logo RIMA
logo UFRRJ

  1. Repositório de Múltiplos Acervos da UFRRJ
  2. Teses e Dissertações
  3. Programa de Pós-Graduação em Agronomia - Ciência do Solo
  4. Doutorado em Agronomia - Ciência do Solo
Please use this identifier to cite or link to this item: https://rima.ufrrj.br/jspui/handle/20.500.14407/20209
Full metadata record
DC FieldValueLanguage
dc.contributor.authorFerreira, Natália dos Santos-
dc.date.accessioned2025-02-26T23:02:00Z-
dc.date.available2025-02-26T23:02:00Z-
dc.date.issued2022-11-29-
dc.identifier.citationFERREIRA, Natália dos Santos. Taxonomia e reclassificação de estirpes do gênero Azospirillum e Nitrospirillum pertencentes ao Centro de Recursos Biológicos Johanna Döbereiner. 2022. 102 f. Tese (Doutorado em Agronomia - Ciência do Solo) - Instituto de Agronomia, Universidade Federal Rural do Rio de Janeiro, Seropédica, 2022.pt_BR
dc.identifier.urihttps://rima.ufrrj.br/jspui/handle/20.500.14407/20209-
dc.description.abstractO Centro de Recursos Biológicos Johanna Döbereiner - CRB-JD, é uma coleção de culturas pertencente ao Centro Nacional de Pesquisa em Agrobiologia (CNPAB), existe oficialmente desde 1960, é mundialmente conhecido por manter uma alta diversidade de bactérias fixadoras de nitrogênio, além de conter espécies microbianas com potencial para serem utilizadas em benefício da sociedade brasileira. Hoje seu acervo abriga cerca de (53) leveduras, (64) fungos filamentosos, (6060) bactérias de diversos gêneros. Grande parte da Coleção foi identificada por meio de características bioquímicas e morfológicas. No entanto, com base nos métodos moleculares atualmente aceitos na análise do genoma, ainda faltam informações taxonômicas sobre as cepas. Diante disso, o presente trabalho propôs, por meio de análise molecular, caracterizar uma parte da coleção de germoplasma para os gêneros Azospirillum e Nitrospirillum. Ambos os gêneros possuem rizobactérias promotoras do crescimento vegetal com capacidade de fixar nitrogênio atmosférico e produzir compostos benéficos para as plantas e estão presentes em diferentes condições edafoclimáticas. As análises moleculares foram baseadas em caracterizações filogenéticas combinadas (16S rRNA, recA); genômica (identidade nucleotídica média (ANI) com valores de circunscrição de 96% e linha de corte de hibridização digital DNA-DNA (dDDH) de 70%, proteoma central). As análises funcionais são definidas apenas para as espécies de Azospirillum, são baseadas em caracterizações fenotípicas e bioquímicas. Este trabalho originou duas propostas de reclassificação taxonômica, definidas como Azospirillum baldaniorum Sp245T e Azospirillum argentinense Az39T , anteriormente classificadas como espécies pertencentes a Azospirillum brasilense. Além da classificação filogenética das cepas dos gêneros Azospirillum e Nitrospirillum, evidenciando a alta diversidade entre cepas das espécies de ambos os gêneros, sugerindo a existência de novas espécies e acrescentando informações ao banco de dados desta coleção de estirpes erroneamente classificadas pertencentes a outros gêneros.pt_BR
dc.description.sponsorshipCoordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPESpt_BR
dc.languageporpt_BR
dc.publisherUniversidade Federal Rural do Rio de Janeiropt_BR
dc.subjectColeção de culturaspt_BR
dc.subjectNovas espéciespt_BR
dc.subjectReclassificação taxonômicapt_BR
dc.subjectAzospirillumpt_BR
dc.subjectNitrospirillumpt_BR
dc.titleTaxonomia e reclassificação de estirpes do gênero Azospirillum e Nitrospirillum pertencentes ao Centro de Recursos Biológicos Johanna Döbereinerpt_BR
dc.title.alternativeTaxonomy and reclassification of strains of the genus Azospirillum and Nitrospirillum belonging to the Johanna Döbereiner Center for Biological Resourcesen
