Soil Organic Matter Constituents Research Articles

Impact of Diverse Agricultural Land Uses on Soil Organic Matter Fractions: A Comprehensive Evaluation

Organic matter is a crucial component of soil that influences various soil properties and functions, including nutrient cycling, soil structure, water holding capacity and microbial activity. Different agricultural land uses significantly influence the quantity and quality of soil organic matter (SOM) fractions. The primary constituent of SOM is humic substances, also known as humus. These are stable compounds originating from the decomposition of organic matter derived from plants, animals, and microorganisms. The soil humic fraction is categorized into humic acid (HA), fulvic acid (FA) and humin (HN) based on the solubility in acid and alkaline medium. The structural arrangement, chemical constitution and stability of the humic substances in soil are affected by various factors, including climate, parent material, altitude, vegetation and the management practices employed in the area. In this context the present study was proposed to assess the impact of various agricultural land use systems on humic acid, fulvic acid and humin fraction in soils of different agro-ecological units (AEUs) of southern Kerala. The study focused on specific AEUs in southern Kerala, including the southern coastal plain (AEU 1), Onattukara sandy plain (AEU 3), southern laterites (AEU 8), south central laterites (AEU 9) and southern and central foothills (AEU 12). Within each AEU, various agricultural land use categories such as, coconut, rice, rubber and uncultivated land were selected as specific focal points for this investigation. The HA, FA and HN content in soil exhibited varying ranges across different AEUs, ranging from 0.57 to 2.06, 0.73 to 2.33, and 0.62 to 1.59 per cent respectively. Among the various land uses, rubber exhibited significantly higher levels of HA (1.72%), FA (2.01%) and HN (1.44%) compared to coconut, rice and uncultivated land. Among the different organic matter fractions, FA (32.30-36.18 %) contributed more towards SOM than HA (29.40-32.51 %) and HN (26.43-29.25 %).

Regional topsoil organic carbon content in the agricultural soils of Slovakia and its drivers, as revealed by the most recent national soil monitoring data

Soil organic carbon (SOC) is a primary constituent of soil organic matter and plays an important role in the regulation of many soil processes, including greenhouse gas emissions. Recently, SOC also became an indicator for monitoring climate change mitigation policies in the agricultural sector. The availability of up-to-date SOC inventories is thus crucial in terms of supporting SOC–related actions at country or sub-country scales. Currently, the National Monitoring System of the Agricultural Soils of Slovakia (CMS-P), whose network of 318 monitoring sites was last surveyed in 2018, is the only available source of up-to-date topsoil SOC data for agricultural land in Slovakia. Although very useful at the national scale, the number of CMS-P observations it contains is too limited for much needed sub-national SOC inventories. We hypothesized that with the aid of well-chosen macro-scale drivers of topsoil SOC accumulation in agricultural land in Slovakia, and by mapping those drivers geographically, we could upscale the CMS-P observations and produce a regional estimate of topsoil SOC. Altitude, land cover, topsoil texture, and soil type were assumed to be the key factors controlling topsoil SOC accumulation in Slovakia, and based on these, the country was classified into 14 macro-scale geographical regions. Typical ranges and mid-class values of 0–30cm topsoil SOC concentrations (%) and stocks (t ha−1) were calculated for each macro-scale region from CMS-P data. The average topsoil SOC content in agricultural land was estimated to be 2.13% (72.9 t ha−1). The highest topsoil SOC stock (> 90 t ha−1) was estimated for the lowlands of Slovakia, and the lowest (< 50 t ha−1) for the shallow and stony soils of mountain regions. When aggregated to 78 administrative regions at LAU1 level, the area-weighted averages ranged between 39.20 t ha−1 and 80.0 t ha−1, with the highest values (> 65 t ha−1) being in LAU1 regions in the south-west, south-east, and north of Slovakia where arable land is most prevalent. Total SOC storage in 0–30cm topsoil of agricultural land in Slovakia was estimated at 118.39 Mt, with two-thirds of this amount stored in arable soils in 33 south-west, south-east, and south LAU1 administrative regions. As there is no alternative and up-to-date dataset on topsoil SOC content in Slovakia, the upscaling algorithm presented in this study is an important step toward utilizing CMS-P data for sub-national SOC inventories. It may also offer a new way of providing inputs to help predict future or alternative regional topsoil SOC accumulation trajectories in Slovakian agricultural land using process-based or statistical models.

