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Volume 73, Issue 11

sp. nov. isolated from poultry manure No Access

Abstract

A polyphasic taxonomic approach was used to characterize a novel bacterium, designated strain CC-YST667, isolated from poultry manure sampled in Taiwan. The cells were observed to be aerobic, motile and non-spore-forming rods, displaying positive reactions for oxidase. Optimal growth of CC-YST667 was observed at 25 °C, pH 8.0 and with 1 % (w/v) NaCl. The polar lipid profile consisted of phosphatidylmonomethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and multiple unidentified polar lipids. The major polyamine was spermidine. The major cellular fatty acids (>5 %) included C, Ccyclo, Ccyclo ω8 and C 3OH/iso-C I. On the basis of the results of analysis of 16S rRNA gene sequences, this isolate showed the closest phylogenetic relationship with ‘ (with 98.2 % similarity) and (with 97.3 % similarity) of the family . The draft genome, (3.3 Mb) with a DNA G+C content of 57.2 mol%, harboured various genes involved in the biodegradation of aromatic hydrocarbons. CC-YST667 shared highest orthologous average nucleotide identity (OrthoANI) with the type strains of species of of the genera (72.4‒77.9 %, =2), (72.8‒73.0 %, =2) and (71.7‒73.0 %, =5). On the basis of its distinct phylogenetic, phenotypic and chemotaxonomic traits together with the results of comparative 16S rRNA gene sequencing, OrthoANI, digital DNA–DNA hybridization (DDH) and the phylogenomic placement, strain CC-YST667 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is CC-YST667 (=BCRC 81321 =JCM 34761).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): aromatic hydrocarbons , Neopusillimonas aromaticivorans , polyphasic taxonomic approach and poultry manure
Funding
This study was supported by the:
  • Innovation and Development Center of Sustainable Agriculture
    • Principle Award Recipient: Chiu-ChungYoung
  • National Science and Technology Council (Award MOST 111-2313-B-005-050)
    • Principle Award Recipient: Chiu-ChungYoung
  • National Science and Technology Council (Award MOST 111-2313-B-005-050)
    • Principle Award Recipient: Shih-YaoLin
© 2023 The Authors
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/content/journal/ijsem/10.1099/ijsem.0.006146
2023-11-14
2024-05-08
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References

