Ecology of the aquatic methane filter: Vertical distribution and temporal dynamics of active methanotroph assemblages in stratified lakes

Abstract

Lakes and impoundments substantially contribute to atmospheric methane concentrations. Methane is responsible for most of the climatic impact of lakes and impoundments due to its high global warming potential. In lacustrine sediments and the anoxic water column methane is produced in large quantities as a final step of organic matter degradation, which is further enhanced by anthropogenic eutrophication of freshwaters. This methane accumulates in oxygen-depleted hypolimnia of stratified lakes, which may reach the atmosphere through different pathways. The major methane sink in the lake are methane-oxidizing bacteria (MOB), which oxidize the methane with oxygen to carbon dioxide. But, most oxygen and methane found in stratified lakes are separated from each other. Oxygen decreases towards the anoxic hypolimnion in which methane starts to increase. Although MOB would be expected to be found directly at the interface of the oxygen and methane reservoirs, MOB are in fact found throughout the water column. This raises the question whether MOB taxa show preferences and adaptations to the different environmental conditions within the counter gradient. Diverse MOB in the water column belonging to distinct phylogenetic groups, mainly Alpha- and Gammaproteobacteria, are generally thought to be responsible for methane oxidation in lakes. A comprehensive knowledge on the ecology of the MOB taxa involved is still missing. Upon autumn lake overturn the methane-rich bottom water is mobilized and transported to the surface layer from where methane may evade into the atmosphere. How much methane outgasses upon autumn overturn is a matter of controversy. The amount of methane outgassing will depend on the response of the MOB assemblage to lake overturn in terms of growth and activity, which remains to be investigated. In future, the number of lakes with methane-rich hypolimnia may increase due to ongoing eutrophication of freshwaters. Therefore, a comprehensive knowledge on the fate of stored methane in permanently and transitionally stratified lakes is paramount. How adaptive MOB are to different environmental conditions is critical for the amount of lacustrine methane reaching the atmosphere. The aim of this thesis was to improve the ecological understanding of the structure and function of the MOB assemblage along the vertical oxygen-methane counter gradient of stratified lakes and the dynamics of the MOB assemblage upon disintegration of the counter gradient during autumn overturn. The vertical distribution of MOB taxa and activity along the oxygen-methane counter gradient were investigated in four eutrophic Swiss lakes (Rotsee, Greifensee, Lake Zug, Lake Lugano). A comprehensive study of the MOB response to autumn overturn and their methane oxidation kinetics was performed in Rotsee. To achieve this, molecular methods, incubations with (radio-) isotopes and physico-chemical measurements were applied. In the present thesis it was shown that the water column of stratified lakes is inhabited by an active MOB assemblage, which changes along the oxygen-methane counter gradient. This indicates specialization within the counter gradient. Further, niche preferences for some common lacustrine MOB taxa were proposed. In conclusion, a structured MOB assemblage presumably based on niche-specific adaptations sustains methane oxidation in the water column. During lake overturn in Rotsee the cooling and expanding mixed layer incorporated methane-rich water from the hypolimnion. This overturn process made oxygen and methane available simultaneously and MOB were able to take advantage and grew to high abundances, thereby oxidizing most of the methane entering the mixed layer. But, the MOB assemblage present during stratification was almost entirely replaced during the autumn overturn. Especially the bottom assemblage was severely reduced. In this chapter is was shown that a new MOB assemblage responded fast enough to lake overturn, which is why most of the mobilized methane was not released to the atmosphere. The same period was tested for differences in methane oxidation kinetics between epi- and hypolimnion, which were found to differ both in space and time. This finding supports the view that ecologically different MOB taxa inhabit the stratified lakes in space and time. High affinity variants of the particulate methane monooxygenase (pMMO) were not detected and the main enzyme transcribed was conventional pMMO. Overall, the results in this thesis suggest that a diverse MOB assemblage, which is spatially and temporally structured, provides an effective methane filter during lake stratification and lake overturn. New insights into the ecology of prevalent and uncultured MOB taxa at a high taxonomic resolution within stratified lakes are given. Many MOB taxa within Gammaproteobacteria, Alphaproteobacteria, and Ca. Methylomirabilis limnetica were detected repeatedly, suggesting that a core set of lacustrine MOB taxa forms the effective methane filter in lakes.