Spotlight On...

Taxonomy and Identification of Plant Pests and Pathogens.

An authoritative identification of the cause of a problem is the first step towards its solution or control and an important element in the study of interactions with other organisms. Further, the name is the key to the accumulated knowledge about an organism.

CABI Bioscience

CABI Bioscience offers a range of services and products that centre around the name of the organism and to obtain what it is necessary to identify it.

Identification Services

CABI Bioscience offers identification services for nematodes, fungi and bacteria (microbial). The service for the identification of insects was transferred to the Natural History Museum in December 2000. Any enquiries should be directed to  Mr Paul Hillyard, Insect Identification Service, Entomology Department, The Natural History Museum, Cromwell Road, London, SW7 5BD. E-mail: Website:

The Nematode Identification Service provides authoritative identifications of plant parasitic nematodes and insect parasitic nematodes, including entomopathogenic nematodes, worldwide. The service accepts:

  • Fixed material extracted from soil, plant tissue or insects;
  • Live material, particularly of entomopathogenic nematodes;
  • Mounted material on glass slides;
  • Soil or plant samples.

The Microbial Identification Service provides identifications of filamentous fungi (excluding most Oomycetes* and any medical fungi), yeasts and plant pathogenic bacteria worldwide. The service accepts:

  • Cultures grown on most media as long as they remain intact, are mite-free and pure;
  • Dried specimens in packets, not plastic bags.

*A Phytophthora identification service is run jointly with the Scottish Crops Research Institute. This service combines morphological investigation and sequencing of the ITS regions of ribosomal RNA. The result is a highly accurate characterization of the isolates based on SCRI抯 extensive database of Phytophthora sequences. For further information visit the online Phytophthora identification website, PhytID:

Most identifications will be completed within 3-4 weeks from receipt but results can be supplied more rapidly if required, for instance for quarantine purposes. In the case of the Microbial Identification Service the time taken to provide an identification will always be determined by how quickly the fungus produces the structures needed for identification.

On completion of the identification a final report will be supplied. This will provide you with a name, usually to species level, together with supplementary information such as habitat, distribution, likely pathogenicity and key literature. An invoice is also sent with further details about payment. There is a scale of charges which is set out below:

Non-Commercial organizations in:

Developing CABI Member Countries �

Developing non-CABI Member Countries �

Developed CABI Member Countries �

Developed Non-CABI Member Countries �0

All Commercial organizations �0

A range of molecular-based services, from strain characterization to DNA sequencing to provide identifications using on-line sequence databases is also offered. Charges for these services are determined on a case by case basis depending upon the numbers of isolates and the kind of service required.

For further information about CABI Bioscience Identification Services please visit or contact Dr David Hunt (Nematodes) � or Dr John David (Microbials) �

CABI Bioscience also offers two diagnostic services. The Plant Disease Diagnostics and Advisory Service (Plant Clinic) investigates the cause of disease in plants, particularly crop plants. Comprehensive information is supplied on pathogens, disease distribution and recommendations made for management. Assistance can also be provided for virus and phytoplasma diseases. For further details, including charges, contact Dr Eric Boa ( or visit the Plant Clinic website, part of the CABI Biosciences website.

The Environmental and Industrial Diagnostics Service assesses samples from industry, manufacturing, or the general environment. It provides information on the significance of the organisms identified together with preventative and control measures. For further details, including charges, contact Dr Joan Kelley ( or Sharon Livingstone (


The provision of identification and diagnostic services by CABI started with the identification of insects by the then Bureau for Entomology, established in 1913. Fungal identifications were commenced with the establishment of the Bureau for Mycology in 1920, nematodes in 1929 by the Bureau of Animal Parasitology and plant pathogenic bacteria in 1959. The latter also being based at the Mycology Institute (CMI, IMI). Since 1999 the services have all been located at the Egham site.

The system of assigning IMI numbers to each fungal and bacterial sample received was started in 1945 and since that time over 385,000 numbers have been issued which gives a good indication of the number of samples received for identification over that time. The remit also has broadened, from the original work in identifying fungi and bacteria on crop plants, so that isolates are now received from a wide range of sources such as air, water, man-made materials, insects, etc. This arises from environmental and biodiversity surveys, quality assessment, quarantine and pre- & post-harvest storage problems. It is still a worldwide service and samples are regularly received from 20-30 different countries every year. Over the past five years the service has assisted 87 different countries.

Biochemical and molecular methods are being increasingly used to improve identifications both for nematodes, fungi and bacteria. For yeasts and bacteria, fatty acid analysis is routinely used and a comprehensive database allows comparison with already known strains. RFLP profiling is regularly used as the first approach to the identification of entomopathogenic nematodes from the genera Steinernema and Heterorhabditis. CABI Bioscience has a comprehensive library of profiles, including many for species yet to be formally described and named. DNA sequencing of filamentous fungi is proving to be a powerful technique for identification, at least to generic level, of isolates that do not sporulate in culture. CABI Bioscience are keen to develop this as a routine part of the identification service.

