Genomic analysis of Sinorhizobium meliloti LPU63, an acid-tolerant and symbiotically efficient alfalfa-nodulating rhizobia

Autores
Cafiero, Juan Hilario; Salvetti Casasco, María; Lozano, Mauricio Javier; Lopez Garcia, Silvina Laura; Vacca, Carolina; Draghi, Walter Omar; Lagares, Antonio; del Papa, Maria Florencia
Año de publicación
2023
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The growth and persistence of alfalfa (Medicago sativa), a perennial legume capable of producing high yields of high-quality forage, is reduced in moderately acidic soils. The low performance of alfalfa at low pH is due to numerous factors that affect the host plant, their rhizobia, and the symbiotic interaction.Sinorhizobium meliloti LPU63 was isolated from acid topsoil (in Argentina) and showed to be a highly competitive and efficient N2-fixing rhizobium under both, neutral and moderately acidic soil conditions. In this study, we obtained a draft of the LPU63 genome sequence using Illumina HiSeq4000. The whole genome phylogenetic analysis confirmed the taxonomic position of LPU63 as a S. meliloti strain and the multilocus sequence analysis confirmed that LPU63 is not related to the strains used in Argentina in bioformulations. The genomic analysis showed that beyond the canonical chromosome, pSymA, and pSymB, LPU63 strain has an accessory plasmid that codes for a repABC origin of replication and a conjugative T4SS, suggesting that this plasmid could be self-transmissible. In addition, the complete denitrification pathway (i.e., the gene clusters nap, nir, nor, and nos), including napC and nosZ, which could be used as an alternative respiration route under hypoxic conditions with moderate N2O emissions was found. Also, genes associated with plant growth-promoting activities (PGPR) and the degradation of phenylacetic acid (PAA) were identified. LPU63 is a highly melanogenic strain, a property that could enhance its survival under soil conditions, and the genome data showed a particular arrangement of the genes involved in melanin production. The information regarding LPU63 activities compatible with plant-growth promotion phenotypes, together with other characteristics mentioned here (melanin production, potential moderate N2O emissions), constitute the basis of future experiments toward the rational design of a novel bioinoculant for the environmentally sustainable production of alfalfa.
Fil: Cafiero, Juan Hilario. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina
Fil: Salvetti Casasco, María. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina
Fil: Lozano, Mauricio Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina
Fil: Lopez Garcia, Silvina Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina
Fil: Vacca, Carolina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina
Fil: Draghi, Walter Omar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina
Fil: Lagares, Antonio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina
Fil: del Papa, Maria Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina
Materia
Rhizobia
Sinorhizobium meliloti
accessory genome
denitrification pathway
PGPR-related genes
Symbiosis
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/230101
Acceder
id CONICETDig_4b679173cdc687cf072f3a7149e7a12f
oai_identifier_str oai:ri.conicet.gov.ar:11336/230101
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repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Genomic analysis of Sinorhizobium meliloti LPU63, an acid-tolerant and symbiotically efficient alfalfa-nodulating rhizobiaCafiero, Juan HilarioSalvetti Casasco, MaríaLozano, Mauricio JavierLopez Garcia, Silvina LauraVacca, CarolinaDraghi, Walter OmarLagares, Antoniodel Papa, Maria FlorenciaRhizobiaSinorhizobium melilotiaccessory genomedenitrification pathwayPGPR-related genesSymbiosishttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1https://purl.org/becyt/ford/4.1https://purl.org/becyt/ford/4The growth and persistence of alfalfa (Medicago sativa), a perennial legume capable of producing high yields of high-quality forage, is reduced in moderately acidic soils. The low performance of alfalfa at low pH is due to numerous factors that affect the host plant, their rhizobia, and the symbiotic interaction.Sinorhizobium meliloti LPU63 was isolated from acid topsoil (in Argentina) and showed to be a highly competitive and efficient N2-fixing rhizobium under both, neutral and moderately acidic soil conditions. In this study, we obtained a draft of the LPU63 genome sequence using Illumina HiSeq4000. The whole genome phylogenetic analysis confirmed the taxonomic position of LPU63 as a S. meliloti strain and the multilocus sequence analysis confirmed that LPU63 is not related to the strains used in Argentina in bioformulations. The genomic analysis showed that beyond the canonical chromosome, pSymA, and pSymB, LPU63 strain has an accessory plasmid that codes for a repABC origin of replication and a conjugative T4SS, suggesting that this plasmid could be self-transmissible. In addition, the complete denitrification pathway (i.e., the gene clusters nap, nir, nor, and nos), including napC and nosZ, which could be used as an alternative respiration route under hypoxic conditions with moderate N2O emissions was found. Also, genes associated with plant growth-promoting activities (PGPR) and the degradation of phenylacetic acid (PAA) were identified. LPU63 is a highly melanogenic strain, a property that could enhance its survival under soil conditions, and the genome data showed a particular arrangement of the genes involved in melanin production. The information regarding LPU63 activities compatible with plant-growth promotion phenotypes, together with other characteristics mentioned here (melanin production, potential moderate N2O emissions), constitute the basis of future experiments toward the rational design of a novel bioinoculant for the environmentally sustainable production of alfalfa.Fil: Cafiero, Juan Hilario. