Skip to content
1887

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

Volume 70, Issue 7

sp. nov., a species isolated from L. rhizosphere in northeast Mexico Free

Abstract

During the isolation of bacteria from the L. rhizosphere in northeast Mexico, four strains with similar BOX-PCR patterns were collected. The 16S rRNA gene sequences of all four strains were very similar to each other and that of the type strains of CH34 (98.49 % sequence similarity) and N-1 (98.35 %). The genome of strain ASC-9842 was sequenced and compared to those of other species. ANIb and ANIm values with the most closely related species were lower than 95%, while the DNA–DNA hybridization values were also much lower than 70 %, consistent with the proposal that they represent a novel species. This conclusion was supported by additional phenotypic and chemotaxonomic analyses. Therefore, the name sp. nov. is proposed with the type strain ASC-9842 (=LMG 26414=CIP 110327).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): agave , Cupriavidus , plant-associated and rhizosphere
Funding
This study was supported by the:
  • Office of Science (Award DE-AC02-05CH11231)
    • Principal Award Recipient: William B. Whitman
  • Secretaría de Investigación y Posgrado, Instituto Politécnico Nacional (Award SIP20196674)
    • Principal Award Recipient: Paulina Estrada de los Santos
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004263
2020-06-15
2026-02-17

Metrics

Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/7/4165.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004263&mimeType=html&fmt=ahah

