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The central carbon (C) metabolic network is responsible for most of the production of energy and biosynthesis in microorganisms and is therefore key to a mechanistic understanding of microbial life in soil communities. Many upland soil communities have shown a relatively high C flux through the pentose phosphate (PP) or the Entner-Doudoroff (ED) pathway, thought to be related to oxidative damage control. We tested the hypothesis that the metabolic organization of the central C metabolic network differed between two ecosystems, an anoxic marsh soil and oxic upland soil, and would be affected by altering oxygen concentrations. We expected there to be high PP/ED pathway activity under high oxygen concentrations and in oxic soils and low PP/ED activity in reduced oxygen concentrations and in marsh soil. Although we found high PP/ED activity in the upland soil and low activity in the marsh soil, lowering the oxygen concentration for the upland soil did not reduce the relative PP/ED pathway activity as hypothesized, nor did increasing the oxygen concentration in the marsh soil increase the PP/ED pathway activity. We speculate that the high PP/ED activity in the upland soil, even when exposed to low oxygen concentrations, was related to a high demand for NADPH for biosynthesis, thus reflecting higher microbial growth rates in C-rich soils than in C-poor sediments. Further studies are needed to explain the observed metabolic diversity among soil ecosystems and determine whether it is related to microbial growth rates.IMPORTANCEWe observed that the organization of the central carbon (C) metabolic processes differed between oxic and anoxic soil. However, we also found that the pentose phosphate pathway/Entner-Doudoroff (PP/ED) pathway activity remained high after reducing the oxygen concentration for the upland soil and did not increase in response to an increase in oxygen concentration in the marsh soil. These observations contradicted the hypothesis that oxidative stress is a main driver for high PP/ED activity in soil communities. We suggest that the high PP/ED activity and NADPH production reflect higher anabolic activities and growth rates in the upland soil compared to the anaerobic marsh soil. A greater understanding of the molecular and biochemical processes in soil communities is needed to develop a mechanistic perspective on microbial activities and their relationship to soil C and nutrient cycling. Such an increased mechanistic perspective is ecologically relevant, given that the central carbon metabolic network is intimately tied to the energy metabolism of microbes, the efficiency of new microbial biomass production, and soil organic matter formation., Competing Interests: The authors declare no conflict of interest.

Soils store more carbon than other terrestrial ecosystems 1,2 . How soil organic carbon (SOC) forms and persists remains uncertain 1,3 , which makes it challenging to understand how it will respond to climatic change 3,4 . It has been suggested that soil microorganisms play an important role in SOC formation, preservation and loss 5-7 . Although microorganisms affect the accumulation and loss of soil organic matter through many pathways 4,6,8-11 , microbial carbon use efficiency (CUE) is an integrative metric that can capture the balance of these processes 12,13 . Although CUE has the potential to act as a predictor of variation in SOC storage, the role of CUE in SOC persistence remains unresolved 7,14,15 . Here we examine the relationship between CUE and the preservation of SOC, and interactions with climate, vegetation and edaphic properties, using a combination of global-scale datasets, a microbial-process explicit model, data assimilation, deep learning and meta-analysis. We find that CUE is at least four times as important as other evaluated factors, such as carbon input, decomposition or vertical transport, in determining SOC storage and its spatial variation across the globe. In addition, CUE shows a positive correlation with SOC content. Our findings point to microbial CUE as a major determinant of global SOC storage. Understanding the microbial processes underlying CUE and their environmental dependence may help the prediction of SOC feedback to a changing climate., (© 2023. The Author(s).)

Plants may slow global warming through enhanced growth, because increased levels of photosynthesis stimulate the land carbon (C) sink. However, how climate warming affects plant C storage globally and key drivers determining the response of plant C storage to climate warming remains unclear, causing uncertainty in climate projections. We performed a comprehensive meta-analysis, compiling 393 observations from 99 warming studies to examine the global patterns of plant C storage responses to climate warming and explore the key drivers. Warming significantly increased total biomass (+8.4 %), aboveground biomass (+12.6 %) and belowground biomass (+10.1 %). The effect of experimental warming on plant biomass was best explained by the availability of soil nitrogen (N) and water. Across the entire dataset, warming-induced changes in total, aboveground and belowground biomass all positively correlated with soil C:N ratio, an indicator of soil N availability. In addition, warming stimulated plant biomass more strongly in humid than in dry ecosystems, and warming tended to decrease root:shoot ratios at high soil C:N ratios. Together, these results suggest dual controls of warming effects on plant C storage; warming increases plant growth in ecosystems where N is limiting plant growth, but it reduces plant growth where water availability is limiting plant growth., Competing Interests: Declaration of competing interest The authors declared no conflict of interests., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Microorganisms drive soil carbon mineralization and changes in their activity with increased temperature could feedback to climate change. Variation in microbial biodiversity and the temperature sensitivities (Q 10 ) of individual taxa may explain differences in the Q 10 of soil respiration, a possibility not previously examined due to methodological limitations. Here, we show phylogenetic and taxonomic variation in the Q 10 of growth (5-35 °C) among soil bacteria from four sites, one from each of Arctic, boreal, temperate, and tropical biomes. Differences in the temperature sensitivities of taxa and the taxonomic composition of communities determined community-assembled bacterial growth Q 10 , which was strongly predictive of soil respiration Q 10 within and across biomes. Our results suggest community-assembled traits of microbial taxa may enable enhanced prediction of carbon cycling feedbacks to climate change in ecosystems across the globe., (© 2021. The Author(s), under exclusive licence to International Society for Microbial Ecology.)

