Molecular insight into soil carbon turnover

Association between soil organic carbon and calcium in acidic grassland soils from Point Reyes National Seashore, CA

Organo-mineral and organo-metal associations play an important role in the retention and accumulation of soil organic carbon (SOC). Recent studies have demonstrated a positive correlation between calcium (Ca) and SOC content in a range of soil types. However, most of these studies have focused on soils that contain calcium carbonate (pH > 6). To assess the importance of Ca-SOC associations in lower pH soils, we investigated their physical and chemical interaction in the grassland soils of Point Reyes National Seashore (CA, USA) at a range of spatial scales. Multivariate analyses of our bulk soil characterisation dataset showed a strong correlation between exchangeable Ca (CaExch; 5-8.3 c.molc kg-1) and SOC (0.6-4%) content. Additionally, linear combination fitting (LCF) of bulk Ca K-edge X-ray absorption near-edge structure (XANES) spectra revealed that Ca was predominantly associated with organic carbon across all samples. Scanning transmission X-ray microscopy near-edge X-ray absorption fine structure spectroscopy (STXM C/Ca NEXAFS) showed that Ca had a strong spatial correlation with C at the microscale. The STXM C NEXAFS K-edge spectra indicated that SOC had a higher abundance of aromatic/olefinic and phenolic C functional groups when associated with Ca, relative to C associated with Fe. In regions of high Ca-C association, the STXM C NEXAFS spectra were similar to the spectrum from lignin, with moderate changes in peak intensities and positions that are consistent with oxidative C transformation. Through this association, Ca thus seems to be preferentially associated with plant-like organic matter that has undergone some oxidative transformation, at depth in acidic grassland soils of California. Our study highlights the importance of Ca-SOC complexation in acidic grassland soils and provides a conceptual model of its contribution to SOC preservation, a research area that has previously been unexplored.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10533-023-01059-2.

Perennial Crops Can Compensate for Low Soil Carbon Inputs from Maize in Ley-Arable Systems

(1) Background: Soil organic carbon (SOC) in agricultural soils plays a crucial role in mitigating global climate change but also, and maybe more importantly, in soil fertility and thus food security. Therefore, the influence of contrasting cropping systems on SOC not only in the topsoil, but also in the subsoil, needs to be understood. (2) Methods: In this study, we analyzed SOC content and δ¹³C values from a crop rotation experiment for biogas production, established in southern Germany in 2004. We compared two crop rotations, differing in their proportions of maize (0 vs. 50%) and perennial legume-grass leys as main crops (75 vs. 25%). Maize was cultivated with an undersown white clover. Both rotations had an unfertilized variant and a variant that was fertilized with biogas digestate according to the nutrient demand of crops. Sixteen years after the experiment was established, the effects of crop rotation, fertilization, and soil depth on SOC were analyzed. Furthermore, we defined a simple carbon balance model to estimate the dynamics of δ¹³C in soil. Simulations were compared to topsoil data (0-30 cm) from 2009, 2017, and 2020, and to subsoil data (30-60 cm) from 2020. (3) Results: Crop rotation and soil depth had significant effects, but fertilization had no effect on SOC content and δ¹³C. SOC significantly differed between the two crop rotations regarding δ¹³C in both depths but not regarding content. Annual enrichment in C₄ (maize) carbon was 290, 34, 353, and 70 kg C ha^-1 per maize year in the topsoil and subsoil of the unfertilized and fertilized treatments, respectively. These amounts corresponded to carbon turnover rates of 0.8, 0.3, 0.9, and 0.5% per maize year. Despite there being 50% maize in the rotation, maize carbon only accounted for 20% of the observed carbon sequestration in the topsoil. Even with pre-defined parameter values, the simple carbon model reproduced observed δ¹³C well. The optimization of model parameters decreased the carbon use efficiency of digestate carbon in the soil, as well as the response of belowground carbon allocation to increased aboveground productivity of maize. (4) Conclusions: Two main findings resulted from this combination of measurement and modelling: (i) the retention of digestate carbon in soil was low and its effect on δ¹³C was negligible, and (ii) soil carbon inputs from maize only responded slightly to increased above-ground productivity. We conclude that SOC stocks in silage maize rotations can be preserved or enhanced if leys with perennial crops are included that compensate for the comparably low maize carbon inputs.

Clarifying the evidence for microbial- and plant-derived soil organic matter, and the path toward a more quantitative understanding

Predicting and mitigating changes in soil carbon (C) stocks under global change requires a coherent understanding of the factors regulating soil organic matter (SOM) formation and persistence, including knowledge of the direct sources of SOM (plants vs. microbes). In recent years, conceptual models of SOM formation have emphasized the primacy of microbial-derived organic matter inputs, proposing that microbial physiological traits (e.g., growth efficiency) are dominant controls on SOM quantity. However, recent quantitative studies have challenged this view, suggesting that plants make larger direct contributions to SOM than is currently recognized by this paradigm. In this review, we attempt to reconcile these perspectives by highlighting that variation across estimates of plant- versus microbial-derived SOM may arise in part from methodological limitations. We show that all major methods used to estimate plant versus microbial contributions to SOM have substantial shortcomings, highlighting the uncertainty in our current quantitative estimates. We demonstrate that there is significant overlap in the chemical signatures of compounds produced by microbes, plant roots, and through the extracellular decomposition of plant litter, which introduces uncertainty into the use of common biomarkers for parsing plant- and microbial-derived SOM, especially in the mineral-associated organic matter (MAOM) fraction. Although the studies that we review have contributed to a deeper understanding of microbial contributions to SOM, limitations with current methods constrain quantitative estimates. In light of recent advances, we suggest that now is a critical time to re-evaluate long-standing methods, clearly define their limitations, and develop a strategic plan for improving the quantification of plant- and microbial-derived SOM. From our synthesis, we outline key questions and challenges for future research on the mechanisms of SOM formation and stabilization from plant and microbial pathways.

