Understanding the rules of life

Bioscience for sustainable agriculture and food

Category: Standard Studentships

Bacterial symbiosis in the soil – unlocking new antibiotics and pesticides

Project No.2239

Primary Supervisor

Dr Simon Moore – University of Kent


Dr Matevz Papp-Rupar – NIAB EMR

Prof Xiangming Xu – NIAB EMR


Impact – Agriculture is worth about £24 billion to the UK bioeconomy, but it is threatened by rising levels of pest resistance, global warming and extreme weather events. Synthetic biology aims to design and engineer new life, using standardised parts and devices tested through the design-build-test-learn cycle approach.  

This project aims to study the microbiome and symbiotic interactions between soil bacteria and strawberry plants (Fragaria x ananassa). Specifically, we will target bacterial symbiotic interactions in commercial strawberry production, which is severely compromised by crown rot pathogen Phytopyhora cactorum leading to losses of up to 30% every year.  

In the build-up to the project, Dr Matevz Papp-Rupar has isolated over 80 Actinomycetes strains, including Streptomyces found to co-localise with plant roots. These bacterial families are a renowned treasure chest of antibiotics and herbicides – providing 2/3 of all clinical antibiotics used today. We aim to characterise the natural Actinobacteria microbiome and exploit novel factors that aid the survival of Actinobacteria, strengthen the symbiosis and protect the plant, through secretion of antifungals or plant growth promoting factors. 

This project has four specific aims: 

  1. Study natural interactions of wild Streptomyces isolates with strawberry roots in microcosm and commercial and track the bacteria with molecular and imaging/fluorescence methods. 
  1. Characterise the secondary metabolites (SMs) produced by the strawberry associated wild Streptomyces isolates (~80 in total) for antibacterial, antifungal, and anti-oomycete activity in-vitro. 
  1. Perform genome sequencing of select strains and analyse the secondary metabolite biosynthetic gene clusters 
  1. Purify natural SMs and characterise by HPLC, Mass Spectroscopy, Nuclear Magnetic Resonance, and bioactivity assays. 

The Moore lab (Uni of Kent) will assist with synthetic biology (integrative plasmid tools) to study how the bacteria co-localise with F. ananassa roots. First, we need to study which wild strains can be genetically modified using conjugation and/or protoplast transformation. Then we can integrate strong expression plasmids making mScarlet-I protein to label and visualise bacterial cells on plant roots.  

Next, the student will assess biocontrol and plant growth promoting activity of the strains in Papp-Rupar / Xu lab. The activity will be assessed in model plant Arabidopsis thaliana and strawberry in-vitro tissue cultures followed by studies in soil and other media in Arabidopsis and strawberry. Sporulating Streptomyces with biocontrol potential will also be screened. The Moore lab has the equipment (preparative HPLC, rotary evaporator, chromatography columns) and expertise to assist with natural product purification and characterisation by NMR at Kent. 

Rationale – Natural symbiotic interactions are severely understudied area of biology but have enormous potential to complement traditional agricultural chemical methods such pesticides and fertiliser. This project will use synthetic biology to study wild symbiotic Streptomyces bacteria and assess their potential to protect strawberry plants and/or provide commercially relevant bioactive natural products.