Metagenomic and 14C tracing evidence for autotrophic microbial CO2 fixation in paddy soils

Autotrophic carbon dioxide (CO₂) fixation by microbes is ubiquitous in the environment and potentially contributes to the soil organic carbon (SOC) pool. However, the multiple autotrophic pathways of microbial carbon assimilation and fixation in paddy soils remain poorly characterized. In this study, we combine metagenomic analysis with ¹⁴C-labelling to investigate all known autotrophic pathways and CO₂ assimilation mechanisms in five typical paddy soils from southern China. Marker genes of six autotrophic pathways are detected in all soil samples, which are dominated by the cbbL genes (67%–82%) coding the ribulose-bisphosphate carboxylase large chain in the Calvin cycle. These marker genes are associated with a broad range of phototrophic and chemotrophic genera. Significant amounts of ¹⁴C-CO₂ are assimilated into SOC (74.3–175.8 mg ¹⁴C kg⁻¹) and microbial biomass (5.2–24.1 mg ¹⁴C kg⁻¹) after 45 days incubation, where more than 70% of ¹⁴C-SOC was concentrated in the relatively stable humin fractions. These results show that paddy soil microbes contain the genetic potential for autotrophic carbon fixation spreading over broad taxonomic ranges, and can incorporate atmospheric carbon into organic components, which ultimately contribute to the stable SOC pool.     

Non-phototrophic CO 2 fixation by soil microorganisms

Although soils are generally known to be a net source of CO₂ due to microbial respiration, CO₂ fixation may also be an important process. The non-phototrophic fixation of CO₂ was investigated in a tracer experiment with ¹⁴CO₂ in order to obtain information about the extent and the mechanisms of this process. Soils were incubated for up to 91 days in the dark. In three independent incubation experiments, a significant transfer of radioactivity from ¹⁴CO₂ to soil organic matter was observed. The process was related to microbial activity and could be enhanced by the addition of readily available substrates such as acetate. CO₂ fixation exhibited biphasic kinetics and was linearly related to respiration during the first phase of incubation (about 20–40 days). The fixation amounted to 3–5% of the net respiration. After this phase, the CO₂ fixation decreased to 1–2% of the respiration. The amount of carbon fixed by an agricultural soil corresponded to 0.05% of the organic carbon present in the soil at the beginning of the experiment, and virtually all of the fixed CO₂ was converted to organic compounds. Many autotrophic and heterotrophic biochemical processes result in the fixation of CO₂. However, the enhancement of the fixation by addition of readily available substrates and the linear correlation with respiration suggested that the process is mainly driven by aerobic heterotrophic microorganisms. We conclude that heterotrophic CO₂ fixation represents a significant factor of microbial activity in soils.     

Application of a two‐pool model to soil carbon dynamics under elevated CO2

Elevated atmospheric CO₂ concentrations increase plant productivity and affect soil microbial communities, with possible consequences for the turnover rate of soil carbon (C) pools and feedbacks to the atmosphere. In a previous analysis (Van Groenigen et al., 2014), we used experimental data to inform a one‐pool model and showed that elevated CO₂ increases the decomposition rate of soil organic C, negating the storage potential of soil. However, a two‐pool soil model can potentially explain patterns of soil C dynamics without invoking effects of CO₂ on decomposition rates. To address this issue, we refit our data to a two‐pool soil C model. We found that CO₂ enrichment increases decomposition rates of both fast and slow C pools. In addition, elevated CO₂ decreased the carbon use efficiency of soil microbes (CUE), thereby further reducing soil C storage. These findings are consistent with numerous empirical studies and corroborate the results from our previous analysis. To facilitate understanding of C dynamics, we suggest that empirical and theoretical studies incorporate multiple soil C pools with potentially variable decomposition rates.     

Functional metagenomic selection of ribulose 1, 5‐bisphosphate carboxylase/oxygenase from uncultivated bacteria

