Global nitrous oxide emissions from livestock manure during 1890-2020: An IPCC tier 2 inventory

Nitrous oxide (N2O) emissions from livestock manure contribute significantly to the growth of atmospheric N2O, a powerful greenhouse gas and dominant ozone-depleting substance. Here, we estimate global N2O emissions from livestock manure during 1890-2020 using the tier 2 approach of the 2019 Refinement to the 2006 IPCC Guidelines. Global N2O emissions from livestock manure increased by ~350% from 451 [368-556] Gg N year-1 in 1890 to 2042 [1677-2514] Gg N year-1 in 2020. These emissions contributed ~30% to the global anthropogenic N2O emissions in the decade 2010-2019. Cattle contributed the most (60%) to the increase, followed by poultry (19%), pigs (15%), and sheep and goats (6%). Regionally, South Asia, Africa, and Latin America dominated the growth in global emissions since the 1990s. Nationally, the largest emissions were found in India (329 Gg N year-1), followed by China (267 Gg N year-1), the United States (163 Gg N year-1), Brazil (129 Gg N year-1) and Pakistan (102 Gg N year-1) in the 2010s. We found a substantial impact of livestock productivity, specifically animal body weight and milk yield, on the emission trends. Furthermore, a large spread existed among different methodologies in estimates of global N2O emission from livestock manure, with our results 20%-25% lower than those based on the 2006 IPCC Guidelines. This study highlights the need for robust time-variant model parameterization and continuous improvement of emissions factors to enhance the precision of emission inventories. Additionally, urgent mitigation is required, as all available inventories indicate a rapid increase in global N2O emissions from livestock manure in recent decades.

Improved scientific knowledge of methanogenesis and methanotrophy needed to slow climate change during the next 30 years

Owing to the high radiative forcing and short atmospheric residence time of methane, abatement of methane emissions offers a crucial opportunity for effective, rapid slowing of climate change. Here, we report on a colloquium jointly sponsored by the American Society for Microbiology and the American Geophysical Union, where 35 national and international experts from academia, the private sector, and government met to review understanding of the microbial processes of methanogenesis and methanotrophy. The colloquium addressed how advanced knowledge of the microbiology of methane production and consumption could inform waste management, including landfills and composts, and three areas of agricultural management: enteric emissions from ruminant livestock, manure management, and rice cultivation. Support for both basic and applied research in microbiology and its applications is urgently needed to accelerate the realization of the large potential for these near-term solutions to counteract climate change.

Global mapping of crop-specific emission factors highlights hotspots of nitrous oxide mitigation

Mitigating soil nitrous oxide (N₂O) emissions is essential for staying below a 2 °C warming threshold. However, accurate assessments of mitigation potential are limited by uncertainty and variability in direct emission factors (EFs). To assess where and why EFs differ, we created high-resolution maps of crop-specific EFs based on 1,507 georeferenced field observations. Here, using a data-driven approach, we show that EFs vary by two orders of magnitude over space. At global and regional scales, such variation is primarily driven by climatic and edaphic factors rather than the well-recognized management practices. Combining spatially explicit EFs with N surplus information, we conclude that global mitigation potential without compromising crop production is 30% (95% confidence interval, 17-53%) of direct soil emissions of N₂O, equivalent to the entire direct soil emissions of China and the United States combined. Two-thirds (65%) of the mitigation potential could be achieved on one-fifth of the global harvested area, mainly located in humid subtropical climates and across gleysols and acrisols. These findings highlight the value of a targeted policy approach on global hotspots that could deliver large N₂O mitigation as well as environmental and food co-benefits.

The increasing global environmental consequences of a weakening US-China crop trade relationship

The consideration of tariffs on China's imports of US agricultural products has focused on economic impacts, while the environmental consequences have received less attention. Here we use a global computable general equilibrium model to evaluate long-term crop portfolio changes induced by China's retaliatory agricultural tariffs and thereby assess the environmental stresses imposed by different crop production portfolios based on region-specific and crop-specific databases. We show that China's tariffs cause unintended increases in nitrogen and phosphorus pollution and blue water extraction in the United States as farmers shift from soybeans to more pollution-causing crops. If diverted to Brazil, China's soybean demands would reduce Brazilian stresses of nitrogen pollution and water use through crop portfolio changes, but may add additional pressures on phosphorus pollution and deforestation. On a global scale, trade policies could help to reduce nutrient pollution and water source depletion by promoting crop production where it is most efficient in terms of nutrient and water use.

Quantification of global and national nitrogen budgets for crop production

Input-output estimates of nitrogen on cropland are essential for improving nitrogen management and better understanding the global nitrogen cycle. Here, we compare 13 nitrogen budget datasets covering 115 countries and regions over 1961-2015. Although most datasets showed similar spatiotemporal patterns, some annual estimates varied widely among them, resulting in large ranges and uncertainty. In 2010, global medians (in TgN yr^-1) and associated minimum-maximum ranges were 73 (64-84) for global harvested crop nitrogen; 161 (139-192) for total nitrogen inputs; 86 (68-97) for nitrogen surplus; and 46% (40-53%) for nitrogen use efficiency. Some of the most uncertain nitrogen budget terms by country showed ranges as large as their medians, revealing areas for improvement. A benchmark nitrogen budget dataset, derived from central tendencies of the original datasets, can be used in model comparisons and inform sustainable nitrogen management in food systems.

