Publications

Here you can view and download data generated from the IsoGenie project, organized by manuscript.

Anthony, K. W., Daanen, R., Anthony, P., von Deimling, T. S., Ping, C.-L., Chanton, J. P., & Grosse,G. (2016). Methane emissions proportional to permafrost carbon thawed in Arctic lakes since the 1950s. Nature Geoscience, Advance online publication. doi:10.1038/ngeo2795

Permafrost thaw exposes previously frozen soil organic matter to microbial decomposition. This process generates methane and carbon dioxide, and thereby fuels a positive feedback process that leads to further warming and thaw1. Despite widespread permafrost degradation during the past ~40 years, the degree to which permafrost thaw may be contributing to a feedback between warming and thaw in recent decades is not well understood. Radiocarbon evidence of modern emissions of ancient permafrost carbon is also sparse5. Here we combine radiocarbon dating of lake bubble trace-gas methane (113 measurements) and soil organic carbon (289 measurements) for lakes in Alaska, Canada, Sweden and Siberia with numerical modelling of thaw and remote sensing of thermokarst shore expansion. Methane emissions from thermokarst areas of lakes that have expanded over the past 60  years were directly proportional to the mass of soil carbon inputs to the lakes from the erosion of thawing permafrost. Radiocarbon dating indicates that methane age from lakes is nearly identical to the age of permafrost soil carbon thawing around them. Based on this evidence of landscape-scale permafrost carbon feedback, we estimate that 0.2 to 2.5 Pg permafrost carbon was released as methane and carbon dioxide in thermokarst expansion zones of pan-Arctic lakes during the past 60 years.

Hodgkins, S. B., Tfaily, M. M., Podgorski, D. C., McCalley, C. K., Saleska, S. R., Crill, P. M. Cooper, W. T. (2016). Elemental composition and optical properties reveal changes in dissolved organic matter along a permafrost thaw chronosequence in a subarctic peatland. Geochimica et Cosmochimica Acta, 187, 123–140.

The fate of carbon stored in permafrost-zone peatlands represents a significant uncertainty in global climate modeling. Given that the breakdown of dissolved organic matter (DOM) is often a major pathway for decomposition in peatlands, knowledge of DOM reactivity under different permafrost regimes is critical for determining future climate feedbacks. To explore the effects of permafrost thaw and resultant plant succession on DOM reactivity, we used a combination of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), UV/Vis absorbance, and excitation-emission matrix spectroscopy (EEMS) to examine the DOM elemental composition and optical properties of 27 pore water samples gathered from various sites along a permafrost thaw sequence in Stordalen Mire, a thawing subarctic peatland in northern Sweden. The presence of dense Sphagnum moss, a feature that is dominant in the intermediate thaw stages, appeared to be the main driver of variation in DOM elemental composition and optical properties at Stordalen. Specifically, DOM from sites with Sphagnum had greater aromaticity, higher average molecular weights, and greater O/C, consistent with a higher abundance of phenolic compounds that likely inhibit decomposition. These compounds are released by Sphagnum and may accumulate due to inhibition of phenol oxidase activity by the acidic pH at these sites. In contrast, sites without Sphagnum, specifically fully-thawed rich fens, had more saturated, more reduced compounds, which were high in N and S. Optical properties at rich fens indicated the presence of microbially-derived DOM, consistent with the higher decomposition rates previously measured at these sites. These results indicate that Sphagnum acts as an inhibitor of rapid decomposition and CH4 release in thawing subarctic peatlands, consistent with lower rates of CO2 and CH4 production previously observed at these sites. However, this inhibitory effect may disappear if Sphagnum-dominated bogs transition to more waterlogged rich fens that contain very little to no living Sphagnum. Release of this inhibition allows for higher levels of microbial activity and potentially greater CH4 release, as has been observed in these fen sites

Bolduc, B., Youens-Clark, K., Roux, S., Hurwitz, B. L., & Sullivan, M. B. (2016). iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure. The ISME Journal. Advance online publication 15 July 2016. doi: 10.1038/ismej.2016.89