Ribulose 1,5‐bisphosphate carboxylase/oxygenase (RubisCO) is a critical yet severely inefficient enzyme that catalyses the fixation of virtually all of the carbon found on Earth. Here, we report a functional metagenomic selection that recovers physiologically active RubisCO molecules directly from uncultivated and largely unknown members of natural microbial communities. Selection is based on CO₂‐dependent growth in a host strain capable of expressing environmental deoxyribonucleic acid (DNA), precluding the need for pure cultures or screening of recombinant clones for enzymatic activity. Seventeen functional RubisCO‐encoded sequences were selected using DNA extracted from soil and river autotrophic enrichments, a photosynthetic biofilm and a subsurface groundwater aquifer. Notably, three related form II RubisCOs were recovered which share high sequence similarity with metagenomic scaffolds from uncultivated members of the Gallionellaceae family. One of the Gallionellaceae RubisCOs was purified and shown to possess CO₂/O₂ specificity typical of form II enzymes. X‐ray crystallography determined that this enzyme is a hexamer, only the second form II multimer ever solved and the first RubisCO structure obtained from an uncultivated bacterium. Functional metagenomic selection leverages natural biological diversity and billions of years of evolution inherent in environmental communities, providing a new window into the discovery of CO₂‐fixing enzymes not previously characterized.     

Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient

Desert soils harbour diverse communities of aerobic bacteria despite lacking substantial organic carbon inputs from vegetation. A major question is therefore how these communities maintain their biodiversity and biomass in these resource-limiting ecosystems. Here, we investigated desert topsoils and biological soil crusts collected along an aridity gradient traversing four climatic regions (sub-humid, semi-arid, arid, and hyper-arid). Metagenomic analysis indicated these communities vary in their capacity to use sunlight, organic compounds, and inorganic compounds as energy sources. Thermoleophilia, Actinobacteria, and Acidimicrobiia were the most abundant and prevalent bacterial classes across the aridity gradient in both topsoils and biocrusts. Contrary to the classical view that these taxa are obligate organoheterotrophs, genome-resolved analysis suggested they are metabolically flexible, with the capacity to also use atmospheric H₂ to support aerobic respiration and often carbon fixation. In contrast, Cyanobacteria were patchily distributed and only abundant in certain biocrusts. Activity measurements profiled how aerobic H₂ oxidation, chemosynthetic CO₂ fixation, and photosynthesis varied with aridity. Cell-specific rates of atmospheric H₂ consumption increased 143-fold along the aridity gradient, correlating with increased abundance of high-affinity hydrogenases. Photosynthetic and chemosynthetic primary production co-occurred throughout the gradient, with photosynthesis dominant in biocrusts and chemosynthesis dominant in arid and hyper-arid soils. Altogether, these findings suggest that the major bacterial lineages inhabiting hot deserts use different strategies for energy and carbon acquisition depending on resource availability. Moreover, they highlight the previously overlooked roles of Actinobacteriota as abundant primary producers and trace gases as critical energy sources supporting productivity and resilience of desert ecosystems.Subject terms: Microbial ecology, Biogeochemistry     

Elevated CO2 impacts ectomycorrhiza-mediated forest soil carbon flow: fungal biomass production,respiration and exudation

Large quantities of carbon are exchanged between terrestrial ecosystems and the atmosphere, and extensive research efforts are made to understand carbon cycling and the impact of elevated atmospheric CO₂ levels. The response of soils to increased carbon availability is largely driven by root associated ectomycorrhizal fungi in forest ecosystems, since they partition host derived carbon belowground. In this review I examine how CO₂ enrichment affects ectomycorrhizal fungal biomass production, exudation, respiration, soil carbon fluxes, and other soil microbes, and the importance of the fungal species in these responses. I briefly discuss the significance of CO₂ alterations in the mycorrhizal symbiosis in the context of consequences for carbon sequestration, and present research priorities.     

Deep Autotrophic Soil Respiration in Shrubland and Woodland Ecosystems in Central New Mexico

Quantifying the controls on soil respiration is important for understanding ecosystem physiology and for predicting the response of soil carbon reservoirs to climate change. The majority of soil respiration is typically considered to occur in the top 20–30 cm of soils. In desert soils, where organic matter concentrations tend to be low and plants are deeply rooted, deeper respiration might be expected. However, little is known about the depth distribution of respiration in dryland soils. Here we show that the average depth of soil respiration between pulse precipitation events is almost always greater than 20 cm and is frequently greater than 50 cm in two central New Mexico desert shrublands. The average depth of soil respiration in a pi?on-juniper woodland was shallower, between 5 and 40 cm. In the shrublands, 8‰ seasonal variations in the carbon isotope composition of soil-respired CO₂ (δ¹³C_r-soil) that correlate with vapor pressure deficit support root/rhizosphere respiration as the dominant source of soil CO₂. Such deep autotrophic respiration indicates that shrubs preferentially allocate photosynthate to deep roots when conditions near the surface are unfavorable. Therefore, respiration rates in these soils are not necessarily correlated with root biomass. The δ¹³C_r-soil values provide no evidence for CO₂ evolved from soil inorganic carbon. Our results also suggest that organic carbon cycling is rapid and efficient in these soils and that the δ¹³C value of CO₂ respired from soils in much of the southwestern US, and perhaps in other semiarid regions, varies seasonally by at least 4‰.     

