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

MICAELA STIEBEN; SOLMI LEANDRO; GÁRRIZ ANDRES; OSCAR A RUIZ; FRANCO R. ROSSI; FERNANDO M. ROMERO

Chapadmalal

Congreso; XVIII Congreso SAMIGE; 2023

Sociedad Argentina de Microbiología General

Endophytic bacteria colonize host tissues internally without causing damage, and insome 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 antimicrobialcompounds. The aim of this work was to analyze the genome of these isolates to properlyidentify them and to search for genes responsible to produce different antimicrobialcompounds and traits related to intra and inter-kingdom interactions.Genomic DNA was purified and whole genome sequencing was performed. Theassembly and annotation were performed using Unicycler and Bakta software respectively. Phylogenetic identity was determined by whole genome-based taxonomic analysis usingType (Strain) Genome Server platform. The genomes were screened for secondarymetabolite and bacteriocin biosynthetic 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 (4,8 Mbp, 55% GC),4,345 CDSs; 339 hypotheticals proteins and 14 pseudogenes were identified. On the otherhand, 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 Bro11genome (4 Mbp, 49% GC) has 3,986 CDSs; 116 hypotheticals proteins and 21pseudogenes. The phylogenetic identity using whole genome sequences revealed thatBru13 belongs to the species Pantoea agglomerans, Bro5 was identified as Bacillusvelezensis and Bro11 as B. subtilis. Since these isolates were able to produce antibioticcompounds against other bacteria and fungi, their genomes were explored searching forsecondary metabolite and bacteriocin clusters. We identified nine regions in Bru13 includingantibiotics and siderophore clusters, whereas the genomes of Bro5 and Bro11 have 13 and11 regions clustering genes with antimicrobial functions. Regarding bacteriocins, weidentified 2 areas of interest in the Bru13 genome (bottromycin and carocin D), other 2 areasin Bro5 genome (amylocyclicin and LCI) and 3 in Bro11 (competence, subtilosin andsporulation killing factor). Finally, we explored the genomes searching for potential genesinvolved in intra and inter-kingdom communication. Thus, Bru13 showed componentsbelonging to type 1, 2, 5 and 6 secretion systems, also, genes involved in flagellum andtype IV pilus. On the other hand, Bro5 and Bro11 genomes showed no components relatedto 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 andbacteriocins in every genome that could be responsible for their antagonistic activity againstphytopathogens.