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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 75, Issue 1

gen. nov., sp. nov.: a novel species of a novel genus in the family , isolated from the sediment of a tidal flat located in Zhoushan, China No Access

Abstract

A Gram-stain-negative, aerobic and rod-shaped bacterium, designated as HZG-20, was isolated from a tidal flat in Zhoushan, Zhejiang Province, China. The 16S rRNA sequence similarities between strain HZG-20 and RR4-56, NNCM2, P31 and X9-2-2 were 98.9, 91.7, 91.0 and 91.0%, respectively. Colonies of strain HZG-20 were 1.4 mm in diameter, milky white, round, smooth and convex after cultivating on marine agar at 30 °C for 48 h. Cells were catalase and oxidase-negative. Growth occurred at 15–37 ℃ (optimum, 28 ℃), pH 5.0–9.0 (optimum, pH 6.0–8.0) and with 0–8% (w/v) NaCl (optimum, 1–3%). It contained Menaquinone-8 (H) as the sole respiratory quinone, and C (11.8–13.6%), C c (6.8–13.3%) and C anteiso (10.9–27.7%) as the major cellular fatty acids. The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid, one unidentified aminolipid, one unidentified phosphoglycolipid, two unidentified glycolipids (GL1–GL2) and three unidentified lipids (L1–L3). The genome of strain HZG-20 was 3 835 886 bp in length, comprised 3746 protein-coding genes, with DNA G+C content of 67.1 mol%. The phylogenetic and phylogenomic trees indicated that strain HZG-20 formed an independent and stable clade with RR4-56. However, the average nucleotide identity, DNA–DNA hybridization and average amino acid identity values between strain HZG-20 and RR4-56, NNCM2, P31 and X9-2-2 were 81.6, 71.1, 68.7 and 69.5%; 23.0, 18.5, 17.9 and 17.5%; and 78.2, 56.8, 56.5 and 61.9%, respectively, together with distinct chemotaxonomic features, indicating strain HZG-20 should not be assigned to known genera. As a result, a novel species of a novel genus within the family , designated as gen. nov., sp. nov., was proposed. The type strain is HZG-20 (MCCC 1K08468=KCTC 82692).

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Keyword(s): Paludibacillus litoralis , Paracoccaceae , tidal flat and Zhoushan
Funding
This study was supported by the:
  • Zhejiang Provincial Natural Science Foundation of China (Award LY24C010002 and LDT23D06025D06)
    • Principal Award Recipient: CongSun
  • National Natural Science Foundation of China (Award 32370006 and U23A2034)
    • Principal Award Recipient: CongSun
© 2025 The Authors
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/content/journal/ijsem/10.1099/ijsem.0.006655
2025-01-27
2026-04-18

