1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 9

sp. nov., a novel indole-acetic acid producing actinobacterium isolated from marine sand No Access

Abstract

A Gram-positive, aerobic, heterotrophic, non-endospore-forming, rod-shaped and indole-acetic acid-producing strain, designated NEAU-184, was isolated from marine sand collected in Sanya, PR China, and its taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence data indicated that strain NEAU-184 should be assigned to the genus and formed a distinct branch with its closest neighbour, NBRC 106452 (99.1 %). 2,4-Diaminobutyric acid, alanine, -glutamic acid and glycine were detected in cell-wall hydrolysate and glucose, rhamnose and xylose were detected in whole-cell hydrolysate. The polar lipids were found to contain diphosphatidylglycerol, glycolipid, phosphatidylglycerol and two unidentified lipids. The major menaquinone was MK-12 and the minor menaquinones were MK-13 and MK-11. The predominant fatty acids were anteiso-C, anteiso-C and iso-C. The DNA G+C content was 71.5 mol%. Furthermore, the strain could be clearly distinguished from its closely related type strains by the combination of DNA–DNA hybridization results and some phenotypic characteristics. Meanwhile, the strain has the ability to produce indole-acetic acid (0.334mg ml). Therefore, strain NEAU-184 represents a novel species of the genus , for which the name sp. nov. is proposed, with strain NEAU-184 (=CGMCC 4.7505=JCM 32546) as the type strain.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Agromyces mariniharenae sp. nov. , indole-acetic acid , polyphasic approach and whole genome analysis
Funding
This study was supported by the:
  • the key program of the national natural science foundation of china (Award 32030090)
    • Principle Award Recipient: WenshengXiang
© 2021 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005026
2021-09-24
2024-05-10
Loading full text...

Full text loading...

