Skip to main content
SpringerLink
Log in

Xanthomonas chitinilytica sp. nov., a novel chitinolytic bacterium isolated from a microbial fermentation bed material

  • Original Paper
  • Published:
Antonie van Leeuwenhoek Aims and scope Submit manuscript

Abstract

A Gram-stain-negative bacterium, H13-6T, was isolated from a microbial fermentation bed material collected from a pig farm located in Yan’an, Shaanxi, China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain H13-6T was affiliated with the genus Xanthomonas and showed highest similarity to strain Xanthomonas maliensis M97T (98.38%), Xanthomonas prunicola CFBP 8353T (98.26%) and Xanthomonas oryzae ATCC 35933T (98.11%). The pairwise ortho Average Nucleotide Identity values and the digital DNA-DNA hybridization values between strain H13-6T and the other Xanthomonas species were all below their respective cut-offs. Two genes encoding for chitinase were found and the strain showed a strong chitin-degrading activity. The major fatty acids were Iso-C15:0 (55.9%), Antesio-C15:0 (7.4%) and Iso-C11:0 (5.5%) and the major polar lipids were diphosphatidylglycerol, phosphatidyglycerol and phosphatidylethanolamine. Based on the phenotypic properties and phylogenetic distinctiveness, Xanthomonas chitinilytica was proposed as a novel species of the genus Xanthomonas, with strain H13-6T (= CGMCC 1.61317T = NBRC 115641T) as type strain.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

Data availability

This Whole Genome Shotgun project of strain H13-6T has been deposited at DDBJ/ENA/GenBank under the accession JAPCHY000000000. The version described in this paper is version JAPCHY000000000.1. The GenBank/EMBL/DDBJ accession numbers for 16S rRNA gene sequence is ON115013. The type strain H13-6T was deposited at the China General Microbiological Culture Collection Centre (CGMCC 1.61317T) and Biological Resource Center, NITE (NBRC 115641T).

References

  • Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477

    Article  CAS  PubMed Central  Google Scholar 

  • Bansal K, Kaur A, Midha S, Kumar S, Korpole S, Patil PB (2021) Xanthomonas sontii sp. nov., a non-pathogenic bacterium isolated from healthy basmati rice (Oryza sativa) seeds from India. Antonie Van Leeuwenhoek 114:1935–1947

    Article  CAS  PubMed  Google Scholar 

  • Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, Van Wezel GP, Medema MH, Weber T (2021) antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 49:W29–W35

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dowson DW (1939) On the systematic position and generic names of the Gram negative bacterial plant pathogens. Zentralblatt Für Bakteriologie U.s.w. 100:17

    Google Scholar 

  • Essakhi S, Cesbron S, Fischer-Le Saux M, Bonneau S, Jacques MA, Manceau C (2015) Phylogenetic and variable-number tandem-repeat analyses identify nonpathogenic Xanthomonas arboricola lineages lacking the canonical type III secretion system. Appl Environ Microbiol 81:5395–5410

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies—an approach using the bootstrap. Evolution 39:783–791

    Article  PubMed  Google Scholar 

  • Fitch WM (1971) Toward defining course of evolution - minimum change for a specific tree topology. Syst Zool 20:406

    Article  Google Scholar 

  • Galperin MY, Makarova KS, Wolf YI, Koonin EV (2014) Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res 43:D261–D269

    Article  PubMed  PubMed Central  Google Scholar 

  • Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91

    Article  CAS  PubMed  Google Scholar 

  • Hauben L, Vauterin L, Swings J, Moore ER (1997) Comparison of 16S ribosomal DNA sequences of all Xanthomonas species. Int J Syst Bacteriol 47:328–335

    Article  CAS  PubMed  Google Scholar 

  • Jain C, Rodriguez RL, Phillippy AM, Konstantinidis KT, Aluru S (2018) High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 9:5114

    Article  PubMed Central  Google Scholar 

  • Kanehisa M, Sato Y, Kawashima M (2021) KEGG mapping tools for uncovering hidden features in biological data. Protein Sci 31:47–53

    Article  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Kotb E, Alabdalall AH, Alghamdi AI, Ababutain IM, Aldakeel SA, Al-Zuwaid SK, Algarudi BM, Algarudi SM, Ahmed AA, Albarrag AM (2023) Screening for chitin degrading bacteria in the environment of Saudi Arabia and characterization of the most potent chitinase from Streptomyces variabilis Am 1. Sci Rep 13:11723

