Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of <italic toggle="yes">Zetaproteobacteria</italic> Iron Mats at Marine Hydrothermal Vents

ABSTRACT Zetaproteobacteria create extensive iron (Fe) oxide mats at marine hydrothermal vents, making them an ideal model for microbial Fe oxidation at circumneutral pH. Comparison of neutrophilic Fe oxidizer isolate genomes has revealed a hypothetical Fe oxidation pathway, featuring a homolog of t...

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Autores principales:	Sean M. McAllister, Shawn W. Polson, David A. Butterfield, Brian T. Glazer, Jason B. Sylvan, Clara S. Chan
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	Cyc2 Fe oxidation pathway biogeochemistry environmental microbiology hydrothermal vent iron cycling iron oxidizers Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/820811a3bfcd4dd6b438106b0bed7a35
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spelling	oai:doaj.org-article:820811a3bfcd4dd6b438106b0bed7a352021-12-02T18:39:47ZValidating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of <italic toggle="yes">Zetaproteobacteria</italic> Iron Mats at Marine Hydrothermal Vents10.1128/mSystems.00553-192379-5077https://doaj.org/article/820811a3bfcd4dd6b438106b0bed7a352020-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00553-19https://doaj.org/toc/2379-5077ABSTRACT Zetaproteobacteria create extensive iron (Fe) oxide mats at marine hydrothermal vents, making them an ideal model for microbial Fe oxidation at circumneutral pH. Comparison of neutrophilic Fe oxidizer isolate genomes has revealed a hypothetical Fe oxidation pathway, featuring a homolog of the Fe oxidase Cyc2 from Acidithiobacillus ferrooxidans. However, Cyc2 function is not well verified in neutrophilic Fe oxidizers, particularly in Fe-oxidizing environments. Toward this, we analyzed genomes and metatranscriptomes of Zetaproteobacteria, using 53 new high-quality metagenome-assembled genomes reconstructed from Fe mats at Mid-Atlantic Ridge, Mariana Backarc, and Loihi Seamount (Hawaii) hydrothermal vents. Phylogenetic analysis demonstrated conservation of Cyc2 sequences among most neutrophilic Fe oxidizers, suggesting a common function. We confirmed the widespread distribution of cyc2 and other model Fe oxidation pathway genes across all represented Zetaproteobacteria lineages. High expression of these genes was observed in diverse Zetaproteobacteria under multiple environmental conditions and in incubations. The putative Fe oxidase gene cyc2 was highly expressed in situ, often as the top expressed gene. The cyc2 gene showed increased expression in Fe(II)-amended incubations, with corresponding increases in carbon fixation and central metabolism gene expression. These results substantiate the Cyc2-based Fe oxidation pathway in neutrophiles and demonstrate its significance in marine Fe-mineralizing environments. IMPORTANCE Iron oxides are important components of our soil, water supplies, and ecosystems, as they sequester nutrients, carbon, and metals. Microorganisms can form iron oxides, but it is unclear whether this is a significant mechanism in the environment. Unlike other major microbial energy metabolisms, there is no marker gene for iron oxidation, hindering our ability to track these microbes. Here, we investigate a promising possible iron oxidation gene, cyc2, in iron-rich hydrothermal vents, where iron-oxidizing microbes dominate. We pieced together diverse Zetaproteobacteria genomes, compared these genomes, and analyzed expression of cyc2 and other hypothetical iron oxidation genes. We show that cyc2 is widespread among iron oxidizers and is highly expressed and potentially regulated, making it a good marker for the capacity for iron oxidation and potentially a marker for activity. These findings will help us understand and potentially quantify the impacts of neutrophilic iron oxidizers in a wide variety of marine and terrestrial environments.Sean M. McAllisterShawn W. PolsonDavid A. ButterfieldBrian T. GlazerJason B. SylvanClara S. ChanAmerican Society for MicrobiologyarticleCyc2 Fe oxidation pathwaybiogeochemistryenvironmental microbiologyhydrothermal ventiron cyclingiron oxidizersMicrobiologyQR1-502ENmSystems, Vol 5, Iss 1 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Cyc2 Fe oxidation pathway biogeochemistry environmental microbiology hydrothermal vent iron cycling iron oxidizers Microbiology QR1-502