References

  1. Gledhill WE, Casida LE. Predominant catalase-negative soil bacteria. III. Agromyces, gen. n., microorganisms intermediary to Actinomyces and Nocardia. Appl Microbiol 1969; 18:340–349 [View Article] [PubMed]
     [Google Scholar]
  2. Zgurskaya HI, Evtushenko LI, Akimov VN, Voyevoda HV, Dobrovolskaya TG et al. Emended description of the genus Agromyces and description of Agromyces cerinus subsp., cerinus sp. nov., subsp. nov., Agromyces cerinus subsp. nitratus sp. nov., subsp. nov., Agromyces fucosus subsp. fucosus sp. nov., subsp. nov., and Agromyces fucosus subsp. hippuratus sp. nov., subsp. nov. Int J Syst Bacteriol 1992; 42:635–641
     [Google Scholar]
  3. Huang J-R, Ming H, Li S, Meng X-L, Zhang J-X et al. Agromyces insulae sp. nov., an actinobacterium isolated from a soil sample. Int J Syst Evol Microbiol 2016; 66:2002–2007 [View Article] [PubMed]
     [Google Scholar]
  4. Chen Z, Guan Y, Wang J, Li J. Agromyces binzhouensis sp. nov. an actinobacterium isolated from a coastal wetland of the yellow river delta. Int J Syst Evol Microbiol 2016; 66:2278–2283 [View Article] [PubMed]
     [Google Scholar]
  5. Corretto E, Antonielli L, Sessitsch A, Compant S, Gorfer M et al. Agromyces aureus sp. nov., isolated from the rhizosphere of Salix caprea L. grown in a heavy-metal-contaminated soil. Int J Syst Evol Microbiol 2016; 66:3749–3754 [View Article] [PubMed]
     [Google Scholar]
  6. Jurado V, Groth I, Gonzalez JM, Laiz L, Schuetze B et al. Agromyces italicus sp. nov., Agromyces humatus sp. nov. and Agromyces lapidis sp. nov., isolated from Roman catacombs. Int J Syst Evol Microbiol 2005; 55:871–875 [View Article] [PubMed]
     [Google Scholar]
  7. Dorofeeva LV, Krausova VI, Evtushenko LI, Tiedje JM. Agromyces albus sp. nov., isolated from a plant (Androsace sp. Int J Syst Evol Microbiol 2003; 53:1435–1438 [View Article] [PubMed]
     [Google Scholar]
  8. Hamada M, Shibata C, Tamura T, Suzuki K. Agromyces marinus sp. nov., a novel actinobacterium isolated from sea sediment. J Antibiot 2014; 67:703–706 [View Article] [PubMed]
     [Google Scholar]
  9. Atlas RM. Handbook of microbiological media. Quart Rev Biol 2006; 2:364–365
     [Google Scholar]
  10. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  11. Jin L, Zhao Y, Song W, Duan L, Jiang S et al. Streptomyces inhibens sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L. Int J Syst Evol Microbiol 2019; 69:688–695 [View Article] [PubMed]
     [Google Scholar]
  12. Jones KL. Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 1949; 57:141–145 [View Article] [PubMed]
     [Google Scholar]
  13. Waksman SA. The Actinomycetes, Vol. 2, Classification, Identification and Descriptions of Genera and Species Baltimore: Williams and Wilkins; 1961
     [Google Scholar]
  14. Waksman SA. The Actinomycetes. A Summary of Current Knowledge New York: Ronald Press; 1967
     [Google Scholar]
  15. Kelly KL. Inter-society Color Council-national Bureau of Standards Color-name Charts Illustrated with Centroid Colors Published in US 1964
     [Google Scholar]
  16. Zhao JW, Han LY, Yu MY, Cao P, Li DM et al. Characterization of Streptomyces sporangiiformans sp. nov., a novel soil actinomycete with antibacterial activity against Ralstonia solanacearum. Microorganisms 2019; 7:360
     [Google Scholar]
  17. Cao P, Li C, Tan K, Liu C, Xu X et al. Characterization, phylogenetic analyses, and pathogenicity of enterobacter cloacae on rice seedlings in Heilongjiang Province, China. Plant Dis 2020; 104:1601–1609 [View Article] [PubMed]
     [Google Scholar]
  18. Ruan Z, Wang Y, Song J, Jiang S, Wang H et al. Kurthia huakuii sp. nov., isolated from biogas slurry, and emended description of the genus Kurthia. Int J Syst Evol Microbiol 2014; 64:518–521 [View Article] [PubMed]
     [Google Scholar]
  19. Gordon RE, Barnett DA, Handerhan JE, Pang C. Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
     [Google Scholar]
  20. Yokota A, Tamura T, Hasegawa T, Huang LH. Catenuloplanes japonicas gen. nov., sp. nov., nom. rev., a new genus of the order Actinomycetales. Int J Syst Bacteriol 1993; 43:805–812
     [Google Scholar]
  21. Williams ST, Goodfellow M, Alderson G. Genus Streptomyces Waksman and Henrici 1943, 339AL. Williams S, Sharpe M, Holt J. eds In Bergey’s Manual of Systematic Bacteriology Vol 4 Baltimore: Williams & Willkins; 1989 pp 2453–2492
     [Google Scholar]
  22. Glickmann E, Dessaux Y. A critical examination of the specificity of the salkowski reagent for indolic compounds produced by phytopathogenic bacteria. Appl Environ Microbiol 1995; 61:793–796 [View Article] [PubMed]
     [Google Scholar]
  23. Gordon SA, Weber RP. Colorimetric estimation of indoleacetic acid. Plant Physio 1951; 26:192 [View Article]
     [Google Scholar]
  24. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
     [Google Scholar]