Different quantification approaches for nitrogen use efficiency lead to divergent estimates with varying advantages

Nitrogen use efficiency (NUE) is a key indicator with which to study nitrogen cycles and inform nitrogen management. However, different quantification approaches may result in substantially divergent NUE values even for the same production system or for the same experimental plot. Based on our investigation of the differences between and connections among the three principal approaches for NUE quantification, we offer recommendations for choosing the appropriate approach and call for long-term observations to assess the impacts of management practices.

COSORE: A community database for continuous soil respiration and other soil-atmosphere greenhouse gas flux data

Globally, soils store two to three times as much carbon as currently resides in the atmosphere, and it is critical to understand how soil greenhouse gas (GHG) emissions and uptake will respond to ongoing climate change. In particular, the soil-to-atmosphere CO₂ flux, commonly though imprecisely termed soil respiration (R_S ), is one of the largest carbon fluxes in the Earth system. An increasing number of high-frequency R_S measurements (typically, from an automated system with hourly sampling) have been made over the last two decades; an increasing number of methane measurements are being made with such systems as well. Such high frequency data are an invaluable resource for understanding GHG fluxes, but lack a central database or repository. Here we describe the lightweight, open-source COSORE (COntinuous SOil REspiration) database and software, that focuses on automated, continuous and long-term GHG flux datasets, and is intended to serve as a community resource for earth sciences, climate change syntheses and model evaluation. Contributed datasets are mapped to a single, consistent standard, with metadata on contributors, geographic location, measurement conditions and ancillary data. The design emphasizes the importance of reproducibility, scientific transparency and open access to data. While being oriented towards continuously measured R_S , the database design accommodates other soil-atmosphere measurements (e.g. ecosystem respiration, chamber-measured net ecosystem exchange, methane fluxes) as well as experimental treatments (heterotrophic only, etc.). We give brief examples of the types of analyses possible using this new community resource and describe its accompanying R software package.

Simultaneous numerical representation of soil microsite production and consumption of carbon dioxide, methane, and nitrous oxide using probability distribution functions

Production and consumption of nitrous oxide (N₂ O), methane (CH₄ ), and carbon dioxide (CO₂ ) are affected by complex interactions of temperature, moisture, and substrate supply, which are further complicated by spatial heterogeneity of the soil matrix. This microsite heterogeneity is often invoked to explain non-normal distributions of greenhouse gas (GHG) fluxes, also known as hot spots and hot moments. To advance numerical simulation of these belowground processes, we expanded the Dual Arrhenius and Michaelis-Menten model, to apply it consistently for all three GHGs with respect to the biophysical processes of production, consumption, and diffusion within the soil, including the contrasting effects of oxygen (O₂ ) as substrate or inhibitor for each process. High-frequency chamber-based measurements of all three GHGs at the Howland Forest (ME, USA) were used to parameterize the model using a multiple constraint approach. The area under a soil chamber is partitioned according to a bivariate log-normal probability distribution function (PDF) of carbon and water content across a range of microsites, which leads to a PDF of heterotrophic respiration and O₂ consumption among microsites. Linking microsite consumption of O₂ with a diffusion model generates a broad range of microsite concentrations of O₂ , which then determines the PDF of microsites that produce or consume CH₄ and N₂ O, such that a range of microsites occurs with both positive and negative signs for net CH₄ and N₂ O flux. Results demonstrate that it is numerically feasible for microsites of N₂ O reduction and CH₄ oxidation to co-occur under a single chamber, thus explaining occasional measurement of simultaneous uptake of both gases. Simultaneous simulation of all three GHGs in a parsimonious modeling framework is challenging, but it increases confidence that agreement between simulations and measurements is based on skillful numerical representation of processes across a heterogeneous environment.

Six years of ecosystem-atmosphere greenhouse gas fluxes measured in a sub-boreal forest

Carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O) are the greenhouse gases largely responsible for anthropogenic climate change. Natural plant and microbial metabolic processes play a major role in the global atmospheric budget of each. We have been studying ecosystem-atmosphere trace gas exchange at a sub-boreal forest in the northeastern United States for over two decades. Historically our emphasis was on turbulent fluxes of CO₂ and water vapor. In 2012 we embarked on an expanded campaign to also measure CH₄ and N₂O. Here we present continuous tower-based measurements of the ecosystem-atmosphere exchange of CO₂ and CH₄, recorded over the period 2012–2018 and reported at a 30-minute time step. Additionally, we describe a five-year (2012–2016) dataset of chamber-based measurements of soil fluxes of CO₂, CH₄, and N₂O (2013–2016 only), conducted each year from May to November. These data can be used for process studies, for biogeochemical and land surface model validation and benchmarking, and for regional-to-global upscaling and budgeting analyses.

