Search

Soils are among the most biodiverse habitats on earth and while the species composition of microbial communities can influence decomposition rates and pathways, the functional significance of many microbial species and phylogenetic groups remains unknown. If bacteria exhibit phylogenetic organization in their function, this could enable ecologically meaningful classification of bacterial clades. Here, we show non-random phylogenetic organization in the rates of relative carbon assimilation for both rapidly mineralized substrates (amino acids and glucose) assimilated by many microbial taxa and slowly mineralized substrates (lipids and cellulose) assimilated by relatively few microbial taxa. When mapped onto bacterial phylogeny using ancestral character estimation this phylogenetic organization enabled the identification of clades involved in the decomposition of specific soil organic matter substrates. Phylogenetic organization in substrate assimilation could provide a basis for predicting the functional attributes of uncharacterized microbial taxa and understanding the significance of microbial community composition for soil organic matter decomposition.

Elevated atmospheric CO2 (eCO2 ) generally increases carbon input in rice paddy soils and stimulates the growth of methane-producing microorganisms. Therefore, eCO2 is widely expected to increase methane (CH4 ) emissions from rice agriculture, a major source of anthropogenic CH4 . Agricultural practices strongly affect CH4 emissions from rice paddies as well, but whether these practices modulate effects of eCO2 is unclear. Here we show, by combining a series of experiments and meta-analyses, that whereas eCO2 strongly increased CH4 emissions from paddies without straw incorporation, it tended to reduce CH4 emissions from paddy soils with straw incorporation. Our experiments also identified the microbial processes underlying these results: eCO2 increased methane-consuming microorganisms more strongly in soils with straw incorporation than in soils without straw, with the opposite pattern for methane-producing microorganisms. Accounting for the interaction between CO2 and straw management, we estimate that eCO2 increases global CH4 emissions from rice paddies by 3.7%, an order of magnitude lower than previous estimates. Our results suggest that the effect of eCO2 on CH4 emissions from rice paddies is smaller than previously thought and underline the need for judicious agricultural management to curb future CH4 emissions.

Plant diversity can increase biomass production in plot-scale studies, but applying these results to ecosystem carbon (C) storage at larger spatial and temporal scales remains problematic. Other ecosystem controls interact with diversity and plant production, and may influence soil pools differently from plant pools. We integrated diversity with the state-factor framework, which identifies key controls, or 'state factors', over ecosystem properties and services such as C storage. We used this framework to assess the effects of diversity, plant traits and state factors (climate, topography, time) on live tree, standing dead, organic horizon and total C in Québec forests. Four patterns emerged: (1) while state factors were usually the most important model predictors, models with both state and biotic factors (mean plant traits and diversity) better predicted C pools; (2) mean plant traits were better predictors than diversity; (3) diversity increased live tree C but reduced organic horizon C; (4) different C pools responded to different traits and diversity metrics. These results suggest that, where ecosystem properties result from multiple processes, no simple relationship may exist with any one organismal factor. Integrating biodiversity into ecosystem ecology and assessing both traits and diversity improves our mechanistic understanding of biotic effects on ecosystems.

Nitrogen (N) is frequently a limiting nutrient in soil; its availability can govern ecosystem functions such as primary production and decomposition. Assimilation of N by microorganisms impacts the availability of N in soil. Despite its established ecological significance, the contributions of microbial taxa to N assimilation are unknown. Here we measure N uptake and use by microbial phylotypes and taxonomic groups within a diverse assemblage of soil microbes through quantitative stable isotope probing (qSIP) with 15 N. Following incubation with 15 NH4+, distinct patterns of 15 N assimilation among taxonomic groups were observed. For instance, glucose addition stimulated 15 N assimilation in most members of Actinobacteria and Proteobacteria but generally decreased 15 N use by Firmicutes and Bacteriodetes. While NH4+ is considered a preferred and universal source of N to prokaryotes, the majority (> 80%) of N assimilation in our soils could be attributed to a handful of active orders. Characterizing N assimilation of taxonomic groups with 15 N qSIP may provide a basis for understanding how microbial community composition influences N availability in the environment.

Contents Summary 507 I. Introduction 507 II. The return on investment approach 508 III. CO2 response spectrum 510 IV. Discussion 516 Acknowledgements 518 References 518 SUMMARY: Land ecosystems sequester on average about a quarter of anthropogenic CO2 emissions. It has been proposed that nitrogen (N) availability will exert an increasingly limiting effect on plants' ability to store additional carbon (C) under rising CO2 , but these mechanisms are not well understood. Here, we review findings from elevated CO2 experiments using a plant economics framework, highlighting how ecosystem responses to elevated CO2 may depend on the costs and benefits of plant interactions with mycorrhizal fungi and symbiotic N-fixing microbes. We found that N-acquisition efficiency is positively correlated with leaf-level photosynthetic capacity and plant growth, and negatively with soil C storage. Plants that associate with ectomycorrhizal fungi and N-fixers may acquire N at a lower cost than plants associated with arbuscular mycorrhizal fungi. However, the additional growth in ectomycorrhizal plants is partly offset by decreases in soil C pools via priming. Collectively, our results indicate that predictive models aimed at quantifying C cycle feedbacks to global change may be improved by treating N as a resource that can be acquired by plants in exchange for energy, with different costs depending on plant interactions with microbial symbionts.

