Chemical Profiling Provides Insights into the Metabolic Machinery of Hydrocarbon-Degrading Deep-Sea Microbes

ABSTRACT Marine microbes are known to degrade hydrocarbons; however, microbes inhabiting deep-sea sediments remain largely unexplored. Previous studies into the classical pathways of marine microbial metabolism reveal diverse chemistries; however, metabolic profiling of marine microbes cultured with...

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Autores principales:	Aldo Moreno-Ulloa, Victoria Sicairos Diaz, Javier A. Tejeda-Mora, Marla I. Macias Contreras, Fernando Díaz Castillo, Abraham Guerrero, Ricardo Gonzalez Sanchez, Omar Mendoza-Porras, Rafael Vazquez Duhalt, Alexei Licea-Navarro
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	16S rRNA deep-sea microbes hydrocarbon degradation marine bacteria mass spectrometry metabolomics Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/ea0ed0dc6a8646d18ecb3ae5e4952c47
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spelling	oai:doaj.org-article:ea0ed0dc6a8646d18ecb3ae5e4952c472021-12-02T18:15:46ZChemical Profiling Provides Insights into the Metabolic Machinery of Hydrocarbon-Degrading Deep-Sea Microbes10.1128/mSystems.00824-202379-5077https://doaj.org/article/ea0ed0dc6a8646d18ecb3ae5e4952c472020-12-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00824-20https://doaj.org/toc/2379-5077ABSTRACT Marine microbes are known to degrade hydrocarbons; however, microbes inhabiting deep-sea sediments remain largely unexplored. Previous studies into the classical pathways of marine microbial metabolism reveal diverse chemistries; however, metabolic profiling of marine microbes cultured with hydrocarbons is limited. In this study, taxonomic (amplicon sequencing) profiles of two environmental deep-sea sediments (>1,200 m deep) were obtained, along with taxonomic and metabolomic (mass spectrometry-based metabolomics) profiles of microbes harbored in deep-sea sediments cultured with hydrocarbons as the sole energy source. Samples were collected from the Gulf of México (GM) and cultured for 28 days using simple (toluene, benzene, hexadecane, and naphthalene) and complex (petroleum API 40) hydrocarbon mixtures as the sole energy sources. The sediment samples harbored diverse microbial communities predominantly classified into Woeseiaceae and Kiloniellaceae families, whereas Pseudomonadaceae and Enterobacteriaceae families prevailed after sediments were cultured with hydrocarbons. Chemical profiling of microbial metabolomes revealed diverse chemical groups belonging primarily to the lipids and lipid-like molecules superclass, as well as the organoheterocyclic compound superclass (ClassyFire annotation). Metabolomic data and prediction of functional profiles indicated an increase in aromatic and alkane degradation in samples cultured with hydrocarbons. Previously unreported metabolites, identified as intermediates in the degradation of hydrocarbons, were annotated as hydroxylated polyunsaturated fatty acids and carboxylated benzene derivatives. In summary, this study used mass spectrometry-based metabolomics coupled to chemoinformatics to demonstrate how microbes from deep-sea sediments could be cultured in the presence of hydrocarbons. This study also highlights how this experimental approach can be used to increase the understanding of hydrocarbon degradation by deep-sea sediment microbes. IMPORTANCE High-throughput technologies and emerging informatics tools have significantly advanced knowledge of hydrocarbon metabolism by marine microbes. However, research into microbes inhabiting deep-sea sediments (>1,000 m) is limited compared to those found in shallow waters. In this study, a nontargeted and nonclassical approach was used to examine the diversity of bacterial taxa and the metabolic profiles of hydrocarbon-degrading deep-sea microbes. In conclusion, this study used metabolomics and chemoinformatics to demonstrate that microbes from deep-sea sediment origin thrive in the presence of toxic and difficult-to-metabolize hydrocarbons. Notably, this study provides evidence of previously unreported metabolites and the global chemical repertoire associated with the metabolism of hydrocarbons by deep-sea microbes.Aldo Moreno-UlloaVictoria Sicairos DiazJavier A. Tejeda-MoraMarla I. Macias ContrerasFernando Díaz CastilloAbraham GuerreroRicardo Gonzalez SanchezOmar Mendoza-PorrasRafael Vazquez DuhaltAlexei Licea-NavarroAmerican Society for Microbiologyarticle16S rRNAdeep-sea microbeshydrocarbon degradationmarine bacteriamass spectrometrymetabolomicsMicrobiologyQR1-502ENmSystems, Vol 5, Iss 6 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	16S rRNA deep-sea microbes hydrocarbon degradation marine bacteria mass spectrometry metabolomics Microbiology QR1-502
