Microbial carbon use efficiency promotes global soil carbon storage.

Soils store more carbon than other terrestrial ecosystems1,2. How soil organic carbon (SOC) forms and persists remains uncertain1,3, which makes it challenging to understand how it will respond to climatic change3,4. It has been suggested that soil microorganisms play an important role in SOC formation, preservation and loss5-7. Although microorganisms affect the accumulation and loss of soil organic matter through many pathways4,6,8-11, microbial carbon use efficiency (CUE) is an integrative metric that can capture the balance of these processes12,13. Although CUE has the potential to act as a predictor of variation in SOC storage, the role of CUE in SOC persistence remains unresolved7,14,15. 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.

Warming and elevated CO2 promote rapid incorporation and degradation of plant-derived organic matter in an ombrotrophic peatland.

Rising temperatures have the potential to directly affect carbon cycling in peatlands by enhancing organic matter (OM) decomposition, contributing to the release of CO2 and CH4 to the atmosphere. In turn, increasing atmospheric CO2 concentration may stimulate photosynthesis, potentially increasing plant litter inputs belowground and transferring carbon from the atmosphere into terrestrial ecosystems. Key questions remain about the magnitude and rate of these interacting and opposing environmental change drivers. Here, we assess the incorporation and degradation of plant- and microbe-derived OM in an ombrotrophic peatland after 4 years of whole-ecosystem warming (+0, +2.25, +4.5, +6.75 and +9°C) and two years of elevated CO2  manipulation (500 ppm above ambient). We show that OM molecular composition was substantially altered in the aerobic acrotelm, highlighting the sensitivity of acrotelm carbon to rising temperatures and atmospheric CO2 concentration. While warming accelerated OM decomposition under ambient CO2 , new carbon incorporation into peat increased in warming × elevated CO2 treatments for both plant- and microbe-derived OM. Using the isotopic signature of the applied CO2 enrichment as a label for recently photosynthesized OM, our data demonstrate that new plant inputs have been rapidly incorporated into peat carbon. Our results suggest that under current hydrological conditions, rising temperatures and atmospheric CO2  levels will likely offset each other in boreal peatlands.

What on Earth Have We Been Burning? Deciphering Sedimentary Records of Pyrogenic Carbon.

Humans have interacted with fire for thousands of years, yet the utilization of fossil fuels marked the beginning of a new era. Ubiquitous in the environment, pyrogenic carbon (PyC) arises from incomplete combustion of biomass and fossil fuels, forming a continuum of condensed aromatic structures. Here, we develop and evaluate 14C records for two complementary PyC molecular markers, benzene polycarboxylic acids (BPCAs) and polycyclic aromatic hydrocarbons (PAHs), preserved in aquatic sediments from a suburban and a remote catchment in the United States (U.S.) from the mid-1700s to 1998. Results show that the majority of PyC stems from local sources and is transferred to aquatic sedimentary archives on subdecadal to millennial time scales. Whereas a small portion stems from near-contemporaneous production and sedimentation, the majority of PyC (∼90%) experiences delayed transmission due to "preaging" on millennial time scales in catchment soils prior to its ultimate deposition. BPCAs (soot) and PAHs (precursors of soot) trace fossil fuel-derived PyC. Both markers parallel historical records of the consumption of fossil fuels in the U.S., yet never account for more than 19% total PyC. This study demonstrates that isotopic characterization of multiple tracers is necessary to constrain histories and inventories of PyC and that sequestration of PyC can markedly lag its production.

Persistence of soil organic matter as an ecosystem property.

Globally, soil organic matter (SOM) contains more than three times as much carbon as either the atmosphere or terrestrial vegetation. Yet it remains largely unknown why some SOM persists for millennia whereas other SOM decomposes readily--and this limits our ability to predict how soils will respond to climate change. Recent analytical and experimental advances have demonstrated that molecular structure alone does not control SOM stability: in fact, environmental and biological controls predominate. Here we propose ways to include this understanding in a new generation of experiments and soil carbon models, thereby improving predictions of the SOM response to global warming.

Interactive effects of elevated CO2 and nitrogen deposition on fatty acid molecular and isotope composition of above- and belowground tree biomass and forest soil fractions.

