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

Volume 75, Issue 6

sp. nov., a novel endophytic actinobacterium isolated from the root nodules of Open Access

Abstract

The root nodules of remain a relatively understudied niche, with poorly described associated microbial communities. In this study, the isolate RTGN1 was recovered from root nodules collected from Gateshead, UK, and was identified as belonging to based on 16S rRNA gene similarity and phylogenomic placement. This isolate was polyphasically characterized, displaying the ability to grow between 12 and 28 °C and pH 6 and 8 and exhibiting the genes necessary to produce the polar lipids phosphatidylethanolamine and phosphatidylglycerophosphate, alongside DL-type peptidoglycan, which are diagnostic of . Overall genomic relatedness index values were below the cut-off value for delineating a novel species. As such, it is proposed that RTGN1 be recognized as the type strain (=CECT 30870=CABI 507287) of sp. nov. The RTGN1 isolate was screened using and methods and was found to possess a number of genes and pathways related to secondary metabolite production and plant growth promotion. Such genes may serve as an avenue of future study regarding biotechnological potential and use as a bioinoculant to increase phytoremediation efficiency.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Alnus glutinosa , Amycolatopsis , endophyte , novel species , phytoremediation and plant growth promotion
Funding
This study was supported by the:
  • Spanish Ministry of Economy, Industry and Competitiveness (Award RYC2019-028468-I)
    • Principle Award Recipient: Mariadel Carmen Montero-Calasanz
  • Natural Environment Research Council (Award NE/S007512/1)
    • Principle Award Recipient: RyanMichael Thompson
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2025-06-16
2025-07-19
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References

  1. Dawson JO. Ecology of actinorhizal plants. Pawlowski K, Newton WE. Nitrogen Fixation: Origins, Applications, and Research Progress 6 Dordrecht, The Netherlands: Springer; 2008199–227
     [Google Scholar]
  2. Dawson JO. Actinorhizal plants: their use in forestry and agriculture. Outlook Agric 1986; 15:202–208 [View Article]
     [Google Scholar]
  3. Zavitkovski J, Newton M. Ecological importance of snowbrush (Ceanothus velutinus) in the Oregon Cascades. Ecology 1968; 49:1134–1145 [View Article]
     [Google Scholar]
  4. Wall LG. The actinorhizal symbiosis. J Plant Growth Regul 2000; 19:167–182 [View Article] [PubMed]
     [Google Scholar]
  5. Thompson RM, George D, Del Carmen Montero-Calasanz M. Actinorhizal plants and frankiaceae: the overlooked future of phytoremediation. Environ Microbiol Rep 2024; 16:e70033 [View Article] [PubMed]
     [Google Scholar]
  6. Ghodhbane-Gtari F, D’Angelo T, Gueddou A, Ghazouani S, Gtari M et al. Alone yet not alone: frankia lives under the same roof with other bacterial in actinorhizal nodules. Front Microbiol 2021; 12:749760 [View Article]
     [Google Scholar]
  7. Lechevalier MP, Prauser H, Labeda DP, Ruan JS. Two new genera of nocardioform actinomycetes: Amycolata gen. nov. and Amycolatopsis gen. nov. Int J Syst Bacteriol 1986; 36:29–37 [View Article]
     [Google Scholar]
  8. Lee SD. Amycolatopsis ultiminotia sp. nov., isolated from rhizosphere soil, and emended description of the genus Amycolatopsis. Int J Syst Evol Microbiol 2009; 59:1401–1404 [View Article]
     [Google Scholar]
  9. Tang SK, Wang Y, Guan TW, Lee JC, Kim CJ et al. Amycolatopsis halophila sp. nov., a halophilic actinomycete isolated from a salt lake. Int J Syst Evol Microbiol 2010; 60:1073–1078 [View Article]
     [Google Scholar]
  10. Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T et al. Genome-based taxonomic classification of the phylum Actinobacteria. Front Microbiol 2018; 9:2007 [View Article]
     [Google Scholar]
  11. 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]
