The chemical ecology of soil organic matter molecular constituents

Permafrost carbon cycle and its dynamics on the Tibetan Plateau

Our knowledge on permafrost carbon (C) cycle is crucial for understanding its feedback to climate warming and developing nature-based solutions for mitigating climate change. To understand the characteristics of permafrost C cycle on the Tibetan Plateau, the largest alpine permafrost region around the world, we summarized recent advances including the stocks and fluxes of permafrost C and their responses to thawing, and depicted permafrost C dynamics within this century. We find that this alpine permafrost region stores approximately 14.1 Pg (1 Pg=1015 g) of soil organic C (SOC) in the top 3 m. Both substantial gaseous emissions and lateral C transport occur across this permafrost region. Moreover, the mobilization of frozen C is expedited by permafrost thaw, especially by the formation of thermokarst landscapes, which could release significant amounts of C into the atmosphere and surrounding water bodies. This alpine permafrost region nevertheless remains an important C sink, and its capacity to sequester C will continue to increase by 2100. For future perspectives, we would suggest developing long-term in situ observation networks of C stocks and fluxes with improved temporal and spatial coverage, and exploring the mechanisms underlying the response of ecosystem C cycle to permafrost thaw. In addition, it is essential to improve the projection of permafrost C dynamics through in-depth model-data fusion on the Tibetan Plateau.

Soil Fungal Community Differences in Manual Plantation Larch Forest and Natural Larch Forest in Northeast China

Soil fungal communities are pivotal components in ecosystems and play an essential role in global biogeochemical cycles. In this study, we determined the fungal communities of a natural larch forest and a manual plantation larch forest in Heilongjiang Zhongyangzhan Black-billed Capercaillie Nature Reserve and Gala Mountain Forest using high-throughput sequencing. The interactions between soil fungal communities were analysed utilising a co-occurrence network. The relationship between soil nutrients and soil fungal communities was determined with the help of Mantel analysis and a correlation heatmap. The Kruskal-Wallis test indicated that different genera of fungi differed in the two forest types. The results show that there was a significant change in the alpha diversity of soil fungal communities in both forests. In contrast, nonmetric multidimensional scaling (NMDS) analysis showed significant differences in the soil fungal community structures between the manual plantation larch forest and the natural larch forest. The soil fungal co-occurrence network showed that the complexity of the soil fungal communities in the manual plantation larch forest decreased significantly compared to those in the natural larch forest. A Mantel analysis revealed a correlation between the soil fungal co-occurrence network, the composition of soil fungi, and soil nutrients. The RDA analysis also showed that AN, TK, and pH mainly influenced the soil fungal community. The null model test results showed the importance of stochastic processes in soil fungal community assembly in manual plantation larch forests. Overall, this study enhances our understanding of the differences in soil fungal communities in manual plantation larch forests and natural larch forests, providing insights into their sustainable management. It also serves as a reminder that the ecological balance of natural ecosystems is difficult to restore through human intervention, so we need to protect natural ecosystems.

Black carbon, soil organic matter molecular signatures under different land uses in Shenyang, China and relationship with PAHs

The content, composition and molecular signatures of soil organic matter (SOM) have important influences on the cycle of soil organic carbon (SOC) and the partitioning of polycyclic aromatic hydrocarbons (PAHs) in soil. Seventy-nine soil samples from farmland, forest and urban areas were collected in Shenyang, China to investigate black carbon (BC) content, SOM molecular signatures varied with land use patterns, as well as the relationship with PAHs. The content of BC in urban soils was significantly higher than that of farmland and forest. BC was a key contributor of urban SOM which accounted for 0.35 ± 0.31 of SOC in urban soil. Based on BC/SOC ratio, the main sources of BC were identified as fossil fuel combustion for urban soils, while for farmland and forest soils, it is the mixed results of fossil fuel combustion and biomass burning. All categories of PAHs in urban soils showed the highest level compared to farmland and forest soils. Pearson's correlation analysis results showed there were significant positive correlations between BC and PAHs categories in urban soils, indicating the important role of BC in the accumulation of PAHs in soil. SOM from each of the two different land use patterns can be distinguished by molecular signatures. Urban SOM had abundant molecular markers derived from condensed organic carbon inputs, which was consistent with the BC/SOC value. Farmland SOM had abundant carbon from vegetation and microorganisms, and forest SOM was rich in organic carbon from fresh plant materials. The markers enriched in urban SOM showed significant correlations with most PAHs categories, highlighting the affinity of urban SOM for PAHs at the molecular level. This study contributed to understanding the impact of land management methods on SOM molecular composition signatures and its influence on PAHs occurrence in soil, providing a theoretical basis for regional soil pollution management.

