Written by Cameron Ferguson. This is the report from a 2020 BSPP Lockdown Bursary. Click here to read more/apply for one yourself.
The microbiota in the rhizosphere (the interface between roots and soil) engages in a range of associations with their host plant, encompassing both mutualism and parasitism. The Bulgarelli’s lab at the University of Dundee, where I worked for the duration of this project, is interested in capitalising on the molecular basis of these associations to sustainably enhance crop production. Pathogen protection is one of the ways in which rhizosphere microbes can promote plant growth: while this phenomenon has been observed for decades, recent advances in microbiota sequencing have provided us with new evidence into the composition of pathogen-suppressing microbes. However, the research in this field remains effectively “fragmented”: individual studies often focus on specific combinations host-pathogen making it difficult to define common recruitment principles of the pathogen-protective microbiota. To tackle this knowledge gap, my project pursued two objectives: a) to perform an appraisal of the literature, assembling a data matrix that will then be analysed for trends across studies, b) perform descriptive statistic analysis (in R 3.6.3) to evaluate how defined factors impact on the distribution of pathogen-protection microorganisms.
I started combing through the literature using a range of search terms and the names of key authors in the field. I initially focused the search in a five-year window from 2015-2020, although this was later expanded to a nine-year window. After this I proceeded to go through all the papers, producing summaries of each paper and creating a table of key information. The next step was to mine the papers for taxonomic information and create a data matrix. I assigned each study an alphanumeric identifier to act as a key for the table. To allow comparisons across the studies I focused on the higher taxonomic ranks such as family’s, for the sake of time I only considered the bacterial family’s in the data matrix. For each study, I would go through and find the information about the species identified that were suspected of having a suppressive effect and try to identify the genera and corresponding family. The matrix was laid out in such a way that if a study had a family with one genera present then it would have a ‘1’ in the corresponding box for that family, if they had two different genera then it would have a ‘2’ and so on.
Firstly I assessed the data file and removed any studies that don’t contain any bacterial family’s. I then performed multidimensional scaling (MDS) which singled out an individual study very different from the other studies and made the data difficult to interpret, so I decided to remove it. I then looked at a range of factors to determine what was driving this separation. I then attempted to identify what family’s where driving the ordination (see Figure 1a) and subsequently created a subset of studies where the pathogen Fusarium was present and performed MDS (see Figure 1b). Interestingly It seems that the type of pathogen, not the host is driving the recruitment of the microbiota, at P <0.05 this appears to be preferentially assembled by members of the Xanthomonadaceae, Streptomycetaceae, Bacillaceae, Nocardioidaceae and Cytophagaceae family’s (see Figure 1a). In the Fusarium Subset, only four of the family’s are present, perhaps unsurprisingly they are all members of family’s known to produce antimicrobial and antifungal compounds. More interestingly though, there appears to be a separation between gram-positive and gram-negative bacterial family’s (see Figure 1b). Although investigations at deeper resolution are needed to firmly infer first principles, my internship developed the basis for hypotheses to be tested under laboratory and field conditions.
In addition to my investigations in silico, I co-directed and produced, with another BSPP lockdown bursary awardee, a short video to promote the activities of my internship to the general public which was featured on the social media channels of the society. I am therefore very grateful to the BSPP for providing funding to support my internship and all the members of the Bulgarelli’s lab who made my “virtual” stay at the University of Dundee/The James Hutton Institute so enjoyable.
University of Dundee