen fixers


31 genera, 57 species, 64 strains; mycorrizal


500 UKFCC)



Links to
in situ

sources for microorganisms were considered more appropriate to be
left to the observati
on databases of the BMS for the fungi and to GBIF for bacteria
and other groups of microorganism. These links can be provided via the GRFA
information portal.


M2.

Determine how existing databases of strains can be mined through the
GRFA portal for relev
ant strains only

It is recommended that the inventory GRFA names list should be the key search
parameter to identify the items that should be recognised as GRFA and give access to
relevant information. To ensure that all relevant organisms are captured an
d access to
strain data is facilitated the fungal names list and the approved list of bacteria names
must be used. Although taxonomic hierarchy could be used as a mechanism for
expanding the search results to include relatives that may be of interest to t
he user this
should be part of the associated information system. It is not appropriate to add
organisms to an inventory by association (evolutionary relationship). An example of
a supporting information system is given in appendix 3 which takes into acc
ount how
the existing internet community address such access problems. It is also
recommended that little data should be stored and maintained centrally thus reducing
maintenance and update responsibilities for the GRFA web site. A periodic search
using
inventory names can be used to update and monitor changes in sources of
MGRFA. Feedback on inventory content can be used as a mechanism to update and

16

identify gaps. The GBIF/WFCC workshop held on October 27
-
28, 2003, "Towards a
Global Infrastructure for M
icrobial Information" in Brussels was attended. It is
evident that GRFA is a specific section of the data they will cover and it would be
appropriate for the GRFA community to be able to target the parts of the data in this
global initiative that they are

interested in. Using the inventory as a search parameter
will enable this to happen.

Parallel initiatives to link general genetic resource content should be taken advantage
of. The World federation for Culture Collections (WFCC) database, the World data

centre for Microorganisms (WDCM) can be used initially, the european electronic
catalogue, Common Access to Biological Resources and Information (CABRI) at
http://www.cabri.org

and eventually the OECD BRC initiative wil
l provide access to
validated high quality data. None of these will highlight GRFA and it will be the
function of the GRFA inventory to access the detailed strain data for the GRFA
subset.


M3.

Determine how the National Collection Network (UK National C
ulture
Collection) can link to the many specialist collections containing MGRFA giving
access to their collection content


The catalogues of the National microbial collections are available on the web either
directly at the collections themselves or throug
h the UK National Culture Collection
web site (http://www.ukncc.co.uk). It was an objective of this study to contact several
of the many collections that are not part of this national network that hold GRFA.
This was done see General Objective 1 above. Ve
ry few of the collections had
information available electronically and they didn’t wish to change this. As an
additional piece of work CABI has digitised the information that the respondent
collections were willing to provide (a database with tables contai
ning 10538
additional strains is provided as an access file separate to this report).


Only a small number of UK microbial collections are able to supply germplasm on a
regular basis. Investment is required to create a network of UK collections beyond
the

UKNCC. If the UK wishes to make available the products of its publicly funded
research, a co
-
ordinated approach to their deposition in publicly accessible collections
is necessary. Reserving part of the research programme funding to facilitate the
ex
si
tu

conservation is a recommended approach. Only when collections are adequately
funded will such resources be properly maintained and made available for further
research. This does not solely rest on core funding but can eventually be supported by
return
on the exploitation of genetic resources if the correct mechanisms are initiated.

Policy for the Conservation and Sustainable Use of e
x situ

Genetic Resources in
UK Biological Resource Centres

Genetic resources (GR) are an important resource for both the U
K and other
countries, and hold potential benefits for farmers, industry and the public at large.
Animals, plants and micro
-
organisms may contain useful genetic traits that can be
identified and used in many ways including breeding programmes aimed at mee
ting
the challenges of new diseases, environmental pressures or changing consumer
demands. They also support scientific research. Some genetic resources should be
conserved for cultural reasons, as part of our heritage. This scoping study emphasises
the
major problems in accessing and bridging gaps in the
ex situ

holdings of UK
genetic resources. There is a need to move away from the
ad hoc

way in which this is

17

currently done and supported. It is necessary to co
-
ordinate the conservation and
sustainable u
se of, and facilitated access to, animal, plant and microbial genetic
resources, to support biotechnology, bioscience industry, education, sustainable
agriculture and horticulture, and to support related environmental improvements, rural
development, scien
tific research and conservation of heritage and biodiversity, now
and in the future. This requires:



