1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 8

, sp. nov., from an air conditioner condensate drain line No Access

Abstract

A Gram-negative, rod-shaped and filamentous bacterium designated MD30B was isolated from a biofilm hanging in water flowing from an air conditioner condensate drain line in Honolulu, Hawai‘i. Based on 1517 nucleotides of the strain’s 16S rRNA gene, its nearest neighbours are T16R-86 (96.7 %), S-52 (96.6 %), ZY74 (96.6 %), JS13-10 (96.6 %) and Gsoil 052 (96.5 %). MD30B cells are non-motile, strictly aerobic, and catalase and oxidase positive. Growth occurs between 10 and 45 °C. Major fatty acids in whole cells of MD30B are 13-methyl tetradecanoic acid (34.1 %), -11-hexadecenoic acid (30.3 %), and 3-hydroxy, 15-methyl hexadecanoic acid (13.3 %). The quinone system contains predominantly menaquinone MK-7. The polar lipid profile contains the major lipids phosphatidylethanolamine, one unidentified lipid lacking a functional group, and two unidentified aminolipids. -Homospermidine is the major polyamine. The G+C content of the genome is 47.58 mol%. Based on phenotypic and genotypic differences between MD30B and extant species in the , we propose that MD30B represents a new species, for which the name sp. nov. is proposed to accommodate strain MD30B as the type strain (DSM 112477=NCTC 14606).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): air conditioner , biofilm , Chitinophaga pendula sp. nov. and Hawai‘i
Funding
This study was supported by the:
  • National Science Foundation (Award 1560491)
    • Principle Award Recipient: P DonachieStuart
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006008
2023-08-14
2024-05-01
Loading full text...

Full text loading...