dc.typeTesept_BR
dc.description.abstractOtherThe Johanna Döbereiner Biological Resource Center - CRB-JD, is a culture collection belonging to the National Center for Research in Agrobiology (CNPAB), it has officially existed since 1960, it is world-renowned for maintaining a high diversity of nitrogen-fixing bacteria, in addition to containing microbial species that have the potential to be used for the benefit of Brazilian society. Today its collection houses about (53) yeasts, (64) filamentous fungi, (6060) bacteria of different genera. Much of the Collection was identified using biochemical and morphological features. However, based on currently accepted molecular methods in genome analysis, taxonomic information on the strains is still lacking. In view of this, the present work proposed, through molecular analysis, to characterize a part of the germplasm collection for the genus Azospirillum and Nitrospirillum. Both genera have plant growth-promoting rhizobacteria with the ability to fix atmospheric nitrogen and produce beneficial compounds for plants and are present in different edaphoclimatic conditions. Molecular analyzes were based on combined phylogenetic characterizations (16S rRNA, use of recA gene); genomics (average nucleotide identity (ANI) with circumscription values of 96% and DNA-DNA digital hybridization (dDDH) cut-line of 70%, core proteome). Functional analyses are defined only for Azospirillum species, are based on phenotypic and biochemical characterizations. This work originated two taxonomic reclassification proposals, defined as Azospirillum baldaniorum Sp245T and Azospirillum argentinense Az39T , previously classified as species belonging to Azospirillum brasilense. In addition to the phylogenetic classification of strains of the genus Azospirillum and Nitrospirillum, evidencing the high diversity between strains of the species of both genera, suggesting the existence of new species and adding information to the database of this collection of wrongly classified strains belonging to other genera.pt_BR
dc.contributor.advisor1Zilli, Jerri Édson-
dc.contributor.advisor1IDhttps://orcid.org/0000-0003-2138-3488pt_BR
dc.contributor.advisor1Latteshttp://lattes.cnpq.br/4935993716536909pt_BR
dc.contributor.advisor-co1Sant’anna, Fernando Hayashi-
dc.contributor.advisor-co1Lattes-pt_BR
dc.contributor.referee1Zilli, Jerri Édson-
dc.contributor.referee1IDhttps://orcid.org/0000-0003-2138-3488pt_BR
dc.contributor.referee1Latteshttp://lattes.cnpq.br/4935993716536909pt_BR
dc.contributor.referee2Coelho, Irene da Silva-
dc.contributor.referee2IDhttp://lattes.cnpq.br/2191695584157582pt_BR
dc.contributor.referee2Latteshttp://lattes.cnpq.br/2191695584157582pt_BR
dc.contributor.referee3Reis, Veronica Massena-
dc.contributor.referee3IDhttps://orcid.org/0000-0003-2149-7725pt_BR
dc.contributor.referee3Latteshttp://lattes.cnpq.br/9099587982889283pt_BR
dc.contributor.referee4Bach, Evelise-
dc.contributor.referee4IDhttps://orcid.org/0000-0002-2502-221Xpt_BR
dc.contributor.referee4Latteshttp://lattes.cnpq.br/6897089273264357pt_BR
dc.contributor.referee5Moreira, Fatima Maria de Souza-
dc.contributor.referee5IDhttps://orcid.org/0000-0003-0159-5811pt_BR
dc.contributor.referee5Latteshttp://lattes.cnpq.br/5206955158181774pt_BR
dc.creator.IDhttps://orcid.org/0000-0003-0764-9278pt_BR
dc.creator.Latteshttp://lattes.cnpq.br/2646047672530138pt_BR
dc.publisher.countryBrasilpt_BR
dc.publisher.departmentInstituto de Agronomiapt_BR
dc.publisher.initialsUFRRJpt_BR
dc.publisher.programPrograma de Pós-Graduação em Agronomia - Ciência do Solopt_BR
