Soil Organic Matter in Its Native State: Unravelling the Most Complex Biomaterial on Earth

Dynamic Behavior and Interaction Mechanism of Soil Organic Matter in Water Systems: A Coarse-Grained Molecular Dynamics Study

Investigating soil organic matter's (SOM) microscale assembly and functionality is challenging due to its complexity. This study constructs comparatively realistic SOM models, including diverse components such as Leonardite humic acid (LHA), lipids, peptides, carbohydrates, and lignin, to unveil their spontaneous self-assembly behavior at the mesoscopic scale through microsecond coarse-grained molecular dynamics simulations. We discovered an ordered SOM aggregation creating a layered phase from its hydrophobic core to the aqueous phase, resulting in an increasing O/C ratio and declining structural amphiphilicity. Notably, the amphiphilic lipids formed a bilayer membrane, partnering with lignin to constitute SOM's hydrophobic core. LHA, despite forming a layer, was embedded within this structure. The formation of such complex architectures was driven by nonbonded interactions between components. Our analysis revealed component-dependent diffusion effects within the SOM system. Lipids, peptides, and lignin showed inhibitory effects on self-diffusion, while carbohydrates facilitated diffusion. This study offers novel insights into the dynamic behavior and assembly of SOM components, introducing an effective approach for studying dynamic SOM mechanisms in aquatic environments.

New approach to soil management focusing on soil health and air quality: one earth one life (critical review)

Soil plays a key role in ecosphere and air quality regulation. Obsolete environmental technologies lead to soil quality loss, air, water, and land systems pollution. Pedosphere and plants are intertwined with the air quality. Ionized O2 is capable to intensify atmosphere turbulence, providing particulate matter (PM2.5) coalescence and dry deposition. Addressing environmental quality, a Biogeosystem Technique (BGT*) heuristic transcendental (nonstandard and not direct imitation of nature) methodology has been developed. A BGT* main focus is an enrichment of Earth's biogeochemical cycles through land use and air cleaning. An intra-soil processing, which provides the soil multilevel architecture, is one of the BGT* ingredients. A next BGT* implementation is intra-soil pulse continuously discrete watering for optimal soil water regime and freshwater saving up to 10-20 times. The BGT* comprises intra-soil dispersed environmentally safe recycling of the PM sediments, heavy metals (HMs) and other pollutants, controlling biofilm-mediated microbial community interactions in the soil. This provides abundant biogeochemical cycle formation and better functioning of the humic substances, biological preparation, and microbial biofilms as a soil-biological starter, ensuring priority plants and trees nutrition, growth and resistance to phytopathogens. A higher underground and aboveground soil biological product increases a reversible C biological sequestration from the atmosphere. An additional light O2 ions photosynthetic production ensures a PM2.5 and PM0.1 coalescence and strengthens an intra-soil transformation of PM sediments into nutrients and improves atmosphere quality. The BGT* provides PM and HMs intra-soil passivation, increases soil biological productivity, stabilizes a climate system of the earth and promotes a green circular economy.

HR-MAS DREAMTIME NMR for Slow Spinning ex Vivo and in Vivo Samples

HR-MAS NMR is a powerful tool, capable of monitoring molecular changes in intact heterogeneous samples. However, one of the biggest limitations of 1H NMR is its narrow spectral width which leads to considerable overlap in complex natural samples. DREAMTIME NMR is a highly selective technique that allows users to isolate suites of metabolites from congested spectra. This permits targeted metabolomics by NMR and is ideal for monitoring specific processes. To date, DREAMTIME has only been employed in solution-state NMR, here it is adapted for HR-MAS applications. At high spinning speeds (>5 kHz), DREAMTIME works with minimal modifications. However, spinning over 3-4 kHz leads to cell lysis, and if maintaining sample integrity is necessary, slower spinning (<2.5 kHz) is required. Very slow spinning (≤500 Hz) is advantageous for in vivo analysis to increase organism survival; however, sidebands from water pose a problem. To address this, a version of DREAMTIME, termed DREAMTIME-SLOWMAS, is introduced. Both techniques are compared at 2500, 500, and 50 Hz, using ex vivo worm tissue. Following this, DREAMTIME-SLOWMAS is applied to monitor key metabolites of anoxic stress in living shrimp at 500 Hz. Thus, standard DREAMTIME works well under MAS conditions and is recommended for samples reswollen in D2O or spun >2500 Hz. For slow spinning in vivo or intact tissue samples, DREAMTIME-SLOWMAS provides an excellent way to target process-specific metabolites while maintaining sample integrity. Overall, DREAMTIME should find widespread application wherever targeted molecular information is required from complex samples with a high degree of spectral overlap.

Bioactivity profile of dissolved organic matter and its relation to molecular composition

Dissolved organic matter (DOM) occupies a huge and uncharted molecular space. Given its properties, DOM can be presented as a promising biotechnological resource. However, research into bioactivities of DOM is still in early stages. In this study, the biotechnological potential of terrestrial and marine DOM, its molecular composition and their relationships are investigated. Samples were screened for their in vitro antibacterial, antifungal, anticancer and antioxidant activities. Antibacterial activity was detected against Staphylococcus aureus in almost all DOM samples, with freshwater DOM showing the lowest IC50 values. Most samples also inhibited Staphylococcus epidermidis, and four DOM extracts showed up to fourfold higher potency than the reference drug. Antifungal activity was limited to only porewater DOM towards human dermatophyte Trichophyton rubrum. No significant in vitro anticancer activity was observed. Low antioxidant potential was exerted. The molecular characterization by FT-ICR MS allowed a broad compositional overview. Three main distinguished groups have been identified by PCoA analyses. Antibacterial activities are related to high aromaticity content and highly-unsaturated molecular formulae (O-poor). Antifungal effect is correlated with highly-unsaturated molecular formulae (O-rich). Antioxidant activity is positively related to the presence of double bonds and polyphenols. This study evidenced for the first time antibacterial and antifungal activity in DOM with potential applications in cosmeceutical, pharmaceutical and aquaculture industry. The lack of cytotoxicity and the almost unlimited presence of this organic material may open new avenues in future marine bioprospecting efforts.

