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

Conceptualizing soil fauna effects on labile and stabilized soil organic matter

Fauna is highly abundant and diverse in soils worldwide, but surprisingly little is known about how it affects soil organic matter stabilization. Here, we review how the ecological strategies of a multitude of soil faunal taxa can affect the formation and persistence of labile (particulate organic matter, POM) and stabilized soil organic matter (mineral-associated organic matter, MAOM). We propose three major mechanisms - transformation, translocation, and grazing on microorganisms - by which soil fauna alters factors deemed essential in the formation of POM and MAOM, including the quantity and decomposability of organic matter, soil mineralogy, and the abundance, location, and composition of the microbial community. Determining the relevance of these mechanisms to POM and MAOM formation in cross-disciplinary studies that cover individual taxa and more complex faunal communities, and employ physical fractionation, isotopic, and microbiological approaches is essential to advance concepts, models, and policies focused on soil organic matter and effectively manage soils as carbon sinks, nutrient stores, and providers of food.

Unlocking complex soil systems as carbon sinks: multi-pool management as the key

Much research focuses on increasing carbon storage in mineral-associated organic matter (MAOM), in which carbon may persist for centuries to millennia. However, MAOM-targeted management is insufficient because the formation pathways of persistent soil organic matter are diverse and vary with environmental conditions. Effective management must also consider particulate organic matter (POM). In many soils, there is potential for enlarging POM pools, POM can persist over long time scales, and POM can be a direct precursor of MAOM. We present a framework for context-dependent management strategies that recognizes soils as complex systems in which environmental conditions constrain POM and MAOM formation.

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.

Phenoloxidase activity and organic carbon dynamics in historic Anthrosols in Scotland, UK

Phenolic compounds are chemical precursor building blocks of soil organic matter. Their occurrence can be inhibitory to certain enzymes present in soil, thereby influencing the rate of decomposition of soil organic matter. Microbe-derived phenoloxidases (laccases) are extracellular enzymes capable of degrading recalcitrant polyphenolic compounds. In this study, our aim was to investigate the relationships between phenoloxidase enzyme activity, organic carbon content and microbial abundance in the context of long-term anthropogenically amended soils. To achieve this, we used a series of complementary biochemical analytical methods including gas chromatography, enzyme assays and solid-state Carbon-13 Cross Polarisation Magic-Angle Spinning Nuclear Magnetic Resonance Spectroscopy (¹³C CPMAS NMR). Using several anthrosols found in St Andrews (Scotland, UK) that had been subjected to intense anthropogenic modification since the medieval period (11^th century AD) to present-day, we were able to scope the impact of past waste disposal on soils. The long-term anthropogenic impact led to organic matter-rich soils. Overall, phenoloxidase activity increased by up to 2-fold with soil depth (up to 100 cm) and was inversely correlated with microbial biomass. Solid-state ¹³C NMR characterisation of carbon species revealed that the observed decline in soil organic matter with depth corresponded to decreases in the labile organic carbon fractions as evidenced by changes in the O/N-alkyl C region of the spectra. The increase in phenoloxidase activity with depth would appear to be a compensatory mechanism for the reduced quantities of organic carbon and lower overall nutrient environment in subsoils. By enzymatically targeting phenolic compounds, microbes can better utilise recalcitrant carbon when other labile soil carbon sources become limited, thereby maintaining metabolic processes.

Can stable isotopes quantify soil carbon build-up from organic fertilizers?

The application of organic fertilizers (OF) can supply carbon (C) to the soil in crop fields. OF-derived C (OF-C) is often estimated using the differential method that can be biased due to indirect effects of OF on soil C. This study tested three methods to quantify OF-C: (i) the widespread differential method, (ii) the synchronic isotope method comparing plots with and without OF and (iii) the asynchronic isotope method mimicking a trial without a control plot. These methods were implemented on an Arenosol and an Andosol supplied during 13 years with slurry or compost. The results highlighted the relevance of using the synchronic isotope method, which focuses on the direct effect of OFs on the soil organic matter (without bias of vegetation change) and considers control soil's evolution. The higher the isotopic difference between soil and OF, the shorter the method implementation time needed: for an initial difference of 7.5 ‰ and 3.5 ‰, quantification is suitable after 4 and 9 years of fertilization respectively. Attention should be paid to OF-δ¹³C variability to guarantee the method validity. The method proved to be suitable to study the factors controlling the OF-C fate in tropical soils.

