Elucidation of bioactive metabolite production potential of endophyte bacterial isolates by whole genome sequencing and polyphasic characterisation

Endophytes include bacterial or fungal microorganisms that live between/inside plant tissues but do not cause visible signs of disease in their host. In this study, whole genome sequencing by next generation sequencing and biochemical characterization of endophyte isolates G56Y1, G106K1, G119Y2T and G129K1-1, which were isolated from various annual plants and produced remarkable results in terms of plant growth promoter (PGP) markers in previous studies, were carried out. In addition, the susceptibilities of the isolates to various antibiotics were tested by standard disc method. As a result of whole genome sequencing using the Illumina HiSeq platform, the draft genome sizes of G56Y1, G106K1, G119Y2T and G129K1-1 coded endophyte isolates were determined as 4.2 Mb (4277605 bp), 4.5 Mb (4582803 bp), 4.8 Mb (4794802 bp) and 3.9 Mb (3886939 bp), respectively. The G+C content of the genomes of G56Y1, G106K1, G119Y2T and G129K1-1 isolates was 45.8%, 66%, 55.2% and 65.7%, respectively. As a result of whole genome based phylogenetic analysis, isolate G56Y1 matched with Bacillus amyloliquefaciens subsp. plantarum FZB42 with a digital DNA-DNA hybridization (dDDH) value of 88.7%; G106K1 isolate matched with Stenotrophomonas lactitubi M15 with a dDDH value of 61.8%; G119Y2T isolate matched with Arthrobacter gandavensis JCM 13316 with a dDDH value of 29.7% and G129K1-1 isolate matched with Pantoea agglomerans NBRC 102470 with a dDDH value of 88.8%. Considering the dDDH values, it was hypothesised that isolates G106K1 and G119Y2T with values of 61.8% and 29.7% could be new species belonging to the genera Stenotrophomonas and Arthrobacter, respectively. Genome analyses revealed that the isolates have gene/gene clusters encoding secondary metabolites of biotechnological importance such as terpene, thiopeptide, siderophore, betalactone, metelophore and arylpolyene. According to the antibiotic susceptibility results of the isolates, the most resistant isolate was G106K1 which showed complete resistance to ampicillin, penicillin G, florfenicol, erythromycin, nitrofurontoin and clindamycin. This isolate was followed by G129K1-1 which showed complete resistance to penicillin G, rifampin, erythromycin, nitrofurontoin and clindamycin. Isolate G119Y2T showed complete resistance only to cefepime antibiotic, while isolate G56Y1 showed complete resistance only to rifampin antibiotic.