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Salvetti Casasco, María. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Lozano, Mauricio Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Lopez Garcia, Silvina Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Vacca, Carolina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Draghi, Walter Omar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Lagares, Antonio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: del Papa, Maria Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFrontiers Media2023-07info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/230101Cafiero, Juan Hilario; Salvetti Casasco, María; Lozano, Mauricio Javier; Lopez Garcia, Silvina Laura; Vacca, Carolina; et al.; Genomic analysis of Sinorhizobium meliloti LPU63, an acid-tolerant and symbiotically efficient alfalfa-nodulating rhizobia; Frontiers Media; Frontiers in Agronomy; 5; 7-2023; 1-142673-32182673-3218CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.frontiersin.org/articles/10.3389/fagro.2023.1175524/abstractinfo:eu-repo/semantics/altIdentifier/doi/10.3389/fagro.2023.1175524info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-15T15:26:41Zoai:ri.conicet.gov.ar:11336/230101instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-10-15 15:26:41.66CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Genomic analysis of Sinorhizobium meliloti LPU63, an acid-tolerant and symbiotically efficient alfalfa-nodulating rhizobia
title Genomic analysis of Sinorhizobium meliloti LPU63, an acid-tolerant and symbiotically efficient alfalfa-nodulating rhizobia
spellingShingle Genomic analysis of Sinorhizobium meliloti LPU63, an acid-tolerant and symbiotically efficient alfalfa-nodulating rhizobia
Cafiero, Juan Hilario
Rhizobia
Sinorhizobium meliloti
accessory genome
denitrification pathway
PGPR-related genes
Symbiosis
title_short Genomic analysis of Sinorhizobium meliloti LPU63, an acid-tolerant and symbiotically efficient alfalfa-nodulating rhizobia
title_full Genomic analysis of Sinorhizobium meliloti LPU63, an acid-tolerant and symbiotically efficient alfalfa-nodulating rhizobia
title_fullStr Genomic analysis of Sinorhizobium meliloti LPU63, an acid-tolerant and symbiotically efficient alfalfa-nodulating rhizobia
title_full_unstemmed Genomic analysis of Sinorhizobium meliloti LPU63, an acid-tolerant and symbiotically efficient alfalfa-nodulating rhizobia
title_sort Genomic analysis of Sinorhizobium meliloti LPU63, an acid-tolerant and symbiotically efficient alfalfa-nodulating rhizobia
dc.creator.none.fl_str_mv Cafiero, Juan Hilario
Salvetti Casasco, María
Lozano, Mauricio Javier
Lopez Garcia, Silvina Laura
Vacca, Carolina
Draghi, Walter Omar
Lagares, Antonio
del Papa, Maria Florencia
author Cafiero, Juan Hilario
author_facet Cafiero, Juan Hilario
Salvetti Casasco, María
Lozano, Mauricio Javier
Lopez Garcia, Silvina Laura
Vacca, Carolina
Draghi, Walter Omar
Lagares, Antonio
del Papa, Maria Florencia
author_role author
author2 Salvetti Casasco, María
Lozano, Mauricio Javier
Lopez Garcia, Silvina Laura
Vacca, Carolina
Draghi, Walter Omar
Lagares, Antonio
del Papa, Maria Florencia
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Rhizobia
Sinorhizobium meliloti
accessory genome
denitrification pathway
PGPR-related genes
Symbiosis
topic Rhizobia
Sinorhizobium meliloti
accessory genome
denitrification pathway
PGPR-related genes
Symbiosis
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
https://purl.org/becyt/ford/4.1
https://purl.org/becyt/ford/4
dc.description.none.fl_txt_mv The growth and persistence of alfalfa (Medicago sativa), a perennial legume capable of producing high yields of high-quality forage, is reduced in moderately acidic soils. The low performance of alfalfa at low pH is due to numerous factors that affect the host plant, their rhizobia, and the symbiotic interaction.Sinorhizobium meliloti LPU63 was isolated from acid topsoil (in Argentina) and showed to be a highly competitive and efficient N2-fixing rhizobium under both, neutral and moderately acidic soil conditions. In this study, we obtained a draft of the LPU63 genome sequence using Illumina HiSeq4000. The whole genome phylogenetic analysis confirmed the taxonomic position of LPU63 as a S. meliloti strain and the multilocus sequence analysis confirmed that LPU63 is not related to the strains used in Argentina in bioformulations. The genomic analysis showed that beyond the canonical chromosome, pSymA, and pSymB, LPU63 strain has an accessory plasmid that codes for a repABC origin of replication and a conjugative T4SS, suggesting that this plasmid could be self-transmissible. In addition, the complete denitrification pathway (i.e., the gene clusters nap, nir, nor, and nos), including napC and nosZ, which could be used as an alternative respiration route under hypoxic conditions with moderate N2O emissions was found. Also, genes associated with plant growth-promoting activities (PGPR) and the degradation of phenylacetic acid (PAA) were identified. LPU63 is a highly melanogenic strain, a property that could enhance its survival under soil conditions, and the genome data showed a particular arrangement of the genes involved in melanin production. The information regarding LPU63 activities compatible with plant-growth promotion phenotypes, together with other characteristics mentioned here (melanin production, potential moderate N2O emissions), constitute the basis of future experiments toward the rational design of a novel bioinoculant for the environmentally sustainable production of alfalfa.