Cadmium Uptake From Soil by Ornamental Metallophytes: A Meta-analytical Approach

Soil pollution by cadmium (Cd) is a serious issue worldwide affecting environmental and human health. Conventional chemical and physical methods of treating contaminated soil are costly, time-consuming, and less effective. Phytoremediation using ornamental plants is a safe and effective method for the treatment of heavy metal-polluted soil due to their rapid growth and accumulation of biomass, high heavy metal tolerance, and non-edible nature. The present study is the first attempt for the meta-analysis of existing literature on Cd accumulation and translocation by ornamental plants. The uptake and transfer capacity of ornamental plants was measured using the bio-concentration factor (BCF) and translocation factor (TF). The results indicate that ornamental plants have varying Cd-absorption capacities. Among the 49 plant species identified from 31 articles, Helianthus annuus (BCF = 5.785), Impatiens glandulifera (BCF = 4.722), and Crassocephalum crepidioides (BCF = 3.623) represented higher accumulation capacity, whereas Rorippa globosa (TF = 1.653) and Sedum spectabile Boreau (TF = 1.579) represented significantly higher translocation capacity for Cd. The contribution of various environmental factors in influencing BCF was obtained through multiple linear regression analysis. Results showed that soil pH was the major factor influencing the BCF. To further explain the influence of four main factors that are soil pH, soil organic matter (SOM), cation exchange capacity (CEC), and soil Cd concentration on the accumulation efficiency of ornamental plants, a subgroup meta-analysis was performed. Results of the subgroup meta-analysis revealed that the BCF is negatively correlated with the soil pH and SOM, while the estimated limit of soil Cd concentration for growing ornamental plants was up to 50 mg/kg. Results of this study indicate that choosing a native hyperaccumulator is not the sole key to the success of a phytoremediation design, rather the conditions of the pedosphere will determine the regulating factor for efficient removal. In order to overcome the issue of recirculation and gradual release in the rhizosphere, it is important to match the type of hyperaccumulators to the soil environment (pH, CEC, SOM, etc.) to achieve maximum translocation and desired removal. This study will help researchers to pair the right plant with environmental conditions and customize more efficient phytoremediation systems.

Organic carbon accumulation and aggregate formation in soils under organic and inorganic fertilizer management practices in a rice-wheat cropping system

Soil organic carbon (C) and aggregates are the important components of soil fertility and the foundation of sustainable agriculture. The storage and protection of SOC in aggregates is widely regarded as the material basis of soil organic C accumulation. However, current understanding of soil aggregate and its associated organic C is insufficient to elucidate the regulation mechanism of soil organic C. A nine-year field experiment including chemical fertilizer (FR) and organic manure (OM) treatments was set up in the eastern plain of Funiu Mountain, central China. Using chemical analysis, physical sieving as well as nuclear magnetic resonance (NMR) methods, we mainly probed into the response of soil organic C concentration and composition, and C functional groups, water-stable aggregates to different treatments. Furthermore, scanning electronic microscopy (SEM) and partial least square structural equation modelling (PLS-SEM) was conducted to characterise the different size aggregates and to analyse the mechanism of soil organic C accumulation and stabilisation at aggregate scales. After nine years of farming, OM treatment substantially increased soil organic C content (by 3.77 g kg^-1) and significantly enhanced the formation of macro-aggregates (> 250 μm), while FR had no significant influence on soil organic C. At the aggregate scale, the amounts of soil organic C, C physical fractions (particulate and mineral-associated organic C), total nitrogen and microbial biomass carbon associated in macro-aggregates (> 250 μm) were obviously higher than that in micro-aggregates and silt + clay fraction, and OM treatment greatly increased the accumulation of soil organic C and its components in macro-aggregates. Moreover, microbial biomass carbon (MBC) amounts in aggregates were remarkably increased (27-116%) by the application of OM. And MBC had a positively effect on the physical fractions of SOC but not on the C chemical structure within aggregates. The present study indicated that soil organic C accumulation mainly rely on macro-aggregates (> 250 μm). Intra-particulate organic carbon (POC) and mineral-associated organic carbon (MOC) within macro-aggregates played an important role in soil organic C accumulation. Meanwhile, soil microbes were a driving force for the accumulation of soil organic C physical fractions (POC and MOC). We concluded that OM treatment accelerated the synergistic process between organic C sequestration and soil aggregation, and showed great potential to increase soil organic C accumulation.

SASSY NMR: Simultaneous Solid and Solution Spectroscopy

Synergism between different phases gives rise to chemical, biological or environmental reactivity, thus it is increasingly important to study samples intact. Here, SASSY (SimultAneous Solid and Solution spectroscopY) is introduced to simultaneously observe (and differentiate) all phases in multiphase samples using standard, solid-state NMR equipment. When monitoring processes, the traditional approach of studying solids and liquids sequentially, can lead to information in the non-observed phase being missed. SASSY solves this by observing the full range of materials, from crystalline solids, through gels, to pure liquids, at full sensitivity in every scan. Results are identical to running separate ¹³ C CP-MAS solid-state and ¹³ C solution-state experiments back-to-back but requires only a fraction of the spectrometer time. After its introduction, SASSY is applied to process monitoring and finally to detect all phases in a living freshwater shrimp. SASSY is simple to implement and thus should find application across all areas of research.

