The first report on the isolation, genomic and biochemical characterization of endophyte Staphylococcus hominis from oat (Avena sativa L. cv. Albatros)

Endophytes include microorganisms that live in/between the tissues of plants but do not cause any visible signs of disease in their host. In this study, in silico analyses were performed on the whole genome data obtained using Illumina HiSeq sequencing technology for Staphylococcus sp. G15S1, isolated as an endophyte from Avena sativa L. cv. Albatros. The isolate was also examined İn vitro for its plant growth promoting (PGP) properties, biochemical characterization, resistance profile to some metals and antibiotics, and ability to synthesize hydrolytic enzymes. Detailed genomic analyses revealed that Staphylococcus sp. G15S1 genome consisted of a circular chromosome (2.21 Mbp; 31.4% G+C content). In the whole genome-based phylogenetic analysis, G15S1 was clustered together with Staphylococcus hominis NCTC 11320 with a digital DNA-DNA hybridization (dDDH) value of 92.9%. Annotation showed that the G15S1 genome consisted of 2199 protein-coding genes, 60 tRNAs, and 9 rRNA operons. Although genomic analyzes predicted that G15S1 encoded genes for phosphate solubility, siderophore, and indole acetic acid (IAA) synthesis, which were useful in promoting plant growth, İn vitro tests were negative for phosphate solubility and IAA synthesis. Genes for production of glutathione peroxidase, superoxide dismutase and peroxidases stress regulator that confer resistance to oxidative stress in plants were also identified in G15S1. Moreover, genes for choline and glycine betaine biosynthesis were also found in the genome related with osmotic stress. The core genome data revealed 44 genes responsible for the defense properties of the G15S1 isolate, including virulence, disease, resistance to antibiotics and toxic compounds. Furthermore, genomic mining for pathogenicity revealed 14 gene clusters encoding proteins such as regulatory protein BlaR1, QacA, beta-lactamase, LysR-type transcriptional regulator, transposase and staphylococcal accessory regulator A proteins. These findings strongly suggested that G15S1 matched with Staphylococcus hominis, might also be a human pathogen. This is the first report of the isolation of S. hominis from Avena sativa L. as an endophyte, supporting the hypothesis that the internal tissues of plants can be a reservoir for opportunistic human pathogenic bacteria.