Competing Interests: The authors declare no conflict of interest.

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., (© 2018 John Wiley & Sons Ltd/CNRS.)

Agricultural and industrial activities have increased atmospheric nitrogen (N) deposition to ecosystems worldwide. N deposition can stimulate plant growth and soil carbon (C) input, enhancing soil C storage. Changes in microbial decomposition could also influence soil C storage, yet this influence has been difficult to discern, partly because of the variable effects of added N on the microbial enzymes involved. We show, using meta-analysis, that added N reduced the activity of lignin-modifying enzymes (LMEs), and that this N-induced enzyme suppression was associated with increases in soil C. In contrast, N-induced changes in cellulase activity were unrelated to changes in soil C. Moreover, the effects of added soil N on LME activity accounted for more of the variation in responses of soil C than a wide range of other environmental and experimental factors. Our results suggest that, through responses of a single enzyme system to added N, soil microorganisms drive long-term changes in soil C accumulation. Incorporating this microbial influence on ecosystem biogeochemistry into Earth system models could improve predictions of ecosystem C dynamics.

Microorganisms perform most decomposition on Earth, mediating carbon (C) loss from ecosystems, and thereby influencing climate. Yet, how variation in the identity and composition of microbial communities influences ecosystem C balance is far from clear. Using quantitative stable isotope probing of DNA, we show how individual bacterial taxa influence soil C cycling following the addition of labile C (glucose). Specifically, we show that increased decomposition of soil C in response to added glucose (positive priming) occurs as a phylogenetically diverse group of taxa, accounting for a large proportion of the bacterial community, shift toward additional soil C use for growth. Our findings suggest that many microbial taxa exhibit C use plasticity, as most taxa altered their use of glucose and soil organic matter depending upon environmental conditions. In contrast, bacteria that exhibit other responses to glucose (reduced growth or reliance on glucose for additional growth) clustered strongly by phylogeny. These results suggest that positive priming is likely the prototypical response of bacteria to sustained labile C addition, consistent with the widespread occurrence of the positive priming effect in nature.

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.

Native soil carbon (C) can be lost in response to fresh C inputs, a phenomenon observed for decades yet still not understood. Using dual-stable isotope probing, we show that changes in the diversity and composition of two functional bacterial groups occur with this 'priming' effect. A single-substrate pulse suppressed native soil C loss and reduced bacterial diversity, whereas repeated substrate pulses stimulated native soil C loss and increased diversity. Increased diversity after repeated C amendments contrasts with resource competition theory, and may be explained by increased predation as evidenced by a decrease in bacterial 16S rRNA gene copies. Our results suggest that biodiversity and composition of the soil microbial community change in concert with its functioning, with consequences for native soil C stability.

Leaf litter decomposition plays a major role in nutrient dynamics in forested streams. The chemical composition of litter affects its processing by microorganisms, which obtain nutrients from litter and from the water column. The balance of these fluxes is not well known, because they occur simultaneously and thus are difficult to quantify separately. Here, we examined C and N flow from streamwater and leaf litter to microbial biofilms during decomposition. We used isotopically enriched leaves ((13)C and (15)N) from two riparian foundation tree species: fast-decomposing Populus fremontii and slow-decomposing Populus angustifolia, which differed in their concentration of recalcitrant compounds. We adapted the isotope pool dilution method to estimate gross elemental fluxes into litter microbes. Three key findings emerged: litter type strongly affected biomass and stoichiometry of microbial assemblages growing on litter; the proportion of C and N in microorganisms derived from the streamwater, as opposed to the litter, did not differ between litter types, but increased throughout decomposition; gross immobilization of N from the streamwater was higher for P. fremontii compared to P. angustifolia, probably as a consequence of the higher microbial biomass on P. fremontii. In contrast, gross immobilization of C from the streamwater was higher for P. angustifolia, suggesting that dissolved organic C in streamwater was used as an additional energy source by microbial assemblages growing on slow-decomposing litter. These results indicate that biofilms on decomposing litter have specific element requirements driven by litter characteristics, which might have implications for whole-stream nutrient retention.

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 (15) N 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 (15) N 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., (© 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.)

Organic carbon (C) and nitrogen (N) are essential for heterotrophic soil microorganisms, and their bioavailability strongly influences ecosystem C and N cycling. We show here that the natural (15)N abundance of the soil microbial biomass is affected by both the availability of C and N and ecosystem N processing. Microbial (15)N enrichment correlated negatively with the C : N ratio of the soil soluble fraction and positively with net N mineralization for ecosystems spanning semiarid, temperate and tropical climates, grassland and forests, and over four million years of ecosystem development. In addition, during soil incubation, large increases in microbial (15)N enrichment corresponded to high net N mineralization rates. These results support the idea that the N isotope composition of an organism is determined by the balance between N assimilation and dissimilation. Thus, (15)N enrichment of the soil microbial biomass integrates the effects of C and N availability on microbial metabolism and ecosystem processes.

