Cargando…
Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture
Polycyclic aromatic hydrocarbons (PAH) such as naphthalene are widespread, recalcitrant pollutants in anoxic and methanogenic environments. A mechanism catalyzing PAH activation under methanogenic conditions has yet to be discovered, and the microbial communities coordinating their metabolism are la...
Autores principales: | , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2018
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6164631/ https://www.ncbi.nlm.nih.gov/pubmed/29996505 http://dx.doi.org/10.3390/microorganisms6030065 |
_version_ | 1783359646504845312 |
---|---|
author | Toth, Courtney R. A. Berdugo-Clavijo, Carolina O’Farrell, Corynne M. Jones, Gareth M. Sheremet, Andriy Dunfield, Peter F. Gieg, Lisa M. |
author_facet | Toth, Courtney R. A. Berdugo-Clavijo, Carolina O’Farrell, Corynne M. Jones, Gareth M. Sheremet, Andriy Dunfield, Peter F. Gieg, Lisa M. |
author_sort | Toth, Courtney R. A. |
collection | PubMed |
description | Polycyclic aromatic hydrocarbons (PAH) such as naphthalene are widespread, recalcitrant pollutants in anoxic and methanogenic environments. A mechanism catalyzing PAH activation under methanogenic conditions has yet to be discovered, and the microbial communities coordinating their metabolism are largely unknown. This is primarily due to the difficulty of cultivating PAH degraders, requiring lengthy incubations to yield sufficient biomass for biochemical analysis. Here, we sought to characterize a new methanogenic naphthalene-degrading enrichment culture using DNA-based stable isotope probing (SIP) and metagenomic analyses. 16S rRNA gene sequencing of fractionated DNA pinpointed an unclassified Clostridiaceae species as a putative naphthalene degrader after two months of SIP incubation. This finding was supported by metabolite and metagenomic evidence of genes predicted to encode for enzymes facilitating naphthalene carboxylic acid CoA-thioesterification and degradation of an unknown arylcarboxyl-CoA structure. Our findings also suggest a possible but unknown role for Desulfuromonadales in naphthalene degradation. This is the first reported functional evidence of PAH biodegradation by a methanogenic consortium, and we envision that this approach could be used to assess carbon flow through other slow growing enrichment cultures and environmental samples. |
format | Online Article Text |
id | pubmed-6164631 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-61646312018-10-10 Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture Toth, Courtney R. A. Berdugo-Clavijo, Carolina O’Farrell, Corynne M. Jones, Gareth M. Sheremet, Andriy Dunfield, Peter F. Gieg, Lisa M. Microorganisms Article Polycyclic aromatic hydrocarbons (PAH) such as naphthalene are widespread, recalcitrant pollutants in anoxic and methanogenic environments. A mechanism catalyzing PAH activation under methanogenic conditions has yet to be discovered, and the microbial communities coordinating their metabolism are largely unknown. This is primarily due to the difficulty of cultivating PAH degraders, requiring lengthy incubations to yield sufficient biomass for biochemical analysis. Here, we sought to characterize a new methanogenic naphthalene-degrading enrichment culture using DNA-based stable isotope probing (SIP) and metagenomic analyses. 16S rRNA gene sequencing of fractionated DNA pinpointed an unclassified Clostridiaceae species as a putative naphthalene degrader after two months of SIP incubation. This finding was supported by metabolite and metagenomic evidence of genes predicted to encode for enzymes facilitating naphthalene carboxylic acid CoA-thioesterification and degradation of an unknown arylcarboxyl-CoA structure. Our findings also suggest a possible but unknown role for Desulfuromonadales in naphthalene degradation. This is the first reported functional evidence of PAH biodegradation by a methanogenic consortium, and we envision that this approach could be used to assess carbon flow through other slow growing enrichment cultures and environmental samples. MDPI 2018-07-10 /pmc/articles/PMC6164631/ /pubmed/29996505 http://dx.doi.org/10.3390/microorganisms6030065 Text en © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Toth, Courtney R. A. Berdugo-Clavijo, Carolina O’Farrell, Corynne M. Jones, Gareth M. Sheremet, Andriy Dunfield, Peter F. Gieg, Lisa M. Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture |
title | Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture |
title_full | Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture |
title_fullStr | Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture |
title_full_unstemmed | Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture |
title_short | Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture |
title_sort | stable isotope and metagenomic profiling of a methanogenic naphthalene-degrading enrichment culture |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6164631/ https://www.ncbi.nlm.nih.gov/pubmed/29996505 http://dx.doi.org/10.3390/microorganisms6030065 |
work_keys_str_mv | AT tothcourtneyra stableisotopeandmetagenomicprofilingofamethanogenicnaphthalenedegradingenrichmentculture AT berdugoclavijocarolina stableisotopeandmetagenomicprofilingofamethanogenicnaphthalenedegradingenrichmentculture AT ofarrellcorynnem stableisotopeandmetagenomicprofilingofamethanogenicnaphthalenedegradingenrichmentculture AT jonesgarethm stableisotopeandmetagenomicprofilingofamethanogenicnaphthalenedegradingenrichmentculture AT sheremetandriy stableisotopeandmetagenomicprofilingofamethanogenicnaphthalenedegradingenrichmentculture AT dunfieldpeterf stableisotopeandmetagenomicprofilingofamethanogenicnaphthalenedegradingenrichmentculture AT gieglisam stableisotopeandmetagenomicprofilingofamethanogenicnaphthalenedegradingenrichmentculture |