Microorganisms and electron acceptors affecting methane oxidation in freshwater and marine systems

Abstract

Methane is a potent greenhouse gas and one of the major contributors to global warming. Aquatic systems, both marine and freshwater, contribute to methane emissions, as methane is produced in anoxic sediments. Methane consumption, which can decrease methane emissions, can take place in both oxic and anoxic environments, and is performed by methane oxidizing archaea or bacteria, called methanotrophs. As methane consumption proceeds via a redox reaction – methane oxidation coupled to the reduction of another compound – the availability of suitable electron acceptors has a large impact on the methane removal rates. When considering relevant electron acceptors for methane oxidation, it is, however, important to know which methanotrophs are present in the system, and which electron acceptors they are capable of using. In this thesis, methane oxidizing bacteria are studied in the eutrophic, temperate zone Lacamas Lake (WA, US). Incubation experiments showed enhanced methane oxidation rates after nitrate or sulfate were added to anoxic water column samples. Genomic analysis showed, however, that no complete denitrification pathway was present in the dominant methanotroph, a Methylobacter species. Enrichment culturing and laboratory incubation experiments were performed to further unravel the interaction between methane oxidation and nitrate. One non-methanotrophic species, belonging to the genus Methylotenera, was discovered to be highly abundant. Further analysis showed that the genome of this species contained all genes required for denitrification. Stable isotope labeling studies showed that methane-derived carbon was incorporated in both Methylobacter and Methylotenera cells, suggesting that the methanotroph Methylobacter produced methane-derived carbon compounds that were used by the non-methanotrophic Methylotenera. This thesis also contains a study on anaerobic methane oxidizing archaea (ANME) of the Black Sea water column. Marine anaerobic methane oxidation (AOM) is generally assumed to be coupled to sulfate reduction, via a consortium of ANME and sulfate reducing bacteria (SRB). ANME-1 are, however, often found as single cells, or only loosely aggregated with SRB, suggesting they perform a form of AOM independent of sulfate reduction. Oxidized metals and humic substances have been suggested as potential electron acceptors for ANME, but up to now, AOM linked to reduction of these compounds has only been shown for the ANME-2 and ANME-3 clades. The Black Sea methanotrophic archaea belong to the ANME-1b clade. Our incubation studies suggest that humic compounds increase methane oxidation rates. Large shifts in the microbial community were observed after the addition of humic substances, opening up the opportunity that partner species may be involved in humic substance stimulated methane oxidation.