Design Type(s)	observational design • data collection and processing objective
Measurement Type(s)	greenhouse gas
Technology Type(s)	environmental monitoring
Factor Type(s)	greenhouse gas • temporal_interval
Sample Characteristic(s)	Howland Forest • forest ecosystem

Machine-accessible metadata file describing the reported data (ISA-Tab format)

Biogeochemical recuperation of lowland tropical forest during succession

High rates of land conversion and land use change have vastly increased the proportion of secondary forest in the lowland tropics relative to mature forest. As secondary forests recover following abandonment, nitrogen (N) and phosphorus (P) must be present in sufficient quantities to sustain high rates of net primary production and to replenish the nutrients lost during land use prior to secondary forest establishment. Biogeochemical theory and results from individual studies suggest that N can recuperate during secondary forest recovery, especially relative to P. Here, we synthesized 23 metrics of N and P in soil and plants from 45 secondary forest chronosequences located in the wet tropics to empirically explore (1) whether there is a consistent change in nutrients and nutrient cycling processes during secondary succession in the biome; (2) which metrics of N and P in soil and plants recuperate most consistently; (3) if the recuperation of nutrients during succession approaches similar nutrient concentrations and fluxes as those in mature forest in ~100 yr following the initiation of succession; and (4) whether site characteristics, including disturbance history, climate, and soil order are significantly related to nutrient recuperation. During secondary forest succession, nine metrics of N and/or P cycling changed consistently and substantially. In most sites, N concentrations and fluxes in both plants and soil increased during secondary succession, and total P concentrations increased in surface soil. Changes in nutrient concentrations and nutrient cycling processes during secondary succession were similar whether mature forest was included or excluded from the analysis, indicating that nutrient recuperation in secondary forest leads to biogeochemical conditions that are similar to those of mature forest. Further, of the N and P metrics that recuperated, only soil total P and foliar δ¹⁵ N were strongly influenced by site characteristics like climate, soils, or disturbance history. Predictable nutrient recuperation across a diverse and productive ecosystem may support future forest growth and could provide a means to quantify successful restoration of ecosystem function in secondary tropical forest beyond biomass or species composition.

Global soil nitrous oxide emissions since the preindustrial era estimated by an ensemble of terrestrial biosphere models: Magnitude, attribution, and uncertainty

Our understanding and quantification of global soil nitrous oxide (N₂ O) emissions and the underlying processes remain largely uncertain. Here, we assessed the effects of multiple anthropogenic and natural factors, including nitrogen fertilizer (N) application, atmospheric N deposition, manure N application, land cover change, climate change, and rising atmospheric CO₂ concentration, on global soil N₂ O emissions for the period 1861-2016 using a standard simulation protocol with seven process-based terrestrial biosphere models. Results suggest global soil N₂ O emissions have increased from 6.3 ± 1.1 Tg N₂ O-N/year in the preindustrial period (the 1860s) to 10.0 ± 2.0 Tg N₂ O-N/year in the recent decade (2007-2016). Cropland soil emissions increased from 0.3 Tg N₂ O-N/year to 3.3 Tg N₂ O-N/year over the same period, accounting for 82% of the total increase. Regionally, China, South Asia, and Southeast Asia underwent rapid increases in cropland N₂ O emissions since the 1970s. However, US cropland N₂ O emissions had been relatively flat in magnitude since the 1980s, and EU cropland N₂ O emissions appear to have decreased by 14%. Soil N₂ O emissions from predominantly natural ecosystems accounted for 67% of the global soil emissions in the recent decade but showed only a relatively small increase of 0.7 ± 0.5 Tg N₂ O-N/year (11%) since the 1860s. In the recent decade, N fertilizer application, N deposition, manure N application, and climate change contributed 54%, 26%, 15%, and 24%, respectively, to the total increase. Rising atmospheric CO₂ concentration reduced soil N₂ O emissions by 10% through the enhanced plant N uptake, while land cover change played a minor role. Our estimation here does not account for indirect emissions from soils and the directed emissions from excreta of grazing livestock. To address uncertainties in estimating regional and global soil N₂ O emissions, this study recommends several critical strategies for improving the process-based simulations.

A world of co-benefits: Solving the global nitrogen challenge

Nitrogen is a critical component of the economy, food security, and planetary health. Many of the world's sustainability targets hinge on global nitrogen solutions, which, in turn, contribute lasting benefits for: (i) world hunger; (ii) soil, air and water quality; (iii) climate change mitigation; and (iv) biodiversity conservation. Balancing the projected rise in agricultural nitrogen demands while achieving these 21^st century ideals will require policies to coordinate solutions among technologies, consumer choice, and socioeconomic transformation.

Deep soils modify environmental consequences of increased nitrogen fertilizer use in intensifying Amazon agriculture

Agricultural intensification offers potential to grow more food while reducing the conversion of native ecosystems to croplands. However, intensification also risks environmental degradation through emissions of the greenhouse gas nitrous oxide (N2O) and nitrate leaching to ground and surface waters. Intensively-managed croplands and nitrogen (N) fertilizer use are expanding rapidly in tropical regions. We quantified fertilizer responses of maize yield, N2O emissions, and N leaching in an Amazon soybean-maize double-cropping system on deep, highly-weathered soils in Mato Grosso, Brazil. Application of N fertilizer above 80 kg N ha-1 yr-1 increased maize yield and N2O emissions only slightly. Unlike experiences in temperate regions, leached nitrate accumulated in deep soils with increased fertilizer and conversion to cropping at N fertilization rates >80 kg N ha-1, which exceeded maize demand. This raises new questions about the capacity of tropical agricultural soils to store nitrogen, which may determine when and how much nitrogen impacts surface waters.

