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Volume 72, Issue 2

sp. nov., an SUF-system-containing bacterium from Antarctic coastal sediment No Access

Abstract

A Gram-stain-negative, heterotrophic, aerobic, non-motile, rod-shaped bacterial strain (GW1-59) belonging to the genus was isolated from coastal sediment collected from the Chinese Great Wall Station, Antarctica. The strain was identified using a polyphasic taxonomic approach. The strain grew well on Reasoner's 2A media and could grow in the presence of 0–4 % (w/v) NaCl (optimum, 1 %), at pH 9.0–11.0 and at 15–37 °C (optimum, 30 °C). Strain GW1-59 possessed ubiquinone-8 as the sole respiratory quinone. The major phospholipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were summed feature 9 (10-methyl C and/or iso-C 9), iso-C, iso-C, iso-C, C and iso-C 3-OH. DNA–DNA relatedness with Ko07, the nearest phylogenetic relative (98.5 % 16S rRNA gene sequence similarity) was 23.4 % (21.1–25.9 %). The average nucleotide identity value between strain GW1-59 and Ko07 was 80.1 %. The physiological and biochemical results and low level of DNA–DNA relatedness suggested the phenotypic and genotypic differentiation of strain GW1-59 from other species. On the basis of phenotypic, phylogenetic and genotypic data, a novel species, sp. nov., is proposed. The type strain is GW1-59 (=CCTCC AB 2019390=KCTC 72831).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Antarctica , Lysobacter , new taxa and polyphasic taxonomy
Funding
This study was supported by the:
  • the National Key R&D Program of China (Award 2018YFC1406705)
    • Principle Award Recipient: JingLi
© 2022 The Authors
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2022-02-16
2024-04-16
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References

  1. Christensen P, Cook FD. Lysobacter, a new genus of nonfruiting, gliding bacteria with a high base ratio. Int J Syst Bacteriol 1978; 28:367–393 [View Article]
     [Google Scholar]
  2. Park JH, Kim R, Aslam Z, Jeon CO, Chung YR et al. Lysobacter capsici sp. nov., with antimicrobial activity, isolated from the rhizosphere of pepper, and emended description of the genus Lysobacter. Int J Syst Evol Microbiol 2008; 58:387–392 [View Article] [PubMed]
     [Google Scholar]
  3. de Bruijn I, Cheng X, de Jager V, Expósito RG, Watrous J et al. Comparative genomics and metabolic profiling of the genus Lysobacter. BMC Genomics 2015; 16:991 [View Article] [PubMed]
     [Google Scholar]
  4. Yoon J. Polyphasic characterization of Lysobacter maris sp. nov., a bacterium isolated from seawater. Curr Microbiol 2016; 72:282–287 [View Article]
     [Google Scholar]
  5. Romanenko LA, Uchino M, Tanaka N, Frolova GM, Mikhailov VV et al. Lysobacter spongiicola sp. nov., isolated from a deep-sea sponge. Int J Syst Evol Microbiol 2008; 58:370–374 [View Article] [PubMed]
     [Google Scholar]
  6. Luo G, Shi Z, Wang G. Lysobacter arseniciresistens sp. nov., an arsenite-resistant bacterium isolated from iron-mined soil. Int J Syst Evol Microbiol 2012; 62:1659–1665 [View Article] [PubMed]
     [Google Scholar]
  7. Zhang L, Bai J, Wang Y, Wu G-L, Dai J et al. Lysobacter korlensis sp. nov. and Lysobacter bugurensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2011; 61:2259–2265 [View Article] [PubMed]
     [Google Scholar]
  8. Liu M, Liu Y, Wang Y, Luo X, Dai J et al. Lysobacter xinjiangensis sp. nov., a moderately thermotolerant and alkalitolerant bacterium isolated from a gamma-irradiated sand soil sample. Int J Syst Evol Microbiol 2011; 61:433–437 [View Article] [PubMed]
     [Google Scholar]
  9. Siddiqi MZ, Im W-T. Lysobacter pocheonensis sp. nov., isolated from soil of a ginseng field. Arch Microbiol 2016; 198:551–557 [View Article] [PubMed]
     [Google Scholar]
  10. Fukuda W, Kimura T, Araki S, Miyoshi Y, Atomi H et al. Lysobacter oligotrophicus sp. nov., isolated from an Antarctic freshwater lake in Antarctica. Int J Syst Evol Microbiol 2013; 63:3313–3318 [View Article] [PubMed]
