Design and evaluation of synthetic bacterial consortia for optimized phenanthrene degradation through the integration of genomics and shotgun proteomics

Autores
Macchi, Marianela; Festa, Sabrina; Nieto, Esteban Emanuel; Irazoqui, José M.; Vega Vela, Nelson E.; Junca, Howard; Valacco, María P.; Amadio, Ariel F.; Morelli, Irma Susana; Coppotelli, Bibiana Marina
Año de publicación
2021
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Two synthetic bacterial consortia (SC) composed of bacterial strains Sphingobium sp. (AM), Klebsiella aerogenes (B), Pseudomonas sp. (Bc-h and T), Burkholderia sp. (Bk) and Inquilinus limosus (Inq) isolated from a natural phenanthrene (PHN)-degrading consortium (CON) were developed and evaluated as an alternative approach to PHN biodegradation in bioremediation processes. A metabolic network showing the potential role of strains was reconstructed by in silico study of the six genomes and classification of dioxygenase enzymes using RHObase and AromaDeg databases. Network analysis suggested that AM and Bk were responsible for PHN initial attack, while Inq, B, T and Bc-h would degrade PHN metabolites. The predicted roles were further confirmed by physiological, RT-qPCR and metaproteomic assays. SC-1 with AM as the sole PHN degrader was the most efficient. The ecological roles inferred in this study can be applied to optimize the design of bacterial consortia and tackle the biodegradation of complex environmental pollutants.
Centro de Investigación y Desarrollo en Fermentaciones Industriales
Comisión de Investigaciones Científicas de la provincia de Buenos Aires
Materia
Química
Synthetic bacterial consortia (SC)
Whole genome sequencing
Metabolic network
RT-qPCR
Shotgun proteomics
Polycyclic aromatic hydrocarbon (PAH)
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-nd/4.0/
Repositorio
SEDICI (UNLP)
Institución
Universidad Nacional de La Plata
OAI Identificador
oai:sedici.unlp.edu.ar:10915/118814
Acceder
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network_acronym_str SEDICI
repository_id_str 1329
network_name_str SEDICI (UNLP)
spelling Design and evaluation of synthetic bacterial consortia for optimized phenanthrene degradation through the integration of genomics and shotgun proteomicsMacchi, MarianelaFesta, SabrinaNieto, Esteban EmanuelIrazoqui, José M.Vega Vela, Nelson E.Junca, HowardValacco, María P.Amadio, Ariel F.Morelli, Irma SusanaCoppotelli, Bibiana MarinaQuímicaSynthetic bacterial consortia (SC)Whole genome sequencingMetabolic networkRT-qPCRShotgun proteomicsPolycyclic aromatic hydrocarbon (PAH)Two synthetic bacterial consortia (SC) composed of bacterial strains Sphingobium sp. (AM), Klebsiella aerogenes (B), Pseudomonas sp. (Bc-h and T), Burkholderia sp. (Bk) and Inquilinus limosus (Inq) isolated from a natural phenanthrene (PHN)-degrading consortium (CON) were developed and evaluated as an alternative approach to PHN biodegradation in bioremediation processes. A metabolic network showing the potential role of strains was reconstructed by in silico study of the six genomes and classification of dioxygenase enzymes using RHObase and AromaDeg databases. Network analysis suggested that AM and Bk were responsible for PHN initial attack, while Inq, B, T and Bc-h would degrade PHN metabolites. The predicted roles were further confirmed by physiological, RT-qPCR and metaproteomic assays. SC-1 with AM as the sole PHN degrader was the most efficient. The ecological roles inferred in this study can be applied to optimize the design of bacterial consortia and tackle the biodegradation of complex environmental pollutants.Centro de Investigación y Desarrollo en Fermentaciones IndustrialesComisión de Investigaciones Científicas de la provincia de Buenos Aires2021info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionArticulohttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://sedici.unlp.edu.ar/handle/10915/118814enginfo:eu-repo/semantics/altIdentifier/issn/2215-017Xinfo:eu-repo/semantics/altIdentifier/doi/10.1016/j.btre.2021.e00588info:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-nd/4.0/Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)reponame:SEDICI (UNLP)instname:Universidad Nacional de La Platainstacron:UNLP2025-09-29T11:27:59Zoai:sedici.unlp.edu.ar:10915/118814Institucionalhttp://sedici.unlp.edu.ar/Universidad públicaNo correspondehttp://sedici.unlp.edu.ar/oai/snrdalira@sedici.unlp.edu.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:13292025-09-29 11:27:59.89SEDICI (UNLP) - Universidad Nacional de La Platafalse
dc.title.none.fl_str_mv Design and evaluation of synthetic bacterial consortia for optimized phenanthrene degradation through the integration of genomics and shotgun proteomics
title Design and evaluation of synthetic bacterial consortia for optimized phenanthrene degradation through the integration of genomics and shotgun proteomics
spellingShingle Design and evaluation of synthetic bacterial consortia for optimized phenanthrene degradation through the integration of genomics and shotgun proteomics
Macchi, Marianela
Química
Synthetic bacterial consortia (SC)
Whole genome sequencing
Metabolic network
RT-qPCR
Shotgun proteomics
Polycyclic aromatic hydrocarbon (PAH)
title_short Design and evaluation of synthetic bacterial consortia for optimized phenanthrene degradation through the integration of genomics and shotgun proteomics
title_full Design and evaluation of synthetic bacterial consortia for optimized phenanthrene degradation through the integration of genomics and shotgun proteomics
title_fullStr Design and evaluation of synthetic bacterial consortia for optimized phenanthrene degradation through the integration of genomics and shotgun proteomics
title_full_unstemmed Design and evaluation of synthetic bacterial consortia for optimized phenanthrene degradation through the integration of genomics and shotgun proteomics
title_sort Design and evaluation of synthetic bacterial consortia for optimized phenanthrene degradation through the integration of genomics and shotgun proteomics
dc.creator.none.fl_str_mv Macchi, Marianela
Festa, Sabrina
Nieto, Esteban Emanuel
Irazoqui, José M.
