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. 2021 Jul 21;3(7):000244.
doi: 10.1099/acmi.0.000244. eCollection 2021.

Using genome comparisons of wild-type and resistant mutants of Methanococcus maripaludis to help understand mechanisms of resistance to methane inhibitors

Affiliations

Using genome comparisons of wild-type and resistant mutants of Methanococcus maripaludis to help understand mechanisms of resistance to methane inhibitors

Feng Long et al. Access Microbiol. .

Abstract

Methane emissions from enteric fermentation in the ruminant digestive system generated by methanogenic archaea are a significant contributor to anthropogenic greenhouse gas emissions. Additionally, methane produced as an end-product of enteric fermentation is an energy loss from digested feed. To control the methane emissions from ruminants, extensive research in the last decades has been focused on developing viable enteric methane mitigation practices, particularly, using methanogen-specific inhibitors. We report here the utilization of two known inhibitors of methanogenic archaea, neomycin and chloroform, together with a recently identified inhibitor, echinomycin, to produce resistant mutants of Methanococcus maripaludis S2 and S0001. Whole-genome sequencing at high coverage (> 100-fold) was performed subsequently to investigate the potential targets of these inhibitors at the genomic level. Upon analysis of the whole-genome sequencing data, we identified mutations in a number of genetic loci pointing to potential mechanisms of inhibitor action and their underlying mechanisms of resistance.

Keywords: chloroform; echinomycin; methanogen; methanogen-specific inhibitors; neomycin; rumen; whole-genome sequencing.

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Conflict of interest statement

The authors declare that there are no conflicts of interest.

Figures

Fig. 1.
Fig. 1.
Strain tree describing the parental M. maripaludis wild-type strains and the corresponding derived resistant mutant strains used in this study. (a) M. maripaludis wild-type S2 strain A and its derived echinomycin-resistant mutants E25 and E26; M. maripaludis wild-type S2 strain B and its derived neomycin resistant mutants Neo1, Neo2, Neo3 and Neo4, together with its derived chloroform resistant mutants Chl1, Chl2, Chl3 and Chl4; M. maripaludis wildtype S2 strain C is a sub-strain of wild-type S2 strain B. (b) M. maripaludis wild-type S0001 strain A and its derived echinomycin-resistant mutants Ech1, Ech2, Ech3 and Ech4; M. maripaludis wild-type S0001 strain B and C are subculture strains of wild-type S0001 strain A. Numbers under the wild-type strains represents the number of SNPs found in the parental strain when compared to the S2 reference genome. The first number under the resistant mutant strains is the number of SNPs found only in the mutant but not in its parental strain, while the second number is the total number of SNPs found in the mutant strain. S2 reference genome [21] was used for comparison for both results.
Fig. 2.
Fig. 2.
Partial genomic map of the region position 1 158 991 to 1 160 125 presenting variant SNPs of re-sequenced Methanococcus maripaludis wild-type strains S2-A, S2-B, S2-C, S0001-A and S0001-B mapped back to the S2 reference genome. Blue rectangles represent the positions 1 158 991 to 1 160 125 of M. maripaludis S2 genome [53]. Green bars stand for the genes in this region on M. maripaludis S2 genome. Orange bars represent variant SNPs of each strain, they were 13, 73, 31, 1, 1, 1 variant SNPs on MMP1176 from top to bottom, with 88.9−99.1 %, 81.8−99.8 %, 88.1−100 %, 14.7, 19.8, 10  % variant frequency, respectively; and 7, 12, 12, 2, 1,2 variant SNPs on MMP1177 from top to bottom, with 89.5−98.6 %, 99.1−99.8 %, 99.5−100 %, 14.70, 71.4–75.8 %, 19.8, 10, 72.3–74.8 % variant frequency, respectively.

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