Precipitation pulse size effects on Sonoran Desert soil microbial crusts

Deserts are characterized by low productivity and substantial unvegetated space, which is often covered by soil microbial crust communities. Microbial crusts are important for nitrogen fixation, soil stabilization and water infiltration, but their role in ecosystem production is not well understood. This study addresses the following questions: what are the CO₂ exchange responses of crusts to pulses of water, does the contribution of crusts to ecosystem flux differ from the soil respiratory flux, and is this contribution pulse size dependent? Following water application to crusts and soils, CO₂ exchange was measured and respiration was partitioned through mixing model analysis of Keeling plots across treatments. Following small precipitation pulse sizes, crusts contributed 80% of soil-level CO₂ fluxes to the atmosphere. However, following a large pulse event, roots and soil microbes contributed nearly 100% of the soil-level flux. Rainfall events in southern Arizona are dominated by small pulse sizes, suggesting that crusts may frequently contribute to ecosystem production. Carbon cycle studies of arid land systems should consider crusts as important contributors because of their dynamic responses to different pulse sizes as compared to the remaining ecosystem components.     

Carbon dioxide consumption during soil development

Carbon is sequestered in soils by accumulation of recalcitrant organic matter and by bicarbonate weathering of silicate minerals. Carbon fixation by ecosystems helps drive weathering processes in soils and that in turn diverts carbon from annual photosynthesis-soil respiration cycling into the long-term geological carbon cycle. To quantify rates of carbon transfer during soil development in moist temperate grassland and desert scrubland ecosystems, we measured organic and inorganic residues derived from the interaction of soil biota and silicate mineral weathering for twenty-two soil profiles in arkosic sediments of differing ages. In moist temperate grasslands, net annual removal of carbon from the atmosphere by organic carbon accumulation and silicate weathering ranges from about 8.5 g m^–2 yr^–1 for young soils to 0.7 g M^–2 yr^–1 for old soils. In desert scrublands, net annual carbon removal is about 0.2 g m^–2 yr^–1 for young soils and 0.01 g m^–2 yr^–1 for old soils. In soils of both ecosystems, organic carbon accumulation exceeds CO₂ removal by weathering, however, as soils age, rates of CO₂ consumption by weathering accounts for greater amounts of carbon sequestration, increasing from 2% to 8% in the grassland soils and from 2% to 40% in the scrubland soils. In soils of desert scrublands, carbonate accumulation far outstrips organic carbon accumulation, but about 90% of this mass is derived from aerosolic sources that do not contribute to long-term sequestration of atmospheric carbon dioxide.     

Soil respiration and the global carbon cycle

Soil respiration is the primary path by which CO₂fixed by land plants returns to the atmosphere. Estimated at approximately 75 × 10¹⁵gC/yr, this large natural flux is likely to increase due changes in the Earth's condition. The objective of this paper is to provide a brief scientific review for policymakers who are concerned that changes in soil respiration may contribute to the rise in CO₂in Earth's atmosphere. Rising concentrations of CO₂in the atmosphere will increase the flux of CO₂from soils, while simultaneously leaving a greater store of carbon in the soil. Traditional tillage cultivation and rising temperature increase the flux of CO₂from soils without increasing the stock of soil organic matter. Increasing deposition of nitrogen from the atmosphere may lead to the sequestration of carbon in vegetation and soils. The response of the land biosphere to simultaneous changes in all of these factors is unknown, but a large increase in the soil carbon pool seems unlikely to moderate the rise in atmospheric CO₂during the next century.     

Shrub expansion stimulates soil C and N storage along a coastal soil chronosequence