Vega Vela, Nelson E.
Junca, Howard
Valacco, María P.
Amadio, Ariel F.
Morelli, Irma Susana
Coppotelli, Bibiana Marina
author Macchi, Marianela
author_facet Macchi, Marianela
Festa, Sabrina
Nieto, Esteban Emanuel
Irazoqui, José M.
Vega Vela, Nelson E.
Junca, Howard
Valacco, María P.
Amadio, Ariel F.
Morelli, Irma Susana
Coppotelli, Bibiana Marina
author_role author
author2 Festa, Sabrina
Nieto, Esteban Emanuel
Irazoqui, José M.
Vega Vela, Nelson E.
Junca, Howard
Valacco, María P.
Amadio, Ariel F.
Morelli, Irma Susana
Coppotelli, Bibiana Marina
author2_role author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Química
Synthetic bacterial consortia (SC)
Whole genome sequencing
Metabolic network
RT-qPCR
Shotgun proteomics
Polycyclic aromatic hydrocarbon (PAH)
topic Química
Synthetic bacterial consortia (SC)
Whole genome sequencing
Metabolic network
RT-qPCR
Shotgun proteomics
Polycyclic aromatic hydrocarbon (PAH)
dc.description.none.fl_txt_mv Two synthetic bacterial consortia (SC) composed of bacterial strains Sphingobium sp. (AM), Klebsiella aerogenes (B), Pseudomonas sp. (Bc-h and T), Burkholderia sp. (Bk) and Inquilinus limosus (Inq) isolated from a natural phenanthrene (PHN)-degrading consortium (CON) were developed and evaluated as an alternative approach to PHN biodegradation in bioremediation processes. A metabolic network showing the potential role of strains was reconstructed by in silico study of the six genomes and classification of dioxygenase enzymes using RHObase and AromaDeg databases. Network analysis suggested that AM and Bk were responsible for PHN initial attack, while Inq, B, T and Bc-h would degrade PHN metabolites. The predicted roles were further confirmed by physiological, RT-qPCR and metaproteomic assays. SC-1 with AM as the sole PHN degrader was the most efficient. The ecological roles inferred in this study can be applied to optimize the design of bacterial consortia and tackle the biodegradation of complex environmental pollutants.
Centro de Investigación y Desarrollo en Fermentaciones Industriales
Comisión de Investigaciones Científicas de la provincia de Buenos Aires
description Two synthetic bacterial consortia (SC) composed of bacterial strains Sphingobium sp. (AM), Klebsiella aerogenes (B), Pseudomonas sp. (Bc-h and T), Burkholderia sp. (Bk) and Inquilinus limosus (Inq) isolated from a natural phenanthrene (PHN)-degrading consortium (CON) were developed and evaluated as an alternative approach to PHN biodegradation in bioremediation processes. A metabolic network showing the potential role of strains was reconstructed by in silico study of the six genomes and classification of dioxygenase enzymes using RHObase and AromaDeg databases. Network analysis suggested that AM and Bk were responsible for PHN initial attack, while Inq, B, T and Bc-h would degrade PHN metabolites. The predicted roles were further confirmed by physiological, RT-qPCR and metaproteomic assays. SC-1 with AM as the sole PHN degrader was the most efficient. The ecological roles inferred in this study can be applied to optimize the design of bacterial consortia and tackle the biodegradation of complex environmental pollutants.
publishDate 2021
dc.date.none.fl_str_mv 2021
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
Articulo
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://sedici.unlp.edu.ar/handle/10915/118814
url http://sedici.unlp.edu.ar/handle/10915/118814
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/issn/2215-017X
info:eu-repo/semantics/altIdentifier/doi/10.1016/j.btre.2021.e00588
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-nd/4.0/
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-nd/4.0/
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:SEDICI (UNLP)
instname:Universidad Nacional de La Plata
instacron:UNLP
reponame_str SEDICI (UNLP)
collection SEDICI (UNLP)
instname_str Universidad Nacional de La Plata
instacron_str UNLP
institution UNLP
repository.name.fl_str_mv SEDICI (UNLP) - Universidad Nacional de La Plata
repository.mail.fl_str_mv alira@sedici.unlp.edu.ar
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