The importance of culture collections

By Joana Vicente and Andrew Aspin

Culture collections are repositories of preserved and authenticated microbes for use in research.  Some of our Bacterial Plant Disease projects are generating large collections of isolates and/or are using isolates from in-house or public collections. For example, the Xanthomonas Threats project is both using and contributing isolates from the Warwick/Wellesbourne culture collection, from the Fera collection and from the National Collection of Plant Pathogenic Bacteria (NCPPB). These are great examples of both private/in-house collections and a public collection that specialises in plant-associated bacteria. Other international collections that are specialised in plant-associated bacteria include the CIRM-CFBP of France, the ICMP of New Zealand and the NRRL of the USA; other non-specialist collections that might have plant pathogenic bacteria are available.

Advantages of using Culture Collections

Using, contributing to and maintaining culture collections has many benefits:

• Culture collections minimise the amount of sub-culturing a strain goes through during the process of being preserved. Repetitive sub-culturing can lead to changes in the more sensitive isolates’ properties through selective propagation, lack of interaction with their host, or just poor maintenance. In addition, repeated sub-culturing introduces the possibility of mislabelling or a contaminant being confused with the desired isolate and the wrong organism being studied.
• Using strains obtained directly from culture collections reduces the chance of non-authentic materials being used. Culture collections specialise in the long-term preservation of organisms and the curators ensure that all the isolates they house are correctly identified and appropriately named.
• Rules and regulations limit the movement, study and holding of many plant pathogenic bacteria. By using established public collections, such as the NCPPB, researchers can ensure they are not inadvertently breaking any rules or laws that might be associated with the organism.
• Collections often become centres for dissemination of knowledge as well as strains.

The Wellesbourne/Warwick Collection

The Wellesbourne/Warwick collection is an example of a large collection, with over 10,000 isolates, that has been kept by Wellesbourne bacteriologists for nearly six decades. The collection was started by John D. Taylor in 1965 with the aim of keeping organisms useful for studies on several important diseases and also as a source of materials to develop diagnostics. The collection was also important to select isolates for disease resistance screening to help identify plants that had useful resistance that could be used in breeding projects.

The great strength of this collection was the careful organisation from the beginning. Isolate books contain details of the samples and also each isolate is maintained in two tubes kept in freezers at -76C. One freezer houses a working collection and the other has a backup copy. A small proportion of isolates have been freeze-dried as an extra back-up, but this number is quite limited due to lack of time of all the staff involved over the years. The information from the isolates books was partially transferred to a digital database and this facilitated finding the information on each isolate.

The maintenance of collections at various research institutions is always complicated as sometimes gaps in funding and lack of continuity in staff can leave the collections unprotected. Over the decades many bacterial isolates have been lost after projects finished, PhD students completed their theses, researchers retired or were made redundant, and the teams evolved or changed completely. The Wellesbourne collection has fortunately been maintained even though part of the work collection had been discarded before the start of the Xanthomonas Threats project in order to make space in a freezer. Fortunately, the archive collection had not been touched and the current project has been using and maintaining this invaluable collection.

National Collection of Plant Pathogenic Bacteria (NCPPB)

The NCPPB was recognised as a National Collection by the Permanent Committee of the Commonwealth Collection of Micro-organisms in 1956.  It has existed since the early 1900s, first as a private collection curated by W. J. Dowson. It then expanded in 1947 when the National Collection of Type Cultures rehoused bacteria that were not related to animal or human health concerns. The NCPPB is a founding member of the UK Biological Resource Centre Network, a member of the European Culture Collections’ Organisation and an affiliate member of the World Federation of Culture Collections. This collection deals specifically with plant pathogenic bacteria whilst many other public collections (e.g. the ATCC in the US, DSMZ in Germany, CECT in Spain) are generalist collections.

The NCPPB currently holds nearly 4,000 strains and approximately 200 Type strains. It is funded through a long-term service agreement between Defra and Fera Science, Sand Hutton, York. The strains are freeze dried and stored at 4°C in the dark. The list of strains is available online and requests are easy to place. Isolates are regularly sent to researchers across the globe. It is also usual practice to exchange isolates between culture collections as a way of maintaining backups to ensure that strains are always available.

Contributions from Xanthomonas Threats

Although sampling and collecting new isolates was not a main part of the project, the Xanthomonas Threats project has added approximately 270 new isolates to the collection. Some of these isolates were obtained from isolations from new field samples whilst others were imported from other institutions’ collections (e.g. some isolates from the Fera collection and isolates imported from Serbia). In addition, some isolates were also added to the Fera collection and the NCPPB collection and we expect that after the data analysis is completed more Xanthomonas isolates will be selected for inclusion in the NCPPB.

With the help of the BPD programme communications manager Sarah McLusky, we have recently added a Wikipedia page for the NCPPB.

Most BPD projects will be making their own contributions to culture collections. Find out more in this blog.