Fingerprinting macrophyte Blue Carbon by pyrolysis-GC-compound specific isotope analysis (Py-CSIA)

There is a need for tools to determine the origin of organic matter (OM) in Blue Carbon Ecosystems (BCE) and marine sediments to (1) facilitate the implementation of Blue Carbon strategies into carbon accounting and crediting schemes and (2) decipher changes in ecosystem condition over decadal to millennial time scales and thus to understand and predict the stability of BCE in a changing world. Pyrolysis-GC-compound specific isotope analysis (Py-CSIA) is applied for the first time in marine environments and BCE research. We studied Australian mangrove, tidal marsh and seagrass sediments, in addition to potential sources of OM (Avicennia, Posidonia, Zostera, Sarcocornia, Ecklonia and Ulva species and seagrass epiphytes), to identify precursors of different biomacromolecule constituents (lignin, polysaccharides and aliphatic structures). Firstly, the link between bulk δ¹³C and δ¹³C reconstructed from compound-specific δ¹³C showed that the pyrolysis approach allows for the isotopic screening of a representative portion of the OM. Secondly, for all samples, the C isotope fingerprint of the carbohydrate products (plant polysaccharides) was the heaviest (¹³C enriched), followed by lignin and aliphatic products. The differences in δ¹³C among macromolecules and the overlap in δ¹³C among putative sources reflect the limitations of bulk δ¹³C analyses for deciphering OM provenance. Thirdly, phanerogams specimen had the heaviest carbohydrate and lignin, confirming that seagrass-derived lignocellulose can be traced based on δ¹³C. Consistent differences for individual compounds were identified between seagrasses and between Avicennia and Sarcocornia using Py-CSIA. Fourth, ecosystem shifts (colonization of seagrass habitats by mangrove) on millenary time scales, hypothesized in previous studies on the basis of bulk δ¹³C and Py-GC-MS, were confirmed by Py-CSIA. We conclude that Py-CSIA is useful in Blue Carbon research to decipher OM sources in marine sediments, identify ecosystem transitions in palaeoenvironmental records, and to understand the role of different OM compounds in Blue Carbon storage.

Roots are key to increasing the mean residence time of organic carbon entering temperate agricultural soils

The ratio of soil organic carbon stock (SOC) to annual carbon input gives an estimate of the mean residence time of organic carbon that enters the soil (MRT_OC ). It indicates how efficiently biomass can be transformed into SOC, which is of particular relevance for mitigating climate change by means of SOC storage. There have been few comprehensive studies of MRT_OC and their drivers, and these have mainly been restricted to the global scale, on which climatic drivers dominate. This study used the unique combination of regional-scale cropland and grassland topsoil (0-30 cm) SOC stock data and average site-specific OC input data derived from the German Agricultural Soil Inventory to elucidate the main drivers of MRT_OC . Explanatory variables related to OC input composition and other soil-forming factors were used to explain the variability in MRT_OC by means of a machine-learning approach. On average, OC entering German agricultural topsoils had an MRT of 21.5 ± 11.6 years, with grasslands (29.0 ± 11.2 years, n = 465) having significantly higher MRT_OC than croplands (19.4 ± 10.7, n = 1635). This was explained by the higher proportion of root-derived OC inputs in grassland soils, which was the most important variable for explaining MRT_OC variability at a regional scale. Soil properties such as clay content, soil group, C:N ratio and groundwater level were also important, indicating that MRT_OC is driven by a combination of site properties and OC input composition. However, the great importance of root-derived OC inputs indicated that MRT_OC can be actively managed, with maximization of root biomass input to the soil being a straightforward means to extend the time that assimilated C remains in the soil and consequently also increase SOC stocks.

Conservation tillage for 17 years alters the molecular composition of organic matter in soil profile

Conservation tillage is considered as a potential measure to mitigate climate change by sequestering soil organic matter (SOM), however its stabilization mechanisms remain elusive. In this study, we revealed the molecular composition of SOM in soil profile (~50 cm depth) from a 17-yr tillage experiment in North China. The soils were collected from 0-10, 10-20, 20-30 and 30-50 cm layers under conventional tillage (CT), and conservation tillage such as rotary tillage (RT) and no-tillage (NT). The sequential solvent extraction and CuO oxidation methods were used to quantify free lipids and lignin-derived phenols. The results showed that NT (cf. CT) increased labile compounds (i.e., carbohydrates) and plant-derived SOM (i.e., long-chain (≥C₂₀) aliphatic lipids and steroids) in the 0-10 and 30-50 cm layers. The RT (cf. CT) increased the total free lipids by 72-133% in the sublayers (>10 cm). The RT (cf. CT and NT) resulted in higher preservation of plant-derived (≥C₂₀ aliphatic lipids and steroids) and microbial-derived compounds (<C₂₀ aliphatic lipids and trehalose) SOM in deep soils (i.e., ≥10 cm). Conservation tillage suppressed lignin degradation, as reflected by 32-137% higher total lignin-derived phenols under RT and NT than CT in the 0-10 and 30-50 cm layers. The NMR revealed higher aliphatic to aromatic C ratio under NT and RT in the whole soil profile, suggesting more aliphatic lipids accumulated. Conservation tillage increased SOC stocks by 10-14% in 0-10 cm layer but not in deeper profiles. These results suggest that conservation tillage have increased plant-derived lipids and lignin accumulation. Our study highlights that conservation tillage (particularly the RT) after 17 years alters SOM molecular compositions and degradation processes in the soil profile. These findings have implications for improving our understanding of C stabilization mechanisms in agroecosystems.

DNA Stable-Isotope Probing Delineates Carbon Flows from Rice Residues into Soil Microbial Communities Depending on Fertilization

Identifying and understanding the active microbial communities and interactions involved in plant residue utilization are key questions to elucidate the transformation of soil organic matter (SOM) in agricultural ecosystems. Microbial community composition responds strongly to management, but little is known about specific microbial groups involved in plant residue utilization and, consequently, microbial functions under different methods of fertilization. We combined DNA stable-isotope (¹³C) probing and high-throughput sequencing to identify active fungal and bacterial groups degrading residues in soils after 3 years of mineral fertilization with and without manure. Manuring changed the active microbial composition and complexified microbial interactions involved in residue C flow. Most fungal genera, especially Chaetomium, Staphylotrichum, Penicillium, and Aspergillus, responded to residue addition faster in soils that historically had received manure. We generated a valuable library of microorganisms involved in plant residue utilization for future targeted research to exploit specific functions of microbial groups in organic matter utilization and C sequestration.

