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Atopomonas sediminilitoris sp. nov., isolated from beach sediment of Zhairuo Island, China

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Abstract

A novel bacterium designated A3.4T was isolated from the beach sediment of Zhairuo Island, which is located in the East China Sea. Strain A3.4T was found to be Gram-stain negative, cream coloured, rod-shaped, aerobic and motile via a single monopolar flagellum. The isolate grows at 20–37 °C (optimum 25–30 °C), at pH 6.0–8.0 (optimum pH 7.0–8.0), and in the presence of 0–5.0% (w/v) NaCl (optimum 0.5–1%). A3.4T has catalase and oxidase activity. The predominant fatty acids (≥ 10%) of the strain were identified as C16:0, summed feature 3 (C16:1 ω7c /C16:1 ω6c) and summed feature 8 (C18:1 ω7c /C18:1 ω6c). Q-9 was identified as the major isoprenoid quinone, with trace levels of Q-8 present. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The draft genome size is 3.55 Mb, with a DNA G + C content of 57.7 mol%. Analysis of the 16S rRNA gene sequence of strain A3.4T indicates that it belongs to the genus Atopomonas and shares high sequence similarity with Atopomonas hussainii JCM 19513T (97.60%). This classification was also supported by phylogenetic analysis using rpoB and several core genes. The genome of strain A3.4T shows an average nucleotide identity of 82.3%, an amino acid identity of 83.0%, and a digital DNA–DNA hybridization value of 22.1% with A. hussainii. In addition, 20 conserved signature indels (CSIs) were identified to be specific for A3.4T and A. hussainii, demonstrating that the strain A3.4T is closely related to A. hussainii rather than other species of family Pseudomonadaceae. Hundreds of unique genes were identified in the genomes of A3.4T and A. hussainii, which may underly multiple phenotypic differences between these strains. Based on phenotypic, chemotaxonomic, phylogenetic, and genomic investigations, strain A3.4T is concluded to represent a novel species of the genus Atopomonas, for which the name Atopomonas sediminilitoris sp. nov. is proposed. The type strain is A3.4T (= LMG 32563T = MCCC 1K07166T).

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References

  • Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  CAS  Google Scholar 

  • Anwar N, Abaydulla G, Zayadan B et al (2016) Pseudomonas populi sp. nov., an endophytic bacterium isolated from populus euphratica. Int J Syst Evol Microbiol 66:1419–1425

    Article  CAS  Google Scholar 

  • Bankevich A, Nurk S, Antipov D et al (2012) SPAdes: a New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. J Comput Biol 19:455–477

    Article  CAS  Google Scholar 

  • Blin K, Shaw S, Steinke K et al (2019) antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acid Res 47:W81–W87

    Article  CAS  Google Scholar 

  • Chun J, Oren A, Ventosa A et al (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466

    Article  CAS  Google Scholar 

  • Debnath SC, Chen C, Liu S-X et al (2019) Flavobacterium sharifuzzamanii sp. nov., Isolated from the Sediments of the East China Sea. Curr Microbiol 76:297–303

    Article  CAS  Google Scholar 

  • Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    Article  CAS  Google Scholar 

  • Fox GE, Wisotzkey JD, Jurtshuk P (1992) How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 42:166–170

    Article  CAS  Google Scholar 

  • Frank JA, Reich CI, Sharma S et al (2008) Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 74:2461–2470

    Article  CAS  Google Scholar 

  • Glaeser SP, Kämpfer P (2015) Multilocus sequence analysis (MLSA) in prokaryotic taxonomy. Syst Appl Microbiol 38:237–245

    Article  CAS  Google Scholar 

  • Gupta RS (2014) Chapter 8–identification of conserved indels that are useful for classification and evolutionary studies. In: Goodfellow M, Sutcliffe I, Chun J (eds) methods in microbiology. Academic Press, pp 153–182

    Google Scholar 

  • Hameed A, Shahina M, Lin S-Y et al (2014) Pseudomonas hussainii sp. nov., isolated from droppings of a seashore bird, and emended descriptions of pseudomonas pohangensis, pseudomonas benzenivorans and pseudomonas segetis. Int J Syst Evol Microbiol 64:2330–2337

    Article  CAS  Google Scholar 

  • Hesse C, Schulz F, Bull CT et al (2018) Genome-based evolutionary history of pseudomonas spp. Environ Microbiol 20:2142–2159

    Article  CAS  Google Scholar 

  • Jain C, Rodriguez-R LM, Phillippy AM et al (2018) High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 9:5114

    Article  Google Scholar 

  • Kamlage B (1996) Methods for general and molecular bacteriology. edited by P. Gerhardt, R. G. E. Murray, W. A. Wood and N. R. Krieg. 791 pages, numerous figures and tables. American Society for Microbiology, Washington, D.C., 1994. Food Nahr 40:103–103

    Article  Google Scholar 

  • Kim J, Na SI, Kim D et al (2021) UBCG2: up-to-date bacterial core genes and pipeline for phylogenomic analysis. J Microbiol 59:609–615

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  CAS  Google Scholar 

  • Komagata K, Suzuki K-I (1988) 4 lipid and cell-wall analysis in bacterial systematics. In: Colwell RR, Grigorova R (eds) methods in microbiology. Academic Press, pp 161–207

    Google Scholar 

  • Li W, O’Neill KR, Haft DH et al (2021) RefSeq: expanding the prokaryotic genome annotation pipeline reach with protein family model curation. Nucleic Acid Res 49:D1020–D1028