Effects of land use change from natural forest to plantation on C, N and natural abundance of 13C and 15N along a climate gradient in eastern China

Soil C and N turnover rates and contents are strongly influenced by climates (e.g., mean annual temperature MAT, and mean annual precipitation MAP) as well as human activities. However, the effects of converting natural forests to intensively human-managed plantations on soil carbon (C), nitrogen (N) dynamics across various climatic zones are not well known. In this study, we evaluated C, N pool and natural abundances of δ¹³C and δ¹⁵N in forest floor layer and 1-meter depth mineral soils under natural forests (NF) and plantation forest (PF) at six sites in eastern China. Our results showed that forest floor had higher C contents and lower N contents in PF compared to NF, resulting in high forest floor C/N ratios and a decrease in the quality of organic materials in forest floor under plantations. In general, soil C, N contents and their isotope changed significantly in the forest floor and mineral soil after land use change (LUC). Soil δ¹³C was significantly enriched in forest floor after LUC while both δ¹³C and δ¹⁵N values were enriched in mineral soils. Linear and non-linear regressions were observed for MAP and MAT in soil C/N ratios and soil δ¹³C, in their changes with NF conversion to PF while soil δ¹⁵N values were positively correlated with MAT. Our findings implied that LUC alters soil C turnover and contents and MAP drive soil δ¹³C dynamic.

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.

Isotopic evidence of biotrophy and unusual nitrogen nutrition in soil-dwelling Hygrophoraceae

Several lines of evidence suggest that the agaricoid, non-ectomycorrhizal members of the family Hygrophoraceae (waxcaps) are biotrophic with unusual nitrogen nutrition. However, methods for the axenic culture and lab-based study of these organisms remain to be developed, so our current knowledge is limited to field-based investigations. Addition of nitrogen, lime or organophosphate pesticide at an experimental field site (Sourhope) suppressed fruiting of waxcap basidiocarps. Furthermore, stable isotope natural abundance in basidiocarps were unusually high in 15 N and low in 13 C, the latter consistent with mycorrhizal nutritional status. Similar patterns were found in waxcap basidiocarps from diverse habitats across four continents. Additional data from 14 C analysis of basidiocarps and 13 C pulse label experiments suggest that these fungi are not saprotrophs but rather biotrophic endophytes and possibly mycorrhizal. The consistently high but variable δ15 N values (10-20‰) of basidiocarps further indicate that N acquisition or processing differ from other fungi; we suggest that N may be derived from acquisition of N via soil fauna high in the food chain.

Natural organic matter contained in clay rock pore water: Direct quantification at the molecular level using electrospray ionization mass spectrometry

RATIONALE

Natural organic matter (NOM) is present in the environment and could influence the migration of heavy metals/radionuclides. The dissolved fraction of NOM (DOM) is usually quantified using total organic carbon analysis or UV-visible spectrometry. Nonetheless, analysis using pattern recognition cannot provide the full spectrum of organic molecules contained in waters, especially low-molecular-weight compounds. In the context of nuclear performance assessment studies, ground waters may contain DOM and a key aspect is to quantify different categories of NOM types in order to further evaluate the transport and fate of radionuclides in the environment.

METHODS

Thus, a method for the quantification of DOM at the molecular level was developed, based on electrospray ionization mass spectrometry (ESI-MS). This method simultaneously gives structural information on DOM and the individual concentrations of these low-molecular-weight compounds without pretreatment and/or preconcentration of the samples.

RESULTS

Several methods of quantification (internal calibration, calibrated addition of external standard, sequential tandem mass spectrometry) have been optimized and successfully applied to real natural samples. They are discussed in this paper with a focus on acidic compounds, which are the compounds that most probably could influence the migration of heavy metals and radionuclides in the clay rock pore water from the French Callovo-Oxfordian (COx) nuclear repository site.

CONCLUSIONS

Quantification of in situ dissolved NOM from the COx has been performed using ESI-MS. For the first time to our knowledge, it was possible to give a quite exhaustive and quantitative inventory of the small organic compounds present without proceeding to any chemical treatment or sample crushing and for naturally occurring concentrations.

Labelled microbial culture as a calibration medium for (13) C-isotope measurement of derivatized compounds: application to tert-butyldimethylsilyl amino acids

RATIONALE

Compound-specific stable carbon isotope analysis by gas chromatography/combustion/isotope ratio mass spectrometry (GC/C/IRMS) is widely used in studies of environmental or biological functioning. In the case of derivatized molecules, a calibration might be required due to added non-analyte carbon and in some cases non-stoichiometric recovery by the mass spectrometer.

