PRIMARY RESEARCH PAPER Multi-scale phylogenetic heterogeneity of archaea, bacteria, methanogens and methanotrophs in lake sediments Elodie Billard • Isabelle Domaizon • Nathalie Tissot • Fabien Arnaud • Emilie Lyautey Received: 11 July 2014 / Revised: 5 January 2015 / Accepted: 13 January 2015 / Published online: 1 February 2015 Ó Springer International Publishing Switzerland 2015 Abstract Understanding spatial microbial commu- nity 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. Com- munity 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 commu- nity 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 struc- tures only differed significantly between the superfi- cial 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 satura- tion), 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. Keywords Spatial distribution Á Microbial diversity Á Freshwater sediment Á Methanotrophy Á Methanogenesis Introduction Microorganisms are involved in the different biogeo- chemical cycles due to their metabolic activities (Fenchel et al., 1998; Madsen, 2011). In aquatic ecosystems, the benthic compartment represents a key area where microbes play crucial roles in the global Handling editor: Stefano Amalfitano Electronic supplementary material The online version of this article (doi:10.1007/s10750-015-2184-6) contains supple- mentary material, which is available to authorized users. E. Billard Á N. Tissot Á E. Lyautey Universite ´ de Savoie, CARRTEL, 73000 Chambe ´ry, France I. Domaizon INRA, CARRTEL, 74200 Thonon-les-Bains, France F. Arnaud CNRS, EDYTEM, 73000 Chambe ´ry, France E. Lyautey (&) UMR 42 CARRTEL, Centre de Recherche sur les Re ´seaux Trophiques et Ecosyste `mes Limniques, Universite ´ de Savoie, 73376 Le Bourget du Lac, France e-mail: emilie.lyautey@univ-savoie.fr 123 Hydrobiologia (2015) 751:159–173 DOI 10.1007/s10750-015-2184-6