How BPD projects are using and contributing to culture collections
By Joana Vicente and Andrew Aspin
As we are approaching the final stages of most of our BPD projects, we are turning our attention to impact, publications, stakeholders’ engagement, and dissemination. Other important aspects of these final stages also involve making large datasets available and dealing with materials like the bacterial isolates generated during the projects. All our BPD projects involve working with bacterial isolates. In some cases, we have used isolates from existing collections or already kept in some of the laboratories, whilst in some cases we imported isolates from overseas, and in others we added or made entire new collections during the projects.
It is important for all BPD projects to consider how these isolates will be maintained in the short, medium and longer term. Hopefully collections of isolates will be kept at least in duplicate, in different freezers and detailed records will be kept for each strain. We also recommend that important strains are sent to one or more official collections like the National Collection of Plant Pathogenic Bacteria (NCPPB) for safe keeping and future distribution. This ensures that the work done currently in the BPD projects will be linked to particular bacterial strains for the years to come and therefore our projects’ long-term impact will increase.
Why culture collections are important for research
As discussed in this blog culture collections are repositories of preserved and authenticated microbes and are an incredibly valuable resource for anyone studying bacterial plant diseases. Depositing isolates in official collections has multiple advantages including securing the long-term maintenance of strains and contributing to global biodiversity and disease records. Frequently isolates used in publications are requested by other researchers and it is easier to distribute them from an official collection that has been set up exactly for that purpose than to have this extra burden for research laboratories.
When publishing any work that deals with bacterial isolates, many studies ignore details on the origin of the isolates. Some have been used so often, that most authors assume the readers already know the background of those strains. This might not be the case. Another important consideration is that in many cases the isolates have been transferred between collections and laboratories and in that process, have been multiplied many times. In some cases, the derived strains are notably different from the original strain due to accumulation of mutations or human errors. In some cases, strains have lost pathogenicity and become ‘laboratory strains’. In most cases the name of the person that has isolated and maintained the strain is never mentioned nor the original references to the strain. Knowing exactly the origin of the strains that are in a laboratory freezer is important for all new studies. Recent open access publications generally have limited space for these details in the main text. However, all the details can easily be included as supplementary materials allowing future researchers to know exactly which strains have been used, their origin (location, year, host, material), isolator, and synonym names and numbers. This will allow culture collections to cross reference the information and link strains to publications and datasets making the information easily accessible for all new researchers.
Isolates used and collected by BPD projects
Brigit, the first BPD project, focused on preparing the UK for the threat of Xylella fastidiosa and used mainly isolates from existing collections although some new isolates were also imported directly from researchers or via the French culture collection, CFBP. These isolates are kept under licence at the NCPPB based at Fera Science, York.
Future Oak and BacStop have assembled a large collection of bacterial isolates associated with oak and some of which might be contributing to Acute Oak Decline (AOD). On the other hand, some isolates obtained in Future Oak might help to control AOD as part of the future management of the disease. Interestingly some isolates found in these projects have been described as new species and no doubt there is a lot more unexplored diversity in the collections from oak.
The DesBL project uses Pectobacterium isolates selected from a large collection of isolates that is maintained at the James Hutton Institute with support from the Scottish Government. The collection includes approximately 1,500 Pectobacterium and Dickeya isolates from the UK, Europe and worldwide that came from various sources including isolates collected by researchers and also isolates from culture collections like the NCPPB and the CFBP.
The Disease Suppressive Soils project works with isolates that cause root mat disease of tomato (Rhizobium radiobacter biovar 1) and also Pseudomonas isolates. This project also has a collection of isolates that may contribute to disease suppression and therefore could be part of the treatments added to create healthy synthetic soils.
The Caliber project used materials held at SASA. Candidatus Liberibacter solanacearum, the causal agent of potato zebra chip, is insect transmitted and cannot be cultured so needs to be maintained in infected plants. This requires active colonies of vectors and plant hosts to produce positive material. This is a real challenge for long term maintenance of these organisms.
The Ralstonia Phage project has access to a large collection of Ralstonia isolates that have been sequenced and characterised in a range of previous projects including two PhD studentships. The isolates are maintained at York University and also at the Fera and NCPPB collections.
The Pseudomonas Prunus project based at NIAB East Malling and Cambridge has also sequenced a large collection of isolates associated with cherry trees. Pathogenicity tests were performed in a selection from these. The large collection assembled before and during this project is a valuable, well characterised resource for studies on bacterial canker and Pseudomonas pathogenicity in general.
The Xanthomonas Threats project is using the large collection of bacterial isolates of the Wellesbourne Campus of Warwick University. In addition, this project is also using isolates from the NCPPB and the Fera collection.
If the isolates obtained, characterised or used in BPD projects are maintained in the long term and continue to be used in future projects and referred to in publications (with full details), or in some cases, are included in synthetic communities that aim at reducing disease levels, the impact of our projects will be long lasting!