Atmospheric carbon dioxide (CO2) and reactive nitrogen (N) concentrations have been increasing due to human activities and impact the global carbon (C) cycle by affecting plant photosynthesis and decomposition processes in soil. Large amounts of C are stored in plants and soils, but the mechanisms behind the stabilization of plant- and microbial-derived organic matter (OM) in soils are still under debate and it is not clear how N deposition affects soil OM dynamics. Here, we studied the effects of 4 years of elevated (13C-depleted) CO2 and N deposition in forest ecosystems established in open-top chambers on composition and turnover of fatty acids (FAs) in plants and soils. FAs served as biomarkers for plant- and microbial-derived OM in soil density fractions. We analyzed above- and belowground plant biomass of beech and spruce trees as well as soil density fractions for the total organic C and FA molecular and isotope (δ13C) composition. FAs did not accumulate relative to total organic C in fine mineral fractions, showing that FAs are not effectively stabilized by association with soil minerals. The δ13C values of FAs in plant biomass increased under high N deposition. However, the N effect was only apparent under elevated CO2 suggesting a N limitation of the system. In soil fractions, only isotope compositions of short-chain FAs (C16+18) were affected. Fractions of 'new' (experimental-derived) FAs were calculated using isotope depletion in elevated CO2 plots and decreased from free light to fine mineral fractions. 'New' FAs were higher in short-chain compared to long-chain FAs (C20-30), indicating a faster turnover of short-chain compared to long-chain FAs. Increased N deposition did not significantly affect the quantity of 'new' FAs in soil fractions, but showed a tendency of increased amounts of 'old' (pre-experimental) C suggesting that decomposition of 'old' C is retarded by high N inputs.

Nitrogen deposition promotes the production of new fungal residues but retards the decomposition of old residues in forest soil fractions.

Atmospheric nitrogen (N) deposition has frequently been observed to increase soil carbon (C) storage in forests, but the underlying mechanisms still remain unclear. Changes in microbial community composition and substrate use are hypothesized to be one of the key mechanisms affected by N inputs. Here, we investigated the effects of N deposition on amino sugars, which are used as biomarkers for fungal- and bacterial-derived microbial residues in soil. We made use of a 4-year combined CO2 enrichment and N deposition experiment in model forest ecosystems, providing a distinct (13) C signal for 'new' and 'old' C in soil organic matter and microbial residues measured in density and particle-size fractions of soils. Our hypothesis was that N deposition decreases the amount of fungal residues in soils, with the new microbial residues being more strongly affected than old residues. The soil fractionation showed that organic matter and microbial residues are mainly stabilized by association with soil minerals in the heavy and fine fractions. Moreover, the bacterial residues are relatively enriched at mineral surfaces compared to fungal residues. The (13) C tracing indicated a greater formation of fungal residues compared to bacterial residues after 4 years of experiment. In contradiction to our hypotheses, N deposition significantly increased the amount of new fungal residues in bulk soil and decreased the decomposition of old microbial residues associated with soil minerals. The preservation of old microbial residues could be due to decreased N limitation of microorganisms and therefore a reduced dependence on organic N sources. This mechanism might be especially important in fine heavy fractions with low C/N ratios, where microbial residues are effectively protected from decomposition by association with soil minerals.

Transformation and stabilization of pyrogenic organic matter in a temperate forest field experiment.

Pyrogenic organic matter (PyOM) decomposes on centennial timescale in soils, but the processes regulating its decay are poorly understood. We conducted one of the first studies of PyOM and wood decomposition in a temperate forest using isotopically labeled organic substrate, and quantified microbial incorporation and physico-chemical transformations of PyOM in situ. Stable-isotope (¹³C and ¹5N) enriched PyOM and its precursor wood were added to the soil at 2 cm depth at ambient (N0) and increased (N+) levels of nitrogen fertilization. The carbon (C) and nitrogen (N) of added PyOM or wood were tracked through soil to 15 cm depth, in physically separated soil density fractions and in benzene polycarboxylic acids (BPCA) molecular markers. After 10 months in situ, more PyOM-derived C (>99% of initial 13C-PyOM) and N (90% of initial ¹5N-PyOM) was recovered than wood derived C (48% of 13C-wood) and N(89% under N0 and 48% under N+). PyOM-C and wood-C migrated at the rate of 126 mm yr ⁻¹ with 3-4% of PyOMC and 4-8% of wood-C recovered below the application depth. Most PyOM C was recovered in the free light fraction(fLF) (74%), with 20% in aggregate-occluded and 6% in mineral associated fractions ­ fractions that typically have much slower turnover times. In contrast, wood C was recovered mainly in occluded (33%) or dense fraction (27%).PyOM addition induced loss of native C from soil (priming effect), particularly in fLF (13%). The total BPCA-C content did not change but after 10 months the degree of aromatic condensation of PyOM decreased, as determined by relative contribution of benzene hexa-carboxylic acid (B6CA) to the total BPCA C. Soil microbial biomass assimilated 6-10% of C from the wood, while PyOM contributions was negligible (0.14­0.18%). The addition of N had no effect on the dynamics of PyOM while limited effect on wood.