Decomposition of crop residues in soil is mediated by microorganisms whose activities vary with fertilization. The complexity of active microorganisms and their interactions utilizing residues is impossible to disentangle without isotope applications. Thus, ¹³C-labeled rice residues were employed, and DNA stable-isotope probing (DNA-SIP) combined with high-throughput sequencing was applied to identify microbes active in assimilating residue carbon (C). Manure addition strongly modified microbial community compositions involved in the C flow from rice residues. Relative abundances of the bacterial genus Lysobacter and fungal genus Syncephalis were increased, but abundances of the bacterial genus Streptomyces and fungal genus Trichoderma were decreased in soils receiving mineral fertilizers plus manure (NPKM) compared to levels in soils receiving only mineral fertilizers (NPK). Microbes involved in the flow of residue C formed a more complex network in NPKM than in NPK soils because of the necessity to decompose more diverse organic compounds. The fungal species (Jugulospora rotula and Emericellopsis terricola in NPK and NPKM soils, respectively) were identified as keystone species in the network and may significantly contribute to residue C decomposition. Most of the fungal genera in NPKM soils, especially Chaetomium, Staphylotrichum, Penicillium, and Aspergillus, responded faster to residue addition than those in NPK soils. This is connected with the changes in the composition of the rice residue during degradation and with fungal adaptation (abundance and activity) to continuous manure input. Our findings provide fundamental information about the roles of key microbial groups in residue decomposition and offer important cues on manipulating the soil microbiome for residue utilization and C sequestration in soil.

IMPORTANCE Identifying and understanding the active microbial communities and interactions involved in plant residue utilization are key questions to elucidate the transformation of soil organic matter (SOM) in agricultural ecosystems. Microbial community composition responds strongly to management, but little is known about specific microbial groups involved in plant residue utilization and, consequently, microbial functions under different methods of fertilization. We combined DNA stable-isotope (¹³C) probing and high-throughput sequencing to identify active fungal and bacterial groups degrading residues in soils after 3 years of mineral fertilization with and without manure. Manuring changed the active microbial composition and complexified microbial interactions involved in residue C flow. Most fungal genera, especially Chaetomium, Staphylotrichum, Penicillium, and Aspergillus, responded to residue addition faster in soils that historically had received manure. We generated a valuable library of microorganisms involved in plant residue utilization for future targeted research to exploit specific functions of microbial groups in organic matter utilization and C sequestration.

Quantification and molecular characterization of organo-mineral associations as influenced by redox oscillations

Organo-mineral association is one of the most important stabilization mechanisms of soil organic matter. However, few studies have been conducted to assess the retention, transformation, and transportation of colloids (1-1000 nm) and associated organic carbon (OC) in soil. Given the particularly significant role that wetland soils play in carbon storage and cycling, we quantified the dynamics of organo-mineral association within colloidal size range by conducting three consecutive 35-day redox (reduction-oxidation) oscillation experiments using a wetland soil. Molecular compositions of natural nanoparticle (NNP, 2.3-100 nm), fine colloid (100-450 nm), and particulate (450-1000 nm) fractions were measured using isotope ratio mass spectrometry (IRMS) and x-ray photoelectron spectroscopy (XPS). Results showed that NNP and fine colloids constituted up to 8.94 ± 0.50% and 22.19 ± 7.52% of bulk C concentration (2.3-1000 nm), respectively; indicating substantial contributions of these two fractions to the operationally defined "dissolved" (<450 nm) fraction. There was significant enrichment in heavier δ¹³C isotopes (p < 0.001) with size: NNP (-29.64 ± 0.32‰) < fine colloid (-28.81 ± 0.31‰) < particulate (-28.34 ± 0.25‰) fractions. NNP had the highest percentages of carbonyl/carboxyl C (C=O); while fine colloid and particulate fractions contained more reduced aromatic or aliphatic C (C-C, C=C, C-H). OC became more enriched (‰) in microbial-derived C (higher δ¹³C) with increasing particle size as well as with repeated redox oscillations. Our findings clearly demonstrate limitations of using the operationally defined "dissolved" fraction (<450 nm) to assess C cycling in ecosystems such as wetlands. Increase in colloid and OC concentrations and presence of more microbial-derived C in larger size fractions additionally imply that redox oscillations promote the formation of molecularly diverse sub-colloid sized organo-mineral associations. Being a composite unit of soil microaggregates, organic-mineral associations can thus influence the overall stability of OC in wetland soils that undergo frequent redox oscillations.

Stable carbon isotope analyses offer insights into net carbon degradation of maize silages in anaerobic batch fermentations

Carbon degradation indicates the efficiency of anaerobic digestion processes. Common carbon degradation determination methods define gross carbon degradation (C deggross) of substrate and inoculum inseparably. The aim of this study was to test an isotope-based method defining solely substrate-based net carbon degradation (C degnet) on maize silage. As the natural abundance of stable isotopes in agricultural substrates vary, the method’s applicability was tested on (i) different maize silages sampled from agricultural farms, (ii) maize silage in fresh (MSfresh) and impaired storage (MSimpaired) conditions.Experiments included six maize silages digested in a total of 19 lab-scale batch reactors, analyzed for digestion parameters, stable isotopes, gross and net carbon degradation. MSimpaired showed significantly different stable carbon isotope composition at the start of the experiments, compared to MSfresh. Both methods indicated quality losses in MSimpaired. Results showed significantly higher C degnet values, ranging from 58.4% to 86.5%, compared to deggross values, ranging from 23.1% to 48.7%. This indicated the applicability of an isotope-based method C degnet to assess net carbon degradation of maize silages more detailed by excluding the masking effect of the inoculum. The isotope-based net carbon degradation method was found applicable on maize silages from (i) different farms and (ii) in different storage qualities.