  12. Duangmal K, Mingma R, Pathom-Aree W, Thamchaipenet A, Inahashi Y et al. Amycolatopsis samaneae sp. nov., isolated from roots of Samanea saman (Jacq.) Merr. Int J Syst Evol Microbiol 2011; 61:951–955 [View Article] [PubMed]
     [Google Scholar]
  13. Chantavorakit T, Suksaard P, Matsumoto A, Duangmal K. Amycolatopsis suaedae sp. nov., an endophytic actinomycete isolated from Suaeda maritima roots. Int J Syst Evol Microbiol 2019; 69:2591–2596 [View Article] [PubMed]
     [Google Scholar]
  14. Song Z, Xu T, Wang J, Hou Y, Liu C et al. Secondary metabolites of the genus Amycolatopsis: structures, bioactivities and biosynthesis. Molecules 2021; 26:1884 [View Article] [PubMed]
     [Google Scholar]
  15. Tan GYA, Goodfellow M. Amycolatopsis. In Bergy’s Manual of Systematics of Archea and Bacteria 2015 pp 1–40 [View Article]
     [Google Scholar]
  16. Vandamme P, Sutcliffe I. Out with the old and in with the new: time to rethink twentieth century chemotaxonomic practices in bacterial taxonomy. Int J Syst Evol Microbiol 2021; 71:005127 [View Article] [PubMed]
     [Google Scholar]
  17. Fotedar R, Caldwell ME, Sankaranarayanan K, Al -Zeyara A, Al-Malki A et al. Ningiella ruwaisensis gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from marine water of the Arabian Gulf. Int J Syst Evol Microbiol 2020; 70:4130–4138 [View Article]
     [Google Scholar]
  18. Lawson PA, Patel NB, Mohammed A, Moore ERB, Lo AS et al. Parapseudoflavitalea muciniphila gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a human peritoneal tumour and reclassification of Pseudobacter ginsenosidimutans as Pseudoflavitalea ginsenosidimutans comb. nov. Int J Syst Evol Microbiol 2020; 70:3639–3646 [View Article]
     [Google Scholar]
  19. Montero-Calasanz MDC, Yaramis A, Rohde M, Schumann P, Klenk HP et al. Genotype-phenotype correlations within the Geodermatophilaceae. Front Microbiol 2022; 13:975365 [View Article] [PubMed]
     [Google Scholar]
  20. Thompson RM, Fox EM, Montero-Calasanz MDMC. Draft genome sequence of amycolatopsis camponoti RTGN1, a bacterial endophyte isolated from Alnus glutinosa nodules. Microbiol Resour Announc 2023; 13:e00470–23 [View Article]
     [Google Scholar]
  21. 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]
  22. Vaas LAI, Sikorski J, Hofner B, Fiebig A, Buddruhs N et al. opm: an R package for analysing OmniLog phenotype microarray data. Bioinformatics 2013; 29:1823–1824 [View Article] [PubMed]
     [Google Scholar]
  23. 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]
  24. Madeira F, Park YM, Lee J, Buso N, Gur T et al. The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Res 2019; 47:W636–W641 [View Article] [PubMed]
     [Google Scholar]
  25. Madeira F, Madhusoodanan N, Lee J, Eusebi A, Niewielska A et al. The EMBL-EBI job dispatcher sequence analysis tools framework in 2024. Nucleic Acids Res 2024; 52:W521–W525 [View Article] [PubMed]
     [Google Scholar]
  26. Yoon SH, Ha SM, 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]
  27. 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]
  28. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  29. Meier-Kolthoff JP, Göker M, Spröer C, Klenk HP. When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 2013; 195:413–418 [View Article] [PubMed]
     [Google Scholar]
  30. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
     [Google Scholar]
  31. Goloboff PA, Farris JS, Nixon KC. TNT, a free program for phylogenetic analysis. Cladistics 2008; 24:774–786 [View Article]
     [Google Scholar]
  32. 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]
  33. 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]
  34. Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4.0 B10 Sunderland: Sinauer Associates Inc; 2002
     [Google Scholar]
  35. Farris JS. Estimating phylogenetic trees from distance matrices. The American Naturalist 1972; 106:645–668 [View Article]
     [Google Scholar]
  36. Lagesen K, Hallin P, Rødland EA, Stærfeldt HH, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article]
     [Google Scholar]
  37. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J et al. BLAST+: architecture and applications. BMC Bioinformatics 2009; 10:412 [View Article]
