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

Abstract

Permafrost contains an estimated 1672 Pg carbon (C),metagenomes converged to be more similar to each other than while they were frozen. We found that multiple genes involved in cycling of C and nitrogen shifted rapidly during thaw. We also constructed the first draft genome from a complex soil metagenome, which corresponded to a novel methanogen. Methane previously accumulated in permafrost was 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.We collected three intact frozen permafrost soil cores with their overlying seasonally thawed active layers from Hess Creek (HC), Alaska. This is a black spruce forest site containing many meters of frozen peat and the C was dated to 1200 ybp 10 .Other soil properties and microbial respiration rates were previously characterized 10 .Frozen active layer and permafrost layer samples from each core were thawed and incubated for 7 days at 5°C under a He headspace. During the incubations, CH 4 ( Fig. 1a) and CO 2 ( Supplementary Fig 1) concentrations were monitored in the headspace and DNA was extracted for 16S ribosomal RNA (rRNA) and metagenome sequencing.There was a burst of CH 4 from the permafrost within 48 h of thaw, followed by a significant (P = 0.05) decrease in concentration from day 2 to day 7 (Fig. 1a). To determine (a) if methane release was due to post-thaw production or from trapped gas, (b)whether the methane was consumed by methanotrophs or anaerobic methane oxidizers, and (c) the CH 4 oxidation potential over time, we treated additional samples with 1500 3 ppm CH 4 and 2-bromoethane sulphonic acid (BES) and measured CH 4 levels daily. BES is an inhibitor of archaeal methanogenesis and methyl-coenzyme M reductase (MCR)-dependent anaerobic methane oxidation. Rapid release of CH 4 from samples treated with BES suggested that the CH 4 primarily originated from gas present in the permafrost prior to thaw ( Supplementary Fig. 2), as previously reported 11 . Subsequent CH 4 consumption in both BES and non-BES-treated samples was indicative of CH 4 oxidation by methanotrophic bacteria (Fig. 1b). The oxygen utilized for methane oxidation presumably originated from permafrost water or aerobic microsites in the samples 12 . Together these data indicate CH 4 levels are dynamic in thawing permafrost.To determine the phylogenetic and functional gene repertoire before and after thaw, we performed deep metagenome sequencing of samples from two of the three replicate cores (cores 1 and 2). DNA was extracted from frozen active layer and permafrost samples and from samples thawed at 5°C for 2 and 7 days. This resulted in 12 samples for metagenome sequencing.Due to low DNA yield we used emulsion PCR (emPCR) to generate random shotgun short insert libraries with minimum amplification bias 13 . Sequencing yielded a total of 176 million reads and 39.8 Gb of raw sequence. The individual metagenome reads were annotated by comparison to protein-coding...

Denitrification Potential and Denitrifier Abundance in Downstream of Dams in Temperate Streams

“…Because the majority of microorganisms in the environment are highly divergent from those of most cultured organisms, the employment of emerging "omics" approaches along with advanced analytical chemistry provides new opportunities to bridge the knowledge gap across scales and to link microbial functions with biogeochemical cycles (Lin et al, 2014). Recently, several metagenomic studies could provide insights into changes of genes associated with metabolic potentials for C and N cycling in response to environmental change (Mackelprang et al, 2011;Fierer et al, 2012). A more comprehensive and complete inventory of microbial genes in soils or sediments is desired by taking advantage of pyrosequencing technique in metagenomic approach (Smith and Osborn, 2009;Myrold et al, 2013).…”

Recruiting Environmental Genomes from Metagenomes

“…As the microbiota of the acid mine drainage was inhabited by only one or two naturally selected microbial groups extensive genome assembly was possible with their accurate taxonomical assignments. Where as in Permafrost analysis [5] a draft genome assembly of a previously unknown methanotroph was obtained using De-Brujin based algorithm and single copy (total 19 genes) gene based validation. Total metagenomic data (pre-processed) was assembled on 41 K-mer length and contigs were taxonomically characterized (at various ranks) using MEGAN [2].…”

Diversity and abundance of microbial eukaryotes in stream sediments from Svalbard

“…Anesio and Laybourn-Parry 2012;Hamilton et al 2013;Jansson and Taş 2014) whose compositions and associated activities are susceptible to external physical and chemical change, for example, permafrost thaw (e.g. Mackelprang et al 2011;Liebner et al 2015). In addition, these microbial communities have been shown to play key roles in biogeochemical cycles, in particular the carbon cycle (McCalley et al 2014).…”

“…Boyd et al 2011;Mackelprang et al 2011;Tveit et al 2013), hydrogen cycling (Telling et al 2015, sulphur cycling (Harrold et al 2016) and carbon cycling (e.g. Boyd et al 2010Boyd et al , 2014Mackelprang et al 2011;Tveit et al 2013). However, there have been comparatively fewer studies conducted on microbial eukaryotes in cold, highlatitude ecosystems despite the potentially important role that they have in nutrient cycling in these environments.…”

“…Skidmore et al 2005;Boyd et al 2014;Hindshaw et al 2016a), nitrogen cycling (e.g. Boyd et al 2011;Mackelprang et al 2011;Tveit et al 2013), hydrogen cycling (Telling et al 2015, sulphur cycling (Harrold et al 2016) and carbon cycling (e.g. Boyd et al 2010Boyd et al , 2014Mackelprang et al 2011;Tveit et al 2013).…”