Multi-scale phylogenetic heterogeneity of archaea, bacteria, methanogens and methanotrophs in lake sediments
Résumé
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 O2 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.