Antibiotic-resistant pathogens increasingly threaten human health. Widespread application of antibiotics to animal populations raised for food, including chickens, cattle, and pigs, selects for resistance and contributes to the evolution of those pathogens. Despite a half century of research establishing the mechanisms and pathways by which antibiotic-resistant bacteria spread from food animals to people, scientists lack the appropriate data and models to estimate the public health burden of antibiotic-resistant human infections attributable to antibiotic use in food-animal production. Genomic technologies are enabling researchers to track the bidirectional transmissions of specific bacterial strains from livestock to people – and from people to livestock – that can amplify resistance traits. Concepts in ecology, which were developed to understand resource subsidies, metapopulations, and biological invasions, provide insight into the epidemiology of antibiotic resistance from genomic data. By applying ecological principles to highly resolved phylogenetic data, researchers can improve strategies for controlling antibiotic resistance.

Rising levels of atmospheric CO2 frequently stimulate plant inputs to soil, but the consequences of these changes for soil carbon (C) dynamics are poorly understood. Plant-derived inputs can accumulate in the soil and become part of the soil C pool (“new soil C”), or accelerate losses of pre-existing (“old”) soil C. The dynamics of the new and old pools will likely differ and alter the long-term fate of soil C, but these separate pools, which can be distinguished through isotopic labeling, have not been considered in past syntheses. Using meta-analysis, we found that while elevated CO2 (ranging from 550 to 800 parts per million by volume) stimulates the accumulation of new soil C in the short term (

Growth of soil microorganisms is often described as carbon limited, and adding labile carbon to soil often results in a transient and large increase in respiration. In contrast, soil microbial biomass changes little, suggesting that growth and respiration are decoupled in response to a carbon pulse. Alternatively, measuring bulk responses of the entire community (total respiration and biomass) could mask ecologically important variation among taxa in response to the added carbon. Here, we assessed taxon-specific variation in cellular growth (measured as DNA synthesis) and metabolic activity (measured as rRNA synthesis) following glucose addition to soil using quantitative stable isotope probing with H218 O. We found that glucose addition altered rates of DNA and rRNA synthesis, but the effects were strongly taxon specific: glucose stimulated growth and rRNA transcription for some taxa, and suppressed these for others. These contrasting taxon-specific responses could explain the small and transient changes in total soil microbial biomass. Responses to glucose were not well predicted by a priori assignments of taxa into copiotrophic or oligotrophic categories. Across all taxa, rates of DNA and rRNA synthesis changed in parallel, indicating that growth and activity were coupled, and the degree of coupling was unaffected by glucose addition. This pattern argues against the idea that labile carbon addition causes a large reduction in metabolic growth efficiency; rather, the large pulse of respiration observed with labile substrate addition is more likely to be the result of rapid turnover of microbial biomass, possibly due to trophic interactions. Our results support a strong connection between rRNA synthesis and bacterial growth, and indicate that taxon-specific responses among soil bacteria can buffer responses at the scale of the whole community.

Identification of microorganisms that facilitate the cycling of nutrients in freshwater is paramount to understanding how these ecosystems function. Here, we identify growing aquatic bacteria using H218O quantitative stable isotope probing. During 8 day incubations in 97 atom % H218O, 54% of the taxa grew. The most abundant phyla among growing taxa were Proteobacteria (45%), Bacteroidetes (30%) and Firmicutes (10%). Taxa differed in isotopic enrichment, reflecting variation in DNA replication of bacterial populations. At the class level, the highest atom fraction excess was observed for OPB41 and δ-Proteobacteria. There was no linear relationship between 18 O incorporation and abundance of taxa. δ-Proteobacteria and OPB41 were not abundant, yet the DNA of both taxa was highly enriched in 18 O. Bacteriodetes, in contrast, were abundant but not highly enriched. Our study shows that a large proportion of the bacterial taxa found on decomposing leaf litter grew slowly, and several low abundance taxa were highly enriched. These findings indicating that rare organisms may be important for the decomposition of leaf litter in streams, and that quantitative stable isotope probing with H218O can be used to advance our understanding of microorganisms in freshwater by identifying species that are growing in complex communities.

Changing climate and a legacy of fire-exclusion have increased the probability of high-severity wildfire, leading to an increased risk of forest carbon loss in ponderosa pine forests in the southwestern USA. Efforts to reduce high-severity fire risk through forest thinning and prescribed burning require both the removal and emission of carbon from these forests, and any potential carbon benefits from treatment may depend on the occurrence of wildfire. We sought to determine how forest treatments alter the effects of stochastic wildfire events on the forest carbon balance. We modeled three treatments (control, thin-only, and thin and burn) with and without the occurrence of wildfire. We evaluated how two different probabilities of wildfire occurrence, 1% and 2% per year, might alter the carbon balance of treatments. In the absence of wildfire, we found that thinning and burning treatments initially reduced total ecosystem carbon (TEC) and increased net ecosystem carbon balance (NECB). In the presence of wildfire, the thin and burn treatment TEC surpassed that of the control in year 40 at 2%/yr wildfire probability, and in year 51 at 1%/yr wildfire probability. NECB in the presence of wildfire showed a similar response to the no-wildfire scenarios: both thin-only and thin and burn treatments increased the C sink. Treatments increased TEC by reducing both mean wildfire severity and its variability. While the carbon balance of treatments may differ in more productive forest types, the carbon balance benefits from restoring forest structure and fire in southwestern ponderosa pine forests are clear.