Soil Carbon Dynamics in Soybean Cropland and Forests in Mato Grosso, Brazil

Climate and land use models predict that tropical deforestation and conversion to cropland will produce a large flux of soil carbon (C) to the atmosphere from accelerated decomposition of soil organic matter (SOM). However, the C flux from the deep tropical soils on which most intensive crop agriculture is now expanding remains poorly constrained. To quantify the effect of intensive agriculture on tropical soil C, we compared C stocks, radiocarbon, and stable C isotopes to 2 m depth from forests and soybean cropland created from former pasture in Mato Grosso, Brazil. We hypothesized that soil disturbance, higher soil temperatures (+2°C), and lower OM inputs from soybeans would increase soil C turnover and deplete C stocks relative to nearby forest soils. However, we found reduced C concentrations and stocks only in surface soils (0-10 cm) of soybean cropland compared with forests, and these differences could be explained by soil mixing during plowing. The amount and Δ14C of respired CO2 to 50 cm depth were significantly lower from soybean soils, yet CO2 production at 2 m deep was low in both forest and soybean soils. Mean surface soil δ13C decreased by 0.5‰ between 2009 and 2013 in soybean cropland, suggesting low OM inputs from soybeans. Together these findings suggest the following: (1) soil C is relatively resistant to changes in land use and (2) conversion to cropland caused a small, measurable reduction in the fast-cycling C pool through reduced OM inputs, mobilization of older C from soil mixing, and/or destabilization of SOM in surface soils.

Seasonality of temperate forest photosynthesis and daytime respiration

Terrestrial ecosystems currently offset one-quarter of anthropogenic carbon dioxide (CO2) emissions because of a slight imbalance between global terrestrial photosynthesis and respiration. Understanding what controls these two biological fluxes is therefore crucial to predicting climate change. Yet there is no way of directly measuring the photosynthesis or daytime respiration of a whole ecosystem of interacting organisms; instead, these fluxes are generally inferred from measurements of net ecosystem-atmosphere CO2 exchange (NEE), in a way that is based on assumed ecosystem-scale responses to the environment. The consequent view of temperate deciduous forests (an important CO2 sink) is that, first, ecosystem respiration is greater during the day than at night; and second, ecosystem photosynthetic light-use efficiency peaks after leaf expansion in spring and then declines, presumably because of leaf ageing or water stress. This view has underlain the development of terrestrial biosphere models used in climate prediction and of remote sensing indices of global biosphere productivity. Here, we use new isotopic instrumentation to determine ecosystem photosynthesis and daytime respiration in a temperate deciduous forest over a three-year period. We find that ecosystem respiration is lower during the day than at night-the first robust evidence of the inhibition of leaf respiration by light at the ecosystem scale. Because they do not capture this effect, standard approaches overestimate ecosystem photosynthesis and daytime respiration in the first half of the growing season at our site, and inaccurately portray ecosystem photosynthetic light-use efficiency. These findings revise our understanding of forest-atmosphere carbon exchange, and provide a basis for investigating how leaf-level physiological dynamics manifest at the canopy scale in other ecosystems.

The economic and environmental consequences of implementing nitrogen-efficient technologies and management practices in agriculture

Technologies and management practices (TMPs) that reduce the application of nitrogen (N) fertilizer while maintaining crop yields can improve N use efficiency (NUE) and are important tools for meeting the dual challenges of increasing food production and reducing N pollution. However, because farmers operate to maximize their profits, incentives to implement TMPs are limited, and TMP implementation will not always reduce N pollution. Therefore, we have developed the NUE Economic and Environmental impact analytical framework (NUE) to examine the economic and environmental consequences of implementing TMPs in agriculture, with a specific focus on farmer profits, N fertilizer consumption, N losses, and cropland demand. Our analytical analyses show that impact of TMPs on farmers' economic decision-making and the environment is affected by how TMPs change the yield ceiling and the N fertilization rate at the ceiling and by how the prices of TMPs, fertilizer, and crops vary. Technologies and management practices that increase the yield ceiling appear to create a greater economic incentive for farmers than TMPs that do not but may result in higher N application rates and excess N losses. Nevertheless, the negative environmental impacts of certain TMPs could be avoided if their price stays within a range determined by TMP yield response, fertilizer price, and crop price. We use a case study on corn production in the midwestern United States to demonstrate how NUE can be applied to farmers' economic decision-making and policy analysis. Our NUE framework provides an important tool for policymakers to understand how combinations of fertilizer, crop, and TMP prices affect the possibility of achieving win-win outcomes for farmers and the environment.

More food, low pollution (mo fo lo Po): a grand challenge for the 21st century

Synthetic nitrogen fertilizer has been a double-edged sword, greatly improving human nutrition during the 20th century but also posing major human health and environmental challenges for the 21st century. In August 2013, about 160 agronomists, scientists, extension agents, crop advisors, economists, social scientists, farmers, representatives of regulatory agencies and nongovernmental organizations (NGOs), and other agricultural experts gathered to discuss the vexing challenge of how to produce more food to nourish a growing population while minimizing pollution to the environment. This collection of 14 papers authored by conference participants provides a much needed analysis of the many technical, economic, and social impediments to improving nitrogen use efficiency (NUE) in crop and animal production systems. These papers demonstrate that the goals of producing more food with low pollution (Mo Fo Lo Po) will not be achieved by technological developments alone but will also require policies that recognize the economic and social factors affecting farmer decision-making. Take-home lessons from this extraordinary interdisciplinary effort include the need (i) to develop partnerships among private and public sectors to demonstrate the most current, economically feasible, best management NUE practices at local and regional scales; (ii) to improve continuing education to private sector retailers and crop advisers; (iii) to tie nutrient management to performance-based indicators on the farm and in the downwind and downstream environment; and (iv) to restore investments in research, education, extension, and human resources that are essential for developing the interdisciplinary knowledge and innovative skills needed to achieve agricultural sustainability goals.

