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

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

Beyond bulk: Density fractions explain heterogeneity in global soil carbon abundance and persistence.

Understanding the controls on the amount and persistence of soil organic carbon (C) is essential for predicting its sensitivity to global change. The response may depend on whether C is unprotected, isolated within aggregates, or protected from decomposition by mineral associations. Here, we present a global synthesis of the relative influence of environmental factors on soil organic C partitioning among pools, abundance in each pool (mg C g-1  soil), and persistence (as approximated by radiocarbon abundance) in relatively unprotected particulate and protected mineral-bound pools. We show that C within particulate and mineral-associated pools consistently differed from one another in degree of persistence and relationship to environmental factors. Soil depth was the best predictor of C abundance and persistence, though it accounted for more variance in persistence. Persistence of all C pools decreased with increasing mean annual temperature (MAT) throughout the soil profile, whereas persistence increased with increasing wetness index (MAP/PET) in subsurface soils (30-176 cm). The relationship of C abundance (mg C g-1  soil) to climate varied among pools and with depth. Mineral-associated C in surface soils (<30 cm) increased more strongly with increasing wetness index than the free particulate C, but both pools showed attenuated responses to the wetness index at depth. Overall, these relationships suggest a strong influence of climate on soil C properties, and a potential loss of soil C from protected pools in areas with decreasing wetness. Relative persistence and abundance of C pools varied significantly among land cover types and soil parent material lithologies. This variability in each pool's relationship to environmental factors suggests that not all soil organic C is equally vulnerable to global change. Therefore, projections of future soil organic C based on patterns and responses of bulk soil organic C may be misleading.

Redox Properties of Pyrogenic Dissolved Organic Matter (pyDOM) from Biomass-Derived Chars.

Chars are ubiquitous in the environment and release significant amounts of redox-active pyrogenic dissolved organic matter (pyDOM). Yet, the redox properties of pyDOM remain poorly characterized. This work provides a systematic assessment of the quantity and redox properties of pyDOM released at circumneutral pH from a total of 14 chars pyrolyzed from wood and grass feedstocks from 200 to 700 °C. The amount of released pyDOM decreased with increasing pyrolysis temperature of chars, reflecting the increasing degree of condensation and decreasing char polarity. Using flow-injection analysis coupled to electrochemical detection, we demonstrated that electron-donating capacities (EDCpyDOM; up to 6.5 mmole-·gC-1) were higher than electron-accepting capacities (EACpyDOM; up to 1.2 mmole-·gC-1) for all pyDOM specimens. The optical properties and low metal contents of the pyDOM implicate phenols and quinones as the major redox-active moieties. Oxidation of a selected pyDOM by the oxidative enzyme laccase resulted in a 1.57 mmole-·gC-1 decrease in EDCpyDOM and a 0.25 mmole-·gC-1 increase in EACpyDOM, demonstrating a largely irreversible oxidation of presumably phenolic moieties. Non-mediated electrochemical reduction of the same pyDOM resulted in a 0.17 mmole-·gC-1 increase in EDCpyDOM and a 0.24 mmole-·gC-1 decrease in EACpyDOM, consistent with the largely reversible reduction of quinone moieties. Our results imply that pyDOM is an important dissolved redox-active phase in the environment and requires consideration in assessing and modeling biogeochemical redox processes and pollutant redox transformations, particularly in char-rich environments.

Simple Plant and Microbial Exudates Destabilize Mineral-Associated Organic Matter via Multiple Pathways.

Most mineral-associated organic matter (MAOM) is protected against microbial attack, thereby contributing to long-term carbon storage in soils. However, the extent to which reactive compounds released by plants and microbes may destabilize MAOM and so enhance microbial access, as well as the underlying mechanisms, remain unclear. Here, we tested the ability of functionally distinct model exudates-ligands, reductants, and simple sugars-to promote microbial utilization of monomeric MAOM, bound via outer-sphere complexes to common iron and aluminum (hydr)oxide minerals. The strong ligand oxalic acid induced rapid MAOM mineralization, coinciding with greater sorption to and dissolution of minerals, suggestive of direct MAOM mobilization mechanisms. In contrast, the simple sugar glucose caused slower MAOM mineralization, but stimulated microbial activity and metabolite production, indicating an indirect microbially-mediated mechanism. Catechol, acting as reductant, promoted both mechanisms. While MAOM on ferrihydrite showed the greatest vulnerability to both direct and indirect mechanisms, MAOM on other (hydr)oxides was more susceptible to direct mechanisms. These findings suggest that MAOM persistence, and thus long-term carbon storage within a given soil, is not just a function of mineral reactivity but also depends on the capacity of plant roots and associated microbes to produce reactive compounds capable of triggering specific destabilization mechanisms.