Microbes affect nutrient and energy transformations throughout the world’s ecosystems, yet they do so under viral constraints. In complex communities, viral metagenome (virome) sequencing is transforming our ability to quantify viral diversity and impacts. Although some bottlenecks, for example, few reference genomes and nonquantitative viromics, have been overcome, the void of centralized data sets and specialized tools now prevents viromics from being broadly applied to answer fundamental ecological questions. Here we present iVirus, a community resource that leverages the CyVerse cyberinfrastructure to provide access to viromic tools and data sets. The iVirus Data Commons contains both raw and processed data from 1866 samples and 73 projects derived from global ocean expeditions, as well as existing and legacy public repositories. Through the CyVerse Discovery Environment, users can interrogate these data sets using existing analytical tools (software applications known as ‘Apps’) for assembly, open reading frame prediction and annotation, as well as several new Apps specifically developed for analyzing viromes. Because Apps are web based and powered by CyVerse supercomputing resources, they enable scalable analyses for a broad user base. Finally, a use-case scenario documents how to apply these advances toward new data. This growing iVirus resource should help researchers utilize viromics as yet another tool to elucidate viral roles in nature.

Rinke C, Low S, Woodcroft BJ, Raina J, Skarshewski A, Le XH, Butler MK, Stocker R, Seymour J, Tyson GW, Hugenholtz P. (2016) Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics. PeerJ 4:e2486

High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. Here we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diverse Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (∼100–1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics.

Trubl, G., Solonenko, N., Chittick, L., Solonenko, S. A., Rich, V. I., & Sullivan, M. B. (2016). Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient. PeerJ, 4, e1999.

Permafrost stores approximately 50% of global soil carbon (C) in a frozen form; it is thawing rapidly under climate change, and little is known about viral communities in these soils or their roles in C cycling. In permafrost soils, microorganisms contribute significantly to C cycling, and characterizing them has recently been shown to improve prediction of ecosystem function. In other ecosystems, viruses have broad ecosystem and community impacts ranging from host cell mortality and organic matter cycling to horizontal gene transfer and reprogramming of core microbial metabolisms. Here we developed an optimized protocol to extract viruses from three types of high organic-matter peatland soils across a permafrost thaw gradient (palsa, moss-dominated bog, and sedge-dominated fen). Three separate experiments were used to evaluate the impact of chemical buffers, physical dispersion, storage conditions, and concentration and purification methods on viral yields. The most successful protocol, amended potassium citrate buffer with bead-beating or vortexing and BSA, yielded on average as much as 2-fold more virus-like particles (VLPs) g−1 of soil than other methods tested. All method combinations yielded VLPs g−1 of soil on the 108 order of magnitude across all three soil types. The different storage and concentration methods did not yield significantly more VLPs g−1 of soil among the soil types. This research provides much-needed guidelines for resuspending viruses from soils, specifically carbon-rich soils, paving the way for incorporating viruses into soil ecology studies.

Woodcroft BJ, Boyd, J, Tyson GW. 2016 OrfM: A fast open reading frame predictor for metagenomic data. Bioinformatics. May 3, 2016

Finding and translating stretches of DNA lacking stop codons is a task common in the analysis of sequence data. However, the computational tools for finding open reading frames are sufficiently slow that they are becoming a bottleneck as the volume of sequence data grows. This computational bottleneck is especially problematic in metagenomics when searching unassembled reads, or screening assembled contigs for genes of interest. Here, we present OrfM, a tool to rapidly identify open reading frames (ORFs) in sequence data by applying the Aho–Corasick algorithm to find regions uninterrupted by stop codons. Benchmarking revealed that OrfM finds identical ORFs to similar tools (‘GetOrf’ and ‘Translate’) but is four-five times faster. While OrfM is sequencing platform-agnostic, it is best suited to large, high quality datasets such as those produced by Illumina sequencers.

Deng J., Li C., and Frolking S. 2015. Modeling impacts of changes in temperature and water table on C gas fluxes in an alaskan peatland. Journal of Geophysical Research: Biogeosciences. 120 (7): 1279-1295.

