Multi-scale phylogenetic heterogeneityof archaea, bacteria, methanogens andmethanotrophs in lake sediments

International audienceUnderstanding spatial microbial communityvariation is necessary to assess diversity patterns.In this study, we investigated spatial heterogeneity andvariability of functional and total microbial benthiccommunity structures in Lake Bourget, France. Communitystructure variability was determined verticallyby comparing three sediment layers per core, andhorizontally at the intra-site level (between up to threecores per sites) and between three sites. Bacterial,archaeal, methanotrophs and methanogens communitystructures were assessed by genotyping the 16SrRNA–23S rRNA intergenic spacer, 16S rRNA, pmoAand mcrA genes, respectively. The consequence ofpooling DNA extracts before genotyping was tested.After pooling, the OTU number decreased for allcommunities, but it had no effect on structure. At thecore scale, bacterial community structure significantlydiffered between the sediment layers, but archaeal,methanogens and methanotrophs community structuresonly differed significantly between the superficialand deeper layers. Changes in environmentalconditions affected microbial community structuresbetween sites (sediment carbonates, total carboncontents, median particle sizes, and water O2 saturation),but not intra-site, as no significant changes wereobserved at the horizontal scale. These spatial scalesshould be considered to understand their importancefor biogeochemical cycle when assessing benthicmicrobial community structure and diversity in lakes