Increased carbon storage in ecosystems due to elevated CO(2) may help stabilize atmospheric CO(2) concentrations and slow global warming. Many field studies have found that elevated CO(2) leads to higher carbon assimilation by plants, and others suggest that this can lead to higher carbon storage in soils, the largest and most stable terrestrial carbon pool. Here we show that 6 years of experimental CO(2) doubling reduced soil carbon in a scrub-oak ecosystem despite higher plant growth, offsetting approximately 52% of the additional carbon that had accumulated at elevated CO(2) in aboveground and coarse root biomass. The decline in soil carbon was driven by changes in soil microbial composition and activity. Soils exposed to elevated CO(2) had higher relative abundances of fungi and higher activities of a soil carbon-degrading enzyme, which led to more rapid rates of soil organic matter degradation than soils exposed to ambient CO(2). The isotopic composition of microbial fatty acids confirmed that elevated CO(2) increased microbial utilization of soil organic matter. These results show how elevated CO(2), by altering soil microbial communities, can cause a potential carbon sink to become a carbon source.

The amount of carbon plants allocate to mycorrhizal symbionts exceeds that emitted by human activity annually. Senescent ectomycorrhizal roots represent a large input of carbon into soils, but their fate remains unknown. Here, we present the surprising result that, despite much higher nitrogen concentrations, roots colonized by ectomycorrhizal (EM) fungi lost only one-third as much carbon as non-mycorrhizal roots after 2 years of decomposition in a piñon pine (Pinus edulis) woodland. Experimentally excluding live mycorrhizal hyphae from litter, we found that live mycorrhizal hyphae may alter nitrogen dynamics, but the afterlife (litter-mediated) effects of EM fungi outweigh the influences of live fungi on root decomposition. Our findings indicate that a shift in plant allocation to mycorrhizal fungi could promote carbon accumulation in soil by this pathway. Furthermore, EM litters could directly contribute to the process of stable soil organic matter formation, a mechanism that has eluded soil scientists.

Rising levels of atmospheric CO2 are thought to increase C sinks in terrestrial ecosystems. The potential of these sinks to mitigate CO2 emissions, however, may be constrained by nutrients. By using metaanalysis, we found that elevated CO2 only causes accumulation of soil C when N is added at rates well above typical atmospheric N inputs. Similarly, elevated CO2 only enhances N2 fixation, the major natural process providing soil N input, when other nutrients (e.g., phosphorus, molybdenum, and potassium) are added. Hence, soil C sequestration under elevated CO2 is constrained both directly by N availability and indirectly by nutrients needed to support N2 fixation.

The growth and physiology of soil microorganisms, which play vital roles in biogeochemical cycling, are shaped by both current and historical soil environmental conditions. Here, we developed and applied a genome-resolved metagenomic implementation of quantitative stable isotope probing (qSIP) with an H218O labeling experiment to identify actively growing soil microorganisms and their genomic capacities. qSIP enabled measurement of taxon-specific growth because isotopic incorporation into microbial DNA requires production of new genome copies. We studied three Mediterranean grassland soils across a rainfall gradient to evaluate the hypothesis that historic precipitation levels are an important factor controlling trait selection. We used qSIP-informed genome-resolved metagenomics to resolve the active subset of soil community members and identify their characteristic ecophysiological traits. Higher year-round precipitation levels correlated with higher activity and growth rates of flagellar motile microorganisms. In addition to heavily isotopically labeled bacteria, we identified abundant isotope-labeled phages, suggesting phage-induced cell lysis likely contributed to necromass production at all three sites. Further, there was a positive correlation between phage activity and the activity of putative phage hosts. Contrary to our expectations, the capacity to decompose the diverse complex carbohydrates common in soil organic matter or oxidize methanol and carbon monoxide were broadly distributed across active and inactive bacteria in all three soils, implying that these traits are not highly selected for by historical precipitation. IMPORTANCE Soil moisture is a critical factor that strongly shapes the lifestyle of soil organisms by changing access to nutrients, controlling oxygen diffusion, and regulating the potential for mobility. We identified active microorganisms in three grassland soils with similar mineral contexts, yet different historic rainfall inputs, by adding water labeled with a stable isotope and tracking that isotope in DNA of growing microbes. By examining the genomes of active and inactive microorganisms, we identified functions that are enriched in growing organisms, and showed that different functions were selected for in different soils. Wetter soil had higher activity of motile organisms, but activity of pathways for degradation of soil organic carbon compounds, including simple carbon substrates, were comparable for all three soils. We identified many labeled, and thus active bacteriophages (viruses that infect bacteria), implying that the cells they killed contributed to soil organic matter. The activity of these bacteriophages was significantly correlated with activity of their hosts.