Belowground plant allocation regulates rice methane emissions from degraded peat soils.

Carbon-rich peat soils have been drained and used extensively for agriculture throughout human history, leading to significant losses of their soil carbon. One solution for rewetting degraded peat is wet crop cultivation. Crops such as rice, which can grow in water-saturated conditions, could enable agricultural production to be maintained whilst reducing CO2 and N2O emissions from peat. However, wet rice cultivation can release considerable methane (CH4). Water table and soil management strategies may enhance rice yield and minimize CH4 emissions, but they also influence plant biomass allocation strategies. It remains unclear how water and soil management influences rice allocation strategies and how changing plant allocation and associated traits, particularly belowground, influence CH4-related processes. We examined belowground biomass (BGB), aboveground biomass (AGB), belowground:aboveground ratio (BGB:ABG), and a range of root traits (root length, root diameter, root volume, root area, and specific root length) under different soil and water treatments; and evaluated plant trait linkages to CH4. Rice (Oryza sativa L.) was grown for six months in field mesocosms under high (saturated) or low water table treatments, and in either degraded peat soil or degraded peat covered with mineral soil. We found that BGB and BGB:AGB were lowest in water saturated conditions where mineral soil had been added to the peat, and highest in low-water table peat soils. Furthermore, CH4 and BGB were positively related, with BGB explaining 60% of the variation in CH4 but only under low water table conditions. Our results suggest that a mix of low water table and mineral soil addition could minimize belowground plant allocation in rice, which could further lower CH4 likely because root-derived carbon is a key substrate for methanogenesis. Minimizing root allocation, in conjunction with water and soil management, could be explored as a strategy for lowering CH4 emissions from wet rice cultivation in degraded peatlands.

Toward a "molecular thermometer" to estimate the charring temperature of wildland charcoals derived from different biomass sources.

The maximum temperature experienced by biomass during combustion has a strong effect on chemical properties of the resulting charcoal, such as sorption capacity (water and nonpolar materials) and microbial degradability. However, information about the formation temperature of natural charcoal can be difficult to obtain in ecosystems that are not instrumented prior to fires. Benzene polycarboxylic acids (BPCA) are molecular markers specific for pyrogenic carbon (PyC) which can provide information on the degree of aromatic condensation in charcoals. Here we apply the BPCA molecular marker method to a set of 10 charcoals produced during an experimental fire in a Pitch pine-scrub oak forest from litter and bark of pitch pine and inkberry plants in the Pinelands National Reserve in New Jersey, USA. We deployed temperature-sensitive crayons throughout the burn site, which recorded the maximum air temperature and made comparisons to the degree of thermal alteration recorded by BPCA molecular markers. Our results show an increase of the degree of aromatic condensation with monitored temperatures for bark biomass, while for needles no clear trend could be observed. For leaf-derived charcoals at increasing monitored fire temperatures, decreasing degree of aromatic condensation was obtained. This suggests that molecular markers can be used to roughly estimate the maximum fire temperatures experienced by bark and wood materials, but not based on leaf- and needle-derived materials. Possible applications include verifying declared pyrolysis temperatures of biochars and evaluating ecosystem fire temperature postburn.

Rapid loss of complex polymers and pyrogenic carbon in subsoils under whole-soil warming.

Subsoils contain more than half of soil organic carbon (SOC) and are expected to experience rapid warming in the coming decades. Yet our understanding of the stability of this vast carbon pool under global warming is uncertain. In particular, the fate of complex molecular structures (polymers) remains debated. Here we show that 4.5 years of whole-soil warming (+4 °C) resulted in less polymeric SOC (sum of specific polymers contributing to SOC) in the warmed subsoil (20-90 cm) relative to control, with no detectable change in topsoil. Warming stimulated the subsoil loss of lignin phenols (-17 ± 0%) derived from woody plant biomass, hydrolysable lipids cutin and suberin, derived from leaf and woody plant biomass (-28 ± 3%), and pyrogenic carbon (-37 ± 8%) produced during incomplete combustion. Given that these compounds have been proposed for long-term carbon sequestration, it is notable that they were rapidly lost in warmed soils. We conclude that complex polymeric carbon in subsoil is vulnerable to decomposition and propose that molecular structure alone may not protect compounds from degradation under future warming.

