Taxonomic and functional analysis of the endophytic microbiome associated with wild cold-adapted Rosaceae plants

Climate change-associated extreme weather events such as early spring frosts have increased in frequency and intensity over the past decades. Cold stress is one of the main limiting factors for fruit crop production worldwide. Plants growing in cold regions, such as alpine regions, are hypothesized to survive cold stress thanks to symbiosis with endophytic microorganisms. However, the structure and function of endophytic microbial communities associated with such plants are poorly understood. Here, we collected three wild cold-adapted Rosaceae plants (Geum montanum, Alchemilla sp. and Dryas octopetala) from seven different sites in Italy from two expositions (North and South). Using 16S rRNA gene amplicon sequencing, we characterized the bacterial community structure across three compartments (flowers, leaves and roots) to identify potential candidate taxa for cold tolerance. We complemented this analysis with a culture-dependent approach, a combination of a low nutrient medium (Reasoner's 2A agar), long incubation time (up to 4 weeks) and low temperature (at 4°C), to recover culturable psychrotolerant bacterial taxa. We successfully established a taxonomically diverse bacterial culture collections representing the majority of dominant genera detectable by culture-independent community profiling, including Pseudomonas, Erwinia, Sphingomonas, Rhizobium, Massilia, Janthinobacterium, Duganella and Flavobacterium. Additional work will test these isolates for their cold stress alleviation capacities on tomato and apple. Understanding the role of microbiomes in cold stress tolerance of plants will help to develop relevant bacterial inoculants for agricultural systems