Stawitz and colleagues (2016) present an analysis of seafood mislabeling and make inferences about its financial and ecological implications. We applaud the authors for tackling this important topic. As presented, however, we have reservations about the research which call into question the main conclusions. First, based on the data and results that are presented, there appear to be errors and some of the conclusions are not supported. Second, there may be a bias in the analyses that favors the conclusions. Third, details are lacking regarding the analyses, challenging their verification. We briefly describe some of the issues. This article is protected by copyright. All rights reserved

Understanding how population‐level dynamics contribute to ecosystem‐level processes is a primary focus of ecological research and has led to important breakthroughs in the ecology of macroscopic organisms. However, the inability to measure population‐specific rates, such as growth, for microbial taxa within natural assemblages has limited ecologists’ understanding of how microbial populations interact to regulate ecosystem processes. Here, we use isotope incorporation within DNA molecules to model taxon‐specific population growth in the presence of 18O‐labeled water. By applying this model to phylogenetic marker sequencing data collected from stable‐isotope probing studies, we estimate rates of growth, mortality, and turnover for individual microbial populations within soil assemblages. When summed across the entire bacterial community, our taxon‐specific estimates are within the range of other whole‐assemblage measurements of bacterial turnover. Because it can be applied to environmental samples, the approach we present is broadly applicable to measuring population growth, mortality, and associated biogeochemical process rates of microbial taxa for a wide range of ecosystems and can help reveal how individual microbial populations drive biogeochemical fluxes.

Studies focusing on seasonal dynamics of microbial communities in terrestrial and marine environments are common; however, little is known about seasonal dynamics in high-temperature environments. Thus, our objective was to document the seasonal dynamics of both the physicochemical conditions and the microbial communities inhabiting hot springs in Tengchong County, Yunnan Province, China. The PhyloChip microarray detected 4882 operational taxonomic units (OTUs) within 79 bacterial phylum-level groups and 113 OTUs within 20 archaeal phylum-level groups, which are additional 54 bacterial phyla and 11 archaeal phyla to those that were previously described using pyrosequencing. Monsoon samples (June 2011) showed increased concentrations of potassium, total organic carbon, ammonium, calcium, sodium and total nitrogen, and decreased ferrous iron relative to the dry season (January 2011). At the same time, the highly ordered microbial communities present in January gave way to poorly ordered communities in June, characterized by higher richness of Bacteria, including microbes related to mesophiles. These seasonal changes in geochemistry and community structure are likely due to high rainfall influx during the monsoon season and indicate that seasonal dynamics occurs in high-temperature environments experiencing significant changes in seasonal recharge. Thus, geothermal environments are not isolated from the surrounding environment and seasonality affects microbial ecology.

Summary Disturbance affects most terrestrial ecosystems and has the potential to shape their responses to chronic environmental change. 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. 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. 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.

Summary 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. 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. 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. 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.

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. 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. 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. 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.

Summary 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. 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. 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. 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.

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.

Breeding high-yielding rice cultivars through increasing biomass is a key strategy to meet rising global food demands. Yet, increasing rice growth can stimulate methane (CH4 ) emissions, exacerbating global climate change, as rice cultivation is a major source of this powerful greenhouse gas. Here, we show in a series of experiments that high-yielding rice cultivars actually reduce CH4 emissions from typical paddy soils. Averaged across 33 rice cultivars, a biomass increase of 10% resulted in a 10.3% decrease in CH4 emissions in a soil with a high carbon (C) content. Compared to a low-yielding cultivar, a high-yielding cultivar significantly increased root porosity and the abundance of methane-consuming microorganisms, suggesting that the larger and more porous root systems of high-yielding cultivars facilitated CH4 oxidation by promoting O2 transport to soils. Our results were further supported by a meta-analysis, showing that high-yielding rice cultivars strongly decrease CH4 emissions from paddy soils with high organic C contents. Based on our results, increasing rice biomass by 10% could reduce annual CH4 emissions from Chinese rice agriculture by 7.1%. Our findings suggest that modern rice breeding strategies for high-yielding cultivars can substantially mitigate paddy CH4 emission in China and other rice growing regions.

Summary Six terrestrial ecosystems in the USA were exposed to elevated atmospheric CO2 in single or multifacto- rial experiments for more than a decade to assess potential impacts. We retrospectively assessed soil bacterial community responses in all six-field experi- ments and found ecosystem-specific and common patterns of soil bacterial community response to elevated CO2. Soil bacterial composition differed greatly across the six ecosystems. No common effect of elevated atmospheric CO2 on bacterial biomass, richness and community composition across all of the ecosystems was identified, although significant responses were detected in individual ecosystems. The most striking common trend across the sites was a decrease of up to 3.5-fold in the relative abundance of Acidobacteria Group 1 bacteria in soils exposed to elevated CO2 or other climate factors. The Acidobac- teria Group 1 response observed in exploratory 16S rRNA gene clone library surveys was validated in one ecosystem by 100-fold deeper sequencing and semi- quantitative PCR assays. Collectively, the 16S rRNA gene sequencing approach revealed influences of elevated CO2 on multiple ecosystems. Although few common trends across the ecosystems were detected in the small surveys, the trends may be har- bingers of more substantive changes in less abun- dant, more sensitive taxa that can only be detected by deeper surveys.

Ambient nitrous oxide (N(2)O) emissions from Great Boiling Spring (GBS) in the US Great Basin depended on temperature, with the highest flux, 67.8 ± 2.6 μmol N(2)O-N m(-2) day(-1) , occurring in the large source pool at 82 °C. This rate of N(2)O production contrasted with negligible production from nearby soils and was similar to rates from soils and sediments impacted with agricultural fertilizers. To investigate the source of N(2)O, a variety of approaches were used to enrich and isolate heterotrophic micro-organisms, and isolates were screened for nitrate reduction ability. Nitrate-respiring isolates were identified by 16S rRNA gene sequencing as Thermus thermophilus (31 isolates) and T. oshimai (three isolates). All isolates reduced nitrate to N(2)O but not to dinitrogen and were unable to grow with N(2)O as a terminal electron acceptor. Representative T. thermophilus and T. oshimai strains contained genes with 96-98% and 93% DNA identity, respectively, to the nitrate reductase catalytic subunit gene (narG) of T. thermophilus HB8. These data implicate T. thermophilus and T. oshimai in high flux of N(2)O in GBS and raise questions about the genetic basis of the incomplete denitrification pathway in these organisms and on the fate of biogenic N(2)O in geothermal environments.