Different Molecular Characterization of Soil Particulate Fractions under N Deposition in a Subtropical Forest

Key Findings: Combining physical fractionation and pyrolysis–gas chromatography/mass spectrometry (py-GC/MS) technique can help better understand the dynamics of soil organic matter (SOM). Background and Objectives: SOM plays a critical role in the global carbon (C) cycle. However, its complexity remains a challenge in characterizing chemical molecular composition within SOM and under nitrogen (N) deposition. Materials and Methods: Three particulate organic matter (POM) fractions within SOM and under N treatments were studied from perspectives of distributions, C contents and chemical signatures in a subtropical forest. N addition experiment was conducted with two inorganic N forms (NH4Cl and NaNO3) applied at three rates of 0, 40, 120 kg N ha−1 yr−1. Three particle-size fractions (>250 μm, 53–250 μm and <53 μm) were separated by a wet-sieving method. Py-GC/MS technique was used to differentiate between chemical composition. Results: A progressive proportion transfer of mineral-associated organic matter (MAOM) to fine POM under N treatment was found. Only C content in fine POM was sensitive to N addition. Principal component analyses (PCA) showed that the coarse POM had the largest plant-derived markers (lignins, phenols, long-chain n-alkanes, and n-alkenes). Short-chain n-alkanes and n-alkenes, benzofurans, aromatics and polycyclic aromatic hydrocarbons mainly from black carbon prevailed in the fine POM. N compounds and polysaccharides from microbial products dominated in the MAOM. Factor analysis revealed that the degradation extent of three fractions was largely distinct. The difference in chemical structure among three particulate fractions within SOM was larger than treatments between control and N addition. In terms of N treatment impact, the MAOM fraction had fewer benzofurans compounds and was enriched in polysaccharides, indicating comparatively weaker mineralization and stronger stabilization of these substances. Conclusions: Our findings highlight the importance of chemical structure in SOM pools and help to understand the influence of N deposition on SOM transformation.

Artificial humification of lignin architecture: Top-down and bottom-up approaches

Humic substances readily identifiable in the environment are involved in several biotic and abiotic reactions affecting carbon turnover, soil fertility, plant nutrition and stimulation, xenobiotic transformation and microbial respiration. Inspired by natural roles of humic substances, several applications of these substances, including crop stimulants, redox mediators, anti-oxidants, human medicines, environmental remediation and fish feeding, have been developed. The annual market for humic substances has grown rapidly for these reasons and due to eco-conscious features, but there is a limited supply of natural coal-related resources such as lignite and leonardite from which humic substances are extracted in bulk. The structural similarity between humic substances and lignin suggests that lignocellulosic refinery resulting in lignin residues as a by-product could be a potential candidate for a bulk source of humic-like substances, but structural differences between the two polymeric materials indicate that additional transformation procedures allowing lignin architecture to fully mimic commercial humic substances are required. In this review, we introduce the emerging concept of artificial humification of lignin-related materials as a promising strategy for lignin valorization. First, the core structural features of humic substances and the relationship between these features and the physicochemical properties, natural functions and versatile applications of the substances are described. In particular, the mechanism by which humic substances stimulate the growth of plants and hence can improve crop productivity is highlighted. Second, top-down and bottom-up transformation pathways for scalable humification of small lignin-derived phenols, technical lignins and lignin-containing plant residues are described in detail. Finally, future directions are suggested for research and development of artificial lignin humification to achieve alternative ways of producing customized analogues of humic substances.

Current and emerging methodologies for estimating carbon sequestration in agricultural soils: A review

This review covers the current and emerging analytical methods used in laboratory, field, landscape and regional contexts for measuring soil organic carbon (SOC) sequestration in agricultural soil. Soil depth plays an important role in estimating SOC sequestration. Selecting appropriate sampling design, depth of soil, use of proper analytical methods and base line selection are prerequisites for estimating accurately the soil carbon stocks. Traditional methods of wet digestion and dry combustion (DC) are extensively used for routine laboratory analysis; the latter is considered to be the "gold standard" and superior to the former for routine laboratory analysis. Recent spectroscopic techniques can measure SOC stocks in laboratory and in-situ even up to a deeper depth. Aerial spectroscopy using multispectral and/or hyperspectral sensors located on aircraft, unmanned aerial vehicles (UAVs) or satellite platforms can measure surface soil organic carbon. Although these techniques' current precision is low, the next generation hyperspectral sensor with improved signal noise ratio will further improve the accuracy of prediction. At the ecosystem level, carbon balance can be estimated directly using the eddy-covariance approach and indirectly by employing agricultural life cycle analysis (LCA). These methods have tremendous potential for estimating SOC. Irrespective of old or new approaches, depending on the resources and research needed, they occupy a unique place in soil carbon and climate research. This paper highlights the overview, potential limitations of various scale-dependent techniques for measuring SOC sequestration in agricultural soil.

Soil Organic Matter Persistence as a Stochastic Process: Age and Transit Time Distributions of Carbon in Soils

The question of why some types of organic matter are more persistent while others decompose quickly in soils has motivated a large amount of research in recent years. Persistence is commonly characterized as turnover or mean residence time of soil organic matter (SOM). However, turnover and residence times are ambiguous measures of persistence, because they could represent the concept of either age or transit time. To disambiguate these concepts and propose a metric to assess SOM persistence, we calculated age and transit time distributions for a wide range of soil organic carbon models. Furthermore, we show how age and transit time distributions can be obtained from a stochastic approach that takes a deterministic model of mass transfers among different pools and creates an equivalent stochastic model at the level of atoms. Using this approach we show the following: (1) Age distributions have relatively old mean values and long tails in relation to transit time distributions, suggesting that carbon stored in soils is on average much older than carbon in the release flux. (2) The difference between mean ages and mean transit times is large, with estimates of soil organic carbon persistence on the order of centuries or millennia when assessed using ages and on the order of decades when using transit or turnover times. (3) The age distribution is an appropriate metric to characterize persistence of SOM. An important implication of our analysis is that random chance is a factor that helps to explain why some organic matter persists for millennia in soil.

