Publications

We present a significant relationship between the natural abundance isotopic composition of ecosystem pools and the abundance of a microbial gene. Natural abundance ¹⁵N of soils and soil DNA were analysed and compared with archaeal ammonia oxidizer abundance along an elevation gradient in northern Arizona and along a substrate age gradient in Hawai'i. There was a significant positive correlation between the abundance of archaeal <em>amoA</em> genes and natural abundance δ¹⁵N of total soil or DNA suggesting that ammonia oxidizing archaea play an important role in ecosystem N release.

Are tundra ecosystems currently a carbon source or sink? What is the future trajectory of tundra carbon fluxes in response to climate change? These questions are of global importance because of the vast quantities of organic carbon stored in permafrost soils. In this meta-analysis, we compile 40 years of CO₂ flux observations from 54 studies spanning 32 sites across northern high latitudes. Using time-series analysis, we investigated if seasonal or annual CO₂ fluxes have changed over time, and whether spatial differences in mean annual temperature could help explain temporal changes in CO₂ flux. Growing season net CO₂ uptake has definitely increased since the 1990s; the data also suggest (albeit less definitively) an increase in winter CO₂ emissions, especially in the last decade. In spite of the uncertainty in the winter trend, we estimate that tundra sites were annual CO₂ sources from the mid-1980s until the 2000s, and data from the last 7 years show that tundra continue to emit CO₂ annually. CO₂ emissions exceed CO₂uptake across the range of temperatures that occur in the tundra biome. Taken together, these data suggest that despite increases in growing season uptake, tundra ecosystems are currently CO₂ sources on an annual basis.

Climate-induced changes to permafrost are altering high latitude landscapes in ways that could increase the vulnerability of the vast soil carbon pools of the region. Permafrost thaw is temporally dynamic and spatially heterogeneous because, in addition to the thickening of the active layer, localized thermokarst features form when ice-rich permafrost thaws and the ground subsides. Thermokarst produces a diversity of landforms and alters the physical environment in dynamic ways. To estimate potential changes to the carbon cycle it is imperative to quantify the size and distribution of thermokarst landforms. By performing a supervised classification on a high resolution IKONOS image, we detected and mapped small, irregular thermokarst features occurring within an upland watershed in discontinuous permafrost of Interior Alaska. We found that 12% of the Eight Mile Lake (EML) watershed has undergone thermokarst, predominantly in valleys where tussock tundra resides. About 35% of the 3.7 km² tussock tundra class has likely transitioned to thermokarst. These landscape level changes created by permafrost thaw at EML have important implications for ecosystem carbon cycling because thermokarst features are forming in carbon-rich areas and are altering the hydrology in ways that increase seasonal thawing of the soil.

Reciprocal subsidies between rivers and terrestrial habitats are common where terrestrial leaf litter provides energy to aquatic invertebrates while emerging aquatic insects provide energy to terrestrial predators (e.g., birds, lizards, spiders). We examined how aquatic insect emergence changed seasonally with litter from two foundation riparian trees, whose litter often dominates riparian streams of the southwestern United States: Fremont (Populus fremontii) and narrowleaf (Populus angustifolia) cottonwood. P. fremontii litter is fast-decomposing and lower in defensive phytochemicals (i.e., condensed tannins, lignin) relative to P. angustifolia. We experimentally manipulated leaf litter from these two species by placing them in leaf enclosures with emergence traps attached in order to determine how leaf type influenced insect emergence. Contrary to our initial predictions, we found that packs with slow-decomposing leaves tended to support more emergent insects relative to packs with fast-decomposing leaves. Three findings emerged. Firstly, abundance (number of emerging insects m−2 day−1) was 25 % higher on narrowleaf compared to Fremont leaves for the spring but did not differ in the fall, demonstrating that leaf quality from two dominant trees of the same genus yielded different emergence patterns and that these patterns changed seasonally. Secondly, functional feeding groups of emerging insects differed between treatments and seasons. Specifically, in the spring collector-gatherer abundance and biomass were higher on narrowleaf leaves, whereas collector-filterer abundance and biomass were higher on Fremont leaves. Shredder abundance and biomass were higher on narrowleaf leaves in the fall. Thirdly, diversity (Shannon’s H′) was higher on Fremont leaves in the spring, but no differences were found in the fall, showing that fast-decomposing leaves can support a more diverse, complex emergent insect assemblage during certain times of the year. Collectively, these results challenge the notion that leaf quality is a simple function of decomposition, suggesting instead that aquatic insects benefit differentially from different leaf types, such that some use slow-decomposing litter for habitat and its temporal longevity and others utilize fast-decomposing litter with more immediate nutrient release.

