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Soil carbon loss is likely to increase due to climate warming, but microbiomes and microenvironments may dampen this effect. In a 30-year warming experiment, physical protection within soil aggregates affected the thermal responses of soil microbiomes and carbon dynamics. In this study, we combined metagenomic analysis with physical characterization of soil aggregates to explore mechanisms by which microbial communities respond to climate warming across different soil microenvironments. Long-term warming decreased the relative abundances of genes involved in degrading labile compounds (e.g. cellulose), but increased those genes involved in degrading recalcitrant compounds (e.g. lignin) across aggregate sizes. These changes were observed in most phyla of bacteria, especially for Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, and Planctomycetes. Microbial community composition was considerably altered by warming, leading to declined diversity for bacteria and fungi but not for archaea. Microbial functional genes, diversity, and community composition differed between macroaggregates and microaggregates, indicating the essential role of physical protection in controlling microbial community dynamics. Our findings suggest that microbes have the capacity to employ various strategies to acclimate or adapt to climate change (e.g. warming, heat stress) by shifting functional gene abundances and community structures in varying microenvironments, as regulated by soil physical protection.

Microbes are responsible for cycling carbon (C) through soils, and predicted changes in soil C stocks under climate change are highly sensitive to shifts in the mechanisms assumed to control the microbial physiological response to warming. Two mechanisms have been suggested to explain the long-term warming impact on microbial physiology: microbial thermal acclimation and changes in the quantity and quality of substrates available for microbial metabolism. Yet studies disentangling these two mechanisms are lacking. To resolve the drivers of changes in microbial physiology in response to long-term warming, we sampled soils from 13- and 28-year-old soil warming experiments in different seasons. We performed short-term laboratory incubations across a range of temperatures to measure the relationships between temperature sensitivity of physiology (growth, respiration, carbon use efficiency, and extracellular enzyme activity) and the chemical composition of soil organic matter. We observed apparent thermal acclimation of microbial respiration, but only in summer, when warming had exacerbated the seasonally-induced, already small dissolved organic matter pools. Irrespective of warming, greater quantity and quality of soil carbon increased the extracellular enzymatic pool and its temperature sensitivity. We propose that fresh litter input into the system seasonally cancels apparent thermal acclimation of C-cycling processes to decadal warming. Our findings reveal that long-term warming has indirectly affected microbial physiology via reduced C availability in this system, implying that earth system models including these negative feedbacks may be best suited to describe long-term warming effects on these soils.

How, where, and why carbon (C) moves into and out of an ecosystem through time are long-standing questions in biogeochemistry. Here, we bring together hundreds of thousands of C-cycle observations at the Harvard Forest in central Massachusetts, USA, a mid-latitude landscape dominated by 80–120-yr-old closed-canopy forests. These data answered four questions: (1) where and how much C is presently stored in dominant forest types; (2) what are current rates of C accrual and loss; (3) what biotic and abiotic factors contribute to variability in these rates; and (4) how has climate change affected the forest’s C cycle? Harvard Forest is an active C sink resulting from forest regrowth following land abandonment. Soil and tree biomass comprise nearly equal portions of existing C stocks. Net primary production (NPP) averaged 680–750 g C·m−2·yr−1; belowground NPP contributed 38–47% of the total, but with large uncertainty. Mineral soil C measured in the same inventory plots in 1992 and 2013 was too heterogeneous to detect change in soil-C pools; however, radiocarbon data suggest a small but persistent sink of 10–30 g C·m−2·yr−1. Net ecosystem production (NEP) in hardwood stands averaged ~300 g C·m−2·yr−1. NEP in hemlock-dominated forests averaged ~450 g C·m−2·yr−1 until infestation by the hemlock woolly adelgid turned these stands into a net C source. Since 2000, NPP has increased by 26%. For the period 1992–2015, NEP increased 93%. The increase in mean annual temperature and growing season length alone accounted for ~30% of the increase in productivity. Interannual variations in GPP and NEP were also correlated with increases in red oak biomass, forest leaf area, and canopy-scale light-use efficiency. Compared to long-term global change experiments at the Harvard Forest, the C sink in regrowing biomass equaled or exceeded C cycle modifications imposed by soil warming, N saturation, and hemlock removal. Results of this synthesis and comparison to simulation models suggest that forests across the region are likely to accrue C for decades to come but may be disrupted if the frequency or severity of biotic and abiotic disturbances increases.