BackgroundAnthropogenic activities have increased the inputs of atmospheric reactive nitrogen (N) into terrestrial ecosystems, affecting soil carbon stability and microbial communities. Previous studies have primarily examined the effects of nitrogen deposition on microbial taxonomy, enzymatic activities, and functional processes. Here, we examined various functional traits of soil microbial communities and how these traits are interrelated in a Mediterranean-type grassland administrated with 14 years of 7 g m-2 year-1 of N amendment, based on estimated atmospheric N deposition in areas within California, USA, by the end of the twenty-first century.ResultsSoil microbial communities were significantly altered by N deposition. Consistent with higher aboveground plant biomass and litter, fast-growing bacteria, assessed by abundance-weighted average rRNA operon copy number, were favored in N deposited soils. The relative abundances of genes associated with labile carbon (C) degradation (e.g., amyA and cda) were also increased. In contrast, the relative abundances of functional genes associated with the degradation of more recalcitrant C (e.g., mannanase and chitinase) were either unchanged or decreased. Compared with the ambient control, N deposition significantly reduced network complexity, such as average degree and connectedness. The network for N deposited samples contained only genes associated with C degradation, suggesting that C degradation genes became more intensely connected under N deposition.ConclusionsWe propose a conceptual model to summarize the mechanisms of how changes in above- and belowground ecosystems by long-term N deposition collectively lead to more soil C accumulation. Video Abstract.

The functioning, health, and productivity of soil are intimately tied to a complex network of interactions, particularly in plant root-associated rhizosphere soil. We conducted a stable-isotope-informed, genome-resolved metagenomic study to trace carbon from Avena fatua grown in a 13CO2 atmosphere into soil. We collected paired rhizosphere and nonrhizosphere soil at 6 and 9 weeks of plant growth and extracted DNA that was then separated by density using ultracentrifugation. Thirty-two fractions from each of five samples were grouped by density, sequenced, assembled, and binned to generate 55 unique bacterial genomes that were ≥70% complete. We also identified complete 18S rRNA sequences of several 13C-enriched microeukaryotic bacterivores and fungi. We generated 10 circularized bacteriophage (phage) genomes, some of which were the most labeled entities in the rhizosphere, suggesting that phage may be important agents of turnover of plant-derived C in soil. CRISPR locus targeting connected one of these phage to a Burkholderiales host predicted to be a plant pathogen. Another highly labeled phage is predicted to replicate in a Catenulispora sp., a possible plant growth-promoting bacterium. We searched the genome bins for traits known to be used in interactions involving bacteria, microeukaryotes, and plant roots and found DNA from heavily 13C-labeled bacterial genes thought to be involved in modulating plant signaling hormones, plant pathogenicity, and defense against microeukaryote grazing. Stable-isotope-informed, genome-resolved metagenomics indicated that phage can be important agents of turnover of plant-derived carbon in soil. IMPORTANCE Plants grow in intimate association with soil microbial communities; these microbes can facilitate the availability of essential resources to plants. Thus, plant productivity commonly depends on interactions with rhizosphere bacteria, viruses, and eukaryotes. Our work is significant because we identified the organisms that took up plant-derived organic C in rhizosphere soil and determined that many of the active bacteria are plant pathogens or can impact plant growth via hormone modulation. Further, by showing that bacteriophage accumulate CO2-derived carbon, we demonstrated their vital roles in redistribution of plant-derived C into the soil environment through bacterial cell lysis. The use of stable-isotope probing (SIP) to identify consumption (or lack thereof) of root-derived C by key microbial community members within highly complex microbial communities opens the way for assessing manipulations of bacteria and phage with potentially beneficial and detrimental traits, ultimately providing a path to improved plant health and soil carbon storage.

Predation structures food webs, influences energy flow, and alters rates and pathways of nutrient cycling through ecosystems, effects that are well documented for macroscopic predators. In the microbial world, predatory bacteria are common, yet little is known about their rates of growth and roles in energy flows through microbial food webs, in part because these are difficult to quantify. Here, we show that growth and carbon uptake were higher in predatory bacteria compared to nonpredatory bacteria, a finding across 15 sites, synthesizing 82 experiments and over 100,000 taxon-specific measurements of element flow into newly synthesized bacterial DNA. Obligate predatory bacteria grew 36% faster and assimilated carbon at rates 211% higher than nonpredatory bacteria. These differences were less pronounced for facultative predators (6% higher growth rates, 17% higher carbon assimilation rates), though high growth and carbon assimilation rates were observed for some facultative predators, such as members of the genera Lysobacter and Cytophaga, both capable of gliding motility and wolf-pack hunting behavior. Added carbon substrates disproportionately stimulated growth of obligate predators, with responses 63% higher than those of nonpredators for the Bdellovibrionales and 81% higher for the Vampirovibrionales, whereas responses of facultative predators to substrate addition were no different from those of nonpredators. This finding supports the ecological theory that higher productivity increases predator control of lower trophic levels. These findings also indicate that the functional significance of bacterial predators increases with energy flow and that predatory bacteria influence element flow through microbial food webs.IMPORTANCE The word "predator" may conjure images of leopards killing and eating impala on the African savannah or of great white sharks attacking elephant seals off the coast of California. But microorganisms are also predators, including bacteria that kill and eat other bacteria. While predatory bacteria have been found in many environments, it has been challenging to document their importance in nature. This study quantified the growth of predatory and nonpredatory bacteria in soils (and one stream) by tracking isotopically labeled substrates into newly synthesized DNA. Predatory bacteria were more active than nonpredators, and obligate predators, such as Bdellovibrionales and Vampirovibrionales, increased in growth rate in response to added substrates at the base of the food chain, strong evidence of trophic control. This work provides quantitative measures of predator activity and suggests that predatory bacteria-along with protists, nematodes, and phages-are active and important in microbial food webs.