A plan to conserve and sustainably utilise the UK's genetic resources



Joint programmes of
in situ

and
ex situ

conservation



Framework for co
-
ordinated resear
ch, knowledge development and gap
analysis



A better understanding on the genetic resource needs of other sectors (Genetic
Resources for Food and Agriculture [GRFA] being addressed) industry,
education, research etc



Priority list of actions to protect and u
tilise the UK's biological resources

Suggested Policy

1.

Co
-
ordinate activities and improved co
-
operation

A large number of bodies exist that independently carry out activities relevant to the
ex situ conservation and understanding of GR and seek co
-
operation

between
stakeholders (Annexe 1). There is a requirement to work with these bodies to help
improve co
-
operation between stakeholders within and between the plant, animal and
microbial sectors. UK Government Departments have disparate responsibility and
g
oals for the different sectors of GR. In consultation with stakeholders the
UK
Government
will set a comprehensive strategy for conservation and utilisation of UK
GR to avoid duplication and the ad hoc approach to managing the UK GR.

To achieve this there

is a need for a co
-
ordinating body for the
ex situ

conservation
and utilisation of GR.

2.

Facilitate sharing of information on GR

A wide range of stakeholders, including
collection holders
,
researchers
,
nature
conservation organisations

and
NGOs
, hold inform
ation on GR and make it
available to others through a range of databases. It is their responsibility to maintain
and up
-
date such databases.
UK Government

will seek to add value to this, and
work with GBIF and the OECD Biological Resource Centre Initiati
ve through which
all such information on GR can be accessed by stakeholders in the UK and overseas.

3.

Compile a National Inventory of GR

There is not a full inventory of UK genetic resources available. There is a need to
develop such an inventory, which wil
l be as complete as possible, covering both
in
situ

and
ex situ

GR, and publish it on the web. The inventory should be dynamic and
up
-
dated from time to time. Input will be required from a wide range of stakeholders,
including
other government agencies
,
researchers
,
collection holders

and
NGOs
.
Collaboration with
GBIF

through the UK
National Biodiversity Institute

will be
necessary.


18

4.

Support conservation of
ex situ

GR

Conservation of
ex situ

GR is currently the responsibility of
research councils
,
collecti
on holders

and
researchers
.
UK Government
will seek to assist these actors
through co
-
ordination and funding to enable them to meet their conservation roles. In
addition, and in consultation with stakeholders,
UK Government

will identify key
collections
whose development may benefit from
UK Government

support.
Ex situ

conservation of GR should be complimentary to
in situ

conservation and a plan to
achieve GR security through a gap analysis will be established.

5.

Support conservation of
in situ

GR

In situ

c
onservation of GR is largely the responsibility of
farmers
,
breed societies
,
nature conservation bodies

and
NGO
s. The UK Biodiversity Action Plan is
managed by the
UK Biodiversity Partnership

and is heavily biased toward
in situ

conservation. This is refle
cted by current UK conservation activities
(http://www.ukbap.org.uk/habitats.htm).
UK Government

will, in consultation with
stakeholders, consider the extent to which it could add value to this activity.
UK
Government

will also develop a policy on
in situ

conservation of microbial genetic
resources, working with stakeholders and, in particular, relevant nature conservation
bodies such as
English Nature
, the
National Trust
,
national park authorities,
wildlife trusts

etc. Policies on
in situ

conservation of
GR will take into account the
ecosystem approach.