Compound-specific stable carbon isotopic signature of carbohydrate pyrolysis products from C3 and C4 plants

BACKGROUND

Pyrolysis-compound specific isotopic analysis (Py-CSIA: Py-GC-(FID)-C-IRMS) is a relatively novel technique that allows on-line quantification of stable isotope proportions in chromatographically separated products released by pyrolysis. Validation of the Py-CSIA technique is compulsory for molecular traceability in basic and applied research. In this work, commercial sucrose from C4 (sugarcane) and C3 (sugarbeet) photosystem plants and admixtures were studied using analytical pyrolysis (Py-GC/MS), bulk δ(13)C IRMS and δ(13)C Py-CSIA.

RESULTS

Major pyrolysis compounds were furfural (F), furfural-5-hydroxymethyl (HMF) and levoglucosan (LV). Bulk and main pyrolysis compound δ(13)C (‰) values were dependent on plant origin: C3 (F, -24.65 ± 0.89; HMF, -22.07 ± 0.41‰; LV, -21.74 ± 0.17‰) and C4 (F, -14.35 ± 0.89‰; HMF, -11.22 ± 0.54‰; LV, -11.44 ± 1.26‰). Significant regressions were obtained for δ(13)C of bulk and pyrolysis compounds in C3 and C4 admixtures. Furfural (F) was found (13)C depleted with respect to bulk and HMF and LV, indicating the incorporation of the light carbon atom in position 6 of carbohydrates in the furan ring after pyrolysis.

CONCLUSION

This is the first detailed report on the δ(13)C signature of major pyrolytically generated carbohydrate-derived molecules. The information provided by Py-CSIA is valuable for identifying source marker compounds of use in food science/fraud detection or in environmental research.

The molecular composition of dissolved organic matter in forest soils as a function of pH and temperature

We examined the molecular composition of forest soil water during three different seasons at three different sites, using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS). We examined oxic soils and tested the hypothesis that pH and season correlate with the molecular composition of dissolved organic matter (DOM). We used molecular formulae and their relative intensity from ESI-FT-ICR-MS for statistical analysis. Applying unconstrained and constrained ordination methods, we observed that pH, dissolved organic carbon (DOC) concentration and season were the main factors correlating with DOM molecular composition. This result is consistent with a previous study where pH was a main driver of the molecular differences between DOM from oxic rivers and anoxic bog systems in the Yenisei River catchment. At a higher pH, the molecular formulae had a lower degree of unsaturation and oxygenation, lower molecular size and a higher abundance of nitrogen-containing compounds. These characteristics suggest a higher abundance of tannin connected to lower pH that possibly inhibited biological decomposition. Higher biological activity at a higher pH might also be related to the higher abundance of nitrogen-containing compounds. Comparing the seasons, we observed a decrease in unsaturation, molecular diversity and the number of nitrogen-containing compounds in the course of the year from March to November. Temperature possibly inhibited biological degradation during winter, which could cause the accumulation of a more diverse compound spectrum until the temperature increased again. Our findings suggest that the molecular composition of DOM in soil pore waters is dynamic and a function of ecosystem activity, pH and temperature.

Measurement of δ13C values of soil amino acids by GC-C-IRMS using trimethylsilylation: a critical assessment

In this study, we evaluated trimethylsilyl (TMS) derivatives as derivatization reagents for the compound-specific stable carbon isotope analysis of soil amino acids by gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS). We used non-proteinogenic amino acids to show that the extraction-derivatization-analysis procedure provides a reliable method to measure δ(13)C values of amino acids extracted from soil. However, we found a number of drawbacks that significantly increase the final total uncertainty. These include the following: production of multiple peaks for each amino acid, identified as di-, tri- and tetra-TMS derivatives; a number of TMS-carbon (TMS-C) atoms added lower than the stoichiometric one, possibly due to incomplete combustion; different TMS-C δ(13)C for di-, tri- and tetra-TMS derivatives. For soil samples, only four amino acids (leucine, valine, threonine and serine) provide reliable δ(13)C values with a total average uncertainty of 1.3 ‰. We conclude that trimethylsilyl derivatives are only suitable for determining the (13)C incorporation in amino acids within experiments using (13)C-labelled tracers but cannot be applied for amino acids with natural carbon isotope abundance until the drawbacks described here are overcome and the measured total uncertainty significantly decreased.

The Microbial Efficiency-Matrix Stabilization (MEMS) framework integrates plant litter decomposition with soil organic matter stabilization: do labile plant inputs form stable soil organic matter?

The decomposition and transformation of above- and below-ground plant detritus (litter) is the main process by which soil organic matter (SOM) is formed. Yet, research on litter decay and SOM formation has been largely uncoupled, failing to provide an effective nexus between these two fundamental processes for carbon (C) and nitrogen (N) cycling and storage. We present the current understanding of the importance of microbial substrate use efficiency and C and N allocation in controlling the proportion of plant-derived C and N that is incorporated into SOM, and of soil matrix interactions in controlling SOM stabilization. We synthesize this understanding into the Microbial Efficiency-Matrix Stabilization (MEMS) framework. This framework leads to the hypothesis that labile plant constituents are the dominant source of microbial products, relative to input rates, because they are utilized more efficiently by microbes. These microbial products of decomposition would thus become the main precursors of stable SOM by promoting aggregation and through strong chemical bonding to the mineral soil matrix.

The source of microbial C has little impact on soil organic matter stabilisation in forest ecosystems

The source of microbial C is thought to impact its stability in soil due to variations in cellular biochemistry. It has been hypothesised that a fungal-dominated community stabilises more C than a bacterial-dominated community, in part due to chemical recalcitrance of their non-living biomass, particularly cell wall components and pigments. We compared the turnover of (13)C-labelled (99.9 atom %) temperate and tropical microbial isolates [i.e. fungi, Gram-positive bacteria (including actinobacteria) and Gram-negative bacteria] in temperate (California) and tropical (Puerto Rico) forest soils. While significant differences in (13)C recovery and mean residence times occurred among some microbial additions, similar turnover rates were observed, and in general, results do not support the view that microbial biochemistry affects soil C maintenance. Different effects by microbial necromass additions in California and Puerto Rico suggest that ecosystem-specific effects may be as important to microbial C stabilisation as its macromolecular composition and recalcitrance.