Microbial activity increases after rewetting dry soil, resulting in a pulse of carbon mineralization and nutrient availability. The biogeochemical responses to wet-up are reasonably well understood and known to be microbially mediated. Yet, the population level dynamics, and the resulting changes in microbial community patterns, are not well understood as ecological phenomena. Here, we used sequencing of 16S rRNA genes coupled with heavy water (H218O) DNA quantitative stable isotope probing to estimate population-specific rates of growth and mortality in response to a simulated wet-up event in a California annual grassland soil. Bacterial growth and mortality responded rapidly to wet-up, within 3 h, and continued throughout the 168 h incubation, with patterns of sequential growth observed at the phylum level. Of the 37 phyla detected in the prewet community, growth was found in 18 phyla while mortality was measured in 26 phyla. Rapid growth and mortality rates were measurable within 3 h of wet-up but had contrasting characteristics; growth at 3 h was dominated by select taxa within the Proteobacteria and Firmicutes, whereas mortality was taxonomically widespread. Furthermore, across the community, mortality exhibited density-independence, consistent with the indiscriminate shock resulting from dry-down and wet-up, whereas growth was density-dependent, consistent with control by competition or predation. Total aggregated growth across the community was highly correlated with total soil CO2 production. Together, these results illustrate how previously "invisible" population responses can translate quantitatively to emergent observations of ecosystem-scale biogeochemistry.

Higher temperatures in northern latitudes will increase permafrost thaw and stimulate above- and belowground plant biomass growth in tundra ecosystems. Higher plant productivity increases the input of easily decomposable carbon (C) to soil, which can stimulate microbial activity and increase soil organic matter decomposition rates. This phenomenon, known as the priming effect, is particularly interesting in permafrost because an increase in C supply to deep, previously frozen soil may accelerate decomposition of C stored for hundreds to thousands of years. The sensitivity of old permafrost C to priming is not well known; most incubation studies last less than one year, and so focus on fast-cycling C pools. Furthermore, the age of respired soil C is rarely measured, even though old C may be vulnerable to labile C inputs. We incubated soil from a moist acidic tundra site in Eight Mile Lake, Alaska for 409 days at 15 °C. Soil from surface (0–25 cm), transition (45–55 cm), and permafrost (65–85 cm) layers were amended with three pulses of uniformly ¹³C-labeled glucose or cellulose every 152 days. Glucose addition resulted in positive priming in the permafrost layer 7 days after each substrate addition, eliciting a two-fold increase in cumulative soil C loss relative to unamended soils with consistent effects across all three pulses. In the transition and permafrost layers, glucose addition significantly decreased the age of soil-respired CO₂-C with Δ¹⁴C values that were 115‰ higher. Previous field studies that measured the age of respired C in permafrost regions have attributed younger Δ¹⁴C ecosystem respiration values to higher plant contributions. However, the results from this study suggest that positive priming, due to an increase in fresh C supply to deeply thawed soil layers, can also explain the respiration of younger C observed at the ecosystem scale. We must consider priming effects to fully understand permafrost C dynamics, or we risk underestimating the contribution of soil C to ecosystem respiration.

The majority of the Earth's terrestrial carbon is stored in the soil. If anthropogenic warming stimulates the loss of this carbon to the atmosphere, it could drive further planetary warming. Despite evidence that warming enhances carbon fluxes to and from the soil, the net global balance between these responses remains uncertain. Here we present a comprehensive analysis of warming-induced changes in soil carbon stocks by assembling data from 49 field experiments located across North America, Europe and Asia. We find that the effects of warming are contingent on the size of the initial soil carbon stock, with considerable losses occurring in high-latitude areas. By extrapolating this empirical relationship to the global scale, we provide estimates of soil carbon sensitivity to warming that may help to constrain Earth system model projections. Our empirical relationship suggests that global soil carbon stocks in the upper soil horizons will fall by 30 ± 30 petagrams of carbon to 203 ± 161 petagrams of carbon under one degree of warming, depending on the rate at which the effects of warming are realized. Under the conservative assumption that the response of soil carbon to warming occurs within a year, a business-as-usual climate scenario would drive the loss of 55 ± 50 petagrams of carbon from the upper soil horizons by 2050. This value is around 12-17 per cent of the expected anthropogenic emissions over this period. Despite the considerable uncertainty in our estimates, the direction of the global soil carbon response is consistent across all scenarios. This provides strong empirical support for the idea that rising temperatures will stimulate the net loss of soil carbon to the atmosphere, driving a positive land carbon-climate feedback that could accelerate climate change.