spellingShingle	Cyc2 Fe oxidation pathway biogeochemistry environmental microbiology hydrothermal vent iron cycling iron oxidizers Microbiology QR1-502 Sean M. McAllister Shawn W. Polson David A. Butterfield Brian T. Glazer Jason B. Sylvan Clara S. Chan Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of <italic toggle="yes">Zetaproteobacteria</italic> Iron Mats at Marine Hydrothermal Vents
description	ABSTRACT Zetaproteobacteria create extensive iron (Fe) oxide mats at marine hydrothermal vents, making them an ideal model for microbial Fe oxidation at circumneutral pH. Comparison of neutrophilic Fe oxidizer isolate genomes has revealed a hypothetical Fe oxidation pathway, featuring a homolog of the Fe oxidase Cyc2 from Acidithiobacillus ferrooxidans. However, Cyc2 function is not well verified in neutrophilic Fe oxidizers, particularly in Fe-oxidizing environments. Toward this, we analyzed genomes and metatranscriptomes of Zetaproteobacteria, using 53 new high-quality metagenome-assembled genomes reconstructed from Fe mats at Mid-Atlantic Ridge, Mariana Backarc, and Loihi Seamount (Hawaii) hydrothermal vents. Phylogenetic analysis demonstrated conservation of Cyc2 sequences among most neutrophilic Fe oxidizers, suggesting a common function. We confirmed the widespread distribution of cyc2 and other model Fe oxidation pathway genes across all represented Zetaproteobacteria lineages. High expression of these genes was observed in diverse Zetaproteobacteria under multiple environmental conditions and in incubations. The putative Fe oxidase gene cyc2 was highly expressed in situ, often as the top expressed gene. The cyc2 gene showed increased expression in Fe(II)-amended incubations, with corresponding increases in carbon fixation and central metabolism gene expression. These results substantiate the Cyc2-based Fe oxidation pathway in neutrophiles and demonstrate its significance in marine Fe-mineralizing environments. IMPORTANCE Iron oxides are important components of our soil, water supplies, and ecosystems, as they sequester nutrients, carbon, and metals. Microorganisms can form iron oxides, but it is unclear whether this is a significant mechanism in the environment. Unlike other major microbial energy metabolisms, there is no marker gene for iron oxidation, hindering our ability to track these microbes. Here, we investigate a promising possible iron oxidation gene, cyc2, in iron-rich hydrothermal vents, where iron-oxidizing microbes dominate. We pieced together diverse Zetaproteobacteria genomes, compared these genomes, and analyzed expression of cyc2 and other hypothetical iron oxidation genes. We show that cyc2 is widespread among iron oxidizers and is highly expressed and potentially regulated, making it a good marker for the capacity for iron oxidation and potentially a marker for activity. These findings will help us understand and potentially quantify the impacts of neutrophilic iron oxidizers in a wide variety of marine and terrestrial environments.
format	article
author	Sean M. McAllister Shawn W. Polson David A. Butterfield Brian T. Glazer Jason B. Sylvan Clara S. Chan
author_facet	Sean M. McAllister Shawn W. Polson David A. Butterfield Brian T. Glazer Jason B. Sylvan Clara S. Chan
author_sort	Sean M. McAllister
title	Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of <italic toggle="yes">Zetaproteobacteria</italic> Iron Mats at Marine Hydrothermal Vents
title_short	Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of <italic toggle="yes">Zetaproteobacteria</italic> Iron Mats at Marine Hydrothermal Vents
title_full	Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of <italic toggle="yes">Zetaproteobacteria</italic> Iron Mats at Marine Hydrothermal Vents
title_fullStr	Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of <italic toggle="yes">Zetaproteobacteria</italic> Iron Mats at Marine Hydrothermal Vents
title_full_unstemmed	Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of <italic toggle="yes">Zetaproteobacteria</italic> Iron Mats at Marine Hydrothermal Vents
title_sort	validating the cyc2 neutrophilic iron oxidation pathway using meta-omics of <italic toggle="yes">zetaproteobacteria</italic> iron mats at marine hydrothermal vents
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/820811a3bfcd4dd6b438106b0bed7a35
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Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of <italic toggle="yes">Zetaproteobacteria</italic> Iron Mats at Marine Hydrothermal Vents

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