The pangenome of environmental Gram-negative bacteria and its hidden, but promising, biotechnological potential

Secondary metabolites (SMs) produced by bacteria from unusual environments can contribute to mitigate some of the health and environmental challenges we face. The knowledge of the diversity and applicability of SMs produced by environmental Gram-negatives is lagging behind that of Gram-positives. Examples include some members of genus Pedobacter that produce nonribosomal peptides active against bacteria listed by the WHO as a priority for R&D of new drugs. Herein, a total of 233 biosynthetic gene clusters (BGCs) were identified in the Pedobacter´s pangenome, which encode the biosynthesis of RiPPs (27%), terpenes (22%), hybrid SMs (17%), PKs (12%), NRPs (9%) and siderophores (6%). Most of BGCs did not have significant hits with MIBiG database, which highlights the novelty of their products. From all species, P. cryoconitis and P. lusitanus encode the highest number and diversity of BGCs. Giving their applicability and ecological roles, the BGCs for the production of siderophores and terpenoids were analysed in detail. It was concluded that some species can be a source of squalene and novel siderophores and carotenoids, which deserve further characterization. This study highlights the genus Pedobacter as a prolific source of SMs, probably with a wide range of biological activities and applications hitherto unknown.