Aim: Potato cultivation in southwest Greenland, at Inneruulalik, omits the use of pesticides while relying on limited crop rotations and despite the presence of plant pathogens in the soil does not suffer from major disease outbreaks. Previously, we have shown that the soil at Inneruulalik is disease suppressive owing to the presence of diverse antimicrobial microorganisms. Using culture-based approaches, the psychrotroph Pseudomonas fluorescens In5 was previously isolated from the soil microbiome. The aim of this study is to unravel key biocontrol traits underpinning the antagonistic activity of this cold-active bacterium against phytopathogens.

Method: A combination of different technologies including genomics, transcriptomics and metabolomics are being used to explore the interaction of the psychrotroph P. fluorescens In5 in dual-culture with diverse plant pathogens. To date, molecular genetics coupled with MALDI imaging mass spectrometry (MALDI-IMS) have successfully identified a large antifungal genomic island encoding two secondary metabolites (nunamycin and nunapeptin) assembled by non-ribosomal peptide synthetases (NRPS). Functional analysis of genes located on the island uncovered a LuxR-type regulator required for secondary metabolite biosynthesis. The development of reporter strains and a microplate reader-based method for studying microbial interactions enabled further characterization of the regulator during bacterial-fungal interactions. Finally, whole-transcriptome analysis using RNA sequencing was conducted to investigate the response of the bacterium to different plant pathogens in dual-culture.

Results/Discussion: Key biocontrol components of P. fluorescens In5 identified to date include the two secondary metabolites nunamycin and nunapeptin that form part of a complex interaction whereby nunamycin appears most active against the basidiomycete Rhizoctonia solani in contrast to nunapeptin, which is most potent against the oomycete Pythium aphanidermatum. Regulation of peptide synthesis is mediated by a LuxR-type regulator that switches on when the bacterium enters the deceleration growth phase and upon physical encounter with fungal hyphae. Furthermore, the regulator is strongly upregulated in response to carbon sources indicating the presence of a fungus suggesting that environmental elicitors may also influence regulator expression, which upon activation controls nunamycin and nunapeptin production required for the growth inhibition of phytopathogens. Recent transcriptomic profiling of In5 in dual-culture with two different phytopathogens revealed the specific response of the bacterium to R. solani and identified novel gene targets for functional analysis that may play specific roles in the bioactivity or alternatively defense of In5 against phytopathogens.

Conclusion: Climate change is altering the Arctic at a rate unmatched anywhere in the world with global warming paving the way for new agricultural opportunities in Low Arctic and Subarctic regions. However, rising temperatures could lead to increased problems with soil-borne pathogens and importantly the application of synthetic fungicides in cold areas may be problematic due to slow degradation. Thus, the application of environmentally friendly biological control agents may provide an alternative sustainable solution for combatting plant pathogenic fungi. Current studies are aimed at unravelling further the complex mode of action underpinning the antagonistic activity of In5 in order to develop effective microbial biocontrol agents (mBCAs) for the management of soil-borne plant diseases.