Roles of Natural Phenolic Compounds in Polycyclic Aromatic Hydrocarbons Abiotic Attenuation at Soil-Air Interfaces through Oxidative Coupling Reactions.

Little information is available on the roles of natural phenolic compounds in polycyclic aromatic hydrocarbons (PAHs) attenuation at dry soil-air interfaces. The purpose of this study was to determine the roles of model phenolic constituents of soil organic matter (SOM) on the abiotic attenuation of PAHs. The phenolic compounds can significantly change the attenuation rates of PAHs, among which hydroquinone was the most effective in promoting anthracene and benzo[a]anthracene attenuation. Product identification and sequential extraction experiments revealed hydroquinone enhanced the formation of oxidative coupling products and promoted the incorporation of PAHs into humic analogues, thereby reducing potential risks to humans and ecosystems. Electron paramagnetic resonance spectroscopy analyses showed both PAHs and phenolic compounds could donate electrons to Lewis acid sites of soil minerals, resulting in the generation of persistent free radicals (PFRs). PFRs could promote the generation of ·OH to enhance PAH oxidation and could cross-couple with PAHs, resulting in high-molecular-weight oxidative coupling products. This study revealed for the first time the reaction mechanism between PAHs and phenolic components of SOM under relatively dry conditions and provided new insights into promoting PAHs detoxification in soils but also a potential strategy to increase the organic carbon sequestration.

Soil metabolomics: A powerful tool for predicting and specifying pesticide sorption

Sorption regulates the dispersion of pesticides from cropped areas to surrounding water bodies as well as their persistence. Assessing the risk of water contamination and evaluating the efficiency of mitigation measures, requires fine-resolution sorption data and a good knowledge of its drivers. This study aimed to assess the potential of a new approach combining chemometric and soil metabolomics to estimate the adsorption and desorption coefficients of a range of pesticides. It also aims to identify and characterise key components of soil organic matter (SOM) driving the sorption of these pesticides. We constituted a dataset of 43 soils from Tunisia, France and Guadeloupe (West Indies), covering extensive ranges of texture, organic carbon and pH. We performed untargeted soil metabolomics by liquid chromatography coupled with high-resolution mass spectrometry (UPLC-HRMS). We measured the adsorption and desorption coefficients of three pesticides namely glyphosate, 2,4-D and difenoconazole for these soils. We developed Partial Least Square Regression (PLSR) models for the prediction of the sorption coefficients from the RT-m/z matrix and conducted further ANOVA analyses to identify, annotate and characterise the most significant constituents of SOM in the PLSR models. The curated metabolomics matrix yielded 1213 metabolic markers. The prediction performance of the PLSR models was generally high for the adsorption coefficients Kdads (0.3 < R2 < 0.8) and for the desorption coefficients Kfdes (0.6 < R2 < 0.8) but low for ndes (0.03 < R2 < 0.3). The most significant features in the predictive models were annotated with a confidence level of 2 or 3. The molecular descriptors of these putative compounds suggest that the pool of SOM compounds driving glyphosate sorption is reduced compared to 2,4-D and difenoconazole, and these compounds are generally more polar. This approach can provide estimates of the adsorption and desorption coefficients of pesticides, including polar pesticide, for contrasted pedoclimates.