Climate warming and elevated CO2 alter peatland soil carbon sources and stability.

Peatlands are an important carbon (C) reservoir storing one-third of global soil organic carbon (SOC), but little is known about the fate of these C stocks under climate change. Here, we examine the impact of warming and elevated atmospheric CO2 concentration (eCO2) on the molecular composition of SOC to infer SOC sources (microbe-, plant- and fire-derived) and stability in a boreal peatland. We show that while warming alone decreased plant- and microbe-derived SOC due to enhanced decomposition, warming combined with eCO2 increased plant-derived SOC compounds. We further observed increasing root-derived inputs (suberin) and declining leaf/needle-derived inputs (cutin) into SOC under warming and eCO2. The decline in SOC compounds with warming and gains from new root-derived C under eCO2, suggest that warming and eCO2 may shift peatland C budget towards pools with faster turnover. Together, our results indicate that climate change may increase inputs and enhance decomposition of SOC potentially destabilising C storage in peatlands.

Stable isotopic analysis of pyrogenic organic matter in soils by liquid chromatography-isotope-ratio mass spectrometry of benzene polycarboxylic acids.

Pyrogenic organic matter (PyOM), the incomplete combustion product of organic materials, is considered stable in soils and represents a potentially important terrestrial sink for atmospheric carbon dioxide. One well-established method of measuring PyOM in the environment is as benzene polycarboxylic acids (BPCAs), a compound-specific method, which allows both qualitative and quantitative estimation of PyOM. Until now, stable isotope measurement of PyOM carbon involved measurement of the trimethylsilyl (TMS) or methyl (Me) polycarboxylic acid derivatives by gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS). However, BPCA derivatives can contain as much as 150% derivative carbon, necessitating post-analysis correction for the accurate measurement of δ¹³C values, leading to increased measurement error. Here, we describe a method for δ¹³C isotope ratio measurement and quantification of BPCAs from soil-derived PyOM, based on ion-exchange chromatography (IEC-IRMS). The reproducibility of the δ¹³C measurement of individual BPCAs by IEC-IRMS was better than 0.35‰ (1σ). The δ¹³C-BPCA analysis of PyOM in soils, including at natural and artificially enriched ¹³C-abundance, produced accurate and precise δ¹³C measurements. Analysis of samples that differed in δ¹³C by as much as 900‰ revealed carryover of <1‰ between samples. The weighted sum of individual δ¹³C-BPCA measurements was correlated with previous isotopic measurements of whole PyOM, providing complementary information for bulk isotopic measurements. We discuss potential applications of δ¹³C-BPCA measurements, including the study of turnover rates of PyOM in soils and the partitioning of PyOM sources based on photosynthetic pathways.

Five years of whole-soil warming led to loss of subsoil carbon stocks and increased CO2 efflux.

Subsoils below 20 cm are an important reservoir in the global carbon cycle, but little is known about their vulnerability under climate change. We measured a statistically significant loss of subsoil carbon (-33 ± 11%) in warmed plots of a conifer forest after 4.5 years of whole-soil warming (4°C). The loss of subsoil carbon was primarily from unprotected particulate organic matter. Warming also stimulated a sustained 30 ± 4% increase in soil CO2 efflux due to increased CO2 production through the whole-soil profile. The observed in situ decline in subsoil carbon stocks with warming is now definitive evidence of a positive soil carbon-climate feedback, which could not be concluded based on increases in CO2 effluxes alone. The high sensitivity of subsoil carbon and the different responses of soil organic matter pools suggest that models must represent these heterogeneous soil dynamics to accurately predict future feedbacks to warming.

Author Correction: Tropical forest soil carbon stocks do not increase despite 15 years of doubled litter inputs.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Tropical forest soil carbon stocks do not increase despite 15 years of doubled litter inputs.

