Defining Genomic and Predicted Metabolic Features of the <italic toggle="yes">Acetobacterium</italic> Genus

ABSTRACT Acetogens are anaerobic bacteria capable of fixing CO2 or CO to produce acetyl coenzyme A (acetyl-CoA) and ultimately acetate using the Wood-Ljungdahl pathway (WLP). Acetobacterium woodii is the type strain of the Acetobacterium genus and has been critical for understanding the biochemistry...

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Autores principales:	Daniel E. Ross, Christopher W. Marshall, Djuna Gulliver, Harold D. May, R. Sean Norman
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	Acetobacterium pan-genome metagenome-assembled genome acetogens Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/3cbf8633f2474f17b610b9d65d4e550a
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spelling	oai:doaj.org-article:3cbf8633f2474f17b610b9d65d4e550a2021-12-02T19:47:36ZDefining Genomic and Predicted Metabolic Features of the <italic toggle="yes">Acetobacterium</italic> Genus10.1128/mSystems.00277-202379-5077https://doaj.org/article/3cbf8633f2474f17b610b9d65d4e550a2020-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00277-20https://doaj.org/toc/2379-5077ABSTRACT Acetogens are anaerobic bacteria capable of fixing CO2 or CO to produce acetyl coenzyme A (acetyl-CoA) and ultimately acetate using the Wood-Ljungdahl pathway (WLP). Acetobacterium woodii is the type strain of the Acetobacterium genus and has been critical for understanding the biochemistry and energy conservation in acetogens. Members of the Acetobacterium genus have been isolated from a variety of environments or have had genomes recovered from metagenome data, but no systematic investigation has been done on the unique and various metabolisms of the genus. To gain a better appreciation for the metabolic breadth of the genus, we sequenced the genomes of 4 isolates (A. fimetarium, A. malicum, A. paludosum, and A. tundrae) and conducted a comparative genome analysis (pan-genome) of 11 different Acetobacterium genomes. A unifying feature of the Acetobacterium genus is the carbon-fixing WLP. The methyl (cluster II) and carbonyl (cluster III) branches of the Wood-Ljungdahl pathway are highly conserved across all sequenced Acetobacterium genomes, but cluster I encoding the formate dehydrogenase is not. In contrast to A. woodii, all but four strains encode two distinct Rnf clusters, Rnf being the primary respiratory enzyme complex. Metabolism of fructose, lactate, and H2:CO2 was conserved across the genus, but metabolism of ethanol, methanol, caffeate, and 2,3-butanediol varied. Additionally, clade-specific metabolic potential was observed, such as amino acid transport and metabolism in the psychrophilic species, and biofilm formation in the A. wieringae clade, which may afford these groups an advantage in low-temperature growth or attachment to solid surfaces, respectively. IMPORTANCE Acetogens are anaerobic bacteria capable of fixing CO2 or CO to produce acetyl-CoA and ultimately acetate using the Wood-Ljungdahl pathway (WLP). This autotrophic metabolism plays a major role in the global carbon cycle and, if harnessed, can help reduce greenhouse gas emissions. Overall, the data presented here provide a framework for examining the ecology and evolution of the Acetobacterium genus and highlight the potential of these species as a source for production of fuels and chemicals from CO2 feedstocks.Daniel E. RossChristopher W. MarshallDjuna GulliverHarold D. MayR. Sean NormanAmerican Society for MicrobiologyarticleAcetobacteriumpan-genomemetagenome-assembled genomeacetogensMicrobiologyQR1-502ENmSystems, Vol 5, Iss 5 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Acetobacterium pan-genome metagenome-assembled genome acetogens Microbiology QR1-502
spellingShingle	Acetobacterium pan-genome metagenome-assembled genome acetogens Microbiology QR1-502 Daniel E. Ross Christopher W. Marshall Djuna Gulliver Harold D. May R. Sean Norman Defining Genomic and Predicted Metabolic Features of the <italic toggle="yes">Acetobacterium</italic> Genus
description	ABSTRACT Acetogens are anaerobic bacteria capable of fixing CO2 or CO to produce acetyl coenzyme A (acetyl-CoA) and ultimately acetate using the Wood-Ljungdahl pathway (WLP). Acetobacterium woodii is the type strain of the Acetobacterium genus and has been critical for understanding the biochemistry and energy conservation in acetogens. Members of the Acetobacterium genus have been isolated from a variety of environments or have had genomes recovered from metagenome data, but no systematic investigation has been done on the unique and various metabolisms of the genus. To gain a better appreciation for the metabolic breadth of the genus, we sequenced the genomes of 4 isolates (A. fimetarium, A. malicum, A. paludosum, and A. tundrae) and conducted a comparative genome analysis (pan-genome) of 11 different Acetobacterium genomes. A unifying feature of the Acetobacterium genus is the carbon-fixing WLP. The methyl (cluster II) and carbonyl (cluster III) branches of the Wood-Ljungdahl pathway are highly conserved across all sequenced Acetobacterium genomes, but cluster I encoding the formate dehydrogenase is not. In contrast to A. woodii, all but four strains encode two distinct Rnf clusters, Rnf being the primary respiratory enzyme complex. Metabolism of fructose, lactate, and H2:CO2 was conserved across the genus, but metabolism of ethanol, methanol, caffeate, and 2,3-butanediol varied. Additionally, clade-specific metabolic potential was observed, such as amino acid transport and metabolism in the psychrophilic species, and biofilm formation in the A. wieringae clade, which may afford these groups an advantage in low-temperature growth or attachment to solid surfaces, respectively. IMPORTANCE Acetogens are anaerobic bacteria capable of fixing CO2 or CO to produce acetyl-CoA and ultimately acetate using the Wood-Ljungdahl pathway (WLP). This autotrophic metabolism plays a major role in the global carbon cycle and, if harnessed, can help reduce greenhouse gas emissions. Overall, the data presented here provide a framework for examining the ecology and evolution of the Acetobacterium genus and highlight the potential of these species as a source for production of fuels and chemicals from CO2 feedstocks.
format	article
author	Daniel E. Ross Christopher W. Marshall Djuna Gulliver Harold D. May R. Sean Norman
author_facet	Daniel E. Ross Christopher W. Marshall Djuna Gulliver Harold D. May R. Sean Norman
author_sort	Daniel E. Ross
title	Defining Genomic and Predicted Metabolic Features of the <italic toggle="yes">Acetobacterium</italic> Genus
title_short	Defining Genomic and Predicted Metabolic Features of the <italic toggle="yes">Acetobacterium</italic> Genus
title_full	Defining Genomic and Predicted Metabolic Features of the <italic toggle="yes">Acetobacterium</italic> Genus
title_fullStr	Defining Genomic and Predicted Metabolic Features of the <italic toggle="yes">Acetobacterium</italic> Genus
title_full_unstemmed	Defining Genomic and Predicted Metabolic Features of the <italic toggle="yes">Acetobacterium</italic> Genus
title_sort	defining genomic and predicted metabolic features of the <italic toggle="yes">acetobacterium</italic> genus
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/3cbf8633f2474f17b610b9d65d4e550a
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Defining Genomic and Predicted Metabolic Features of the <italic toggle="yes">Acetobacterium</italic> Genus

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