  1. Stolz A, Bürger S, Kuhm A, Kämpfer P, Busse H-J. Pusillimonas noertemannii gen. nov., sp. nov., a new member of the family Alcaligenaceae that degrades substituted salicylates. Int J Syst Evol Microbiol 2005; 55:1077–1081 [View Article] [PubMed]
     [Google Scholar]
  2. Karvelis L, Gasparavičiūtė R, Klimavičius A, Jančienė R, Stankevičiūtė J et al. Pusillimonas sp. 5HP degrading 5-hydroxypicolinic acid. Biodegradation 2014; 25:11–19 [View Article] [PubMed]
     [Google Scholar]
  3. Ma Y, Wen R, Qiu J, Hong J, Liu M et al. Biodegradation of nicotine by a novel strain Pusillimonas. Res Microbiol 2015; 166:67–71 [View Article] [PubMed]
     [Google Scholar]
  4. Lin S-Y, Hameed A, Tsai C-F, Tang Y-S, Young C-C. Pusillimonas faecipullorum sp. nov., isolated from the poultry manure. Arch Microbiol 2022; 204:256 [View Article] [PubMed]
     [Google Scholar]
  5. Jin L, Ko S-R, Cui Y, Lee CS, Oh H-M et al. Pusillimonas caeni sp. nov., isolated from a sludge sample of a biofilm reactor. Antonie van Leeuwenhoek 2017; 110:125–132 [View Article] [PubMed]
     [Google Scholar]
  6. Srinivasan S, Kim MK, Sathiyaraj G, Kim Y-J, Yang D-C. Pusillimonas ginsengisoli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2010; 60:1783–1787 [View Article] [PubMed]
     [Google Scholar]
  7. Park MS, Park Y-J, Jung JY, Lee SH, Park W et al. Pusillimonas harenae sp. nov., isolated from a sandy beach, and emended description of the genus Pusillimonas. Int J Syst Evol Microbiol 2011; 61:2901–2906 [View Article] [PubMed]
     [Google Scholar]
  8. Li JY, Qi MM, Lai QL, Dong CM, Liu XP et al. Pusillimonas maritima sp. nov., isolated from surface seawater. Int J Syst Evol Microbiol 2020; 70:3483–3490 [View Article] [PubMed]
     [Google Scholar]
  9. Yao L, Jia Y, Lai Y, Xue F, Wang J. Pusillimonas minor sp. nov., a novel member of the genus Pusillimonas isolated from activated sludge. Int J Syst Evol Microbiol 2022; 72: [View Article]
     [Google Scholar]
  10. Lee M, Woo S-G, Chae M, Ten LN. Pusillimonas soli sp. nov., isolated from farm soil. Int J Syst Evol Microbiol 2010; 60:2326–2330 [View Article] [PubMed]
     [Google Scholar]
  11. Koh H-W, Song M-S, Do K-T, Kim H, Park S-J. Pusillimonas thiosulfatoxidans sp. nov., a thiosulfate oxidizer isolated from activated sludge. Int J Syst Evol Microbiol 2019; 69:1041–1046 [View Article] [PubMed]
     [Google Scholar]
  12. Babich TL, Grouzdev DS, Sokolova DS, Tourova TP, Poltaraus AB et al. Genome analysis of Pollutimonas subterranea gen. nov., sp. nov. and Pollutimonas nitritireducens sp. nov., isolated from nitrate- and radionuclide-contaminated groundwater, and transfer of several Pusillimonas species into three new genera Allopusillimonas, Neopusillimonas, and Mesopusillimonas. Antonie van Leeuwenhoek 2023; 116:109–127 [View Article]
     [Google Scholar]
  13. Zhang D-C, Busse H-J, Wieser C, Liu H-C, Zhou Y-G et al. Candidimonas bauzanensis sp. nov., isolated from soil, and emended description of the genus Candidimonas Vaz-Moreira et al. 2011. Int J Syst Evol Microbiol 2012; 62:2084–2089 [View Article] [PubMed]
     [Google Scholar]
  14. Kämpfer P, Busse H-J, McInroy JA, Glaeser SP. Paracandidimonas soli gen. nov., sp. nov., isolated from soil. Int J Syst Evol Microbiol 2017; 67:1740–1745 [View Article] [PubMed]
     [Google Scholar]
  15. Kim SJ, Yoo SH, Weon HY, Kim YS, Anandham R et al. Paralcaligenes ureilyticus gen. nov., sp. nov. isolated from soil of a Korean ginseng field. J Microbiol 2011; 49:502–507 [View Article] [PubMed]
     [Google Scholar]
  16. Edwards U, Rogall T, Blöcker H, Emde M, Böttger EC. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 1989; 17:7843–7853 [View Article] [PubMed]
     [Google Scholar]
  17. Heiner CR, Hunkapiller KL, Chen SM, Glass JI, Chen EY. Sequencing multimegabase-template DNA with BigDye terminator chemistry. Genome Res 1998; 8:557–561 [View Article] [PubMed]
     [Google Scholar]
  18. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
     [Google Scholar]
  19. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article] [PubMed]
     [Google Scholar]
  20. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
     [Google Scholar]
  21. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
     [Google Scholar]
  22. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  23. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  24. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HN. eds Mammalian Protein Metabolism vol 3 New York: Academic Press; 1969 pp 21–132 [View Article]
     [Google Scholar]
  25. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  26. De Coster W, D’Hert S, Schultz DT, Cruts M, Van Broeckhoven C. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics 2018; 34:2666–2669 [View Article] [PubMed]
     [Google Scholar]
  27. Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 2019; 37:540–546 [View Article] [PubMed]
     [Google Scholar]
  28. Vaser R, Sović I, Nagarajan N, Šikić M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res 2017; 27:737–746 [View Article] [PubMed]
     [Google Scholar]
  29. Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 2018; 34:3094–3100 [View Article] [PubMed]
     [Google Scholar]
  30. Huang Y-T, Liu P-Y, Shih P-W. Homopolish: a method for the removal of systematic errors in nanopore sequencing by homologous polishing. Genome Biol 2021; 22:95 [View Article] [PubMed]
     [Google Scholar]
  31. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article] [PubMed]
     [Google Scholar]
  32. Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 2015; 31:3210–3212 [View Article] [PubMed]
     [Google Scholar]
  33. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
     [Google Scholar]
  34. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  35. Medlar AJ, Törönen P, Holm L. AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination. Nucleic Acids Res 2018; 46:W479–W485 [View Article] [PubMed]
     [Google Scholar]
  36. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
     [Google Scholar]
  37. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  38. Kanehisa M, Sato Y, Kawashima M. KEGG mapping tools for uncovering hidden features in biological data. Protein Sci 2022; 31:47–53 [View Article] [PubMed]
     [Google Scholar]
  39. Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol 2021; 38:5825–5829 [View Article] [PubMed]
     [Google Scholar]
  40. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article] [PubMed]
     [Google Scholar]
  41. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article] [PubMed]
     [Google Scholar]
  42. Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol 2011; 7:e1002195 [View Article] [PubMed]
     [Google Scholar]
  43. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article] [PubMed]
     [Google Scholar]
  44. Price MN, Dehal PS, Arkin AP. FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS One 2010; 5:e9490 [View Article] [PubMed]
     [Google Scholar]
  45. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article] [PubMed]
     [Google Scholar]
  46. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586 [View Article] [PubMed]
     [Google Scholar]
  47. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note vol 101 Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  48. Paisley R. MIS Whole Cell Fatty Acid Analysis by Gas Chromatography Training Manual Newark, DE: MIDI; 1996
     [Google Scholar]
  49. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
  50. Scherer P, Kneifel H. Distribution of polyamines in methanogenic bacteria. J Bacteriol 1983; 154:1315–1322 [View Article] [PubMed]
     [Google Scholar]
  51. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
     [Google Scholar]
  52. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 1994; 44:846–849 [View Article]
     [Google Scholar]
  53. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  54. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
     [Google Scholar]
  55. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
     [Google Scholar]
  56. Seo J-S, Keum Y-S, Li QX. Bacterial degradation of aromatic compounds. Int J Environ Res Public Health 2009; 6:278–309 [View Article] [PubMed]
     [Google Scholar]
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Neopusillimonas aromaticivorans sp. nov. isolated from poultry manure
Int J Syst Evol Microbiol 73, 006146 (2023); https://doi.org/10.1099/ijsem.0.006146
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