Revisit soil organic matter

<p indent="0mm">The accurate and comprehensive understanding of the molecular composition, source, and stabilization mechanism of soil organic matter (SOM) is vital for soil management and the preservation of organic carbon. Currently, a series of key scientific issues concerning the formation and stabilization of SOM is highly contentious. This review summarized the advances in the sources and molecular structure of SOM, and presented a systematic analysis of the different views, conflicts, and problems concerning soil humic substances in the past decades. The traditional view of soil science believes that SOMs are mainly composed of humic substances which are macromolecular compounds and are derived from plant and animal residues through a series of mineralization and humification processes. Soil enzymes and minerals, including phenol oxidase, laccase, peroxidase, iron oxide, manganese oxide, promote the polymerization of organic molecules through additive nucleophilic reactions and free radical catalyzation. ¹³C-NMR and FT-ICR-MS analyses supported the existence of humic substances in soils based on the structure and the molecular composition of SOM. However, with the application of biomarker analysis, high-resolution mass spectrometry, spatial resolution spectroscopy, and other advanced techniques, there is an emergence of new perspectives on the source and the structure of SOM. HPLC-SEC showed the average molecular weight of Aldrich humic acid was significantly smaller than previously thought and the aggregation of humic substances was affected by acetic acid, pH and ionic strength. These evidences suggest that humic substances are aggregates of small organic compounds with a molecular weight of hundreds to thousands of Daltons, rather than macromolecules of tens to hundreds of thousands of Daltons. Furthermore, <italic>in situ</italic> observation of soil particles by STXM revealed significant heterogeneity of SOM at <sc>50 nm</sc> spatial resolution. In terms of the origin of SOM, model calculations and biomarker analysis have indicated that microbial necromass is the major constituent of SOM which accounts for ~33%–62% of SOM in different ecosystems. Collectively, microbial residues may contribute predominantly to the SOM pool and traditional concept “humification” may not occur in the soil. These new findings are contrary to the traditional theory of soil chemistry and soil biochemistry and subvert our understanding of SOM. Therefore, it is imperative to perform further in-depth studies to fill the knowledge gaps regarding the sources, formation processes, and molecular structures of humus. However, further intensive investigations on SOM are restricted by the lack of efficient and reliable extraction procedures. In addition, the conversion coefficients from biomarker to necromass are not accurate and mass spectrometry could not provide a comprehensive analysis on the whole organic molecules in the soil. The studies on enzymatic reactions and microbial synthesis were mainly performed in simple suspension systems, which could not simulate the complex soil matrix. Consequently, future studies are needed to improve the efficiency and accuracy of the extraction and analysis of SOM and to develop a real-time study platform for the interfacial reactions among minerals, organic matters and microorganisms. Meanwhile, <italic>in situ</italic> characterization techniques and modeling should be employed and combined to clarify the sources and the underlying mechanisms of SOM stabilization at molecular level.

Temperature sensitivity of Antarctic soil-humic substance degradation by cold-adapted bacteria.

Heteropolymer humic substances (HS) are the largest constituents of soil organic matter and are key components that affect plant and microbial growth in maritime Antarctic tundra. We investigated HS decomposition in Antarctic tundra soils from distinct sites by incubating samples at 5°C or 8°C (within a natural soil thawing temperature range of -3.8°C to 9.6°C) for 90 days (average Antarctic summer period). This continuous 3-month artificial incubation maintained a higher total soil temperature than that in natural conditions. The long-term warming effects rapidly decreased HS content during the initial incubation, with no significant difference between 5°C and 8°C. In the presence of Antarctic tundra soil heterogeneity, the relative abundance of Proteobacteria (one of the major bacterial phyla in cold soil environments) increased during HS decomposition, which was more significant at 8°C than at 5°C. Contrasting this, the relative abundance of Actinobacteria (another major group) did not exhibit any significant variation. This microcosm study indicates that higher temperatures or prolonged thawing periods affect the relative abundance of cold-adapted bacterial communities, thereby promoting the rate of microbial HS decomposition. The resulting increase in HS-derived small metabolites will possibly accelerate warming-induced changes in the Antarctic tundra ecosystem.

Short-term cellulose addition decreases microbial diversity and network complexity in an Ultisol following 32-year fertilization

Cellulose is an essential component of plant cell walls, and one of the major constituents of soil organic matter. Decomposition of cellulose, mediated by microorganisms, is critical to the sustainable development of arable soils. However, how exogenous cellulose addition, as a surrogate for organic material amendment, influences the diversity and community compositions of soil microorganisms and their network complexity remains largely unknown. To bridge this knowledge gap, we conducted a microcosm experiment incubated with soils that had been subjected to long-term mineral or organic fertilization. Cellulose addition increased the cumulative CO2 emission in all treatments, with the highest value found in the pig manure amended soils. Cellulose addition significantly reduced the alpha diversity of bacteria and fungi across all fertilization treatments, with a more pronounced effect observed for fungi. Moreover, cellulose addition strongly altered bacterial community structure by increasing the relative abundance of copiotrophic bacteria such as Actinobacteria and Proteobacteria while reducing that of oligotrophic bacteria (e.g., Chloroflexi). Compared with no-fertilizer treatment, the influence of cellulose addition on bacterial and fungal community structure was stronger in long-term mineral or organic fertilized soils. Cellulose addition altered the relative abundance of bacterial and fungal functional groups by generally enriching microbes involved in chemoheterotrophy and suppressing those involved in methylotrophy, pathotroph, saprotroph-symbiotroph, and saprotroph-pathotroph. In addition, cellulose addition decreased soil microbial complexity and the number of potential keystone species, but did not change the key role of Chloroflexi in soil microbial network. Overall, our results demonstrated that cellulose addition decreased soil microbial diversity and network complexity, with possible short-term negative consequences for ecosystem functioning in Ultisols.