<ul id="nph12246-list-0001" class="u-list--bullet o-list--paragraph"> <li>Uncertainty surrounds belowground plant responses to rising atmospheric CO₂ because roots are difficult to measure, requiring frequent monitoring as a result of fine root dynamics and long-term monitoring as a result of sensitivity to resource availability.</li> <li>We report belowground plant responses of a scrub-oak ecosystem in Florida exposed to 11 yr of elevated atmospheric CO₂ using open-top chambers. We measured fine root production, turnover and biomass using minirhizotrons, coarse root biomass using ground-penetrating radar and total root biomass using soil cores.</li> <li>Total root biomass was greater in elevated than in ambient plots, and the absolute difference was larger than the difference aboveground. Fine root biomass fluctuated by more than a factor of two, with no unidirectional temporal trend, whereas leaf biomass accumulated monotonically. Strong increases in fine root biomass with elevated CO₂ occurred after fire and hurricane disturbance. Leaf biomass also exhibited stronger responses following hurricanes.</li> <li>Responses after fire and hurricanes suggest that disturbance promotes the growth responses of plants to elevated CO₂. Increased resource availability associated with disturbance (nutrients, water, space) may facilitate greater responses of roots to elevated CO₂. The disappearance of responses in fine roots suggests limits on the capacity of root systems to respond to CO₂ enrichment.</li> </ul>

The effects of elevated CO₂ on ecosystem element stocks are equivocal, in part because cumulative effects of CO₂ on element pools are difficult to detect. We conducted a complete above and belowground inventory of non-nitrogen macro- and micronutrient stocks in a subtropical woodland exposed to twice-ambient CO₂ concentrations for 11 years. We analyzed a suite of nutrient elements and metals important for nutrient cycling in soils to a depth of ∼2 m, in leaves and stems of the dominant oaks, in fine and coarse roots, and in litter. In conjunction with large biomass stimulation, elevated CO₂ increased oak stem stocks of Na, Mg, P, K, V, Zn and Mo, and the aboveground pool of K and S. Elevated CO₂ increased root pools of most elements, except Zn. CO₂-stimulation of plant Ca was larger than the decline in the extractable Ca pool in soils, whereas for other elements, increased plant uptake matched the decline in the extractable pool in soil. We conclude that elevated CO₂ caused a net transfer of a subset of nutrients from soil to plants, suggesting that ecosystems with a positive plant growth response under high CO₂ will likely cause mobilization of elements from soil pools to plant biomass.

Thawing permafrost represents a poorly understood feedback mechanism of climate change in the Arctic, but with a potential impact owing to stored carbon being mobilized^{<a id="ref-link-1" title="Tarnocai, C. et al. Soil organic carbon pools in the northern circumpolar permafrost region. Glob. Biogeochem. Cycle 23, GB2023 (2009)." href="http://www.nature.com/nclimate/journal/v3/n10/full/nclimate1955.html#ref1">1</a>, <a id="ref-link-2" title="Schuur, E. A. G. et al. The effect of permafrost thaw on old carbon release and net carbon exchange from tundra. Nature 459, 556-559 (2009)." href="http://www.nature.com/nclimate/journal/v3/n10/full/nclimate1955.html#ref2">2</a>, <a id="ref-link-3" title="Schuur, E. A. G. et al. Vulnerability of permafrost carbon to climate change: Implications for the global carbon cycle. BioScience 58, 701-714 (2008)." href="http://www.nature.com/nclimate/journal/v3/n10/full/nclimate1955.html#ref3">3</a>, <a id="ref-link-4" title="Hollesen, J., Elberling, B. &amp; Jansson, P. E. Future active layer dynamics and CO2 production from thawing permafrost layers in Northeast Greenland. Glob. Change Biol. 17, 911-926 (2011)." href="http://www.nature.com/nclimate/journal/v3/n10/full/nclimate1955.html#ref4">4</a>, <a id="ref-link-5" title="Elberling, B., Christiansen, H. H. &amp; Hansen, B. U. High nitrous oxide production from thawing permafrost. Nature Geosci. 3, 332-335 (2010)." href="http://www.nature.com/nclimate/journal/v3/n10/full/nclimate1955.html#ref5">5</a>}. We have quantified the long-term loss of carbon (C) from thawing permafrost in Northeast Greenland from 1996 to 2008 by combining repeated sediment sampling to assess changes in C stock and &gt;12 years of CO₂ production in incubated permafrost samples. Field observations show that the active-layer thickness has increased by &gt;1<span class="mb"><span class="mb"> </span></span>cm<span class="mb"><span class="mb"> </span></span>yr⁻¹ but thawing has not resulted in a detectable decline in C stocks. Laboratory mineralization rates at 5<span class="mb"><span class="mb"> </span></span>°C resulted in a C loss between 9 and 75<span class="mb">%</span>, depending on drainage, highlighting the potential of fast mobilization of permafrost C under aerobic conditions, but also that C at near-saturated conditions may remain largely immobilized over decades. This is confirmed by a three-pool C dynamics model that projects a potential C loss between 13 and 77<span class="mb">%</span> for 50 years of incubation at 5<span class="mb"><span class="mb"> </span></span>°C.