    Article  CAS  Google Scholar 

  • Macián M, Arahal D, Garay E et al (2005) Thalassobacter stenotrophicus gen. nov., sp. nov., a novel marine α-proteobacterium isolated from mediterranean sea water. Int J Syst Evol Microbiol 55:105–110

    Article  Google Scholar 

  • Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60

    Article  Google Scholar 

  • Minnikin DE, Odonnell AG, Goodfellow M et al (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Method 2:233–241

    Article  CAS  Google Scholar 

  • Raghunath P (2014) Roles of thermostable direct hemolysin (TDH) and TDH-related hemolysin (TRH) in Vibrio parahaemolyticus. Front Microbiol 5:805

    Google Scholar 

  • Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106:19126–19131

    Article  CAS  Google Scholar 

  • Rodriguez-R LM, Konstantinidis KT (2014) Bypassing cultivation to identify bacterial species. Microbe 9:111–118

    Google Scholar 

  • Rudra B, Gupta RS (2021) Phylogenomic and comparative genomic analyses of species of the family Pseudomonadaceae: proposals for the genera Halopseudomonas gen. nov. and Atopomonas gen. nov., merger of the genus Oblitimonas with the genus Thiopseudomonas, and transfer of some misclassified species of the genus Pseudomonas into other genera. Int J Syst Evol Microbiol 71 9 005011

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  Google Scholar 

  • Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 20:1–6

    Google Scholar 

  • Sethi D, Mahajan S, Singh C et al (2016) Lipoprotein LprI of mycobacterium tuberculosis acts as a lysozyme inhibitor*. J Biol Chem 291:2938–2953

    Article  CAS  Google Scholar 

  • Sofi MY, Shafi A, Masoodi KZ (2022) Chapter 8–CLUSTALW software. In: Sofi MY, Shafi A, Masoodi KZ (eds) bioinformatics for everyone. Academic Press, pp 75–84

    Chapter  Google Scholar 

  • Sudan SK, Pal D, Bisht B et al (2018) Pseudomonas fluvialis sp. nov., a novel member of the genus Pseudomonas isolated from the river Ganges. India Int J Syst Evol Microbiol 68:402–408

    Article  CAS  Google Scholar 

  • Xia X (2018) Maximum parsimony method in phylogenetics. In: Xia X (ed) Bioinformatics and the cell: modern computational approaches in genomics, proteomics and transcriptomics. Springer International Publishing, Cham, pp 327–341

    Chapter  Google Scholar 

  • Ye Y, Chen C, Ren Y et al (2019) Pseudomonas mangrovi sp. nov., isolated from mangrove soil. Int J Syst Evol Microbiol 69:377–383

    Article  CAS  Google Scholar 

  • Yoon S-H, Ha S-M, Kwon S et al (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617

    Article  CAS  Google Scholar 

  • Yu X-Y, Zhai J-Y, Wu C et al (2018) Pseudomonas pharmafabricae sp. nov., isolated from pharmaceutical wastewater. Curr Microbiol 75:1119–1125

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank Dr. Xu Youping (Analysis Center of Agrobiology and Environmental Sciences, Faculty of Agriculture, Life and Environment Sciences, Zhejiang University) for fatty acid analysis. We also thank the equipment support of the Field Scientific Observation and Research Station of Ministry of Education of Marine Ecosystem in Zhoushan Islands, Zhejiang Province.

Funding

This study was supported by a grant from the National Key research and development Program of China (2021YFA0909500), Fundamental Research Funds for the Central Universities (2021XZZX018), and the National Natural Science Foundation of China Grants (32022004 and 32170078).

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Authors and Affiliations

  1. Hainan Institute of Zhejiang University, Sanya, 572000, China

    Kejing Li, Zhenbo Ye, Gen Chen, Kaiwen Zheng, Jun Yin, Cen Yan, Yi Hong, Zhen Guo, Pinmei Wang & Daoqiong Zheng

  2. Ocean College, Zhejiang University, Room 303, Marine Science Building, No.1 Zheda Road, Dinghai District, Zhoushan, 316021, Zhejiang, China

    Kejing Li, Gen Chen, Kaiwen Zheng, Jun Yin, Sanjit Chandra Debnath, Cen Yan, Pinmei Wang & Daoqiong Zheng

  3. ZJU-Hangzhou Global Scientific and Technological Innovation Center, No.733 Jianshe San Road, Xiaoshan District, Hangzhou, 311200, Zhejiang, China

    Kejing Li, Fabai Wu & Daoqiong Zheng

  4. Biosciences, Geoffrey Pope Building, University of Exeter, Exeter, EX4 4HB, Devon, UK

    Sanjit Chandra Debnath

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  1. Kejing Li
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Contributions

Sanjit Chandra Debnath isolated the bacterium; Kejing Li performed the phenotypic and biochemical experiments, analysed the data, and drafted the manuscript; Zhenbo Ye, Gen Chen, Kaiwen Zheng, Jun Yin, Cen Yan, Yi Hong and Zhen Guo provided supports during the experiments performing and data analysis; Daoqiong Zheng, Fabai Wu and Pinmei wang designed and supervised the study and edited the original draft.

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Correspondence to Fabai Wu or Daoqiong Zheng.

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Li, K., Ye, Z., Chen, G. et al. Atopomonas sediminilitoris sp. nov., isolated from beach sediment of Zhairuo Island, China. Antonie van Leeuwenhoek 116, 97–107 (2023). https://doi.org/10.1007/s10482-022-01780-2

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