Written by Alessandro Passera at the University of Milan. This is the report from a BSPP Incoming Fellowship. Click here to read more/apply for one yourself.
In recent years it has become increasingly clear how plants host myriad of different microbes, collectively referred to as the plant microbiome. The ‘who-is-who’ in the plant microbiome is now at centre-stage in both basic science and translational applications. For instance, we’re often asking ourselves what kind of microbes are interacting with the plants, where and when these interactions take place, and most importantly how they take place and which effect they can have on the health and yield of plants, especially crops.
One of the models of my lab is maize, a staple crop globally, whose yields are threatened by losses derived from fungal infections both in the field and in post-harvest. Perhaps more dreadful are the consequences of the infection of pathogenic fungi such as Aspergillus spp. and Fusarium spp. capable of producing extremely stable mycotoxins that are known to be carcinogenic and to accumulate in food containing or derived from infected kernels.
Former investigations in the lab led to the discovery of locally adapted maize landraces displaying different degree of resistance towards these pathogenic fungi. Intriguingly, host genetics alone couldn’t explain such degree of resistance and this prompted me to ask whether the plant microbiome, in particular the seed microbiome, contributed to the protection of the plant.
What fascinates me is that tackling this question requires the application of next-generation sequencing and bioinformatics approaches, an area of experimental of science I wanted to learn more of to strengthen my existing skills. I therefore seized the opportunity to apply for the BSPP Incoming Fellowship to visit for three months the lab of Davide Bulgarelli at the University of Dundee/The James Hutton Institute, to capitalise on and learn from their expertise and tools to study the plant microbiome.
Pleased with the positive outcome of application, I moved to Dundee bringing with me the raw sequencing data of the bacterial communities inhabiting maize seeds (i.e. 16S rRNA gene profiles) that needed to be analysed but, much to our dismay, it turned out that the embryos of maize are a difficult starting material for microbiome profiling. In particular, the vast majority of the results were sequences belonging to the plant itself, even when employing countermeasures designed especially to reduce the number of plant-derived sequences.
We swiftly decided to overcome this limitation by generating a new sequencing library from my original DNA preparations. I mined the existing literature and found approaches optimised for inhibiting the cross amplification of mitochondrial and plastidial sequences, the main source of “plant-contamination”, from rice. I reasoned that this approach would have been more effective in maize, a monocot like rice. I then left the computer desk where I spent the initial part of the fellowship and moved back to the lab where I was able to generate a new sequencing library prior my departure. These data (under processing at the time of writing this report) will integrate the initial data and will provide us with a clearer picture of the bacterial communities populating maize seeds.
Still, the initial data analysis provide some hints on bacteria of the seed maize microbiome, in particular members of the families Propionibacteraceae and Moraxellaceae, differentially associated to maize landraces, and, in turn, their potential contribution to host disease resistance. Back in my lab in Italy, this crucial piece of information will allow me to interrogate existing bacterial collection derived from maize seeds and identify members to be tested for their presumed contribution to pathogen protection.
In addition, during my stay in Dundee I had the chance to not only gain knowledge on how to use microbiome sequencing data, but also to contribute to the activities of the lab by sharing my experience in working with plant growth promoting and biocontrol bacteria. Finally, I was delighted to participate in the annual outreach activity organised by the Division of Plant Sciences at Dundee Botanic Garden where I raised the awareness of the general public on the contribution of plant pathology to sustainable agriculture and development. I am therefore very grateful to the BSPP for providing funding to support my visit and all the members of the Bulgarelli’s lab who made my stay at the University of Dundee/The James Hutton Institute so enjoyable.
University of Milan