     [Google Scholar]
  38. 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]
     [Google Scholar]
  39. 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]
     [Google Scholar]
  40. Kreft Ł, Botzki A, Coppens F, Vandepoele K, Bel M. PhyD3: a phylogenetic tree viewer with extended phyloxml support for functional genomics data visualization. Bioinformatics 2017; 33:2946–2947 [View Article]
     [Google Scholar]
  41. 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]
  42. 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]
  43. 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]
  44. Nordberg H, Cantor M, Dusheyko S, Hua S, Poliakov A et al. The genome portal of the department of energy joint genome institute: 2014 updates. Nucleic Acids Res 2014; 42:D26–31 [View Article] [PubMed]
     [Google Scholar]
  45. Chen I-MA, Chu K, Palaniappan K, Ratner A, Huang J et al. The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities. Nucleic Acids Res 2021; 49:D751–D763 [View Article] [PubMed]
     [Google Scholar]
  46. Mukherjee S, Stamatis D, Bertsch J, Ovchinnikova G, Sundaramurthi JC et al. Genomes OnLine Database (GOLD) v.8: overview and updates. Nucleic Acids Res 2021; 49:D723–D733 [View Article] [PubMed]
     [Google Scholar]
  47. Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 2017; 45:D353–D361 [View Article] [PubMed]
     [Google Scholar]
  48. UniProt Consortium UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res 2021; 49:D480–D489 [View Article] [PubMed]
     [Google Scholar]
  49. Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ et al. GenBank. Nucleic Acids Res 2013; 41:D36–42 [View Article] [PubMed]
     [Google Scholar]
  50. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: a fast phage search tool. Nucleic Acids Res 2011; 39:W347–52 [View Article] [PubMed]
     [Google Scholar]
  51. Arndt D, Grant JR, Marcu A, Sajed T, Pon A et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 2016; 44:W16–W21 [View Article]
     [Google Scholar]
  52. 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]
  53. Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 2014; 58:3895–3903 [View Article] [PubMed]
     [Google Scholar]
  54. Grissa I, Vergnaud G, Pourcel C. CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 2007; 36:W145–W148 [View Article]
     [Google Scholar]
  55. Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 2007; 35:W52–7 [View Article] [PubMed]
     [Google Scholar]
  56. Grissa I, Vergnaud G, Pourcel C. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics 2007; 8:172 [View Article] [PubMed]
     [Google Scholar]
  57. 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]
  58. Zankari E, Allesøe R, Joensen KG, Cavaco LM, Lund O et al. PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens. J Antimicrob Chemother 2017; 72:2764–2768 [View Article] [PubMed]
     [Google Scholar]
  59. Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 2020; 48:D517–D525 [View Article] [PubMed]
     [Google Scholar]
  60. Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S et al. ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 2020; 75:3491–3500 [View Article] [PubMed]
     [Google Scholar]
  61. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
     [Google Scholar]
  62. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–14 [View Article] [PubMed]
     [Google Scholar]
  63. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015; 5:8365 [View Article] [PubMed]
     [Google Scholar]
  64. The Uniprot Consortium Uniprot: the universal protein knowledge in 2023. Nucleic Acids Res 2023; 51:D523–31 [View Article]
     [Google Scholar]
  65. Sayers EW, Bolton EE, Brister JR, Canese K, Chan J et al. Database resources of the national center for biotechnology information. Nucleic Acids Res 2022; 50:D20–D26 [View Article] [PubMed]
     [Google Scholar]
  66. Patil C, Suryawanshi R, Koli S, Patil S. Improved method for effective screening of ACC (1-aminocyclopropane-1-carboxylate) deaminase producing microorganisms. J Microbiol Methods 2016; 131:102–104 [View Article] [PubMed]