A big-microsite framework for soil carbon modeling

Soil carbon cycling processes potentially play a large role in biotic feedbacks to climate change, but little agreement exists at present on what the core of numerical soil C cycling models should look like. In contrast, most canopy models of photosynthesis and leaf gas exchange share a common 'Farquhaur-model' core structure. Here, we explore why a similar core model structure for heterotrophic soil respiration remains elusive and how a pathway to that goal might be envisioned. The spatial and temporal variation in soil microsite conditions greatly complicates modeling efforts, but we believe it is possible to develop a tractable number of parameterizable equations that are organized into a coherent, modular, numerical model structure. First, we show parallels in insights gleaned from linking Arrhenius and Michaelis-Menten kinetics for both photosynthesis and soil respiration. Additional equations and layers of complexity are then added to simulate substrate supply. For soils, model modules that simulate carbon stabilization processes will be key to estimating the fraction of soil C that is accessible to enzymes. Potential modules for dynamic photosynthate input, wetting-event inputs, freeze-thaw impacts on substrate diffusion, aggregate turnover, soluble-C sorption, gas transport, methane respiration, and microbial dynamics are described for conceptually and numerically linking our understanding of fast-response processes of soil gas exchange with longer-term dynamics of soil carbon and nitrogen stocks.

Modeling the impact of net primary production dynamics on post-disturbance Amazon savannization

Amazon tropical forests are being replaced by pasturelands and croplands, but they sometimes revert to regrowth forest when abandoned after a period of agricultural use. Research suggests that this secondary regrowth is limited by climate and nutrient availability and, using a coupled biosphere-atmosphere model, we investigated patterns in the regrowth of the Amazon rainforest after a full deforestation event, considering different types of nutrient stress. We found that, over a 50 year regrowth period, the reduction of precipitation caused by large-scale deforestation was not sufficient to prevent secondary forest regrowth, but this decrease in precipitation combined with nutrient limitation, due to logging and frequent fires, did indeed prevent forest regrowth in central and southern Amazonia, leading to a savannization. These results are concerning, as the northern Mato Grosso region has the highest clearing rate in Amazonia. The low resilience of the forest under nutrient stress indicates that a large scale disturbance could greatly expand the area suitable for cropland, accelerating forest disappearance.

Long-term changes in forest carbon under temperature and nitrogen amendments in a temperate northern hardwood forest

Currently, forests in the northeastern United States are net sinks of atmospheric carbon. Under future climate change scenarios, the combined effects of climate change and nitrogen deposition on soil decomposition, aboveground processes, and the forest carbon balance remain unclear. We applied carbon stock, flux, and isotope data from field studies at the Harvard forest, Massachusetts, to the ForCent model, which integrates above- and belowground processes. The model was able to represent decadal-scale measurements in soil C stocks, mean residence times, fluxes, and responses to a warming and N addition experiment. The calibrated model then simulated the longer term impacts of warming and N deposition on the distribution of forest carbon stocks. For simulation to 2030, soil warming resulted in a loss of soil organic matter (SOM), decreased allocation to belowground biomass, and gain of aboveground carbon, primarily in large wood, with an overall small gain in total system carbon. Simulated nitrogen addition resulted in a small increase in belowground carbon pools, but a large increase in aboveground large wood pools, resulting in a substantial increase in total system carbon. Combined warming and nitrogen addition simulations showed a net gain in total system carbon, predominately in the aboveground carbon pools, but offset somewhat by losses in SOM. Hence, the impact of continuation of anthropogenic N deposition on the hardwood forests of the northeastern United States may exceed the impact of warming in terms of total ecosystem carbon stocks. However, it should be cautioned that these simulations do not include some climate-related processes, different responses from changing tree species composition. Despite uncertainties, this effort is among the first to use decadal-scale observations of soil carbon dynamics and results of multifactor manipulations to calibrate a model that can project integrated aboveground and belowground responses to nitrogen and climate changes for subsequent decades.

Watershed responses to Amazon soya bean cropland expansion and intensification

The expansion and intensification of soya bean agriculture in southeastern Amazonia can alter watershed hydrology and biogeochemistry by changing the land cover, water balance and nutrient inputs. Several new insights on the responses of watershed hydrology and biogeochemistry to deforestation in Mato Grosso have emerged from recent intensive field campaigns in this region. Because of reduced evapotranspiration, total water export increases threefold to fourfold in soya bean watersheds compared with forest. However, the deep and highly permeable soils on the broad plateaus on which much of the soya bean cultivation has expanded buffer small soya bean watersheds against increased stormflows. Concentrations of nitrate and phosphate do not differ between forest or soya bean watersheds because fixation of phosphorus fertilizer by iron and aluminium oxides and anion exchange of nitrate in deep soils restrict nutrient movement. Despite resistance to biogeochemical change, streams in soya bean watersheds have higher temperatures caused by impoundments and reduction of bordering riparian forest. In larger rivers, increased water flow, current velocities and sediment flux following deforestation can reshape stream morphology, suggesting that cumulative impacts of deforestation in small watersheds will occur at larger scales.