spellingShingle	16S rRNA deep-sea microbes hydrocarbon degradation marine bacteria mass spectrometry metabolomics Microbiology QR1-502 Aldo Moreno-Ulloa Victoria Sicairos Diaz Javier A. Tejeda-Mora Marla I. Macias Contreras Fernando Díaz Castillo Abraham Guerrero Ricardo Gonzalez Sanchez Omar Mendoza-Porras Rafael Vazquez Duhalt Alexei Licea-Navarro Chemical Profiling Provides Insights into the Metabolic Machinery of Hydrocarbon-Degrading Deep-Sea Microbes
description	ABSTRACT Marine microbes are known to degrade hydrocarbons; however, microbes inhabiting deep-sea sediments remain largely unexplored. Previous studies into the classical pathways of marine microbial metabolism reveal diverse chemistries; however, metabolic profiling of marine microbes cultured with hydrocarbons is limited. In this study, taxonomic (amplicon sequencing) profiles of two environmental deep-sea sediments (>1,200 m deep) were obtained, along with taxonomic and metabolomic (mass spectrometry-based metabolomics) profiles of microbes harbored in deep-sea sediments cultured with hydrocarbons as the sole energy source. Samples were collected from the Gulf of México (GM) and cultured for 28 days using simple (toluene, benzene, hexadecane, and naphthalene) and complex (petroleum API 40) hydrocarbon mixtures as the sole energy sources. The sediment samples harbored diverse microbial communities predominantly classified into Woeseiaceae and Kiloniellaceae families, whereas Pseudomonadaceae and Enterobacteriaceae families prevailed after sediments were cultured with hydrocarbons. Chemical profiling of microbial metabolomes revealed diverse chemical groups belonging primarily to the lipids and lipid-like molecules superclass, as well as the organoheterocyclic compound superclass (ClassyFire annotation). Metabolomic data and prediction of functional profiles indicated an increase in aromatic and alkane degradation in samples cultured with hydrocarbons. Previously unreported metabolites, identified as intermediates in the degradation of hydrocarbons, were annotated as hydroxylated polyunsaturated fatty acids and carboxylated benzene derivatives. In summary, this study used mass spectrometry-based metabolomics coupled to chemoinformatics to demonstrate how microbes from deep-sea sediments could be cultured in the presence of hydrocarbons. This study also highlights how this experimental approach can be used to increase the understanding of hydrocarbon degradation by deep-sea sediment microbes. IMPORTANCE High-throughput technologies and emerging informatics tools have significantly advanced knowledge of hydrocarbon metabolism by marine microbes. However, research into microbes inhabiting deep-sea sediments (>1,000 m) is limited compared to those found in shallow waters. In this study, a nontargeted and nonclassical approach was used to examine the diversity of bacterial taxa and the metabolic profiles of hydrocarbon-degrading deep-sea microbes. In conclusion, this study used metabolomics and chemoinformatics to demonstrate that microbes from deep-sea sediment origin thrive in the presence of toxic and difficult-to-metabolize hydrocarbons. Notably, this study provides evidence of previously unreported metabolites and the global chemical repertoire associated with the metabolism of hydrocarbons by deep-sea microbes.
format	article
author	Aldo Moreno-Ulloa Victoria Sicairos Diaz Javier A. Tejeda-Mora Marla I. Macias Contreras Fernando Díaz Castillo Abraham Guerrero Ricardo Gonzalez Sanchez Omar Mendoza-Porras Rafael Vazquez Duhalt Alexei Licea-Navarro
author_facet	Aldo Moreno-Ulloa Victoria Sicairos Diaz Javier A. Tejeda-Mora Marla I. Macias Contreras Fernando Díaz Castillo Abraham Guerrero Ricardo Gonzalez Sanchez Omar Mendoza-Porras Rafael Vazquez Duhalt Alexei Licea-Navarro
author_sort	Aldo Moreno-Ulloa
title	Chemical Profiling Provides Insights into the Metabolic Machinery of Hydrocarbon-Degrading Deep-Sea Microbes
title_short	Chemical Profiling Provides Insights into the Metabolic Machinery of Hydrocarbon-Degrading Deep-Sea Microbes
title_full	Chemical Profiling Provides Insights into the Metabolic Machinery of Hydrocarbon-Degrading Deep-Sea Microbes
title_fullStr	Chemical Profiling Provides Insights into the Metabolic Machinery of Hydrocarbon-Degrading Deep-Sea Microbes
title_full_unstemmed	Chemical Profiling Provides Insights into the Metabolic Machinery of Hydrocarbon-Degrading Deep-Sea Microbes
title_sort	chemical profiling provides insights into the metabolic machinery of hydrocarbon-degrading deep-sea microbes
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/ea0ed0dc6a8646d18ecb3ae5e4952c47
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Chemical Profiling Provides Insights into the Metabolic Machinery of Hydrocarbon-Degrading Deep-Sea Microbes

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