     [Google Scholar]
  67. Penrose DM, Glick BR. Methods for isolating and characterizing ACC deaminase‐containing plant growth‐promoting rhizobacteria. Physiol Plant 2003; 118:10–15 [View Article] [PubMed]
     [Google Scholar]
  68. Nautiyal CS. An efficient microbiological growth medium for screening phosphate solubilizing microorganisms. FEMS Microbiol Lett 1999; 170:265–270 [View Article] [PubMed]
     [Google Scholar]
  69. Alexander DB, Zuberer DA. Use of chrome azurol S reagents to evaluate siderophore production by rhizosphere bacteria. Biol Fert Soils 1991; 12:39–45 [View Article]
     [Google Scholar]
  70. Patten CL, Glick BR. Role of Pseudomonas putida indoleacetic acid in development of the host plant root system. Appl Environ Microbiol 2002; 68:3795–3801 [View Article] [PubMed]
     [Google Scholar]
  71. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–9
     [Google Scholar]
  72. Oyuntsetseg B, Lee HB, Kim SB. Amycolatopsis mongoliensis sp. nov., a novel actinobacterium with antifungal activity isolated from a coal mining site in Mongolia. Int J Syst Evol Microbiol 2024; 74:006266 [View Article] [PubMed]
     [Google Scholar]
  73. Zakalyukina YV, Osterman IA, Wolf J, Neumann-Schaal M, Nouioui I et al. Amycolatopsis camponoti sp. nov., new tetracenomycin-producing actinomycete isolated from carpenter ant Camponotus vagus. Antonie Van Leeuwenhoek 2022; 115:533–544 [View Article] [PubMed]
     [Google Scholar]
  74. Labeda DP, Donahue JM, Williams NM, Sells SF, Henton MM. Amycolatopsis kentuckyensis sp. nov., Amycolatopsis lexingtonensis sp. nov. and Amycolatopsis pretoriensis sp. nov., isolated from equine placentas. Int J Syst Evol Microbiol 2003; 53:1601–1605 [View Article] [PubMed]
     [Google Scholar]
  75. Ngamcharungchit C, Kanto H, Také A, Intra B, Matsumoto A et al. Amycolatopsis iheyensis sp. nov., isolated from soil on Iheya island, Japan. Int J Syst Evol Microbiol 2023; 73:005757 [View Article] [PubMed]
     [Google Scholar]
  76. Tan GYA, Robinson S, Lacey E, Goodfellow M. Amycolatopsis australiensis sp. nov., an actinomycete isolated from arid soils. Int J Syst Evol Microbiol 2006; 56:2297–2301 [View Article] [PubMed]
     [Google Scholar]
  77. Ren L, Peng C, Hu X, Han Y, Huang H. Microbial production of vitamin K2: current status and future prospects. Biotechnol Adv 2020; 39:107453 [View Article] [PubMed]
     [Google Scholar]
  78. Upadhyay A, Fontes FL, Gonzalez-Juarrero M, McNeil MR, Crans DC et al. Partial saturation of menaquinone in Mycobacterium tuberculosis: function and essentiality of a novel reductase, MenJ. ACS Cent Sci 2015; 1:292–302 [View Article] [PubMed]
     [Google Scholar]
  79. Egan AJF, Biboy J, van’t Veer I, Breukink E, Vollmer W. Activities and regulation of peptidoglycan synthases. Philos Trans R Soc Lond B Biol Sci 2015; 370:20150031 [View Article] [PubMed]
     [Google Scholar]
  80. ANTIA M, HOARE DS, WORK E. The stereoisomers of αε-diaminopimelic acid. 3. Properties and distribution of diaminopimelic acid racemase, an enzyme causing interconversion of the LL and meso isomers. Biochem J 1957; 65:448–459 [View Article] [PubMed]
     [Google Scholar]
  81. Arthur M, Reynolds PE, Depardieu F, Evers S, Dutka-Malen S et al. Mechanisms of glycopeptide resistance in enterococci. J Infect 1996; 32:11–16 [View Article] [PubMed]
     [Google Scholar]
  82. Gudeta DD, Moodley A, Bortolaia V, Guardabassi L. a new glycopeptide resistance operon in environmental Rhodococcus equi isolates. Antimicrob Agents Chemother 2014; 58:1768–1770 [View Article] [PubMed]
     [Google Scholar]
  83. Courvalin P. Vancomycin resistance in gram-positive cocci. Clin Infect Dis 2006; 42 Suppl 1:S25–34 [View Article] [PubMed]
     [Google Scholar]
  84. Kalan L, Ebert S, Kelly T, Wright GD. Noncanonical vancomycin resistance cluster from Desulfitobacterium hafniense Y51. Antimicrob Agents Chemother 2009; 53:2841–2845 [View Article] [PubMed]
     [Google Scholar]
