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Pedobacter segetis sp. nov., a Novel Bacterium Isolated from Soil

  • 'Open Collection': Novel Prokaryotic Taxa
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Abstract

A Gram-negative, motile by gliding, rod-shaped, aerobic bacterium, designated SD-bT, was isolated from a soil sample collected on Dokdo Island, South Korea. A polyphasic approach based on phenotypic, phylogenetic, and genomic analyses was used to characterize the new isolate. Phylogenetic analysis of 16S rRNA gene sequence showed that strain SD-bT belonged to the family Sphingobacteriaceae and most closely related to Pedobacter psychrophilus P4487AT (95.9% similarity). The isolate contained MK-7 as the predominant respiratory quinone; its main polar lipid was phosphatidylethanolamine; and the major fatty acids were summed feature 3 (C16:1 ω7c/C16:1 ω6c; 32.0%), C15:0 iso (19.1%), C17:0 iso 3-OH (8.3%), and C16:0 (8.2%). The draft genome had a length of 3,842,102 bp with a G+C content of 36.0 mol%, predicting 3282 coding sequences, 3 rRNA genes, 3 ncRNAs, and 36 tRNAs genes. The digital DNA–DNA hybridization and average nucleotide identity values between strain SD-bT and P. psychrophilus LMG 29436T were 22.0% and 78.9%, respectively. The results of phenotypic properties, genotypic distinctiveness, and chemotaxonomic features support the discrimination of SD-bT from its phylogenetic relatives. Pedobacter segetis sp. nov. is therefore proposed with SD-bT (= KCTC 82351T = JCM 34283T) as the type strain.

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Data Availability

The 16S rRNA gene sequence of strain SD-bT has been deposited in NCBI GenBank/EMBL/DDBJ under the accession number LC578312. The Whole Genome Shotgun project number of strain SD-bT in GenBank/EMBL/DDBJ is JAEHFY000000000. The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain SD-bT is LC578312. The Whole Genome Shotgun project of strain SD-bT has been deposited at GenBank/EMBL/DDBJ under the accession number JAEHFY000000000. The datasets used or analyzed during the current study are available from the corresponding author on reasonable request.

Code Availability

Not applicable.

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Funding

This work was supported by the Brain Pool Program (Grant No. 2020H1D3A2A01103925) through the National Research Foundation (NRF) funded by the Ministry of Science and ICT, Republic of Korea.

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Author notes

  1. Leonid N. Ten and Weilan Li have contributed equally to this work.

Authors and Affiliations

  1. School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea

    Leonid N. Ten, Weilan Li, Soo-Min Hong, Seung-Yeol Lee & Hee-Young Jung

  2. Department of Bio and Environmental Technology, Seoul Women’s University, Seoul, 01797, Republic of Korea

    Myung Kyum Kim

  3. Institute of Plant Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea

    Seung-Yeol Lee & Hee-Young Jung

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  1. Leonid N. Ten
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  2. Weilan Li
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Contributions

All the authors contributed to the study conception and design. LNT analyzed the data and wrote the manuscript, WL performed the experiments and wrote the manuscript, SMH carried out polar lipid analysis and API tests, MKK analyzed chemotaxonomic data, SYL performed 16S rRNA phylogeny, HYJ designed, planned the study, and reviewed the manuscript. All authors read and approved the final version of the manuscript.

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Correspondence to Hee-Young Jung.

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Ten, L.N., Li, W., Hong, SM. et al. Pedobacter segetis sp. nov., a Novel Bacterium Isolated from Soil. Curr Microbiol 79, 71 (2022). https://doi.org/10.1007/s00284-021-02753-w

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