Land application of industrial wastes: impacts on soil quality, biota, and human health

Globally, waste disposal options such as landfill, incineration, and discharge to water, are not preferred long-term solutions due to their social, environmental, political, and economic implications. However, there is potential for increasing the sustainability of industrial processes by considering land application of industrial wastes. Applying waste to land can have beneficial outcomes including reducing waste sent to landfill and providing alternative nutrient sources for agriculture and other primary production. However, there are also potential hazards, including environmental contamination. This article reviewed the literature on industrial waste applications to soils and assessed the associated hazards and benefits. The review investigated wastes in relation to soil characteristics, dynamics between soils and waste constituents, and possible impacts on plants, animals, and humans. The current body of literature demonstrates the potential for the application of industrial waste into agricultural soils. The main challenge for applying industrial wastes to land is the presence of contaminants in some wastes and managing these to enhance positive effects and reduce negative outcomes to within acceptable limits. Examination of the literature also revealed several gaps in the research and opportunities for further investigation: specifically, a lack of long-term experiments and mass balance assessments, variable waste composition, and negative public opinion.

Pesticide sorption and mitigation efficiency of a detention pond in a Champagne vineyard catchment

Detention ponds (DPs) are used to reduce the pesticide inputs from runoff to surface water. This study aimed to assess the role of the sorption process in the mitigation of a DP made up of four successive units and built at the outlet of a vineyard catchment in Champagne (France) to treat runoff waters. Sorption kinetics and isotherms were studied for four pesticides with contrasting properties, cyazofamid (CYA), fludioxonil (FLX), fluopicolide (FLP) and oryzalin (ORY), in the presence of copper in sediments and four emergent macrophyte roots and rhizomes sampled in the DP units 2 (photodegradation) and 3 (phytoremediation). The adsorption equilibrium time (from 24 to 96 h) was less than the hydraulic residence times in the two units (6 and 18 days on average) between November 2016 and November 2017. Sorption equilibrium could then be reached in situ in 85 % of cases. The K_d coefficients of the four pesticides were overall greater in plant roots (14–6742 L kg⁻¹) than in sediments (6–163 L kg⁻¹) because of their affinity for organic matter and the molecular and porous structure of the plant matrices. Typha latifolia and Iris pseudacorus exhibited greater K_d coefficients than Mentha aquatica and Phragmites australis, probably due to their greater specific surface area. The pesticide adsorption capacity in sediments and in T. latifolia and I. pseudacorus roots (ORY ≥ FLX > CYA > FLP) was linked to their K_ow. The estimated total annual amounts of the four pesticides adsorbed in situ were determined to be 1236 mg for unit 2 and 1570 mg for unit 3. The four plants improved the removal efficiency of the unit 3 by 33%. Thus, the establishment of suitable and effective plants should be promoted to optimize sorption processes and DP efficiency in reducing water pollution.

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Pesticide sorption on various substrates of a vineyard detention pond was assessed.

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The measured equilibrium time was less than the in situ hydraulic residence time.

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Plant roots and rhizomes showed greater pesticide adsorption capacity than sediments.

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Sorption capacity was higher on cattail and iris than on mint and reed.

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Affinity of selected pesticides for roots and sediments was related to their Kow.

The migration and microbiological degradation of dissolved organic matter in riparian soils

Riparian zones are important natural means of water purification, by decreasing the aqueous concentration of terrestrial organic matter (OM) through adsorption and microbial degradation of the organic matter within the aquatic ecosystem. Limited studies have been reported so far concerning the migration of dissolved organic matter (DOM) in the horizontal and vertical planes of riparian zones. In this study, the migration of DOM in riparian zones, from forest soil to wetland soil, and with soil depth, were explored, based on a case study reservoir. Results showed that riparian wetlands can absorb the OM from the forest soils and adjacent reservoir, and act as a major OM sink through microbial action. Methylomirabilota and GAL15 bacteria increased with soil depth for the two soil systems, and the wetland soil system also contained microbial sulfates, nitrates and carbonates. These microorganisms successfully utilize the Fe³⁺, SO₄^-, and CO₃^- as electron acceptors in the wetland system, resulting in enhanced OM removal. Although the variation of soil DOM in the vertical direction was the same for both forest and wetland soils, the Chemical structure of the DOM was found to be significantly different. Furthermore, the soil was found to be the main source of DOM in the forest ecosystem, with lignin as the main ingredient. The lignin structure was gradually oxidized and decomposed, with an increase in carboxyl groups, as the lignin diffused down into the soil and the adjacent reservoir. PLS-PM analysis showed that the soil physicochemical properties were the main factors affecting DOM transformation. However, microbial metabolism was still the goes deeper affecting factor. This study will contribute to the analysis that migration and transform of soil organic matter in riparian zone.

