Crop Genebank Knowledge Base

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Non-plant taxa for food and agriculture

Contact person for Non-plant taxa for food and agriculture: Fen Beed, IITA, Uganda

Contributors to this section: IITA, Uganda (Fen Beed, Muris Korkaric).

Agriculture and food production are facing numerous challenges. The World Bank estimates that the global demand for food will double within the next 50 years. At the same time arable land is decreasing due to land pressure and loss of fertile soil through unsustainable farming practices, and pests and diseases continue to cause loss of agricultural products. Climate change and increased globalization and cross border trade are likely to add new layers of complexity to these challenges. Consequently, agriculture and food production will have to be intensified. Not only will existing technologies and knowledge have to be improved and implemented, but agriculture will also need innovative approaches to move from short-sighted and unsustainable farming towards a system which can meet future challenges.

Therefore, a greater understanding is needed which views agriculture as a complex system of interactions. To optimize this system, all of it components have to be understood and their importance acknowledged. Crops are at the end point of food production and therefore naturally in focus, but throughout their development uncountable direct and indirect interactions with other organisms occur. Microorganism and insects provide important functions and services for agriculture and they are inextricably connected with ecosystem resilience, crop health, soil fertility, productivity and food quality. Unfortunately, this important role is largely underestimated and their potential to solve problems of modern agriculture has still not been sufficiently exploited.

“Non-plant taxa” in the context of this report are bacteria, fungi, oomycetes, viruses, insects and nematodes. These can be found in almost every compartment of the world and their diversity far exceeds those of plants. In one single gram of soil over a billion bacteria can be found, but fewer than 5% have been described or named. For fungi it is estimated that there are about 1.5 million species and only 5% are described. In comparison, almost all of the estimated 420,000 existing seed plants are known and described. From this still largely untapped pool of genetic resources modern agriculture uses only a fraction. Therefore the potential to use non-plant taxa genetic resources to improve agriculture and provide new solutions is enormous.

In their relevance to food and agriculture, organisms of the non-plant taxa can be divided into beneficials – those that support crop and forage production – and those that hinder food production, pathogenic and spoilage organisms. The beneficials perform many functions and services for food and agriculture. A few examples:

  • Microbes can enhance the nutrient supply to plants. Examples are nitrogen fixing Rhizobia or arbuscular mycorrhizal fungi that are associated with the provision of phosphorus to the plant roots.
  • The maintenance of a high diversity of plant species requires a correspondingly high level of diversity in the soil microbial community.
  • Microorganisms can confer enhanced disease resistance to plants by inducing systemic resistance.
  • Entomopathogenic nematodes and fungi are used in integrated pest management to control insect pests.
  • Biopesticides not only increase yields, but also decrease the use of fungicides and pesticides, reducing their health risks to farmers and consumers.
  • The value of insects as pollinators has been estimated at US$208 billion, which equals about 10% of the total global value of agricultural food production. Insects have further importance as biocontrol agents and as soil ecosystem engineers and regulators.
  • Pests and disease causing organisms are needed for resistance breeding.

Currently there are no common strategies, policies or best practices for the management of these genetic resources but international standards are documented and followed in many cases. A recent survey collected information on the current inventories held across the CGIAR and its partners and compared management procedures with international repositories.

Useful web linkages for collection management

Collection guidelines
OECD: Best practices guidelines for BRCs - The most recent best practices for quality management, biosecurity, building capacity, preservation of biological resources and data management.

The UKNCC Biological Resource: Properties, Maintenance and Management. Provides all the information required to run a biological resource collection. Details techniques used for preservation and characterization of strains and lists the uses and properties of over 5000 micro-organisms.

Guidelines for Collection Quality Management Standards and Catalogue production - CABRI (Common Access to Biological Resources and Information) guidelines.

World federation for culture collections (WFCC) Guidelines for the establishment and operation of collections of cultures of microorganisms - 2nd Edition, June 1999 Revised by the WFCC Executive Board.

ISO 9000. ISO 9000 is a family of standards for quality management systems, maintained by the International Organization for Standardization and is administered by accreditation and certification bodies.

MINE (Microbial Information Network for Europe). The MINE project developed standards (e.g. Minimal Data Sets) for information related to microorganisms. (Gams, W. et al. 1988. Structuring strain data for storage and retrieval of information on fungi and yeasts in MINE, the Microbial Information Network Europe. Journal of General Microbiology 134, 1667-1689)

Collecting and preserving Insects and Mites - Produced by the Agricultural Research Service of the United States Department of Agriculture. Can be accessed online 

Collecting and Preserving. Nematodes - A Manual for Nematology by. SAFRINET, the Southern African (SADC) LOOP of BioNET-INTERNATIONAL. Compiled by the National Collection of Nematodes Biosystematic Division; ARC – Plant Protection Research Institute Pretoria, South Africa.