A significant amount of the material identified is held in CABI Bioscience Reference Collections: for fungi there is a dried reference collection (herbarium) and the Genetic Resources Collection (GRC). The former contains approximately 35,000 species, which is about 10% of the number of known fungi, and 7500 type specimens by which such names are interpreted. The GRC has some 21,000 isolates most of which are also stored in the herbarium so that the identity of the isolates can always be checked. You can search these databases on-line at CABI Bioscience also has the Nematode type slide collection which has been built up since the 1960s and currently comprises over 2500 type slides and is the second largest in the UK. The majority of the species represented are plant parasitic or soil dwelling forms, although there are also many parasitic species from insects and other arthropods.

Expertise & Resources

CABI Bioscience has one bacteriologist, seven mycologists and two nematologists whom are internationally acknowledged experts in the systematics of these groups. Their experience makes them fundamental to the authority of the identifications provided. This expertise is backed up by the reference collections mentioned above, an extensive library and electronic databases. Most significant of the latter is the database of fungal names and literature available at our website, This is based on CABI Bioscience抯 role as an indexing authority for all published fungal names.

Nematode identifications from the early 1960s are held on a computerized database. Most of these records relate to collections from the tropics and subtropics.


CABI Bioscience抯 systematic expertise is central to a number of projects as well as in collaborations with a wide range of organizations around the world. This enables CABI Bioscience to transfer skills to less advantaged areas as well as to build capacity so that these regions can develop their own taxonomic resources. In this CABI Bioscience are also working with BioNET International, an organization established to deliver this kind of assistance ( Some key projects are:

Species 2000. This is a programme that comprises a federation of database owners and plans to compile an electronic checklist � the 慍atalogue of Life�. This will be composed and maintained from a distributed array of existing taxonomic databases, each enhanced on a continuing basis by experts. It will allow users to look up the existence, accepted names, synonyms, and common names of any species, and also to obtain basic factual data about them. CABI Bioscience, through its role as the compiler of Index of Fungi and its comprehensive database of fungal names will contribute the data for fungi both from internal sources and by collaboration with several groups in other parts of the world.

Iwokrama. CABI Bioscience is assisting in a major biodiversity inventory and bioprospecting programme funded by the EU in the Iwokrama Forest Reserve, Guyana, in collaboration with the Iwokrama International Centre, the Institute of Applied Science and Technology, Guyana, the University of Guyana, the University of the West Indies, the Royal Botanic Gardens, Kew and Imperial College. The programme focuses strongly on fungi. A series of integrated investigations into interactions between fungi, plants and insects targets endophytes of indigenous plants, saprobes of fallen leaves, leaf-cutting ants and their associated fungi, and correlations between ant food preferences, endophytes and leaf secondary metabolites. The bioprospecting programme makes use of fungal cultures produced from the inventory process, looking for biologically active compounds. A central theme of both programmes is technology transfer, with staff from Guyana and neighbouring countries trained in survey, isolation, culture and screening techniques, and appropriate facilities set up within the country.

See also: and


CABI Bioscience抯 systematic expertise is a vital element of its training programme as the scientists are major contributors to sessions giving participants an insight on identification. Specially tailored programmes can be run for individuals and small groups to study at the UK Centres for scholars at postgraduate, post doctoral and visiting scientist level.

International Course on the Identification of Fungi of Agricultural and Environmental Significance. (16 July � 24 August, 2001). In just six weeks participants will gain the ability to identify a wide range of microfungi of importance to agriculture, the environment and industry � worldwide. In particular, they will learn how to identify fungi that are important to crop protection and those that are difficult to identify. The course has been run and developed over 25 years at the International Mycological Institute (IMI) now integrated into CABI Bioscience and has been taught to participants from over 50 countries.

Identification and Diagnosis of Plant and Insect Nematodes of Economic Importance. Individual training courses on request. These are usually for three weeks and intensive. Content is adjusted according to need and a copy of the full training manual is provided. Cost is about �00 (depending on content) and includes self-catering accommodation (i.e. meals and transport not included).

Further courses planned for 2002 are:

  • Isolation from Natural Habitats
  • PCR/Modern Methods

For further details contact Stephanie Groundwater, e-mail: or visit the Training website, part of the CABI Bioscience website

CABI Publishing

Identification Keys and related products

Glossary of Plant Nematodes
Root knot Nematode Taxonomic Database (CD-ROM)
Descriptions of Fungi and Bacteria
Index of Fungi
Bibliography of Systematic Mycology
Distribution Maps of Plant Diseases
Distribution Maps of Plant Pests


Details of the following publications are available at the Online Bookshop:

A full list of CABI Publishing book titles can browsed at the Online Bookshop.


The Crop Protection Compendium is an encyclopaedic, multimedia tool that brings together a wide range of different types of science-based information on all aspects of crop protection. It includes comprehensive information on over 1500 pests, diseases, weeds and natural enemies of worldwide or regional importance, each with text, illustrations and a distribution map. Outline data is available for 10,000 species, all contained in an intelligent taxonomic framework. Data is included for more than 150 crops and countries. A novel system of hyperlinking allows dynamic links to be created in real time. Arrangement of the content in a large relational database facilitates identification of potential plant disease/pest problems, and points to control methods.

Related items included in PEST CABWeb�/strong>:

The following abstract journals all contain specific chapters covering the world's literature on the taxonomy and morphology of insects, plant pathogens, weeds and nematodes:

All journals are now available via the internet with an extended backfile containing 10 years' of data.