dc.relation.referencesALVES, L. P. S.; ALMEIDA, A. T.; CRUZ, L. M.; PEDROSA, F. O.; DE SOUZA, E. M. A simple and efficient method for poly-3-hydroxybutyrate quantification in diazotrophic bacteria within 5 minutes using flow cytometry. Braz J Med Biol 50. 2017. ANANDHAM, R.; HEO, J.; KRISHNAMOORTHY, R.; SENTHILKUMAR, M.; GOPAL, N. O.; KIM, S. J.; KWON, S. W. Azospirillum ramasamyi sp. nov., a novel diazotrophic bacterium isolated from fermented bovine products. Int J Syst Evol Microbiol. 69:1369-1375. 2019. BALDANI, J. I.; KRIEG, N. R.; BALDANI, V. L. D.; HARTMANN, A.; DÖBEREINER, J. Azospirillum. Bergey’s Manual of Systematics of Archaea and Bacteria, pp. 1-35. 2015. BEIJERINCK, M. W. Über ein Spirillum, whelches freien Stickstoff binden kann. Zentralbl Bakteriol Parasitenkd Infektionskr 63:535. 1925. CASSÁN, F.; CONIGLIO, A.; LÓPEZ, G.; MOLINA, R.; NIEVAS, S.; DE CARLAN, C. L. N. Everything you must know about Azospirillum and its impact on agriculture and beyond. Biol Fertil Soils 56:461-79. 2020. CASSÁN, F.; DIAZ-ZORITA, M. Azospirillum sp. in current agriculture: From the laboratory to the field. Soil Biol Biochem 103:117-30. 2016. CASSÁN, F.; MAIALE, S.; MASCIARELLI, O.; VIDAL, A.; LUNA, V.; RUIZ, O. Cadaverine production by Azospirillum brasilense and its possible role in plant growth promotion and osmotic stress mitigation. Eur J Soil Biol 45:12-9. 2009. CASSÁN, F.; PERRIG, D.; SGROY, V.; MASCIARELLI O, PENNA C, LUNA V. Azospirillum brasilense Az39 and Bradyrhizobium japonicum E109, inoculated singly or in combination, promote seed germination and early seedling growth in corn (Zea mays L.) and soybean (Glycine max L.). Eur J Soil Biol 45:28-35. 2009. CASSÁN F.; VANDERLEYDEN, J.; SPAEPEN S. Physiological and Agronomical Aspects of Phytohormone Production by Model Plant-Growth-Promoting Rhizobacteria (PGPR) Belonging to the Genus Azospirillum. J Plant Growth Regul 33:440-459. 2014. CASSAN, F. D.; CONIGLIO, A.; AMAVIZCA, E.; MARONICHE, G.; CASCALES, E.; BASHAN, Y. et al. The Azospirillum brasilense type VI secretion system promotes cell aggregation, biocontrol protection against phytopathogens and attachment to the microalgae Chlorella sorokiniana. Environ Microbiol 23:6257-74. 2021. CHOWDHURY, S. P.; NAGARAJAN, T.; TRIPATHI, R.; MISHRA, M. N.; LE RUDULIER, D.; TRIPATHI, A. K. Strain-specific salt tolerance and osmoregulatory mechanisms in Azospirillum brasilense. FEMS Microbiology Letters 267:72-79. 2007. CIUFO, S.; KANNAN, S.; SHARMA, S.; BADRETDIN, A.; CLARK, K.; TURNER, S. Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI. Int J Syst Evol Microbiol 68:2386-92. 2018. 70 CLSI Performance Standards for Antimicrobial Disk Susceptibility Tests; Approved Standard - Eleventh edition. CLSI document M02 - A11. Wayne, PA, USA: Clinical and Laboratory Standards Institute, 2012. CONTRERAS-MOREIRA, B.; VINUESA, P. GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis. Appl Environ Microbiol 79:7696. 2013. DÍAZ-ZORITA, M.; FERNÁNDEZ-CANIGIA, M. V. Field performance of a liquid formulation of Azospirillum brasilense on dryland wheat productivity. Eur J Soil Biol 45:3 11. 2009. EDGAR, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-7. 2004. FERREIRA, N. D. S.; SANT’ANNA, F. H.; REIS, V. M.; AMBROSINI, A.; VOLPIANO, C. G. Genome-based reclassification of Azospirillum brasilense Sp245 as the type strain of Azospirillum baldaniorum sp. nov. Int J Syst Evol Microbiol 70:6203-6212. 2020. GARCÍA, J. E.; LABARTHE, M. M.; PAGNUSSAT, L. A.; AMENTA, M.; CREUS, C. M.; MARONICHE, G. A. Signs of a phyllospheric lifestyle in the genome of the stress-tolerant strain Azospirillum brasilense Az19. Syst Appl Microbiol 43. 2020. GARCÍA, J. E.; MARONICHE, G.; CREUS, C.; SUÁREZ-RODRÍGUEZ, R.; RAMIREZ TRUJILLO, J. A.; GROPPA, M. D. In vitro PGPR properties and osmotic tolerance of different Azospirillum native strains and their effects on growth of maize under drought stress. Microbiol Res 202:21-9. 