Genome features
Genome features of strain PIT were depicted in Supplementary Table S1. The genome size of the strain PIT was 2809662 bp consisting of 2653 genes which include 39 tRNAs genes, 2 sRNA genes and 4 rRNA genes (one 5S, one 16S and two 23S rRNA genes). The N50 value was 308341 bp and the N90 value was 96858 bp. The depth of sequencing coverage was 549 ×. The gene length distribution of strain PIT was mainly concentrated in the range of 300–800 bp and more than 2000 bp (more than 200 bp), the detailed information was depicted in supplementary materials (Fig. S4). The secondary function of strain PIT according to KEGG consisted of metabolism, genetic information processing, environmental information processing, cellular processes, human diseases and organismal systems. There were 2730 genes described by KEGG result annotation, in which 444 genes were related to metabolic pathways, 203 genes were related to biosynthesis of secondary metabolites, 149 genes were related to biosynthesis of antibiotics and 113 genes were related to microbial metabolism in diverse environments. Virulence Factors of Pathogenic Bacteria (VFDB) analysis indicated that strain PIT possessed virulence related genes, which involved in induction of apoptosis, proteolysis, immune system evasion, efflux pump, glycosylation of the flagellin, biofilm formation, cellular invasion, cell adhesion, resistance to serum killing and antibiotic susceptibility. The secondary metabolite of strain PIT was predicted to be arylpolyene and siderophore, which was consisted 12 and 49 genes, respectively. The resistance genes of strain PIT determined its resistance to fluoroquinolone, beta-lactam, isoniazid, aminoglycoside and glycopeptide (Details in Table S3). The Cluster of Orthologous Groups of proteins (COG) of strain PIT included 24 function classifications, for instance, those involved in posttranslational modification, protein turnover, chaperones, transcription, lipid transport and metabolism, coenzyme transport and metabolism, secondary metabolites biosynthesis, transport and catabolism (detailed in Fig. S5).
The DNA G + C content of strain PIT was 48.5 mol%, which was within the range of DNA G + C contents for species of the genus Kangiella (43–49 mol%) previously reported. The AAI value between strain PIT and the most related type strain K. sediminilitoris was 83.9% (between 90% and 60%, which were probably the threshold value for species and genus, respectively) (Rodríguez-R and Konstantinidis 2014a). The ANI values between strain PIT and the reference strains of K. sediminilitoris, K. aquimarina and K. taiwanensis were 76.9%, 71.0% and 74.6%, respectively, which were far below the described ANI values (95.0–96.0%) for species classification (Kim et al. 2014). The dDDH values between strain PIT and K. sediminilitoris, K. aquimarina and K. taiwanensis were 19.8%, 19.1% and 18.7%, respectively, which were lower than the prescribed species delineation standard of 70% (Meier-Kolthoff et al. 2013). The specific result of ANI, dDDH and AAI values between strain PIT and neighbour type strains were depicted in supplementary materials (Table S2). Based on the analysis of genome sequence, strain PIT was proposed to accommodate the novel strains of genus Kangiella. A complete 16S rRNA gene sequence (1564 bp) obtained from the genome sequence was 99.8% similar with the clone sequence (1525 bp) deposited in GenBank under accession number JACNML000000000.
Description of Kangiella shandongensis sp. nov
Kangiella shandongensis (shan.dong.en’sis. N.L. fem. adj. shandongensis pertaining to Shandong, where the type strain was isolated).
Cells (0.4–0.5 µm×1.0–2.0 µm) are Gram-staining negative, aerobic, motile, rod-shaped and non-spore-forming. The colonies are wheat, circular, flat, smooth, opaque and 1–2 mm in diameter after cultured on MA at 30 ℃ for 3 days. Growth occurs at 4–45℃ (optimum 33℃), pH 6.0–9.0 (optimum 7.0) and 1.0–11.0% (w/v) NaCl (optimum 3.0%). The predominant ubiquinone is Q-8 and the major fatty acids are iso-C15:0, iso-C11:0 3-OH, and Summed Feature 9 (iso-C17:1ω9c). The major polar lipids are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine and phosphatidylinositol. The DNA G + C content is 45.8 mol%.
The type strain is PIT (= KCTC 82509T = MCCC 1K04352T), isolated from saline silt samples collected in saltern in Yantai, Shandong, China. The 16S rRNA gene and genome sequences of strain PIT were submitted to GenBank with accession numbers MW407073 and JACNML000000000 respectively.