A new perspective on the photocatalytic action of titanium dioxide on phenol elucidated using comprehensive multiphase NMR

Comprehensive Multiphase NMR (CMP-NMR) is a recently developed technique capable of simultaneously observing different phases - solutions, gels, and solids - while providing the chemical specificity of traditional NMR. With this new tool, the heterogeneous photocatalysis of phenol by titanium dioxide (P25 TiO₂) is re-examined to gain information about the occurrence of reaction at different regions between the catalyst and the solution. It was found that the proportion of phenol in different phases changes over the course of the photodegradation period. The photocatalyst appears to preferentially degrade phenol molecules that are weakly associated with the surface, such that they have restricted mobility in a 'gel-like' state. Diffusion Ordered Spectroscopy (DOSY) corroborates the relative change in phenol signals between freely diffusing solution and diffusion restricted gels as measured using CMP-NMR. The surface of P25 TiO₂ was found to foul over the course of the 200-hour photodegradation period that was monitored using the solid-state capabilities of the CMP-NMR. Finally, CMP-NMR showed differences in the photodegradation of phenol by P25 TiO₂ to that of a TiO₂-nitrogen doped graphene quantum dot (NGQD) composite. With the latter composite, no fouling of the surface was seen over time. This application of CMP-NMR to the field of catalysis demonstrates its potential to better understand and study photocatalytic systems in general.

Speciation of heavy metals in soils and their immobilization at micro-scale interfaces among diverse soil components

Heavy metal (HM) pollution of soils is a globally important ecological and environmental problem. Previous studies have focused on i) tracking pollution sources in HM-contaminated soils, ii) exploring the adsorption capacity and distribution of HMs, and iii) assessing phyto-uptake of HMs and their ecotoxicity. However, few reviews have systematically summarized HM pollution in soil-plant systems over the past decade. Understanding the mechanisms of interaction between HMs and solid soil components is consequently key to effectively controlling and remediating HM pollution. However, the compositions of solid soil phases are diverse, their structures are complex, and their spatial arrangements are heterogeneous, all leading to the formation of soil micro-domains that exhibit different particle sizes and surface properties. The various soil components and their interactions ultimately control the speciation, transformation, and bioavailability of HMs in soils. Over the past few decades, the extensive application of advanced instrumental techniques and methods has greatly expanded our understanding of the behavior of HMs in organic mineral assemblages. In this review, studies investigating the immobilization of HMs by minerals, organic compounds, microorganisms, and their associated complexes are summarized, with a particular emphasis on the interfacial adsorption and immobilization of HMs. In addition, methods for analyzing the speciation and distribution of HMs in aggregates of natural soils with different particle sizes are also discussed. Moreover, we also review the methods for speciating HMs at mineral-organic micro-scale interfaces. Lastly, developmental prospects for HM research at inorganic-organic interfaces are outlined. In future research, the most advanced methods should be used to characterize the interfaces and in situ characteristics of metals and metal complexes. In particular, the roles and contributions of microorganisms in the immobilization of HMs at complex mineral-organic interfaces require significant further investigation.

NMR spectroscopy of wastewater: A review, case study, and future potential

NMR spectroscopy is arguably the most powerful tool for the study of molecular structures and interactions, and is increasingly being applied to environmental research, such as the study of wastewater. With over 97% of the planet's water being saltwater, and two thirds of freshwater being frozen in the ice caps and glaciers, there is a significant need to maintain and reuse the remaining 1%, which is a precious resource, critical to the sustainability of most life on Earth. Sanitation and reutilization of wastewater is an important method of water conservation, especially in arid regions, making the understanding of wastewater itself, and of its treatment processes, a highly relevant area of environmental research. Here, the benefits, challenges and subtleties of using NMR spectroscopy for the analysis of wastewater are considered. First, the techniques available to overcome the specific challenges arising from the nature of wastewater (which is a complex and dilute matrix), including an examination of sample preparation and NMR techniques (such as solvent suppression), in both the solid and solution states, are discussed. Then, the arsenal of available NMR techniques for both structure elucidation (e.g., heteronuclear, multidimensional NMR, homonuclear scalar coupling-based experiments) and the study of intermolecular interactions (e.g., diffusion, nuclear Overhauser and saturation transfer-based techniques) in wastewater are examined. Examples of wastewater NMR studies from the literature are reviewed and potential areas for future research are identified. Organized by nucleus, this review includes the common heteronuclei (¹³C, ¹⁵N, ¹⁹F, ³¹P, ²⁹Si) as well as other environmentally relevant nuclei and metals such as ²⁷Al, ⁵¹V, ²⁰⁷Pb and ¹¹³Cd, among others. Further, the potential of additional NMR methods such as comprehensive multiphase NMR, NMR microscopy and hyphenated techniques (for example, LC-SPE-NMR-MS) for advancing the current understanding of wastewater are discussed. In addition, a case study that combines natural abundance (i.e. non-concentrated), targeted and non-targeted NMR to characterize wastewater, along with in vivo based NMR to understand its toxicity, is included. The study demonstrates that, when applied comprehensively, NMR can provide unique insights into not just the structure, but also potential impacts, of wastewater and wastewater treatment processes. Finally, low-field NMR, which holds considerable future potential for on-site wastewater monitoring, is briefly discussed. In summary, NMR spectroscopy is one of the most versatile tools in modern science, with abilities to study all phases (gases, liquids, gels and solids), chemical structures, interactions, interfaces, toxicity and much more. The authors hope this review will inspire more scientists to embrace NMR, given its huge potential for both wastewater analysis in particular and environmental research in general.