Fluorescence properties of humic substances transformed in ectohumus horizons of Podzols affected by alkaline fly‐ash

AbstractLignite burning is still the main source of energy in many countries, generating huge amounts of alkaline residues deposited in dumping sites, which affects the surrounding environment. There are only a few publications dealing with the effects on pH changes of surface horizons, but there are no reports on the impact on other soil properties. The aim of this paper was to characterize the changes occurring in the soil organic matter (SOM) of ectohumus horizons of Podzols located near the dumping site and at the control site. Conventional one‐dimensional, synchronous, and three‐dimensional fluorescence can provided a new information on differences in the structure of humic substances (HS), which are crucial constituents of SOM. Humic acid (HA) and fulvic acid (FA), originally present in the ectohumus horizon, indicated a lower degree of humification, and were characterized by a looser structure, than HS that were extracted from soils affected by fly‐ash. The neutralization of the soil reaction resulting from the deposition of fly‐ash favored the formation of higher humified HS, characterized by a higher concentration of aromatic rings in the core of the molecule and the presence of double conjugated bonds. The fluorescence technique could be applicable to monitor the chemical modification of soils in regions affected by ashes but also all factors changing soil pH. The conducted research has shown that fluorescence spectroscopy can be successfully used as a sensitive technique to characterize qualitatively structures of different organic substances present in terrestrial and aquatic systems.

Bacillus aryabhattai TFG5-mediated synthesis of humic substances from coir pith wastes

BackgroundHumic substances (HS) form the largest proportion among all the constituents of soil organic matter and are a key component of the terrestrial ecosystem. HS plays a multifunctional role in the environment by controlling the biogeochemical carbon cycle, providing nutrients and bio-stimulants for plant growth, and interacting with inorganic and organic pollutants. The rate of formation of HS in soils determines its productivity and carbon sequestration capacity. Enhancement of HS synthesis in the soil through the microbial route not only increases CO2 sequestration but also mitigates the greenhouse gas emissions in the environment.ResultIn this study, we attempted to understand the mechanism of formation and enhancement of HS from coir pith wastes using the tyrosinase produced by Bacillus aryabhattai TFG5. The bacterium TFG5 isolated from the termite garden produced the tyrosinase (1.34 U mL−1) and laccase (2.1 U mL−1) at 48 h and 60 h of fermentation, respectively. The extracellular tyrosinase from B. aryabhattai TFG5 was designated as TyrB. Homology modeling of TyrB revealed a structure with a predicted molecular mass of 35.23 kDa and two copper ions in the active center with its conserved residues required for the tyrosinase activity. TyrB efficiently transformed and polymerized standard phenols, such as p-cresol, p-hydroxyl benzoic acid, Levo DOPA, and 2,6 DMP, besides transforming free phenols in coir pith wash water (CWW). Additionally, UV–Vis and FT-IR spectra of the degradation products of the coir pith treated with TyrB revealed the formation of HS within 3 days of incubation. Furthermore, the E472/664 ratio of the degradation products revealed a higher degree of condensation of the aromatic carbons and the presence of more aliphatic structures in the HS.ConclusionThe results confirmed the influence of TyrB for the effective synthesis of HS from coir pith wastes. The results of the present study also confirm the recently accepted theory of humification proposed by the International Humic Substances Society.