Summary Elevated atmospheric CO2 generally increases plant productivity and subsequently increases the avail- ability of cellulose in soil to microbial decomposers. As key cellulose degraders, soil fungi are likely to be one of the most impacted and responsive microbial groups to elevated atmospheric CO2. To investigate the impacts of ecosystem type and elevated atmo- spheric CO2 on cellulolytic fungal communities, we sequenced 10 677 cbhI gene fragments encoding the catalytic subunit of cellobiohydrolase I, across five distinct terrestrial ecosystem experiments after a decade of exposure to elevated CO2. The cbhI composition of each ecosystem was distinct, as supported by weighted Unifrac analyses (all P-values; < 0.001), with few operational taxonomic units (OTUs) being shared across ecosystems. Using a 114-member cbhI sequence database compiled from known fungi, less than 1% of the environmental sequences could be classified at the family level indi- cating that cellulolytic fungi in situ are likely domi- nated by novel fungi or known fungi that are not yet recognized as cellulose degraders. Shifts in fungal cbhI composition and richness that were correlated with elevated CO2 exposure varied across the ecosys- tems. In aspen plantation and desert creosote bush soils, cbhI gene richness was significantly higher after exposure to elevated CO2 (550 mmol mol -1 ) than under ambient CO2 (360 mmol mol -1 CO2). In contrast, while the richness was not altered, the relative abun- dance of dominant OTUs in desert soil crusts was significantly shifted. This suggests that responses are complex, vary across different ecosystems and, in at least one case, are OTU-specific. Collectively, our results document the complexity of cellulolytic fungal communities in multiple terrestrial ecosystems and the variability of their responses to long-term exposure to elevated atmospheric CO2.

thermophilus narG revealed sediment populations of 1.3-1.7 ¥ 10 6 copies g -1 sediment. These data indicate a highly active nitrogen cycle (N-cycle) in these springs and suggest that ammonia oxidation may be a major source of energy fuelling primary production.

Global mean temperature is predicted to increase by 2–71C and precipitation to change across the globe by the end of this century. To quantify climate effects on ecosystem processes, a number of climate change experiments have been established around the world in various ecosystems. Despite these efforts, general responses of terrestrial ecosystems to changes in temperature and precipitation, and especially to their combined effects, remain unclear. We used metaanalysis to synthesize ecosystem-level responses to warming, altered precipitation, and their combination. We focused on plant growth and ecosystem carbon (C) balance, including biomass, net primary production (NPP), respiration, net ecosystem exchange (NEE), and ecosystem photosynthesis, synthesizing results from 85 studies. We found that experimental warming and increased precipitation generally stimulated plant growth and ecosystem C fluxes, whereas decreased precipitation had the opposite effects. For example, warming significantly stimulated total NPP, increased ecosystem photosynthesis, and ecosystem respiration. Experimentally reduced precipitation suppressed aboveground NPP (ANPP) and NEE, whereas supplemental precipitation enhanced ANPP and NEE. Plant productivity and ecosystem C fluxes generally showed higher sensitivities to increased precipitation than to decreased precipitation. Interactive effects of warming and altered precipitation tended to be smaller than expected from additive, single-factor effects, though low statistical power limits the strength of these conclusions. New experiments with combined temperature and precipitation manipulations are needed to conclusively determine the importance of temperature–precipitation interactions on the C balance of terrestrial ecosystems under future climate conditions.

Ecologists often equate litter quality with decomposition rate. In soil and sediments, litter that is rapidly decomposed by microbes often has low concentrations of tannin and lignin and low C:N ratios. Do these same traits also favor element transfer to higher trophic levels in streams, where many insects depend on litter as their primary food source? We test the hypothesis that slow decomposition rates promote element transfer from litter to insects, whereas rapid decomposition favors microbes. We measured carbon and nitrogen fluxes from four plant species to a leaf‐shredding caddisfly using isotopically labeled litter. Caddisflies assimilated a higher percentage of litter carbon and nitrogen lost from slowly decomposing litters (Platanus wrightii and Quercus gambelii). In contrast, rapidly decomposing litters (Fraxinus velutina and Populus fremontii) supported higher microbial biomass. These results challenge the view that rapidly decomposing litter is higher quality by demonstrating that slowly decomposing litters provide a critical resource for insects.

Soil is the largest reservoir of organic carbon (C) in the terrestrial biosphere and soil C has a relatively long mean residence time. Rising atmospheric carbon dioxide (CO2) concentrations generally increase plant growth and C input to soil, suggesting that soil might help mitigate atmospheric CO2 rise and global warming. But to what extent mitigation will occur is unclear. The large size of the soil C pool not only makes it a potential buffer against rising atmospheric CO2, but also makes it difficult to measure changes amid the existing background. Meta-analysis is one tool that can overcome the limited power of single studies. Four recent meta-analyses addressed this issue but reached somewhat different conclusions about the effect of elevated CO2 on soil C accumulation, especially regarding the role of nitrogen (N) inputs. Here, we assess the extent of differences between these conclusions and propose a new analysis of the data. The four meta-analyses included different studies, derived different effect size estimates from common studies, used different weighting functions and metrics of effect size, and used different approaches to address nonindependence of effect sizes. Although all factors influenced the mean effect size estimates and subsequent inferences, the approach to independence had the largest influence. We recommend that meta-analysts critically assess and report choices about effect size metrics and weighting functions, and criteria for study selection and independence. Such decisions need to be justified carefully because they affect the basis for inference. Our new analysis, with a combined data set, confirms that the effect of elevated CO2 on net soil C accumulation increases with the addition of N fertilizers. Although the effect at low N inputs was not significant, statistical power to detect biogeochemically important effect sizes at low N is limited, even with meta-analysis, suggesting the continued need for long-term experiments.