Organic matter biomarker and 13C NMR characteristics of soil and sediment standard reference materials from China

Soil and sediment organic matter (OM) in terrestrial environments represent two critical organic carbon pools on Earth and are likely subject to distinct degrees of oxidation and modification. However, few studies have identified critical molecular-level characteristics that differentiate soil and sediment OM from various climate zones. Using biomarkers and solid-state ¹³C nuclear magnetic resonance (NMR) spectroscopy analyses, we studied the OM characteristics of 11 soil and 7 sediment standard reference materials (SRMs) originating from various geographical locations in China. Results showed significantly higher concentrations of lignin phenols in sediment OM than in soil OM, which may result from protection by higher contents of CaO and less microbial degradation in sediments. Nevertheless, the relative abundances of solvent-extractable lipids (alkanes, alkanols, and alkanoic acids) and ester-bound cutin and suberin biomarkers did not differ significantly between soil and sediment SRMs. The concentrations of lignin biomarkers decreased with increasing weathering degree of the soil, while cutin biomarkers increased with mean annual temperature and precipitation. This phenomenon was not observed in sediment SRMs. This study reveals the distinct OM characteristics between Chinese soil and sediment SRMs and provides fundamental data for future studies to link OM characteristics and functions.

Divergent Trajectory of Soil Autotrophic and Heterotrophic Respiration upon Permafrost Thaw

Warming-induced permafrost thaw may stimulate soil respiration (Rs) and thus cause a positive feedback to climate warming. However, due to the limited in situ observations, it remains unclear about how Rs and its autotrophic (Ra) and heterotrophic (Rh) components change upon permafrost thaw. Here we monitored variations in Rs and its components along a permafrost thaw sequence on the Tibetan Plateau, and explored the potential linkage of Rs components (i.e., Ra and Rh) with biotic (e.g., plant functional traits and soil microbial diversity) and abiotic factors (e.g., substrate quality). We found that Ra and Rh exhibited divergent responses to permafrost collapse: Ra increased with the time of thawing, while Rh exhibited a hump-shaped pattern along the thaw sequence. We also observed different drivers of thaw-induced changes in the ratios of Ra:Rs and Rh:Rs. Except for soil water status, plant community structure, diversity, and root properties explained the variation in Ra:Rs ratio, soil substrate quality and microbial diversity were key factors associated with the dynamics of Rh:Rs ratio. Overall, these findings demonstrate divergent patterns and drivers of Rs components as permafrost thaw prolongs, which call for considerations in Earth system models for better forecasting permafrost carbon-climate feedback.

Plant and microbial regulations of soil carbon dynamics under warming in two alpine swamp meadow ecosystems on the Tibetan Plateau

Increasing temperature plays important roles in affecting plant and soil microbial communities as well as ecological processes and functions in terrestrial ecosystems. However, mechanisms of warming influencing soil carbon dynamics associated with plant-microbe interactions remain unclear. In this study, open-top chambers (OTCs) experiments were carried out to detect the responses of plants, soil microbes, and SOC contents, physical fractions (by particle-size fractionation) and chemical composition (by solid-state ¹³C NMR spectroscopy) to warming in two alpine swamp meadows (Kobresia humilis vs K. tibetica) on the Tibetan Plateau. Our results showed that four years of warming had significant influences on plant belowground biomass, microbial community and SOC contents in the K. humilis swamp meadow, but had much weaker or minor effects in the K. tibetica swamp meadow with water-logged status and lower level of warming. In the K. humilis swamp meadow, warming increased microbial biomass, C-hydrolysis gene abundance and N-acetylglucosaminidase enzyme activity. These positive effects of warming on microbial biomass and functions further increased soil dissolved inorganic nitrogen and alleviated the nitrogen limitation for plant growth, potentially leading to higher plant biomass. Therefore, increases in SOC and particulate organic carbon (POC) under warming were likely attributed to the higher C input with promoted plant biomass overweighting the simultaneous higher C degradation and release in the K. humilis swamp meadow. Conversely, warming marginally reduced soil alkyl C, which was likely associated with enhanced decomposition by fungi and gram-positive bacteria. Overall, the increases in unprotected POC and decreases in recalcitrant alkyl C demonstrate the sensitivity of SOC physical fractions as well as chemical composition to climate warming in the K. humilis alpine swamp meadow, and suggest that the overall stability of SOC might be lower despite the gain in the content of SOC after climate warming in this alpine swamp meadow.

Molecular insight into the interfacial chemical functionalities regulating heterogeneous calcium-arsenate nucleation

Heterogeneous nucleation induced by natural organic matter (NOM) can lower the energy barrier for calcium arsenate (Ca-As) precipitation, which aids in immobilizing arsenate (As^Ⅴ). However, it remains unclear how certain chemical functionalities of NOM affect Ca-As nucleation at the molecular scale. By analyzing changes in the local supersaturation and/or interfacial energy, the present work investigates the Ca-As heterogeneous nucleation kinetics and mechanisms on functional-group-modified model surfaces. Mica surfaces modified by functional groups of amine (NH₂), hydroxyl (OH), or carboxyl (COOH) through self-assembled monolayers were used to investigate how chemical functionalities affect the Ca-As heterogeneous nucleation, in which the distributions of formation kinetics and size (as measured by the change in particle height) of nucleated Ca-As particles were measured by using in situ atomic force microscopy. In a parallel analysis, a quartz-crystal microbalance with dissipation was used to detect the buildup of Ca²⁺ and/or HAsO₄^2- ions at the solid-fluid interface. PeakForce quantitative nanomechanical mapping and dynamic force spectroscopy using functional-group-modified tips made it possible to calculate the binding energies holding functional groups to Ca-As particles. Nucleated Ca-As particles were characterized by using Raman spectroscopy and high-resolution transmission electron microscopy. The results indicate that the height of amorphous Ca-As particles formed on a modified mica surface may be ranked in descending order as NH₂ > OH > bare mica > COOH, as determined by the buildup of Ca²⁺ and HAsO₄^2- ions at the solid-fluid interface and the decrease of interfacial energy due to the functional groups. These nanoscale observations and molecular-scale determinations improve our understanding of the roles played by chemical functionalities on NOM in immobilizing dissolved As through heterogeneous nucleation in soil and water.