The long atmospheric residence time of CO2 creates an urgent need to add atmospheric carbon drawdown to CO2 regulatory strategies. Synthetic and systems biology (SSB), which enables manipulation of cellular phenotypes, offers a powerful approach to amplifying and adding new possibilities to current land management practices aimed at reducing atmospheric carbon. The participants (in attendance: Christina Agapakis, George Annas, Adam Arkin, George Church, Robert Cook-Deegan, Charles DeLisi, Dan Drell, Sheldon Glashow, Steve Hamburg, Henry Jacoby, Henry Kelly, Mark Kon, Todd Kuiken, Mary Lidstrom, Mike MacCracken, June Medford, Jerry Melillo, Ron Milo, Pilar Ossorio, Ari Patrinos, Keith Paustian, Kristala Jones Prather, Kent Redford, David Resnik, John Reilly, Richard J. Roberts, Daniel Segre, Susan Solomon, Elizabeth Strychalski, Chris Voigt, Dominic Woolf, Stan Wullschleger, and Xiaohan Yang) identified a range of possibilities by which SSB might help reduce greenhouse gas concentrations and which might also contribute to environmental sustainability and adaptation. These include, among other possibilities, engineering plants to convert CO2 produced by respiration into a stable carbonate, designing plants with an increased root-to-shoot ratio, and creating plants with the ability to self-fertilize. A number of serious ecological and societal challenges must, however, be confronted and resolved before any such application can be fully assessed, realized, and deployed.

Nitrogen (N) availability exerts strong control on carbon storage in the forests of Northern Eurasia. Here, using a process-based model, we explore how three factors that alter N availability-permafrost degradation, atmospheric N deposition, and the abandonment of agricultural land to forest regrowth (land-use legacy)-affect carbon storage in the region's forest vegetation over the 21st century within the context of two IPCC global-change scenarios (RCPs 4.5 and 8.5). For RCP4.5, enhanced N availability results in increased tree carbon storage of 27.8 Pg C, with land-use legacy being the most important factor. For RCP8.5, enhanced N availability results in increased carbon storage in trees of 13.4 Pg C, with permafrost degradation being the most important factor. Our analysis reveals complex spatial and temporal patterns of regional carbon storage. This study underscores the importance of considering carbon-nitrogen interactions when assessing regional and sub-regional impacts of global change policies.

Global soil carbon (C) stocks are expected to decline with warming, and changes in microbial processes are key to this projection. However, warming responses of critical microbial parameters such as carbon use efficiency (CUE) and biomass turnover (rB) are not well understood. Here, we determine these parameters using a probabilistic inversion approach that integrates a microbial-enzyme model with 22 years of carbon cycling measurements at Harvard Forest. We find that increasing temperature reduces CUE but increases rB, and that two decades of soil warming increases the temperature sensitivities of CUE and rB. These temperature sensitivities, which are derived from decades-long field observations, contrast with values obtained from short-term laboratory experiments. We also show that long-term soil C flux and pool changes in response to warming are more dependent on the temperature sensitivity of CUE than that of rB. Using the inversion-derived parameters, we project that chronic soil warming at Harvard Forest over six decades will result in soil C gain of

Many serious ecosystem consequences of climate change will take decades or even centuries to emerge. Long-term ecological responses to global change are strongly regulated by slow processes, such as changes in species composition, carbon dynamics in soil and by long-lived plants, and accumulation of nutrient capitals. Understanding and predicting these processes require experiments on decadal time scales. But decadal experiments by themselves may not be adequate because many of the slow processes have characteristic time scales much longer than experiments can be maintained. This article promotes a coordinated approach that combines long-term, large-scale global change experiments with process studies and modeling. Long-term global change manipulative experiments, especially in high-priority ecosystems such as tropical forests and high-latitude regions, are essential to maximize information gain concerning future states of the earth system. The long-term experiments should be conducted in tandem with complementary process studies, such as those using model ecosystems, species replacements, laboratory incubations, isotope tracers, and greenhouse facilities. Models are essential to assimilate data from long-term experiments and process studies together with information from long-term observations, surveys, and space-for-time studies along environmental and biological gradients. Future research programs with coordinated long-term experiments, process studies, and modeling have the potential to be the most effective strategy to gain the best information on long-term ecosystem dynamics in response to global change.