Microstructural and biochemical diversity of forest soil organic surface layers revealed by density fractionation

Particularly on sites with shallow, nutrient-poor soils, forest soil organic surface layers (O layers) are important for the storage of plant-available nutrients and water, and thus for forest vitality and productivity. O layers can contain up to 70 mass percent of inorganic compounds (minerals) which may be spatially separated from or closely associated with soil organic matter (SOM). O layer SOM may differ in biochemical properties and resistance against mineralization, depending on the extent of organo-mineral association. Moreover, type and intensity of SOM-mineral mixing in O layers conveys information about biological activity. Here, for the first time we present detailed density fractionation results to distinguish SOM constituents in O layers with different chemical properties and likely also different degrees of organo-mineral association. Additionally, we characterized spatial association patterns of the SOM fractions. We investigated samples of Of (Oe) and Oh (Oa) horizons of temperate forest soils with different parent materials (basalt, gneiss, andesite, Pleistocene gravel, dolomite). The samples were distinguished into six density fractions (ρ < 0.8 g cm−3; 0.8–1.0 g cm−3; 1.0–1.2 g cm−3; 1.2–1.4 g cm−3; 1.4–1.6 g cm−3; >1.6 g cm−3) by sequential treatment with deionized H2O (ρ = 1.0 g cm−3), 1-propanol (ρ = 0.8 g cm−3), and sodium polytungstate (SPT) solution of increasing density (ρ = 1.2, 1.4, 1.6 g cm−3). The procedure is characterized by a mass recovery of 93 ± 5% and an organic carbon (OC) recovery of 90 ± 9%. In each fraction, we analyzed the concentrations of C, N, metal cations (Fe, Al, Ca, Mg), C speciation (13C NMR spectroscopy), as well as abundances of 13C and 15N. For selected fractions, we additionally determined the radiocarbon age and acquired microscopic images. From the Of to the Oh horizons, the contribution of heavy fractions (>1.4 g cm−3) to total soil mass and total SOC increased, indicating augmented organo–mineral association with progressive SOM decomposition state. Compared to bulk soil, heavier fractions >1.4 g cm−3 were characterized by smaller SOC concentrations, whereas concentrations of Al and Fe were increased for fractions >1.4 g cm−3 in the of and >1.6 g cm−3 in the Oh horizon. The SOM in the heavy fractions was enriched in N, carboxyl C, and alkyl C, but depleted in O/N-alkyl C and aryl C. Smaller mean particle sizes and C/N ratios as well as increased alkyl C / O/N-alkyl C ratios and 13C and 15N abundances indicate an advanced SOM decomposition state and enrichment of microbial-derived SOM in heavier fractions. However, according to its 14C signature, in contrast to high-density (ρ > 1.6 g cm−3) SOM in the mineral soil, forest floor SOM with high density is a rapidly cycling SOM pool with a turnover time <50 years.

Susceptible soil organic matter, SOM, fractions to agricultural management practices in salt-affected soils

In the recent decades, soil salinity became the main human-induced soil degradation causes in Egypt’s Nile Delta Valley (ENDV) by affecting the stabilization processes of soil organic matter (SOM). However, soil organic carbon (SOC) is highly conserved by aggregating the stabilized organic molecules under sound agricultural management. In particular, labile SOM fractions assumed to be dually influenced by salinity and agricultural management practices other than the stabilized fractions. This work aimed to study various labile and stable SOM fractions that are more susceptible to the current agricultural practices in salt-affected soils of the ENDV area. Three different agro-ecological sites were studied: Eastern (EH, EM soils) and Western (WM, WL soils) Delta regions dominated by Vertic Torrifluvents, and Coastal region (NCH, NCM soils) dominated by Typic Calcitorrerts of high CaCO3 contents. Two different salinity levels were detected in each site; low in WL soils, medium in WM, NCM, and EM soils, and high in EH and NCH soils. The least values in EM, WL, and NCM soils were due to the recurrent legume applications. The carbon content of glomalin-related soil protein (GRSP) (C-GRSP) was positively correlated with SOC and water-extractable organic carbon (WEOC) fraction confirming the contribution of GRSP to the stabilization of SOM. The lower soil β-glucosidase, phosphatase, and protease enzymes activities were in those soils with larger salinity levels in each site as NCH < NCM, WM < WL, and EH < EM reflecting the effect of soil salinity and CaCO3 contents on soil metabolic activities. Extracted organic carbon (EOC) in both humic and fulvic fractions was higher in EH, WM, WL, and EM soils than in NCH and NCM soils. The chemical composition of SOM obtained by the pyrolysis gas chromatography showed that lignocellulosic and condensed aromatic structures in SOM increased significantly with CaCO3 and salinity. In conclusion, the considered SOM fractions such as WEOC, EOC, GRSP, C-GRSP, together with the pyrolytic results can be considered as significant indicators in the dynamic stability of SOM. Intercropping with legumes may increase the stability of SOM fractions in salt-affected soils of degraded lands. In calcareous soils, severe alteration in SOC conservation was observed and negatively influenced the active constituents of SOM.