A meta-analysis about the accumulation of heavy metals uptake by Sedum alfredii and Sedum plumbizincicola in contaminated soil

Sedum alfredii and Sedum plumbizincicola typically have high heavy metal (such as Zn and Cd) accumulation capacities with fast growth rates and relatively high Pb tolerance in contaminated soils. We compared the accumulation characteristics of heavy metals in Sedum species through meta-analysis. Furthermore, we analyzed the effects of soil organic matter (SOM) and soil pH on Cd, Pb and Zn accumulation by S. alfredii and S. plumbizincicola and the correlation between various metals. Results showed that the accumulations of Cd and Zn in shoots were higher than that of roots, but Pb accumulated in roots more than shoots. Moreover, there is a significant positive correlation between the accumulation of Zn and Cd in shoots. We found that the heavy metal accumulation rate in shoots was higher with lower soil pH. Sedum species had the highest Cd adsorption capacity in 20-30 g/kg SOM and the highest Zn adsorption capacity in SOM less than 20 g/kg. The accumulation rate of Cd in shoots of S. plumbizincicola was increased with exposure time, while the accumulation rate of Zn was slightly decreased.

Carbon Budget and Molecular Structure of Natural Organic Matter in Bank Infiltrated Groundwater

Managed aquifer recharge (MAR) provides means to remove natural organic matter (NOM) from surface waters. Recent studies have explored the degree of NOM removal in groundwater. In this study, we further elaborate the NOM removal at a lakeside natural bank infiltration site that functions as a surrogate for MAR. Our objective was to quantify the carbon budget in the aquifer based on concentration measurements of dissolved (in)organic carbon, and the molecular changes in NOM using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). According to the carbon budget, only 25% of the dissolved carbon entering the aquifer was organic, and it predominantly originated from lake water. Of the inorganic majority, on average 40% was produced in the vadose zone above the groundwater table, 31% in the lake bank, 22% in the aquifer as a result of degrading organic matter of lake water, and 7% in the lake. Seasonal concentration variations suggested that the lake bank was the main carbon source in the summer, increasing the carbon concentration of infiltrating lake water, that is, 3.0 mg/L to 7.9 mg/L. FT-ICR MS results showed 4960 to 5330 individual compounds in lake and groundwater. NOM removal in the aquifer was selective: the relative abundance of oxygen-containing species decreased from 75 to 31%, while the relative abundance of sulfur-containing species increased from 15 to 57%. The average molecular weights of both species remained unchanged. The study highlighted the role of lake bank processes and sulfur-containing species in groundwater quality.

Soil Organic Matter Characterization by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR MS): A Critical Review of Sample Preparation, Analysis, and Data Interpretation

The biogeochemical cycling of soil organic matter (SOM) plays a central role in regulating soil health, water quality, carbon storage, and greenhouse gas emissions. Thus, many studies have been conducted to reveal how anthropogenic and climate variables affect carbon sequestration and nutrient cycling. Among the analytical techniques used to better understand the speciation and transformation of SOM, Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) is the only technique that has sufficient mass resolving power to separate and accurately assign elemental compositions to individual SOM molecules. The global increase in the application of FTICR MS to address SOM complexity has highlighted the many challenges and opportunities associated with SOM sample preparation, FTICR MS analysis, and mass spectral interpretation. Here, we provide a critical review of recent strategies for SOM characterization by FTICR MS with emphasis on SOM sample collection, preparation, analysis, and data interpretation. Data processing and visualization methods are presented with suggested workflows that detail the considerations needed for the application of molecular information derived from FTICR MS. Finally, we highlight current research gaps, biases, and future directions needed to improve our understanding of organic matter chemistry and cycling within terrestrial ecosystems.

Comprehensive Multiphase NMR Probehead with Reduced Radiofrequency Heating Improves the Analysis of Living Organisms and Heat-Sensitive Samples

Comprehensive multiphase (CMP) NMR, first described in 2012, combines all of the hardware components necessary to analyze all phases (solid, gel, and solution) in samples in their natural state. In combination with spectral editing experiments, it can fully differentiate phases and study the transfer of chemical species across and between phases, providing unprecedented molecular-level information in unaltered natural systems. However, many natural samples, such as swollen soils, plants, and small organisms, contain water, salts, and ionic compounds, making them electrically lossy and susceptible to RF heating, especially when using high-strength RF fields required to select the solid domains. While dedicated reduced-heating probes have been developed for solid-state NMR, to date, all CMP-NMR probes have been based on solenoid designs, which can lead to problematic sample heating. Here, a new prototype CMP probe was developed, incorporating a loop gap resonator (LGR) for decoupling. Temperature increases are monitored in salt solutions analogous to those in small aquatic organisms and then tested in vivo on Hyalella azteca (freshwater shrimp). In the standard CMP probe (solenoid), 80% of organisms died within 4 h under high-power decoupling, while in the LGR design, all organisms survived the entire test period of 12 h. The LGR design reduced heating by a factor of ∼3, which allowed 100 kHz decoupling to be applied to salty samples with generally ≤10 °C sample heating. In addition to expanding the potential for in vivo research, the ability to apply uncompromised high-power decoupling could be beneficial for multiphase samples containing true crystalline solids that require the strongest possible decoupling fields for optimal detection.