Diel patterns of autotrophic and heterotrophic respiration among phenological stages

Improved understanding of the links between aboveground production and allocation of photosynthate to belowground processes and the temporal variation in those links is needed to interpret observations of belowground carbon cycling processes. Here, we show that combining a trenching manipulation with high-frequency soil respiration measurements in a temperate hardwood forest permitted identification of the temporally variable influence of roots on diel and seasonal patterns of soil respiration. The presence of roots in an untrenched plot caused larger daily amplitude and a 2-3 h delay in peak soil CO2 efflux relative to a root-free trenched plot. These effects cannot be explained by differences in soil temperature, and they were significant only when a canopy was present during the growing season. This experiment demonstrated that canopy processes affect soil CO2 efflux rates and patterns at hourly and seasonal time scales, and it provides evidence that root and microbial processes respond differently to environmental factors.

Foundation species loss affects vegetation structure more than ecosystem function in a northeastern USA forest

Loss of foundation tree species rapidly alters ecological processes in forested ecosystems. Tsuga canadensis, an hypothesized foundation species of eastern North American forests, is declining throughout much of its range due to infestation by the nonnative insect Adelges tsugae and by removal through pre-emptive salvage logging. In replicate 0.81-ha plots, T. canadensis was cut and removed, or killed in place by girdling to simulate adelgid damage. Control plots included undisturbed hemlock and mid-successional hardwood stands that represent expected forest composition in 50–100 years. Vegetation richness, understory vegetation cover, soil carbon flux, and nitrogen cycling were measured for two years prior to, and five years following, application of experimental treatments. Litterfall and coarse woody debris (CWD), including snags, stumps, and fallen logs and branches, have been measured since treatments were applied. Overstory basal area was reduced 60%–70% in girdled and logged plots. Mean cover and richness did not change in hardwood or hemlock control plots but increased rapidly in girdled and logged plots. Following logging, litterfall immediately decreased then slowly increased, whereas in girdled plots, there was a short pulse of hemlock litterfall as trees died. CWD volume remained relatively constant throughout but was 3–4× higher in logged plots. Logging and girdling resulted in small, short-term changes in ecosystem dynamics due to rapid regrowth of vegetation but in general, interannual variability exceeded differences among treatments. Soil carbon flux in girdled plots showed the strongest response: 35% lower than controls after three years and slowly increasing thereafter. Ammonium availability increased immediately after logging and two years after girdling, due to increased light and soil temperatures and nutrient pulses from leaf-fall and reduced uptake following tree death. The results from this study illuminate ecological processes underlying patterns observed consistently in region-wide studies of adelgid-infested hemlock stands. Mechanisms of T. canadensis loss determine rates, magnitudes, and trajectories of ecological changes in hemlock forests. Logging causes abrupt, large changes in vegetation structure whereas girdling (and by inference, A. tsugae) causes sustained, smaller changes. Ecosystem processes depend more on vegetation cover per se than on species composition. We conclude that the loss of this late-successional foundation species will have long-lasting impacts on forest structure but subtle impacts on ecosystem function.

Rate my data: quantifying the value of ecological data for the development of models of the terrestrial carbon cycle

Primarily driven by concern about rising levels of atmospheric CO2, ecologists and earth system scientists are collecting vast amounts of data related to the carbon cycle. These measurements are generally time consuming and expensive to make, and, unfortunately, we live in an era where research funding is increasingly hard to come by. Thus, important questions are: "Which data streams provide the most valuable information?" and "How much data do we need?" These questions are relevant not only for model developers, who need observational data to improve, constrain, and test their models, but also for experimentalists and those designing ecological observation networks. Here we address these questions using a model-data fusion approach. We constrain a process-oriented, forest ecosystem C cycle model with 17 different data streams from the Harvard Forest (Massachusetts, USA). We iteratively rank each data source according to its contribution to reducing model uncertainty. Results show the importance of some measurements commonly unavailable to carbon-cycle modelers, such as estimates of turnover times from different carbon pools. Surprisingly, many data sources are relatively redundant in the presence of others and do not lead to a significant improvement in model performance. A few select data sources lead to the largest reduction in parameter-based model uncertainty. Projections of future carbon cycling were poorly constrained when only hourly net-ecosystem-exchange measurements were used to inform the model. They were well constrained, however, with only 5 of the 17 data streams, even though many individual parameters are not constrained. The approach taken here should stimulate further cooperation between modelers and measurement teams and may be useful in the context of setting research priorities and allocating research funds.

Interactions between repeated fire, nutrients, and insect herbivores affect the recovery of diversity in the southern Amazon

Surface fires burn extensive areas of tropical forests each year, altering resource availability, biotic interactions, and, ultimately, plant diversity. In transitional forest between the Brazilian cerrado (savanna) and high stature Amazon forest, we took advantage of a long-term fire experiment to establish a factorial study of the interactions between fire, nutrient availability, and herbivory on early plant regeneration. Overall, five annual burns reduced the number and diversity of regenerating stems. Community composition changed substantially after repeated fires, and species common in the cerrado became more abundant. The number of recruits and their diversity were reduced in the burned area, but burned plots closed to herbivores with nitrogen additions had a 14 % increase in recruitment. Diversity of recruits also increased up to 50 % in burned plots when nitrogen was added. Phosphorus additions were related to an increase in species evenness in burned plots open to herbivores. Herbivory reduced seedling survival overall and increased diversity in burned plots when nutrients were added. This last result supports our hypothesis that positive relationships between herbivore presence and diversity would be strongest in treatments that favor herbivory--in this case herbivory was higher in burned plots which were initially lower in diversity. Regenerating seedlings in less diverse plots were likely more apparent to herbivores, enabling increased herbivory and a stronger signal of negative density dependence. In contrast, herbivores generally decreased diversity in more species rich unburned plots. Although this study documents complex interactions between repeated burns, nutrients, and herbivory, it is clear that fire initiates a shift in the factors that are most important in determining the diversity and number of recruits. This change may have long-lasting effects as the forest progresses through succession.

