SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter

ABSTRACT Deep-ocean regions beyond the reach of sunlight contain an estimated 615 Pg of dissolved organic matter (DOM), much of which persists for thousands of years. It is thought that bacteria oxidize DOM until it is too dilute or refractory to support microbial activity. We analyzed five single-a...

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Autores principales:	Zachary Landry, Brandon K. Swan, Gerhard J. Herndl, Ramunas Stepanauskas, Stephen J. Giovannoni
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	bathypelagic Chloroflexi dissolved organic matter mesopelagic monooxygenase SAR202 Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/10f8eacdbc3347819b8bcf7734eddd29
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spelling	oai:doaj.org-article:10f8eacdbc3347819b8bcf7734eddd292021-11-15T15:51:00ZSAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter10.1128/mBio.00413-172150-7511https://doaj.org/article/10f8eacdbc3347819b8bcf7734eddd292017-05-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00413-17https://doaj.org/toc/2150-7511ABSTRACT Deep-ocean regions beyond the reach of sunlight contain an estimated 615 Pg of dissolved organic matter (DOM), much of which persists for thousands of years. It is thought that bacteria oxidize DOM until it is too dilute or refractory to support microbial activity. We analyzed five single-amplified genomes (SAGs) from the abundant SAR202 clade of dark-ocean bacterioplankton and found they encode multiple families of paralogous enzymes involved in carbon catabolism, including several families of oxidative enzymes that we hypothesize participate in the degradation of cyclic alkanes. The five partial genomes encoded 152 flavin mononucleotide/F420-dependent monooxygenases (FMNOs), many of which are predicted to be type II Baeyer-Villiger monooxygenases (BVMOs) that catalyze oxygen insertion into semilabile alicyclic alkanes. The large number of oxidative enzymes, as well as other families of enzymes that appear to play complementary roles in catabolic pathways, suggests that SAR202 might catalyze final steps in the biological oxidation of relatively recalcitrant organic compounds to refractory compounds that persist. IMPORTANCE Carbon in the ocean is massively sequestered in a complex mixture of biologically refractory molecules that accumulate as the chemical end member of biological oxidation and diagenetic change. However, few details are known about the biochemical machinery of carbon sequestration in the deep ocean. Reconstruction of the metabolism of a deep-ocean microbial clade, SAR202, led to postulation of new biochemical pathways that may be the penultimate stages of DOM oxidation to refractory forms that persist. These pathways are tied to a proliferation of oxidative enzymes. This research illuminates dark-ocean biochemistry that is broadly consequential for reconstructing the global carbon cycle.Zachary LandryBrandon K. SwanGerhard J. HerndlRamunas StepanauskasStephen J. GiovannoniAmerican Society for MicrobiologyarticlebathypelagicChloroflexidissolved organic mattermesopelagicmonooxygenaseSAR202MicrobiologyQR1-502ENmBio, Vol 8, Iss 2 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	bathypelagic Chloroflexi dissolved organic matter mesopelagic monooxygenase SAR202 Microbiology QR1-502
spellingShingle	bathypelagic Chloroflexi dissolved organic matter mesopelagic monooxygenase SAR202 Microbiology QR1-502 Zachary Landry Brandon K. Swan Gerhard J. Herndl Ramunas Stepanauskas Stephen J. Giovannoni SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter
description	ABSTRACT Deep-ocean regions beyond the reach of sunlight contain an estimated 615 Pg of dissolved organic matter (DOM), much of which persists for thousands of years. It is thought that bacteria oxidize DOM until it is too dilute or refractory to support microbial activity. We analyzed five single-amplified genomes (SAGs) from the abundant SAR202 clade of dark-ocean bacterioplankton and found they encode multiple families of paralogous enzymes involved in carbon catabolism, including several families of oxidative enzymes that we hypothesize participate in the degradation of cyclic alkanes. The five partial genomes encoded 152 flavin mononucleotide/F420-dependent monooxygenases (FMNOs), many of which are predicted to be type II Baeyer-Villiger monooxygenases (BVMOs) that catalyze oxygen insertion into semilabile alicyclic alkanes. The large number of oxidative enzymes, as well as other families of enzymes that appear to play complementary roles in catabolic pathways, suggests that SAR202 might catalyze final steps in the biological oxidation of relatively recalcitrant organic compounds to refractory compounds that persist. IMPORTANCE Carbon in the ocean is massively sequestered in a complex mixture of biologically refractory molecules that accumulate as the chemical end member of biological oxidation and diagenetic change. However, few details are known about the biochemical machinery of carbon sequestration in the deep ocean. Reconstruction of the metabolism of a deep-ocean microbial clade, SAR202, led to postulation of new biochemical pathways that may be the penultimate stages of DOM oxidation to refractory forms that persist. These pathways are tied to a proliferation of oxidative enzymes. This research illuminates dark-ocean biochemistry that is broadly consequential for reconstructing the global carbon cycle.
format	article
author	Zachary Landry Brandon K. Swan Gerhard J. Herndl Ramunas Stepanauskas Stephen J. Giovannoni
author_facet	Zachary Landry Brandon K. Swan Gerhard J. Herndl Ramunas Stepanauskas Stephen J. Giovannoni
author_sort	Zachary Landry
title	SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter
title_short	SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter
title_full	SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter
title_fullStr	SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter
title_full_unstemmed	SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter
title_sort	sar202 genomes from the dark ocean predict pathways for the oxidation of recalcitrant dissolved organic matter
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/10f8eacdbc3347819b8bcf7734eddd29
work_keys_str_mv	AT zacharylandry sar202genomesfromthedarkoceanpredictpathwaysfortheoxidationofrecalcitrantdissolvedorganicmatter AT brandonkswan sar202genomesfromthedarkoceanpredictpathwaysfortheoxidationofrecalcitrantdissolvedorganicmatter AT gerhardjherndl sar202genomesfromthedarkoceanpredictpathwaysfortheoxidationofrecalcitrantdissolvedorganicmatter AT ramunasstepanauskas sar202genomesfromthedarkoceanpredictpathwaysfortheoxidationofrecalcitrantdissolvedorganicmatter AT stephenjgiovannoni sar202genomesfromthedarkoceanpredictpathwaysfortheoxidationofrecalcitrantdissolvedorganicmatter
_version_	1718427382228975616

SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter

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