6. Support characterisation and evaluation of GR

Characterisation and evaluation of GR is a responsibility for
levy bodies
,
research
organisations
,
collection holders
, and
UK Government
. It should have pa
rticular
focus on GR that are of environmental, bioscience industry and educational
importance.
UK Government

will seek to co
-
ordinate these efforts into a
programmed approach. Within such an approach, the
private sector

and
levy bodies

should focus on co
mmercial benefits while
UK Government

should focus on public
good benefits.

7. Raise awareness of the importance of GR

All stakeholders

should contribute to raising awareness of the importance of
conservation and sustainable use of GR

with the public, s
cientific community,
breeders, consumers, and food industry and within government.
UK Government

will seek to co
-
ordinate and support activity, working closely with, in particular,
NGOs
,
farm parks
,
National Trust
,
national park authorities,

horticultural
and
botanical gardens
,
microbial resource collections,

relevant
museums,
the
retail
sector

and
consumer groups
.

8. Support GR through other UK Government policies and programmes

With input from stakeholders the
UK Government

departments should seek to
in
fluence, as far as possible, all
UK Government

policies and programmes to be
supportive of the conservation and sustainable use of GR.


19

9. Ensure GR are managed in compliance with international treaties and
conventions and national law

There are over 30
treaties, conventions or legislation that impact upon the access,
management or distribution of GR (Annexe 3). Cohesive policy must be in place to
facilitate use and access but is compliant with legislation. The UK Government will
liase with GR stakehold
ers and put in place such mechanisms.
UK Government

should put in place mechanisms that compensate collection holders for services
provided to Government that help meet UK Government obligations to conventions,
treaties and national law.


Recommendations



Initially, the UKFCC should be given the role to work with the UKNCC to
strengthen the UK network of microbial collections



UK Government should establish a policy on the ex situ conservation and
utilisation of genetic resources that links with the UK in si
tu actions in the UK
Biodiversity Action Plan.


M4.

Gap analysis for MGRFA in the UK

Information in electronic form is currently available on around 100000 of the 525000
strains of microorganisms over the Internet. However, not all of the data is relevant
as
GRFA but dividing the task is not really a practical solution. An initiative to digitise
all data, for example through GBIF, is more appropriate, or perhaps through organism
domain for example the fungi through the Global Strategy for Plant Conservation
,
where an objective is to create a fungal portal. Additionally, there is still a huge gap
between the described organisms and those that are not yet culturable and that exist in
the environment providing vital roles relevant to GRFA. It is therefore ess
ential that
ex situ

conservation must be intrinsically linked to
in situ

programmes. It is essential
to have further information on
in situ

conservation of microbial diversity and how it
might be balanced with
ex situ

conservation. At the very least import
ant microbial
GRFA should be backed up in
ex situ

collections. Only a few strains of microbial
GRFA are adequately cryopreserved in national collections and most of the
production strains are kept locally. There is also a huge information gap on how
micr
obial diversity impacts on GRFA. Access to such information is essential to
ensure that key elements remain available if environmental change threatens their
existence. It is clear that the UK requires a co
-
ordinated strategy for the management
and
ex si
tu

conservation of its microbial genetic resources.


Cryopreservation of Genetic Resources for Food and Agriculture extension
report


CABI Bioscience was tasked with the collection of data on the cryopreservation of
Genetic Resources for Food and Agricultu
re (GRFA) in order to make
recommendations on the needs for cryobiology research and ex situ conservation of
GRFA.


A compilation of the institutions that are working in the field of low temperature
biology was made. Sixty
-
three organisations were identifi
ed through internet
searches, review of the membership list of the Cryobiology and Low Temperature
Biology membership lists. Thirty
-
three were active in animal preservation research,

20

17 in plant and 12 in microorganisms. A search for all publications was
made through
Google and the CABI Abstracts and Medline databases.


