Methanotrophs enrichments from methanogenic lake sediments

Here, we investigated the diversity and the genomic-based function of aerobic methanotrophs enriched from highly reduced Lake Kinneret sediments. These sediments served as inoculum in two enrichment experiments i) an aerobic enrichment with ambient air, combined with DNA stable isotope probing (DNA-SIP), and ii) a hypoxic enrichment using repeated spiking with 1% oxygen. We explored the genetic mechanisms that may facilitate survival in hypoxic environments predicted by the metagenome-assembled genomes (MAGs) of five LK-enriched Methylococcales and conducted a metabolic comparison with an additional 62 Methylococcales MAGs previously curated from various environments. This comparative analysis suggests the prevalence of various mechanisms to hypoxia across Methylococcales MAGs, including strategies such as high-affinity cytochrome bd, oxygen binding proteins, fermentation-based methane oxidation, motility, glycogen utilization, and alternative electron acceptors. These last ones include the possibility of using nitrate, nitrite, nitrous oxide, and potentially metals and humic substances as electron acceptors through outer membrane multi-heme cytochromes, Type I secretion system, or secretion of Riboflavins. These mechanisms may enable methanotrophs to inhabit ecological niches previously considered unsuitable for their growth.