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References

  1. Göker M. Filling the gaps: missing taxon names at the ranks of class, order and family. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  2. Mergaert S. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2007; 57:1 [View Article]
     [Google Scholar]
  3. Elifantz H, Horn G, Ayon M, Cohen Y, Minz D. Rhodobacteraceae are the key members of the microbial community of the initial biofilm formed in Eastern Mediterranean coastal seawater. FEMS Microbiol Ecol 2013; 85:348–357 [View Article] [PubMed]
     [Google Scholar]
  4. Breider S, Scheuner C, Schumann P, Fiebig A, Petersen J et al. Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov. Front Microbiol 2014; 5:416 [View Article] [PubMed]
     [Google Scholar]
  5. Albuquerque L, Rainey FA, Nobre MF, da Costa MS. Oceanicella actignis gen. nov., sp. nov., a halophilic slightly thermophilic member of the Alphaproteobacteria. Syst Appl Microbiol 2012; 35:385–389 [View Article] [PubMed]
     [Google Scholar]
  6. Albuquerque L, França L, Taborda M, La Cono V, Yakimov M et al. Palleronia abyssalis sp. nov., isolated from the deep Mediterranean Sea and the emended description of the genus Palleronia and of the species Palleronia marisminoris. Antonie Van Leeuwenhoek 2015; 107:633–642 [View Article] [PubMed]
     [Google Scholar]
  7. Liang HY, Sun C, Xu L, Xu XW, Cheng H et al. Pontibrevibacter nitratireducens gen a member of the family Rhodobacteraceae isolated from seawater of the Indian Ocean and intertidal zone. Int J Syst Evol Microbiol 2022; 72:5341 [View Article]
     [Google Scholar]
  8. Liao H, Li Y, Lin X, Lai Q, Tian Y. Zhengella mangrovi gen. nov., sp. nov., a novel member of family Phyllobacteriaceae isolated from mangrove sediment. Int J Syst Evol Microbiol 2018; 68:2819–2825 [View Article]
     [Google Scholar]
  9. Lim J-M, Jeon CO, Jang HH, Park D-J, Shin YK et al. Albimonas donghaensis gen. nov., sp. nov., a non-photosynthetic member of the class Alphaproteobacteria isolated from seawater. Int J Syst Evol Microbiol 2008; 58:282–285 [View Article] [PubMed]
     [Google Scholar]
  10. Park J, Kim Y-S, Kim S-J, Kim S-E, Jung H-K et al. Pikeienuella piscinae gen. nov., sp. nov., a novel genus in the family Rhodobacteraceae. J Microbiol 2021; 59:546–551 [View Article]
     [Google Scholar]
  11. Sun F, Du Y, Liu X, Lai Q, Shao Z. Halovulum dunhuangense gen. nov., sp. nov., isolated from a saline terrestrial spring. Int J Syst Evol Microbiol 2015; 65:2810–2816 [View Article] [PubMed]
     [Google Scholar]
  12. Sun H, Zheng H, Liao B, Chen B, Li A et al. Algiphilus acroporae sp. nov. and Coraliihabitans acroporae gen. nov. sp. nov., isolated from scleractinian coral Acropora digitifera. Int J Syst Evol Microbiol 2022; 72: [View Article]
     [Google Scholar]
  13. Suzuki T, Muroga Y, Takahama M, Nishimura Y. Roseigium denhamense gen. nov., sp. nov. and Roseibium hemelinense sp. nov., aerobic bacteriochlorophyll-containing bacteria isolated from the east and west coasts of Australia. Int J Syst Evol Microbiol 2000; 50:2151–2156 [View Article]
     [Google Scholar]
  14. Wei TT, Fan XB, Quan ZX. Abyssibius alkaniclasticus gen. nov., sp. nov., a novel member of the family Rhodobacteraceae, isolated from the Mariana Trench. Int J Syst Evol Microbiol 2023; 73:5715 [View Article] [PubMed]
     [Google Scholar]
  15. Lai Q, Wang L, Liu Y, Yuan J, Sun F et al. Parvibaculum indicum sp. nov., isolated from deep-sea water. Int J Syst Evol Microbiol 2011; 61:271–274 [View Article]
     [Google Scholar]
  16. Weerawongwiwat V, Kim J-H, Yoon J-H, Suh MK, Kim HS et al. Roseibium limicola sp. nov., isolated from tidal mudflat. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
     [Google Scholar]
  17. Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold L-M et al. Analysis of 1,000+ type-strain genomes substantially improves taxonomic classification of Alphaproteobacteria. Front Microbiol 2020; 11:468 [View Article] [PubMed]
     [Google Scholar]
  18. Zhang Y, Hua J, Ying J-J, Dong H, Li H et al. Erythrobacter aurantius sp. nov., isolated from intertidal seawater in Taizhou. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  19. Huang M-M, Guo L-L, Wu Y-H, Lai Q-L, Shao Z-Z et al. Pseudooceanicola lipolyticus sp. nov., a marine alphaproteobacterium, reclassification of Oceanicola flagellatus as Pseudooceanicola flagellatus comb. nov. and emended description of the genus Pseudooceanicola. Int J Syst Evol Microbiol 2018; 68:409–415 [View Article] [PubMed]
     [Google Scholar]
  20. Romero S, Schell RF, Pennell DR. Rapid method for the differentiation of gram-positive and gram-negative bacteria on membrane filters. J Clin Microbiol 1988; 26:1378–1382 [View Article] [PubMed]
     [Google Scholar]
  21. Sun C, Xu L, Yu XY, Zhao Z, Wu YH et al. Minwuia thermotolerans gen. nov., sp. nov., a marine bacterium forming a deep branch in the Alphaproteobacteria, and proposal of Minwuiaceae fam. nov. and Minwuiales ord. nov. Int J Syst Evol Microbiol 2018; 68:3856–3862 [View Article]