The literature survey revealed many protocols that were being used by the different
collections and researchers to preserve their biological materials. It was evident that
cross disciplin
e technology transfer would enhance our ability to preserve recalcitrant
organisms or their replicable parts. In this exercise over 210 cryopreservation
protocols have been identified. Some are general techniques where routine protocols
have been develop
ed for specific groups of organisms others address specific species.
Specific protocols were identified for 106 species of microoraganism, 44 species of
animal and 15 plant species. There were 29 general procedures recommended for
specific groups of micro
organism, 9 for animals, including spermatozoa and embryos,
and 4 for plants including seeds, tissues, meristems and shoot tips. Over 20 different
chemical cryoprotectants were used either singularly in different concentrations or as
various mixtures. A fu
ll report on the cryopreservation study extension is provided
electronically as an annexe to this report.


Recommendations from the crypreservation ad
-
on study

Cryopreservation research on Genetic Resources for Food and Agriculture should be
drawn together

under the auspices of DEFRA’s GRFA Framework. Research is
needed to develop protocols for preservation recalcitrant fungi and post preservation
stability testing at the molecular level.


A strategy to ensure GRFA is backed up as cryopreserved germplasm in

ex situ
collections is needed. Again this could fall under DEFRA’s GRFA Framework.


Mechanisms for the transfer of cryopreservation technology between GRFA domains
should be established.


Outputs from the GRFA cryopreservation study



Preservation protocols

and reference list



Publications database



Cryopreservation research group activity list


Conclusions of the cryopreservation information study

There is a great deal of research activity in cryopreservation research but little has
been done to co
-
ordinate i
t or focus it on GRFA. Additionally, technology transfer
will provide solutions to the preservation of preservation recalcitrant GRFA
germplasm. A GRFA cryopreservation Research Group should be established and the
outputs from this study should be made a
vailable on the GRFA information web site.


Conclusions and recommendations


A simple inventory has been constructed with little associated information that will
require little maintenance but regular update via an uncomplicated process. It is
currently a

snap shot in time and needs further input. The latter can be achieved by
interacting with the visitors to the inventory web pages asking them to provide data
that has been missed or to supplement the inventory information. Periodic internet
searches usi
ng the inventory names will help identify new sources of biological
materials and associated information.


21


The inventory will serve as a useful source of information to those working with
GRFA but creating an associated information portal would expand its
usefulness to
the GRFA community. It is recommended that all the recommendations made by the
three domains are considered by DEFRA’s GRFA stakeholder group for further
action under the framework for GRFA.


Recommendations


1.

A mechanism should be establishe
d to update the inventory on a regular basis

2.

An associated information portal/system should be established to provide the
additional information requested by survey respondents

3.

Work with the Global Biodiversity Information Facility (GBIF) to ensure
mechani
sms are in place for data access and that co
-
ordinated programmes are in
place to digitise the UK’s biodiversity data inclusive of that considered to be
GRFA.

4.

Link the inventory to a taxonomic hierarchy that enables the user to trace
taxonomic relatives of

those organisms already used as GRFA.

5.

Call for bids to establish the prescribed information system on the DEFRA web
site to support the GRFA community

6.

Place the three inventories on the DEFRA web site for access via a single page.

7.

Initially, the UKFCC sho
uld be given the role to work with the UKNCC to
strengthen the UK network of microbial collections

8.

Cryopreservation research on Genetic Resources for Food and Agriculture should
be drawn together under the auspices of DEFRA’s GRFA Framework. Research is
ne
eded to develop protocols for preservation recalcitrant fungi and post
preservation stability testing at the molecular level.

9.

A strategy to ensure GRFA is backed
-
up as cryopreserved germplasm in
ex situ

collections is needed. Again this could fall under DE
FRA’s GRFA Framework.

10.

Mechanisms for the transfer of cryopreservation technology between GRFA
domains should be established.


22

Appendix 1

UK Culture Collections

Collection Usage and Activity Profile


The
Aim

of this survey is the Establishment of an Invento
ry for Microbial

Genetic Resources for Food & Agriculture (MGRFA) and Scope a GFRA

Information System


The
objectives

are to create a list of microorganisms that are used directly as
food, in the food industry, indirectly in food, or in agriculture, and
secondly to design an information system that will provide relevant
information to GRFA.