The pyrolytic profile of lyophilized and deep-frozen compact part of the human bone

Background. Bone grafts are used in the treatment of nonunion of fractures, bone tumors and in arthroplasty. Tissues preserved by lyophilization or deep freezing are used as implants nowadays. Lyophilized grafts are utilized in the therapy of birth defects and bone benign tumors, while deep-frozen ones are applied in orthopedics. The aim of the study was to compare the pyrolytic pattern, as an indirect means of the analysis of organic composition of deep-frozen and lyophilized compact part of the human bone. Methods. Samples of preserved bone tissue were subjected to thermolysis and tetrahydroammonium-hydroxide- (TMAH-) associated thermochemolysis coupled with gas chromatography and mass spectrometry (Py-GC/MS). Results. Derivatives of benzene, pyridine, pyrrole, phenol, sulfur compounds, nitriles, saturated and unsaturated aliphatic hydrocarbons, and fatty acids (C12–C20) were identified in the pyrolytic pattern. The pyrolyzates were the most abundant in derivatives of pyrrole and nitriles originated from proteins. The predominant product in pyrolytic pattern of the investigated bone was pyrrolo[1,2-α]piperazine-3,6-dione derived from collagen. The content of this compound significantly differentiated the lyophilized graft from the deep-frozen one. Oleic and palmitic acid were predominant among fatty acids of the investigated samples. The deep-frozen implants were characterized by higher percentage of long-chain fatty acids than lyophilized grafts.

Simultaneous determination of the quantity and isotopic signature of dissolved organic matter from soil water using high-performance liquid chromatography/isotope ratio mass spectrometry

We assessed the accuracy and utility of a modified high-performance liquid chromatography/isotope ratio mass spectrometry (HPLC/IRMS) system for measuring the amount and stable carbon isotope signature of dissolved organic matter (DOM) <1 µm. Using a range of standard compounds as well as soil solutions sampled in the field, we compared the results of the HPLC/IRMS analysis with those from other methods for determining carbon and (13)C content. The conversion efficiency of the in-line wet oxidation of the HPLC/IRMS averaged 99.3% for a range of standard compounds. The agreement between HPLC/IRMS and other methods in the amount and isotopic signature of both standard compounds and soil water samples was excellent. For DOM concentrations below 10 mg C L(-1) (250 ng C total) pre-concentration or large volume injections are recommended in order to prevent background interferences. We were able to detect large differences in the (13)C signatures of soil solution DOM sampled in 10 cm depth of plots with either C3 or C4 vegetation and in two different parent materials. These measurements also demonstrated changes in the (13)C signature that demonstrate rapid loss of plant-derived C with depth. Overall the modified HLPC/IRMS system has the advantages of rapid sample preparation, small required sample volume and high sample throughput, while showing comparable performance with other methods for measuring the amount and isotopic signature of DOM.

Applications of stable isotope ratio mass spectrometry in cattle dung carbon cycling studies

Understanding the fate of dung carbon (C) in soils is challenging due to the ubiquitous presence of the plant-derived organic matter (OM), the source material from which both dung-derived OM and soil organic matter (SOM) predominantly originate. A better understanding of the fate of specific components of this substantial source of OM, and thereby its contribution to C cycling in terrestrial ecosystems, can only be achieved through the use of labelled dung treatments. In this short review, we consider analytical approaches using bulk and compound-specific stable carbon isotope analysis that have been utilised to explore the fate of dung-derived C in soils. Bulk stable carbon isotope analyses are now used routinely to explore OM matter cycling in soils, and have shown that up to 20% of applied dung C may be incorporated into the surface soil horizons several weeks after application, with up to 8% remaining in the soil profile after one year. However, whole soil delta(13)C values represent the average of a wide range of organic components with varying delta(13)C values and mean residence times in soils. Several stable (13)C isotope ratio mass spectrometric methods have been developed to qualify and quantify different fractions of OM in soils and other complex matrices. In particular, thermogravimetry-differential scanning calorimetry-isotope ratio mass spectrometry (TG-DSC-IRMS) and gas chromatography-combustion-IRMS (GC-C-IRMS) analyses have been applied to determine the incorporation and turnover of polymeric plant cell wall materials from C(4) dung into C(3) grassland soils using natural abundance (13)C isotope labelling. Both approaches showed that fluxes of C derived from polysaccharides, i.e. as cellulose or monosaccharide components, were more similar to the behaviour of bulk dung C in soil than lignin. However, lignin and its 4-hydroxypropanoid monomers were unexpectedly dynamic in soil. These findings provide further evidence for emerging themes in biogeochemical investigations of soil OM dynamics that challenge perceived concepts of recalcitrance of C pools in soils, which may have profound implications for the assessment of the potential of agricultural soils to influence terrestrial C sinks.

Molecular turnover time of soil organic matter in particle-size fractions of an arable soil

The composition and molecular residence time of soil organic matter (SOM) in four particle-size fractions (POM >200 microm, POM 63-200 microm, silt and clay) were determined using Curie-point pyrolysis/gas chromatography coupled on-line to mass spectrometry. The fractions were isolated from soils, either continuously with a C(3) wheat (soil (13)C value = -26.4 per thousand), or transferred to a C(4) maize (soil (13)C value = -20.2 per thousand) cropping system 23 years ago. Pyrograms contained up to 45 different pyrolysis peaks; 37 (ca. 85%) were identifiable compounds. Lignins and carbohydrates dominated the POM fractions, proteins were abundant, but lignin was (nearly) absent in the silt and clay fractions. The mean turnover time (MRT) for the pyrolysis products in particulate organic matter (POM) was generally <15 years (fast C pool) and 20-300 years (medium or slow C pools) in silt and clay fractions. Methylcyclopentenone (carbohydrate) in the clay fraction and benzene (mixed source) in the silt fraction exhibited the longest MRTs, 297 and 159 years, respectively. Plant-derived organic matter was not stored in soils, but was transformed to microbial remains, mainly in the form of carbohydrates and proteins and held in soil by organo-mineral interactions. Selective preservation of plant-derived OM (i.e. lignin) based on chemical recalcitrance was not observed in these arable soils. Association/presence of C with silt or clays in soils clearly increased MRT values, but in an as yet unresolved manner (i.e. 'truly' stabilized, or potentially still 'labile' but just not accessible C).