Expanding current applications and permitting the analysis of larger intact samples by means of a 7 mm CMP-NMR probe

Comprehensive multiphase NMR combines the ability to study and differentiate all phases (solids, gels, and liquids) using a single NMR probe. The general goal of CMP-NMR is to study intact environmental and biological samples to better understand conformation, organization, association, and transfer between and across phases/interfaces that may be lost with conventional sample preparation such as drying or solubilization. To date, all CMP-NMR studies have used 4 mm probes and rotors. Here, a larger 7 mm probehead is introduced which provides ∼3 times the volume and ∼2.4 times the signal over a 4 mm version. This offers two main advantages: (1) the additional biomass reduces experiment time, making 13C detection at natural abundance more feasible; (2) it allows the analysis of larger samples that cannot fit within a 4 mm rotor. Chicken heart tissue and Hyalella azteca (freshwater shrimp) are used to demonstrate that phase-based spectral editing works with 7 mm rotors and that the additional biomass from the larger volumes allows detection with 13C at natural abundance. Additionally, a whole pomegranate seed berry (aril) and an intact softgel capsule of hydroxyzine hydrochloride are used to demonstrate the analysis of samples too large to fit inside a conventional 4 mm CMP probe. The 7 mm version introduced here extends the range of applications and sample types that can be studied and is recommended when 4 mm CMP probes cannot provide adequate signal-to-noise (S/N), or intact samples are simply too big for 4 mm rotors.

Assessment of Aqueous Extraction Methods on Extractable Organic Matter and Hydrophobic/Hydrophilic Fractions of Virgin Forest Soils

The assessment of water-extractable organic matter using an autoclave can provide useful information on physical, chemical, and biological changes within the soil. The present study used virgin forest soils from Chini Forest Reserve, Langkawi Island, and Kenyir Forest Reserve (Malaysia), extracted using different extraction methods. The dissolved organic carbon (DOC), total dissolved nitrogen (TDN), total dissolved phosphorus (TDP), and ammonium-nitrate content were higher in the autoclave treatments, up to 3.0, 1.3, 1.2, and 1.4 times more than by natural extraction (extracted for 24 h at room temperature). Overall, the highest extractable DOC, TDN, TDP, ammonium and nitrate could be seen under autoclaved conditions 121 °C 2×, up to 146.74 mg C/L, 8.97 mg N/L, 0.23 mg P/L, 5.43 mg N mg/L and 3.47 N mg/L, respectively. The soil extracts became slightly acidic with a higher temperature and longer duration. Similar trends were observed in the humic and nonhumic substances, where different types of soil extract treatments influenced the concentrations of the fractions. Different soil extraction methods can provide further details, thus widening the application of soil extracts, especially in microbes.

Solution-state NMR evaluation of molecular interaction between monoaromatic carboxylic acids and dissolved humic acid

Understanding the nature of interactions between the aromatic organic pollutants with dissolved humic acid (HA) is fundamental for the prediction of their environmental fate and subsequent development of efficient remediation methods. The present study employs solution-state ¹H/¹⁹F NMR methods to investigate the non-covalent interaction between aqueous peat humic acid (Aldrich HA) and monoaromatic carboxylic acids (CA), viz., 2, 6 diflourobenzoic acid (DFBA) and its non-fluorinated analog, benzoic acid (BA). NMR self-diffusion measurement of HA protons confirmed micellar nature indicating possibility of encapsulation of small molecules through host-guest interaction. ¹⁹F-¹H and ¹H-¹H saturation transfer difference (STD) experiments reveal the mode of insertion of CA into HA superstructure. The strength of interaction has been evaluated by analyzing T₁/T₂ relaxation times and self-diffusion coefficients of CA as a function of HA concentration. Association constants extracted for CA-HA complexes from NMR diffusion experiments reflected that the association between DFBA-HA (2.34 mM^-1) is significantly higher than that of BA-HA (0.97 mM^-1). The experimental outcome reiterated that substitution of -H with halogen atoms (-F in specific) to aromatic ring plays a dominant role in modulating the strength of association and mode of insertion of organic pollutants into HA superstructure. The present study emphasizes that AHA can be a potential remediating agent for organic contaminants due to its superior binding affinity compared to less humified extracted HA (EHA) from Karwar, Rajasthan, India.

Supramolecular aggregation of colloidal natural organic matter masks priority pollutants released in water from peat soil

Natural organic matter (NOM) from Sphagnum peat soil is extracted in water and subjected to several investigations to obtain structural and conformational information. Data show that the extracted NOM is self-organized in colloidal aggregates of variable sizes (from nano to micro scales, depending on the solvent composition, i.e., ultrapure water, solutions with denaturing agents, acetone, ethanol). Aggregates are formed by highly heterogeneous classes of organic compounds. According to the results of nuclear magnetic resonance and fluorescence measurements, the three-dimensional structure of aggregates, revealed by scanning electron microscope imaging, is supposed to be stabilized by the exposition of polar functional groups to the solvent, with consequent formation of hydrogen bonds, dipole-interactions and cation bridging. In contrast, the inner part of the aggregates displays hydrophobic features and is hypothesized to be further reinforced by the establishment of π-stacking interactions. The structure is assumed to be a supramolecular aggregation of small-medium oligomeric fragments (Max 750 Da) in which priority pollutants are entrapped by dispersive forces. The structures are shown to be nanosized spheroidal particles further aggregated to form higher dimension supra-structures. Carbohydrates play primary role, stabilizing the structure and giving marked hydrophilic properties to the aggregates.