Why have you been contacted?
You have been identified as holding a collection
relevant to GRFA.


Please Complete Details Below:


1.

List of Micro
-
organism Genetic Reso
urces Used Positively for Food &

Agriculture and their quantities (approximate figures are acceptable where
exact details are not known)




Direct Use as Food Number

Starter Cultures

100

Nut
iceuticals

5

Single cell protein
-

meat substitutes

0

Other

70



Use in Agriculture Number

Biocontrol Agents

207

Competitors

200

Other

3416


Indirect use as Food i.e. food production

Number

Or as ingredients e.g. food colourings

Cheese ripeners

0

Brewers

62

Fermentation products e.g. soy sauce, bread,
beverages, yeast extract

0

Algae in larva bread

0

Organic aci
ds and enzymes for food processing
or as ingredients; food colourings

0

Totals

4060


23

2.

Number of strains held in the collection




Actinomycetes

19,000

Plant Cell Lines

0

Algae

450

Plasmids

2050

Animal Cell lines

20

Protozoa

4

Archaea

10

Yeasts

210

B
acteria

15087

Viruses

140

Bacteriophage

151

Other (e.g. DNA)

0

Cyanobacteria

1

Non filamentus

20

Filamentous fungi

4638



Human cell lines

0



Mycoplasma

50




Total

30687

Total made available to outside users

14,565


3.

Preservation techniques used


Su
bculture



6

Oil layer


1


Water


0

Air dried



0

Vacuum dried 1


Freeze dried


4

Frozen

20ºC



4

Frozen

70ºC 8


Frozen

135ºC

1

Frozen below

140ºC 4


4.

Number of strains distributed annually


Internally to you
r organisation:

386.5

Externally:




545








5.

Current funding: grant vs commercal income


Proportion (%) grant


592


Proportion (%) sales of cultures

5


Proportion (%) sales of services

103

Other (please specify)


100


6.

Number of new strains added to the
collection each year




Actinomycetes

200

Plant Cell Lines

0

Algae

10

Plasmids

205

Animal Cell lines

1

Protozoa

2

Archaea

0

Yeasts

5

Bacteria

1320

Viruses

15

Bacteriophage

5

Other (e.g. DNA)

5

Cyanobacteria

0



Filamentous fungi

125



Human cell li
nes

1



Mycoplasma

20




Total

1809



24


7.

Number of staff dedicated to the collection

6.75




8.

Does the collection operate a quality system?

If so which?



ISO 9000 series


1


CABRI Guidelines


0

ISO standard e.g. 17025

0


WFCC standard


0

GMP




0


Your ow
n standard


9

GLP




1


Other




0

UKNCC System


0



9.

Do you publish a catalogue? If yes, is it paper or electronic?
Yes 2 No 8




9.

Do you have a database? If yes does it contain strain property data?

Yes 5 No 5



Please provide a link to the database
or forward a copy:

…………………………………………………………………………………………..



Please confirm whether your list of relevant strains can be added to the DEFRA

Inventory:












Yes


6

No


4


Please be advised that your data will be acknowledgeable and remain your

copyrig
ht.
The intention of the inventory is create a link from the DEFRA
website to their live data.


11.

Long
-
term security: Do you consider your collection to be:


Safe

3 Relatively safe 5 Endangered 1 Imminent threat 0 Unknown 1


12.

Please s
ummarise your main areas of activity and interest.

Molecular Genetics of Streptomyces

Biocontrol of food borne pathogens

Plant Pathogen acteria

Taxonomy

Rumen

Biocontrol feed supply, fermented foods

Plant, Insect Pathogens aand Basidiomycete
(Agariou
s bisporus)

Marine Algae, food and biotechnology

Biocontrol of weeds

Vetenary antimicrobial agents



25

13.