<div data-canvas-width="78.4225">Branched glycerol dialkyl glycerol tetraethers (bGDGTs) are membrane-spanning lipids that likely stabilize membranes of some bacteria. Although bGDGTs have been reported previously in certain geothermal environments, it has been suggested that they may derive from surrounding soils since bGDGTs are known to be produced by soil bacteria.  To test the hypothesis that bGDGTs can be produced by thermophiles in geothermal environments, we examined the distribution and abundance of bGDGTs, along with extensive geochemical data, in 40 sediment and mat samples collected from geothermal systems in the U.S. Great Basin (temperature: 31–95◦C; pH: 6.8–10.7). bGDGTs were found in 38 out of 40 samples at concentrations up to 824 ng/g sample dry mass and comprised up to 99.5% of total GDGTs (branched plus isoprenoidal). The wide distribution of bGDGTs in hot springs, strong correlation between core and polar lipid abundances, distinctness of bGDGT profiles compared to nearby soils, and higher concentration of bGDGTs in hot springs compared to nearby soils provided evidence of in situ production,</div> <div data-canvas-width="19.563666666666666">particularly for the minimally methylated bGDGTs I, Ib, and Ic. Polar bGDGTs were found almost exclusively in samples ≤70◦C and the absolute abundance of polar bGDGTs correlated negatively with properties of chemically reduced, high temperature spring sources (temperature, H2S/HS−) and positively with properties of oxygenated, low temperature sites (O2, NO−3). Two-way cluster analysis and nonmetric multidimensional scaling based on relative abundance of polar bGDGTs supported these relationships and showed a negative relationship between the degree of methylation and temperature, suggesting a higher abundance for minimally methylated bGDGTs at high temperature.  This study presents evidence of the widespread production of bGDGTs in mats and sediments of natural geothermal springs in the U.S. Great Basin, especially in oxygenated, low-temperature sites (70◦C).</div>

Ecosystem respiration (<em>R</em>_eco) is one of the largest terrestrial carbon (<span class="fixed-roman">C</span>) fluxes. The effect of climate change on <em>R</em>_eco depends on the responses of its autotrophic and heterotrophic components. How autotrophic and heterotrophic respiration sources respond to climate change is especially important in ecosystems underlain by permafrost. Permafrost ecosystems contain vast stores of soil <span class="fixed-roman">C</span> (1672 Pg) and are located in northern latitudes where climate change is accelerated. Warming will cause a positive feedback to climate change if heterotrophic respiration increases without corresponding increases in primary production. We quantified the response of autotrophic and heterotrophic respiration to permafrost thaw across the 2008 and 2009 growing seasons. We partitioned <em>R</em>_eco using Δ¹⁴<span class="fixed-roman">C</span> and δ¹³<span class="fixed-roman">C</span> into four sources–two autotrophic (above – and belowground plant structures) and two heterotrophic (young and old soil). We sampled the Δ¹⁴<span class="fixed-roman">C</span> and δ¹³<span class="fixed-roman">C</span> of sources using incubations and the Δ¹⁴<span class="fixed-roman">C</span> and δ¹³<span class="fixed-roman">C</span> of <em>R</em>_eco using field measurements. We then used a Bayesian mixing model to solve for the most likely contributions of each source to <em>R</em>_eco. Autotrophic respiration ranged from 40 to 70% of <em>R</em>_eco and was greatest at the height of the growing season. Old soil heterotrophic respiration ranged from 6 to 18% of <em>R</em>_eco and was greatest where permafrost thaw was deepest. Overall, growing season fluxes of autotrophic and old soil heterotrophic respiration increased as permafrost thaw deepened. Areas with greater thaw also had the greatest primary production. Warming in permafrost ecosystems therefore leads to increased plant and old soil respiration that is initially compensated by increased net primary productivity. However, barring large shifts in plant community composition, future increases in old soil respiration will likely outpace productivity, resulting in a positive feedback to climate change.