Abstract: Leaf litter provides an important nutrient subsidy to headwater streams, but little is known about how tree genetics influence energy pathways from litter to higher trophic levels. Despite the charge to quantify carbon (C) and nitrogen (N) pathways from decomposing litter, the relationship between litter decomposition and aquatic consumers remains unresolved. We measured litter preference (attachments to litter), C and N assimilation rates, and growth rates of a shredding caddisfly (Hesperophylax magnus, Limnephilidae) in response to leaf litter of different chemical and physical phenotypes using Populus cross types (P. fremontii, P. angustifolia, and F1 hybrids) and genotypes within P. angustifolia. We combined laboratory mesocosm studies using litter from a common garden with a field study using doubly labeled litter (13C and 15N) grown in a greenhouse and incubated in Oak Creek, Arizona, USA. We found that, in the lab, shredders initially chose relatively labile (low lignin and condensed tannin concentrations, rapidly decomposing) cross type litter, but preference changed within 4 d to relatively recalcitrant (high lignin and condensed tannin concentrations, slowly decomposing) litter types. Additionally, in the lab, shredder growth rates were higher on relatively recalcitrant compared to labile cross type litter. Over the course of a three‐week field experiment, shredders also assimilated more C and N from relatively recalcitrant compared to labile cross type litter. Finally, among P. angustifolia genotypes, N assimilation by shredders was positively related to litter lignin and C:N, but negatively related to condensed tannins and decomposition rate. C assimilation was likewise positively related to litter C:N, and also to litter %N. C assimilation was not associated with condensed tannins or lignin. Collectively, these findings suggest that relatively recalcitrant litter of Populus cross types provides more nutritional benefit, in terms of N fluxes and growth, than labile litter, but among P. angustifolia genotypes the specific trait of litter recalcitrance (lignin or tannins) determines effects on C or N assimilation. As shredders provide nutrients and energy to higher trophic levels, the influence of these genetically based plant decomposition pathways on shredder preference and performance may affect community and food web structure. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The article highlights forest managers on stabilizing the forest carbon emission. Topics discussed include forest carbon stored by protecting carbon in soil and in large, old trees; small-tree carbon which is unstable and reason for shifting the natural disturbance from low to high intensity fire; and cost reduction in risk which provides a financial mechanism to stabilize forest carbon stores.

Projecting the response of forests to changing climate requires understanding how biotic and abiotic controls on tree growth will change over time. As temperature and interannual precipitation variability increase, the overall forest response is likely to be influenced by species-specific responses to changing climate. Management actions that alter composition and density may help buffer forests against the effects of changing climate, but may require tradeoffs in ecosystem services. We sought to quantify how projected changes in climate and different management regimes would alter the composition and productivity of Puget Lowland forests in Washington State, USA. We modeled forest responses to four treatments (control, burn-only, thin-only, thin-and-burn) under five different climate scenarios: baseline climate (historical) and projections from two climate models (CCSM4 and CNRM-CM5), driven by moderate (RCP 4.5) and high (RCP 8.5) emission scenarios. We also simulated the effects of intensive management to restore Oregon white oak woodlands ( Quercus garryana ) for the western gray squirrel ( Sciurus griseus ) and quantified the effects of these treatments on the probability of oak occurrence and carbon sequestration. At the landscape scale we found little difference in carbon dynamics between baseline and moderate emission scenarios. However, by late-century under the high emission scenario, climate change reduced forest productivity and decreased species richness across a large proportion of the study area. Regardless of the climate scenario, we found that thinning and burning treatments increased the carbon sequestration rate because of decreased resource competition. However, increased productivity with management was not sufficient to prevent an overall decline in productivity under the high emission scenario. We also found that intensive oak restoration treatments were effective at increasing the probability of oak presence and that the limited extent of the treatments resulted in small declines in total ecosystem carbon across the landscape as compared to the thin-and-burn treatment. Our research suggests that carbon dynamics in this system under the moderate emission scenario may be fairly consistent with the carbon dynamics under historical climate, but that the high emission scenario may alter the successional trajectory of these forests. [ABSTRACT FROM AUTHOR]

Carbon uptake by forests is a major sink in the global carbon cycle, helping buffer the rising concentration of CO2 in the atmosphere, yet the potential for future carbon uptake by forests is uncertain. Climate warming and drought can reduce forest carbon uptake by reducing photosynthesis, increasing respiration, and by increasing the frequency and intensity of wildfires, leading to large releases of stored carbon. Five years of eddy covariance measurements in a ponderosa pine ( Pinus ponderosa)-dominated ecosystem in northern Arizona showed that an intense wildfire that converted forest into sparse grassland shifted site carbon balance from sink to source for at least 15 years after burning. In contrast, recovery of carbon sink strength after thinning, a management practice used to reduce the likelihood of intense wildfires, was rapid. Comparisons between an undisturbed-control site and an experimentally thinned site showed that thinning reduced carbon sink strength only for the first two posttreatment years. In the third and fourth posttreatment years, annual carbon sink strength of the thinned site was higher than the undisturbed site because thinning reduced aridity and drought limitation to carbon uptake. As a result, annual maximum gross primary production occurred when temperature was 3 °C higher at the thinned site compared with the undisturbed site. The severe fire consistently reduced annual evapotranspiration (range of 12-30%), whereas effects of thinning were smaller and transient, and could not be detected in the fourth year after thinning. Our results show large and persistent effects of intense fire and minor and short-lived effects of thinning on southwestern ponderosa pine ecosystem carbon and water exchanges. [ABSTRACT FROM AUTHOR]

Escherichia coli cells were forced to mineralize or assimilate nitrogen in vitro by manipulating substrate carbon and nitrogen availability. When grown on an organic nitrogen source, E. coli cells released NH4+ and were enriched in 15N relative to the nitrogen source (1.6–3.1‰). However, when cells were grown on an inorganic nitrogen source, the biomass was depleted (6.1–9.1‰) relative to the source. By measuring 15N enrichment of microorganisms relative to nitrogen pools, ecosystem ecologists may be able to determine if microorganisms are assimilating or mineralizing nitrogen. [ABSTRACT FROM AUTHOR]