Nine years of in situ soil warming and topography impact the temperature sensitivity and basal respiration rate of the forest floor in a Canadian boreal forest

The forest floor of boreal forest stores large amounts of organic C that may react to a warming climate and increased N deposition. It is therefore crucial to assess the impact of these factors on the temperature sensitivity of this C pool to help predict future soil CO2 emissions from boreal forest soils to the atmosphere. In this study, soil warming (+2-4°C) and canopy N addition (CNA; +0.30-0.35 kg·N·ha-1·yr-1) were replicated along a topographic gradient (upper, back and lower slope) in a boreal forest in Quebec, Canada. After nine years of treatment, the forest floor was collected in each plot, and its organic C composition was characterized through solid-state 13C nuclear magnetic resonance (NMR) spectroscopy. Forest floor samples were incubated at four temperatures (16, 24, 32 and 40°C) and respiration rates (RR) measured to assess the temperature sensitivity of forest floor RR (Q10 = e10k) and basal RR (B). Both soil warming and CNA had no significant effect on forest floor chemistry (e.g., C, N, Ca and Mg content, amount of soil organic matter, pH, chemical functional groups). The NMR analyses did not show evidence of significant changes in the forest floor organic C quality. Nonetheless, a significant effect of soil warming on both the Q10 of RR and B was observed. On average, B was 72% lower and Q10 45% higher in the warmed, versus the control plots. This result implies that forest floor respiration will more strongly react to changes in soil temperature in a future warmer climate. CNA had no significant effect on the measured soil and respiration parameters, and no interaction effects with warming. In contrast, slope position had a significant effect on forest floor organic C quality. Upper slope plots had higher soil alkyl C:O-alkyl C ratios and lower B values than those in the lower slope, across all different treatments. This result likely resulted from a relative decrease in the labile C fraction in the upper slope, characterized by lower moisture levels. Our results point towards higher temperature sensitivity of RR under warmer conditions, accompanied by an overall down-regulation of RR at low temperatures (lower B). Since soil C quantity and quality were unaffected by the nine years of warming, the observed patterns could result from microbial adaptations to warming.

Temperature sensitivity of SOM decomposition governed by aggregate protection and microbial communities

Temperature sensitivity (Q ₁₀) of soil organic matter (SOM) decomposition is a crucial parameter for predicting the fate of soil carbon (C) under global warming. However, our understanding of its regulatory mechanisms remains inadequate, which constrains its accurate parameterization in Earth system models and induces large uncertainties in predicting terrestrial C-climate feedback. Here, we conducted a long-term laboratory incubation combined with a two-pool model and manipulative experiments to examine potential mechanisms underlying the depth-associated Q ₁₀ variations in active and slow soil C pools. We found that lower microbial abundance and stronger aggregate protection were coexisting mechanisms underlying the lower Q ₁₀ in the subsoil. Of them, microbial communities were the main determinant of Q ₁₀ in the active pool, whereas aggregate protection exerted more important control in the slow pool. These results highlight the crucial role of soil C stabilization mechanisms in regulating temperature response of SOM decomposition, potentially attenuating the terrestrial C-climate feedback.

Soil organic carbon depletion and degradation in surface soil after long-term non-growing season warming in High Arctic Svalbard

Arctic tundra active-layer soils are at risk of soil organic carbon (SOC) depletion and degradation upon global climate warming because they are in a stage of relatively early decomposition. Non-growing season (NGS) warming is particularly pronounced, and observed increases of CO₂ emissions during experimentally warmed NGSs give concern for great SOC losses to the atmosphere. Here, we used snow fences in Arctic Spitsbergen dwarf shrub tundra to simulate 1.86 °C NGS warming for 9 consecutive years, while growing season temperatures remained unchanged. In the snow fence treatment, the 4-11 cm thick A-horizon had a 2% lower SOC concentration and a 0.48 kg C m^-2 smaller pool size than the controls, indicating SOC pool depletion. The snow fence treatment's A-horizon's alkyl/O-alkyl ratio was also significantly increased, indicating an advance of SOC degradation. The underlying 5 cm of B/C-horizon did not show these effects. Our results support the hypothesis that SOC depletion and degradation are connected to the long-term transience of observed ecosystem respiration (ER) increases upon soil warming. We suggest that the bulk of warming induced ER increases may originate from surface and not deep active layer or permafrost horizons. The observed losses of SOC might be significant for the ecosystem in question, but are in magnitude comparatively small relative to anthropogenic greenhouse gas enrichment of the atmosphere. We conclude that a positive feedback of carbon losses from surface soils of Arctic dwarf shrub tundra to anthropogenic forcing will be minor, but not negligible.