     [Google Scholar]
  11. Fang B-Z, Xie Y-G, Zhou X-K, Zhang X-T, Liu L et al. Lysobacter prati sp. nov., isolated from a plateau meadow sample. Antonie van Leeuwenhoek 2020; 113:763–772 [View Article] [PubMed]
     [Google Scholar]
  12. Lin S-Y, Hameed A, Wen C-Z, Liu Y-C, Hsu Y-H et al. Lysobacter lycopersici sp. nov., isolated from tomato plant Solanum lycopersicum. Antonie van Leeuwenhoek 2015; 107:1261–1270 [View Article] [PubMed]
     [Google Scholar]
  13. Singh H, Du J, Ngo HTT, Won K, Yang J-E et al. Lysobacter fragariae sp. nov. and Lysobacter rhizosphaerae sp. nov. isolated from rhizosphere of strawberry plant. Antonie van Leeuwenhoek 2015; 107:1437–1444 [View Article] [PubMed]
     [Google Scholar]
  14. Singh H, Won K, Du J, Yang J-E, Akter S et al. Lysobacter agri sp. nov., a bacterium isolated from soil. Antonie van Leeuwenhoek 2015; 108:553–561 [View Article] [PubMed]
     [Google Scholar]
  15. Ngo HTT, Won K, Du J, Son H-M, Park Y et al. Lysobacter terrae sp. nov. isolated from Aglaia odorata rhizosphere soil. Int J Syst Evol Microbiol 2015; 65:587–592 [View Article] [PubMed]
     [Google Scholar]
  16. Kim I, Choi J, Chhetri G, Seo T. Lysobacter helvus sp. nov. and Lysobacter xanthus sp. nov., isolated from soil in South Korea. Antonie van Leeuwenhoek 2019; 112:1253–1262 [View Article]
     [Google Scholar]
  17. Ahmed K, Chohnan S, Ohashi H, Hirata T, Masaki T et al. Purification, bacteriolytic activity, and specificity of beta-lytic protease from Lysobacter sp. IB-9374. J Biosci Bioeng 2003; 95:27–34 [View Article] [PubMed]
     [Google Scholar]
  18. Panthee S, Hamamoto H, Paudel A, Sekimizu K. Lysobacter species: a potential source of novel antibiotics. Arch Microbiol 2016; 198:839–845 [View Article] [PubMed]
     [Google Scholar]
  19. Xie Y, Wright S, Shen Y, Du L. Bioactive natural products from Lysobacter. Nat Prod Rep 2012; 29:1277–1287 [View Article] [PubMed]
     [Google Scholar]
  20. Sun W, Dai S, Jiang S, Wang G, Liu G et al. Culture-dependent and culture-independent diversity of Actinobacteria associated with the marine sponge Hymeniacidon perleve from the South China Sea. Antonie van Leeuwenhoek 2010; 98:65–75 [View Article] [PubMed]
     [Google Scholar]
  21. Benndorf R, Guo H, Sommerwerk E, Weigel C, Garcia-Altares M et al. Natural products from actinobacteria associated with fungus-growing termites. Antibiotics 2018; 7:83 [View Article] [PubMed]
     [Google Scholar]
  22. 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]
  23. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  24. 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]
  25. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
     [Google Scholar]
  26. Thompson J. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 1997; 25:4876–4882 [PubMed]
     [Google Scholar]
  27. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 2017; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  28. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010; 20:265–272 [View Article] [PubMed]
     [Google Scholar]
  29. 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]
  30. Lee I, Chalita M, Ha S-M, Na S-I, Yoon S-H et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [View Article] [PubMed]
     [Google Scholar]
  31. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [View Article] [PubMed]
     [Google Scholar]
  32. Kalvari I, Argasinska J, Quinones-Olvera N, Nawrocki EP, Rivas E et al. Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. Nucleic Acids Research 2018; 46:D335–D342 [View Article] [PubMed]
     [Google Scholar]
  33. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Research 2021; 49:W29–W35 [View Article] [PubMed]
     [Google Scholar]
  34. Besemer J. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Research 2001; 29:2607–2618 [View Article] [PubMed]
     [Google Scholar]