Stoichiometric patterns in foliar nutrient resorption across multiple scales

• Nutrient resorption is a fundamental process through which plants withdraw nutrients from leaves before abscission. Nutrient resorption patterns have the potential to reflect gradients in plant nutrient limitation and to affect a suite of terrestrial ecosystem functions. • Here, we used a stoichiometric approach to assess patterns in foliar resorption at a variety of scales, specifically exploring how N : P resorption ratios relate to presumed variation in N and/or P limitation and possible relationships between N : P resorption ratios and soil nutrient availability. • N : P resorption ratios varied significantly at the global scale, increasing with latitude and decreasing with mean annual temperature and precipitation. In general, tropical sites (absolute latitudes < 23°26') had N : P resorption ratios of < 1, and plants growing on highly weathered tropical soils maintained the lowest N : P resorption ratios. Resorption ratios also varied with forest age along an Amazonian forest regeneration chronosequence and among species in a diverse Costa Rican rain forest. • These results suggest that variations in N : P resorption stoichiometry offer insight into nutrient cycling and limitation at a variety of spatial scales, complementing other metrics of plant nutrient biogeochemistry. The extent to which the stoichiometric flexibility of resorption will help regulate terrestrial responses to global change merits further investigation.

An in vitro autogene

Recent technological advances have allowed development of increasingly complex systems for in vitro evolution. Here, we describe an in vitro autogene composed of a self-amplifying T7 RNA polymerase system. Functional autogene templates in cell-free lysate produce T7 RNA polymerase, which amplifies the autogene genetic information through a positive feedback architecture. Compartmentalization of individual templates within a water-in-oil emulsion links genotype and phenotype, allowing evolution.

Climate change impacts of US reactive nitrogen

Fossil fuel combustion and fertilizer application in the United States have substantially altered the nitrogen cycle, with serious effects on climate change. The climate effects can be short-lived, by impacting the chemistry of the atmosphere, or long-lived, by altering ecosystem greenhouse gas fluxes. Here we develop a coherent framework for assessing the climate change impacts of US reactive nitrogen emissions, including oxides of nitrogen, ammonia, and nitrous oxide (N(2)O). We use the global temperature potential (GTP), calculated at 20 and 100 y, in units of CO(2) equivalents (CO(2)e), as a common metric. The largest cooling effects are due to combustion sources of oxides of nitrogen altering tropospheric ozone and methane concentrations and enhancing carbon sequestration in forests. The combined cooling effects are estimated at -290 to -510 Tg CO(2)e on a GTP(20) basis. However, these effects are largely short-lived. On a GTP(100) basis, combustion contributes just -16 to -95 Tg CO(2)e. Agriculture contributes to warming on both the 20-y and 100-y timescales, primarily through N(2)O emissions from soils. Under current conditions, these warming and cooling effects partially offset each other. However, recent trends show decreasing emissions from combustion sources. To prevent warming from US reactive nitrogen, reductions in agricultural N(2)O emissions are needed. Substantial progress toward this goal is possible using current technology. Without such actions, even greater CO(2) emission reductions will be required to avoid dangerous climate change.

The Amazon basin in transition

Agricultural expansion and climate variability have become important agents of disturbance in the Amazon basin. Recent studies have demonstrated considerable resilience of Amazonian forests to moderate annual drought, but they also show that interactions between deforestation, fire and drought potentially lead to losses of carbon storage and changes in regional precipitation patterns and river discharge. Although the basin-wide impacts of land use and drought may not yet surpass the magnitude of natural variability of hydrologic and biogeochemical cycles, there are some signs of a transition to a disturbance-dominated regime. These signs include changing energy and water cycles in the southern and eastern portions of the Amazon basin.

Soil moisture depletion under simulated drought in the Amazon: impacts on deep root uptake

*Deep root water uptake in tropical Amazonian forests has been a major discovery during the last 15 yr. However, the effects of extended droughts, which may increase with climate change, on deep soil moisture utilization remain uncertain. *The current study utilized a 1999-2005 record of volumetric water content (VWC) under a throughfall exclusion experiment to calibrate a one-dimensional model of the hydrologic system to estimate VWC, and to quantify the rate of root uptake through 11.5 m of soil. *Simulations with root uptake compensation had a relative root mean square error (RRMSE) of 11% at 0-40 cm and < 5% at 350-1150 cm. The simulated contribution of deep root uptake under the control was c. 20% of water demand from 250 to 550 cm and c. 10% from 550 to 1150 cm. Furthermore, in years 2 (2001) and 3 (2002) of throughfall exclusion, deep root uptake increased as soil moisture was available but then declined to near zero in deep layers in 2003 and 2004. *Deep root uptake was limited despite high VWC (i.e. > 0.30 cm(3) cm(-3)). This limitation may partly be attributable to high residual water contents (theta(r)) in these high-clay (70-90%) soils or due to high soil-to-root resistance. The ability of deep roots and soils to contribute increasing amounts of water with extended drought will be limited.