The detrital input and removal treatment (DIRT) network: Insights into soil carbon stabilization

Ecological research networks functioning across climatic and edaphic gradients are critical for improving predictive understanding of biogeochemical cycles at local through global scales. One international network, the Detrital Input and Removal Treatment (DIRT) Project, was established to assess how rates and sources of plant litter inputs influence accumulations or losses of organic matter in forest soils. DIRT employs chronic additions and exclusions of aboveground litter inputs and exclusion of root ingrowth to permanent plots at eight forested and two shrub/grass sites to investigate how soil organic matter (SOM) dynamics are influenced by plant detrital inputs across ecosystem and soil types. Across the DIRT network described here, SOM pools responded only slightly, or not at all, to chronic doubling of aboveground litter inputs. Explanations for the slow or even negative response of SOM to litter additions include increased decomposition of new inputs and priming of old SOM. Evidence of priming includes increased soil respiration in litter addition plots, decreased dissolved organic carbon (DOC) output from increased microbial activity, and biochemical markers in soil indicating enhanced SOM degradation. SOM pools decreased in response to chronic exclusion of aboveground litter, which had a greater effect on soil C than did excluding roots, providing evidence that root-derived C is not more critical than aboveground litter C to soil C sequestration. Partitioning of belowground contributions to total soil respiration were predictable based on site-level soil C and N as estimates of site fertility; contributions to soil respiration from root respiration were negatively related to soil fertility and inversely, contributions from decomposing aboveground litter in soil were positively related to site fertility. The commonality of approaches and manipulations across the DIRT network has provided greater insights into soil C cycling than could have been revealed at a single site.

Nutrient Dependent Cross-Kingdom Interactions: Fungi and Bacteria From an Oligotrophic Desert Oasis

Microbial interactions play a key role in ecosystem functioning, with nutrient availability as an important determinant. Although phylogenetically distant bacteria and fungi commonly co-occur in nature, information on their cross-kingdom interactions under unstable, extreme environments remains poor. Hence, the aims of this work were to evaluate potential in vitro interactions among fungi and bacteria isolated from a phosphorous oligotrophic aquatic system in the Cuatro Ciénegas Basin, Mexico, and to test the nutrients-based shifts. We assessed growth changes in bacteria (Aeromonas and Vibrio) and fungi (Coprinellus micaceus, Cladosporium sp., and Aspergillus niger) on co-cultures in relation to monocultures under diverse nutrient scenarios on Petri dishes. Interactions were explored using a network analysis, and a metabolome profiling for specific taxa. We identified nutrient-dependent patterns, as beneficial interactions dominated in low-nutrients media and antagonistic interactions dominated in rich media. This suggests that cross-kingdom synergistic interactions might favor microbial colonization and growth under low nutrient conditions, representing an adaptive trait to oligotrophic environments. Moreover, our findings agree with the stress-gradient hypothesis, since microbial interactions shifted from competition to cooperation as environmental stress (expressed as low nutrients) increased. At a functional level consistent differences were detected in the production of secondary metabolites, agreeing with plate bioassays. Our results based on culture experiments, provides evidence to understand the complexity of microbial dynamics and survival in phosphorous-depleted environments.

Environmental Nuclear Magnetic Resonance Spectroscopy: An Overview and a Primer

NMR spectroscopy is a versatile tool for the study of structure and interactions in environmental media such as air, soil, and water as well as monitoring the metabolic responses of living organisms to an ever changing environment. Part review, part perspective, and part tutorial, this Feature is aimed at nonspecialists who are interested in learning more about the potential and impact of NMR spectroscopy in environmental research.

Plant litter chemistry alters the content and composition of organic carbon associated with soil mineral and aggregate fractions in invaded ecosystems

