Large‐scale biogeography and environmental regulation of methanotrophic bacteria across boreal inland waters

Abstract

Aerobic methanotrophic bacteria (methanotrophs) use methane as a source of carbon and energy, thereby mitigating net methane emissions from natural sources. Methanotrophs represent a widespread and phylogenetically complex guild, yet the biogeography of this functional group and the factors that explain the taxonomic structure of the methanotrophic assemblage are still poorly understood. Here, we used high‐throughput sequencing of the 16S rRNA gene of the bacterial community to study the methanotrophic community composition and the environmental factors that influence their distribution and relative abundance in a wide range of freshwater habitats, including lakes, streams and rivers across the boreal landscape. Within one region, soil and soil water samples were additionally taken from the surrounding watersheds in order to cover the full terrestrial–aquatic continuum. The composition of methanotrophic communities across the boreal landscape showed only a modest degree of regional differentiation but a strong structuring along the hydrologic continuum from soil to lake communities, regardless of regions. This pattern along the hydrologic continuum was mostly explained by a clear niche differentiation between type I and type II methanotrophs along environmental gradients in pH, and methane concentrations. Our results suggest very different roles of type I and type II methanotrophs within inland waters, the latter likely having a terrestrial source and reflecting passive transport and dilution along the aquatic networks, but this is an unresolved issue that requires further investigation.

Efficiency of crustacean zooplankton in transferring allochthonous carbon in a boreal lake

“…As Lake Simoncouche is shallow and well oxygenated, anaerobic metabolism is likely limited compared to aerobic metabolism. Moreover, Crevecoeur et al (2019) recently showed that methanotrophs on the surface waters only constitute for about 0.1% of the bacterial community in Quebec lakes. Because of the depleted 13 C values of methane (about À70&), zooplankton biomass found with methane contribution in a boreal lake has consequently very depleted 13 C values (about À50&; Kankaala et al 2006).…”

Candidatus Methylumidiphilus Drives Peaks in Methanotrophic Relative Abundance in Stratified Lakes and Ponds Across Northern Landscapes

“…However, the impact of those environmental parameters on the methanotrophic communities is still unclear and often seems contradictory (Ho et al, 2013). Furthermore, most studies on freshwater MO neglect the potential importance of anaerobic MO and Verrucomicrobia as they are less abundant (Ho et al, 2013;Knief, 2015;Crevecoeur et al, 2017Crevecoeur et al, , 2019Reis et al, 2020). As the role of rare microorganisms is still poorly understood (Galand et al, 2009), there is a pressing need to include those into the analyses for a complete understanding of the functioning and interactions in the methanotrophic community.…”

“…Rare taxa can also serve as a seed for when conditions change (Graf et al, 2018;Mayr et al, 2020b) and should therefore be considered. Also, methodological issues should be taken into account as most previous studies on methanotrophs have been done using PCR-based methods looking into the diversity of 16S rRNA or pmoA genes (Crevecoeur et al, 2017(Crevecoeur et al, , 2019Rissanen et al, 2018;Mayr et al, 2020c). While being a well-established method in microbial ecology, it introduces biases to the data, especially in primer mismatches and problems related to coverage of especially new and poorly known taxa (Bourne et al, 2001;Wang et al, 2017).…”

“…Studies looking into the ecology of methanotrophs using shotgun metagenomics are still rare (Rissanen et al, 2018;Mayr et al, 2020b). Last but not least, all known previous studies focus on one or a small number of lakes in a limited geographic area (Tsutsumi et al, 2011;Crevecoeur et al, 2017;Oswald et al, 2017;Samad and Bertilsson, 2017;Graf et al, 2018;Mayr et al, 2020c;Rissanen et al, 2020) or look only at the top layer of the studied water bodies (Crevecoeur et al, 2019), restraining the identification of factors that could be used for global estimations of the abundance and distribution of methanotrophs.…”

Abundance and biogeography of methanogenic and methanotrophic microorganisms across European streams

“…Aerobic MOX, often inhabiting anoxic–oxic interfaces such as the upper sediment layers, are known to support a high potential for CH 4 oxidation in riverbeds (Trimmer et al., 2015). Furthermore, a large‐scale study on methanotrophic communities in boreal inland waters in Canada highlighted a clear niche differentiation between type I and type II methanotrophs in water and river sediments (Crevecoeur et al., 2019). Besides these works on specific groups, however, the taxonomic composition/distribution of both, methanogens and methanotrophs and the respective predominant key players in different streams across ecoregions have not yet been examined.…”