Expansion of woody vegetation in grasslands is a worldwide phenomenon with implications for C and N cycling at local, regional and global scales. Although woody encroachment is often accompanied by increased annual net primary production (ANPP) and increased inputs of litter, mesic ecosystems may become sources for C after woody encroachment because stimulation of soil CO₂ efflux releases stored soil carbon. Our objective was to determine if young, sandy soils on a barrier island became a sink for C after encroachment of the nitrogen‐fixing shrub Morella cerifera, or if associated stimulation of soil CO₂ efflux mitigated increased litterfall. We monitored variations in litterfall in shrub thickets across a chronosequence of shrub expansion and compared those data to previous measurements of ANPP in adjacent grasslands. In the final year, we quantified standing litter C and N pools in shrub thickets and soil organic matter (SOM), soil organic carbon (SOC), soil total nitrogen (TN) and soil CO₂ efflux in shrub thickets and adjacent grasslands. Heavy litterfall resulted in a dense litter layer storing an average of 809 g C m^?2 and 36 g N m^?2. Although soil CO₂ efflux was stimulated by shrub encroachment in younger soils, soil CO₂ efflux did not vary between shrub thickets and grasslands in the oldest soils and increases in CO₂ efflux in shrub thickets did not offset contributions of increased litterfall to SOC. SOC was 3.6–9.8 times higher beneath shrub thickets than in grassland soils and soil TN was 2.5–7.7 times higher under shrub thickets. Accumulation rates of soil and litter C were highest in the youngest thicket at 101 g m^?2 yr^?1 and declined with increasing thicket age. Expansion of shrubs on barrier islands, which have low levels of soil carbon and high potential for ANPP, has the potential to significantly increase ecosystem C sequestration.     

自养微生物同化CO_2的分子生态研究及同化碳在土壤中的转化

大气中CO2浓度持续升高和全球气候变暖是亟待解决的重大环境问题。自养微生物在环境中广泛分布,能直接参与CO2的同化,因此研究自养微生物同化CO2的分子生态学机制具有重大的科学意义。以往对自养微生物的研究多针对基因组DNA,从DNA水平揭示了不同生态系统中碳同化自养微生物的种群结构和多样性,但这些微生物在生态系统中的具体功能有待进一步的研究。近年来,随着转录组学研究技术和稳定同位素探针技术(SIP)的发展,自养微生物同化CO2的生态机理研究不断深入,这些研究明确揭示了碳同化自养微生物是河流、湖泊和海洋生态系统中CO2固定作用的驱动者,并新发现了一些具有CO2同化功能的微生物群落。基于国内外有关研究进展,从DNA和RNA水平上对自养微生物同化CO2的分子机理以及稳定同位素探针技术(SIP)在碳同化微生物研究中的应用进行了分析和总结,初步展望了RNA-SIP技术在陆地生态系统碳同化微生物分子生态学研究中的前景。同时,探讨了陆地生态系统同化碳的转化和稳定性机理,以期为深入了解生态系统碳循环过程和应对气候变化提供理论依据。     

Dark microbial CO2 fixation in temperate forest soils increases with CO2 concentration

Dark, that is, nonphototrophic, microbial CO₂ fixation occurs in a large range of soils. However, it is still not known whether dark microbial CO₂ fixation substantially contributes to the C balance of soils and what factors control this process. Therefore, the objective of this study was to quantitate dark microbial CO₂ fixation in temperate forest soils, to determine the relationship between the soil CO₂ concentration and dark microbial CO₂ fixation, and to estimate the relative contribution of different microbial groups to dark CO₂ fixation. For this purpose, we conducted a ¹³C‐CO₂ labeling experiment. We found that the rates of dark microbial CO₂ fixation were positively correlated with the CO₂ concentration in all soils. Dark microbial CO₂ fixation amounted to up to 320 µg C kg^?1 soil day^?1 in the Ah horizon. The fixation rates were 2.8–8.9 times higher in the Ah horizon than in the Bw1 horizon. Although the rates of dark microbial fixation were small compared to the respiration rate (1.2%–3.9% of the respiration rate), our findings suggest that organic matter formed by microorganisms from CO₂ contributes to the soil organic matter pool, especially given that microbial detritus is more stable in soil than plant detritus. Phospholipid fatty acid analyses indicated that CO₂ was mostly fixed by gram‐positive bacteria, and not by fungi. In conclusion, our study shows that the dark microbial CO₂ fixation rate in temperate forest soils increases in periods of high CO₂ concentrations, that dark microbial CO₂ fixation is mostly accomplished by gram‐positive bacteria, and that dark microbial CO₂ fixation contributes to the formation of soil organic matter.     

CO₂ utilizing microbes--a comprehensive review

CO₂ fixing microbes are the species primarily engaged in complexing the inorganic carbon dioxide to organic carbon compounds. There are many microorganisms from archaeal and bacterial domain that can fix carbon dioxide through six known CO₂ fixing pathways. These organisms are ubiquitous and can survive in wide range of aerobic and anaerobic habitats. This review focuses on the prior research, that has been conducted in this field and presents a summarized overview of all the mechanisms (along with their genes and enzymes) used by these microbes for CO₂ incorporation. In addition, this review provides a better understanding of diversity and taxonomy of CO₂ fixing microorganisms. The information presented here will motivate researchers to further explore the diversity of CO₂ fixing microorganisms as well as to decipher the underlying mechanisms of CO₂ utilization.     

