Abstract
Acetogenic bacteria are obligate anaerobes with the ability of converting carbon dioxide and other one‐carbon substrates into acetate through the Wood–Ljungdahl (WL) pathway. These substrates are becoming increasingly important feedstock in industrial microbiology. The main potential industrial application of acetogenic bacteria is the production of metabolites that constitute renewable energy sources (biofuel); such bacteria are of particular interest for this purpose thanks to their low energy requirements for large‐scale cultivation. Here, we report new genome sequences for four species, three of them are reported for the first time, namely Acetobacterium paludosum DSM 8237, Acetobacterium tundrae DSM 917, Acetobacterium bakii DSM 8239, and Alkalibaculum bacchi DSM 221123. We performed a comparative genomic analysis focused on the WL pathway's genes and their encoded proteins, using Acetobacterium woodii as a reference genome. The Average Nucleotide Identity (ANI) values ranged from 70% to 95% over an alignment length of 5.4–6.5 Mbp. The core genome consisted of 363 genes, whereas the number of unique genes in a single genome ranged from 486 in A. tundrae to 2360 in A.bacchi. No significant rearrangements were detected in the gene order for the Wood–Ljungdahl pathway however, two species showed variations in genes involved in formate metabolism: A. paludosum harbor two copies of fhs1, and A. bakii a truncated fdhF1. The analysis of protein networks highlighted the expansion of protein orthologues in A. woodii compared to A. bacchi, whereas protein networks involved in the WL pathway were more conserved. This study has increased our understanding on the evolution of the WL pathway in acetogenic bacteria.
Highlights
Acetogenic bacteria, or acetogens, are obligate anaerobes converting one‐carbon substrates, such as carbon dioxide, formate, methyl groups, or carbon monoxide into acetate using molecular hydrogen as electron donor through the Wood–Ljungdahl (WL) pathway, a process known as acetogenesis (Ragsdale & Pierce, 2008)
The main potential industrial application of acetogenic bacteria is the production of metabolites that constitute renewable energy sources; such bacteria are of particular interest for this purpose thanks to their low energy requirements for large‐scale cultivation
The analysis of protein networks highlighted the expansion of protein orthologues in A. woodii compared to A. bacchi, whereas protein networks involved in the WL pathway were more con‐ served
Summary
Acetogenic bacteria, or acetogens, are obligate anaerobes converting one‐carbon substrates, such as carbon dioxide, formate, methyl groups, or carbon monoxide into acetate using molecular hydrogen as electron donor through the Wood–Ljungdahl (WL) pathway, a process known as acetogenesis (Ragsdale & Pierce, 2008). The main advantages of the WL pathway include the following: its versatility; it can be cou‐ pled to methanogenesis or to energy conservation via generation of electrochemical gradients; its modularity, since some species utilize partial WL pathways to channel electrons produced during fermen‐ tation to CO2; its flexibility, as several organisms use different coen‐ zymes and/or electron carriers, and in some cases the WL pathway is reversed (e.g., it generates molecular hydrogen and carbon dioxide from acetate for energy production (Schuchmann & Mueller, 2016). Cluster I consists of 7 genes encoding formate dehydrogenase and accessory enzymes catalyzing the reduction of carbon dioxide to for‐ mate. Cluster III encodes the enzymes involved in carbon fixation and production of acetate from acetyl‐CoA (Poehlein et al, 2012). We report new genome sequences of four aceto‐ genic bacteria and perform a comparative genomic analysis focused on the gene clusters and protein networks of the WL pathway
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