Distinct depth profile of bacterial and archaeal communities between four Alaskan soil cores

Abstract

Microbial response to permafrost thaw driven by climate warming varies by sites. Although a great deal of environmental heterogeneity is found across permafrost regions, vertical variation of microbial communities in permafrost affected soils is not well understood. Here, we sampled soil cores at four different sites including both continuous and discontinuous permafrost regions in Alaska. Abundance and community structure of soil bacteria and archaea were compared between cores at different depths using MiSeq sequencing and quantitative PCR targeting 16S rRNA gene. Abundance of bacteria and archaea overall changed in a similar way but did not show any directional pattern across depth. Both bacteria and archaeal communities were primarily structured by site difference, followed by depth and soil chemical properties. Interestingly, there were dramatic shifts in bacterial phyla dominance around permafrost table in two permafrost affected soils. Relative abundance of Chloroflexi was reduced to a great extent, while Caldiserica and Firmicutes markedly increased below 58 cm depth in a tussock tundra site. In a Sphagnum-dominated bog site, Verrcomicrobia and Planctomycetes almost disappeared, while Chloroflexi and candidate phylum AD3 dominated below 72 cm depth. These site-specific vertical variations of microbial community structure will be an important resource to predict how soil microbes respond to permafrost thaw.