References

  1. Fulthorpe RR, Roesch LFW, Riva A, Triplett EW. Distantly sampled soils carry few species in common. ISME J 2008; 2:901–910 [View Article] [PubMed]
     [Google Scholar]
  2. Fujii K, Satomi M, Fukui Y, Matsunobu S, Morifuku Y et al. Streptomyces abietis sp. nov., a cellulolytic bacterium isolated from soil of a pine forest. Int J Syst Evol Microbiol 2013; 63:4754–4759 [View Article] [PubMed]
     [Google Scholar]
  3. Ahnia H, Bourebaba Y, Durán D, Boulila F, Palacios JM et al. Bradyrhizobium algeriense sp. nov., a novel species isolated from effective nodules of Retama sphaerocarpa from Northeastern Algeria. Syst Appl Microbiol 2018; 41:333–339 [View Article] [PubMed]
     [Google Scholar]
  4. Ping W, Zhang Y, Pang H, Zhang J, Li D et al. Chitinophaga solisilvae sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2020; 70:4808–4815 [View Article] [PubMed]
     [Google Scholar]
  5. Bromfield ESP, Cloutier S. Bradyrhizobium septentrionale sp. nov. (sv. septentrionale) and Bradyrhizobium quebecense sp. nov. (sv. septentrionale) associated with legumes native to Canada possess rearranged symbiosis genes and numerous insertion sequences. Int J Syst Evol Microbiol 2021; 71:004831 [View Article] [PubMed]
     [Google Scholar]
  6. Ivanova EP, Romanenko LA, Chun J, Matte MH, Matte GR et al. Idiomarina gen. nov., comprising novel indigenous deep-sea bacteria from the Pacific Ocean, including descriptions of two species, Idiomarina abyssalis sp. nov. and Idiomarina zobellii sp. nov. Int J Syst Evol Microbiol 2000; 50 Pt 2:901–907 [View Article] [PubMed]
     [Google Scholar]
  7. Furuhata K, Miyamoto H, Goto K, Kato Y, Hara M et al. Roseomonas stagni sp. nov., isolated from pond water in Japan. J Gen Appl Microbiol 2008; 54:167–171 [View Article]
     [Google Scholar]
  8. Subhash Y, Bang JJ, You TH, Lee S-S. Roseomonas rubra sp. nov., isolated from lagoon sediments. Int J Syst Evol Microbiol 2016; 66:3821–3827 [View Article] [PubMed]
     [Google Scholar]
  9. Donachie SP, Bowman JP, Alam M. Psychroflexus tropicus, sp. nov., a new, obligately halophilic CFB group bacterium isolated from an Hawaiian hypersaline lake. Int J Syst Evol Microbiol 2004; 54:935–940
     [Google Scholar]
  10. Donachie SP, Hou S, Lee KS, Riley CW, Pikina A et al. The Hawaiian Archipelago: a microbial diversity hotspot. Microb Ecol 2004; 48:509–520 [View Article] [PubMed]
     [Google Scholar]
  11. Donachie SP, Bowman JP, On SLW, Alam M. Arcobacter halophilus sp. nov., the first obligate halophile in the genus Arcobacter. Int J Syst Evol Microbiol 2005; 55:1271–1277 [View Article] [PubMed]
     [Google Scholar]
  12. King GM. Urban microbiomes and urban ecology: how do microbes in the built environment affect human sustainability in cities?. J Microbiol 2014; 52:721–728 [View Article] [PubMed]
     [Google Scholar]
  13. Brenner DJ, Steigerwalt AG, McDade JE. Classification of the Legionnaires’ disease bacterium: Legionella pneumophila, genus novum, species nova, of the family Legionellaceae, familia nova. Ann Intern Med 1979; 90:656–658 [View Article] [PubMed]
     [Google Scholar]
  14. Khan MAA, Hussain M, Djavanroodi F. Microbiologically influenced corrosion in oil and gas industries: a review. Int J Corros Scale Inhib 2021; 10:80–106 [View Article]
     [Google Scholar]
  15. Langfeldt A, Gold JAW, Chiller T. Emerging fungal infections: from the fields to the clinic, resistant Aspergillus fumigatus and Dermatophyte species: a one health perspective on an urgent public health problem. Curr Clin Microbiol Rep 2022; 9:46–51 [View Article] [PubMed]
     [Google Scholar]
  16. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
     [Google Scholar]
  17. Lewin RA. A classification of flexibacteria. J Gen Microbiol 1969; 58:189–206 [View Article] [PubMed]
     [Google Scholar]
  18. Li L, Sun L, Shi N, Liu L, Guo H et al. Chitinophaga cymbidii sp. nov., isolated from Cymbidium goeringii roots. Int J Syst Evol Microbiol 2013; 63:1800–1804 [View Article] [PubMed]
     [Google Scholar]
  19. Wang Q, Cheng C, He L-Y, Huang Z, Sheng X-F. Chitinophaga jiangningensis sp. nov., a mineral-weathering bacterium. Int J Syst Evol Microbiol 2014; 64:260–265 [View Article] [PubMed]
     [Google Scholar]
  20. Li N, Chen T, Cheng D, Xu X-J, He J. Chitinophaga sedimenti sp. nov., isolated from sediment. Int J Syst Evol Microbiol 2017; 67:3485–3489 [View Article] [PubMed]
     [Google Scholar]
  21. Jin D, Kong X, Wang J, Sun J, Yu X et al. Chitinophaga caeni sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2018; 68:2209–2213 [View Article] [PubMed]
     [Google Scholar]
  22. Tran TLQ, Anani H, Trinh HT, Pham TPT, Dang VK et al. Chitinophaga vietnamensis sp. nov., a multi-drug resistant bacterium infecting humans. Int J Syst Evol Microbiol 2020; 70:1758–1768 [View Article]
     [Google Scholar]
  23. Wan X, Darris M, Hou S, Donachie SP. Draft genome sequence of a novel Chitinophaga sp. strain, MD30, isolated from a biofilm in an air conditioner condensate pipe. Genome Announc 2017; 5:e01161-17 [View Article] [PubMed]
     [Google Scholar]
  24. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991 pp 115–175
     [Google Scholar]
  25. Zhang Z, Schwartz S, Wagner L, Miller W. A greedy algorithm for aligning DNA sequences. J Comput Biol 2000; 7:203–214 [View Article] [PubMed]
     [Google Scholar]
  26. 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]
  27. Stackebrandt E. Defining taxonomic ranks. In Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E. eds The ProkaryotesSymbiotic Associations, Biotechnology, Applied Microbiology, 3rd edition. vol 1 New York: Springer; 2006 pp 29–57 [View Article]
     [Google Scholar]
  28. Tindall BJ, Rosselló-Móra R, Busse HJ, Ludwig W, Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:249–266 [View Article]
     [Google Scholar]
  29. Kim M, Oh H-S, Park S-C, 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]
  30. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
     [Google Scholar]
  31. 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]