The effects of elevated CO 2 on plant growth and insect herbivory have been frequently investigated over the past 20 years. Most studies have shown an increase in plant growth, a decrease in plant nitrogen concentration, an increase in plant secondary metabolites and a decrease in herbivory. However, such studies have generally overlooked the fact that increases in plant production could cause increases of herbivores per unit area of habitat. Our study investigated leaf production, herbivory levels and herbivore abundance per unit area of leaf litter in a scrub-oak system at Kennedy Space Center, Florida, under conditions of ambient and elevated CO 2 , over an 11-year period, from 1996 to 2007. In every year, herbivory, that is leafminer and leaftier abundance per 200 leaves, was lower under elevated CO 2 than ambient CO 2 for each of three species of oaks, Quercus myrtifolia, Quercus chapmanii and Quercus geminata. However, leaf litter production per 0.1143 m 2 was greater under elevated CO 2 than ambient CO 2 for Q. myrtifolia and Q. chapmanii, and this difference increased over the 11 years of the study. Leaf production of Q. geminata under elevated CO 2 did not increase. Leafminer densities per 0.1143 m 2 of litterfall for Q. myrtifolia and Q. chapmanii were initially lower under elevated CO 2 . However, shortly after canopy closure in 2001, leafminer densities per 0.1143 m 2 of litter fall became higher under elevated CO 2 and remained higher for the remainder of the experiment. Leaftier densities per 0.1143 m 2 were also higher under elevated CO 2 for Q. myrtifolia and Q. chapmanii over the last 6 years of the experiment. There were no differences in leafminer or leaftier densities per 0.1143 m 2 of litter for Q. geminata. These results show three phenomena. First, they show that elevated CO 2 decreases herbivory on all oak species in the Florida scrub-oak system. Second, despite lower numbers of herbivores per 200 leaves in elevated CO 2 increased leaf production resulted in higher herbivore densities per unit area of leaf litter for two oak species. Third, they corroborate other studies which suggest that the effects of elevated CO 2 on herbivores are species specific, meaning they depend on the particular plant species involved. Two oak species showed increases in leaf production and herbivore densities per 0.1143 m 2 in elevated CO 2 over time while another oak species did not. Our results point to a future world of elevated CO 2 where, despite lower plant herbivory, some insect herbivores may become more common.

A scrub-oak woodland has maintained higher aboveground biomass accumulation after 11 years of atmospheric CO 2 enrichment (ambient + 350 μmol CO 2 mol ―1 ), despite the expectation of strong nitrogen (N) limitation at the site. We hypothesized that changes in plant available N and exploitation of deep sources of inorganic N in soils have sustained greater growth at elevated CO 2 . We employed a suite of assays performed in the sixth and 11th year of a CO 2 enrichment experiment designed to assess soil N dynamics and N availability in the entire soil profile. In the 11th year, we found no differences in gross N flux, but significantly greater microbial respiration (P≤0.01) at elevated CO 2 . Elevated CO 2 lowered extractable inorganic N concentrations (P = 0.096) considering the whole soil profile (0―190 cm). Conversely, potential net N mineralization, although not significant in considering the entire profile (P = 0.460), tended to be greater at elevated CO 2 . Ion-exchange resins placed in the soil profile for approximately 1 year revealed that potential N availability at the water table was almost 3 x greater than found elsewhere in the profile, and we found direct evidence using a 15 N tracer study that plants took up N from the water table. Increased microbial respiration and shorter mean residence times of inorganic N at shallower depths suggests that enhanced SOM decomposition may promote a sustained supply of inorganic N at elevated CO 2 . Deep soil N availability at the water table is considerable, and provides a readily available source of N for plant uptake. Increased plant growth at elevated CO 2 in this ecosystem may be sustained through greater inorganic N supply from shallow soils and N uptake from deep soil.

This study reports the aboveground biomass response of a fire-regenerated Florida scruboak ecosystem exposed to elevated CO2 (1996‐2007), from emergence after fire through canopy closure. Eleven years exposure to elevated CO2 caused a 67% increase in aboveground shoot biomass. Growth stimulation was sustained throughout the experiment; although there was significant variability between years. The absolute stimulation of aboveground biomass generally declined over time, reflecting increasing environmental limitations to long-term growth response. Extensive defoliation caused by hurricanes in September 2004 was followed by a strong increase in shoot density in 2005 that may have resulted from reopening the canopy and relocating nitrogen from leaves to the nutrientpoor soil. Biomass response to elevated CO2 was driven primarily by stimulation of growth of the dominant species, Quercus myrtifolia, while Quercus geminata, the other co-dominant oak, displayed no significant CO2 response. Aboveground growth also displayed interannual variation, which was correlated with total annual rainfall. The

Management of forests for carbon uptake is an important tool in the effort to slow the increase in atmospheric CO2 and global warming. However, some current policies governing forest carbon credits actually promote avoidable CO2 release and punish actions that would increase long-term carbon storage. In fire-prone forests, management that reduces the risk of catastrophic carbon release resulting from stand-replacing wild-fire is considered to be a CO2 source, according to current accounting practices, even though such management may actually increase long-term carbon storage. Examining four of the largest wildfires in the US in 2002, we found that, for forest land that experienced catastrophic stand-replacing fire, prior thinning would have reduced CO2 release from live tree biomass by as much as 98%. Altering carbon accounting practices for forests that have historically experienced frequent, low-severity fire could provide an incentive for forest managers to reduce the risk of catastrophic fire and asso...

