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Summary: Lake methane (CH4) emissions are largely controlled by aerobic methane‐oxidizing bacteria (MOB) which mostly belong to the classes Alpha‐ and Gammaproteobacteria (Alpha‐ and Gamma‐MOB). Despite the known metabolic and ecological differences between the two MOB groups, their main environmental drivers and their relative contribution to CH4 oxidation rates across lakes remain unknown. Here, we quantified the two MOB groups through CARD‐FISH along the water column of six temperate lakes and during incubations in which we measured ambient CH4 oxidation rates. We found a clear niche separation of Alpha‐ and Gamma‐MOB across lake water columns, which is mostly driven by oxygen concentration. Gamma‐MOB appears to dominate methanotrophy throughout the water column, but Alpha‐MOB may also be an important player particularly in well‐oxygenated bottom waters. The inclusion of Gamma‐MOB cell abundance improved environmental models of CH4 oxidation rate, explaining part of the variation that could not be explained by environmental factors alone. Altogether, our results show that MOB composition is linked to CH4 oxidation rates in lakes and that information on the MOB community can help predict CH4 oxidation rates and thus emissions from lakes. [ABSTRACT FROM AUTHOR]

Catalysed reporter deposition-fluorescence in situ hybridization ( CARD-FISH) is a powerful approach to quantify bacterial taxa. In this study, we compare the performance of the widely used B acteroidetes CF319 a probe with the new CF968 probe. In silico analyses and tests with isolates demonstrate that CF319 a hybridizes with non- B acteroidetes sequences from the R hodobacteraceae and A lteromonadaceae families. We test the probes' accuracy in 37 globally distributed marine samples and over two consecutive years at the Blanes Bay Microbial Observatory ( NW Mediterranean). We also compared the CARD-FISH data with the B acteroidetes 16 S rRNA gene sequences retrieved from 27 marine metagenomes from the TARA Oceans expedition. We find no significant differences in abundances between both approaches, although CF319 a targeted some unspecific sequences and both probes displayed different abundances of specific B acteroidetes phylotypes. Our results demonstrate that quantitative estimations by using both probes are significantly different in certain oceanographic regions ( Mediterranean Sea, Red Sea and Arabian Sea) and that CF968 shows seasonality within marine B acteroidetes, notably large differences between summer and winter that is overlooked by CF319 a. We propose CF968 as an alternative to CF319 a for targeting the whole B acteroidetes phylum since it has better coverage, greater specificity and overall better quantifies marine B acteroidetes. [ABSTRACT FROM AUTHOR]