Direct measurement of the in situ decomposition of microbial-derived soil organic matter

Soil organic matter (SOM) is the dominant reservoir of terrestrial organic carbon and nitrogen, and microbial necromass represents a primary input to it. However, knowledge of stabilization mechanisms and direct measurements of the decomposition of microbial-derived SOM are lacking. Here we report a novel 15N isotope pool dilution approach using labeled amino sugars and muropeptides as tracers to quantify the decomposition of proteins and microbial cell walls, which allows to estimate in situ decomposition rates of microbial-derived SOM. Our results demonstrate that microbial cell walls are as recalcitrant as soil protein, exhibiting comparable turnover times across various ecosystems. The bacterial peptidoglycan in soils was primarily decomposed to muropeptides which can be directly utilized by microbes without being further depolymerized to free amino compounds. Moreover, bacterial peptidoglycan decomposition was correlated with soil microbial biomass while fungal chitin and soil protein decomposition were correlated with high soil pH and fine soil texture. This approach thereby provides new insights into the decomposition pathways and stabilization mechanisms of microbial-derived SOM constituents pertaining to SOM persistence.

Mulching-induced preservation of soil organic matter quality in a burnt eucalypt plantation in central Portugal

Mulching has amply proven its effectiveness to mitigate post-fire soil erosion but its impacts on soil organic matter (SOM) quality and quantity continue poorly studied. The present study addressed this knowledge gap for a eucalypt plantation in central Portugal that had been burnt and, immediately after the wildfire, mulched with 13.6 Mg ha−1 of eucalypt logging residues some five years before. This was done by performing a range of analytical techniques (elemental and isotope analyses, analytical pyrolysis and 13C NMR spectroscopy) not only on the bulk soil samples but also on their humic acids (HAs) and free organic matter (FOM) fractions. While mulching reduced soil and SOM losses with 91 and 93%, respectively, it also improved SOM quality of the topsoil, in particular in terms of HAs and FOM. At 0–4 cm depth, both HAs and FOM contents were roughly twice as high in the mulched plots as in the control plots. The effects of mulching on the molecular composition of HAs and FOM fractions, however, varied markedly. Analytical pyrolysis (Py-GC/MS) revealed that mulching had led to a noticeable accumulation of labile, aliphatic SOM constituents such as carbohydrate-derived and alkyl compounds (fatty acids and n-alkanes) but that it hardly affected the composition of HAs. Even so, solid-state 13C NMR spectroscopy showed that mulching had resulted in a relative increase in aryl C in the FOM fraction, suggesting an enhanced preservation of the pyrogenic OM. Overall, the combined use of a range of analytical techniques allowed to conclude that, five years after their application, the forest logging residues had led to a greater preservation of the fire-derived pyrogenic OM (mainly aromatic compounds) in the topsoil as well as to higher contents of SOM's most labile molecular constituents (mainly carbohydrates and n-alkyl compounds). The former reflected the reduced erosion rates, while the latter was probably due to a combination of reduced erosion rates with the additional input of fresh organic matter.

Untargeted Soil Metabolomics Using Liquid Chromatography-Mass Spectrometry and Gas Chromatography-Mass Spectrometry.

The molecular composition of soil organic matter (SOM) sets the foundation for terrestrial microbial community structures and carbon cycling dynamics. However, the specific chemical constituents of SOM are underexplored. In this chapter we present a protocol for the extraction of small molecule metabolites from soil followed by compound detection and identification using liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry. There are options within the protocol to assess either the extracellular pool of metabolites or the total pool (including intracellular) and either polar or nonpolar metabolites, depending on the reader's research interests. These methods can be followed individually for a more targeted analysis or all methods can be combined to obtain a more comprehensive understanding of SOM metabolite composition (such as amino acids, nucleobases, organic acids, fatty acids, carbohydrates, secondary metabolites, and antibiotics).