Organic compounds alter the preference and rates of heavy metal adsorption on ferrihydrite

The availability of heavy metals in terrestrial environments is largely controlled by their interactions with minerals and organic matter, with iron minerals having a particularly strong role in heavy metal fate. Because soil organic matter contains a variety of compounds that differ in their chemical properties, the underlying impact organic matter-soil mineral associations bestow on heavy metal binding is still unresolved. Here, we systematically examine the binding of Cd, Zn and Ni by a suite of organic-ferrihydrite assemblages, chosen to account for various compound chemistries within soil organic matter. We posited that organic compound functionality would dictate the extent of association with the organic-ferrihydrite assemblages. Increased heavy metal binding to the assemblages was observed and attributed to the introduction of additional binding sites by the organic functional groups with differing metal affinities. The relative increase depended on the metal's Lewis acidity and followed the order Cd > Zn > Ni, whereas the reverse order was obtained for metal binding by pristine ferrihydrite (Ni > Zn > Cd). Citric acid-, aspartic acid- and cysteine-ferrihydrite assemblages also enhanced the metal binding rate. X-ray absorption spectroscopy revealed that the organic coating contributed significantly to Zn binding by the assemblages, despite relatively low organic surface coverage. Our findings provide valuable information on the nature of heavy metal-organic-mineral interactions and metal adsorption processes regulating their bioavailability and transport.

Identification of Organic Matter Dispersions Based on Light Scattering Matrices Focusing on Soil Organic Matter Management

The origin of organic matter, its spread, scattering, and functioning are influenced by the physical structure of liquid or dispersed media of organic matter. Refractive indices of fodder yeast grown on paraffin oil (paprin) and natural gas (gaprin) as well as Lycoperdon spore and organelles were measured by laser phase microscopy. The scattering matrices of aqueous suspensions of paprin, gaprin, and Lycoperdon spores were measured using a laser polarimeter with the scattering angle ranging from 20 to 150°. The experimentally measured scattering matrices have been approximated by the weighted sum of theoretically calculated scattering matrices using the T-matrix code developed by Mishchenko. Most of the particle radii in the filtered fraction of paprin and gaprin were within the range of about 0.05-0.12 μm. Particle radii of the Lycoperdon spore suspension were within the range of 0.4-2.4 μm, which corresponded to both whole spores and their separate organelles. A possibility of identifying a suspension by its scattering matrices was shown for a small difference in the real parts of the refractive index in the example of paprin and gaprin. The measurements of the light scattering matrix showed that for a small size parameter of about 1, the identification of paprin and gaprin can be based only on a difference in the particle shape. Refractive index difference is manifested for the size parameter values higher than 3. An example of a suspension consisting of micron-sized spores and their submicron organelles shows high sensitivity of the scattering matrix to the composition of the dispersed material. The presented data and models help to extrapolate the results of the light scattering matrix study to a vast spectrum of media of organic matter origin and functioning. This study focused on the Biogeosystem Technique (BGT*) transcendental methodology to manage soil as an arena of biodegradation and organic synthesis. A BGT*-based robotic system for intra-soil pulse continuous-discrete water and matter supply directly into the dispersed-aggregated physical structure of the soil media was developed. The system enables transformation of soil into a stable highly productive organic chemical bioreactor for better controlled nanoparticle biomolecular interactions and adsorption by biological and mineral media. The scattering matrix measurement unit is supposed to be used in the robotic system as a diagnostic tool for the dispersion composition of soil organic components.

Vienna soil organic matter modeler 2 (VSOMM2)

Soil Organic Matter (SOM) plays an important role in several biogeochemical processes by directly affecting the microbial activity, soil aggregation, plant growth and carbon storage. Despite of its importance, our understanding of its composition and structure is still incomplete. Several experiments using elemental analysis, nuclear magnetic resonance (NMR) and mass spectrometry (MS) shed light on the structure of organic matter. In this context, the Vienna Soil-Organic-Matter Modeler (https://somm.boku.ac.at/) is a website that generates condensed phase computer models of Soil-Organic-Matter (SOM). Most of the data comes from standardized samples by the International Humic Substances Association (IHSS), which uses a specific methodology to extract organic compounds from soil, called humic substances. We have improved the modeler by increasing the pool of elemental units that compose our SOM molecules called building blocks, and also by implementing a genetic algorithm that increases the chemical and geometric diversity of the models. This allowed us to create models using the IHSS data as well as different types of soil. The webserver uses as an input principally the elemental and organic composition and offers input files needed to run molecular dynamic (MD) simulations of solvated and neutralized SOM within the framework of the GROMOS 54A7 forcefield and the GROMOS and GROMACS simulation packages.

Spectroscopic response of soil organic matter in mining area to Pb/Cd heavy metal interaction: A mirror of coherent structural variation

Understanding the interaction between heavy metals and soil organic matter (SOM) in mining area is important for the clarification of the environmental behaviors of heavy metals. In this work, the coherence of structural changes of SOM during interaction with Pb²⁺ and Cd²⁺ ions were examined by using UV-vis/fluorescence spectroscopy coupled with correlation analyses. The result showed that phenolic- and carboxylic-like groups of SOM were engaged in the complexation of heavy metals (Pb²⁺ and Cd²⁺) with SOM, resulting in the formation of highly conjugated macromolecules/aggregates and an increase in molecular weight/size. Fluorescent humic-like, fulvic-like, and protein-like species were involved in the binding with Pb²⁺/Cd²⁺ ions, which were closely correlated with phenolic-like and carboxylic-like constitutes. SOM was more favorable to bind with Pb²⁺ ions than Cd²⁺ ions, with a less susceptive of SOM structure to Pb²⁺/Cd²⁺ ions in the mining area compared to those off the mining area under heavy metal stress. These results may provide a new insight for the treatment and remediation of heavy metal-polluted soil in mining area.