Northern peatlands have accumulated a large amount of organic carbon (C) in their thick peat profile. Climate change and associated variations in soil environments are expected to have significant impacts on the C balance of these ecosystems, but the magnitude is still highly uncertain. Verifying and understanding the influences of changes in environmental factors on C gas fluxes in biogeochemical models are essential for forecasting feedbacks between C gas fluxes and climate change. In this study, we applied a biogeochemical model, DeNitrification-DeComposition (DNDC), to assess impacts of air temperature (TA) and water table (WT) on C gas fluxes in an Alaskan peatland. DNDC was validated against field measurements of net ecosystem exchange of CO2 (NEE) and CH4 fluxes under manipulated surface soil temperature and WT conditions in a moderate rich fen. The validation demonstrates that DNDC was able to capture the observed impacts of the manipulations in soil environments on C gas fluxes. To investigate responses of C gas fluxes to changes in TA and soil water condition, we conducted a series of simulations with varying TA and WT. The results demonstrate that (1) uptake rates of CO2 at the site were reduced by either too colder or warmer temperatures and generally increased with increasing soil moisture; (2) CH4 emissions showed an increasing trend as TA increased or WT rose toward the peat surface; and (3) the site could shift from a net greenhouse gas (GHG) sink into a net GHG source under some warm and/or dry conditions. A sensitivity analysis evaluated the relative importance of TA and WT to C gas fluxes. The results indicate that both TA and WT played important roles in regulating NEE and CH4 emissions and that within the investigated ranges of the variations in TA and WT, changes in WT showed a greater impact than changes in TA on NEE, CH4 fluxes, and net C gas fluxes at the study fen.

Hodgkins SB, Chanton JP, Langford LC, McCalley CK, Saleska SR, Rich VI, Crill PM, Cooper WT. 2015. Soil incubations reproduce field methane dynamics in a subarctic wetland. Biogeochemistry. 126: 241-249

A major challenge in peatland carbon cycle modeling is the estimation of subsurface methane (CH4) and carbon dioxide (CO2) production and consumption rates and pathways. The most common methods for modeling these processes are soil incubations and stable isotope modeling, both of which may involve departures from field conditions. To explore the impacts of these departures, we measured CH4/CO2 concentration ratios and 13C fractionation factors (aC, indicating CH4 production pathways) in field pore water from a thawing subarctic peatland, and compared these values to those observed in incubations of corresponding peat samples. Incubations bation CH4/CO2 production ratios were significantly and positively correlated with observed field CH4/CO2 concentration ratios, though observed field ratios were ~20 % of those in incubations due to CH4’s lower solubility in pore water. After correcting the field ratios for CH4 loss with an isotope mass balance model, the incubation CH4/CO2 ratios and aC were both significantly positively correlated with field ratios and aC (respectively), both with slopes indistinguishable from 1. Although CH4/CO2 ratios and aC were slightly higher in the incubations, these shifts were consistent along the thaw progression, indicating that ex situ incubations can replicate trends in in situ CH4 production.

Kao-Kniffin, J., Woodcroft, B. J., Carver, S. M., Bockheim, J. G., Handelsman, J., Tyson, G. W., … Mueller, C. W. (2015). Archaeal and bacterial communities across a chronosequence of drained lake basins in Arctic Alaska. Scientific Reports, 5, 18165.

We examined patterns in soil microbial community composition across a successional gradient of drained lake basins in the Arctic Coastal Plain. Analysis of 16S rRNA gene sequences revealed that methanogens closely related to Candidatus ‘Methanoflorens stordalenmirensis’ were the dominant archaea, comprising >50% of the total archaea at most sites, with particularly high levels in the oldest basins and in the top 57 cm of soil (active and transition layers). Bacterial community composition was more diverse, with lineages from OP11, Actinobacteria, Bacteroidetes, and Proteobacteria found in high relative abundance across all sites. Notably, microbial composition appeared to converge in the active layer, but transition and permafrost layer communities across the sites were significantly different to one another. Microbial biomass using fatty acid-based analysis indicated that the youngest basins had increased abundances of gram-positive bacteria and saprotrophic fungi at higher soil organic carbon levels, while the oldest basins displayed an increase in only the gram-positive bacteria. While this study showed differences in microbial populations across the sites relevant to basin age, the dominance of Candidatus ‘M. stordalenmirensis’ across the chronosequence indicates the potential for changes in local carbon cycling, depending on how these methanogens and associated microbial communities respond to warming temperatures.

Tfaily, M. M., Corbett, J. E., & Wilson, R. (2015). Utilization of PARAFAC‐Modeled Excitation‐Emission Matrix (EEM) Fluorescence Spectroscopy to Identify Biogeochemical Processing of Dissolved Organic Matter in a Northern Peatland. Photochemistry and Photobiology, 91(3), 684-695.