Increased carbon storage in ecosystems due to elevated CO2 may help stabilize atmospheric CO2 concentrations and slow global warming. Many field studies have found that elevated CO2 leads to higher carbon assimilation by plants, and others suggest that this can lead to higher carbon storage in soils, the largest and most stable terrestrial carbon pool. Here we show that 6 years of experimental CO2 doubling reduced soil carbon in a scrub-oak ecosystem despite higher plant growth, offsetting ≈52% of the additional carbon that had accumulated at elevated CO2 in aboveground and coarse root biomass. The decline in soil carbon was driven by changes in soil microbial composition and activity. Soils exposed to elevated CO2 had higher relative abundances of fungi and higher activities of a soil carbon- degrading enzyme, which led to more rapid rates of soil organic matter degradation than soils exposed to ambient CO2. The isotopic composition of microbial fatty acids confirmed that elevated CO2 increased microbial utilization of soil organic matter. These results show how elevated CO2. by altering soil microbial communities, can cause a potential carbon sink to become a carbon source. [ABSTRACT FROM AUTHOR]

Elevated CO2 can increase fine root biomass but responses of fine roots to exposure to increased CO2 over many years are infrequently reported. We investigated the effect of elevated CO2 on root biomass and N and P pools of a scrub-oak ecosystem on Merritt Island in Florida, USA, after 7 years of CO2 treatment. Roots were removed from 1-m deep soil cores in 10-cm increments, sorted into different categories (<0.25 mm, 0.25–1 mm, 1–2 mm, 2 mm to 1 cm, >1 cm, dead roots, and organic matter), weighed, and analyzed for N, P and C concentrations. With the exception of surface roots <0.25 mm diameter, there was no effect of elevated CO2 on root biomass. There was little effect on C, N, or P concentration or content with the exception of dead roots, and <0.25 mm and 1–2 mm diameter live roots at the surface. Thus, fine root mass and element content appear to be relatively insensitive to elevated CO2. In the top 10 cm of soil, biomass of roots with a diameter of <0.25 mm was depressed by elevated CO2. Elevated CO2 tended to decrease the mass and N content of dead roots compared to ambient CO2. A decreased N concentration of roots <0.25 mm and 1–2 mm in diameter under elevated CO2 may indicate reduced N supply in the elevated CO2 treatment. Our study indicated that elevated CO2 does not increase fine root biomass or the pool of C in fine roots. In fact, elevated CO2 tends to reduce biomass and C content of the most responsive root fraction (<0.25 mm roots), a finding that may have more general implications for understanding C input into the soil at higher atmospheric CO2 concentrations. [ABSTRACT FROM AUTHOR]

Interactions involving carbon (C) and nitrogen (N) likely modulate terrestrial ecosystem responses to elevated atmospheric carbon dioxide (CO2) levels at scales from the leaf to the globe and from the second to the century. In particular, response to elevated CO2 may generally be smaller at low relative to high soil N supply and, in turn, elevated CO2 may influence soil N processes that regulate N availability to plants. Such responses could constrain the capacity of terrestrial ecosystems to acquire and store C under rising elevated CO2 levels. This review highlights the theory and empirical evidence behind these potential interactions. We address effects on photosynthesis, primary production, biogeochemistry, trophic interactions, and interactions with other resources and environmental factors, focusing as much as possible on evidence from long-term field experiments. [ABSTRACT FROM AUTHOR]

Elevated CO2 can increase fine root biomass but responses of fine roots to exposure to increased CO2 over many years are infrequently reported. We investigated the effect of elevated CO2 on root biomass and N and P pools of a scrub-oak ecosystem on Merritt Island in Florida, USA, after 7 years of CO2 treatment. Roots were removed from 1-m deep soil cores in 10-cm increments, sorted into different categories (<0.25 mm, 0.25–1 mm, 1–2 mm, 2 mm to 1 cm, >1 cm, dead roots, and organic matter), weighed, and analyzed for N, P and C concentrations. With the exception of surface roots <0.25 mm diameter, there was no effect of elevated CO2 on root biomass. There was little effect on C, N, or P concentration or content with the exception of dead roots, and <0.25 mm and 1–2 mm diameter live roots at the surface. Thus, fine root mass and element content appear to be relatively insensitive to elevated CO2. In the top 10 cm of soil, biomass of roots with a diameter of <0.25 mm was depressed by elevated CO2. Elevated CO2 tended to decrease the mass and N content of dead roots compared to ambient CO2. A decreased N concentration of roots <0.25 mm and 1–2 mm in diameter under elevated CO2 may indicate reduced N supply in the elevated CO2 treatment. Our study indicated that elevated CO2 does not increase fine root biomass or the pool of C in fine roots. In fact, elevated CO2 tends to reduce biomass and C content of the most responsive root fraction (<0.25 mm roots), a finding that may have more general implications for understanding C input into the soil at higher atmospheric CO2 concentrations. [ABSTRACT FROM AUTHOR]

