Skip to content
1887

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

Volume 75, Issue 3

sp. nov., isolated from the China Space Station No Access

Abstract

Understanding the characteristics of microbes during long-term space missions is essential for safeguarding the health of astronauts and maintaining the functionality of spacecraft. In this study, a Gram-positive, aerobic, spore-forming, rod-shaped strain JL1B1071 was isolated from the surface of hardware on the China Space Station. This strain belongs to the genus , with its closest relative being ATCC 4513. The genome of JL1B1071 is 5 166 230 bp in size, with a G+C content of 35.6 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between JL1B1071 and ATCC 4513 are 83.3 and 27.5%, respectively, both below the recommended thresholds for species delineation. The major cellular fatty acids were anteiso-C and iso-C. The major quinone was menaquinone-7 (MK-7). Notably, strain JL1B1071 demonstrates a unique ability to hydrolyse gelatin, suggesting that it can utilize gelatin as a substrate in nutrient-limited environments. Genomic analysis of JL1B1071 revealed two conserved signature indels in the GAF domain-containing protein and DNA ligase D protein, which are specific to the genus . Additionally, structural and functional differences in proteins BshB1 and SplA were identified, which may enhance biofilm formation, oxidative stress response and radiation damage repair, thereby aiding its survival in the space environment. Based on phenotypic, physiological and chemotaxonomic characteristics, as well as genome annotation, strain JL1B1071 was considered a novel species within the genus and is proposed to be named sp. nov. The type strain is JL1B1071 (=GDMCC 1.4642=KCTC 43715).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): biotechnological application , China Space Station , Niallia and novel species
Funding
This study was supported by the:
  • China Space Station engineering aerospace technology test field project (Award NO.2019HJS002)
    • Principal Award Recipient: NotApplicable
© 2025 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006693
2025-03-03
2025-12-15

Metrics

Loading full text...

Full text loading...

