Bradyrhizobium nivariense sp. nov., predominant species nodulating Cytisus supranubius in the high mountain ecosystem of Tenerife (Canary Islands)

References

1. Stępkowski T, Banasiewicz J, Granada CE, Andrews M, Passaglia LMP. Phylogeny and phylogeography of rhizobial symbionts nodulating legumes of the tribe genisteae. Genes 2018; 9:163 [View Article] [PubMed]
   [Google Scholar]
2. Acebes J, León M, Rodríguez M, Arco M, García A. Ptridophyta, Spermatophyta. In Arechavaleta M, Rodríguez N, Zurita N, García A. eds Lista de especies silvestres de Canarias. Hongos, plantas y animales terrestres 2010 pp 119–172
   [Google Scholar]
3. Jarabo-Lorenzo A, Pérez-Galdona R, Donate-Correa J, Rivas R, Velázquez E et al. Genetic diversity of bradyrhizobial populations from diverse geographic origins that nodulate Lupinus spp. and Ornithopus spp. Syst Appl Microbiol 2003; 26:611–623 [View Article] [PubMed]
   [Google Scholar]
4. Jarabo-Lorenzo A, Velázquez E, Pérez-Galdona R, Vega-Hernández MC, Martínez-Molina E et al. Restriction fragment length polymorphism analysis of 16S rDNA and low molecular weight RNA profiling of rhizobial isolates from shrubby legumes endemic to the Canary islands. Syst Appl Microbiol 2000; 23:418–425 [View Article] [PubMed]
   [Google Scholar]
5. Vinuesa P, Rademaker J, Bruijn FJ, Werner D. Genotypic characterization of bradyrhizobium strains nodulating endemic woody legumes of the canary islands by PCR-restriction fragment length. Appl Environ Microbiol 1998; 64:2096–2104 [View Article]
   [Google Scholar]
6. Vinuesa P, León-Barrios M, Silva C, Willems A, Jarabo-Lorenzo A et al. Bradyrhizobium canariense sp. nov., an acid-tolerant endosymbiont that nodulates endemic genistoid legumes (Papilionoideae: Genisteae) from the Canary Islands, along with Bradyrhizobium japonicum bv. genistearum, Bradyrhizobium genospecies alpha and Bradyrhizobium genospecies beta. Int J Syst Evol Microbiol 2005; 55:569–575 [View Article] [PubMed]
   [Google Scholar]
7. Wheeler C, Dickson J. Symbiotic nitrogen fixation and distribution of Spartocytisus supranubius on Las Cañadas, Tenerife. Vieraea 1990; 19:309–314
   [Google Scholar]
8. Pulido-Suárez L, Notario Del Pino J, Díaz-Peña FJ, Perdomo-González A, González-Rodríguez ÁM et al. High diversity of bradyrhizobial species fix nitrogen with woody legume Spartocytisus supranubius in a high mountain ecosystem. Microorganisms 2023; 11:1–18 [View Article] [PubMed]
   [Google Scholar]
9. Pulido-Suárez L, Díaz-Peña F, Pino JN, Medina-Cabrera A, León-Barrios M. Alteration of soil rhizobial populations by rabbit latrines could impair symbiotic nitrogen fixation in the insular alpine ecosystem of Teide National Park. Appl Soil Ecol 2021; 160:103850 [View Article]
   [Google Scholar]
10. Ormeño-Orrillo E, Martínez-Romero E. A genomotaxonomy view of the Bradyrhizobium genus. Front Microbiol 2019; 10:1–13 [View Article]
    [Google Scholar]
11. Somasegaran P, Hoben HJ. Counting rhizobia by a plant infection method. In Handbook for Rhizobia Springer-Verlag; 1994 pp 58–64 [View Article]
    [Google Scholar]
12. Pulido-Suárez L, González-Rodríguez ÁM, Cubas J, del Arco-Aguilar M, Martín-Esquivel JL et al. Applying agronomic principles of rhizobial inoculation to the conservation of a keystone legume species in a high mountain ecosystem on an oceanic island. Front Agron 2021; 3:660574 [View Article]
    [Google Scholar]
13. de Lajudie PM, Andrews M, Ardley J, Eardly B, Jumas-Bilak E et al. Minimal standards for the description of new genera and species of rhizobia and agrobacteria. Int J Syst Evol Microbiol 2019; 69:1852–1863 [View Article] [PubMed]
    [Google Scholar]
14. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article] [PubMed]