     [Google Scholar]
  22. 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]
  23. Komagata K, Suzuki K-I. 4 Lipid and cell-wall analysis in bacterial systematics. In Colwell RR, Grigorova R. eds Methods in Microbiology Academic Press; 1988 pp 161–207
     [Google Scholar]
  24. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
     [Google Scholar]
  25. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
     [Google Scholar]
  26. Mise K, Iwasaki W. Environmental atlas of prokaryotes enables powerful and intuitive habitat-based analysis of community structures. iScience 2020; 23:101624 [View Article] [PubMed]
     [Google Scholar]
  27. Riesco R, Trujillo ME. Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2024; 74:006300 [View Article] [PubMed]
     [Google Scholar]
  28. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article] [PubMed]
     [Google Scholar]
  29. 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]
  30. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009; 25:1972–1973 [View Article] [PubMed]
     [Google Scholar]
  31. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article]
     [Google Scholar]
  32. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article] [PubMed]
     [Google Scholar]
  33. Zhou Z, Tran PQ, Breister AM, Liu Y, Kieft K et al. METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks. Microbiome 2022; 10:33 [View Article]
     [Google Scholar]
  34. Zheng J, Ge Q, Yan Y, Zhang X, Huang L et al. dbCAN3: automated carbohydrate-active enzyme and substrate annotation. Nucleic Acids Res 2023; 51:W115–W121 [View Article]
     [Google Scholar]
  35. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article] [PubMed]
     [Google Scholar]
  36. 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. International Journal of Systematic and Evolutionary Microbiology 2017; 67:1613–1617 [View Article]
     [Google Scholar]
  37. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article] [PubMed]
     [Google Scholar]
  38. 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]
  39. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  40. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
     [Google Scholar]
  41. Do KA. A simulation study of balanced and antithetic bootstrap resampling methods. J Stat Comput Simul 1992; 40:153–166 [View Article]
     [Google Scholar]
  42. 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]
  43. 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]
  44. 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]
  45. Breton C, Šnajdrová L, Jeanneau C, Koča J, Imberty A. Structures and mechanisms of glycosyltransferases. Glycobiology 2006; 16:29R–37R [View Article]
     [Google Scholar]
  46. van Wyk N, Drancourt M, Henrissat B, Kremer L. Current perspectives on the families of glycoside hydrolases of Mycobacterium tuberculosis : their importance and prospects for assigning function to unknowns. Glycobiology 2017; 27:112–122 [View Article]
     [Google Scholar]
  47. Zhong Z-P, Liu Y, Liu H-C, Wang F, Zhou Y-G et al. Roseibium aquae sp. nov., isolated from a saline lake. Int J Syst Evol Microbiol 2014; 64:2812–2818 [View Article]
     [Google Scholar]
  48. Lee MW, Kim JM, Kim KH, Choi DG, Lee JK. Roseibium algicola sp. nov. and Roseibium porphyridii sp. nov., isolated from marine red algae. Int J Syst Evol Microbiol 2024; 74:6283 [View Article]
     [Google Scholar]
  49. Fan J, Liu X, Wang Z, Cui N, Zhang Y et al. Roseibium algae sp. nov., isolated from a marine alga (Grateloupia sp.). Int J Syst Evol Microbiol 2024; 74:6475 [View Article]
     [Google Scholar]
  50. Duan L, Li J-L, Li X, Dong L, Fang B-Z et al. Roseibium aestuarii sp. nov., isolated from Pearl River Estuary. Int J Syst Evol Microbiol 2020; 70:2896–2900 [View Article] [PubMed]
     [Google Scholar]
  51. Schleheck D, Tindall BJ, Rosselló-Mora R, Cook AM. Parvibaculum lavamentivorans gen. nov., sp. nov., a novel heterotroph that initiates catabolism of linear alkylbenzenesulfonate. Int J Syst Evol Microbiol 2004; 54:1489–1497 [View Article] [PubMed]
     [Google Scholar]
  52. Rosario-Passapera R, Keddis R, Wong R, Lutz RA, Starovoytov V et al. Parvibaculum hydrocarboniclasticum sp. nov., a mesophilic, alkane-oxidizing alphaproteobacterium isolated from a deep-sea hydrothermal vent on the East Pacific Rise. Int J Syst Evol Microbiol 2012; 62:2921–2926 [View Article] [PubMed]
     [Google Scholar]
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Paludibacillus litoralis gen. nov., sp. nov.: a novel species of a novel genus in the family Paracoccaceae, isolated from the sediment of a tidal flat located in Zhoushan, China
Int J Syst Evol Microbiol 75, 006655 (2025); https://doi.org/10.1099/ijsem.0.006655
/content/journal/ijsem/10.1099/ijsem.0.006655
/content/journal/ijsem/10.1099/ijsem.0.006655
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