The mechanisms of humic substances self-assembly with biological molecules: The case study of the prion protein.

Humic substances (HS) are the largest constituent of soil organic matter and are considered as a key component of the terrestrial ecosystem. HS may facilitate the transport of organic and inorganic molecules, as well as the sorption interactions with environmentally relevant proteins such as prions. Prions enter the environment through shedding from live hosts, facilitating a sustained incidence of animal prion diseases such as Chronic Wasting Disease and scrapie in cervid and ovine populations, respectively. Changes in prion structure upon environmental exposure may be significant as they can affect prion infectivity and disease pathology. Despite its relevance, the mechanisms of prion interaction with HS are still not completely understood. The goal of this work is to advance a structural-level picture of the encapsulation of recombinant, non-infectious, prion protein (PrP) into different natural HS. We observed that PrP precipitation upon addition of HS is mainly driven by a mechanism of “salting-out” whereby PrP molecules are rapidly removed from the solution and aggregate in insoluble adducts with humic molecules. Importantly, this process does not alter the protein folding since insoluble PrP retains its α-helical content when in complex with HS. The observed ability of HS to promote PrP insolubilization without altering its secondary structure may have potential relevance in the context of “prion ecology”. These results suggest that soil organic matter interacts with prions possibly without altering the protein structures. This may facilitate prions preservation from biotic and abiotic degradation leading to their accumulation in the environment.

The relation of structural mobility and water sorption of soil organic matter studied by 1H and 13C solid-state NMR

The impact of low water contents on the molecular mobility of soil organic matter (SOM) and its most frequent components was investigated. Combined 1H, 2H, and 13C solid-state nuclear magnetic resonance (NMR) techniques allow for an advanced insight into mechanisms of water uptake under defined atmospheres and its effect on SOM segment mobility. The major individual organic components of two peats, a gleyic podsol and a number of model substances (cutin, suberin, wood and cellulose) were distinguished with respect to their contribution to the 1H and 13C NMR spectra. Water molecules and mobile polymer constituents of SOM contribute to the mobile fraction in 1H NMR wide line spectra. Poly(methylene), being most probably part of amphiphilic molecules, have been identified as SOM components that are mobilized in the presence of water. Even though being of hydrophobic nature, water acts as a plasticizer on such long chain aliphatic soil components. Differential scanning calorimetry measurements of SOM samples support this insight in terms of a thermal step transition. Based on our findings, comparison of experimental results from different soils with varying water contents and soil composition should consider mobility effects of both, aliphatic moieties as well as polar moieties of SOM.

Iron addition to soil specifically stabilized lignin

The importance of lignin as a recalcitrant constituent of soil organic matter (SOM) remains contested. Associations with iron (Fe) oxides have been proposed to specifically protect lignin from decomposition, but impacts of Fe-lignin interactions on mineralization rates remain unclear. Oxygen (O2) fluctuations characteristic of humid tropical soils drive reductive Fe dissolution and precipitation, facilitating multiple types of Fe-lignin interactions that could variably decompose or protect lignin. We tested impacts of Fe addition on 13C methoxyl-labeled lignin mineralization in soils that were exposed to static or fluctuating O2. Iron addition suppressed lignin mineralization to 21% of controls, regardless of O2 availability. However, Fe addition had no effect on soil CO2 production, implying that Fe oxides specifically protected lignin methoxyls but not bulk SOM. Iron oxide-lignin interactions represent a specific mechanism for lignin stabilization, linking SOM biochemical composition to turnover via geochemistry.

Complex Forms of Soil Organic Phosphorus-A Major Component of Soil Phosphorus.