A method for (13)C-labeling of metabolic carbohydrates within French bean leaves (Phaseolus vulgaris L.) for decomposition studies in soils

The molecular composition of plant residues is suspected to largely govern the fate of their constitutive carbon (C) in soils. Labile compounds, such as metabolic carbohydrates, are affected differently from recalcitrant and structural compounds by soil-C stabilisation mechanisms. Producing (13)C-enriched plant residues with specifically labeled fractions would help us to investigate the fate in soils of the constitutive C of these compounds. The objective of the present research was to test (13)C pulse chase labeling as a method for specifically enriching the metabolic carbohydrate components of plant residues, i.e. soluble sugars and starch. Bean plants were exposed to a (13)CO(2)-enriched atmosphere for 0.5, 1, 2, 3 and 21 h. The major soluble sugars were then determined on water-soluble extracts, and starch on HCl-hydrolysable extracts. The results show a quick differential labeling between water-soluble and water-insoluble compounds. For both groups, (13)C-labeling increased linearly with time. The difference in delta(13)C signature between water-soluble and insoluble fractions was 7 per thousand after 0.5 h and 70 per thousand after 21 h. However, this clear isotopic contrast masked a substantial labeling variability within each fraction. By contrast, metabolic carbohydrates on the one hand (i.e. soluble sugars + starch) and other fractions (essentially cell wall components) on the other hand displayed quite homogeneous signatures within fractions, and a significant difference in labeling between fractions: delta(13)C = 414 +/- 3.7 per thousand and 56 +/- 5.5 per thousand, respectively. Thus, the technique generates labeled plant residues displaying contrasting (13)C-isotopic signatures between metabolic carbohydrates and other compounds, with homogenous signatures within each group. Metabolic carbohydrates being labile compounds, our findings suggest that the technique is particularly appropriate for investigating the effect of compound lability on the long-term storage of their constitutive C in soils.

Isotopic evidences for microbiologically mediated and direct C input to soil compounds from three different leaf litters during their decomposition

We show the potentiality of coupling together different compound-specific isotopic analyses in a laboratory experiment, where (13)C-depleted leaf litter was incubated on a (13)C-enriched soil. The aim of our study was to identify the soil compounds where the C derived from three different litter species is retained. Three (13)C-depleted leaf litter (Liquidambar styraciflua L., Cercis canadensis L. and Pinus taeda L., delta(13)C(vsPDB) approximately -43 per thousand), differing in their degradability, were incubated on a C4 soil (delta(13)C(vsPDB) approximately -18 per thousand) under laboratory-controlled conditions for 8 months. At harvest, compound-specific isotope analyses were performed on different classes of soil compounds [i.e. phospholipids fatty acids (PLFAs), n-alkanes and soil pyrolysis products]. Linoleic acid (PLFA 18:2omega6,9) was found to be very depleted in (13)C (delta(13)C(vsPDB) approximately from -38 to -42 per thousand) compared to all other PLFAs (delta(13)C(vsPDB) approximately from -14 to -35 per thousand). Because of this, fungi were identified as the first among microbes to use the litter as source of C. Among n-alkanes, long-chain (C27-C31) n-alkanes were the only to have a depleted delta(13)C. This is an indication that not all of the C derived from litter in the soil was transformed by microbes. The depletion in (13)C was also found in different classes of pyrolysis products, suggesting that the litter-derived C is incorporated in less or more chemically stable compounds, even only after 8 months decomposition.

Off-line pyrolysis and compound-specific stable carbon isotope analysis of lignin moieties: a new method for determining the fate of lignin residues in soil

Off-line pyrolysis was used to liberate lignin moieties from dung and soil and, after trimethylsilylation, the delta(13)C values of these derivatives were determined by gas chromatography-combustion-isotope ratio mass spectrometry. Initial delta(13)C values determined for 4-vinylphenol, syringol, 4-vinylguaiacol, 4-acetylsyringol, 4-vinylsyringol, 4-(2-Z-propenyl)syringol, 4-(2-E-propenyl)syringol and 4-(2-propenone)syringol pyrolysis products of the lignin polyphenol structure from C(4) (delta(13)C(bulk) = -12.6%) and C(3) (delta(13)C(bulk) = -30.1 per thousand) dung confirmed the robust and reproducible nature of the off-line preparation technique. C(4) dung was used as a treatment in a randomised field experiment to assess the short-term sequestration of dung carbon in managed grasslands. Since lignin was on average 3.5 per thousand depleted in (13)C compared with bulk dung delta(13)C values, this may have resulted in an under-estimation of dung C incorporation based on bulk delta(13)C values. Therefore, an investigation of the compound-specific delta(13)C values of dung-derived lignin moieties extracted from soils sampled up to 372 days was undertaken. Delta(13)C values between lignin moieties extracted from treated and untreated soils showed that dung-derived lignin was not especially resistant to degradation and suggested that individual moieties of the lignin macromolecule must: (i) move into soil, (ii) be degraded, or (iii) be transformed diagenetically at different rates. This adds to a gathering body of evidence that lignin is not particularly stable in soils, which has considerable significance for the perceived role of different biochemical components in the cycling of C in soils.