  35. Bagheri H, Dyer R, Severin A, Rajan H. Comprehensive analysis of non redundant protein database. In Review 2020
     [Google Scholar]
  36. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M et al. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007; 35:W182–5 [View Article] [PubMed]
     [Google Scholar]
  37. Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 2019; 47:D309–D314 [View Article] [PubMed]
     [Google Scholar]
  38. UniProt Consortium UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res 2019; 47:D506–D515 [View Article] [PubMed]
     [Google Scholar]
  39. Conesa A, Götz S. Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics 2008; 2008:1–12 [View Article] [PubMed]
     [Google Scholar]
  40. 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]
  41. Meier-Kolthoff JP, Göker M, Spröer C, Klenk H-P. When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 2013; 195:413–418 [View Article] [PubMed]
     [Google Scholar]
  42. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J et al. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
     [Google Scholar]
  43. 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]
  44. Meier-Kolthoff JP, Klenk H-P, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352–356 [View Article] [PubMed]
     [Google Scholar]
  45. Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol 2015; 16:157 [View Article] [PubMed]
     [Google Scholar]
  46. Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J et al. 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]
  47. Goel AK, Rajagopal L, Nagesh N, Sonti RV. Genetic locus encoding functions involved in biosynthesis and outer membrane localization of xanthomonadin in Xanthomonas oryzae pv. oryzae. J Bacteriol 2002; 184:3539–3548 [View Article] [PubMed]
     [Google Scholar]
  48. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  49. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 2014; 64:316–324 [View Article] [PubMed]
     [Google Scholar]
  50. Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Krichevsky MI et al. Report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
     [Google Scholar]
  51. Li J, Gu X, Gui Y. Prokaryotic diversity and composition of sediments from Prydz Bay, the Antarctic Peninsula Region, and the Ross Sea, Southern Ocean. Front Microbiol 2020; 11:783 [View Article] [PubMed]
     [Google Scholar]
  52. Ward BB. Chapter 5 - Nitrification in marine systems. In Capone DG, Bronk DA, Mulholland MR, Carpenter EJ. eds Nitrogen in the Marine Environment, 2nd edn. San Diego: Academic Press; 2008 pp 199–261
     [Google Scholar]
  53. Shaw DR, Ali M, Katuri KP, Gralnick JA, Reimann J et al. Extracellular electron transfer-dependent anaerobic oxidation of ammonium by anammox bacteria. Nat Commun 2020; 11:2058 [View Article] [PubMed]
     [Google Scholar]
  54. Park D, Kim H, Yoon S. Nitrous oxide reduction by an obligate aerobic bacterium, Gemmatimonas aurantiaca strain T-27. Appl Environ Microbiol 2017; 83:e00502-17 [View Article] [PubMed]
     [Google Scholar]
  55. Garber AI, Zehnpfennig JR, Sheik CS, Henson MW, Ramírez GA et al. Metagenomics of antarctic marine sediment reveals potential for diverse chemolithoautotrophy. mSphere 2021; 6:e0077021 [View Article] [PubMed]
     [Google Scholar]
  56. Smith JA, Graham AGC, Post AL, Hillenbrand C-D, Bart PJ et al. The marine geological imprint of Antarctic ice shelves. Nat Commun 2019; 10:5635 [View Article] [PubMed]
     [Google Scholar]
  57. Burdon RH. The heat shock proteins. Endeavour 1988; 12:133–138 [View Article] [PubMed]
     [Google Scholar]
  58. Sakthivel K, Watanabe T, Nakamoto H. A small heat-shock protein confers stress tolerance and stabilizes thylakoid membrane proteins in cyanobacteria under oxidative stress. Arch Microbiol 2009; 191:319–328 [View Article] [PubMed]
     [Google Scholar]