2017. GUALPA, J.; LOPEZ, G.; NIEVAS, S.; CONIGLIO, A.; HALLIDAY, N.; CÁMARA, M. Azospirillum brasilense Az39, a model rhizobacterium with AHL quorum-quenching capacity. J Appl Microbiol 126:1850-60. 2020. HARDY, R. W. F.; BURNS, R. C.; HOLSTEN, R. D. Applications of the acetylene-ethylene assay for measurement of nitrogen fixation. Soil Biol Biochem 5:47-81. 1973. HÖRDT, A.; LÓPEZ, M. G.; MEIER-KOLTHOFF, J. P.; SCHLEUNING, M.; WEINHOLD, L. M. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Front Microbiol 11:468. 2020. JENSEN, J. B.; EGSGAARD, H.; VAN ONCKELEN, H.; JOCHIMSEN, B. U. Catabolism of indole-3-acetic acid and 4- and 5-chloroindole-3-acetic acid in Bradyrhizobium japonicum. J. Bacteriol. 177:5762. 1995. KWAK, Y.; SHIN, J. H. First Azospirillum genome from aquatic environments: Whole genome sequence of Azospirillum thiophilum BV-ST, a novel diazotroph harboring a capacity of sulfur-chemolithotrophy from a sulfide spring. Marine Genomics 25:21-24. 2016. KOCH, B.; EVANS, H. J. Reduction of Acetylene to Ethylene by Soybean Root Nodules. Plant Physiol 41:1748-50. 1966. 71 KUMAR, S.; STECHER, G.; LI, M.; KNYAZ, C.; TAMURA, K. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol 35:1547-9. 2018. LEE, I.; KIM, Y. O.; PARK, S. C.; CHUN, J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100-3. 2016. LIN, S. Y.; HAMEED, A.; SHEN, F. T.; LIU, Y. C.; HSU, Y. H. Description of Niveispirillum fermenti gen. nov., sp. nov., isolated from a fermentor in Taiwan, transfer of Azospirillum irakense (1989) as Niveispirillum irakense comb. nov., and reclassification of Azospirillum amazonense (1983) as Nitrospirillum amazonense gen. nov. Antonie van Leeuwenhoek 105. 2014. LIN, S. Y.; SHEN, F. T.; YOUNG, L. S.; ZHU, Z. L.; CHEN, W. M.; YOUNG, C. C. Azospirillum formosense sp. nov., a diazotroph from agricultural soil. Int J Syst Evol Microbiol 62:1185-1190. 012. LU, Y. K.; MARDEN, J.; HAN, M.; SWINGLEY, W. D.; MASTRIAN, S. D.; CHOWDHURY, S.; TOUCHMAN, J. W. Metabolic flexibility revealed in the genome of the cyst-forming alpha-1 proteobacterium Rhodospirillum centenum. BMC Genom 11:325. 2010. MICHEL, D. C.; PASSOS, S. R.; SIMÕES-ARAUJO, J. L.; BARAÚNA, A. C.; DA SILVA, K. Bradyrhizobium centrolobii and Bradyrhizobium macuxiense sp. nov. isolated from Centrolobium paraense grown in soil of Amazonia, Brazil. Arch Microbiol 199:657-64. 2017. MOLINA, R.; LÓPEZ, G.; RODRIGUEZ, B.; ROSAS, S.; MORA, V.; CASSÁN, F. Evaluation of growth and motility in non-photosynthetic Azospirillum brasilense exposed to red, blue, and white light. Arch Microbiol 202:1193-1201. 2020. MURRAY, R.; DOETSCH, R.; ROBINOW, C. Determinative and cytological light microscopy. In: GERHARDT, P. (Ed.). Methods for General and Molecular Bacteriology, Washington: ASM Press; pp. 21-41. 1994. NA, S. I.; KIM, Y. O.; YOON, S. H.; HA, S.; MIN BAEK. I.; CHUN, J. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J. Microbiol. 56:281 5. 2018. OKON, Y.; LABANDERA-GONZALEZ, C. A. Agronomic applications of Azospirillum: An evaluation of 20 years worldwide field inoculation. Soil Biol Biochem 26:1591-601. 1994. PARTE, A. C.; CARBASSE, J. S.; MEIER-KOLTHOFF, J. P.; REIMER, L. C.; GÖKER, M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 70:5607-12. 2020. PERRIG, D.; BOIERO, M. L.; MASCIARELLI, O. A.; PENNA, C.; RUIZ, O. A. Plant growth-promoting compounds produced by two agronomically important strains of Azospirillum brasilense, and implications for inoculant formulation. Appl Microbiol Biotechnol 75:1143-50. 2007. 72 PEDRAZA, R. O.; MOTOK, J.; TORTORA, M. L.; SALAZAR, S. M.; DÍAZ-RICCI, J. C. Natural occurrence of Azospirillum brasilense in strawberry plants. Plant and Soil 295: 169 178. 