The defining genomic and predicted metabolic features of the Acetobacterium genus

Abstract

AbstractAcetogens are anaerobic bacteria capable of fixing CO2or 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.Acetobacterium woodii, which is a member of theEubacteriaceaefamily and type strain of theAcetobacteriumgenus, has been critical for understanding the biochemistry and energy conservation in acetogens. Other members of theAcetobacteriumgenus have been isolated from a variety of environments or have had genomes recovered from metagenome data, but no systematic investigation has been done into the unique and varying metabolisms of the genus. Using the 4 sequenced isolates and 5 metagenome-assembled genomes available, we sequenced the genomes of an additional 4 isolates (A. fimetarium, A. malicum, A. paludosum,andA. tundrae) and conducted a comparative genome analysis of 13 differentAcetobacteriumgenomes to obtain better phylogenomic resolution and understand the metabolic diversity of theAcetobacteriumgenus. Our findings suggest that outside of the reductive acetyl-CoA (Wood-Ljungdahl) pathway, theAcetobacteriumgenus is more phylogenetically and metabolically diverse than expected, with metabolism of fructose, lactate, and H2:CO2constant across the genus, and ethanol, methanol, caffeate, and 2,3-butanediol varying across the genus. While the gene arrangement and predicted proteins of the methyl (Cluster II) and carbonyl (Cluster III) branches of the Wood Ljungdahl pathway are highly conserved across all sequencedAcetobacteriumgenomes, Cluster 1, encoding the formate dehydrogenase, is not. Furthermore, the accessory WLP components, including the Rnf cluster and electron bifurcating hydrogenase, were also well conserved, though all but four strains encode for two Rnf clusters. Additionally, comparative genomics revealed clade-specific potential functional capabilities, such as amino acid transport and metabolism in the psychrophilic group, and biofilm formation in theA. wieringaeclade, which may afford these groups an advantage in low-temperature growth or attachment to solid surfaces, respectively. Overall, the data presented herein provides a framework for examining the ecology and evolution of theAcetobacteriumgenus and highlights the potential of these species as a source of fuels and chemicals from CO2-feedstocks.