  85. Singh MP, Petersen PJ, Weiss WJ, Janso JE, Luckman SW et al. Mannopeptimycins, new cyclic glycopeptide antibiotics produced by Streptomyces hygroscopicus LL-AC98: antibacterial and mechanistic activities. Antimicrob Agents Chemother 2003; 47:62–69 [View Article] [PubMed]
     [Google Scholar]
  86. Doyle D, McDowall KJ, Butler MJ, Hunter IS. Characterization of an oxytetracycline-resistance gene, otrA, of Streptomyces rimosus. Mol Microbiol 1991; 5:2923–2933 [View Article] [PubMed]
     [Google Scholar]
  87. Zhao Y-F, Lu D-D, Bechthold A, Ma Z, Yu X-P. Impact of otrA expression on morphological differentiation, actinorhodin production, and resistance to aminoglycosides in Streptomyces coelicolor M145. J Zhejiang Univ Sci B 2018; 19:708–717 [View Article] [PubMed]
     [Google Scholar]
  88. Proctor R, Craig W, Kunin C. Cetocycline, tetracycline analog: in vitro studies of antimicrobial activity, serum binding, lipid solubility, and uptake by bacteria. Antimicrob Agents Chemother 1978; 13:598–604 [View Article] [PubMed]
     [Google Scholar]
  89. Birnie CR, Malamud D, Schnaare RL. Antimicrobial evaluation of N-alkyl betaines and N-alkyl-N, N-dimethylamine oxides with variations in chain length. Antimicrob Agents Chemother 2000; 44:2514–2517 [View Article] [PubMed]
     [Google Scholar]
  90. Dieuleveux V, Lemarinier S, Guéguen M. Antimicrobial spectrum and target site of D-3-phenyllactic acid. Int J Food Microbiol 1998; 40:177–183 [View Article] [PubMed]
     [Google Scholar]
  91. Lavermicocca P, Valerio F, Evidente A, Lazzaroni S, Corsetti A et al. Purification and characterization of novel antifungal compounds from the sourdough Lactobacillus plantarum strain 21B. Appl Environ Microbiol 2000; 66:4084–4090 [View Article] [PubMed]
     [Google Scholar]
  92. Sakko M, Tjäderhane L, Sorsa T, Hietala P, Järvinen A et al. 2-hydroxyisocaproic acid (HICA): a new potential topical antibacterial agent. Int J Antimicrob Agents 2012; 39:539–540 [View Article] [PubMed]
     [Google Scholar]
  93. Heeb S, Fletcher MP, Chhabra SR, Diggle SP, Williams P et al. Quinolones: from antibiotics to autoinducers. FEMS Microbiol Rev 2011; 35:247–274 [View Article] [PubMed]
     [Google Scholar]
  94. Xuan LJ, Xu SH, Zhang HL, Xu YM, Chen MQ. Dutomycin, a new anthracycline antibiotic from Streptomyces. J Antibiot 1992; 45:1974–1976 [View Article]
     [Google Scholar]
  95. Sasikala C, Ramana CV, Rao PR. 5-aminolevulinic acid: a potential herbicide/insecticide from microorganisms. Biotechnol Prog 1994; 10:451–459 [View Article]
     [Google Scholar]
  96. Mascal M, Dutta S. Synthesis of the natural herbicide δ-aminolevulinic acid from cellulose-derived 5-(chloromethyl)furfural. Green Chem 2011; 13:40–41 [View Article]
     [Google Scholar]
  97. Miyazawa M, Shimamura H, Nakamura S, Kameoka H. Antimutagenic activity of (+)-β-eudesmol and paeonol from Dioscorea japonica. J Agric Food Chem 1996; 44:1647–1650 [View Article]
     [Google Scholar]
  98. Hsieh C-L, Cheng C-Y, Tsai T-H, Lin I, Liu C-H et al. Paeonol reduced cerebral infarction involving the superoxide anion and microglia activation in ischemia-reperfusion injured rats. J Ethnopharmacol 2006; 106:208–215 [View Article] [PubMed]
     [Google Scholar]
  99. Sova M, Saso L. Natural sources, pharmacokinetics, biological activities and health benefits of hydroxycinnamic acids and their metabolites. Nutrients 2020; 12:2190 [View Article] [PubMed]
     [Google Scholar]
  100. Antelmann H, Scharf C, Hecker M. Phosphate starvation-inducible proteins of bacillus subtilis: proteomics and transcriptional analysis. J Bacteriol 2000; 182:4478–4490 [View Article] [PubMed]
     [Google Scholar]
  101. Santos-Beneit F. The pho regulon: a huge regulatory network in bacteria. Front Microbiol 2015; 6:402 [View Article]
     [Google Scholar]
  102. Alipour Kafi S, Karimi E, Akhlaghi Motlagh M, Amini Z, Mohammadi A et al. Isolation and identification of Amycolatopsis sp. strain 1119 with potential to improve cucumber fruit yield and induce plant defense responses in commercial greenhouse. Plant Soil 2021; 468:125–145 [View Article]