Other comments:


Contact name:
Keith Chater


Address:
John Innes Centre
,
Norwic
h Research Park
,
Norwich Research
Park
,
Norwich
,
NR4 7UH

Telephone:
01603 450297

Fax:
01603 450297

Email:
mailto:keith.chater
@bbsrc.ac.uk



Contact name:
Dr. M. A Collins


Address:
Northern Ireland Horticultural & Plant Breeding Station
,
,
,
,

Telephone:
2890255314

Fax:
20890255009

Email:
mailto:martin.collins@dardni.gov.uk



Contact name:
Andy Aspin


Address:
NCPPB
,
CSL Sand York
,
York
,
,
YO41 1LZ

Telephone:
01904 462344

Fax:
01904 462111

Email:
mailto:ncppb@csl.gov.uk



Contact name:
Sophie Kemp


Address:
Royal Botanic Gardens
,
Kew
,
Richmond
,
Surrey
,
TW9 3AB

Telephone:
0208 332 5000

Fax:
0208 332 5278

Email:
mailto:s.kemp@rbgkew.org.uk



Contact name:
John Wallace


Address:
Rowett Research Institute
,
Aberdeen
,
,
,
AB21 9SB

Telephone:
01224 716656

Fax:
01224 716687

Email:
mailto:john.wallace@rowett.ac.uk



Con
tact name:
Dr. D. R. Davis


Address:
Plas Gogerddan
,
Aberysyth
,
Ceredigan
,
,
SY26 3EB

Telephone:
01
970 823061

Fax:

Email:
mailto:david.davies@bbsrc.ac.uk



Contact name:
Prof. Peter. R. Mills


Address:
HRI Warwick
,
Wellesbourne
,
Warwick
,
,
CV35 9EF

Telephone:
024 765 74455

Fax:
02476 574500

Email:
mailto:peter.mills@warwick.ac.uk



Contact name:
Dr. R. K. Pipe


Address:
MBA
,
Citadel Hi;;
Plymouth
,
,
PL1 2PB

Telephone:
01752 633217

Fax:
01752 633102

Email:
mailto:rkpi@mba.ac.uk


26


Contact name:
Prof. P John


Address:
School of Plant Sciences
,
University of Reading
,
,
,
RG6 6AS

Telephone:
0118 378 8098

Fax:
0118 3778 8169

Email:
mailto:p.john@reading.ac.uk



Contact name:
Dr. Andrew Prid
more


Address:
Don Whitley Scientific Ltd
,
14 Otley Road
,
Shipley
,
West
Yorkshire
,
BD17 7SE

Telephone:
01274 595728

Fa
x:
01274 531197

Email:
mailto:andrew_pridmore@dwscientific.co.uk


Additional UKFCC collections contacted


Collection

Holdings

Considered GRFA

Department of Plant Biology, University of
Bath, Culture Collection

500

-

Department of Botany, University of
Edinburgh

1200

-

Department of Microbiology, The
University, Bristol,

100+

-

Hull: Collection of Slerotia
-
Forming Fungi,
The University

300

-

Queen Mary and Westfield College,
University Of London

130

-

RCS Impe
rial College of Science &
Technology.

100

-

RLCC Roussel Laboratories Culture
Collection

550

-

Strathclyde: Division of Applied
Microbiology

250

-

Tate and Lyle Ltd. Group Culture
Collection, Reading

100

-

Total

3230




27

Appendix 2. MGRFA Inventory


O
rganism

Type

Property

Numbe
r


of
strains

Absidia californica

Fungus

Biodeteriorgen

1

Acetobacter calcoaeticus

Bacterium

Biodegrader

1

Acetobacter diazotrophicus

Bacterium

Nitrogen fixer

1

Achromobacter cholinophagum

Bacterium

Biodegrader

1

Acinetobac
ter

Bacterium

Biodegrader

1

Acinetobacter baumanni

Bacterium

Biodegrader

3

Acinetobacter sp.

