Complementing culture-dependent and -independent approaches is essential when assessing bacterial community potential functions in chronically polycyclic aromatic hydrocarbon-conta...

Autores: Festa, Sabrina; Nieto, Esteban; Raposeiras Aldorino, Penélope; Cuadros Orellana, Sara; Irazoqui, Jose Matias; Quevedo, Claudio; Coppotelli, Bibiana Marina; Morelli, Irma Susana
Año de publicación: 2025
Idioma: inglés
Tipo de recurso: artículo
Estado: versión publicada
Descripción: Bioremediation is an eco-friendly alternative for soil restoration; however, its outcomes are still variable. Different bioremediation strategies were used in a chronically polycyclic aromatic hydrocarbon (PAH)-contaminated soil, and no degradation was achieved. This work attempts to study whether the soil bacterial community has the genetic potential for aromatic compound degradation (ACD). While 16S rRNA metabarcoding of that soil showed a predominance of Proteobacteria, shotgun metagenomics indicated that 99.5% of the sequences were taxonomically assigned to Streptomycetales, and almost all genes for ACD were assigned to the latter. As comprehension of the composition and metabolic potential of a soil community can be enhanced by exploring enrichment cultures of that soil, a culture approach followed by a shotgun metagenomic analysis was performed. These enrichment cultures were obtained by sequential transfers with pyrene conducted every 7 days (r-EFP) and every 28 days (k-MSP2). Both r-EFP and k-MSP2 demonstrated the ability to degrade pyrene and the presence of genes related to ACD. While in r-EFP Pseudomonas and Olivibacter were the predominant genera, Mycobacterium, Chitoniphaga, Bacillus, and Pseudoxanthomonas were predominant in k-MSP2. This study demonstrated the soil bacterial community’s potential to degrade PAHs of three and four rings; therefore, exploration of bioremediation strategies aimed at activating this potential would be worthwhile. It was confirmed that shotgun metagenomics may not fully reveal potential bacterial functions when characterizing impacted soil microbiomes. Additionally, culture-based methods complemented and increased the knowledge obtained from culture-independent approaches, demonstrating their utility for bioprospecting PAH degraders and designing microbiome engineering strategies.
EEA Rafaela
Fil: Festa, Sabrina. Universidad Nacional de La Plata (UNLP). Centro de Investigación y Desarrollo en Fermentaciones Industriales; Argentina
Fil: Festa, Sabrina. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Centro de Investigación y Desarrollo en Fermentaciones Industriales; Argentina
Fil: Nieto, Esteban. Universidad Nacional de La Plata (UNLP). Centro de Investigación y Desarrollo en Fermentaciones Industriales; Argentina
Fil: Nieto, Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Centro de Investigación y Desarrollo en Fermentaciones Industriales; Argentina
Fil: Raposeiras Aldorino, Penélope. Universidad Nacional de La Plata (UNLP). Centro de Investigación y Desarrollo en Fermentaciones Industriales; Argentina
Fil: Raposeiras Aldorino, Penélope. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Centro de Investigación y Desarrollo en Fermentaciones Industriales; Argentina
Fil: Raposeiras Aldorino, Penélope. Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC); Argentina
Fil: Cuadros Orellana, Sara. Universidad Católica del Maule. Facultad de Ciencias Agrarias y Forestales. Centro de Biotecnología de los Recursos Naturales; Chile
Fil: Irazoqui, Jose Matias. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela. Instituto de Investigación de la Cadena Láctea (IDICAL); Argentina
Fil: Irazoqui, Jose Matias. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Instituto de Investigación de la Cadena Láctea (IDICAL); Argentina
Fil: Quevedo, Claudio. Universidad Católica del Maule. Facultad de Ciencias Agrarias y Forestales. Centro de Biotecnología de los Recursos Naturales; Chile
Fil: Coppotelli, Bibiana Marina. Universidad Nacional de La Plata (UNLP). Centro de Investigación y Desarrollo en Fermentaciones Industriales; Argentina
Fil: Coppotelli, Bibiana Marina. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Centro de Investigación y Desarrollo en Fermentaciones Industriales; Argentina