Soil respiration at mean annual temperature predicts annual total across vegetation types and biomes

Soil respiration (SR) constitutes the largest flux of CO(2) from terrestrial ecosystems to the atmosphere. However, there still exist considerable uncertainties as to its actual magnitude, as well as its spatial and interannual variability. Based on a reanalysis and synthesis of 80 site-years for 57 forests, plantations, savannas, shrublands and grasslands from boreal to tropical climates we present evidence that total annual SR is closely related to SR at mean annual soil temperature (SR(MAT)), irrespective of the type of ecosystem and biome. This is theoretically expected for non water-limited ecosystems within most of the globally occurring range of annual temperature variability and sensitivity (Q(10)). We further show that for seasonally dry sites where annual precipitation (P) is lower than potential evapotranspiration (PET), annual SR can be predicted from wet season SR(MAT) corrected for a factor related to P/PET. Our finding indicates that it can be sufficient to measure SR(MAT) for obtaining a well constrained estimate of its annual total. This should substantially increase our capacity for assessing the spatial distribution of soil CO(2) emissions across ecosystems, landscapes and regions, and thereby contribute to improving the spatial resolution of a major component of the global carbon cycle.

Environmental Parameters Regulating Gaseous Nitrogen Losses from Two Forested Ecosystems via Nitrification and Denitrification

Gaseous N losses from disturbed and reference forested watersheds at the Coweeta Hydrologic Laboratory in western North Carolina were studied by in situ N(2)O diffusion measurements and laboratory incubations throughout a 10-month period. Soil temperature, percent base saturation, and water-filled pore space accounted for 43% of the variation in in situ N(2)O diffusion measurements. Laboratory incubations distinguished the gaseous N products of nitrification and denitrification. Nitrifying activity, ambient NO(3), and nitrification N(2)O were positively correlated with percent base saturation. However, differences between watersheds in soil N substrate caused by presence of leguminous black locust in the disturbed watershed were confounded with differences in soil acidity. Denitrification was most strongly affected by soil moisture, which in turn was determined by precipitation events and slope position. Gaseous N losses from well-drained midslope and toeslope landscape positions appeared to be minor relative to other N transformations. Favorable conditions for denitrification occurred at a poorly drained site near the stream of the disturbed watershed. Laboratory incubations revealed high rates of NO(3) reduction in these soils. We speculate that the riparian zone is a major site of depletion of NO(3) from the soil solution via denitrification.

Emulsion based selection of T7 promoters of varying activity

The ability to build and control complex biological systems is greatly enhanced by the generation of related parts with varying strengths. In this way, various parts can be strung together and the connectivity and expression levels can be matched for the desired system performance. Engineered gene circuits, both in vivo and in vitro, often utilize the T7 RNA polymerase in tandem with the T7 promoter for transcription. In this work, we describe the selection of T7 promoter variants of varying strength by emulsifying in vitro transcription with subsequent fluorescence activated cell sorting (FACS) to enrich for active promoters. Such variant promoters should be of use to synthetic biologists for both in vivo and in vitro applications.

Directed evolution of proteins in vitro using compartmentalization in emulsions

This unit describes a protocol for the directed evolution of proteins utilizing in vitro compartmentalization. This method uses a large number of independent in vitro transcription and translation (IVTT) reactions in water droplets suspended in an oil emulsion to enable selection of proteins that bind a target molecule. Protein variants that bind the target also bind to and allow recovery of the genes that encoded them. This protocol serves as a basis for carrying out selections in emulsions, and can potentially be modified to select for other functionalities, including catalysis. This selection method is advantageous compared to alternative selection protocols due to the ability to screen through very large-size libraries and the ability to express and screen or select for functions that would otherwise be toxic or inaccessible to in vivo selections and screens.

Drought effects on litterfall, wood production and belowground carbon cycling in an Amazon forest: results of a throughfall reduction experiment

The Amazon Basin experiences severe droughts that may become more common in the future. Little is known of the effects of such droughts on Amazon forest productivity and carbon allocation. We tested the prediction that severe drought decreases litterfall and wood production but potentially has multiple cancelling effects on belowground production within a 7-year partial throughfall exclusion experiment. We simulated an approximately 35-41% reduction in effective rainfall from 2000 through 2004 in a 1ha plot and compared forest response with a similar control plot. Wood production was the most sensitive component of above-ground net primary productivity (ANPP) to drought, declining by 13% the first year and up to 62% thereafter. Litterfall declined only in the third year of drought, with a maximum difference of 23% below the control plot. Soil CO2 efflux and its 14C signature showed no significant treatment response, suggesting similar amounts and sources of belowground production. ANPP was similar between plots in 2000 and declined to a low of 41% below the control plot during the subsequent treatment years, rebounding to only a 10% difference during the first post-treatment year. Live aboveground carbon declined by 32.5Mgha-1 through the effects of drought on ANPP and tree mortality. Results of this unreplicated, long-term, large-scale ecosystem manipulation experiment demonstrate that multi-year severe drought can substantially reduce Amazon forest carbon stocks.