Bacterium

Biodegrader

1

Acinobacter sp.

Bacterium

Biodegrader

19

Acremonium strictum

Fungus

Biodeteriogen

3

Actinobacter sp.

Bacterium

Biodegrader

2

Aeromona
s caviae

Bacterium

Biodegrader

2

Aeromonas sp.

Bacterium

Biodegrader

1

Agaricus campestris

Fungus

Food strain

1

Agaricus arvensis

Fungus

Food strain

1

Agaricus augustus

Fungus

Food strain

1

Agaricus bitorquis

Fungus

Food strain

1

Agaricus brunnescen
s

Fungus

Food strain

1

Agaricus campestris

Fungus

Food strain

1

Agaricus impudicus

Fungus

Food strain

1

Agaricus macrosporus

Fungus

Food strain

1

Agaricus silvaticus

Fungus

Food strain

1

Agaricus silvicola

Fungus

Food strain

1

Agaricus
sp
.

Fungus

Foo
d s t rain

1

Agrobact eri um radi obact er

Bact erium

Biocont rol agent

1

Agrobact eri um
s p.

Bact erium

Biodegrader

1

Agrocybe aegeri t a

Fungus

Food s t rain

1

Agromonas ol i got rophi ca

Bact erium

Nit rogen fixer

1

Al cal i genes eut rophus

Bact erium

Biodegrader

1

Al cal i
genes faeci al i s

Bact erium

Biodegrader

1

Al cal i genes faeci al i s
s ubs p.

faeci al i s

Bact erium

Biodegrader

1

Al cal i genes l at us

Bact erium

Nit rogen fixer

1

Al cal i genes
s p.

Bact erium

Biodegrader

2

Al cal i genes xyl osoxi dans subsp.
deni t ri fi cans

Bact erium

Biodegra
der

5

Al cal i gens
s p.

Bact erium

Biodegrader

2

Al euri a aurant i a

Fungus

Food s t rain

1

Al t ermonas
s p.

Bact erium

Biodegrader

1

Al t ernari a al t ernat a

Fungus

Biodegrader; Biodet eriogen;
Plant pat hogen indigenous t o
t he UK. Mus t be s ent

21

Alteromonas carragen
ovora

Bacterium

Biodegrader

1

Alteromonas
sp.

Bacterium

Biodegrader

5

Amanita
sp.

Fungus

Food strain

1

Aminobacter aminovorans

Bacterium

Biodegrader

6

Aminomonas aminovorus

Bacterium

Biodegrader

2

Amorpotheca resinae

Fungus

Biodeteriogen

28

Amycolata

sp.
p.sp.sp.
hydrocarbonoxydans

Bacterium

Biodegrader

3

Amylocolapsis methalonica

Bacterium

Biodegrader

1

Ancycobacter
sp.

Bacterium

Biodegrader

1

Aplosporella
sp.

Fungus

Biodegrader

1

Armallaria
sp.

Fungus

Food strain

1


28

Arthrobacter
sp.