Long-term field fertilization alters the diversity of autotrophic bacteria based on the ribulose-1,5-biphosphate carboxylase/oxygenase (RubisCO) large-subunit genes in paddy soil

Carbon dioxide (CO₂) assimilation by autotrophic bacteria is an important process in the soil carbon cycle with major environmental implications. The long-term impact of fertilizer on CO₂ assimilation in the bacterial community of paddy soils remains poorly understood. To narrow this knowledge gap, the composition and abundance of CO₂-assimilating bacteria were investigated using terminal restriction fragment length polymorphism and quantitative PCR of the cbbL gene [that encodes ribulose-1,5-biphosphate carboxylase/oxygenase (RubisCO)] in paddy soils. Soils from three stations in subtropical China were used. Each station is part of a long-term fertilization experiment with three treatments: no fertilizer (CK), chemical fertilizers (NPK), and NPK combined with rice straw (NPKM). At all of the stations, the cbbL-containing bacterial communities were dominated by facultative autotrophic bacteria such as Rhodopseudomonas palustris, Bradyrhizobium japonicum, and Ralstonia eutropha. The community composition in the fertilized soil (NPK and NPKM) was distinct from that in unfertilized soil (CK). The bacterial cbbL abundance (3–8?×?10⁸ copies g soil^?1) and RubisCO activity (0.40–1.76 nmol CO₂ g soil^?1 min^?1) in paddy soils were significantly positively correlated, and both increased with the addition of fertilizer. Among the measured soil parameters, soil organic carbon and pH were the most significant factors influencing the community composition, abundance, and activity of the cbbL-containing bacteria. These results suggest that long-term fertilization has a strong impact on the activity and community of cbbL-containing bacterial populations in paddy soils, especially when straw is combined with chemical fertilizers.     

A multiyear synthesis of soil respiration responses to elevated atmospheric CO2 from four forest FACE experiments

The rapidly rising concentration of atmospheric CO₂ has the potential to alter forest and global carbon cycles by altering important processes that occur in soil. Forest soils contain the largest and longest lived carbon pools in terrestrial ecosystems and are therefore extremely important to the land–atmosphere exchange of carbon and future climate. Soil respiration is a sensitive integrator of many soil processes that control carbon storage in soil, and is therefore a good metric of changes to soil carbon cycling. Here, we summarize soil respiration data from four forest free‐air carbon dioxide enrichment (FACE) experiments in developing and established forests that have been exposed to elevated atmospheric [CO₂] (168 μL L^?1 average enrichment) for 2–6 years. The sites have similar experimental design and use similar methodology (closed‐path infrared gas analyzers) to measure soil respiration, but differ in species composition of the respective forest communities. We found that elevated atmospheric [CO₂] stimulated soil respiration at all sites, and this response persisted for up to 6 years. Young developing stands experienced greater stimulation than did more established stands, increasing 39% and 16%, respectively, averaged over all years and communities. Further, at sites that had more than one community, we found that species composition of the dominant trees was a major controller of the absolute soil CO₂ efflux and the degree of stimulation from CO₂ enrichment. Interestingly, we found that the temperature sensitivity of bulk soil respiration appeared to be unaffected by elevated atmospheric CO₂. These findings suggest that stage of stand development and species composition should be explicitly accounted for when extrapolating results from elevated CO₂ experiments or modeling forest and global carbon cycles.     

Efficiency of CO2 fixation in a glycollate oxidoreductase mutant of Alcaligenes eutrophus which exports fixed carbon as glycollate

Mutant strains of the facultative autotrophic bacterium Alcaligenes eutrophus blocked in glycollate utilization were isolated and characterized. One of the strains, AE161, which lacked glycollate oxidoreductase activity, excreted up to 1.2mol glycollate/mg cell protein per hour during autotrophic growth. This mutant strain was used to study the efficiency of CO₂ fixation in terms of how much of the fixed carbon was excreted as glycollate under different conditions. Glycollate excretion was not detected during heterotrophic growth. Only 1% of the total CO₂ fixed was excreted as glycollate in an atmosphere of 4% CO₂ plus 20% O₂. The rate of glycollate excretion showed a large increase and CO₂ fixation decreased as the CO₂ concentration was lowered. Almost half (40–50%) of the total CO₂ fixed was excreted as glycollate in an atmosphere of 0.07% CO₂ plus 20% O₂.Abbreviations HPMS 2-pyridyl-hydroxymethane sulphonic acid - RuBP ribulose 1,5-bisphosphate To whom offprint requests are to be sent     