Forest ecosystems assimilate more CO2 from the atmosphere and store more carbon in woody biomass than most nonforest ecosystems, indicating strong potential for afforestation to serve as a carbon management tool. However, converting grasslands to forests could affect ecosystem‐atmosphere exchanges of other greenhouse gases, such as nitrous oxide and methane (CH4), effects that are rarely considered. Here, we show that afforestation on a well-aerated grassland in Siberia reduces soil CH4 uptake by a factor of 3 after 35 years of tree growth. The decline in CH4 oxidation was observed both in the field and in laboratory incubation studies under controlled environmental conditions, suggesting that not only physical but also biological factors are responsible for the observed effect. Using incubation experiments with 13 CH4 and tracking 13 C incorporation into bacterial phospholipid fatty acid (PLFA), we found that, at low CH4 concentrations, most of the 13 C was incorporated into only two PLFAs, 18:1x7 and 16:0. High CH4 concentration increased total 13 C incorporation and the number of PLFA peaks that became labeled, suggesting that the microbial assemblage oxidizing CH4 shifts with ambient CH4 concentration. Forests and grasslands exhibited similar labeling profiles for the high-affinity methanotrophs, suggesting that largely the same general groups of methanotrophs were active in both ecosystems. Both PLFA concentration and labeling patterns indicate a threefold decline in the biomass of active methanotrophs due to afforestation, but little change in the methanotroph community. Because the grassland consumed CH4 at a rate five times higher than forest soils under laboratory conditions, we concluded that not only biomass but also cell-specific activity was higher in grassland than in afforested plots. While the decline in biomass of active methanotrophs can be explained by site preparation (plowing), inorganic N (especially NH4 1 ) could be responsible for the change in cell-specific activity. Overall, the negative effect of afforestation of upland grassland on soil CH4 uptake can be largely explained by the reduction in biomass and to a lesser extent by reduced cell-specific activity of CH4-oxidizing bacteria.

Ponderosa pine (Pinus ponderosa) forests of the southwestern United States are a mosaic of stands where undisturbed forests are carbon sinks, and stands recovering from wildfires may be sources of carbon to the atmosphere for decades after the fire. However, the relative magnitude of these sinks and sources has never been directly measured in this region, limiting our understanding of the role of fire in regional and US carbon budgets. We used the eddy covariance technique to measure the CO2 exchange of two forest sites, one burned by fire in 1996, and an unburned forest. The fire was a high-intensity stand-replacing burn that killed all trees. Ten years after the fire, the burned site was still a source of CO2 to the atmosphere [109±6 (SEM) g C m−2 yr−1], whereas the unburned site was a sink (−164±23 g C m−2 yr−1). The fire reduced total carbon storage and shifted ecosystem carbon allocation from the forest floor and living biomass to necromass. Annual ecosystem respiration was lower at the burned site (480±5 g C m−2 yr−1) than at the unburned site (710±54 g C m−2 yr−1), but the difference in gross primary production was even larger (372±13 g C m−2 yr−1 at the burned site and 858±37 g C m−2 yr−1at the unburned site). Water availability controlled carbon flux in the warm season at both sites, and the burned site was a source of carbon in all months, even during the summer, when wet and warm conditions favored respiration more than photosynthesis. Our study shows that carbon losses following stand-replacing fires in ponderosa pine forests can persist for decades due to slow recovery of the gross primary production. Because fire exclusion is becoming increasingly difficult in dry western forests, a large US forest carbon sink could shift to a decadal-scale carbon source.

Summary 1. Ecological restoration often involves returning ecosystem structure to some predisturbance reference state, but ecosystem function must also recover if restoration efforts are to be self-sustaining over the long term. In the south-western United States, ponderosa pine forest structure was altered by disruption of the fire regime following Euro-American settlement. Forest structure is now being restored to presettlement conditions through the application of thinning and burning treatments. However, the effects of these treatments on below-ground ecosystem processes remain unclear. 2. We conducted a water and nitrogen (N) addition experiment in adjacent restored and unrestored ponderosa pine stands and compared soil CO 2 efflux in response to these treatments over a 13-month period. Our goals were to (i) quantify water and N limitation to below-ground carbon (C) cycling in contemporary high-density ponderosa pine forests; and (ii) determine if restoration alleviates water and N limitations. 3. Restoration thinning and burning increased soil CO 2 efflux, along with surface soil water content, temperature and herbaceous fine root biomass, while total fine root biomass decreased as a result of restoration. 4. Water and N additions increased C flux from soils to a similar degree in both restored and unrestored ponderosa pine stands, but the increase was relatively small when compared to that stimulated by restoration. 5. Synthesis and applications. An understanding of how ecosystem processes respond to treatments designed to restore ecosystem structure is critical in ensuring the long-term success of restoration efforts. Here we show that, although water and N stimulate C flux from soils in these semi-arid forests, restoration treatments have a much greater effect on soil C balance than increased water and N availability by themselves. This suggests that increased quality of C inputs from a recovering understorey herbaceous community is a key component of restoring ecosystem function (e.g. below-ground C cycling) in south-western ponderosa pine forests.