<span class="paraNumber">[1]</span> Permafrost thaw can affect decomposition rates by changing environmental conditions and litter quality. As permafrost thaws, soils warm and thermokarst (ground subsidence) features form, causing some areas to become wetter while other areas become drier. We used a common substrate to measure how permafrost thaw affects decomposition rates in the surface soil in a natural permafrost thaw gradient and a warming experiment in Healy, Alaska. Permafrost thaw also changes plant community composition. We decomposed 12 plant litters in a common garden to test how changing plant litter inputs would affect decomposition. We combined species' tissue-specific decomposition rates with species and tissue-level estimates of aboveground net primary productivity to calculate community-weighted decomposition constants at both the thaw gradient and warming experiment. Moisture, specifically growing season precipitation and water table depth, was the most significant driver of decomposition. At the gradient, an increase in growing season precipitation from 200 to 300 mm increased mass loss of the common substrate by 100%. At the warming experiment, a decrease in the depth to the water table from 30 to 15 cm increased mass loss by 100%. At the gradient, community-weighted decomposition was 21% faster in extensive than in minimal thaw, but was similar when moss production was included. Overall, the effect of climate change and permafrost thaw on surface soil decomposition are driven more by precipitation and soil environment than by changes to plant communities. Increasing soil moisture is thereby another mechanism by which permafrost thaw can become a positive feedback to climate change.

The Rehai and Ruidian geothermal fields, located in Tengchong County, Yunnan Province, China, host a variety of geochemically distinct hot springs. In this study, we report a comprehensive, cultivation-independent census of microbial communities in 37 samples collected from these geothermal fields, encompassing sites ranging in temperature from 55.1 to 93.6°C, in pH from 2.5 to 9.4, and in mineralogy from silicates in Rehai to carbonates in Ruidian. Richness was low in all samples, with 21–123 species-level OTUs detected. The bacterial phylum <em>Aquificae</em> or archaeal phylum <em>Crenarchaeota</em> were dominant in Rehai samples, yet the dominant taxa within those phyla depended on temperature, pH, and geochemistry. Rehai springs with low pH (2.5–2.6), high temperature (85.1–89.1°C), and high sulfur contents favored the crenarchaeal order <em>Sulfolobales,</em> whereas those with low pH (2.6–4.8) and cooler temperature (55.1–64.5°C) favored the <em>Aquificae</em> genus <em>Hydrogenobaculum</em>. Rehai springs with neutral-alkaline pH (7.2–9.4) and high temperature (&gt;80°C) with high concentrations of silica and salt ions (Na, K, and Cl) favored the <em>Aquificae</em> genus <em>Hydrogenobacter</em> and crenarchaeal orders <em>Desulfurococcales</em> and <em>Thermoproteales</em>. <em>Desulfurococcales</em> and <em>Thermoproteales</em> became predominant in springs with pH much higher than the optimum and even the maximum pH known for these orders. Ruidian water samples harbored a single <em>Aquificae</em> genus <em>Hydrogenobacter</em>, whereas microbial communities in Ruidian sediment samples were more diverse at the phylum level and distinctly different from those in Rehai and Ruidian water samples, with a higher abundance of uncultivated lineages, close relatives of the ammonia-oxidizing archaeon “<em>Candidatus</em> Nitrosocaldus yellowstonii”, and candidate division O1aA90 and OP1. These differences between Ruidian sediments and Rehai samples were likely caused by temperature, pH, and sediment mineralogy. The results of this study significantly expand the current understanding of the microbiology in Tengchong hot springs and provide a basis for comparison with other geothermal systems around the world.

<ul id="nph12409-list-0001" class="u-list--bullet o-list--paragraph"> <li>Disturbance affects most terrestrial ecosystems and has the potential to shape their responses to chronic environmental change.</li> <li>Scrub-oak vegetation regenerating from fire disturbance in subtropical Florida was exposed to experimentally elevated carbon dioxide (CO₂) concentration (+350 μl l⁻¹) using open-top chambers for 11 yr, punctuated by hurricane disturbance in year 8. Here, we report the effects of elevated CO₂ on aboveground and belowground net primary productivity (NPP) and nitrogen (N) cycling during this experiment.</li> <li>The stimulation of NPP and N uptake by elevated CO₂ peaked within 2 yr after disturbance by fire and hurricane, when soil nutrient availability was high. The stimulation subsequently declined and disappeared, coincident with low soil nutrient availability and with a CO₂-induced reduction in the N concentration of oak stems.</li> <li>These findings show that strong growth responses to elevated CO₂ can be transient, are consistent with a progressively limited response to elevated CO₂ interrupted by disturbance, and illustrate the importance of biogeochemical responses to extreme events in modulating ecosystem responses to global environmental change.</li> </ul>