Fil: Morelli, Irma Susana. Universidad Nacional de La Plata (UNLP). Centro de Investigación y Desarrollo en Fermentaciones Industriales; Argentina
Fil: Morelli, Irma Susana. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Centro de Investigación y Desarrollo en Fermentaciones Industriales; Argentina
Fil: Morelli, Irma Susana. Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC); Argentina
Fuente: Pedosphere 35 (6) : 931-944. (December 2025)
Materia: Biodecontaminación
Bacteria
Suelo Contaminado
Hidrocarburo Aromático Policíclico
Metagenómica
Técnicas de Cultivo
Bioremediation
Polluted Soils
Polycyclic Aromatic Hydrocarbons
Metagenomics
Culture Techniques
Aromatic Compound Degradation (ACD)
Nivel de accesibilidad: acceso restringido
Condiciones de uso: http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
Institución: Instituto Nacional de Tecnología Agropecuaria
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spelling	Complementing culture-dependent and -independent approaches is essential when assessing bacterial community potential functions in chronically polycyclic aromatic hydrocarbon-contaminated soilsFesta, SabrinaNieto, EstebanRaposeiras Aldorino, PenélopeCuadros Orellana, SaraIrazoqui, Jose MatiasQuevedo, ClaudioCoppotelli, Bibiana MarinaMorelli, Irma SusanaBiodecontaminaciónBacteriaSuelo ContaminadoHidrocarburo Aromático PolicíclicoMetagenómicaTécnicas de CultivoBioremediationPolluted SoilsPolycyclic Aromatic HydrocarbonsMetagenomicsCulture TechniquesAromatic Compound Degradation (ACD)Bioremediation is an eco-friendly alternative for soil restoration; however, its outcomes are still variable. Different bioremediation strategies were used in a chronically polycyclic aromatic hydrocarbon (PAH)-contaminated soil, and no degradation was achieved. This work attempts to study whether the soil bacterial community has the genetic potential for aromatic compound degradation (ACD). While 16S rRNA metabarcoding of that soil showed a predominance of Proteobacteria, shotgun metagenomics indicated that 99.5% of the sequences were taxonomically assigned to Streptomycetales, and almost all genes for ACD were assigned to the latter. As comprehension of the composition and metabolic potential of a soil community can be enhanced by exploring enrichment cultures of that soil, a culture approach followed by a shotgun metagenomic analysis was performed. These enrichment cultures were obtained by sequential transfers with pyrene conducted every 7 days (r-EFP) and every 28 days (k-MSP2). Both r-EFP and k-MSP2 demonstrated the ability to degrade pyrene and the presence of genes related to ACD. While in r-EFP Pseudomonas and Olivibacter were the predominant genera, Mycobacterium, Chitoniphaga, Bacillus, and Pseudoxanthomonas were predominant in k-MSP2. This study demonstrated the soil bacterial community’s potential to degrade PAHs of three and four rings; therefore, exploration of bioremediation strategies aimed at activating this potential would be worthwhile. It was confirmed that shotgun metagenomics may not fully reveal potential bacterial functions when characterizing impacted soil microbiomes. Additionally, culture-based methods complemented and increased the knowledge obtained from culture-independent approaches, demonstrating their utility for bioprospecting PAH degraders and designing microbiome engineering strategies.EEA RafaelaFil: Festa, Sabrina. Universidad Nacional de La Plata (UNLP). Centro de Investigación y Desarrollo en Fermentaciones Industriales; ArgentinaFil: Festa, Sabrina. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Centro de Investigación y Desarrollo en Fermentaciones Industriales; ArgentinaFil: Nieto, Esteban. Universidad Nacional de La Plata (UNLP). Centro de Investigación y Desarrollo en Fermentaciones Industriales; ArgentinaFil: Nieto, Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Centro de Investigación y Desarrollo en Fermentaciones Industriales; ArgentinaFil: Raposeiras Aldorino, Penélope. Universidad Nacional de La Plata (UNLP). Centro de Investigación y Desarrollo en Fermentaciones Industriales; ArgentinaFil: Raposeiras Aldorino, Penélope. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Centro de Investigación y Desarrollo en Fermentaciones Industriales; ArgentinaFil: Raposeiras Aldorino, Penélope. Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC); ArgentinaFil: Cuadros Orellana, Sara. Universidad Católica del Maule. Facultad de Ciencias Agrarias y Forestales. Centro de Biotecnología de los Recursos Naturales; ChileFil: Irazoqui, Jose Matias. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela. Instituto de Investigación de la Cadena Láctea (IDICAL); ArgentinaFil: Irazoqui, Jose Matias. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Instituto de Investigación de la Cadena Láctea (IDICAL); ArgentinaFil: Quevedo, Claudio. Universidad Católica del Maule. Facultad de Ciencias Agrarias y Forestales. Centro de Biotecnología de los Recursos Naturales; ChileFil: Coppotelli, Bibiana Marina. Universidad Nacional de La Plata (UNLP). Centro de Investigación y Desarrollo en Fermentaciones Industriales; ArgentinaFil: Coppotelli, Bibiana Marina. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Centro de Investigación y Desarrollo en Fermentaciones Industriales; ArgentinaFil: Morelli, Irma Susana. Universidad Nacional de La Plata (UNLP). Centro de Investigación y Desarrollo en Fermentaciones Industriales; ArgentinaFil: Morelli, Irma Susana. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Centro de Investigación y Desarrollo en Fermentaciones Industriales; ArgentinaFil: Morelli, Irma Susana. Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC); ArgentinaElsevier2026-03-10T14:02:44Z2026-03-10T14:02:44Z2025-12info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/25415https://www.sciencedirect.com/science/article/abs/pii/S1002016024000791?via%3Dihub1002-0160https://doi.org/10.1016/j.pedsph.2024.08.005Pedosphere 35 (6) : 931-944. (December 2025)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/restrictedAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2026-03-26T11:25:30Zoai:localhost:20.500.12123/25415instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2026-03-26 11:25:30.407INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv	Complementing culture-dependent and -independent approaches is essential when assessing bacterial community potential functions in chronically polycyclic aromatic hydrocarbon-contaminated soils
title	Complementing culture-dependent and -independent approaches is essential when assessing bacterial community potential functions in chronically polycyclic aromatic hydrocarbon-contaminated soils
spellingShingle	Complementing culture-dependent and -independent approaches is essential when assessing bacterial community potential functions in chronically polycyclic aromatic hydrocarbon-contaminated soils Festa, Sabrina Biodecontaminación Bacteria Suelo Contaminado Hidrocarburo Aromático Policíclico Metagenómica Técnicas de Cultivo Bioremediation Polluted Soils Polycyclic Aromatic Hydrocarbons Metagenomics Culture Techniques Aromatic Compound Degradation (ACD)
title_short	Complementing culture-dependent and -independent approaches is essential when assessing bacterial community potential functions in chronically polycyclic aromatic hydrocarbon-contaminated soils
title_full	Complementing culture-dependent and -independent approaches is essential when assessing bacterial community potential functions in chronically polycyclic aromatic hydrocarbon-contaminated soils
title_fullStr	Complementing culture-dependent and -independent approaches is essential when assessing bacterial community potential functions in chronically polycyclic aromatic hydrocarbon-contaminated soils
title_full_unstemmed	Complementing culture-dependent and -independent approaches is essential when assessing bacterial community potential functions in chronically polycyclic aromatic hydrocarbon-contaminated soils
title_sort	Complementing culture-dependent and -independent approaches is essential when assessing bacterial community potential functions in chronically polycyclic aromatic hydrocarbon-contaminated soils
dc.creator.none.fl_str_mv	Festa, Sabrina Nieto, Esteban Raposeiras Aldorino, Penélope Cuadros Orellana, Sara Irazoqui, Jose Matias Quevedo, Claudio Coppotelli, Bibiana Marina Morelli, Irma Susana
author	Festa, Sabrina
author_facet	Festa, Sabrina Nieto, Esteban Raposeiras Aldorino, Penélope Cuadros Orellana, Sara Irazoqui, Jose Matias Quevedo, Claudio Coppotelli, Bibiana Marina Morelli, Irma Susana
