Genomes of Planktonic <italic toggle="yes">Acidimicrobiales</italic>: Widening Horizons for Marine <italic toggle="yes">Actinobacteria</italic> by Metagenomics

ABSTRACT The genomes of four novel marine Actinobacteria have been assembled from large metagenomic data sets derived from the Mediterranean deep chlorophyll maximum (DCM). These are the first marine representatives belonging to the order Acidimicrobiales and only the second group of planktonic mari...

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Autores principales:	Carolina Megumi Mizuno, Francisco Rodriguez-Valera, Rohit Ghai
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2015
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/2ef2e846fa1b4b36bb1083219fb158cc
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spelling	oai:doaj.org-article:2ef2e846fa1b4b36bb1083219fb158cc2021-11-15T15:41:19ZGenomes of Planktonic <italic toggle="yes">Acidimicrobiales</italic>: Widening Horizons for Marine <italic toggle="yes">Actinobacteria</italic> by Metagenomics10.1128/mBio.02083-142150-7511https://doaj.org/article/2ef2e846fa1b4b36bb1083219fb158cc2015-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.02083-14https://doaj.org/toc/2150-7511ABSTRACT The genomes of four novel marine Actinobacteria have been assembled from large metagenomic data sets derived from the Mediterranean deep chlorophyll maximum (DCM). These are the first marine representatives belonging to the order Acidimicrobiales and only the second group of planktonic marine Actinobacteria to be described. Their streamlined genomes and photoheterotrophic lifestyle suggest that they are planktonic, free-living microbes. A novel rhodopsin clade, acidirhodopsins, related to freshwater actinorhodopsins, was found in these organisms. Their genomes suggest a capacity to assimilate C2 compounds, some using the glyoxylate bypass and others with the ethylmalonyl-coenzyme A (CoA) pathway. They are also able to derive energy from dimethylsulfopropionate (DMSP), sulfonate, and carbon monoxide oxidation, all commonly available in the marine habitat. These organisms appear to be prevalent in the deep photic zone at or around the DCM. The presence of sister clades to the marine Acidimicrobiales in freshwater aquatic habitats provides a new example of marine-freshwater transitions with potential evolutionary insights. IMPORTANCE Despite several studies showing the importance and abundance of planktonic Actinobacteria in the marine habitat, a representative genome was only recently described. In order to expand the genomic repertoire of marine Actinobacteria, we describe here the first Acidimicrobidae genomes of marine origin and provide insights about their ecology. They display metabolic versatility in the acquisition of carbon and appear capable of utilizing diverse sources of energy. One of the genomes harbors a new kind of rhodopsin related to the actinorhodopsin clade of freshwater origin that is widespread in the oceans. Our data also support their preference to inhabit the deep chlorophyll maximum and the deep photic zone. This work contributes to the perception of marine actinobacterial groups as important players in the marine environment with distinct and important contributions to nutrient cycling in the oceans.Carolina Megumi MizunoFrancisco Rodriguez-ValeraRohit GhaiAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 6, Iss 1 (2015)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Carolina Megumi Mizuno Francisco Rodriguez-Valera Rohit Ghai Genomes of Planktonic <italic toggle="yes">Acidimicrobiales</italic>: Widening Horizons for Marine <italic toggle="yes">Actinobacteria</italic> by Metagenomics
description	ABSTRACT The genomes of four novel marine Actinobacteria have been assembled from large metagenomic data sets derived from the Mediterranean deep chlorophyll maximum (DCM). These are the first marine representatives belonging to the order Acidimicrobiales and only the second group of planktonic marine Actinobacteria to be described. Their streamlined genomes and photoheterotrophic lifestyle suggest that they are planktonic, free-living microbes. A novel rhodopsin clade, acidirhodopsins, related to freshwater actinorhodopsins, was found in these organisms. Their genomes suggest a capacity to assimilate C2 compounds, some using the glyoxylate bypass and others with the ethylmalonyl-coenzyme A (CoA) pathway. They are also able to derive energy from dimethylsulfopropionate (DMSP), sulfonate, and carbon monoxide oxidation, all commonly available in the marine habitat. These organisms appear to be prevalent in the deep photic zone at or around the DCM. The presence of sister clades to the marine Acidimicrobiales in freshwater aquatic habitats provides a new example of marine-freshwater transitions with potential evolutionary insights. IMPORTANCE Despite several studies showing the importance and abundance of planktonic Actinobacteria in the marine habitat, a representative genome was only recently described. In order to expand the genomic repertoire of marine Actinobacteria, we describe here the first Acidimicrobidae genomes of marine origin and provide insights about their ecology. They display metabolic versatility in the acquisition of carbon and appear capable of utilizing diverse sources of energy. One of the genomes harbors a new kind of rhodopsin related to the actinorhodopsin clade of freshwater origin that is widespread in the oceans. Our data also support their preference to inhabit the deep chlorophyll maximum and the deep photic zone. This work contributes to the perception of marine actinobacterial groups as important players in the marine environment with distinct and important contributions to nutrient cycling in the oceans.
format	article
author	Carolina Megumi Mizuno Francisco Rodriguez-Valera Rohit Ghai
author_facet	Carolina Megumi Mizuno Francisco Rodriguez-Valera Rohit Ghai
author_sort	Carolina Megumi Mizuno
title	Genomes of Planktonic <italic toggle="yes">Acidimicrobiales</italic>: Widening Horizons for Marine <italic toggle="yes">Actinobacteria</italic> by Metagenomics
title_short	Genomes of Planktonic <italic toggle="yes">Acidimicrobiales</italic>: Widening Horizons for Marine <italic toggle="yes">Actinobacteria</italic> by Metagenomics
title_full	Genomes of Planktonic <italic toggle="yes">Acidimicrobiales</italic>: Widening Horizons for Marine <italic toggle="yes">Actinobacteria</italic> by Metagenomics
title_fullStr	Genomes of Planktonic <italic toggle="yes">Acidimicrobiales</italic>: Widening Horizons for Marine <italic toggle="yes">Actinobacteria</italic> by Metagenomics
title_full_unstemmed	Genomes of Planktonic <italic toggle="yes">Acidimicrobiales</italic>: Widening Horizons for Marine <italic toggle="yes">Actinobacteria</italic> by Metagenomics
title_sort	genomes of planktonic <italic toggle="yes">acidimicrobiales</italic>: widening horizons for marine <italic toggle="yes">actinobacteria</italic> by metagenomics
publisher	American Society for Microbiology
publishDate	2015
url	https://doaj.org/article/2ef2e846fa1b4b36bb1083219fb158cc
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Genomes of Planktonic <italic toggle="yes">Acidimicrobiales</italic>: Widening Horizons for Marine <italic toggle="yes">Actinobacteria</italic> by Metagenomics

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