Niche partitioning of methane-oxidizing bacteria along the oxygen–methane counter gradient of stratified lakes

• Published in: The ISME Journal Vol. 14; no. 1; pp. 274 - 287
• Main Authors: Mayr, Magdalena J., Zimmermann, Matthias, Guggenheim, Carole, Brand, Andreas, Bürgmann, Helmut
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01-01-2020; Nature Publishing Group
• Subjects: 45/77; 631/326/171/1878; 704/158/855; Bacteria; Biomedical and Life Sciences; Differential distribution; Distribution patterns; Ecology; Ecosystem; Evolutionary Biology; Gammaproteobacteria - isolation & purification; Lakes; Lakes - chemistry; Lakes - microbiology; Life Sciences; Methane; Methane - analysis; Methane - metabolism; Methylococcaceae; Methylococcaceae - genetics; Methylococcaceae - isolation & purification; Methylococcaceae - metabolism; Microbial Ecology; Microbial Genetics and Genomics; Microbiology; Niche overlap; Niches; Oxidation; Oxidation-Reduction; Oxygen; Oxygen - analysis; Phylogeny; Resource consumption; RNA, Ribosomal, 16S - genetics; Vertical distribution; Water column
• ISSN: 1751-7362; 1751-7370
• DOI: 10.1038/s41396-019-0515-8

Lakes are a significant source of atmospheric methane, although methane-oxidizing bacteria consume most methane diffusing upward from anoxic sediments. Diverse methane-oxidizing bacteria form an effective methane filter in the water column of stratified lakes, yet, niche partitioning of different methane-oxidizing bacteria along the oxygen–methane counter gradient remains poorly understood. In our study, we reveal vertical distribution patterns of active methane-oxidizing bacteria along the oxygen–methane counter gradient of four lakes, based on amplicon sequencing analysis of 16S rRNA and
pmoA
genes, and 16S rRNA and
pmoA
transcripts, and potential methane oxidation rates. Differential distribution patterns indicated that ecologically different methane-oxidizing bacteria occupied the methane-deficient and oxygen-deficient part above and below the oxygen–methane interface. The interface sometimes harbored additional taxa. Within the dominant
Methylococcales
, an uncultivated taxon (CABC2E06) occurred mainly under methane-deficient conditions, whereas Crenothrix-related taxa preferred oxygen-deficient conditions.
Candidatus
Methylomirabilis limnetica (NC10 phylum) abundantly populated the oxygen-deficient part in two of four lakes. We reason that the methane filter in lakes is structured and that methane-oxidizing bacteria may rely on niche-specific adaptations for methane oxidation along the oxygen–methane counter gradient. Niche partitioning of methane-oxidizing bacteria might support greater overall resource consumption, contributing to the high effectivity of the lacustrine methane filter.