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Pedobacter paludis sp. nov., isolated from wetland soil

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Abstract

A Gram-stain-negative, aerobic, non-motile, rod-shaped and non-spore-forming bacterium, designated YXT, was isolated from wetland soil. Compared to strain YXT, Pedobacter yonginense HMD1002T had the highest 16S rRNA gene sequence identity (97.8%), and the remaining strains had the identities below 97%. Phylogenetic analysis of the 16S rRNA gene sequences showed that strain YXT grouped with P. yonginense HMD1002T. The values of DNA–DNA hybridization and genomic orthologous average nucleotide identity (orthoANI) between strain YXT and Pedobacter yonginense KCTC 22721T were 58.5% and 82.0%, respectively. The genome size of strain YXT was 5.0 Mb, comprising 4369 predicted genes with a DNA G+C content of 37.3 mol %. Strain YXT had menaquinone-7 as the only respiratory quinone and polar lipids of phosphatidylethanolamine, sphingolipid, aminolipid and three unidentified lipids. The predominant cellular fatty acids (> 10%) of strain YXT were summed feature 3 (iso-C15:0 2-OH and/or C16:1ω7c), iso-C15:0 and iso-C17:0 3-OH. Strain YXT could be distinguished from the other Pedobacter members based on the data of phylogenetic distance, DNA–DNA hybridization, genomic orthoANI, RecA MLSA, core-protein comparison, and hydrolyses of l-arginine, utilization of d/l-lactate, l-alanine, 5-ketonic gluconate and glycogen. Therefore, strain YXT represents a novel species of the genus Pedobacter, for which the name Pedobacter paludis sp. nov. is proposed. The type strain is YXT (= KCTC 62520T = CCTCC AB 2018029T).

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Acknowledgements

We are grateful to Professor Prof. Bernhard Schink for the Latin construction of the species name. Fatty acids and polar lipid analyses were performed by Guangdong Detection Centre of Microbiology, P. R. China. This work was financially supported by the National Key Research and Development Program of China (2016YFD0800702) and National Natural Science Foundation of China (31870086).

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Authors and Affiliations

  1. State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People’s Republic of China

    Yuxiao Zhang, Jingxin Li & Gejiao Wang

  2. College of Basic Science, Huazhong Agricultural University, Wuhan, 430070, People’s Republic of China

    Jinling Wang

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  1. Yuxiao Zhang
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Correspondence to Gejiao Wang.

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Additional information

Communicated by Erko Stackebrandt.

The GenBank/EMBL/DDBJ accession number of the 16S rRNA gene sequence of strain YXT is MH307976. The genome numbers of strain YXT and Pedobacter yonginense KCTC 22721T are QGNY00000000 and QGNZ00000000, respectively.

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Zhang, Y., Li, J., Wang, J. et al. Pedobacter paludis sp. nov., isolated from wetland soil. Arch Microbiol 201, 349–355 (2019). https://doi.org/10.1007/s00203-018-1605-0

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