author_role	author
author2	Nieto, Esteban Raposeiras Aldorino, Penélope Cuadros Orellana, Sara Irazoqui, Jose Matias Quevedo, Claudio Coppotelli, Bibiana Marina Morelli, Irma Susana
author2_role	author author author author author author author
dc.subject.none.fl_str_mv	Biodecontaminación Bacteria Suelo Contaminado Hidrocarburo Aromático Policíclico Metagenómica Técnicas de Cultivo Bioremediation Polluted Soils Polycyclic Aromatic Hydrocarbons Metagenomics Culture Techniques Aromatic Compound Degradation (ACD)
topic	Biodecontaminación Bacteria Suelo Contaminado Hidrocarburo Aromático Policíclico Metagenómica Técnicas de Cultivo Bioremediation Polluted Soils Polycyclic Aromatic Hydrocarbons Metagenomics Culture Techniques Aromatic Compound Degradation (ACD)
dc.description.none.fl_txt_mv	Bioremediation is an eco-friendly alternative for soil restoration; however, its outcomes are still variable. Different bioremediation strategies were used in a chronically polycyclic aromatic hydrocarbon (PAH)-contaminated soil, and no degradation was achieved. This work attempts to study whether the soil bacterial community has the genetic potential for aromatic compound degradation (ACD). While 16S rRNA metabarcoding of that soil showed a predominance of Proteobacteria, shotgun metagenomics indicated that 99.5% of the sequences were taxonomically assigned to Streptomycetales, and almost all genes for ACD were assigned to the latter. As comprehension of the composition and metabolic potential of a soil community can be enhanced by exploring enrichment cultures of that soil, a culture approach followed by a shotgun metagenomic analysis was performed. These enrichment cultures were obtained by sequential transfers with pyrene conducted every 7 days (r-EFP) and every 28 days (k-MSP2). Both r-EFP and k-MSP2 demonstrated the ability to degrade pyrene and the presence of genes related to ACD. While in r-EFP Pseudomonas and Olivibacter were the predominant genera, Mycobacterium, Chitoniphaga, Bacillus, and Pseudoxanthomonas were predominant in k-MSP2. This study demonstrated the soil bacterial community’s potential to degrade PAHs of three and four rings; therefore, exploration of bioremediation strategies aimed at activating this potential would be worthwhile. It was confirmed that shotgun metagenomics may not fully reveal potential bacterial functions when characterizing impacted soil microbiomes. Additionally, culture-based methods complemented and increased the knowledge obtained from culture-independent approaches, demonstrating their utility for bioprospecting PAH degraders and designing microbiome engineering strategies. EEA Rafaela Fil: Festa, Sabrina. Universidad Nacional de La Plata (UNLP). Centro de Investigación y Desarrollo en Fermentaciones Industriales; Argentina Fil: Festa, Sabrina. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Centro de Investigación y Desarrollo en Fermentaciones Industriales; Argentina Fil: Nieto, Esteban. Universidad Nacional de La Plata (UNLP). Centro de Investigación y Desarrollo en Fermentaciones Industriales; Argentina Fil: Nieto, Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Centro de Investigación y Desarrollo en Fermentaciones Industriales; Argentina Fil: Raposeiras Aldorino, Penélope. Universidad Nacional de La Plata (UNLP). Centro de Investigación y Desarrollo en Fermentaciones Industriales; Argentina Fil: Raposeiras Aldorino, Penélope. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Centro de Investigación y Desarrollo en Fermentaciones Industriales; Argentina Fil: Raposeiras Aldorino, Penélope. Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC); Argentina Fil: Cuadros Orellana, Sara. Universidad Católica del Maule. Facultad de Ciencias Agrarias y Forestales. Centro de Biotecnología de los Recursos Naturales; Chile Fil: Irazoqui, Jose Matias. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela. Instituto de Investigación de la Cadena Láctea (IDICAL); Argentina Fil: Irazoqui, Jose Matias. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Instituto de Investigación de la Cadena Láctea (IDICAL); Argentina Fil: Quevedo, Claudio. Universidad Católica del Maule. Facultad de Ciencias Agrarias y Forestales. Centro de Biotecnología de los Recursos Naturales; Chile Fil: Coppotelli, Bibiana Marina. Universidad Nacional de La Plata (UNLP). Centro de Investigación y Desarrollo en Fermentaciones Industriales; Argentina Fil: Coppotelli, Bibiana Marina. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Centro de Investigación y Desarrollo en Fermentaciones Industriales; Argentina Fil: Morelli, Irma Susana. Universidad Nacional de La Plata (UNLP). Centro de Investigación y Desarrollo en Fermentaciones Industriales; Argentina Fil: Morelli, Irma Susana. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Centro de Investigación y Desarrollo en Fermentaciones Industriales; Argentina Fil: Morelli, Irma Susana. Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC); Argentina
description	Bioremediation is an eco-friendly alternative for soil restoration; however, its outcomes are still variable. Different bioremediation strategies were used in a chronically polycyclic aromatic hydrocarbon (PAH)-contaminated soil, and no degradation was achieved. This work attempts to study whether the soil bacterial community has the genetic potential for aromatic compound degradation (ACD). While 16S rRNA metabarcoding of that soil showed a predominance of Proteobacteria, shotgun metagenomics indicated that 99.5% of the sequences were taxonomically assigned to Streptomycetales, and almost all genes for ACD were assigned to the latter. As comprehension of the composition and metabolic potential of a soil community can be enhanced by exploring enrichment cultures of that soil, a culture approach followed by a shotgun metagenomic analysis was performed. These enrichment cultures were obtained by sequential transfers with pyrene conducted every 7 days (r-EFP) and every 28 days (k-MSP2). Both r-EFP and k-MSP2 demonstrated the ability to degrade pyrene and the presence of genes related to ACD. While in r-EFP Pseudomonas and Olivibacter were the predominant genera, Mycobacterium, Chitoniphaga, Bacillus, and Pseudoxanthomonas were predominant in k-MSP2. This study demonstrated the soil bacterial community’s potential to degrade PAHs of three and four rings; therefore, exploration of bioremediation strategies aimed at activating this potential would be worthwhile. It was confirmed that shotgun metagenomics may not fully reveal potential bacterial functions when characterizing impacted soil microbiomes. Additionally, culture-based methods complemented and increased the knowledge obtained from culture-independent approaches, demonstrating their utility for bioprospecting PAH degraders and designing microbiome engineering strategies.
publishDate	2025
dc.date.none.fl_str_mv	2025-12 2026-03-10T14:02:44Z 2026-03-10T14:02:44Z
dc.type.none.fl_str_mv	info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion 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://hdl.handle.net/20.500.12123/25415 https://www.sciencedirect.com/science/article/abs/pii/S1002016024000791?via%3Dihub 1002-0160 https://doi.org/10.1016/j.pedsph.2024.08.005
url	http://hdl.handle.net/20.500.12123/25415 https://www.sciencedirect.com/science/article/abs/pii/S1002016024000791?via%3Dihub https://doi.org/10.1016/j.pedsph.2024.08.005
identifier_str_mv	1002-0160
dc.language.none.fl_str_mv	eng
language	eng
dc.rights.none.fl_str_mv	info:eu-repo/semantics/restrictedAccess http://creativecommons.org/licenses/by-nc-sa/4.0/ Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
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rights_invalid_str_mv	http://creativecommons.org/licenses/by-nc-sa/4.0/ Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv	application/pdf
dc.publisher.none.fl_str_mv	Elsevier
publisher.none.fl_str_mv	Elsevier
dc.source.none.fl_str_mv	Pedosphere 35 (6) : 931-944. (December 2025) reponame:INTA Digital (INTA) instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str	INTA Digital (INTA)
collection	INTA Digital (INTA)
instname_str	Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv	INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv	tripaldi.nicolas@inta.gob.ar
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Complementing culture-dependent and -independent approaches is essential when assessing bacterial community potential functions in chronically polycyclic aromatic hydrocarbon-conta...

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