  25. Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes. Dietz A, Thayer D. eds In Actinomycete Taxonomy (Special publication vol 6) Arlington: Society of Industrial Microbiology; 1980 pp 227–291
     [Google Scholar]
  26. 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
     [Google Scholar]
  27. Collins MD. Isoprenoid quinone analyses in bacterial classification and identification. Goodfellow M, Minnikin D. eds In Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp 267–284
     [Google Scholar]
  28. Wu C, Lu X, Qin M, Wang Y, Ruan J. Analysis of menaquinone compound in microbial cells by HPLC. Microbiology 1989; 16:176–178
     [Google Scholar]
  29. Gao R, Liu C, Zhao J, Jia F, Yu C et al. Micromonospora jinlongensis sp. nov., isolated from muddy soil in China and emended description of the genus Micromonospora. Antonie van Leeuwenhoek 2014; 105:307–315 [View Article] [PubMed]
     [Google Scholar]
  30. Zhuang X, Peng C, Wang Z, Zhao J, Shen Y et al. Actinomadura physcomitrii sp. nov., a novel actinomycete isolated from moss [Physcomitrium sphaericum (Ludw) Fuernr]. Antonie van Leeuwenhoek 2020; 113:677–685 [View Article] [PubMed]
     [Google Scholar]
  31. Kim SB, Brown R, Oldfield C, Gilbert SC, Iliarionov S et al. Gordonia amicalis sp. nov., a novel dibenzothiophene-desulphurizing actinomycete. Int J Syst Evol Microbiol 2000; 50 Pt 6:2031–2036 [View Article] [PubMed]
     [Google Scholar]
  32. Rivas R, Sánchez M, Trujillo ME, Zurdo-Piñeiro JL, Mateos PF et al. Xylanimonas cellulosilytica gen. nov., sp. nov., a xylanolytic bacterium isolated from a decayed tree (Ulmus nigra). Int J Syst Evol Microbiol 2003; 53:99–103 [View Article] [PubMed]
     [Google Scholar]
  33. Thompson JD, Higgins DG, Gibson TJ. CLUSTALW: 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]
  34. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  35. 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]
  36. Sudhir K, Glen S, Michael L, Christina K, Koichiro T. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 6:1547–1549
     [Google Scholar]
  37. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:83–791 [View Article]
     [Google Scholar]
  38. 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]
  39. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article] [PubMed]
     [Google Scholar]
  40. Chen XY, Zhou YK, Zheng FC. Comparison of two extracting methods for soil microbial total. DNA Chin J Trop Agric 2008; 28:41–43
     [Google Scholar]
  41. 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]
  42. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article] [PubMed]
     [Google Scholar]
  43. 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]
  44. Medema MH, Ka B, Peter C, Victor de J, Piotr Z et al. AntiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 2011; 39:W339–W346 [View Article]
     [Google Scholar]
  45. 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]
  46. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
     [Google Scholar]
  47. 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]
  48. De Ley J, Cattoir H, Reynaerts A. The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 1970; 12:133–142 [View Article] [PubMed]
     [Google Scholar]
  49. Huss VAR, Festl H, Schleifer KH. Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 1983; 4:184–192 [View Article] [PubMed]
     [Google Scholar]
  50. Thomas EA, Alvarez CE, Sutcliffe JG. Evolutionarily distinct classes of S27 ribosomal proteins with differential mrna expression in rat hypothalamus. J Neurochem 2000; 74:2259–2267 [View Article] [PubMed]
     [Google Scholar]
  51. Hamada M, Shibata C, Ishida Y, Tamura T, Yamamura H et al. Agromyces iriomotensis sp. nov. and Agromyces subtropicus sp. nov., isolated from soil. Int J Syst Evol Microbiol 2014; 64:833–838 [View Article] [PubMed]
     [Google Scholar]
  52. 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 Bacteriol 1987; 37:463–464
     [Google Scholar]
  53. 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]
  54. 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]
  55. Duca D, Lorv J, Patten CL, Rose D, Glick BR. Indole-3-acetic acid in plant-microbe interactions. Antonie van Leeuwenhoek 2014; 106:85–125
     [Google Scholar]
  56. Zhang D-C, Schumann P, Liu H-C, Xin Y-H, Zhou Y-G et al. Agromyces bauzanensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2010; 60:2341–2345 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005026
Loading
Agromyces mariniharenae sp. nov., a novel indole-acetic acid producing actinobacterium isolated from marine sand
Int J Syst Evol Microbiol 71, 005026 (2021); https://doi.org/10.1099/ijsem.0.005026
/content/journal/ijsem/10.1099/ijsem.0.005026
/content/journal/ijsem/10.1099/ijsem.0.005026
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