<ul id="nph12333-list-0001" class="u-list--bullet o-list--paragraph"> <li>Rising atmospheric carbon dioxide (CO₂) could alter the carbon (C) and nitrogen (N) content of ecosystems, yet the magnitude of these effects are not well known. We examined C and N budgets of a subtropical woodland after 11 yr of exposure to elevated CO₂.</li> <li>We used open-top chambers to manipulate CO₂ during regrowth after fire, and measured C, N and tracer ¹⁵N in ecosystem components throughout the experiment.</li> <li>Elevated CO₂ increased plant C and tended to increase plant N but did not significantly increase whole-system C or N. Elevated CO₂ increased soil microbial activity and labile soil C, but more slowly cycling soil C pools tended to decline. Recovery of a long-term ¹⁵N tracer indicated that CO₂ exposure increased N losses and altered N distribution, with no effect on N inputs.</li> <li>Increased plant C accrual was accompanied by higher soil microbial activity and increased C losses from soil, yielding no statistically detectable effect of elevated CO₂ on net ecosystem C uptake. These findings challenge the treatment of terrestrial ecosystems responses to elevated CO₂ in current biogeochemical models, where the effect of elevated CO₂ on ecosystem C balance is described as enhanced photosynthesis and plant growth with decomposition as a first-order response.</li> </ul>

A forest carbon (C) offset is a quantifiable unit of C that is commonly developed at the local or regional project scale and is designed to counterbalance anthropogenic C emissions by sequestering C in trees. In cap-and-trade programs, forest offsets have market value if the sequestered C is additional (more than would have occurred in the absence of the project) and permanent (sequestered within the project boundary for a specified period of time). Local management and ecological context determine the rate of C sequestration, risk of loss, and hence the market value. An understanding of global C dynamics can inform policy but may not be able to effectively price an ecosystem service, such as C sequestration. Appropriate pricing requires the assistance of ecologists to assess C stock abundance and stability over spatial and temporal scales appropriate for the regional market. We use the risk that sequestered C will be emitted as a result of wildfire (reversal risk) to show how ecological context can influence market valuation in offset programs.

Male circumcision reduces female-to-male HIV transmission. Hypothesized mechanisms for this protective effect include decreased HIV target cell recruitment and activation due to changes in the penis microbiome. We compared the coronal sulcus microbiota of men from a group of uncircumcised controls (<em>n</em> = 77) and from a circumcised intervention group (<em>n</em> = 79) at enrollment and year 1 follow-up in a randomized circumcision trial in Rakai, Uganda. We characterized microbiota using16S rRNA gene-based quantitative PCR (qPCR) and pyrosequencing, log response ratio (LRR), Bayesian classification, nonmetric multidimensional scaling (nMDS), and permutational multivariate analysis of variance (PerMANOVA). At baseline, men in both study arms had comparable coronal sulcus microbiota; however, by year 1, circumcision decreased the total bacterial load and reduced microbiota biodiversity. Specifically, the prevalence and absolute abundance of 12 anaerobic bacterial taxa decreased significantly in the circumcised men. While aerobic bacterial taxa also increased postcircumcision, these gains were minor. The reduction in anaerobes may partly account for the effects of circumcision on reduced HIV acquisition.

Retail poultry products are known sources of antibiotic-resistant <em>Escherichia coli</em>, a major human health concern. Consumers have a range of choices for poultry, including conventional, organic, kosher, and raised without antibiotics (RWA) – designations that are perceived to indicate differences in quality and safety. However, whether these categories vary in the frequency of contamination with antibiotic-resistant <em>E. coli</em> is unknown. We examined the occurrence of antibiotic-resistant <em>E. coli</em> on raw chicken marketed as conventional, organic, kosher and RWA. From April – June 2012, we purchased 213 samples of raw chicken from 15 locations in the New York City metropolitan area. We screened <em>E. coli</em> isolates from each sample for resistance to 12 common antibiotics. Although the organic and RWA labels restrict the use of antibiotics, the frequency of antibiotic-resistant <em>E. coli</em> tended to be only slightly lower for RWA, and organic chicken was statistically indistinguishable from conventional products that have no restrictions. Kosher chicken had the highest frequency of antibiotic-resistant <em>E. coli</em>, nearly twice that of conventional products, a result that belies the historical roots of kosher as a means to ensure food safety. These results indicate that production methods influence the frequency of antibiotic-resistant <em>E. coli </em>on poultry products available to consumers. Future research to identify the specific practices that cause the high frequency of antibiotic-resistant <em>E. coli</em> in kosher chicken could promote efforts to reduce consumer exposure to this potential pathogen.