Soil organic carbon (SOC) dynamics represent a persisting uncertainty in our understanding of the global carbon cycle. SOC storage is strongly linked to plant inputs via the formation of soil organic matter, but soil geochemistry also plays a critical role. In tropical soils with rapid SOC turnover, the association of organic matter with soil minerals is particularly important for stabilising SOC but projected increases in tropical forest productivity could trigger feedbacks that stimulate the release of stored SOC. Here, we demonstrate limited additional SOC storage after 13-15 years of experimentally doubled aboveground litter inputs in a lowland tropical forest. We combined biological, physical, and chemical methods to characterise SOC along a gradient of bioavailability. After 13 years of monthly litter addition treatments, most of the additional SOC was readily bioavailable and we observed no increase in mineral-associated SOC. Importantly, SOC with weak association to soil minerals declined in response to long-term litter addition, suggesting that increased plant inputs could modify the formation of organo-mineral complexes in tropical soils. Hence, we demonstrate the limited capacity of tropical soils to sequester additional C inputs and provide insights into potential underlying mechanisms.

Marked isotopic variability within and between the Amazon River and marine dissolved black carbon pools.

Riverine dissolved organic carbon (DOC) contains charcoal byproducts, termed black carbon (BC). To determine the significance of BC as a sink of atmospheric CO2 and reconcile budgets, the sources and fate of this large, slow-cycling and elusive carbon pool must be constrained. The Amazon River is a significant part of global BC cycling because it exports an order of magnitude more DOC, and thus dissolved BC (DBC), than any other river. We report spatially resolved DBC quantity and radiocarbon (Δ14C) measurements, paired with molecular-level characterization of dissolved organic matter from the Amazon River and tributaries during low discharge. The proportion of BC-like polycyclic aromatic structures decreases downstream, but marked spatial variability in abundance and Δ14C values of DBC molecular markers imply dynamic sources and cycling in a manner that is incongruent with bulk DOC. We estimate a flux from the Amazon River of 1.9-2.7 Tg DBC yr-1 that is composed of predominately young DBC, suggesting that loss processes of modern DBC are important.

The MICE facility - a new tool to study plant-soil C cycling with a holistic approach.

Plant-soil interactions are recognized to play a crucial role in the ecosystem response to climate change. We developed a facility to disentangle the complex interactions behind the plant-soil C feedback mechanisms. The MICE ('Multi-Isotope labelling in a Controlled Environment') facility consists of two climate chambers with independent control of the atmospheric conditions (light, CO2, temperature, humidity) and the soil environment (temperature, moisture). Each chamber holds 15 plant-soil systems with hermetical separation of the shared above ground (shoots) from the individual belowground compartments (roots, rhizosphere, soil). Stable isotopes (e.g. 13C, 15N, 2H, 18O) can be added to either compartment and traced within the whole system. The soil CO2 efflux rate is monitored, and plant material, leached soil water and gas samples are taken frequently. The facility is a powerful tool to improve our mechanistic understanding of plant-soil interactions that drive the C cycle feedback to climate change.

Characterization, Quantification and Compound-specific Isotopic Analysis of Pyrogenic Carbon Using Benzene Polycarboxylic Acids (BPCA).

Fire-derived, pyrogenic carbon (PyC), sometimes called black carbon (BC), is the carbonaceous solid residue of biomass and fossil fuel combustion, such as char and soot. PyC is ubiquitous in the environment due to its long persistence, and its abundance might even increase with the projected increase in global wildfire activity and the continued burning of fossil fuel. PyC is also increasingly produced from the industrial pyrolysis of organic wastes, which yields charred soil amendments (biochar). Moreover, the emergence of nanotechnology may also result in the release of PyC-like compounds to the environment. It is thus a high priority to reliably detect, characterize and quantify these charred materials in order to investigate their environmental properties and to understand their role in the carbon cycle. Here, we present the benzene polycarboxylic acid (BPCA) method, which allows the simultaneous assessment of PyC's characteristics, quantity and isotopic composition ((13)C and (14)C) on a molecular level. The method is applicable to a very wide range of environmental sample materials and detects PyC over a broad range of the combustion continuum, i.e., it is sensitive to slightly charred biomass as well as high temperature chars and soot. The BPCA protocol presented here is simple to employ, highly reproducible, as well as easily extendable and modifiable to specific requirements. It thus provides a versatile tool for the investigation of PyC in various disciplines, ranging from archeology and environmental forensics to biochar and carbon cycling research.