References

  1. Gupta RS, Patel S, Saini N, Chen S. Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species. Int J Syst Evol Microbiol 2020; 70:5753–5798 [View Article]
     [Google Scholar]
  2. Jordan E. A report on certain species of bacteria observed in sewage. A report of the biological work of the Lawrence experiment etation, including an account of methods employed and results obtained in the microscopical and bacteriological investigation of sewage and water, report on water supply and sewerage (Part II). In: Sedgewick W (editor). Massachusetts; 1890 pp 821–844
  3. Ma L, Xi J-Q, Cao Y-H, Wang X-Y, Zheng S-C et al. Bacillus endozanthoxylicus sp. nov., an endophytic bacterium isolated from Zanthoxylum bungeanum Maxim leaves. Int J Syst Evol Microbiol 2017; 67:3699–3705 [View Article] [PubMed]
     [Google Scholar]
  4. Venkateswaran K, Kempf M, Chen F, Satomi M, Nicholson W et al. Bacillus nealsonii sp. nov., isolated from a spacecraft-assembly facility, whose spores are gamma-radiation resistant. Int J Syst Evol Microbiol 2003; 53:165–172 [View Article] [PubMed]
     [Google Scholar]
  5. Patel S, Gupta RS. A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. Int J Syst Evol Microbiol 2020; 70:406–438 [View Article]
     [Google Scholar]
  6. Khurana H, Sharma M, Verma H, Lopes BS, Lal R et al. Genomic insights into the phylogeny of Bacillus strains and elucidation of their secondary metabolic potential. Genomics 2020; 112:3191–3200 [View Article] [PubMed]
     [Google Scholar]
  7. Li Y, Zhang D, Bo D, Peng D, Sun M et al. A taxonomic note on the order Caryophanales: description of 12 novel families and emended description of 21 families. Int J Syst Evol Microbiol 2024; 74:006539 [View Article] [PubMed]
     [Google Scholar]
  8. Tuo L, Liu F, Yan X-R, Liu Y. Bacillus taxi sp. nov., a novel endophytic bacterium isolated from root of Taxus chinensis (Pilger) Rehd. Int J Syst Evol Microbiol 2020; 70:481–486 [View Article]
     [Google Scholar]
  9. Srivastava S, Dafale NA. Genomic dissection of Niallia sp. for potential application in lignocellulose hydrolysis and bioremediation. Arch Microbiol 2024; 206: [View Article]
     [Google Scholar]
  10. Hossain MI, Saleh NUA, Numan A, Hossain MM, Uddin MA et al. Bombyx mori as a model for Niallia circulans pathogenicity. Drug Discov Ther 2023; 17:18–25 [View Article]
     [Google Scholar]
  11. Harirchi S, Sar T, Ramezani M, Aliyu H, Etemadifar Z et al. Bacillales: from taxonomy to biotechnological and industrial perspectives. Microorganisms 2022; 10:2355 [View Article] [PubMed]
     [Google Scholar]
  12. Harwood CR. Bacillus New York: Springer; 2013
     [Google Scholar]
  13. Sarmiento-López LG, López-Meyer M, Maldonado-Mendoza IE, Quiroz-Figueroa FR, Sepúlveda-Jiménez G et al. Production of indole-3-acetic acid by Bacillus circulans E9 in a low-cost medium in a bioreactor. J Biosci Bioeng 2022; 134:21–28 [View Article] [PubMed]
     [Google Scholar]
  14. Patel D, Patil KS, Madamwar D, Desai C. Electrogenic degradation of reactive red 152 dye by Niallia circulans DC10 and its genome sequence analysis reveals genes mediating dye degradation and anodic electron transfer. J Water Process Eng 2022; 47:102690 [View Article]
     [Google Scholar]
  15. Stott KV, Morgan L, Shearer C, Steadham MB, Ballarotto M et al. Qualification of membrane filtration for planetary protection flight implementation. Front Microbiol 2022; 13:871110 [View Article] [PubMed]
     [Google Scholar]
  16. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74:2461–2470 [View Article] [PubMed]
     [Google Scholar]
  17. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J et al. BLAST+: architecture and applications. BMC Bioinf 2009; 10:1–9 [View Article]
     [Google Scholar]
  18. Thorat V, Kirdat K, Tiwarekar B, Dhanavade P, Karodi P. Paenibacillus albicereus sp. nov. and Niallia alba sp. nov., isolated from digestive syrup. Arch Microbiol 2022; 204:127 [View Article]
     [Google Scholar]
  19. 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]
  20. 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]
  21. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH et al. Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation. Genome Res 2017; 27:722–736 [View Article] [PubMed]
     [Google Scholar]
  22. Chin C-S, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods 2016; 13:1050–1054 [View Article] [PubMed]
     [Google Scholar]
  23. Van der Auwera G, O’Connor B. Genomics in the Cloud: Using Docker, GATK, and WDL in Terra, 1st edition O’Reilly Media; 2020
     [Google Scholar]
  24. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article] [PubMed]
     [Google Scholar]
  25. Nandi T, Ong C, Singh AP, Boddey J, Atkins T et al. A genomic survey of positive selection in Burkholderia pseudomallei provides insights into the evolution of accidental virulence. PLoS Pathog 2010; 6:e1000845 [View Article] [PubMed]
     [Google Scholar]
  26. Johnson JS, Spakowicz DJ, Hong B-Y, Petersen LM, Demkowicz P et al. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat Commun 2019; 10:5029 [View Article] [PubMed]
     [Google Scholar]
  27. 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]
  28. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International committee on systematic bacteriology. 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]
  29. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
     [Google Scholar]
  30. Robert X, Gouet P. Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res 2014; 42:W320–4 [View Article] [PubMed]
     [Google Scholar]
  31. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B et al. The COG database: an updated version includes eukaryotes. BMC Bioinf 2003; 4:41 [View Article]
     [Google Scholar]
  32. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V et al. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res 2009; 37:D233–8 [View Article] [PubMed]
     [Google Scholar]
  33. Drula E, Garron M-L, Dogan S, Lombard V, Henrissat B et al. The carbohydrate-active enzyme database: functions and literature. Nucleic Acids Res 2022; 50:D571–D577 [View Article] [PubMed]
     [Google Scholar]
  34. Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res 2018; 46:W296–W303 [View Article] [PubMed]
     [Google Scholar]
  35. Systèmes D. Dassault systèmes BIOVIA, discovery studio modeling environment San Diego: 2023
  36. Woodward RL, Castleman MM, Meloche CE, Karpen ME, Carlson CG et al. X-ray crystallographic structure of BshB, the zinc-dependent deacetylase involved in bacillithiol biosynthesis. Protein Sci 2020; 29:1035–1039 [View Article] [PubMed]
     [Google Scholar]
  37. Chandrangsu P, Loi VV, Antelmann H, Helmann JD. The role of bacillithiol in gram-positive Firmicutes. Antioxid Redox Signal 2018; 28:445–462 [View Article] [PubMed]
     [Google Scholar]
  38. Fajardo-Cavazos P, Nicholson WL. The TRAP-like SplA protein is a trans-acting negative regulator of spore photoproduct lyase synthesis during Bacillus subtilis sporulation. J Bacteriol 2000; 182:555–560 [View Article] [PubMed]
     [Google Scholar]
  39. Qing R, Hao S, Smorodina E, Jin D, Zalevsky A et al. Protein design: from the aspect of water solubility and stability. Chem Rev 2022; 122:14085–14179 [View Article] [PubMed]
     [Google Scholar]
  40. Gratkowski H, Lear JD, DeGrado WF. Polar side chains drive the association of model transmembrane peptides. Proc Natl Acad Sci USA 2001; 98:880–885 [View Article] [PubMed]
     [Google Scholar]
  41. KOVACS N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703 [View Article] [PubMed]
     [Google Scholar]
  42. 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]
  43. Kuykendall LD, Roy MA, O’neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Evol Microbiol 1988; 38:358–361 [View Article]
     [Google Scholar]
  44. 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]
  45. Tindall B. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
     [Google Scholar]
  46. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
     [Google Scholar]
  47. Komagata K, Suzuki K-I. Lipid and Cell-Wall Analysis in Bacterial Systematics Elsevier; 1988
     [Google Scholar]
  48. Schumann P. Peptidoglycan structure. Method Microbiol 2011; 38:101–129 [View Article]
     [Google Scholar]
  49. Stickler DJ. Bacterial biofilms in patients with indwelling urinary catheters. Nat Clin Pract Urol 2008; 5:598–608 [View Article] [PubMed]
     [Google Scholar]
  50. Kart D, Kuştimur AS. Investigation of gelatinase gene expression and growth of Enterococcus faecalis clinical isolates in biofilm models. Turk J Pharm Sci 2019; 16:356–361 [View Article] [PubMed]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006693
Loading
Niallia tiangongensis sp. nov., isolated from the China Space Station
Int J Syst Evol Microbiol 75, 006693 (2025); https://doi.org/10.1099/ijsem.0.006693
/content/journal/ijsem/10.1099/ijsem.0.006693
/content/journal/ijsem/10.1099/ijsem.0.006693
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An error occurred
Approval was partially successful, following selected items could not be processed due to error