<div data-canvas-width="203.71166666666667">Isoprenoidal glycerol dialkyl glycerol tetra ethers (iGDGTs) are core membrane lipids of many archaea that enhance the integrity of cytoplasmic membranes in extreme environments. We examined the iGDGT profiles and corresponding aqueous geochemistry in 40 hot spring sediment and microbial mat samples from the U.S. Great Basin with temperatures ranging from 31 to 95◦C and pH ranging from 6.8 to 10.7. The absolute abundance of iGDGTs correlated negatively with pH and positively with temperature.  High lipid concentrations, distinct lipid profiles, and a strong relationship between polar and core lipids in hot spring samples suggested in situ production of most iGDGTs rather than contamination from local soils. Two-way cluster analysis and non-metric multidimensional scaling (NMS) of polar iGDGTs indicated that the relative abundance of individual lipids was most strongly related to temperature (r2=0.546), with moderate correlations with pH (r2=0.359), nitrite (r2=0.286), oxygen (r2=0.259), and nitrate(r2=0.215). Relative abundance profiles of individual polar iGDGTs indicated potential temperature optima for iGDGT-0 (≤70◦C), iGDGT-3 (≥55◦C), and iGDGT-4 (≥60◦C). These relationships likely reflect both physiological adaptations and community-level population shifts in response to temperature differences, such as a shift from cooler samples with more abundant methanogens to higher-temperature samples with more abundant Crenarchaeota. Crenarchaeol was widely distributed across the temperature gradient, which is consistent with other reports of abundant crenarchaeol in Great Basin hot springs and suggests a wide distribution for thermophilic ammonia-oxidizing archaea (AOA).</div>

Soil organic matter (SOM) is heterogeneous in structure and has been considered to consist of various pools with different intrinsic turnover rates. Although those pools have been conceptually expressed in models and analyzed according to soil physical and chemical properties, separation of SOM into component pools is still challenging. In this study, we conducted inverse analyses with data from a long-term (385 days) incubation experiment with two types of soil (from plant interspace and from underneath plants) to deconvolute soil carbon (C) efflux into different source pools. We analyzed the two datasets with one-, two- and three-pool models and used probability density functions as a criterion to judge the best model to fit the datasets. Our results indicated that soil C release trajectories over the 385 days of the incubation study were best modeled with a two-pool C model. For both soil types, released C within the first 10 days of the incubation study originated from the labile pool. Decomposition of C in the recalcitrant pool was modeled to contribute to the total CO₂ efflux by 9–11 % at the beginning of the incubation. At the end of the experiment, 75–85 % of the initial soil organic carbon (SOC) was modeled to be released over the incubation period. Our modeling analysis also indicated that the labile C-pool in the soil underneath plants was larger than that in soil from interspace. This deconvolution analysis was based on information contained in incubation data to separate carbon pools and can facilitate integration of results from incubation experiments into ecosystem models with improved parameterization.

Approximately 1700 Pg of soil carbon (C) are stored in the northern circumpolar permafrost zone, more than twice as much C than in the atmosphere. The overall amount, rate, and form of C released to the atmosphere in a warmer world will influence the strength of the permafrost C feedback to climate change. We used a survey to quantify variability in the perception of the vulnerability of permafrost C to climate change. Experts were asked to provide quantitative estimates of permafrost change in response to four scenarios of warming. For the highest warming scenario (RCP 8.5), experts hypothesized that C release from permafrost zone soils could be 19–45 Pg C by 2040, 162–288 Pg C by 2100, and 381–616 Pg C by 2300 in CO₂ equivalent using 100-year CH₄ global warming potential (GWP). These values become 50 % larger using 20-year CH₄ GWP, with a third to a half of expected climate forcing coming from CH₄ even though CH₄ was only 2.3 % of the expected C release. Experts projected that two-thirds of this release could be avoided under the lowest warming scenario (RCP 2.6). These results highlight the potential risk from permafrost thaw and serve to frame a hypothesis about the magnitude of this feedback to climate change. However, the level of emissions proposed here are unlikely to overshadow the impact of fossil fuel burning, which will continue to be the main source of C emissions and climate forcing.