     [Google Scholar]
  103. Zhang Y, Chen F-S, Wu X-Q, Luan F-G, Zhang L-P et al. Isolation and characterization of two phosphate-solubilizing fungi from rhizosphere soil of moso bamboo and their functional capacities when exposed to different phosphorus sources and pH environments. PLoS ONE 2018; 13:e0199625 [View Article]
     [Google Scholar]
  104. Chen W, Yang F, Zhang L, Wang J. Organic acid secretion and phosphate solubilizing efficiency of pseudomonas sp. PSB12: effects of phosphorus forms and carbon source. Geomicrobiol J 2016; 33:870–877 [View Article]
     [Google Scholar]
  105. Behera BC, Yadav H, Singh SK, Mishra RR, Sethi BK et al. Phosphate solubilization and acid phosphatase activity of Serratia sp. isolated from mangrove soil of Mahanadi river delta, Odisha, India. J Genet Eng Biotechnol 2017; 15:169–178 [View Article] [PubMed]
     [Google Scholar]
  106. Jiang Y, Zhao X, Zhou Y, Ding C. Effect of the phosphate solubilization and mineralization synergistic mechanism of Ochrobactrum sp. on the remediation of lead. Environ Sci Pollut Res 2022; 29:58037–58052 [View Article]
     [Google Scholar]
  107. Wannawong T, Mhuantong W, Macharoen P, Niemhom N, Sitdhipol J et al. Comparative genomics reveals insight into the phylogeny and habitat adaptation of novel Amycolatopsis species, an endophytic actinomycete associated with scab lesions on potato tubers. Front Plant Sci 2024; 15:1346574 [View Article] [PubMed]
     [Google Scholar]
  108. Mano Y, Nemoto K. The pathway of auxin biosynthesis in plants. J Exp Bot 2012; 63:2853–2872 [View Article] [PubMed]
     [Google Scholar]
  109. Chaiya L, Kumla J, Suwannarach N, Kiatsiriroat T, Lumyong S. Isolation, characterization, and efficacy of actinobacteria associated with arbuscular mycorrhizal spores in promoting plant growth of chili (Capsicum flutescens L). Microorganisms 2021; 9:1274 [View Article] [PubMed]
     [Google Scholar]
  110. Basavarajappa DS, Kumar RS, Nayaka S. Formulation-based antagonistic endophyte Amycolatopsis sp. SND-1 triggers defense response in Vigna radiata (L.) R. Wilczek (Mung bean) against Cercospora leaf spot disease. Arch Microbiol 2023; 205:77 [View Article] [PubMed]
     [Google Scholar]
  111. Raklami A, Quintas-Nunes F, Nascimento FX, Jemo M, Oufdou K et al. Assessing the growth-promoting traits of actinobacteria spp. isolated from Cleome africana: Implications on growth and root enhancement of Medicago sativa. J King Saud Univ Sci 2023; 35:102722 [View Article]
     [Google Scholar]
  112. Sun Y, Wu H, Zhou W, Yuan Z, Hao J et al. Effects of indole derivatives from Purpureocillium lilacinum in controlling tobacco mosaic virus. Pestic Biochem Physiol 2022; 183:105077 [View Article] [PubMed]
     [Google Scholar]
  113. Kundu A, Mishra S, Kundu P, Jogawat A, Vadassery J. Piriformospora indica recruits host-derived putrescine for growth promotion in plants. Plant Physiol 2022; 188:2289–2307 [View Article]
     [Google Scholar]
  114. Hallmark HT, Rashotte AM. Cytokinin isopentenyladenine and its glucoside isopentenyladenine-9G delay leaf senescence through activation of cytokinin-associated genes. Plant Direct 2020; 4: [View Article]
     [Google Scholar]
  115. Yu Y, Jin C, Sun C, Wang J, Ye Y et al. Inhibition of ethylene production by putrescine alleviates aluminium-induced root inhibition in wheat plants. Sci Rep 2016; 6:18888 [View Article]
     [Google Scholar]
  116. Letunic I, Bork P. Interactive tree of life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res 2024; 52:W78–W82 [View Article] [PubMed]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006810
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Amycolatopsis ponsaeliensis sp. nov., a novel endophytic actinobacterium isolated from the root nodules of Alnus glutinosa
Int J Syst Evol Microbiol 75, 006810 (2025); https://doi.org/10.1099/ijsem.0.006810
/content/journal/ijsem/10.1099/ijsem.0.006810
/content/journal/ijsem/10.1099/ijsem.0.006810
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