Through the input of disproportionate quantities of chemically distinct litter, invasive plants may potentially influence the fate of organic matter associated with soil mineral and aggregate fractions in some of the ecosystems they invade. Although context dependent, these native ecosystems subjected to prolonged invasion by exotic plants may be instrumental in distinguishing the role of plant-microbe-mineral interactions from the broader edaphic and climatic influences on the formation of soil organic matter (SOM). We hypothesized that the soils subjected to prolonged invasion by an exotic plant that input recalcitrant litter (Japanese knotweed, Polygonum cuspidatum) would have a greater proportion of plant-derived carbon (C) in the aggregate fractions, as compared with that in adjacent soil inhabited by native vegetation that input labile litter, whereas the soils under an invader that input labile litter (kudzu, Pueraria lobata) would have a greater proportion of microbial-derived C in the silt-clay fraction, as compared with that in adjacent soils that receive recalcitrant litter. At the knotweed site, the higher C content in soils under P. cuspidatum, compared with noninvaded soils inhabited by grasses and forbs, was limited to the macroaggregate fraction, which was abundant in plant biomarkers. The noninvaded soils at this site had a higher abundance of lignins in mineral and microaggregate fractions and suberin in the macroaggregate fraction, partly because of the greater root density of the native species, which might have had an overriding influence on the chemistry of the above-ground litter input. At the kudzu site, soils under P. lobata had lower C content across all size fractions at a 0-5 cm soil depth despite receiving similar amounts of Pinus litter. Contrary to our prediction, the noninvaded soils receiving recalcitrant Pinus litter had a similar abundance of plant biomarkers across both mineral and aggregate fractions, potentially because of the higher surface area of soil minerals at this site. The plant biomarkers were lower in the aggregate fractions of the P. lobata-invaded soils, compared with noninvaded pine stands, potentially suggesting a microbial co-metabolism of pine-derived compounds. These results highlight the complex interactions among litter chemistry, soil biota, and minerals in mediating soil C storage in unmanaged ecosystems; these interactions are particularly important under global changes that may alter plant species composition and hence the quantity and chemistry of litter inputs in terrestrial ecosystems.

Influence of Organic Chemicals on Water Molecule Bridges in Soil Organic Matter of a Sapric Histosol

Water molecules in soil organic matter (SOM) can form clusters bridging neighboring molecular segments (water molecule bridges, WaMBs). WaMBs are hypothesized to enhance the physical entrapment of organic chemicals and to control the rigidity of the SOM supramolecular structure. However, the understanding of WaMBs dynamics in SOM is still limited. We investigated the relation between WaMBs stability and the physicochemical properties of their environment by treating a sapric histosol with various solvents and organic chemicals. On the basis of predictions from molecular modeling, we hypothesized that the stability of WaMBs, measured by differential scanning calorimetry, increases with the decreasing ability of a chemical to interact with water molecules of the WaMBs. The interaction ability between WaMBs and the chemicals was characterized by linear solvation energy relationships. The WaMBs stability in solvent-treated samples was found to decrease with increasing ability of a solvent to undergo H-donor/acceptor interactions. Spiking with an organic chemical stabilized (naphthalene) or destabilized (phenol) the WaMBs. The WaMBs stability and matrix rigidity were generally reduced strongly and quickly when hydrophilic chemicals entered the soil. The physicochemical aging following this destabilization is slow but leads to successive WaMBs stabilization and matrix stiffening.

Molecular composition of soil organic matter with land-use change along a bi-continental mean annual temperature gradient

Soil organic matter (SOM) is critical for maintaining soil fertility and long-term agricultural sustainability. The molecular composition of SOM is likely altered due to global climate and land-use change; but rarely are these two aspects studied in tandem. Here we used molecular-level techniques to examine SOM composition along a bi-continental (from North to South America) mean annual temperature (MAT) gradient from seven native grassland/forest and cultivated/pasture sites. Biomarker methods included solvent extraction, base hydrolysis and cupric (II) oxide oxidation for the analysis of free lipids of plant and microbial origin, ester-bound lipids from cutin and suberin, and lignin-derived phenols, respectively. Solid-state ¹³C nuclear magnetic resonance (NMR) was used to examine the overall composition of SOM. Soil cultivation was found to increase the amount of microbial-derived compounds at warmer temperatures (up to 17% increase). The cultivated soils were characterized by much lower contributions of plant-derived SOM components compared to the native soils (up to 64% lower at the coldest site). In addition, cultivation caused an increase in lignin and cutin degradation (up to 68 and 15% increase, respectively), and an increase in the amount of suberin-derived inputs (up to 54% increase). Clear differences in the molecular composition of SOM due to soil cultivation were observed in soils of varying mineral composition and were attributed to disturbance, different vegetation inputs, soil aggregate destruction and MAT. A high organic allophanic tropical soil was characterized by its protection of carbohydrates and nitrogen-containing compounds. The conversion of native to cultivated land shows significant shifts in the degradation stage of SOM. In particular, cutin-derived compounds which are believed to be part of the stable SOM pool may undergo enhanced degradation with long-term cultivation and disruption of soil aggregates. On a per year basis, the total amount of cutin decreased only at the two forest sites that were converted to pasture, likely due to cutin degradation or to changes in vegetation and litter quality associated with land-use change. Overall, our study highlights that the implementation of different agricultural management practices enhances the degradation of recalcitrant SOM compounds that may become a source of atmospheric CO₂ with increasing land-use and climate change.