In this study, we contrast the fluorescent properties of dissolved organic matter (DOM) in fens and bogs in a Northern Minnesota peatland using excitation emission matrix fluorescence spectroscopy with parallel factor analysis (EEM-PARAFAC). EEM-PARAFAC identified four humic-like components and one protein-like component and the dynamics of each were evaluated based on their distribution with depth as well as across sites differing in hydrology and major biological species. The PARAFAC-EEM experiments were supported by dissolved organic carbon measurements (DOC), optical spectroscopy (UV-Vis), and compositional characterization by ultrahigh resolution Fourier transform ion cyclotron resonance mass spectroscopy (FT-ICR MS). The FT-ICR MS data indicate that metabolism in peatlands reduces the molecular weights of individual components of DOM, and oxygen-rich less aromatic molecules are selectively biodegraded. Our data suggest that different hydrologic and biological conditions within the larger peat ecosystem drive molecular changes in DOM, resulting in distinctly different chemical compositions and unique fluorescent fingerprints. PARAFAC modeling of EEM data coupled with ultrahigh resolution FT-ICR MS has the potential to provide significant molecular-based information on DOM composition that will support efforts to better understand the composition, sources, and diagenetic status of DOM from different terrestrial and aquatic systems.

Frolking S., Talbot J., and Subin Z.M. 2014. Exploring the relationship between peatland net carbon balance and apparent carbon accumulation rate at centry to millennial time scales. Holocene. 24 (9): 1167-1173.

Each year, a peatland has an annual net carbon balance (NCB), which can be positive (net uptake), zero or negative. Over centuries to millennia, this NCB accumulates as a peat profile. Contemporary peatlands can be sampled (cored), and the past apparent carbon accumulation rate (aCAR) can be determined as the quantity of peat carbon in any particular dated interval down the core profile. We use a process-based peatland carbon and water cycle model to compare peatland annual NCB during millennia of peat accumulation to the contemporary estimate of aCAR, resulting from this accumulation. Integrating over the entire profile, the accumulated NCB must equal the aCAR, but for shorter time intervals, these two quantities can diverge. A climate variation/ perturbation that leads to persistent, slow carbon loss or negligible carbon gain through enhanced decomposition will necessarily reduce the aCAR for time periods before the climate variation/perturbation occurred. This can compromise peatland climate–carbon balance relationships inferred from joint analysis of peat cores and paleoclimate reconstructions.

Hodgkins, S.B. M.M. Tfaily, C. K. McCalley, T.A. Logan, P.M. Crill, S.R. Saleska, V.I. Rich, and J.P. Chanton. 2014. Changes in peat chemistry associated with permafrost thaw increase greenhouse gas production. Proc. Nat. Acad. Sci. 111 (16): 5819-5824.

Carbon release due to permafrost thaw represents a potentially major positive climate change feedback. The magnitude of carbon loss and the proportion lost as methane (CH4) vs. carbon dioxide (CO2) depend on factors including temperature, mobilization of previously frozen carbon, hydrology, and changes in organic matter chemistry associated with environmental responses to thaw. While the first three of these effects are relatively well understood, the effect of organic matter chemistry remains largely unstudied. To address this gap, we examined the biogeochemistry of peat and dissolved organic matter (DOM) along a ∼40-y permafrost thaw progression from recently- to fully thawed sites in Stordalen Mire (68.35°N, 19.05°E), a thawing peat plateau in northern Sweden. Thaw-induced subsidence and the resulting inundation along this progression led to succession in vegetation types accompanied by an evolution in organic matter chemistry. Peat C/N ratios decreased whereas humification rates increased, and DOM shifted toward lower molecular weight compounds with lower aromaticity, lower organic oxygen content, and more abundant microbially produced compounds. Corresponding changes in decomposition along this gradient included increasing CH4 and CO2 production potentials, higher relative CH4/CO2 ratios, and a shift in CH4 production pathway from CO2 reduction to acetate cleavage. These results imply that subsidence and thermokarst-associated increases in organic matter lability cause shifts in biogeochemical processes toward faster decomposition with an increasing proportion of carbon released as CH4. This impact of permafrost thaw on organic matter chemistry could intensify the predicted climate feedbacks of increasing temperatures, permafrost carbon mobilization, and hydrologic changes.