Phosphorus (P) is an essential element for life, an innate constituent of soil organic matter, and a major anthropogenic input to terrestrial ecosystems. The supply of P to living organisms is strongly dependent on the dynamics of soil organic P. However, fluxes of P through soil organic matter remain unclear because only a minority (typically <30%) of soil organic P has been identified as recognizable biomolecules of low molecular weight (e.g., inositol hexakisphosphates). Here, we use (31)P nuclear magnetic resonance spectroscopy to determine the speciation of organic P in soil extracts fractionated into two molecular weight ranges. Speciation of organic P in the high molecular weight fraction (>10 kDa) was markedly different to that of the low molecular weight fraction (<10 kDa). The former was dominated by a broad peak, which is consistent with P bound by phosphomonoester linkages of supra-/macro-molecular structures, whereas the latter contained all of the sharp peaks that were present in unfractionated extracts, along with some broad signal. Overall, phosphomonoesters in supra-/macro-molecular structures were found to account for the majority (61% to 73%) of soil organic P across the five diverse soils. These soil phosphomonoesters will need to be integrated within current models of the inorganic-organic P cycle of soil-plant terrestrial ecosystems.

Will changes in climate and land use affect soil organic matter composition? Evidence from an ecotonal climosequence

As the largest actively cycling pool of terrestrial C, the response of soil organic matter (SOM) to climate change may greatly affect global C cycling and climate change feedbacks. Despite the influence of SOM chemistry—here defined as soil organic C (SOC) and soil organic N (SON) functional groups and compounds—on decomposition, uncertainty exists regarding the response of SOM chemistry to climate change and associated land use shifts. Here, we adopt a climosequence approach, using latitude along a uniform glacial till deposit at the grassland–forest ecotone in central Canada as a surrogate for the effects of climate change on SOM chemistry. Additionally, we evaluate differences in SOM chemistry from paired native grassland, native trembling aspen (Populus tremuloides) forest, and arable soil profiles to investigate the effects of likely climate-induced land use alterations.The combination of C and N K-edge X-ray absorption near edge structure (XANES) with pyrolysis-field ionization mass spectrometry (Py-FIMS) techniques was used to examine SOM chemistry at atomic and molecular scales, respectively. These techniques revealed only modest differences in surface SOM chemistry related to land use and latitude. Greater variation was apparent in the vertical stratification of SOM constituents from soil depth profiles. These findings indicate that pedon-scale processes have greater control over SOM chemistry than do processes operating on landscape (e.g. land use) and regional (e.g. climate) scales. Additionally they imply that SOM chemistry is largely unresponsive to climatic change on the magnitude of the mean annual temperature (MAT) gradient under study (~0.7°C), despite its location at the grassland–forest boundary highlighting its sensitivity, and is similarly unresponsive to associated land use shifts.

Temporal changes in soil bacterial diversity and humic substances degradation in subarctic tundra soil.

Humic substances (HS), primarily humic acids (HA) and fulvic acids (FA), are the largest constituent of soil organic matter. In microcosm systems with subarctic HS-rich tundra soil (site AK 1-75; approximately 5.6 °C during the thawing period) from Council, Alaska, the HA content significantly decreased to 48% after a 99-day incubation at 5 °C as part of a biologically mediated process. Accordingly, levels of FA, a putative byproduct of HA degradation, consistently increased to 172% during an identical incubation process. Culture-independent microbial community analysis showed that during the microcosm experiments, the relative abundance of phyla Proteobacteria (bacteria) and Euryarchaeota (archaea) largely increased, indicating their involvement in HS degradation. When the indigenous bacteria in AK 1-75 were enriched in an artificial mineral medium spiked with HA, the changes in relative abundance were most conspicuous in Proteobacteria (from 60.2 to 79.0%), specifically Betaproteobacteria-related bacteria. One hundred twenty-two HA-degrading bacterial strains, primarily from the genera Paenibacillus (phylum Firmicutes) and Pseudomonas (class Gammaproteobacteria), were cultivated from AK 1-75 and nearby sites. Through culture-dependent analysis with these bacterial isolates, we observed increasing HS-degradation rates in parallel with rising temperatures in a range of 0 °C to 20 °C, with the most notable increase occurring at 8 °C compared to 6 °C. Our results indicate that, although microbial-mediated HS degradation occurs at temperature as low as 5 °C in tundra ecosystems, increasing soil temperature caused by global climate change could enhance HS degradation rates. Extending the thawing period could also increase degradation activity, thereby directly affecting nearby microbial communities and rhizosphere environments.