Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean
ABSTRACT Microbes play a significant role in the degradation of petroleum hydrocarbons in the oceans, yet little is known about the native bacteria that metabolize hydrocarbons before an oil spill. The Faroe-Shetland Channel (FSC) is a deepwater subarctic region of the North Atlantic with prominent...
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ftdoajarticles:oai:doaj.org/article:86683d2a849b4bada2aa3666584f5104 2023-11-12T04:21:55+01:00 Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean Mirna Vázquez Rosas Landa Valerie De Anda Robin R. Rohwer Angelina Angelova Georgia Waldram Tony Gutierrez Brett J. Baker 2023-10-01T00:00:00Z https://doi.org/10.1128/msystems.00619-23 https://doaj.org/article/86683d2a849b4bada2aa3666584f5104 EN eng American Society for Microbiology https://journals.asm.org/doi/10.1128/msystems.00619-23 https://doaj.org/toc/2379-5077 doi:10.1128/msystems.00619-23 2379-5077 https://doaj.org/article/86683d2a849b4bada2aa3666584f5104 mSystems, Vol 8, Iss 5 (2023) oil spills stable-isotope probing (SIP) metagenomics assembled genomes hydrocarbon degradation Microbiology QR1-502 article 2023 ftdoajarticles https://doi.org/10.1128/msystems.00619-23 2023-10-29T00:38:15Z ABSTRACT Microbes play a significant role in the degradation of petroleum hydrocarbons in the oceans, yet little is known about the native bacteria that metabolize hydrocarbons before an oil spill. The Faroe-Shetland Channel (FSC) is a deepwater subarctic region of the North Atlantic with prominent oil production and a diverse microbial community associated with the degradation of petroleum. Here, we combine DNA-based stable-isotope probing (DNA-SIP) with metagenomics to elucidate the metabolic underpinnings of native alkane-degrading bacteria from the FSC. From two 13C n-hexadecane SIP experiments using seawater from 5 and 700 m depths in the FSC, we obtained 42 metagenome-assembled genomes (MAGs) belonging to 19 genera, including two previously overlooked hydrocarbon-degrading bacteria, Lentibacter (Alphaproteobacteria) and Dokdonia (Bacteroidetes). Diversity surveys indicated Lentibacter were dominant members of the FSC, constituting up to 17% of these communities. Many of the SIP-enriched MAGs (20/42) encoded a complete alkane oxidation pathway, including alkane monooxygenase (AlkB), rubredoxin reductase (AlkT), and rubredoxin-2 (AlkG). Fourteen Aphaproteobacteria MAGs lacked AlkG for electron transfer. Instead, they encoded novel disulfide isomerases with iron-binding cysteine motifs conserved across rubredoxins. Dokdonia lacked AlkT and AlkG, however, their central alkane-degradation catabolic pathways were complete. We describe previously unrecognized bacteria capable of hydrocarbon degradation, including the dominant genera Lentibacter, which may continuously purge hydrocarbons released from oil exploration activities in the FSC. This advances the understanding of the diversity and physiologies of alkane degradation in the North Atlantic and provides evidence of new mechanisms used to metabolize alkanes. IMPORTANCE Petroleum pollution in the ocean has increased because of rapid population growth and modernization, requiring urgent remediation. Our understanding of the metabolic response of native ... Article in Journal/Newspaper North Atlantic Subarctic Directory of Open Access Journals: DOAJ Articles mSystems 8 5 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
oil spills stable-isotope probing (SIP) metagenomics assembled genomes hydrocarbon degradation Microbiology QR1-502 |
spellingShingle |
oil spills stable-isotope probing (SIP) metagenomics assembled genomes hydrocarbon degradation Microbiology QR1-502 Mirna Vázquez Rosas Landa Valerie De Anda Robin R. Rohwer Angelina Angelova Georgia Waldram Tony Gutierrez Brett J. Baker Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean |
topic_facet |
oil spills stable-isotope probing (SIP) metagenomics assembled genomes hydrocarbon degradation Microbiology QR1-502 |
description |
ABSTRACT Microbes play a significant role in the degradation of petroleum hydrocarbons in the oceans, yet little is known about the native bacteria that metabolize hydrocarbons before an oil spill. The Faroe-Shetland Channel (FSC) is a deepwater subarctic region of the North Atlantic with prominent oil production and a diverse microbial community associated with the degradation of petroleum. Here, we combine DNA-based stable-isotope probing (DNA-SIP) with metagenomics to elucidate the metabolic underpinnings of native alkane-degrading bacteria from the FSC. From two 13C n-hexadecane SIP experiments using seawater from 5 and 700 m depths in the FSC, we obtained 42 metagenome-assembled genomes (MAGs) belonging to 19 genera, including two previously overlooked hydrocarbon-degrading bacteria, Lentibacter (Alphaproteobacteria) and Dokdonia (Bacteroidetes). Diversity surveys indicated Lentibacter were dominant members of the FSC, constituting up to 17% of these communities. Many of the SIP-enriched MAGs (20/42) encoded a complete alkane oxidation pathway, including alkane monooxygenase (AlkB), rubredoxin reductase (AlkT), and rubredoxin-2 (AlkG). Fourteen Aphaproteobacteria MAGs lacked AlkG for electron transfer. Instead, they encoded novel disulfide isomerases with iron-binding cysteine motifs conserved across rubredoxins. Dokdonia lacked AlkT and AlkG, however, their central alkane-degradation catabolic pathways were complete. We describe previously unrecognized bacteria capable of hydrocarbon degradation, including the dominant genera Lentibacter, which may continuously purge hydrocarbons released from oil exploration activities in the FSC. This advances the understanding of the diversity and physiologies of alkane degradation in the North Atlantic and provides evidence of new mechanisms used to metabolize alkanes. IMPORTANCE Petroleum pollution in the ocean has increased because of rapid population growth and modernization, requiring urgent remediation. Our understanding of the metabolic response of native ... |
format |
Article in Journal/Newspaper |
author |
Mirna Vázquez Rosas Landa Valerie De Anda Robin R. Rohwer Angelina Angelova Georgia Waldram Tony Gutierrez Brett J. Baker |
author_facet |
Mirna Vázquez Rosas Landa Valerie De Anda Robin R. Rohwer Angelina Angelova Georgia Waldram Tony Gutierrez Brett J. Baker |
author_sort |
Mirna Vázquez Rosas Landa |
title |
Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean |
title_short |
Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean |
title_full |
Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean |
title_fullStr |
Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean |
title_full_unstemmed |
Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean |
title_sort |
exploring novel alkane-degradation pathways in uncultured bacteria from the north atlantic ocean |
publisher |
American Society for Microbiology |
publishDate |
2023 |
url |
https://doi.org/10.1128/msystems.00619-23 https://doaj.org/article/86683d2a849b4bada2aa3666584f5104 |
genre |
North Atlantic Subarctic |
genre_facet |
North Atlantic Subarctic |
op_source |
mSystems, Vol 8, Iss 5 (2023) |
op_relation |
https://journals.asm.org/doi/10.1128/msystems.00619-23 https://doaj.org/toc/2379-5077 doi:10.1128/msystems.00619-23 2379-5077 https://doaj.org/article/86683d2a849b4bada2aa3666584f5104 |
op_doi |
https://doi.org/10.1128/msystems.00619-23 |
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mSystems |
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8 |
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5 |
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1782337129441918976 |