Journal
MICROORGANISMS
Volume 10, Issue 5, Pages -Publisher
MDPI
DOI: 10.3390/microorganisms10050955
Keywords
methanotroph; glyoxylate shunt; paddy soil; metagenome-assembled genome; pmoA
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Funding
- National Science Foundation of China [41877062, 91751204]
- Youth Innovation Promotion Association, CAS [2019311]
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We reconstructed the nearly complete genome of a Beijerinckiaceae methanotroph labeled as MO3_YZ.1 and found its close relationship with MO3 lineage and Methylocapsa based on phylogeny analysis. The MO3_YZ.1 strain has multiple metabolic pathways, including serine cycle for carbon assimilation and glyoxylate shunt for glyoxylate regeneration, as well as the potential ability to utilize acetate.
Although the study of aerobic methane-oxidizing bacteria (MOB, methanotrophs) has been carried out for more than a hundred years, there are many uncultivated methanotrophic lineages whose metabolism is largely unknown. Here, we reconstructed a nearly complete genome of a Beijerinckiaceae methanotroph from the enrichment of paddy soil by using nitrogen-free M2 medium. The methanotroph labeled as MO3_YZ.1 had a size of 3.83 Mb, GC content of 65.6%, and 3442 gene-coding regions. Based on phylogeny of pmoA gene and genome and the genomic average nucleotide identity, we confirmed its affiliation to the MO3 lineage and a close relationship to Methylocapsa. MO3_YZ.1 contained mxaF- and xoxF-type methanol dehydrogenase. MO3_YZ.1 used the serine cycle to assimilate carbon and regenerated glyoxylate through the glyoxylate shunt as it contained isocitrate lyase and complete tricarboxylic acid cycle-coding genes. The ethylmalonyl-CoA pathway and Calvin-Benson-Bassham cycle were incomplete in MO3_YZ.1. Three acetate utilization enzyme-coding genes were identified, suggesting its potential ability to utilize acetate. The presence of genes for N-2 fixation, sulfur transformation, and poly-beta-hydroxybutyrate synthesis enable its survival in heterogeneous habitats with fluctuating supplies of carbon, nitrogen, and sulfur.
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