The C:N:P:S stoichiometry of soil organic matter

The formation and turnover of soil organic matter (SOM) includes the biogeochemical processing of the macronutrient elements nitrogen (N), phosphorus (P) and sulphur (S), which alters their stoichiometric relationships to carbon (C) and to each other. We sought patterns among soil organic C, N, P and S in data for c. 2000 globally distributed soil samples, covering all soil horizons. For non-peat soils, strong negative correlations (p < 0.001) were found between N:C, P:C and S:C ratios and % organic carbon (OC), showing that SOM of soils with low OC concentrations (high in mineral matter) is rich in N, P and S. The results can be described approximately with a simple mixing model in which nutrient-poor SOM (NPSOM) has N:C, P:C and S:C ratios of 0.039, 0.0011 and 0.0054, while nutrient-rich SOM (NRSOM) has corresponding ratios of 0.12, 0.016 and 0.016, so that P is especially enriched in NRSOM compared to NPSOM. The trends hold across a range of ecosystems, for topsoils, including O horizons, and subsoils, and across different soil classes. The major exception is that tropical soils tend to have low P:C ratios especially at low N:C. We suggest that NRSOM comprises compounds selected by their strong adsorption to mineral matter. The stoichiometric patterns established here offer a new quantitative framework for SOM classification and characterisation, and provide important constraints to dynamic soil and ecosystem models of carbon turnover and nutrient dynamics.

Isotope-filtered nD NMR spectroscopy of complex mixtures to unravel the molecular structures of phenolic compounds in tagged soil organic matter

Unravelling structures of molecules contained in complex, chromatographically inseparable mixtures is a challenging task. Due to the number of overlapping resonances in NMR spectra of these mixtures, unambiguous chemical shift correlations attributable to individual molecules cannot be achieved and thus their structure determination is elusive by this technique. Placing a tag carrying an NMR active nucleus onto a subset of molecules enables (i) to eliminate signals from the non-tagged molecules, and (ii) to obtain a set of correlated chemical shifts and coupling constants belonging to a single molecular type. This approach provides an opportunity for structure determination without the need for compound separation. Focusing on the most abundant functional groups of natural organic matter molecules, the carboxyl and hydroxyl groups were converted into esters and ethers, respectively by introducing (13)CH3O groups. A set of (13)C-filtered nD NMR experiments was designed yielding structures/structural motives of tagged molecules. The relative sensitivity of these experiments was compared and a step-by-step guide how to use these experiments to analyse the structures of methylated phenolics is provided. The methods are illustrated using an operational fraction of soil organic matter, fulvic acid isolated from a Scottish peat bog. Analysis of 33 structures identified in this sample revealed a correlation between the position of the methoxy cross-peaks in the (1)H, (13)C HSQC spectra and the compound type. This information enables profiling of phenolic compounds in natural organic matter without the need to acquire a full set of experiments described here or access to high field cryoprobe NMR spectrometers.

The effect of composition on stability ((14)C activity) of soil organic matter fractions from the albic and black soils

The importance of the composition of soil organic matter (SOM) for carbon (C) cycling is still under debate. Here a single soil source was used to examine the specific influence of its composition on stability ((14)C activity) of SOM fractions while constraining other influential C turnover factors such as mineral, climate and plant input. The following SOM fractions were isolated from two soil samples: four humic acids, two humins, non-hydrolyzable carbon, and the demineralized fraction. We examined the isotope ratios of SOM fractions in relation to composition (such as aliphatic and aromatic C content) using solid state (13)C nuclear magnetic resonance (NMR) and thermal analysis. The Δ(14)C values of the fractions isolated from both an albic soil (SOMs-A) and a black soil (SOMs-B) correlated negatively with their peak temperature of decomposition and the temperature where half of the total heat of reaction was evolved, implying a potential link between thermal and biogeochemical stability of SOM fractions. Aryl C contents of SOMs-A determined using (13)C NMR varied inversely with δ(15)N values and directly with δ(13)C values, suggesting that part of aryl C of SOMs-A might be fire-derived. The Δ(14)C values of SOMs-A correlated positively with aliphatic C content and negatively with aromatic C content. We therefore concluded that fire-derived aromatic C in SOMs-A appeared to be more stable than microbially-derived aliphatic C. The greater decomposition of SOMs-B fractions weakened the relationship of their Δ(14)C values with alkyl and aryl C contents. Hence, the role of the composition of SOM fractions in regulating stability might be dependent on the source of specific C forms and their stage of decomposition.

A phospholipid uptake system in the model plant Arabidopsis thaliana

Plants use solar energy to produce lipids directly from inorganic elements and are not thought to require molecular systems for lipid uptake from the environment. Here we show that Arabidopsis thaliana Aminophospholipid ATPase10 (ALA10) is a P4-type ATPase flippase that internalizes exogenous phospholipids across the plasma membrane, after which they are rapidly metabolized. ALA10 expression and phospholipid uptake are high in the epidermal cells of the root tip and in guard cells, the latter of which regulate the size of stomatal apertures to modulate gas exchange. ALA10-knockout mutants exhibit reduced phospholipid uptake at the root tips and guard cells and are affected in growth and transpiration. The presence of a phospholipid uptake system in plants is surprising. Our results suggest that one possible physiological role of this system is to internalize lysophosphatidylcholine, a signalling lipid involved in root development and stomatal control.