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kovacs N (1956) Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 178:703–703

    Article  CAS  PubMed  Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee I, Ouk Kim Y, Park SC, Chun J (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103

    Article  CAS  PubMed  Google Scholar 

  • Lopez MM, Lopez-Soriano P, Garita-Cambronero J, Beltran C, Taghouti G, Portier P, Cubero J, Fischer-LeSaux M, Marco-Noales E (2018) Xanthomonas prunicola sp. nov., a novel pathogen that affects nectarine (Prunus persica var. nectarina) trees. Int J Syst Evolut Microbiol 68:1857–1866

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  • Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, GöKER M (2021) TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 50:D801–D807

    Article  PubMed Central  Google Scholar 

  • Merda D, Bonneau S, Guimbaud J-F, Durand K, Brin C, Boureau T, Lemaire C, Jacques MA, Fischer-Le Saux M (2016) Recombination-prone bacterial strains form a reservoir from which epidemic clones emerge in agroecosystems. Environ Microbiol Rep 8(5):572–581

    Article  PubMed  Google Scholar 

  • Powers EM (1995) Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 61:3756–3758

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rana R, Madhavan VN, Saroha T, Bansal K, Kaur A, Sonti RV, Patel HK, Patil PB (2022) Xanthomonas indica sp. nov., a novel member of non-pathogenic Xanthomonas community from healthy rice seeds. Curr Microbiol 79:304

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rossello-Mora R, Amann R (2015) Past and future species definitions for Bacteria and Archaea. Syst Appl Microbiol 38:209–216

    Article  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. Usfcc Newsl

  • Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 8:6–9

    Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vauterin L, Hoste B, Kersters K, Swings J (1995) Reclassification of Xanthomonas. Int J Syst Evol Microbiol 45:472–489

    CAS  Google Scholar 

  • Vauterin L, Rademaker J, Swings J (2000) Synopsis on the taxonomy of the genus Xanthomonas. Phytopathology 90:677–682

    Article  CAS  PubMed  Google Scholar 

  • Wilson KH, Blitchington RB, Greene RC (1990) Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction. J Clin Microbiol 28:1942–1946

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xia X (2020) Maximum parsimony method in phylogenetics. In: A Mathematical primer of molecular phylogenetics

  • Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017a) 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  PubMed  PubMed Central  Google Scholar 

  • Yoon SH, Ha SM, Lim J, Kwon S, Chun J (2017b) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek Int J Gen Mol Microbiol 110:1281–1286

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported financially by Special scientific Research Project of Education Department of Shaanxi Province (No. 21JK0992), Special fund for science and technology of Yan’an City (No.2019-27; No.203010105), Doctor Support Project of Yan’an University (No. YDBK2019-43, YDBK2019-44).

Author information

Author notes

  1. Xiaodong Liu and Xin Liu have contributed equally to this work.

Authors and Affiliations

  1. College of Life Sciences, Yan’an University, Yan’an, 716000, China

    Xiaodong Liu, Zhenshan Deng, Xiaolong He & Yingying Jiang

  2. Shaanxi Key Laboratory of Chinese Jujube, Yan’an University, Yan’an, 716000, Shaanxi, China

    Xiaodong Liu, Zhenshan Deng, Xiaolong He & Yingying Jiang

  3. Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan’an University, Yan’an, 716000, China

    Xiaodong Liu, Zhenshan Deng, Xiaolong He & Yingying Jiang

  4. Research and Development Department, Shandong Xianglong Pharmaceutical Research Institute Co., Ltd, Yantai, 264003, China

    Xin Liu

Authors
  1. Xiaodong Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xin Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Zhenshan Deng
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Xiaolong He
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yingying Jiang
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

ZD performed Material preparation. XL, XH and XL performed Data collection and analysis. XL and YJ wrote the main manuscript text. YJ designed and supervised the study. All authors reviewed the manuscript.

Corresponding author

Correspondence to Yingying Jiang.

Ethics declarations

Conflict of interest

The authors declare that there are no conflicts of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 11693 kb)

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Liu, X., Liu, X., Deng, Z. et al. Xanthomonas chitinilytica sp. nov., a novel chitinolytic bacterium isolated from a microbial fermentation bed material. Antonie van Leeuwenhoek 117, 17 (2024). https://doi.org/10.1007/s10482-023-01904-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s10482-023-01904-2

Keywords

Search

Navigation