MINING THE GENOME OF THREE ENDOPHYTIC BACTERIA FROM Brassica CROPS THAT SHOW ANTAGONISTIC ACTIVITY AGAINST PHYTOPATHOGENS

STIEBEN M; SOLMI L; GÁRRIZ A; RUIZ OA; ROSSI FR; ROMERO FM

Chapadmalal

Congreso; XVIII Congreso de la Sociedad Argentina de Microbiolgía General; 2023

Sociedad Argentina de Microbiolgía General

Endophyticbacteria colonize host tissues internally without causing damage, and in somecases, they promote plant growth and confer protection against pathogens.Previously, we have selected 3 isolates with different plant-growth promotiontraits: Bru13, Bro5 and Bro11. These were able to produce both soluble andvolatile antimicrobial compounds. The aim of this work was to analyze thegenome of these isolates to properly identify them and to search for genesresponsible to produce different antimicrobial compounds and traits related tointra and inter-kingdom interactions. Genomic DNA was purified and whole genomesequencing was performed. The assembly and annotation were performed usingUnicycler and Bakta software respectively. Phylogenetic identity was determinedby whole genome-based taxonomic analysis using Type (Strain) Genome Serverplatform. The genomes were screened for secondary metabolite and bacteriocinbiosynthetic clusters using AntiSMASH 2.0 and BAGEL4, respectively.Identification of potential secretion systems was performed on the webserverTXSScan. The genome assembly for Bru13 resulted in three circular contigs (4,8Mbp, 55% GC), 4,345 CDSs; 339 hypotheticals proteins and 14 pseudogenes wereidentified. On the other hand, Bro5 and Bro11 resulted in one circular contigeach. Bro5 genome (4,2 Mbp, 46% GC) contains 4,061 CDSs; 341 hypotheticalsproteins and 23 pseudogenes. While Bro11 genome (4 Mbp, 49% GC) has 3,986 CDSs;116 hypotheticals proteins and 21 pseudogenes. The phylogenetic identity usingwhole genome sequences revealed that Bru13 belongs to the species Pantoea agglomerans, Bro5 was identified as Bacillus velezensis and Bro11 as B.subtilis. Since these isolates were able to produceantibiotic compounds against other bacteria and fungi, their genomes wereexplored searching for secondary metabolite and bacteriocin clusters. Weidentified nine regions in Bru13 including antibiotics and siderophoreclusters, whereas the genomes of Bro5 and Bro11 have 13 and 11 regionsclustering genes with antimicrobial functions. Regarding bacteriocins, weidentified 2 areas of interest in the Bru13 genome (bottromycin and carocin D),other 2 areas in Bro5 genome (amylocyclicin and LCI) and 3 in Bro11(competence, subtilosin and sporulation killing factor). Finally, we exploredthe genomes searching for potential genes involved in intra and inter-kingdomcommunication. Thus, Bru13 showed components belonging to type 1, 2, 5 and 6secretion systems, also, genes involved in flagellum and type IV pilus. On theother hand, Bro5 and Bro11 genomes showed no components related to secretionsystems, but genes involved in flagellum and competence machinery. Inconclusion, we were able to identify our isolates using the whole genomesequence. Also, we identified potential genes involved in the production ofsecondary metabolites and bacteriocins in every genome that could beresponsible for their antagonistic activity against phytopathogens.