An isotopic method for testing the influence of leaf litter quality on carbon fluxes during decomposition

During microbial breakdown of leaf litter a fraction of the C lost by the litter is not released to the atmosphere as CO(2) but remains in the soil as microbial byproducts. The amount of this fraction and the factors influencing its size are not yet clearly known. We performed a laboratory experiment to quantify the flow of C from decaying litter into the soil, by means of stable C isotopes, and tested its dependence on litter chemical properties. Three sets of (13)C-depleted leaf litter (Liquidambar styraciflua L., Cercis canadensis L. and Pinus taeda L.) were incubated in the laboratory in jars containing (13)C-enriched soil (i.e. formed C4 vegetation). Four jars containing soil only were used as a control. Litter chemical properties were measured using thermogravimetry (Tg) and pyrolysis-gas chromatography/mass spectrometry-combustion interface-isotope ratio mass spectrometry (Py-GC/MS-C-IRMS). The respiration rates and the delta(13)C of the respired CO(2) were measured at regular intervals. After 8 months of incubation, soils incubated with both L. styraciflua and C. canadensis showed a significant change in delta(13)C (delta(13)C(final) = -20.2 +/- 0.4 per thousand and -19.5 +/- 0.5 per thousand, respectively) with respect to the initial value (delta(13)C(initial) = -17.7 +/- 0.3 per thousand); the same did not hold for soil incubated with P. taeda (delta(13)C(final:)-18.1 +/- 0.5 per thousand). The percentages of litter-derived C in soil over the total C loss were not statistically different from one litter species to another. This suggests that there is no dependence of the percentage of C input into the soil (over the total C loss) on litter quality and that the fractional loss of leaf litter C is dependent only on the microbial assimilation efficiency. The percentage of litter-derived C in soil was estimated to be 13 +/- 3% of total C loss.

Gas chromatography coupled to mass spectrometry for analyses of organic compounds and biomarkers as tracers for geological, environmental, and forensic research

Gas chromatography, especially when coupled with mass spectrometry, is the analytical method of choice for elucidation of biomarker compounds present in organic mixtures extracted from geological, environmental, and biological samples. This review describes the biomarker concept, i. e., the precursor natural products to the geological/environmental derivatives, and their application as multi-tracers in the geosphere and ambient environment. The mass spectrometric methods currently utilized for such analyses are reviewed with a general key to the literature, and typical examples of applications using GC-MS are also described.

Isotope fractionation and 13C enrichment in soil profiles during the decomposition of soil organic matter

The mechanisms behind the (13)C enrichment of organic matter with increasing soil depth in forests are unclear. To determine if (13)C discrimination during respiration could contribute to this pattern, we compared delta(13)C signatures of respired CO(2) from sieved mineral soil, litter layer and litterfall with measurements of delta(13)C and delta(15)N of mineral soil, litter layer, litterfall, roots and fungal mycelia sampled from a 68-year-old Norway spruce forest stand planted on previously cultivated land. Because the land was subjected to ploughing before establishment of the forest stand, shifts in delta(13)C in the top 20 cm reflect processes that have been active since the beginning of the reforestation process. As (13)C-depleted organic matter accumulated in the upper soil, a 1.0 per thousand delta(13)C gradient from -28.5 per thousand in the litter layer to -27.6 per thousand at a depth of 2-6 cm was formed. This can be explained by the 1 per thousand drop in delta(13)C of atmospheric CO(2) since the beginning of reforestation together with the mixing of new C (forest) and old C (farmland). However, the isotopic change of the atmospheric CO(2) explains only a portion of the additional 1.0 per thousand increase in delta(13)C below a depth of 20 cm. The delta(13)C of the respired CO(2) was similar to that of the organic matter in the upper soil layers but became increasingly (13)C enriched with depth, up to 2.5 per thousand relative to the organic matter. We hypothesise that this (13)C enrichment of the CO(2) as well as the residual increase in delta(13)C of the organic matter below a soil depth of 20 cm results from the increased contribution of (13)C-enriched microbially derived C with depth. Our results suggest that (13)C discrimination during microbial respiration does not contribute to the (13)C enrichment of organic matter in soils. We therefore recommend that these results should be taken into consideration when natural variations in delta(13)C of respired CO(2) are used to separate different components of soil respiration or ecosystem respiration.

Application of simultaneous thermal analysis mass spectrometry and stable carbon isotope analysis in a carbon sequestration study

The simultaneous analysis of evolved gases and the determination of stable isotope composition (delta13C) as part of a thermal analysis experiment have been used to (a) distinguish bulk chemical hosts for carbon (C) and nitrogen (N) within a soil and (b) track labelled C within a soil sequestration experiment. C3 and C4 dung was applied to a pasture soil, and soil samples taken for analysis. The results of thermogravimetry-differential scanning calorimetry-quadrupole mass spectrometry-isotope ratio mass spectrometry (TG-DSC-QMS-IRMS) show that the proportion of more refractory C (lignin-like) is greater for the dungs than for the soil organic matter (SOM), and that this increases with time within the soil. Analysis of evolved gases shows that nitrogen is associated with the decomposition of more refractory C, and is not so strongly associated with the labile C component. IRMS analysis distinguished C3 and C4 dung, and allowed the amount of C from these sources to be estimated for the soil samples. Most dung C enters the refractory SOM fraction. This paper demonstrates the potential of TG-DSC-QMS-IRMS in the investigation of SOM.

Post-photosynthetic fractionation of stable carbon isotopes between plant organs--a widespread phenomenon

Discrimination against 13C during photosynthesis is a well-characterised phenomenon. It leaves behind distinct signatures in organic matter of plants and in the atmosphere. The former is depleted in 13C, the latter is enriched during periods of preponderant photosynthetic activity of terrestrial ecosystems. The intra-annual cycle and latitudinal gradient in atmospheric 13C resulting from photosynthetic and respiratory activities of terrestrial plants have been exploited for the reconstruction of sources and sinks through deconvolution by inverse modelling. Here, we compile evidence for widespread post-photosynthetic fractionation that further modifies the isotopic signatures of individual plant organs and consequently leads to consistent differences in delta13C between plant organs. Leaves were on average 0.96 per thousand and 1.91 per thousand more depleted than roots and woody stems, respectively. This phenomenon is relevant if the isotopic signature of CO2-exchange fluxes at the ecosystem level is used for the reconstruction of individual sources and sinks. It may also modify the parameterization of inverse modelling approaches if it leads to different isotopic signatures of organic matter with different residence times within the ecosystems and to a respiratory contribution to the average difference between the isotopic composition of plant organic matter and the atmosphere. We discuss the main hypotheses that can explain the observed inter-organ differences in delta13C.