<ul id="nph12295-list-0001" class="u-list--bullet o-list--paragraph"> <li>Increasing atmospheric CO₂ concentrations alter leaf physiology, with effects that cascade to communities and ecosystems. Yet, responses over cycles of disturbance and recovery are not well known, because most experiments span limited ecological time. We examined the effects of CO₂ on root growth, herbivory and arthropod biodiversity in a woodland from 1996 to 2006, and the legacy of CO₂ enrichment on these processes during the year after the CO₂ treatment ceased.</li> <li>We used minirhizotrons to study root growth, leaf censuses to study herbivory and pitfall traps to determine the effects of elevated CO₂ on arthropod biodiversity.</li> <li>Elevated CO₂ increased fine root biomass, but decreased foliar nitrogen and herbivory on all plant species. Insect biodiversity was unchanged in elevated CO₂. Legacy effects of elevated CO₂ disappeared quickly as fine root growth, foliar nitrogen and herbivory levels recovered in the next growing season following the cessation of elevated CO₂.</li> <li>Although the effects of elevated CO₂ cascade through plants to herbivores, they do not reach other trophic levels, and biodiversity remains unchanged. The legacy of 10 yr of elevated CO₂ on plant–herbivore interactions in this system appear to be minimal, indicating that the effects of elevated CO₂ may not accumulate over cycles of disturbance and recovery.</li> </ul>

Stocks of soil organic carbon represent a large component of the carbon cycle that may participate in climate change feedbacks, particularly on decadal and centennial timescales. For Earth system models (ESMs), the ability to accurately represent the global distribution of existing soil carbon stocks is a prerequisite for accurately predicting future carbon–climate feedbacks. We compared soil carbon simulations from 11 model centers to empirical data from the Harmonized World Soil Database (HWSD) and the Northern Circumpolar Soil Carbon Database (NCSCD). Model estimates of global soil carbon stocks ranged from 510 to 3040 Pg C, compared to an estimate of 1260 Pg C (with a 95% confidence interval of 890–1660 Pg C) from the HWSD. Model simulations for the high northern latitudes fell between 60 and 820 Pg C, compared to 500 Pg C (with a 95% confidence interval of 380–620 Pg C) for the NCSCD and 290 Pg C for the HWSD. Global soil carbon varied 5.9 fold across models in response to a 2.6-fold variation in global net primary productivity (NPP) and a 3.6-fold variation in global soil carbon turnover times. Model–data agreement was moderate at the biome level (<i>R</i>² values ranged from 0.38 to 0.97 with a mean of 0.75); however, the spatial distribution of soil carbon simulated by the ESMs at the 1° scale was not well correlated with the HWSD (Pearson correlation coefficients less than 0.4 and root mean square errors from 9.4 to 20.8 kg C m⁻²). In northern latitudes where the two data sets overlapped, agreement between the HWSD and the NCSCD was poor (Pearson correlation coefficient 0.33), indicating uncertainty in empirical estimates of soil carbon. We found that a reduced complexity model dependent on NPP and soil temperature explained much of the 1° spatial variation in soil carbon within most ESMs (<i>R</i>² values between 0.62 and 0.93 for 9 of 11 model centers). However, the same reduced complexity model only explained 10% of the spatial variation in HWSD soil carbon when driven by observations of NPP and temperature, implying that other drivers or processes may be more important in explaining observed soil carbon distributions. The reduced complexity model also showed that differences in simulated soil carbon across ESMs were driven by differences in simulated NPP and the parameterization of soil heterotrophic respiration (inter-model <i>R</i>² = 0.93), not by structural differences between the models. Overall, our results suggest that despite fair global-scale agreement with observational data and moderate agreement at the biome scale, most ESMs cannot reproduce grid-scale variation in soil carbon and may be missing key processes. Future work should focus on improving the simulation of driving variables for soil carbon stocks and modifying model structures to include additional processes.

Tillage practices and straw management can affect soil microbial activities with consequences for soil organic carbon (C) dynamics. Microorganisms metabolize soil organic C and in doing so gain energy and building blocks for biosynthesis, and release CO₂ to the atmosphere. Insight into the response of microbial metabolic processes and C use efficiency (CUE; microbial C produced per substrate C utilized) to management practices may therefore help to predict long term changes in soil C stocks. In this study, we assessed the effects of reduced (RT) and conventional tillage (CT) on the microbial central C metabolic network, using soil samples from a 12-year-old field experiment in an Irish winter wheat cropping system. Straw was removed from half of the RT and CT plots after harvest or incorporated into the soil in the other half, resulting in four treatment combinations. We added 1-¹³C and 2,3-¹³C pyruvate and 1-¹³C and U-¹³C glucose as metabolic tracer isotopomers to composite soil samples taken at two depths (0–15 cm and 15–30 cm) from each of the treatments and used the rate of position-specific respired ¹³CO₂ to parameterize a metabolic model. Model outcomes were then used to calculate CUE of the microbial community. Whereas the composite samples differed in CUE, the changes were small, with values ranging between 0.757 and 0.783 across treatments and soil depth. Increases in CUE were associated with a reduced tricarboxylic acid cycle and reductive pentose phosphate pathway activity and increased consumption of metabolic intermediates for biosynthesis. Our results suggest that RT and straw incorporation do not substantially affect CUE.

