Pantoea endophytica sp. nov., novel endophytic bacteria isolated from maize planting in different geographic regions of northern China

• Published in: Systematic and applied microbiology 2019-07, Vol.42 (4), p.488-494
• Main Authors: Gao, Jun-lian, Xue, Jing, Yan, Hui, Tong, Shuai, Sayyar Khan, Mohammad, Wang, Li-wei, Mao, Xiao-jie, Zhang, Xiuhai, Sun, Jian-guang
• Format: Article
• Language: English
• Subjects: Genome; Pantoea endophytica; Phylogeny; Polyphasic approach; Zea mays L
• ISSN: 0723-2020; 1618-0984
• DOI: 10.1016/j.syapm.2019.06.001

Four endophytic bacterial strains were isolated from root, stem and leaf of maize planted in different regions of northern China. The four strains possessed almost identical 16S rRNA gene sequences. However, REP-PCR fingerprint patterns discriminated that they were not from one clonal origin. Furthermore, the average nucleotide identity (ANI) values among them were higher than 95%, suggesting they all belong to one species. Based on 16S rRNA gene phylogeny, the four strains were clustered together with Pantoea rodasii LMG 26273T and Pantoea rwandensis LMG 26275T, but on a separate branch. Multilocus sequence analysis (MLSA) indicated that the four strains form a novel Pantoea species. Authenticity of the novel species was confirmed by ANI comparisons between strain 596T and its closest relatives, since obtained values were considerably below the proposed thresholds for the species delineation. The genome size of 596T was 5.1Mbp, comprising 4896 predicted genes with DNA G+C content of 57.8mol%. The respiratory quinone was ubiquinone-8 (Q-8) and the polar lipid profile consisted of phosphatidylethanolamin, diphosphatidylglycerol, phosphatidylglycerol, unidentified aminophospholipid and unidentified phospholipid. The major fatty acids of strain 596T were C16:0, summed feature 2 (C12:0 aldehyde), summed feature 3 (C16:1ω7c and/or C16:1ω6c) and summed feature 8 (C18:1ω7c and/or C18:1ω6c). Based on phylogenetic, genomic, phenotypic and chemotaxonomic data, the four isolates are considered to represent a novel species of the genus Pantoea, for which the name Pantoea endophytica sp. nov., is proposed, with 596T (=DSM 100,785T=CGMCC 1.15280T) as type strain.