  32. Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V et al. Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 2014; 9:2 [View Article] [PubMed]
     [Google Scholar]
  33. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
     [Google Scholar]
  34. 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]
  35. Goloboff PA, Farris JS, Nixon KC. TNT, a free program for phylogenetic analysis. Cladistics 2008; 24:774–786 [View Article]
     [Google Scholar]
  36. Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME, Stamatakis A. How many bootstrap replicates are necessary?. J Comput Biol 2010; 17:337–354 [View Article] [PubMed]
     [Google Scholar]
  37. Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony (*and other methods), version 4.0 Beta 10. Sinauer Associates, Sunderland; 2002
  38. 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]
     [Google Scholar]
  39. Bushnell B. BBMap: a fast, accurate, splice-aware aligner. United States: Joint Genome Institute, 829 Department of Energy. N. p., 2014. Web;
  40. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
     [Google Scholar]
  41. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 2016; 17:132 [View Article] [PubMed]
     [Google Scholar]
  42. 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]
  43. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J et al. BLAST+: architecture and applications. BMC Bioinformatics 2009; 10:421 [View Article] [PubMed]
     [Google Scholar]
  44. 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]
  45. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article] [PubMed]
     [Google Scholar]
  46. 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 Bacteriol 1987; 37:463–464 [View Article]
     [Google Scholar]
  47. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article]
     [Google Scholar]
  48. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  49. 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]
  50. Li P-E, Lo C-C, Anderson JJ, Davenport KW, Bishop-Lilly KA et al. Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform. Nucleic Acids Res 2017; 45:67–80 [View Article] [PubMed]
     [Google Scholar]
  51. 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 Res 2021; 49:W29–W35 [View Article] [PubMed]
     [Google Scholar]
  52. Snyder LR, Kirkland JJ. Preparing buffered mobile phases. In Practical HPLC Method Development, 2nd edn. Hoboken NJ: John Wiley & Sons, Inc; 1997 pp 735–739
     [Google Scholar]
  53. Gerhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA. eds Manual of Methods for General Bacteriology Washington, DC: American Society for Microbiology; 1981 p 524
     [Google Scholar]
  54. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note vol 101 Newark, DE: MIDI, Inc; 1997
     [Google Scholar]
  55. Busse H-J, Auling G. Polyamine pattern as a chemotaxonomic marker within the proteobacteria. Syst Appl Microbiol 1988; 11:1–8 [View Article]
     [Google Scholar]
  56. Busse H-J, Bunka S, Hensel A, Lubitz W. Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 1997; 47:698–708 [View Article]
     [Google Scholar]
  57. 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]
  58. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
     [Google Scholar]
  59. Altenburger P, Kämpfer P, Makristathis A, Lubitz W, Busse H-J. Classification of bacteria isolated from a medieval wall painting. J Biotechnol 1996; 47:39–52 [View Article]
     [Google Scholar]
  60. Stolz A, Busse H-J, Kämpfer P. Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 2007; 57:572–576 [View Article] [PubMed]
     [Google Scholar]
  61. An D-S, Im W-T, Lee S-T, Choi W-Y, Yoon M-H. Chitinophaga soli sp. nov. and Chitinophaga terrae sp. nov., isolated from soil of a ginseng field in Pocheon Province, Korea. J Microbiol Biotechnol 2007; 17:705–711 [PubMed]
     [Google Scholar]
  62. Yasir M, Chung EJ, Song GC, Bibi F, Jeon CO et al. Chitinophaga eiseniae sp. nov., isolated from vermicompost. Int J Syst Evol Microbiol 2011; 61:2373–2378 [View Article] [PubMed]
     [Google Scholar]
  63. Chung EJ, Park TS, Jeon CO, Chung YR. Chitinophaga oryziterrae sp. nov., isolated from the rhizosphere soil of rice (Oryza sativa L.). Int J Syst Evol Microbiol 2012; 62:3030–3035 [View Article] [PubMed]
     [Google Scholar]
  64. Lee H-G, An D-S, Im W-T, Liu Q-M, Na J-R et al. Chitinophaga ginsengisegetis sp. nov. and Chitinophaga ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea. Int J Syst Evol Microbiol 2007; 57:1396–1401 [View Article] [PubMed]
     [Google Scholar]
  65. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972; 106:645–668 [View Article]
     [Google Scholar]
  66. Kreft L, Botzki A, Coppens F, Vandepoele K, Van Bel M. PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization. Bioinformatics 2017; 33:2946–2947 [View Article] [PubMed]
     [Google Scholar]
  67. Kim S-J, Cho H, Ahn J-H, Weon H-Y, Joa J-H et al. Chitinophaga rhizosphaerae sp. nov., isolated from rhizosphere soil of a tomato plant. Int J Syst Evol Microbiol 2017; 67:3435–3439 [View Article] [PubMed]
     [Google Scholar]
  68. Dahal RH, Kim J. Chitinophaga caseinilytica sp. nov., a casein hydrolysing bacterium isolated from forest soil. Arch Microbiol 2018; 200:645–651 [View Article] [PubMed]
     [Google Scholar]
  69. Zong Y, Wu M, Liu X, Jin Y, Wang G et al. Chitinophaga lutea sp. nov., isolated from arsenic-contaminated soil. Int J Syst Evol Microbiol 2019; 69:2114–2119 [View Article] [PubMed]
     [Google Scholar]
  70. Weon H-Y, Yoo S-H, Kim Y-J, Son J-A, Kim B-Y et al. Chitinophaga niabensis sp. nov. and Chitinophaga niastensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2009; 59:1267–1271 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006008
Loading
Chitinophaga pendula, sp. nov., from an air conditioner condensate drain line
Int J Syst Evol Microbiol 73, 006008 (2023); https://doi.org/10.1099/ijsem.0.006008
/content/journal/ijsem/10.1099/ijsem.0.006008
/content/journal/ijsem/10.1099/ijsem.0.006008
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