Hartley et al. question whether reduction in Rmass, under experimental warming, arises because of the biomass method. We show the method they treat as independent yields the same result. We describe why the substrate-depletion hypothesis may not solely explain observed responses, and urge caution in interpretation of the seasonal data. © 2009 Blackwell Publishing Ltd/CNRS.

In the short-term heterotrophic soil respiration is strongly and positively related to temperature. In the long-term, its response to temperature is uncertain. One reason for this is because in field experiments increases in respiration due to warming are relatively short-lived. The explanations proposed for this ephemeral response include depletion of fast-cycling, soil carbon pools and thermal adaptation of microbial respiration. Using a > 15 year soil warming experiment in a mid-latitude forest, we show that the apparent 'acclimation' of soil respiration at the ecosystem scale results from combined effects of reductions in soil carbon pools and microbial biomass, and thermal adaptation of microbial respiration. Mass-specific respiration rates were lower when seasonal temperatures were higher, suggesting that rate reductions under experimental warming likely occurred through temperature-induced changes in the microbial community. Our results imply that stimulatory effects of global temperature rise on soil respiration rates may be lower than currently predicted.

Agricultural soils play a dual role in regulating the Earth's climate by releasing or sequestering carbon dioxide (CO2) in soil organic carbon (SOC) and emitting non‐CO2 greenhouse gases (GHGs) such as nitrous oxide (N2O) and methane (CH4). To understand how agricultural soils can play a role in climate solutions requires a comprehensive assessment of net soil GHG balance (i.e., sum of SOC‐sequestered CO2 and non‐CO2 GHG emissions) and the underlying controls. Herein, we used a model‐data integration approach to understand and quantify how natural and anthropogenic factors have affected the magnitude and spatiotemporal variations of the net soil GHG balance in U.S. croplands during 1960–2018. Specifically, we used the dynamic land ecosystem model for regional simulations and used field observations of SOC sequestration rates and N2O and CH4 emissions to calibrate, validate, and corroborate model simulations. Results show that U.S. agricultural soils sequestered 13.2±1.16$$ 13.2\pm 1.16 $$ Tg CO2‐C year−1 in SOC (at a depth of 3.5 m) during 1960–2018 and emitted 0.39±0.02$$ 0.39\pm 0.02 $$ Tg N2O‐N year−1 and 0.21±0.01$$ 0.21\pm 0.01 $$ Tg CH4‐C year−1, respectively. Based on the GWP100 metric (global warming potential on a 100‐year time horizon), the estimated national net GHG emission rate from agricultural soils was 122.3±11.46$$ 122.3\pm 11.46 $$ Tg CO2‐eq year−1, with the largest contribution from N2O emissions. The sequestered SOC offset ~28% of the climate‐warming effects resulting from non‐CO2 GHG emissions, and this offsetting effect increased over time. Increased nitrogen fertilizer use was the dominant factor contributing to the increase in net GHG emissions during 1960–2018, explaining ~47% of total changes. In contrast, reduced cropland area, the adoption of agricultural conservation practices (e.g., reduced tillage), and rising atmospheric CO2 levels attenuated net GHG emissions from U.S. croplands. Improving management practices to mitigate N2O emissions represents the biggest opportunity for achieving net‐zero emissions in U.S. croplands. Our study highlights the importance of concurrently quantifying SOC‐sequestered CO2 and non‐CO2 GHG emissions for developing effective agricultural climate change mitigation measures. [ABSTRACT FROM AUTHOR]