METHODS

Two biological materials of known isotopic composition were produced by microbial cell cultures on either (13) C-labelled glucose or non-labelled glucose as sole source of carbon. Subsequent hydrolyzed amino acids were derivatized as tert-butyldimethylsilyl (tBDMSi) derivatives and analyzed by GC/C/IRMS. The (13) C-enrichment measurements were used as a direct calibration to calculate the original (13) C/(12) C ratios of individual amino acids. We tested this calibration on both known and unknown samples.

RESULTS

For the main proteinogenic amino acids we could determine the number of non-analyte added carbon atoms and assess the non-stoichiometrical recovery of tBDMSi carbon atoms, due to their incomplete oxidation in the combustion step of GC/C/IRMS. The calibration enabled the determination of the natural abundances (δ(13) C values) of amino acids with an average accuracy of ±1.1 ‰. We illustrate the application of the calibration to determine the (13) C/(12) C ratios of amino acids, and the associated uncertainty, in biological and plant materials.

CONCLUSIONS

The analysis of a labelled microbial cell culture offers a straightforward, rapid and reliable estimate of non-analyte carbon contribution to stable isotope composition. We recommend this method as a calibration or a control in artificial or natural (13) C-tracing experiments. Copyright © 2016 John Wiley & Sons, Ltd.

A Diverse Soil Microbiome Degrades More Crude Oil than Specialized Bacterial Assemblages Obtained in Culture

Soil microbiome modification may alter system function, which may enhance processes like bioremediation. In this study, we filled microcosms with gamma-irradiated soil that was reinoculated with the initial soil or cultivated bacterial subsets obtained on regular media (REG-M) or media containing crude oil (CO-M). We allowed 8 weeks for microbiome stabilization, added crude oil and monoammonium phosphate, incubated the microcosms for another 6 weeks, and then measured the biodegradation of crude oil components, bacterial taxonomy, and functional gene composition. We hypothesized that the biodegradation of targeted crude oil components would be enhanced by limiting the microbial taxa competing for resources and by specifically selecting bacteria involved in crude oil biodegradation (i.e., CO-M). Postincubation, large differences in taxonomy and functional gene composition between the three microbiome types remained, indicating that purposeful soil microbiome structuring is feasible. Although phylum-level bacterial taxonomy was constrained, operational taxonomic unit composition varied between microbiome types. Contrary to our hypothesis, the biodegradation of C10 to C50 hydrocarbons was highest when the original microbiome was reinoculated, despite a higher relative abundance of alkane hydroxylase genes in the CO-M microbiomes and of carbon-processing genes in the REG-M microbiomes. Despite increases in the relative abundances of genes potentially linked to hydrocarbon processing in cultivated subsets of the microbiome, reinoculation of the initial microbiome led to maximum biodegradation.

IMPORTANCE

In this study, we show that it is possible to sustainably modify microbial assemblages in soil. This has implications for biotechnology, as modification of gut microbial assemblages has led to improved treatments for diseases like Clostridium difficile infection. Although the soil environment determined which major phylogenetic groups of bacteria would dominate the assemblage, we saw differences at lower levels of taxonomy and in functional gene composition (e.g., genes related to hydrocarbon degradation). Further studies are needed to determine the success of such an approach in nonsterile environments. Although the biodegradation of certain crude oil fractions was still the highest when we inoculated with the diverse initial microbiome, the possibility of discovering and establishing microbiomes that are more efficient in crude oil degradation is not precluded.

Long-term management changes topsoil and subsoil organic carbon and nitrogen dynamics in a temperate agricultural system

Soil organic carbon (SOC) and nitrogen (N) contents are controlled partly by plant inputs that can be manipulated in agricultural systems. Although SOC and N pools occur mainly in the topsoil (upper 0.30 m), there are often substantial pools in the subsoil that are commonly assumed to be stable. We tested the hypothesis that contrasting long-term management systems change the dynamics of SOC and N in the topsoil and subsoil (to 0.75 m) under temperate conditions. We used an established field experiment in the UK where control grassland was changed to arable (59 years before) and bare fallow (49 years before) systems. Losses of SOC and N were 65 and 61% under arable and 78 and 74% under fallow, respectively, in the upper 0.15 m when compared with the grass land soil, whereas at 0.3-0.6-m depth losses under arable and fallow were 41 and 22% and 52 and 35%, respectively. The stable isotopes ¹³C and ¹⁵N showed the effects of different treatments. Concentrations of long-chain n-alkanes C₂₇, C₂₉ and C₃₁ were greater in soil under grass than under arable and fallow. The dynamics of SOC and N changed in both topsoil and subsoil on a decadal time-scale because of changes in the balance between inputs and turnover in perennial and annual systems. Isotopic and geochemical analyses suggested that fresh inputs and decomposition processes occur in the subsoil. There is a need to monitor and predict long-term changes in soil properties in the whole soil profile if soil is to be managed sustainably.