2007. PFENNIG, N.; TRUPER, H. G. Higher Taxa of the Phototrophic Bacteria. Int J Syst Evol Microbiol 21:17-8. 1971. PRITCHARD, L.; GLOVER, R. H.; HUMPHRIS, S.; ELPHINSTONE, J. G.; TOTH, I. K. Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods 8:12-24. 2015. REIS, V. M.; DÖBEREINER, J. Effect of high sugar concentration on nitrogenase activity of Acetobacter diazotrophicus. Arch Microbiol 171:13-8. 1998. RIVERA, D.; MORA, V.; LOPEZ, G.; ROSAS, S.; SPAEPEN, S.; VANDERLEYDEN, J. New insights into indole-3-acetic acid metabolism in Azospirillum brasilense. J Appl Microbiol 125:1774-1785. 2018. RIVERA, D.; REVALE, S.; MOLINA, R.; GUALPA, J.; PUENTE, M. Complete Genome Sequence of the Model Rhizosphere Strain Azospirillum brasilense Az39, Successfully Applied in Agriculture. Genome Announc 2:e00683-14. 2014. RODRÍGUEZ CÁCERES, E. A.; DI CIOCCO, C. A.; CARLETTI, S. M. 25 años de investigación de Azospirillum brasilense AZ 39 en Argentina. In: CASSÁN, F. D.; GARCÍA, D. E.; SALAMONE, I. (Eds.) Azospirillum sp.: cell physiology, plant interactions and agronomic research in Argentina. I International Workshop on Azospirillum: cell physiology, plant response and agronomic research. 1st ed., Argentina: Asociación Argentina de Microbiología p. 179-87. 2008. SANT’ANNA, F. H.; AMBROSINI, A.; DE SOUZA, R.; FERNANDES, G. E. C.; BACH, E. Reclassification of Paenibacillus riograndensis as a genomovar of Paenibacillus sonchi: Genome-based metrics improve bacterial taxonomic classification. Front Microbiol 8:1849. 2017. SASSER M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids. Technical Note # 101 Microbial ID, Inc., Newark, Del. USA. 2001. SINGH, C.; PANDEY, P.; SINGH, D. N.; PANDEY, R.; SHASANY, A. K.; TRIPATHI, A. K. Whole-Genome Sequences of Four Indian Isolates of Azospirillum brasilense. Microbiology Resource Announcements 8: e00633-19. 2019. 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 10:512-26. 1993. TAMURA, K.; STECHER, G.; KUMAR, S. MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Mol Biol Evol 38:3022-7. 2021. TARRAND, J. J.; KRIEG, N. R.; DOBEREINER, J. A taxonomic study of the Spirillum lipoferum group, with descriptions of a new genus, Azospirillum gen. nov. and two species, 73 Azospirillum lipoferum (Beijerinck) comb. nov. and Azospirillum brasilense sp. nov. Can J Microbiol 24:967-80. 1978. TIKHONOVA, E. N.; GROUZDEV, D. S.; KRAVCHENKO, I. K. Azospirillum palustre sp. nov., a methylotrophic nitrogen-fixing species isolated from raised bog. Int J Syst Evol Microbiol 69:2787-2793. 2019. VARGHESE, N. J.; MUKHERJEE, S.; IVANOVA N, KONSTANTINIDIS K. T.; MAVROMMATIS K. Microbial species delineation using whole genome sequences. Nucleic Acids Res 43:6761-71. 2015. VINUESA, P.; CONTRERAS-MOREIRA, B. Robust identification of orthologues and paralogues for microbial pan-genomics using GET_HOMOLOGUES: A case study of pIncA/C plasmids. Methods Mol Biol 1231:203-32. 2015. VOLPIANO, C. G.; SANT’ANNA, F. H.; AMBROSINI, A.; DE SÃO JOSÉ, J. F. B.; BENEDUZI, A. Genomic Metrics Applied to Rhizobiales (Hyphomicrobiales): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains. Front Microbiol 12. 2012. YOON, S. H.; HA, S.; MIN, L. I. M. J.; KWON, S.; CHUN, J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281-6. 2017.pt_BR
dc.subject.cnpqAgronomiapt_BR
Appears in Collections:Doutorado em Agronomia - Ciência do Solo

Se for cadastrado no RIMA, poderá receber informações por email.
Se ainda não tem uma conta, cadastre-se aqui!

Files in This Item:
File Description SizeFormat 
2022 - Natália dos Santos Ferreira.Pdf4.62 MBAdobe PDFThumbnail
View/Open
Show simple item record


Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.