Genomic adaptation in the CAZyome and specialised metabolism of the plant-associated Streptomyces violaceusniger clade

Streptomycetes are Gram-positive actinobacteria largely represented in the plant root microbiota. The genetic determinants involved in the presence of Streptomyces in the rhizosphere are largely unknown and can rely on the ability to degrade plant-derived compounds such as cell-wall polysaccharides and on the production of specialised metabolites. To address whether Streptomyces strains recruited into root microbiota share genomic specificities related to these two functions, we engaged a comparative genomic analysis using a newly sequenced rhizospheric strain, Streptomyces sp. AgN23 and strains from the phylogenetically related S. violaceusniger clade. This analysis enlightens a shared prominent CAZyome potentially involved in plant polysaccharides degradation and a strong conservation of antimicrobials biosynthetic clusters (rustmicin, mediomycin, niphimycin, nigericin) as well as plant bioactive compounds (nigericin, echosides, elaiophylin). Taken together, our work supports the hypothesis that specific hydrolytic enzymes and specialised metabolites repertoires may play important roles in the development of Streptomyces strains in the rhizosphere. ### Competing Interest Statement The following information may be foreseen as competing interest. B. Dumas is one of inventors of the patent WO2015044585A1 relating the use of AgN23 in Agriculture. T. Rey and D. Gayrard are full-time researchers in the AgChem company De Sangosse (Pont-Du-Casse, France), which registers and markets crop-protection products.