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; 2022

Sociedad Argentina de Microbiolgía General

Endophytic bacteria colonize host tissues internally without causing damage, and in some cases, they promote plant growth and confer protection against pathogens. Previously, we have selected 3 isolates with different plant-growth promotion traits: Bru13, Bro5 and Bro11. These were able to produce both soluble and volatile antimicrobial compounds. The aim of this work was to analyze the genome of these isolates to properly identify them and to search for genes responsible to produce different antimicrobial compounds and traits related to intra and inter-kingdom interactions.Genomic DNA was purified and whole genome sequencing was performed. The assembly and annotation were performed using Unicycler and Bakta software respectively. Phylogenetic identity was determined by whole genome-based taxonomic analysis using Type (Strain) Genome Server platform. The genomes were screened for secondary metabolite and bacteriocin biosynthetic clusters using AntiSMASH 2.0 and BAGEL4, respectively. Identification of potential secretion systems was performed on the webserver TXSScan.The genome assembly for Bru13 resulted in three circular contigs (4,8 Mbp, 55% GC), 4,345 CDSs; 339 hypotheticals proteins and 14 pseudogenes were identified. On the other hand, Bro5 and Bro11 resulted in one circular contig each. Bro5 genome (4,2 Mbp, 46% GC) contains 4,061 CDSs; 341 hypotheticals proteins and 23 pseudogenes. While Bro11 genome (4 Mbp, 49% GC) has 3,986 CDSs; 116 hypotheticals proteins and 21 pseudogenes. The phylogenetic identity using whole 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 produce antibiotic compounds against other bacteria and fungi, their genomes were explored searching for secondary metabolite and bacteriocin clusters. We identified nine regions in Bru13 including antibiotics and siderophore clusters, whereas the genomes of Bro5 and Bro11 have 13 and 11 regions clustering genes with antimicrobial functions. Regarding bacteriocins, we identified 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 explored the genomes searching for potential genes involved in intra and inter-kingdom communication. Thus, Bru13 showed components belonging to type 1, 2, 5 and 6 secretion systems, also, genes involved in flagellum and type IV pilus. On the other hand, Bro5 and Bro11 genomes showed no components related to secretion systems, but genes involved in flagellum and competence machinery.In conclusion, we were able to identify our isolates using the whole genome sequence. Also, we identified potential genes involved in the production of secondary metabolites and bacteriocins in every genome that could be responsible for their antagonistic activity against phytopathogens.