Hurricane disturbances have profound impacts on ecosystem structure and function, yet their effects on ecosystem CO2 exchange have not been reported. In September 2004, our research site on a fire-regenerated scrub-oak ecosystem in central Florida was struck by Hurricane Frances with sustained winds of 113kmh � 1 and wind gusts as high as 152kmh � 1 . We quantified the hurricane damage on this ecosystem resulting from defoliation: we measured net ecosystem CO2 exchange, the damage and recovery of leaf area, and determined whether growth in elevated carbon dioxide concentration in the atmosphere (Ca) altered this disturbance. The hurricane decreased leaf area index (LAI) by 21%, which was equal to 60% of seasonal variation in canopy growth during the previous 3 years, but stem damage was negligible. The reduction in LAI led to a 22% decline in gross primary production (GPP) and a 25% decline in ecosystem respiration (Re). The compensatory declines in GPP and Re resulted in no significant change in net ecosystem production (NEP). Refoliation began within a month after the hurricane, although this period was out of phase with the regular foliation period, and recovered 20% of the defoliation loss within 2.5 months. Full recovery of LAI, ecosystem CO2 assimilation, and ecosystem respiration did not occur until the next growing season. Plants exposed to elevated Ca did not sustain greater damage, nor did they recover faster than plants grown under ambient Ca. Thus, our results indicate that hurricanes capable of causing significant defoliation with negligible damage to stems have negligible effects on NEP under current or future CO2-enriched environment.

free air carbon dioxide enrichment (FACE) and open top chamber (OTC) studies are valuable tools for evaluating the impact of elevated atmospheric CO2 on nutrient cycling in terrestrial ecosystems. Using meta-analytic techniques, we summarized the results of 117 studies on plant biomass production, soil organic matter dynamics and biological N2 fixation in FACE and OTC experiments. The objective of the analysis was to determine whether elevated CO2 alters nutrient cycling between plants and soil and if so, what the implications are for soil carbon (C) sequestration. Elevated CO2 stimulated gross N immobilization by 22%, whereas gross and net N mineralization rates remained unaffected. In addition, the soil C:N ratio and microbial N contents increased under elevated CO2 by 3.8% and 5.8%, respectively. Microbial C contents and soil respiration increased by 7.1% and 17.7%, respectively. Despite the stimulation of microbial activity, soil C input still caused soil C contents to increase by 1.2%yr � 1 . Namely, elevated CO2 stimulated overall above- and belowground plant biomass by 21.5% and 28.3%, respectively, thereby outweighing the increase in CO2 respiration. In addition, when comparing experiments under both low and high N availability, soil C contents (12.2%yr � 1 ) and above- and belowground plant growth (120.1% and 133.7%) only increased under elevated CO2 in experiments receiving the high N treatments. Under low N availability, above- and belowground plant growth increased by only 8.8% and 14.6%, and soil C contents did not increase. Nitrogen fixation was stimulated by elevated CO2 only when additional nutrients were supplied. These results suggest that the main driver of soil C sequestration is soil C input through plant growth, which is strongly controlled by nutrient availability. In unfertilized ecosystems, microbial N immobilization enhances acclimation of plant growth to elevated CO2 in the long-term. Therefore, increased soil C input and soil C sequestration under elevated CO2 can only be sustained in the long-term when additional nutrients are supplied. Nomenclature FACE 5 free air carbon dioxide enrichment; OTC 5 open top chamber; SOM 5 soil organic matter; SOC 5 soil organic carbon

Elevated atmospheric carbon dioxide (CO2) often stimulates the growth of fine roots, yet there are few reports of responses of intact root systems to long-term CO2 exposure. We investigated the effects of elevated CO2 on fine root growth using open top chambers in a scrub oak ecosystem at Kennedy Space Center, Florida for more than 7 years. CO2 enrichment began immediately after a controlled burn, which simulated the natural disturbance that occurs in this system every 10‐15 years. We hypothesized that (1) root abundance would increase in both treatments as the system recovered from fire; (2) elevated CO2 would stimulate root growth; and (3) elevated CO2 would alter root distribution. Minirhizotron tubes were used to measure fine root length density (mmcm � 2 ) every three months. During the first 2 years after fire recovery, fine root abundance increased in all treatments and elevated CO2 significantly enhanced root abundance, causing a maximum stimulation of 181% after 20 months. The CO2 stimulation was initially more pronounced in the top 10cm and 38‐49cm below the soil surface. However, these responses completely disappeared during the third year of experimental treatment: elevated CO2 had no effect on root abundance or on the depth distribution of fine roots during years 3‐7. The results suggest that, within a few years following fire, fine roots in this scrub oak ecosystem reach closure, defined here as a dynamic equilibrium between production and mortality. These results further suggest that elevated CO2 hastens root closure but does not affect maximum root abundance. Limitation of fine root growth by belowground resources ‐ particularly nutrients in this nutrient-poor soil ‐ may explain the transient response to elevated CO2.

The availability of C and N to the soil microbial biomass is an important determinant of the rates of soil N transformations. Here, we present evidence that changes in C and N availability affect the 15 N natural abundance of the microbial biomass relative to other soil N pools. We analysed the 15 N natural abundance signature of the chloroform-labile, extractable, NO 3 - , NH 4 + and soil total N pools across a cattle manure gradient associated with a water reservoir in semiarid, high-desert grassland. High levels of C and N in soil total, extractable, NO 3 - , NH 4 + and chloroform-labile fractions were found close to the reservoir. The δ 15 N value of chloroform-labile N was similar to that of extractable (organic + inorganic) N and NO 3 - at greater C availability close to the reservoir, but was 15 N-enriched relative to these N-pools at lesser C availability farther away. Possible mechanisms for this variable 15 N-enrichment include isotope fractionation during N assimilation and dissimilation, and changes in substrate use from a less to a more 15 N-enriched substrate with decreasing C availability.

