Assigning ecological roles to the populations belonging to a phenanthrene-degrading bacterial consortium using omic approaches
The present study describes the behavior of a natural phenanthrene-degrading consortium (CON), a synthetic consortium (constructed with isolated strains from CON) and an isolated strain form CON (Sphingobium sp. AM) in phenanthrene cultures to understand the interactions among the microorganisms pre...
Guardado en:
| Autores principales: | , , , , , , , |
|---|---|
| Formato: | JOUR |
| Materias: | |
| Acceso en línea: | http://hdl.handle.net/20.500.12110/paper_19326203_v12_n9_p_Festa |
| Aporte de: |
| id |
todo:paper_19326203_v12_n9_p_Festa |
|---|---|
| record_format |
dspace |
| spelling |
todo:paper_19326203_v12_n9_p_Festa2023-10-03T16:34:52Z Assigning ecological roles to the populations belonging to a phenanthrene-degrading bacterial consortium using omic approaches Festa, S. Coppotelli, B.M. Madueño, L. Loviso, C.L. Macchi, M. Neme Tauil, R.M. Valacco, M.P. Morelli, I.S. bacterial DNA carbon catechol phenanthrene polycyclic aromatic hydrocarbon bacterial DNA phenanthrene derivative Article bacterial genome bacterium culture bacterium isolation Betaproteobacteria biodegradation Burkholderia carbon source controlled study ecology energy resource gene cluster genetic similarity metagenomics microbial consortium nonhuman omics open reading frame organismal interaction proteomics Sphingobium Sphingomonadales bacterial gene bacterium bioremediation classification DNA sequence gene order genetics metabolism metagenome microbiology phylogeny procedures Bacteria Biodegradation, Environmental DNA, Bacterial Gene Order Genes, Bacterial Metagenome Metagenomics Microbial Consortia Phenanthrenes Phylogeny Proteomics Sequence Analysis, DNA Soil Microbiology The present study describes the behavior of a natural phenanthrene-degrading consortium (CON), a synthetic consortium (constructed with isolated strains from CON) and an isolated strain form CON (Sphingobium sp. AM) in phenanthrene cultures to understand the interactions among the microorganisms present in the natural consortium during phenanthrene degradation as a sole carbon and energy source in liquid cultures. In the contaminant degradation assay, the defined consortium not only achieved a major phenanthrene degradation percentage (> 95%) but also showed a more efficient elimination of the intermediate metabolite. The opposite behavior occurred in the CON culture where the lowest phenanthrene degradation and the highest HNA accumulation were observed, which suggests the presence of positive and also negative interaction in CON. To consider the uncultured bacteria present in CON, a metagenomic library was constructed with total CON DNA. One of the resulting scaffolds (S1P3) was affiliated with the Betaproteobacteria class and resulted in a significant similarity with a genome fragment from Burkholderia sp. HB1 chromosome 1. A complete gene cluster, which is related to one of the lower pathways (meta-cleavage of catechol) involved in PAH degradation (ORF 31–43), mobile genetic elements and associated proteins, was found. These results suggest the presence of at least one other microorganism in CON besides Sphingobium sp. AM, which is capable of degrading PAH through the meta-cleavage pathway. Burkholderiales order was further found, along with Sphingomonadales order, by a metaproteomic approach, which indicated that both orders were metabolically active in CON. Our results show the presence of negative interactions between bacterial populations found in a natural consortium selected by enrichment techniques; moreover, the synthetic syntrophic processing chain with only one microorganism with the capability of degrading phenanthrene was more efficient in contaminant and intermediate metabolite degradation than a generalist strain (Sphingobium sp. AM). © 2017 Festa et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_19326203_v12_n9_p_Festa |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
bacterial DNA carbon catechol phenanthrene polycyclic aromatic hydrocarbon bacterial DNA phenanthrene derivative Article bacterial genome bacterium culture bacterium isolation Betaproteobacteria biodegradation Burkholderia carbon source controlled study ecology energy resource gene cluster genetic similarity metagenomics microbial consortium nonhuman omics open reading frame organismal interaction proteomics Sphingobium Sphingomonadales bacterial gene bacterium bioremediation classification DNA sequence gene order genetics metabolism metagenome microbiology phylogeny procedures Bacteria Biodegradation, Environmental DNA, Bacterial Gene Order Genes, Bacterial Metagenome Metagenomics Microbial Consortia Phenanthrenes Phylogeny Proteomics Sequence Analysis, DNA Soil Microbiology |
| spellingShingle |
bacterial DNA carbon catechol phenanthrene polycyclic aromatic hydrocarbon bacterial DNA phenanthrene derivative Article bacterial genome bacterium culture bacterium isolation Betaproteobacteria biodegradation Burkholderia carbon source controlled study ecology energy resource gene cluster genetic similarity metagenomics microbial consortium nonhuman omics open reading frame organismal interaction proteomics Sphingobium Sphingomonadales bacterial gene bacterium bioremediation classification DNA sequence gene order genetics metabolism metagenome microbiology phylogeny procedures Bacteria Biodegradation, Environmental DNA, Bacterial Gene Order Genes, Bacterial Metagenome Metagenomics Microbial Consortia Phenanthrenes Phylogeny Proteomics Sequence Analysis, DNA Soil Microbiology Festa, S. Coppotelli, B.M. Madueño, L. Loviso, C.L. Macchi, M. Neme Tauil, R.M. Valacco, M.P. Morelli, I.S. Assigning ecological roles to the populations belonging to a phenanthrene-degrading bacterial consortium using omic approaches |