Bacterium

Bio
degrader

24

Arthrobacter globiformis

Bacterium

Biodegrader

1

Arthrobacter nicotianae

Bacterium

Biodegrader

1

Arthrobacter ureafaciens

Bacterium

Biodegrader

2

Arthrobotrys javinica

Fungus

Biodeteriogen

1

Aspergillus awamori

Fungus

Food strain

2

Asperg
illus fischeri

Fungus

Biodeteriogen

1

Aspergillus fischeri
var

glaber

Fungus

Biodeteriogen

2

Aspergillus fischeri
var

spinosus

Fungus

Biodeteriogen

2

Aspergillus foetidus

Fungus

Food strain

3

Aspergillus fumigatus

Fungus

Biodeteriogen

7

Aspergillus ma
ngini

Fungus

Biodeteriogen

2

Aspergillus niger

Fungus

Bioremediators

52

Aspergillus oryzae

Fungus

Food strain

15

Aspergillus parasiticus

Fungus

Food strain

2

Aspergillus spectabilis

Fungus

Biodeteriogen

1

Aspergillus tamarii

Fungus

Biodeteriogen

6

As
pergillus terreus

Fungus

Biodeteriogen

6

Aspergillus tonophilus

Fungus

Biodeteriogen

2

Aspergillus unguis

Fungus

Biodeteriogen

1

Aspergillus ustus

Fungus

Biodeteriogen

6

Aspergillus versicolor

Fungus

Biodeteriogen

14

Aspergillus wentii

Fungus

Biodeter
iogen

1

Aureobacterium barkeri

Bacterium

Biodegrader

1

Aureobasidium pullans

Fungus

Biodeteriogen

6

Auricularia auricula
-
judae

Fungus

Food strain

1

Auricularia polytricha

Fungus

Food strain

1

Azospirillum brasilense

Bacterium

Nitrogen fixer

1

Azospir
illum lipoferum

Bacterium

Nitrogen fixer

1

Azotobacter chroococcum

Bacterium

Biodegrader

1

Azotomonas agillis

Bacterium

Nitrogen fixer

1

Bacillus alginolyticus

Bacterium

Biodegrader

1

Bacillus azotofixans

Bacterium

Nitrogen fixer

1

Bacillus benzoevora
ns

Bacterium

Biodegrader

4

Bacillus cereus

Bacterium

Biocontrol agent

2

Bacillus cereus
subsp
. fluorescens

Bacterium

Food strain

1

Bacillus chondroitinus

Bacterium

Biodegrader

2

Bacillus circulans

Bacterium

Biodegrader

3

Bacillus fastidiosis

Bacterium

Biodegrader

4

Bacillus gibsonii

Bacterium

Nitrogen fixer

1

Bacillus gordonae

Bacterium

Biodegrader

4

Bacillus lichenformis

Bacteria

Food strain

2

Bacillus macerans

Bacterium

Nitrogen fixer

3

Bacillus megaterium

Bacterium

Biodegrader

1

Bacillus metha
nolicus

Bacterium

Biodegrader

1

Bacillus niacini

Bacterium

Biodegrader

1

Bacillus polymyxa

Bacterium

Nitrogen fixer

4

Bacillus pumilus

Bacterium

Biocontrol agent

3

Bacillus
sp.

Bacterium

Biodegrader

9

Bacillus sphaericus

Bacterium

Biodegrader

5

Bacil
lus subtilis

Bacterium

Biodeteriogen; Food strain

3


29

Bacterium

Bacterium

Biodegrader

1

Beauveria bassiana

Fungus

Biocontrol agent

3

Beauveria brongniartii

Fungus

Biocontrol agent

1

Beauveria densa

Fungus

Biocontrol agent

1

Beijerinckia acida

Bacterium

Nitrogen fixer

1

Beijerinckia congensis

Bacterium

Nitrogen fixer

1

Beijerinckia derxii

Bacterium

Nitrogen fixer

1

Beijerinckia fluminensis

Bacterium

Nitrogen fixer

1

Beijerinckia indica

Bacterium

Nitrogen fixer

1

Beijerinckia indica subsp. lacticogene
s

Bacterium

Nitrogen fixer

1

Beijerinckia mobilis

Bacterium

Nitrogen fixer

1

Boletus edulis

Fungus

Food strain

1

Boletus
sp.

Fungus

Food strain

1

Botryotrichum piluliferum

Fungus

Biodeteriogen

3

Brachionus plicatilus

Alga

Food strain

1

Brachybacteriu
m faecium

Bacterium

Biodegrader

3

Bradyrhizobium japonicum

Bacterium

Nitrogen fixer

1

Brettanomyces anomalus

Bacteria

Food strain

1

Brevibacterium linens

Bacterium

Biodegrader

1

Calcarisporium thermophilium

Fungus

Biodegrader

1

Calocybe gambosa

Fungus

Food strain

1

Calvatia
sp