Identification of the dominant methanotrophs in trichloroethene degrading enrichment cultures from multiple sources

The current study examined the potential of bioremediation to clean up trichloroethene (TCE) contaminated sites using co-metabolic TCE biodegradation in methanotrophic enrichment cultures. Methanotrophic cultures were developed from both uncontaminated soils (agricultural soils) and impacted sediment from two sites. Following the enrichment of methanotrophs, the cultures were tested for their ability to degrade TCE. Whole genome sequencing data indicated the dominance of the genus Methylocystis and, to a lesser extent, the genera Methylobacter and Methylomicrobium. Fourteen Methylocystis, Methylobacter and Methylomicrobium metagenome assembled genomes (MAGs) were obtained. Twelve particulate methane monooxygenase operons (pmoCAB) were also obtained. The collected operons contained sequences similar to those classifying within the genera Methylocystis, Methylobacter and Methylomicrobium phylotypes. Three operons (mmoXYBZDC) were obtained for soluble methane monooxygenase, with mmoX classifying most closely to other Methylocystis mmoX genes. The newly obtained sequences were compared to commonly used primers for the biomarkers pmoA (A189f and mb661r) and mmoX (536 f and 898r). In summary, TCE degrading methanotrophic cultures were easily developed from both uncontaminated soils and impacted sediments and whole genome sequencing data indicated the importance of the genus Methylocystis across many of the methanotrophic enrichments.