Comparative Omics Along a Thaw Gradient of Alaskan Permafrost – Implications to Climate Change.

The fate of organic carbon reserves sequestered in permafrost is uncertain yet critically important for addressing terrestrial feedbacks to climate change. With warming there is an increased probability of thermokarst formation, and an increase in CO2 and CH4 flux to the atmosphere. However, we understand little of the underlying microbial controls on nitrogen or carbon cycling in permafrost soils. We applied a variety of “omics” methods to study microbial communities, their functions and activity in permafrost soils collected from two sites in Alaska: a stable, low productivity black spruce forest, and a thermokarst bog at the Bonanza Creek LTER Station outside of Fairbanks. Permafrost samples were taken from both the active and the permafrost layers. Our aim was to understand microbial functions in the longer-term thaw processes that are ongoing in the arctic. In total, over 170,000 pyrotags were sequenced and >40 Gb of shotgun metagenome data was obtained. Additionally, shotgun metatranscriptomic and metaproteome approaches were used to examine expression patterns in the different samples. The pyrotag results indicated that the bacterial communities in the permafrost and bog samples were more similar to each other than to the active layer. The bog samples had a different archaeal community compared to the other sample types, with a predominance of methanogens. This is consistent with the bog environment being an area of high CH4 production. An uncultured representative of the Chloroflexi phylum was found to be cosmopolitan and highly abundant (up to 15% of total pyrotag reads) in all sites. When looking at the metagenome gene content, bog and permafrost samples were more similar. There were more differences between the replicate cores in bog than in permafrost and active layers, indicative of greater functional differences in the bog site. We binned the metagenomic contigs based on tetranucelotide frequency, and taxonomic assignment of the largest bins were to uncultured Deltaproteobacteria and Actinobacteria. Microbes from these groups were also found to be active based on the metatranscriptomic sequencing. Metaproteomes were analyzed from 6 samples resulting in close to 800 protein IDs in active layer samples and 450 in permafrost. Analysis of the metaproteomes revealed methanogenesis to be occurring in thermokarst bog, and methane to be actively oxidized in the active layer. In the permafrost samples (depth 70 cm) the expressed proteins were involved in membrane transport and sugar transport. Overall we found that permafrost soils harbor unique microbial communities that do not contain the diversity of archaea present in thermokarst bogs. Therefore important shifts in community composition occur following thaw and before the initiation of methane production.