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...

Over 20% of Earth's terrestrial surface is underlain by permafrost with vast stores of carbon that, once thawed, may represent the largest future transfer of carbon from the biosphere to the atmosphere. This process is largely dependent on microbial responses, but we know little about microbial activity in intact, let alone in thawing, permafrost. Molecular approaches have recently revealed the identities and functional gene composition of microorganisms in some permafrost soils and a rapid shift in functional gene composition during short-term thaw experiments. However, the fate of permafrost carbon depends on climatic, hydrological and microbial responses to thaw at decadal scales. Here we use the combination of several molecular 'omics' approaches to determine the phylogenetic composition of the microbial communities, including several draft genomes of novel species, their functional potential and activity in soils representing different states of thaw: intact permafrost, seasonally thawed active layer and thermokarst bog. The multi-omics strategy reveals a good correlation of process rates to omics data for dominant processes, such as methanogenesis in the bog, as well as novel survival strategies for potentially active microbes in permafrost.

A new functional gene database, FOAM (Functional Ontology Assignments for Metagenomes), was developed to screen environmental metagenomic sequence datasets. FOAM provides a new functional ontology dedicated to classify gene functions relevant to environmental microorganisms based on Hidden Markov Models (HMMs). Sets of aligned protein sequences (i.e. ‘profiles’) were tailored to a large group of target KEGG Orthologs (KOs) from which HMMs were trained. The alignments were checked and curated to make them specific to the targeted KO. Within this process, sequence profiles were enriched with the most abundant sequences available to maximize the yield of accurate classifier models. An associated functional ontology was built to describe the functional groups and hierarchy. FOAM allows the user to select the target search space before HMM-based comparison steps and to easily organize the results into different functional categories and subcategories. FOAM is publicly available at http://portal.nersc.gov/project/m1317/FOAM/.

Salinity is one of the strongest environmental drivers of microbial evolution and community composition. Here we aimed to determine the impact of salt concentrations (2.5, 7.5, and 33.2%) on the microbial community structure of reclaimed saltern ponds near San Francisco, California, and to discover prospective enzymes with potential biotechnological applications. Community compositions were determined by 16S rRNA amplicon sequencing revealing both higher richness and evenness in the pond sediments compared to the water columns. Co-occurrence network analysis additionally uncovered the presence of microbial seed bank communities, potentially primed to respond to rapid changes in salinity. In addition, functional annotation of shotgun metagenomic DNA showed different capabilities if the microbial communities at different salinities for methanogenesis, amino acid metabolism, and carbohydrate-active enzymes. There was an overall shift with increasing salinity in the functional potential for starch degradation, and a decrease in degradation of cellulose and other oligosaccharides. Further, many carbohydrate-active enzymes identified have acidic isoelectric points that have potential biotechnological applications, including deconstruction of biofuel feedstocks under high ionic conditions. Metagenome-assembled genomes (MAGs) of individual halotolerant and halophilic microbes were binned revealing a variety of carbohydrate-degrading potential of individual pond inhabitants.

Summary The bioremediation of chloroethene contaminants in groundwater polluted systems is still a serious environmental challenge. Many previous studies have shown that cooperation of several dechlorinators is crucial for complete dechlorination of trichloroethene to ethene. In the present study, we used an explorative functional DNA microarray (DechloArray) to examine the composition of specific functional genes in groundwater samples in which chloroethene bioremediation was enhanced by delivery of hydrogen‐releasing compounds. Our results demonstrate for the first time that complete biodegradation occurs through spatial and temporal variations of a wide diversity of dehalorespiring populations involving both Sulfurospirillum, Dehalobacter, Desulfitobacterium, Geobacter and Dehalococcoides genera. Sulfurospirillum appears to be the most active in the highly contaminated source zone, while Geobacter was only detected in the slightly contaminated downstream zone. The concomitant detection of both bvcA and vcrA genes suggests that at least two different Dehalococcoides species are probably responsible for the dechlorination of dichloroethenes and vinyl chloride to ethene. These species were not detected on sites where cis‐dichloroethene accumulation was observed. These results support the notion that monitoring dechlorinators by the presence of specific functional biomarkers using a powerful tool such as DechloArray will be useful for surveying the efficiency of bioremediation strategies.