As a result of climate change, large amounts of carbon sequestered in permafrost (~50% of global soil carbon) are becoming available for microbial degradation. One of the primary results of permafrost thaw is the production of the potent greenhouse gas methane, forming a positive feedback to climate change. We used paired meta-omic and geochemical techniques to elucidate tangible links between microbiology and geochemistry along a natural permafrost thaw gradient in northern Sweden.
We analysed ~2 Tbp of shotgun metagenomes from 214 samples taken across the permafrost thaw gradient transitioning through intact palsa, partially thawed sphagnum-dominated bog and fully thawed eriophorum-dominated fen. The samples span several depths from triplicate soil cores taken monthly during the summer thaw over several consecutive years. A comparison of metagenome-derived community profiles with 16S rRNA amplicons revealed strong amplification biases. We developed a new method (SingleM) which uses the nucleotide sequences of ribosomal protein reads to attain community profiles at higher resolution than that provided by 16S rRNA amplicons. The operational taxonomic units (OTUs) recovered de novo can be used as input for ecological diversity measures.
Assembly and genome binning of the metagenomes enabled the recovery of 1,529 high quality population genomes (>70% completeness & <10% contamination), including genomes from three phyla that currently lack sequenced representatives. By linking the SingleM-derived OTU sequences to the recovered genomes, we assessed how representative the recovered population genomes were of these communities. Our results indicate that the majority of these complex microbial communities are represented by at least one population genome within the same genus.
Correlating relative abundances of microbial lineages against paired biogeochemical measurements revealed specific links between geochemistry and microbiology. Relative abundance of the uncharacterised Chloroflexi group 'Ellin6529' correlated with the dissolved CH4:CO2 concentration ratio, a key parameter in global climate models, in the partially thawed bog. Members of the Acidobacteriaceae correlated with the C-isotopic ratio of methane from the same sites and relative abundance of the recently described Archaea Ca. 'Methanoflorens'. We are currently working to understand the metabolism of these lineages by interrogating their genomes.
These genome-centric approaches are furthering our understanding of thawing permafrost communities, allowing us to more fully elucidate the relationships between the geochemistry, microbial ecology and global climate models.
URL: http://ecogenomic.org/melting-permafrost