HIGHLIGHTS

Land-use change affects soil organic carbon and nitrogen, but usually the topsoil only is considered.Grassland cultivated to arable and fallow lost 13-78% SOC and N to 0.6 m depth within decades.Isotopic and biomarker analyses suggested changes in delivery and turnover of plant-derived inputs.The full soil profile must be considered to assess soil quality and sustainability.

Contrasting temperature responses of dissolved organic carbon and phenols leached from soils

BACKGROUND AND AIMS

Plant-derived phenols are a major input to the terrestrial carbon cycle that might be expected to contribute substantially to dissolved organic carbon (DOC) losses from soils. This study investigated changes in DOC and phenols in leachates from soil treated with individual plant litter types under seasonal temperature change.

METHODS

Senescing grass, buttercup, ash and oak litters were applied to soil lysimeters. Leachates were collected over 22 months and analysed for DOC and phenols. Phenols in litter and DOC were analysed using on-line thermally assisted hydrolysis and methylation with tetramethylammonium hydroxide (TMAH).

RESULTS

Mass loss differed between litter type (buttercup>ash>grass>oak). Phenol concentrations in the senescing litters (<2 % TOC) were small, resulting in minor losses to water. Seasonal soil temperature positively correlated with DOC loss from litter-free soils. An initial correlation between temperature change and total phenol concentration in grass and ash litter treatment leachates diminished with time. Dissolved phenol variety in all litter-amended soil leachates increased with time.

CONCLUSIONS

Plant-derived phenols from senescing litter made a minor contribution to DOC loss from soils. The strength of the relationship between seasonal temperature change and phenol type and abundance in DOC changed with time and was influenced by litter type.

Long-term release of carbon from grassland soil amended with different slurry particle size fractions: a laboratory incubation study

Application of animal manure to agricultural soils enhances both native soil carbon (C) and overall (native soil C and added C) respiration. CO(2) effluxes were measured in a laboratory incubation study for 1465 days after the application of different slurry fractions (>2000, 425-2000, 250-425, 150-250, 45-150 and <45 µm) to a grassland soil. The slurry-derived C present in the soil was traced using the natural abundance δ(13)C method. We used two kinetic (single and two pool) models to fit the experimental data and to test the model validity with respect to long-term data sets. Mean residence times (MRTs) of the particle size based slurry-C fractions were estimated using these models and a linear (13)C natural abundance based approach. The results showed that slurry-C degradation in soil over time varied between the different particle size based slurry treatments. The two kinetic soil-C models were successful to predict medium- to long-term carbon release from soil amended with animal slurry. The estimated MRTs did vary between the linear (3.8-5.6 years) and non-linear based (0.8-3.8 years) (model) approaches. Slurry-derived C could still be (isotopically) detected in the soil 4 years after slurry application using the natural abundance δ(13)C method. This suggests that it may take a decadal timescale or longer before the entire amount of C introduced through whole slurry amendments to grassland soils is fully dissipated.

Non-disturbing characterization of natural organic matter (NOM) contained in clay rock pore water by mass spectrometry using electrospray and atmospheric pressure chemical ionization modes

We have investigated the composition of the mobile natural organic matter (NOM) present in Callovo-Oxfodian pore water using electrospray ionization mass spectrometry (ESI-MS), atmospheric pressure chemical ionization mass spectrometry (APCI-MS) and emission-excitation matrix (EEM) spectroscopy. The generation of knowledge of the composition, structure and size of mobile NOM is necessary if one wants to understand the interactions of these compounds with heavy metals/radionuclides, in the context of environmental studies, and particularly how the mobility of these trace elements is affected by mobile NOM. The proposed methodology is very sensitive in unambiguously identifying the in situ composition of dissolved NOM in water even at very low NOM concentration, due to innovative non-disturbing water sampling and ionization (ESI/APCI-MS) techniques. It was possible to analyze a quite exhaustive inventory of the small organic compounds of clay pore water without proceeding to any chemical treatment at naturally occurring concentration levels. The structural features observed were mainly acidic compounds and fatty acids as well as aldehydes and amino acids.