Increased atmospheric CO₂ and rising temperatures are expected to affect rice yields and greenhouse-gas (GHG) emissions from rice paddies^{<a title="Van Groenigen, K. J., Osenberg, C. W. &amp; Hungate, B. A. Increased soil emissions of potent greenhouse gases under increased atmospheric CO2. Nature 475, 214-216 (2011)." href="http://www.nature.com/nclimate/journal/v3/n3/full/nclimate1712.html#ref1">1</a>, <a title="Lobell, D. B. &amp; Field, C. B. Global scale climate[mdash]crop yield relationships and the impacts of recent warming. Environ. Res. Lett. 2, 014002 (2007)." href="http://www.nature.com/nclimate/journal/v3/n3/full/nclimate1712.html#ref2">2</a>, <a title="Ainsworth, E. A. Rice production in a changing climate: A meta-analysis of responses to elevated carbon dioxide and elevated ozone concentration. Glob. Change Biol. 14, 1642-209 (2008)." href="http://www.nature.com/nclimate/journal/v3/n3/full/nclimate1712.html#ref3">3</a>, <a title="Peng, S. et al. Rice yields decline with higher night temperature from global warming. Proc. Natl Acad. Sci. USA 101, 9971-9975 (2004)." href="http://www.nature.com/nclimate/journal/v3/n3/full/nclimate1712.html#ref4">4</a>}. This is important, because rice cultivation is one of the largest human-induced sources of the potent GHG methane^{<a title="EPA Global Anthropogenic non-CO2 Greenhouse Gas Emissions: 1990-2020, EPA 430-R-06-003 (United States Environmental Protection Agency, 2006)." href="http://www.nature.com/nclimate/journal/v3/n3/full/nclimate1712.html#ref5">5</a>} (CH₄) and rice is the world’s second-most produced staple crop^{<a title="http://faostat.fao.org/site/567/default.aspx[num]ancor." href="http://www.nature.com/nclimate/journal/v3/n3/full/nclimate1712.html#ref6">6</a>}. The need for meeting a growing global food demand^{<a title="Cassman, K. G., Dobermann, A., Walters, D. T. &amp; Yang, H. Meeting cereal demand while protecting natural resources and improving environmental quality. Annu. Rev. Environ. Resour. 28, 315-358 (2003)." href="http://www.nature.com/nclimate/journal/v3/n3/full/nclimate1712.html#ref7">7</a>} argues for assessing GHG emissions from croplands on the basis of yield rather than land area^{<a title="Van Groenigen, J. W., Velthof, G. L., Oenema, O., van Groenigen, K. J. &amp; van Kessel, C. Towards an agronomic assessment of N2O emissions: A case study for arable crops. Eur. J. Soil Sci. 61, 903-913 (2010)." href="http://www.nature.com/nclimate/journal/v3/n3/full/nclimate1712.html#ref8">8</a>, <a title="Mosier, A. R., Halvorson, A. D., Reule, C.A. &amp; Liu, X. J. J. Net global warming potential and greenhouse gas intensity in irrigated cropping systems in northeastern Colorado. J. Environ. Qual. 35, 1584-1598 (2006)." href="http://www.nature.com/nclimate/journal/v3/n3/full/nclimate1712.html#ref9">9</a>, <a title="Grassini, P. &amp; Cassman, K. G. High-yield maize with large net energy yield and small global warming intensity. Proc. Natl Acad. USA 109, 1074-1079 (2012)." href="http://www.nature.com/nclimate/journal/v3/n3/full/nclimate1712.html#ref10">10</a>}, such that efforts to reduce GHG emissions take into consideration the consequences for food production. However, it is unclear whether or how the GHG intensity (that is, yield-scaled GHG emissions) of cropping systems will be affected by future atmospheric conditions. Here we show, using meta-analysis, that increased atmospheric CO₂ (ranging from 550 to 743<span class="mb"><span class="mb"> </span></span>ppmV) and warming (ranging from +0.8<span class="mb"><span class="mb"> </span></span>°C to +6<span class="mb"><span class="mb"> </span></span>°C) both increase the GHG intensity of rice cultivation. Increased atmospheric CO₂ increased GHG intensity by 31.4<span class="mb">%</span>, because CH₄ emissions are stimulated more than rice yields. Warming increased GHG intensity by 11.8<span class="mb">%</span> per 1<span class="mb"><span class="mb"> </span></span>°C, largely owing to a decrease in yield. This analysis suggests that rising CO₂ and warming will approximately double the GHG intensity of rice production by the end of the twenty-first century, stressing the need for management practices that optimize rice production while reducing its GHG intensity as the climate continues to change.