| topic_facet |
bacterial DNA carbon catechol phenanthrene polycyclic aromatic hydrocarbon bacterial DNA phenanthrene derivative Article bacterial genome bacterium culture bacterium isolation Betaproteobacteria biodegradation Burkholderia carbon source controlled study ecology energy resource gene cluster genetic similarity metagenomics microbial consortium nonhuman omics open reading frame organismal interaction proteomics Sphingobium Sphingomonadales bacterial gene bacterium bioremediation classification DNA sequence gene order genetics metabolism metagenome microbiology phylogeny procedures Bacteria Biodegradation, Environmental DNA, Bacterial Gene Order Genes, Bacterial Metagenome Metagenomics Microbial Consortia Phenanthrenes Phylogeny Proteomics Sequence Analysis, DNA Soil Microbiology |
| description |
The present study describes the behavior of a natural phenanthrene-degrading consortium (CON), a synthetic consortium (constructed with isolated strains from CON) and an isolated strain form CON (Sphingobium sp. AM) in phenanthrene cultures to understand the interactions among the microorganisms present in the natural consortium during phenanthrene degradation as a sole carbon and energy source in liquid cultures. In the contaminant degradation assay, the defined consortium not only achieved a major phenanthrene degradation percentage (> 95%) but also showed a more efficient elimination of the intermediate metabolite. The opposite behavior occurred in the CON culture where the lowest phenanthrene degradation and the highest HNA accumulation were observed, which suggests the presence of positive and also negative interaction in CON. To consider the uncultured bacteria present in CON, a metagenomic library was constructed with total CON DNA. One of the resulting scaffolds (S1P3) was affiliated with the Betaproteobacteria class and resulted in a significant similarity with a genome fragment from Burkholderia sp. HB1 chromosome 1. A complete gene cluster, which is related to one of the lower pathways (meta-cleavage of catechol) involved in PAH degradation (ORF 31–43), mobile genetic elements and associated proteins, was found. These results suggest the presence of at least one other microorganism in CON besides Sphingobium sp. AM, which is capable of degrading PAH through the meta-cleavage pathway. Burkholderiales order was further found, along with Sphingomonadales order, by a metaproteomic approach, which indicated that both orders were metabolically active in CON. Our results show the presence of negative interactions between bacterial populations found in a natural consortium selected by enrichment techniques; moreover, the synthetic syntrophic processing chain with only one microorganism with the capability of degrading phenanthrene was more efficient in contaminant and intermediate metabolite degradation than a generalist strain (Sphingobium sp. AM). © 2017 Festa et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
| format |
JOUR |
| author |
Festa, S. Coppotelli, B.M. Madueño, L. Loviso, C.L. Macchi, M. Neme Tauil, R.M. Valacco, M.P. Morelli, I.S. |
| author_facet |
Festa, S. Coppotelli, B.M. Madueño, L. Loviso, C.L. Macchi, M. Neme Tauil, R.M. Valacco, M.P. Morelli, I.S. |
| author_sort |
Festa, S. |
| title |
Assigning ecological roles to the populations belonging to a phenanthrene-degrading bacterial consortium using omic approaches |
| title_short |
Assigning ecological roles to the populations belonging to a phenanthrene-degrading bacterial consortium using omic approaches |
| title_full |
Assigning ecological roles to the populations belonging to a phenanthrene-degrading bacterial consortium using omic approaches |
| title_fullStr |
Assigning ecological roles to the populations belonging to a phenanthrene-degrading bacterial consortium using omic approaches |
| title_full_unstemmed |
Assigning ecological roles to the populations belonging to a phenanthrene-degrading bacterial consortium using omic approaches |
| title_sort |
assigning ecological roles to the populations belonging to a phenanthrene-degrading bacterial consortium using omic approaches |
| url |
http://hdl.handle.net/20.500.12110/paper_19326203_v12_n9_p_Festa |
| work_keys_str_mv |
AT festas assigningecologicalrolestothepopulationsbelongingtoaphenanthrenedegradingbacterialconsortiumusingomicapproaches AT coppotellibm assigningecologicalrolestothepopulationsbelongingtoaphenanthrenedegradingbacterialconsortiumusingomicapproaches AT maduenol assigningecologicalrolestothepopulationsbelongingtoaphenanthrenedegradingbacterialconsortiumusingomicapproaches AT lovisocl assigningecologicalrolestothepopulationsbelongingtoaphenanthrenedegradingbacterialconsortiumusingomicapproaches AT macchim assigningecologicalrolestothepopulationsbelongingtoaphenanthrenedegradingbacterialconsortiumusingomicapproaches AT nemetauilrm assigningecologicalrolestothepopulationsbelongingtoaphenanthrenedegradingbacterialconsortiumusingomicapproaches AT valaccomp assigningecologicalrolestothepopulationsbelongingtoaphenanthrenedegradingbacterialconsortiumusingomicapproaches AT morelliis assigningecologicalrolestothepopulationsbelongingtoaphenanthrenedegradingbacterialconsortiumusingomicapproaches |
| _version_ |
1782025608803385344 |