Organic matter source and degradation as revealed by molecular biomarkers in agricultural soils of Yuanyang terrace

Three soils with different tillage activities were collected and compared for their organic matter sources and degradation. Two soils (TD and TP) with human activities showed more diverse of chemicals in both free lipids and CuO oxidation products than the one (NS) without human activities. Branched alkanoic acids only accounted for less than 5% of lipids, indicating limited microbial inputs in all three investigated soils. The degradation of lignin in NS and TD was relatively higher than TP, probably because of the chemical degradation, most likely UV light-involved photodegradation. Lignin parameters obtained from CuO oxidation products confirmed that woody gymnosperm tissue (such as pine trees) may be the main source for NS, while angiosperm tissues from vascular plant may be the predominant source for the lignins in TD and TP. Analysis of BPCAs illustrated that BC in NS may be mainly originated from soot or other fossil carbon sources, whereas BC in TD and TP may be produced during corn stalk and straw burning. BC was involved in mineral interactions for TD and TP. The dynamics of organic matter needs to be extensively examined for their nonideal interactions with contaminants.

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.

Cadmium adsorption on plant- and manure-derived biochar and biochar-amended sandy soils: impact of bulk and surface properties

To investigate the role of the bulk and surface composition of both biochar and biochar-amended soils in the adsorption of Cd(2+), as well as the influence of different biochars added to the soils on Cd(2+) adsorption, swine-manure-derived biochars (BSs) and wheat-straw-derived biochars (BWs) were produced at 300, 450, and 600°C. These biochars were added to a sandy soil to investigate the effect of biochars on the adsorption of Cd(2+) by soil. The significantly higher surface C content of the amended soils compared to their bulk C content suggests that the minerals of the biochar-amended soils are most likely covered primarily by biochars. The maximum adsorption capacity (Qmax,total) of the BSs was 10-15 times higher than that of the BWs due to the high polarity and ash content of the BSs. The polarity ((N+O)/C) of the low-temperature biochars greatly affected their Cd(2+) adsorption. The Qmax,total of the BS-amended soils increased with increasing dose, whereas the Qmax,total of the BW-amended soils showed the opposite behavior, which was attributed to the different surface composition characteristics of the two types of soil. The BSs were more effective in immobilizing Cd(2+) upon application to the soil relative to the BWs. This study elucidates the spatial distribution of biochars in biochar-amended soils and highlights the importance of the surface composition of the investigated samples in Cd(2+) adsorption.

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.

Lignin: characterization of a multifaceted crop component

Lignin is a plant component with important implications for various agricultural disciplines. It confers rigidity to cell walls, and is therefore associated with tolerance to abiotic and biotic stresses and the mechanical stability of plants. In animal nutrition, lignin is considered an antinutritive component of forages as it cannot be readily fermented by rumen microbes. In terms of energy yield from biomass, the role of lignin depends on the conversion process. It contains more gross energy than other cell wall components and therefore confers enhanced heat value in thermochemical processes such as direct combustion. Conversely, it negatively affects biological energy conversion processes such as bioethanol or biogas production, as it inhibits microbial fermentation of the cell wall. Lignin from crop residues plays an important role in the soil organic carbon cycling, as it constitutes a recalcitrant carbon pool affecting nutrient mineralization and carbon sequestration. Due to the significance of lignin in several agricultural disciplines, the modification of lignin content and composition by breeding is becoming increasingly important. Both mapping of quantitative trait loci and transgenic approaches have been adopted to modify lignin in crops. However, breeding goals must be defined considering the conflicting role of lignin in different agricultural disciplines.

High affinity sorption domains in soil are blocked by polar soil organic matter components

Reported correlations between organic contaminant sorption affinity and soil organic matter (OM) structure vary widely, suggesting the importance of OM physical conformation and accessibility. Batch equilibration experiments were used to examine the sorption affinity of bisphenol A, atrazine, and diuron to five soils of varying OM composition. (13)C cross-polarization magic angle spinning NMR spectroscopy was used to characterize the organic carbon chemistry of the soil samples. High sorption by a soil low in O-alkyl components suggested that these structures may block high affinity sorption sites in soil OM. As such, soil samples were subjected to acid hydrolysis, and NMR results showed a decrease in the O-alkyl carbon signal intensity for all soils. Subsequent sorption experiments revealed that organic carbon-normalized distribution coefficient (K(OC)) values increased for all three contaminants. Before hydrolysis, K(OC) values correlated positively with soil aromatic carbon content and negatively with polar soil O-alkyl carbon content. While these correlations were weaker after hydrolysis, the correlation between K(OC) values and soil alkyl carbon content improved. This study suggests that hydrolyzable O-alkyl soil OM components may block high affinity sorption sites and further highlights the importance of OM physical conformation and accessibility with respect to sorption processes.