Experimentally increasing atmospheric CO2 often stimulates plant growth and ecosystem carbon (C) uptake. Biogeochemical theory predicts that these initial responses will immobilize nitrogen (N) in plant biomass and soil organic matter, causing N availability to plants to decline, and reducing the long-term CO2-stimulation of C storage in N limited ecosystems. While many experiments have examined changes in N cycling in response to elevated CO2, empirical tests of this theoretical prediction are scarce. During seven years of postfire recovery in a scrub oak ecosystem, elevated CO2 initially increased plant N accumulation and plant uptake of tracer 15N, peaking after four years of CO2 enrichment. Between years four and seven, these responses to CO2 declined. Elevated CO2 also increased N and tracer 15N accumulation in the O horizon, and reduced 15N recovery in underlying mineral soil. These responses are consistent with progressive N limitation: the initial CO2 stimulation of plant growth immobilized N in plant biomass and in the O horizon, progressively reducing N availability to plants. Litterfall production (one measure of aboveground primary productivity) increased initially in response to elevated CO2, but the CO2 stimulation declined during years five through seven, concurrent with the accumulation of N in the O horizon and the apparent restriction of plant N availability. Yet, at the level of aboveground plant biomass (estimated by allometry), progressive N limitation was less apparent, initially because of increased N acquisition from soil and later because of reduced N concentration in biomass as N availability declined. Over this seven-year period, elevated CO2 caused a redistribution of N within the ecosystem, from mineral soils, to plants, to surface organic matter. In N limited ecosystems, such changes in N cycling are likely to reduce the response of plant production to elevated CO2.

Rising atmospheric CO2 and temperatures are probably altering ecosystem carbon cycling, causing both positive and negative feedbacks to climate. Below-ground processes play a key role in the global carbon (C) cycle because they regulate storage of large quantities of C, and are potentially very sensitive to direct and indirect effects of elevated CO2 and temperature. Soil organic matter pools, roots and associated rhizosphere organisms all have distinct responses to environmental change drivers, although availability of C substrates will regulate all the responses. Elevated CO2 increases C supply below-ground, whereas warming is likely to increase respiration and decomposition rates, leading to speculation that these effects will moderate one another. However, indirect effects on soil moisture availability and nutrient supply may alter processes in unexpected directions. Detailed, mechanistic understanding and modelling of below-ground flux components, pool sizes and turnover rates is needed to adequately predict long-term, net C storage in ecosystems. In this synthesis, we discuss the current status of below-ground responses to elevated CO2 and temperature and potential feedback effects, methodological challenges, and approaches to integrating models and measurements.

Elevated carbon dioxide (CO2) caused greater accumulation of carbon (C) and nutrients in both vegetation and O horizons over a 5-yr sampling period in a scrub oak ecosystem in Florida. Elevated CO2 had no effect on any measured soil property except extractable phosphorus (P), which was lower with elevated CO2 after five years. Anion and cation exchange membranes showed lower available nitrogen (N) and zinc (Zn) with elevated CO2. Soils in both elevated and ambient CO2 showed decreases in total C, N, sulfur (S), and cation exchange capacity, and increases in base saturation, exchangeable Ca2+, and Mg2+ over the 5-yr sampling period. We hypothesize that these soil changes were a delayed response to prescribed fire, which was applied to the site just before the initiation of the experiment. In the ambient CO2 treatment, the increases in vegetation and O horizon C, N, and S were offset by the losses of soil total C, N, and S, resulting in no statistically significant net changes in ecosystem C, N, or S over t...

Plant productivity and ecosystem productivity are strongly influenced by nutrient availability, which is largely determined by the decomposition rate of plant litter. Belowground litter inputs (dead roots, mycorrhizae, and exudates) are larger than above- ground litterfall in many systems. Chemical quality and diameter primarily control decom- position for coarse roots, but these patterns do not hold for finer classes of roots, which are frequently colonized by mycorrhizae. Though mycorrhizal status is known to drastically alter root chemistry, morphology, life span, and exudation, it has never been explicitly considered as a factor affecting root decomposition. We hypothesize that mycorrhizal status substantially influences fine root decomposition rates. Both ectomycorrhizal (EM) and arbuscular mycorrhizal (AM) fungi can change root properties but do so in different ways. Dominant tree species of most cold and temperate forests rely heavily on EM associations. EM fungi form massive structures that envelop fine roots. Roots infected by ectomycorrhizae have higher nitrogen concentrations than nonmycorrhizal roots, which would be expected to increase decomposition rates, but much of this nitrogen is bound in recalcitrant forms, such as chitin, so the net effect on decom- position is difficult to predict. AM fungi lack elaborate, macroscopic structures and may not alter root chemistry as profoundly. In addition to mycorrhizal roots, external fungal hyphae can contribute significantly to ecosystem carbon budgets and thereby influence rates of soil carbon turnover. Hyphae have commonly been considered a rapidly decomposing carbon pool, though this has never been demonstrated experimentally. If hyphae are produced at the expense of rapidly decomposing root exudates, then the net effect of hyphal litter production might be to reduce soil microbial activity and overall carbon cycling rates. Based on known differences in morphology and chemistry, EM hyphae may be more recalcitrant than AM hyphae. In summary, we submit that mycorrhizal status could substantially influence fine root decomposition and soil carbon processing rates, potentially explaining some of the variation observed within and among individual plant species and ecosystems.