    [Google Scholar]
15. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J et al. The sequence alignment/map format and SAMtools. Bioinformatics 2009; 25:2078–2079 [View Article] [PubMed]
    [Google Scholar]
16. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLOS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
    [Google Scholar]
17. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genom 2008; 9:1–15 [View Article] [PubMed]
    [Google Scholar]
18. Haft DH, DiCuccio M, Badretdin A, Brover V, Chetvernin V et al. RefSeq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res 2018; 46:D851–D860 [View Article] [PubMed]
    [Google Scholar]
19. 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]
    [Google Scholar]
20. Carattoli A, Hasman H. PlasmidFinder and In Silico pMLST: identification and typing of plasmid replicons in whole-genome sequencing (WGS). Methods Mol Biol 2020; 2075:285–294 [View Article] [PubMed]
    [Google Scholar]
21. Guo J, Bolduc B, Zayed AA, Varsani A, Dominguez-Huerta G et al. VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome 2021; 9:37 [View Article] [PubMed]
    [Google Scholar]
22. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
23. 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]
24. 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]
25. Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics 2022; 38:5315–5316 [View Article] [PubMed]
    [Google Scholar]
26. 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]
27. Riesco R, Trujillo ME. Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2024; 74:006300 [View Article] [PubMed]
    [Google Scholar]
28. Grant JR, Stothard P. The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Research 2008; 36:W181–W184 [View Article]
    [Google Scholar]
29. Petkau A, Stuart-Edwards M, Stothard P, Van Domselaar G. Interactive microbial genome visualization with GView. Bioinformatics 2010; 26:3125–3126 [View Article] [PubMed]
    [Google Scholar]
30. Sharma S, Sathyanarayana BK, Bird JG, Hoskins JR, Lee B et al. Plasmid P1 RepA is homologous to the F plasmid RepE class of initiators. J Biol Chem 2004; 279:6027–6034 [View Article]
    [Google Scholar]
31. Xu L, Dong Z, Fang L, Luo Y, Wei Z et al. OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res 2019; 47:W52–W58 [View Article] [PubMed]
    [Google Scholar]
32. Pulido-Suárez L, Flores-Félix JD, Socas-Pérez N, Igual JM, Velázquez E et al. Endophytic Bosea spartocytisi sp. nov. coexists with rhizobia in root nodules of Spartocytisus supranubius growing in soils of Teide National Park (Canary Islands). Syst Appl Microbiol 2022; 45:126374 [View Article] [PubMed]
    [Google Scholar]
33. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC News 20011–6
    [Google Scholar]
34. Tighe SW, de Lajudie P, Dipietro K, Lindström K, Nick G et al. Analysis of cellular fatty acids and phenotypic relationships of Agrobacterium, Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium species using the Sherlock Microbial Identification System. Int J Syst Evol Microbiol 2000; 50:787–801 [View Article] [PubMed]
    [Google Scholar]
35. Doetsch RN. Determinative methods of light microscopy. In Gerhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA et al. eds Manual of Methods for General Bacteriology Washington (DC): American Society for Microbiology; 1981 pp 21–33
    [Google Scholar]
36. Vincent J. A Manual for the Practical Study of the Root-Nodule Bacteria Oxford, UK: Blackwell Scientific Publications; 1970
    [Google Scholar]
37. Bergersen F. The growth of rhizobium in synthetic media. Aust J Biol Sci 1961; 14:349–360 [View Article]
    [Google Scholar]