Journal Article

Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw

Rubin, Edward M., David, Maude M., Mackelprang, Rachel, Chavarria, Krystle L., DeAngelis, Kristen M., Jansson, Janet K., Waldrop, Mark P., Blazewicz, Steven J.

2011

Overview

Permafrost microbes await the thaw Permafrost soil in the Arctic contains a huge reservoir of carbon. If the climate warms and the permafrost thaws, this carbon would become accessible to microbial degradation, releasing greenhouse gases in the process. The microbes responsible for this process are largely unknown. Metagenomic analysis of DNA isolated from two permafrost soils collected in Alaska reveals a rapid microbial response to thawing, with many functional gene abundances increasing. A draft genome of a novel methanogen was constructed from the sequence data. This study highlights the importance of rapid cycling of methane and nitrogen in thawing permafrost. Permafrost contains an estimated 1672 Pg carbon (C), an amount roughly equivalent to the total currently contained within land plants and the atmosphere 1 , 2 , 3 . This reservoir of C is vulnerable to decomposition as rising global temperatures cause the permafrost to thaw 2 . During thaw, trapped organic matter may become more accessible for microbial degradation and result in greenhouse gas emissions 4 , 5 . Despite recent advances in the use of molecular tools to study permafrost microbial communities 6 , 7 , 8 , 9 , their response to thaw remains unclear. Here we use deep metagenomic sequencing to determine the impact of thaw on microbial phylogenetic and functional genes, and relate these data to measurements of methane emissions. Metagenomics, the direct sequencing of DNA from the environment, allows the examination of whole biochemical pathways and associated processes, as opposed to individual pieces of the metabolic puzzle. Our metagenome analyses reveal that during transition from a frozen to a thawed state there are rapid shifts in many microbial, phylogenetic and functional gene abundances and pathways. After one week of incubation at 5 °C, permafrost metagenomes converge to be more similar to each other than while they are frozen. We find that multiple genes involved in cycling of C and nitrogen shift rapidly during thaw. We also construct the first draft genome from a complex soil metagenome, which corresponds to a novel methanogen. Methane previously accumulated in permafrost is released during thaw and subsequently consumed by methanotrophic bacteria. Together these data point towards the importance of rapid cycling of methane and nitrogen in thawing permafrost.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/326/2565/2142 / 631/326/2565/855 / 631/326/47 / 704/172 / Alaska / Analysis / Animal, plant and microbial ecology / Arctic Regions / Bacteria / Bacteria - genetics / Bacteria - isolation & purification / Bacteria - metabolism / Biological and medical sciences / Carbon - metabolism / Carbon Cycle - genetics / Chemical properties / DNA - analysis / DNA - genetics / DNA repair / Emission measurements / Environmental aspects / Freezing / Frozen ground / Fundamental and applied biological sciences. Psychology / Genes, rRNA - genetics / Genetic aspects / Genomes / Global temperatures / Greenhouse gases / Growth / Humanities and Social Sciences / Influence / letter / Metagenome - genetics / Metagenomics / Methane / Methane - metabolism / Methods / Microbial activity / Microbial colonies / Microbial degradation / Microbial ecology / Microbial genetics / Microbiology / multidisciplinary / Nitrogen / Nitrogen - metabolism / Nitrogen Cycle - genetics / Observations / Organic matter / Oxidation-Reduction / Permafrost / Phylogeny / RNA, Ribosomal, 16S - genetics / Science / Soil - chemistry / Soil Microbiology / Temperature / Thawing / Thermal properties / Time Factors / Various environments (extraatmospheric space, air, water)