McCalley, C.K., Woodcroft BJ, Hodgkins SB, Wehr, R.A., Kim EH, Mondav, R.; Crill PM, Chanton J, Rich VI, Tyson GW, Saleska SR, 2014. Methane dynamics regulated by microbial community response to permafrost thaw, Nature, doi:10.1038/nature13798

Permafrostcontains about 50%of the global soil carbon. It is thought that the thawing of permafrost can lead to a loss of soil carbon in the form of methane and carbon dioxide emissions. The magnitude of the resulting positive climate feedback of such greenhouse gas emissions is still unknown and may to a large extent depend on the poorly understood role of microbial community compositionin regulating the metabolic processes that drive such ecosystem-scale greenhouse gas fluxes. Here we show that changes in vegetation and increasing methane emissions with permafrost thaw are associated with a switch from hydrogenotrophic to partly acetoclastic methanogenesis, resulting in a large shift in the d13C signature (10–15%) of emitted methane. We used a natural landscape gradient of permafrost thaw in northern Sweden as a model to investigate the role of microbial communities in regulating methane cycling, and to test whether aknowledge of community dynamics coul dimprove predictions of carbon emissions under loss of permafrost. Abundance of the methanogen Candidatus Methanoflorens stordalenmirensis is a key predictor of the shifts in methane isotopes, which in turn predicts the proportions of carbon emitted as methane and as carbon dioxide, an important factor for simulating the climate feedback associated with permafrost thaw in global models. By showing that the abundance of key microbial lineages can be used to predict atmospherically relevant patterns in methane isotopes and the proportion of carbon metabolized to methane during permafrost thaw, we establish a basis for scaling changing microbial communities to ecosystem isotope dynamics. Our findings indicate that microbial ecology may be important in ecosystem-scale responses to global change.

Mondav R, Woodcroft BJ, Kim EH, McCalley CK, Hodgkins SB, Crill PM, Chanton J, Hurst GB, Verberkmoes NC, Saleska SR, Hugenholtz P, Rich VI, Tyson GW. 2014. Discovery of a novel methanogen prevalent in thawing permafrost. Nature Communications. 5: 3212.

Thawing permafrost promotes microbial degradation of cryo-sequestered and new carbon leading to the biogenic production of methane, creating a positive feedback to climate change. Here we determine microbial community composition along a permafrost thaw gradient in northern Sweden. Partially thawed sites were frequently dominated by a single archaeal phylotype, Candidatus 'Methanoflorens stordalenmirensis' gen. nov. sp. nov., belonging to the uncultivated lineage 'Rice Cluster II' (Candidatus 'Methanoflorentaceae' fam. nov.). Metagenomic sequencing led to the recovery of its near-complete genome, revealing the genes necessary for hydrogenotrophic methanogenesis. These genes are highly expressed and methane carbon isotope data are consistent with hydrogenotrophic production of methane in the partially thawed site. In addition to permafrost wetlands, 'Methanoflorentaceae' are widespread in high methane-flux habitats suggesting that this lineage is both prevalent and a major contributor to global methane production. In thawing permafrost, Candidatus 'M. stordalenmirensis' appears to be a key mediator of methane-based positive feedback to climate warming.

J. Deng, C. Li, S. Frolking, y. Zhang, K. Bäckstrand, and P. Crill. 2014. Assessing effects of permafrost thaw on C fluxes on multiyear modeling across a permafrost thaw gradient at stordalen, Sweden. Biogeosciences. 5: 4753-4770.

Northern peatlands in permafrost regions contain a large amount of organic carbon (C) in the soil. Climate warming and associated permafrost degradation are expected to have significant impacts on the C balance of these ecosystems, but the magnitude is uncertain. We incorporated a permafrost model, Northern Ecosystem Soil Temperature (NEST), into a biogeochemical model, DeNitrification-DeComposition (DNDC), to model C dynamics in high-latitude peatland ecosystems. The enhanced model was applied to assess effects of permafrost thaw on C fluxes of a subarctic peatland at Stordalen, Sweden. DNDC simulated soil freeze–thaw dynamics, net ecosystem exchange of CO2 (NEE), and CH4 fluxes across three typical land cover types, which represent a gradient in the process of ongoing permafrost thaw at Stordalen. Model results were compared with multiyear field measurements, and the validation indicates that DNDC was able to simulate observed differences in seasonal soil thaw, NEE, and CH4 fluxes across the three land cover types. Consistent with the results from field studies, the modeled C fluxes across the permafrost thaw gradient demonstrate that permafrost thaw and the associated changes in soil hydrology and vegetation not only increase net uptake of C from the atmosphere but also increase the annual to decadal radiative forcing impacts on climate due to increased CH4 emissions. This study indicates the potential of utilizing biogeochemical models, such as DNDC, to predict the soil thermal regime in permafrost areas and to investigate impacts of permafrost thaw on ecosystem C fluxes after incorporating a permafrost component into the model framework.