Ex vivo Comprehensive Multiphase NMR of whole organisms: A complementary tool to in vivo NMR

Nuclear Magnetic Resonance (NMR) spectroscopy is a non-invasive analytical technique which allows for the study of intact samples. Comprehensive Multiphase NMR (CMP-NMR) combines techniques and hardware from solution state and solid state NMR to allow for the holistic analysis of all phases (i.e. solutions, gels and solids) in unaltered samples. This study is the first to apply CMP-NMR to deceased, intact organisms and uses ¹³C enriched Daphnia magna (water fleas) as an example. D. magna are commonly used model organisms for environmental toxicology studies. As primary consumers, they are responsible for the transfer of nutrients across trophic levels, and a decline in their population can potentially impact the entire freshwater aquatic ecosystem. Though in vivo research is the ultimate tool to understand an organism’s most biologically relevant state, studies are limited by conditions (i.e. oxygen requirements, limited experiment time and reduced spinning speed) required to keep the organisms alive, which can negatively impact the quality of the data collected. In comparison, ex vivo CMP-NMR is beneficial in that; organisms do not need oxygen (eliminating air holes in rotor caps and subsequent evaporation); samples can be spun faster, leading to improved spectral resolution; more biomass per sample can be analyzed; and experiments can be run for longer. In turn, higher quality ex vivo NMR, can provide more comprehensive NMR assignments, which in many cases could be transferred to better understand less resolved in vivo signals. This manuscript is divided into three sections: 1) multiphase spectral editing techniques, 2) detailed metabolic assignments of 2D NMR of ¹³C enriched D. magna and 3) multiphase biological changes over different life stages, ages and generations of D. magna. In summary, ex vivo CMP-NMR proves to be a very powerful approach to study whole organisms in a comprehensive manner and should provide very complementary information to in vivo based research.

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Comprehensive Multiphase NMR detects all phases (solid/liquid/gel) in whole samples.

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Deceased organisms are not subjected to the limitations of in vivo NMR studies.

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2D ex vivo NMR offer increased spectral resolution, improving metabolite assignment.

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Holistic analysis shows biological changes in D. magna over different life stages.

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Ex vivo NMR can be a complementary tool for in vivo NMR metabolomic studies.

In vivo comprehensive multiphase NMR

Traditionally, due to different hardware requirements, nuclear magnetic resonance (NMR) has developed as two separate fields: one dealing with solids, and one with solutions. Comprehensive multiphase (CMP) NMR combines all electronics and hardware (magic angle spinning [MAS], gradients, high power Radio Frequency (RF) handling, lock, susceptibility matching) into a universal probe that permits a comprehensive study of all phases (i.e., liquid, gel-like, semisolid, and solid), in intact samples. When applied in vivo, it provides unique insight into the wide array of bonds in a living system from the most mobile liquids (blood, fluids) through gels (muscle, tissues) to the most rigid (exoskeleton, shell). In this tutorial, the practical aspects of in vivo CMP NMR are discussed including: handling the organisms, rotor preparation, sample spinning, water suppression, editing experiments, and finishes with a brief look at the potential of other heteronuclei (² H, ¹⁵ N, ¹⁹ F, ³¹ P) for in vivo research. The tutorial is aimed as a general resource for researchers interested in developing and applying MAS-based approaches to living organisms. Although the focus here is CMP NMR, many of the approaches can be adapted (or directly applied) using conventional high-resolution magic angle spinning, and in some cases, even standard solid-state NMR probes.

"-Omics" workflow for paleolimnological and geological archives: A review

"-Omics" is a powerful screening method with applications in molecular biology, toxicology, wildlife biology, natural product discovery, and many other fields. Genomics, proteomics, metabolomics, and lipidomics are common examples included under the "-omics" umbrella. This screening method uses combinations of untargeted, semi-targeted, and targeted analyses paired with data mining to facilitate researchers' understanding of the genome, proteins, and small organic molecules in biological systems. Recently, however, the use of "-omics" has expanded into the fields of geology, specifically petrology, and paleolimnology. Specifically, untargeted analyses stand to transform these fields as petroleomics, and sediment-"omics" become more prevalent. "-Omics" facilitates the visualization of small molecule profiles from environmental matrices (i.e. oil and sediment). Small molecule profiles can provide improved understanding of small molecules distributions throughout the environment, and how those compositions can change depending on conditions (i.e. climate change, weathering, etc.). "-Omics" also facilities discovery of next-generation biomarkers that can be used for oil source identification and as proxies for reconstructing past environmental changes. Untargeted analyses paired with data mining and multivariate statistical analyses represents a powerful suite of tools for hypothesis generation, and new method development for environmental reconstructions. Here we present an introduction to "-omics" methodology, technical terms, and examples of applications to paleolimnology and petrology. The purpose of this review is to highlight the important considerations at each step in the "-omics" workflow to produce high quality and statistically powerful data for petrological and paleolimnological applications.

