Methanotrophs and methanogens are differently affected by small-scale heterogeneities in transiently flooded kettle holes

Kettle holes are small depressions, frequently surrounded by agricultural fields and often classified as wetlands. Kettle holes can emit substantial amounts of the greenhouse gas methane and may contribute markedly to methane budgets at the landscape scale. Yet, their actual methane emissions are difficult to predict, as they are shaped by large spatial heterogeneities and fluctuating water tables, which likely impact methane-producing and -consuming microorganisms. To understand the relevance of spatial heterogeneities as determinants for methane cycling communities, we analyzed their abundance and community structure in three kettle holes, covering variation in soil horizon structure and inundation history. Abundance patterns of aerobic methanotrophs varied with pedogenesis above the peat horizons. Abundances of anaerobic methanotroph Ca . Methanoperedens were increased in peat, though this varied by kettle hole. Methanogen abundances were increased in the upper buried peat and correlated with plant cover. Besides the parameter kettle hole, soil horizon explained significant variation in the community structures of prokaryotes (R 2 = 0.274), methanogens (R 2 = 0.301) and methanotrophs (R 2 = 0.192), while sampling site explained more variance for methanotrophs (R 2 = 0.237; all p = 0.001). Reflecting this variability, no methanotrophic genus was differentially abundant between the horizons. Methanogenic genera associated with oxygen tolerance ( Methanosarcina, Methanobacterium ) were dominant especially in surface-near horizons. Our results indicate that abundance patterns of methanogens, aerobic and anaerobic methanotrophs and thus the potential for methane production and consumption cannot be generalized across kettle holes based on easily observable features (e.g. hydrogeomorphic type, horizon composition), but that their community structures vary with the small-scale heterogeneities within kettle holes.