  59. Chen Z, Yu H, Li L, Hu S, Dong X et al. The genome and transcriptome of a newly described psychrophilic archaeon, Methanolobus psychrophilus R15, reveal its cold adaptive characteristics. Environ Microbiol Rep 2012; 4:633–641 [View Article] [PubMed]
     [Google Scholar]
  60. Li J, Qi L, Guo Y, Yue L, Li Y et al. Global mapping transcriptional start sites revealed both transcriptional and post-transcriptional regulation of cold adaptation in the methanogenic archaeon Methanolobus psychrophilus. Sci Rep 2015; 5:9209 [View Article] [PubMed]
     [Google Scholar]
  61. Pérard J, Ollagnier de Choudens S. Iron-sulfur clusters biogenesis by the SUF machinery: close to the molecular mechanism understanding. J Biol Inorg Chem 2018; 23:581–596 [View Article] [PubMed]
     [Google Scholar]
  62. Williams TJ, Allen MA, Ivanova N, Huntemann M, Haque S et al. Genome analysis of a verrucomicrobial endosymbiont with a tiny genome discovAnalysis of a verrucomicrobial endosymbiont with a tiny genome discovered in an Antarctic lake. Front Microbiol 2021; 12:674758 [View Article] [PubMed]
     [Google Scholar]
  63. Anand K, Tripathi A, Shukla K, Malhotra N, Jamithireddy AK et al. Mycobacterium tuberculosis SufR responds to nitric oxide via its 4Fe-4S cluster and regulates Fe-S cluster biogenesis for persistence in mice. Redox Biol 2021; 46:102062 [View Article] [PubMed]
     [Google Scholar]
  64. Alex A, Antunes A. Genus-wide comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine invertebrate hosts. PLoS One 2018; 13:e0194368 [View Article] [PubMed]
     [Google Scholar]
  65. Qin Q-L, Li Y, Sun L-L, Wang Z-B, Wang S et al. Trophic specialization results in genomic reduction in free-living marine Idiomarina bacteria. mBio 2019; 10:e02545-18 [View Article] [PubMed]
     [Google Scholar]
  66. Leifson E. Atlas of Bacterial Flagellation New York: Academic Press; 1960 [View Article]
     [Google Scholar]
  67. Hoffmann T, Frankenberg N, Marino M, Jahn D. Ammonification in Bacillus subtilis utilizing dissimilatory nitrite reductase is dependent on resDE. J Bacteriol 1998; 180:186–189 [View Article] [PubMed]
     [Google Scholar]
  68. Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family “Oxalobacteraceae” isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article] [PubMed]
     [Google Scholar]
  69. Fautz E, Reichenbach H. A simple test for flexirubin-type pigments. FEMS Microbiol Lett 1980; 8:87–91 [View Article]
     [Google Scholar]
  70. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids.Technical Note 101. Microbial ID, inc Newark, Del: 2001
     [Google Scholar]
  71. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article] [PubMed]
     [Google Scholar]
  72. Wink J, Schumann P, Atasayar E, Klenk H-P, Zaburannyi N et al. “Streptomyces caelicus”, an antibiotic-producing species of the genus Streptomyces, and Streptomyces canchipurensis Li et al. 2015 are later heterotypic synonyms of Streptomyces muensis Ningthoujam et al. 2014. Int J Syst Evol Microbiol 2017; 67:548–556 [View Article] [PubMed]
     [Google Scholar]
  73. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of cellulomonas. J Appl Bacteriol 1979; 47:87–95
     [Google Scholar]
  74. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
     [Google Scholar]
  75. Lin S-Y, Hameed A, Shahina M, Liu Y-C, Hsu Y-H et al. Description of Luteimonas pelagia sp. nov., isolated from marine sediment, and emended descriptions of Luteimonas aquatica, Luteimonas composti, Luteimonas mephitis, Lysobacter enzymogenes and Lysobacter panaciterrae. Int J Syst Evol Microbiol 2016; 66:645–651 [View Article] [PubMed]
     [Google Scholar]
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Lysobacter antarcticus sp. nov., an SUF-system-containing bacterium from Antarctic coastal sediment
Int J Syst Evol Microbiol 72, 005250 (2022); https://doi.org/10.1099/ijsem.0.005250
/content/journal/ijsem/10.1099/ijsem.0.005250
/content/journal/ijsem/10.1099/ijsem.0.005250
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