Fil: Cafiero, Juan Hilario. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina
Fil: Salvetti Casasco, María. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina
Fil: Lozano, Mauricio Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina
Fil: Lopez Garcia, Silvina Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina
Fil: Vacca, Carolina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina
Fil: Draghi, Walter Omar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina
Fil: Lagares, Antonio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina
Fil: del Papa, Maria Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina
description The growth and persistence of alfalfa (Medicago sativa), a perennial legume capable of producing high yields of high-quality forage, is reduced in moderately acidic soils. The low performance of alfalfa at low pH is due to numerous factors that affect the host plant, their rhizobia, and the symbiotic interaction.Sinorhizobium meliloti LPU63 was isolated from acid topsoil (in Argentina) and showed to be a highly competitive and efficient N2-fixing rhizobium under both, neutral and moderately acidic soil conditions. In this study, we obtained a draft of the LPU63 genome sequence using Illumina HiSeq4000. The whole genome phylogenetic analysis confirmed the taxonomic position of LPU63 as a S. meliloti strain and the multilocus sequence analysis confirmed that LPU63 is not related to the strains used in Argentina in bioformulations. The genomic analysis showed that beyond the canonical chromosome, pSymA, and pSymB, LPU63 strain has an accessory plasmid that codes for a repABC origin of replication and a conjugative T4SS, suggesting that this plasmid could be self-transmissible. In addition, the complete denitrification pathway (i.e., the gene clusters nap, nir, nor, and nos), including napC and nosZ, which could be used as an alternative respiration route under hypoxic conditions with moderate N2O emissions was found. Also, genes associated with plant growth-promoting activities (PGPR) and the degradation of phenylacetic acid (PAA) were identified. LPU63 is a highly melanogenic strain, a property that could enhance its survival under soil conditions, and the genome data showed a particular arrangement of the genes involved in melanin production. The information regarding LPU63 activities compatible with plant-growth promotion phenotypes, together with other characteristics mentioned here (melanin production, potential moderate N2O emissions), constitute the basis of future experiments toward the rational design of a novel bioinoculant for the environmentally sustainable production of alfalfa.
publishDate 2023
dc.date.none.fl_str_mv 2023-07
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
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info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/230101
Cafiero, Juan Hilario; Salvetti Casasco, María; Lozano, Mauricio Javier; Lopez Garcia, Silvina Laura; Vacca, Carolina; et al.; Genomic analysis of Sinorhizobium meliloti LPU63, an acid-tolerant and symbiotically efficient alfalfa-nodulating rhizobia; Frontiers Media; Frontiers in Agronomy; 5; 7-2023; 1-14
2673-3218
2673-3218
CONICET Digital
CONICET
url http://hdl.handle.net/11336/230101
identifier_str_mv Cafiero, Juan Hilario; Salvetti Casasco, María; Lozano, Mauricio Javier; Lopez Garcia, Silvina Laura; Vacca, Carolina; et al.; Genomic analysis of Sinorhizobium meliloti LPU63, an acid-tolerant and symbiotically efficient alfalfa-nodulating rhizobia; Frontiers Media; Frontiers in Agronomy; 5; 7-2023; 1-14
2673-3218
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://www.frontiersin.org/articles/10.3389/fagro.2023.1175524/abstract
info:eu-repo/semantics/altIdentifier/doi/10.3389/fagro.2023.1175524
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
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rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Frontiers Media
publisher.none.fl_str_mv Frontiers Media
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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