Codh/Acs-Deficient Methanogens Are Prevalent in Anaerobic Digesters

Abstract

Methanogens are archaea that grow by producing methane as a catabolic end product and thrive in diverse anaerobic habitats, including soil, sediments, oil reservoirs, digestive tracts, and anaerobic digesters. Methanogens have typically been classified into three types—namely, hydrogenotrophic, acetoclastic, and methylotrophic methanogens. In addition, studies have found methanogens that require both hydrogen/CO2 and organics, such as acetate, for growth. Genomic analyses have shown that these methanogens lack genes for carbon monoxide dehydrogenase/acetyl-CoA synthase (Codh/Acs), one of the oldest enzymes that catalyzes the central step in the Wood–Ljungdahl pathway. Since these methanogens have been found dominant in such habitats as digestive tracts and anaerobic digesters, it is suggested that the loss of Codh/Acs confers ecological advantages on methanogens in these habitats. Comparisons in genomes of methanogens suggest the possibility that these methanogens have emerged recently in anaerobic digesters and are currently under the process of prevalence. We propose that an understanding of the genetic and ecological processes associated with the emergence and prevalence of these methanogens in anaerobic digesters would offer novel evolutionary insights into microbial ecology.

Current status of carbon monoxide dehydrogenases (CODH) and their potential for electrochemical applications

“…CO 2 can then be converted into formyl-methanofuran to enter the pathway for CH 4 production. In addition, CO 2 can be used for carbon assimilation directly by bifunctional CODH/ACS complexes or coming from methylene–tetrahydromethanopterin (Nagoya et al 2021 ). These reactions are fueled by electrons, which are generated via H 2 oxidation.…”

“…These reactions are fueled by electrons, which are generated via H 2 oxidation. This H 2 oxidation can be carried out by various hydrogenases, including membrane-bound EcH, F 420 -non-reducing hydrogenases, cytoplasmatic F 420 -reducing hydrogenases as well as cytochrome-b-containing heterodisulfide reductases (Schöne and Rother 2018 ; Nagoya et al 2021 ). Finally, ATP is generated by either a H + or Na + translocating ATPase, where Na + is provided by the membrane-bound methyl-H4MPT:coenzyme M methyltransferase.…”

“…This process is also described as fermentation, since acetate is cleaved and methyl groups are reduced to methane with electrons derived from the oxidation of the carbonyl group to CO 2 . The cleavage of the activated acetate is performed by phosphotransacetylase and acetate kinase, while a bifunctional CODH/ACS complex (Lyu et al 2018 ; Nagoya et al 2021 ) subsequently converts acetyl-CoA into CO, methyl-group and coenzyme A. Later, CODH/ACS then oxidizes this CO to CO 2 .…”

Methanolobususe unspecific methyltransferases to produce methane from dimethylsulfide

“…All genes except for acs were expressed at <0.1%, while acs was expressed at 4.9% (Supplementary Figure 7a). It should, however, be kept in mind that methylotrophic methanogens also possess the acs gene 55 .…”

Microbial Genetics and Evolution

“…The observed patchy distribution of this gene suggested a possible loss of this gene during the evolution of several bacterial phyla and/or an ancient horizontal transfer [ 13 ]. Comparative genome analyses have also been performed to better characterize microorganisms belonging to the bacterial Aminobacter genus [ 14 ], Vibrio parahaemolyticus isolates from seafood [ 15 ], and methanogenic archaea [ 16 ]. Different genetic markers have been used to assess their phylogeny, e.g., clustered regularly interspaced short palindromic repeats (CRISPR), 16S rRNA genes, or the whole genome.…”