Characterization and genome analysis of a psychrophilic methanotroph representing a ubiquitous Methylobacter spp. cluster in boreal lake ecosystems

Abstract

Lakes and ponds are considered as a major natural source of CH4 emissions, particularly during the ice-free period in boreal ecosystems. Aerobic methane oxidizing bacteria (MOB), which utilize CH4 using oxygen as an electron acceptor, are one of dominant microorganisms in the CH4-rich water columns. The metagenome-assembled genomes (MAGs) have revealed the genetic potential of MOB from boreal aquatic ecosystems for various microaerobic/anaerobic metabolic functions; however, the experimental validation of the process has not been succeeded. Additionally, psychrophilic (i.e., cold loving) MOB isolates and their CH4 oxidizing process have rarely been investigated. In this study, we isolated, provided taxonomic description, and analyzed the genome of Methylobacter sp. S3L5C, a psychrophilic MOB, from a boreal lake in Finland. Based on phylogenomic comparisons to MAGs, Methylobacter sp. S3L5C represented a ubiquitous cluster of Methylobacter spp. in boreal aquatic ecosystems. At optimal temperatures (3-12 {degrees}C) and pH (6.8-8.3), the specific growth rates () and CH4 utilization rate were in the range of 0.018-0.022 h-1 and 0.66-1.52 mmol l-1 d-1, respectively. In batch cultivation, the isolate could produce organic acids and the concentrations were elevated after replenishing CH4 and air into headspace. The highest concentrations of 4.1 mM acetate, 0.02 mM malate and 0.07 mM propionate were observed at the end of the cultivation period under the optimal operational conditions. The results herein highlight the key role of Methylobacter spp. in regulating CH4 emissions and their potential to provide CH4-derived organic carbon compounds to surrounding heterotrophic microorganisms in cold ecosystems.