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

Abstract: We used metabolic tracers and modeling to analyze the response of soil metabolism to a sudden change in temperature from 4 to 20°C. We hypothesized that intact soil microbial communities would exhibit shifts in pentose phosphate pathway and glycolysis activity in the same way as is regularly observed for individual microorganisms in pure culture. We also hypothesized that increased maintenance respiration at higher temperature would result in greater energy production and reduced carbon use efficiency (CUE). Two hours after temperature increase, respiration increased almost 10-fold. Although all metabolic processes were increased, the relative activity of metabolic processes, biosynthesis, and energy production changed. Pentose phosphate pathway was reduced (17–20%), while activities of specific steps in glycolysis (51%) and Krebs cycle (7–13%) were increased. In contrast, only small but significant changes in biosynthesis (+2%), ATP production (−3%) and CUE (+2%) were observed. In a second experiment, we compared the metabolic responses to temperature increases in soils from high and low elevation. The shift in activity from pentose phosphate pathway to glycolysis with higher temperature was confirmed in both soils, but the responses of Krebs cycle, biosynthesis, ATP production, and CUE were site dependent. Our results indicate that 1) in response to temperature, communities behave biochemically similarly to single species and, 2) our understanding of temperature effects on CUE, energy production and use for maintenance and growth processes is still incomplete. [Copyright &y& Elsevier]

Abstract: Most organic carbon (C) in soils eventually turns into CO2 after passing through microbial metabolic pathways, while providing cells with energy and biosynthetic precursors. Therefore, detailed insight into these metabolic processes may help elucidate mechanisms of soil C cycling processes. Here, we describe a modeling approach to quantify the C flux through metabolic pathways by adding 1-13C and 2,3-13C pyruvate and 1-13C and U-13C glucose as metabolic tracers to intact soil microbial communities. The model calculates, assuming steady-state conditions and glucose as the only substrate, the reaction rates through glycolysis, Krebs cycle, pentose phosphate pathway, anaplerotic activity through pyruvate carboxylase, and various biosynthesis reactions. The model assumes a known and constant microbial proportional precursor demand, estimated from literature data. The model is parameterized with experimentally determined ratios of 13CO2 production from pyruvate and glucose isotopologue pairs. Model sensitivity analysis shows that metabolic flux patterns are especially responsive to changes in experimentally determined 13CO2 ratios from pyruvate and glucose. Calculated fluxes are far less sensitive to assumptions concerning microbial chemical and community composition. The calculated metabolic flux pattern for a young volcanic soil indicates significant pentose phosphate pathway activity in excess of pentose precursor demand and significant anaplerotic activity. These C flux patterns can be used to calculate C use efficiency, energy production and consumption for growth and maintenance purposes, substrate consumption, nitrogen demand, oxygen consumption, and microbial C isotope composition. The metabolic labeling and modeling methods may improve our ability to study the biochemistry and ecophysiology of intact and undisturbed soil microbial communities. [Copyright &y& Elsevier]

Abstract: In order to study controls on metabolic processes in soils, we determined the dynamics of 13CO2 production from two position-specific 13C-labeled pyruvate isotopologues in the presence and absence of glucose, succinate, pine, and legume leaf litter, and under anaerobic conditions. We also compared 13CO2 production in soils along a semiarid substrate age gradient in Arizona. We observed that the C from the carboxyl group (C1) of pyruvate was lost as CO2 much faster than its other C atoms (C2,3). Addition of glucose, pine and legume leaf litter reduced the ratio between 13CO2 production from 1-13C pyruvate and 2,3-13C pyruvate (C1/C2,3 ratio), whereas anaerobic conditions increased this ratio. Young volcanic soils exhibited a lower C1/C2,3 ratio than older volcanic soils. We interpret a low C1/C2,3 ratio as an indication of increased Krebs cycle activity in response to carbon inputs, while the higher ratio implies a reduced Krebs cycle activity in response to anaerobic conditions. Succinate, a gluconeogenic substrate, reduced 13CO2 production from pyruvate to near zero, likely reflecting increased carbohydrate biosynthesis from Krebs cycle intermediates. The difference in 13CO2 production rate from pyruvate isotopologues disappeared 4–5 days after pyruvate addition, indicating that C positions were scrambled by ongoing soil microbial transformations. This work demonstrates that metabolic tracers such as pyruvate can be used to determine qualitative aspects of C flux patterns through metabolic pathways of soil microbial communities. Understanding the controls over metabolic processes in soil may improve our understanding of soil C cycling processes. [ABSTRACT FROM AUTHOR]

Abstract: Stable isotope analysis is a powerful tool in the study of soil organic matter formation. It is often observed that more decomposed soil organic matter is 13C, and especially 15N-enriched relative to fresh litter and recent organic matter. We investigated whether this shift in isotope composition relates to the isotope composition of the microbial biomass, an important source for soil organic matter. We developed a new approach to determine the natural abundance C and N isotope composition of the microbial biomass across a broad range of soil types, vegetation, and climates. We found consistently that the soil microbial biomass was 15N-enriched relative to the total (3.2 ‰) and extractable N pools (3.7 ‰), and 13C-enriched relative to the extractable C pool (2.5 ‰). The microbial biomass was also 13C-enriched relative to total C for soils that exhibited a C3-plant signature (1.6 ‰), but 13C-depleted for soils with a C4 signature (−1.1 ‰). The latter was probably associated with an increase of annual C3 forbs in C4 grasslands after an extreme drought. These findings are in agreement with the proposed contribution of microbial products to the stabilized soil organic matter and may help explain the shift in isotope composition during soil organic matter formation. [Copyright &y& Elsevier]