CBOL (Consortium for the Barcode of Life). CBOL is an international initiative devoted to developing DNA barcoding as a global standard for the identification of biological species.

QBOL (Quarantine Barcoding of Life). QBOL is a project financed by the 7th Framework Program of the European Union that makes collections harboring plant-pathogenic quarantine organisms available. Informative genes from selected species on the EU Directive and EPPO lists are DNA barcoded from vouchered specimens. In the next 3 year the sequences, together with taxonomic
features, will be included in an internet-based database system.

Databases, federations and information networks
WFCC – (World Federation of Culture Collections). The WFCC is a Multidisciplinary Commission of the International Union of Biological Sciences (IUBS) and a Federation within the International Union of Microbiological Societies (IUMS). The WFCC is concerned with the collection, authentication, maintenance and distribution of cultures of microorganisms and cultured cells. Its aim is to promote and support the establishment of culture collections and related services, to provide liaison and set up an information network between the collections and their users, to organize workshops and conferences, publications and newsletters and work to ensure the long term perpetuation of important collections.

WDCM – (World Data Centre for Microorganisms). The WDCM is a comprehensive worldwide directory of culture collections and holdings, and links to databases on microorganisms, biodiversity, molecular biology and genome projects. 

ECCO – (European Culture Collection Organisation). The aim of the organisation is to promote collaboration and exchange of ideas and information about all aspects of culture collection activity.

UKNCC – (United Kingdom National Culture Collection). The UKNCC co-ordinates the activities, marketing and research of the UK national service collections, with links to strain databases and affiliated collections.

MIRCEN – (UNESCO Microbial Resource Centers). Global network in environmental, applied microbiological and biotechnological research.

GBRCN – (Global Biological Resource Centre Network). The aim of the GBRCN is to publicize the benefit of micro-organisms. Provides publicity accreditation quality and authenticity and alleviates bioterrorism suspicion.

EMbaRC - (European Consortium of Microbial Resources Centres). EMbaRC aims at harmonizing the systems for conserving and identifying bacteria and microscopic fungi in the different European countries and also at developing DNA banks and reinforcing biosafety. The goal is also to preserve and valorize microbiological biodiversity. - The Bioportal currently integrates data from 55 Biological Resource Centres (BRCs) into an integrated strain database. A single portal interface, with direct pointers to the relevant information at the collections' websites, and provides both historical traces and geographic distribution of the strains they keep in culture. In addition, this information is automatically linked to related sequences in the public domain and refers to all known scientific publications that deal with the organism.

Access and benefit sharing
CBD – (Convention on Biological Diversity). Website of the Convention on Biological Diversity.

MOSAICC - (Micro-Organisms Sustainable use and Access regulation International Code of Conduct). MOSAICC is a voluntary Code of Conduct, a tool to support the implementation of the Convention on Biological Diversity at the microbial level, in accordance with other relevant rules of international and national laws.

Bonn Guidelines: The "Bonn Guidelines on Access to Genetic Resources and Fair and Equitable Sharing of the Benefits Arising out of their Utilization" are voluntary guidelines to assist governments in the structuring of national and regional legislation and mechanisms to ensure fair access to genetic resources, and sharing of benefits from these resources.


References and further reading

Barba M, Van den Bergh I, Belisario A, Beed F. 2010. The need for culture collections to support plant pathogen diagnostic networks. Research in Microbiology. Institut Pasteur. Microbial research commons: From strain isolation to practical use. 161; (6) p 472 - 479.

FAO. 2009. Background Study Paper No. 48 for the Secretariat of the Comission on genetic resources for food and agriculture: The Impact of Climate Change on Countries’ Interdependence on Genetic Resources for Food and Agriculture. Chapter 5 authored by Fen Beed: The Impact of Climate Change on Interdependence for Microbial Genetic Resources for Agriculture. pp 37 - 47.  Available here.   

Feed B. 2009.  Impact of Climate Change on the Interdependency between Countries in the Use and Exchange of Microorganisms – presentation given at the Global Microbial Commons Workshop, 25-26th March, Brussels, 2009. Available:

Korkaric M, Beed F. 2010. Why manage non crop biodiversity? IITA R4D Edition 4 - March 2010, p 15-18. Available here (2.3 MB).

Miller SE, Beed FD, Harmon CL. 2009. Plant Disease Diagnostic Capabilities and Networks. Annual Review of Phytopathology 47: 15-38.

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