Interannual variability in global soil respiration, 1980–94

We used a climate‐driven regression model to develop spatially resolved estimates of soil‐CO₂ emissions from the terrestrial land surface for each month from January 1980 to December 1994, to evaluate the effects of interannual variations in climate on global soil‐to‐atmosphere CO₂ fluxes. The mean annual global soil‐CO₂ flux over this 15‐y period was estimated to be 80.4 (range 79.3–81.8) Pg C. Monthly variations in global soil‐CO₂ emissions followed closely the mean temperature cycle of the Northern Hemisphere. Globally, soil‐CO₂ emissions reached their minima in February and peaked in July and August. Tropical and subtropical evergreen broad‐leaved forests contributed more soil‐derived CO₂ to the atmosphere than did any other vegetation type (～30% of the total) and exhibited a biannual cycle in their emissions. Soil‐CO₂ emissions in other biomes exhibited a single annual cycle that paralleled the seasonal temperature cycle. Interannual variability in estimated global soil‐CO₂ production is substantially less than is variability in net carbon uptake by plants (i.e., net primary productivity). Thus, soils appear to buffer atmospheric CO₂ concentrations against far more dramatic seasonal and interannual differences in plant growth. Within seasonally dry biomes (savannas, bushlands and deserts), interannual variability in soil‐CO₂ emissions correlated significantly with interannual differences in precipitation. At the global scale, however, annual soil‐CO₂ fluxes correlated with mean annual temperature, with a slope of 3.3 Pg C y^?1 per °C. Although the distribution of precipitation influences seasonal and spatial patterns of soil‐CO₂ emissions, global warming is likely to stimulate CO₂ emissions from soils.     

Synthetic biology for CO2 fixation

Recycling of carbon dioxide (CO₂) into fuels and chemicals is a potential approach to reduce CO₂ emission and fossil-fuel consumption. Autotrophic microbes can utilize energy from light, hydrogen, or sulfur to assimilate atmospheric CO₂ into organic compounds at ambient temperature and pressure. This provides a feasible way for biological production of fuels and chemicals from CO₂ under normal conditions. Recently great progress has been made in this research area, and dozens of CO₂-derived fuels and chemicals have been reported to be synthesized by autotrophic microbes. This is accompanied by investigations into natural CO₂-fixation pathways and the rapid development of new technologies in synthetic biology. This review first summarizes the six natural CO₂-fixation pathways reported to date, followed by an overview of recent progress in the design and engineering of CO₂-fixation pathways as well as energy supply patterns using the concept and tools of synthetic biology. Finally, we will discuss future prospects in biological fixation of CO₂.     

Isotopic evidence for increased carbon and nitrogen exchanges between peatland plants and their symbiotic microbes with rising atmospheric CO2 concentrations since 15,000 cal. year BP

Whether nitrogen (N) availability will limit plant growth and removal of atmospheric CO₂ by the terrestrial biosphere this century is controversial. Studies have suggested that N could progressively limit plant growth, as trees and soils accumulate N in slowly cycling biomass pools in response to increases in carbon sequestration. However, a question remains over whether longer-term (decadal to century) feedbacks between climate, CO₂ and plant N uptake could emerge to reduce ecosystem-level N limitations. The symbioses between plants and microbes can help plants to acquire N from the soil or from the atmosphere via biological N₂ fixation—the pathway through which N can be rapidly brought into ecosystems and thereby partially or completely alleviate N limitation on plant productivity. Here we present measurements of plant N isotope composition (δ¹⁵N) in a peat core that dates to 15,000 cal. year BP to ascertain ecosystem-level N cycling responses to rising atmospheric CO₂ concentrations. We find that pre-industrial increases in global atmospheric CO₂ concentrations corresponded with a decrease in the δ¹⁵N of both Sphagnum moss and Ericaceae when constrained for climatic factors. A modern experiment demonstrates that the δ¹⁵N of Sphagnum decreases with increasing N₂-fixation rates. These findings suggest that plant-microbe symbioses that facilitate N acquisition are, over the long term, enhanced under rising atmospheric CO₂ concentrations, highlighting an ecosystem-level feedback mechanism whereby N constraints on terrestrial carbon storage can be overcome.