Humic Substances Extracted by Alkali Are Invalid Proxies for the Dynamics and Functions of Organic Matter in Terrestrial and Aquatic Ecosystems

The conceptual rigor of using organic materials extracted from soil by alkali, called , as proxies for soil organic matter has been questioned for almost 180 years. However, the humic substances paradigm, i.e., the understanding that alkali-extracted humic substances are newly synthesized materials with unique properties that are distinct from non-humic organic matter, continues to be propagated throughout the literature. Here, we revisit the mechanistic background of the extraction process to show that alkaline extraction is unable to discriminate for the chemical history of a compound. For this reason, alkaline extraction cannot distinguish between (i) materials that have undergone secondary synthesis or humification ("humic" substances), and (ii) materials that are decorated with ionizable functional groups for other reasons, such as oxidative depolymerization ("non-humic" substances). While this mechanistic consideration alone renders invalid a distinction between humic substances and non-humic substances based on alkaline extraction, we further show that the evidence available to date does not support the assumption that processes of secondary synthesis create quantitatively significant proportions of "chemically reactive, yet recalcitrant" materials in natural environments. Any definition of humic substances that invokes both alkaline extraction and secondary synthesis is thus flawed on at least two accounts: (i) alkaline extraction is unable to achieve its purpose of separating humic from non-humic substances, and (ii) the assertion that the extracted materials have unique molecular properties as a consequence of secondary synthesis cannot be proven because alkaline extraction cannot separate materials created by secondary synthesis from other, ionizable organic compounds. Finally, we point out that since the definition of humic substances is tied to the alkaline-extraction procedure, neither the existence of operationally defined humic substances in the environment nor their chemical integrity during the course of alkaline extraction can be independently verified. We conclude that organic materials extracted by alkali require appropriate nomenclature and rigorous definition to merit consideration in teaching, research, and application.

In-Vivo NMR Spectroscopy: A Powerful and Complimentary Tool for Understanding Environmental Toxicity

Part review, part perspective, this article examines the applications and potential of in-vivo Nuclear Magnetic Resonance (NMR) for understanding environmental toxicity. In-vivo NMR can be applied in high field NMR spectrometers using either magic angle spinning based approaches, or flow systems. Solution-state NMR in combination with a flow system provides a low stress approach to monitor dissolved metabolites, while magic angle spinning NMR allows the detection of all components (solutions, gels and solids), albeit with additional stress caused by the rapid sample spinning. With in-vivo NMR it is possible to use the same organisms for control and exposure studies (controls are the same organisms prior to exposure inside the NMR). As such individual variability can be reduced while continual data collection over time provides the temporal resolution required to discern complex interconnected response pathways. When multidimensional NMR is combined with isotopic labelling, a wide range of metabolites can be identified in-vivo providing a unique window into the living metabolome that is highly complementary to more traditional metabolomics studies employing extracts, tissues, or biofluids.

Strontium adsorption and desorption in wetlands: Role of organic matter functional groups and environmental implications

Strontium (Sr) is a chemical element that is often used as a tracer in hydrogeochemical studies, and is ubiquitously distributed as a radioactive contaminant in nuclear sites in the form of strontium-90 (Sr-90). At the interface between groundwater and surface water, wetlands possess unique hydrogeochemical properties whose impact on Sr transport has not been investigated thoroughly. In this study, the adsorption and desorption of Sr was investigated on six natural wetland substrates and two mixes of exogenous media and wetland sediment: winter and summer wetland sediments, decayed cattails, wood, leaf litter, moss, bone charcoal, and clinoptilolite. The composition of the organic matter was characterized using carbon-13, solid phase Nuclear Magnetic Resonance analysis. The range of the substrates' adsorption coefficients obtained could be explained by factors indicative of proteins in the organic matter, which were shown to support strong and poorly reversible Sr adsorption. In contrast, the proportion of carbohydrates and lignin were found to be indicative of lower adsorption coefficients and higher desorption. The implications of these results for Sr pollution remediation in wetlands are discussed.

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.

Residual hydrophobic organic contaminants in soil: Are they a barrier to risk-based approaches for managing contaminated land?

Risk-based approaches to managing contaminated land, rather than approaches based on complete contaminant removal, have gained acceptance as they are likely to be more feasible and cost effective. Risk-based approaches aim to minimise risks of exposure of a specified contaminant to humans. However, adopting a risk-based approach over alternative overly-conservative approaches requires that associated uncertainties in decision making are understood and minimised. Irrespective of the nature of contaminants, a critical uncertainty is whether there are potential risks associated with exposure to the residual contaminant fractions in soil to humans and other ecological receptors, and how they should be considered in the risk assessment process. This review focusing on hydrophobic organic contaminants (HOCs), especially polycyclic aromatic hydrocarbons (PAHs), suggests that there is significant uncertainty on the residual fractions of contaminants from risk perspectives. This is because very few studies have focused on understanding the desorption behaviour of HOCs, with few or no studies considering the influence of exposure-specific factors. In particular, it is not clear whether the exposure of soil-associated HOCs to gastrointestinal fluids and enzyme processes release bound residues. Although, in vitro models have been used to predict PAH bioaccessibility, and chemical extractions have been used to determine residual fractions in various soils, there are still doubts about what is actually being measured. Therefore it is not certain which bioaccessibility method currently represents the best choice, or provides the best estimate, of in vivo PAH bioavailability. It is suggested that the fate and behaviour of HOCs in a wide range of soils, and that consider exposure-specific scenarios, be investigated. Exposure-specific scenarios are important for validation purposes, which may be useful for the development of standardised methods and procedures for HOC bioaccessibility determinations. Research is needed to propose the most appropriate testing methods and for assessing potential risks posed by residual fractions of HOCs. Such investigations may be useful for minimising uncertainties associated with a risk-based approach, so that consideration may then be given to its adoption on a global scale. This review critically appraises existing information on the bioavailability of HOC residues in soil to establish whether there may be risks from highly sequestered contaminant residues.