References

  1. Monchy S, Benotmane MA, Janssen P, Vallaeys T, Taghavi S et al. Plasmids pMOL28 and pMOL30 of Cupriavidus metallidurans are specialized in the maximal viable response to heavy metals. J Bacteriol 2007; 189:7417–7425 [View Article][PubMed]
     [Google Scholar]
  2. Zhang Y, Rodionov DA, Gelfand MS, Gladyshev VN. Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization. BMC Genomics 2009; 10:78 [View Article][PubMed]
     [Google Scholar]
  3. Chen WM, Laevens S, Lee TM, Coenye T, De Vos P et al. Ralstonia taiwanensis sp. nov., isolated from root nodules of Mimosa species and sputum of a cystic fibrosis patient. Int J Syst Evol Microbiol 2001; 51:1729–1735 [View Article][PubMed]
     [Google Scholar]
  4. Chen W-M, Moulin L, Bontemps C, Vandamme P, Béna G et al. Legume symbiotic nitrogen fixation by beta-Proteobacteria is widespread in nature. J Bacteriol 2003; 185:7266–7272 [View Article][PubMed]
     [Google Scholar]
  5. Coenye T, Vandamme P, LiPuma JJ. Ralstonia respiraculi sp. nov., isolated from the respiratory tract of cystic fibrosis patients. Int J Syst Evol Microbiol 2003; 53:1339–1342 [View Article][PubMed]
     [Google Scholar]
  6. Estrada-de Los Santos P, Vacaseydel-Aceves NB, Martínez-Aguilar L, Cruz-Hernández MA, Mendoza-Herrera A et al. Cupriavidus and Burkholderia species associated with agricultural plants that grow in alkaline soils. J Microbiol 2011; 49:867–876 [View Article][PubMed]
     [Google Scholar]
  7. Estrada-de los Santos P, Martínez-Aguilar L, López-Lara IM, Caballero-Mellado J. Cupriavidus alkaliphilus sp. nov., a new species associated with agricultural plants that grow in alkaline soils. Syst Appl Microbiol 2012; 35:310–314 [View Article][PubMed]
     [Google Scholar]
  8. Estrada-de Los Santos P, Solano-Rodríguez R, Matsumura-Paz LT, Vásquez-Murrieta MS, Martínez-Aguilar L. Cupriavidus plantarum sp. nov., a plant-associated species. Arch Microbiol 2014; 196:811–817 [View Article][PubMed]
     [Google Scholar]
  9. De Meyer SE, Ruthrof KX, Edwards T, Hopkins AJM, Hardy G et al. Diversity of endemic rhizobia on Christmas island: implications for agriculture following phosphate mining. Syst Appl Microbiol 2018; 41:641–649 [View Article][PubMed]
     [Google Scholar]
  10. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics. Wiley New York: 1991 pp 115–175
     [Google Scholar]
  11. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003; 52:696–704 [View Article][PubMed]
     [Google Scholar]
  12. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
     [Google Scholar]
  13. Okonechnikov K, Golosova O, Fursov M. UGENE team Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 2012; 28:1166–1167 [View Article][PubMed]
     [Google Scholar]
  14. Darriba D, Taboada GL, Doallo R, Posada D. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 2012; 9:772 [View Article][PubMed]
     [Google Scholar]
  15. Akaike H. A new look at the statistical model identification. IEEE Trans Automat Contr 1974; 19:716–723 [View Article]
     [Google Scholar]
  16. Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M et al. Beast 2.5: an advanced software platform for Bayesian evolutionary analysis. PLoS Comput Biol 2019; 15:e1006650 [View Article][PubMed]
     [Google Scholar]
  17. Versalovic J, Schneider M, de Bruijn FJ, Lupski JR. Genomic fingerprinting of bacteria using repetitive sequence-based PCR (REP-PCR). Methods Mol Cell Biol 1994; 5:25–40
     [Google Scholar]
  18. Whitman WB, Woyke T, Klenk H-P, Zhou Y, Lilburn TG et al. Genomic encyclopedia of bacterial and archaeal type strains, phase III: the genomes of soil and plant-associated and newly described type strains. Stand Genomic Sci 2015; 10:26 [View Article][PubMed]
     [Google Scholar]
  19. Rojas-Rojas FU, Huntemann M, Clum A, Pillay M, Palaniappan K et al. Draft genome sequence of heavy metal-resistant Cupriavidus alkaliphilus ASC-732T, isolated from agave rhizosphere in the northeast of Mexico. Genome Announc 2016; 4:e01013–01016 [View Article][PubMed]
     [Google Scholar]
  20. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article][PubMed]
     [Google Scholar]
  21. 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; 14:260 [View Article]
     [Google Scholar]
  22. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article][PubMed]
     [Google Scholar]
  23. Muñoz-Ramírez ZY, Mendez-Tenorio A, Kato I, Bravo MM, Rizzato C et al. Whole genome sequence and phylogenetic analysis show Helicobacter pylori strains from Latin America have followed a unique evolution pathway. Front Cell Infect Microbiol 2017; 7:50 [View Article][PubMed]
     [Google Scholar]
  24. Rojas-Rojas FU, Salazar-Gómez A, Vargas-Díaz ME, Vásquez-Murrieta MS, Hirsch AM et al. Broad-spectrum antimicrobial activity by Burkholderia cenocepacia TAtl-371, a strain isolated from the tomato rhizosphere. Microbiology 2018; 164:1072–1086 [View Article][PubMed]
     [Google Scholar]
  25. Lukasz D, Liwia R, Aleksandra M, Aleksandra S. Dissolution of arsenic minerals mediated by dissimilatory arsenate reducing bacteria: estimation of the physiological potential for arsenic mobilization. Biomed Res Int 2014; 2014:112 [View Article][PubMed]
     [Google Scholar]
  26. Trujillo-Cabrera Y, Ponce-Mendoza A, Vásquez-Murrieta MS, Rivera-Orduña FN, Wang ET. Diverse cellulolytic bacteria isolated from the high humus, alkaline-saline chinampa soils. Ann Microbiol 2013; 63:779–792 [View Article]
     [Google Scholar]
  27. Castro-González R, Martínez-Aguilar L, Ramírez-Trujillo A, Estrada-de los Santos P, Caballero-Mellado J. High diversity of culturable Burkholderia species associated with sugarcane. Plant Soil 2011; 345:155–169 [View Article]
     [Google Scholar]
  28. Estrada-De Los Santos P, Bustillos-Cristales R, Caballero-Mellado J. Burkholderia, a genus rich in plant-associated nitrogen FiXeRs with wide environmental and geographic distribution. Appl Environ Microbiol 2001; 67:2790–2798 [View Article][PubMed]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.004263
Loading
Cupriavidus agavae sp. nov., a species isolated from Agave L. rhizosphere in northeast Mexico
Int J Syst Evol Microbiol 70, 4165 (2020); https://doi.org/10.1099/ijsem.0.004263
/content/journal/ijsem/10.1099/ijsem.0.004263
/content/journal/ijsem/10.1099/ijsem.0.004263
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