Multi-scale phylogenetic heterogeneity of archaea, bacteria, methanogens and methanotrophs in lake sediments

Understanding spatial microbial community variation is necessary to assess diversity patterns. In this study, we investigated spatial heterogeneity and variability of functional and total microbial benthic community structures in Lake Bourget, France. Community structure variability was determined vertically by comparing three sediment layers per core, and horizontally at the intra-site level (between up to three cores per sites) and between three sites. Bacterial, archaeal, methanotrophs and methanogens community structures were assessed by genotyping the 16S rRNA-23S rRNA intergenic spacer, 16S rRNA, pmoA and mcrA genes, respectively. The consequence of pooling DNA extracts before genotyping was tested. After pooling, the OTU number decreased for all communities, but it had no effect on structure. At the core scale, bacterial community structure significantly differed between the sediment layers, but archaeal, methanogens and methanotrophs community structures only differed significantly between the superficial and deeper layers. Changes in environmental conditions affected microbial community structures between sites (sediment carbonates, total carbon contents, median particle sizes, and water O-2 saturation), but not intra-site, as no significant changes were observed at the horizontal scale. These spatial scales should be considered to understand their importance for biogeochemical cycle when assessing benthic microbial community structure and diversity in lakes.