Enzymes, Manganese, or Iron? Drivers of Oxidative Organic Matter Decomposition in Soils.

Oxidative decomposition of soil organic matter determines the proportion of carbon that is either stored or emitted to the atmosphere as CO2. Full conversion of organic matter to CO2 requires oxidative mechanisms that depolymerize complex molecules into smaller, soluble monomers that can be respired by microbes. Current models attribute oxidative depolymerization largely to the activity of extracellular enzymes. Here we show that reactive manganese (Mn) and iron (Fe) intermediates, rather than other measured soil characteristics, best predict oxidative activity in temperate forest soils. Combining bioassays, spectroscopy, and wet-chemical analysis, we found that oxidative activity in surface litters was most significantly correlated to the abundance of reactive Mn(III) species. In contrast, oxidative activity in underlying mineral soils was most significantly correlated to the abundance of reactive Fe(II/III) species. Positive controls showed that both Mn(III) and Fe(II/III) species are equally potent in generating oxidative activity, but imply conventional bioassays have a systematic bias toward Fe. Combined, our results highlight the coupled biotic-abiotic nature of oxidative mechanisms, with Mn-mediated oxidation dominating within Mn-rich organic soils and Fe-mediated oxidation dominating Fe-rich mineral soils. These findings suggest microbes rely on different oxidative strategies depending on the relative availability of Fe and Mn in a given soil environment.

Networking our science to characterize the state, vulnerabilities, and management opportunities of soil organic matter.

Soil organic matter (SOM) supports the Earth's ability to sustain terrestrial ecosystems, provide food and fiber, and retains the largest pool of actively cycling carbon. Over 75% of the soil organic carbon (SOC) in the top meter of soil is directly affected by human land use. Large land areas have lost SOC as a result of land use practices, yet there are compensatory opportunities to enhance productivity and SOC storage in degraded lands through improved management practices. Large areas with and without intentional management are also being subjected to rapid changes in climate, making many SOC stocks vulnerable to losses by decomposition or disturbance. In order to quantify potential SOC losses or sequestration at field, regional, and global scales, measurements for detecting changes in SOC are needed. Such measurements and soil-management best practices should be based on well established and emerging scientific understanding of processes of C stabilization and destabilization over various timescales, soil types, and spatial scales. As newly engaged members of the International Soil Carbon Network, we have identified gaps in data, modeling, and communication that underscore the need for an open, shared network to frame and guide the study of SOM and SOC and their management for sustained production and climate regulation.

Manganese-Driven Carbon Oxidation at Oxic-Anoxic Interfaces.

The formation of reactive manganese (Mn) species is emerging as a key regulator of carbon oxidation rates, and thus CO2 emissions, in soils and sediments. Many subsurface environments are characterized by steep oxygen gradients, forming oxic-anoxic interfaces that enable rapid redox cycling of Mn. Here, we examined the impact of Mn(II)aq oxidation along oxic-anoxic interfaces on carbon oxidation in soils using laboratory-based diffusion reactors. A combination of cyclic voltammetry, X-ray absorption spectroscopy, and X-ray microprobe imaging revealed a tight coupling between Mn(II)aq oxidation and carbon oxidation at the oxic-anoxic interface. Specifically, zones of Mn(II)aq oxidation across the oxic-anoxic transition also exhibited the greatest lignin oxidation potential, carbon solubilization, and oxidation. Microprobe imaging further revealed that the generation of Mn(III)-dominated precipitates coincided with carbon oxidation. Combined, our findings demonstrate that biotic Mn(II)aq oxidation, specifically the formation of Mn(III) species, contributes to carbon oxidation along oxic-anoxic interfaces in soils and sediments. Our results suggest that we should regard carbon oxidation not merely as a function of molecular composition, which insufficiently predicts rates, but in relation to microenvironments favoring the formation of critically important oxidants such as Mn(III).

Long-term litter decomposition controlled by manganese redox cycling.

Litter decomposition is a keystone ecosystem process impacting nutrient cycling and productivity, soil properties, and the terrestrial carbon (C) balance, but the factors regulating decomposition rate are still poorly understood. Traditional models assume that the rate is controlled by litter quality, relying on parameters such as lignin content as predictors. However, a strong correlation has been observed between the manganese (Mn) content of litter and decomposition rates across a variety of forest ecosystems. Here, we show that long-term litter decomposition in forest ecosystems is tightly coupled to Mn redox cycling. Over 7 years of litter decomposition, microbial transformation of litter was paralleled by variations in Mn oxidation state and concentration. A detailed chemical imaging analysis of the litter revealed that fungi recruit and redistribute unreactive Mn(2+) provided by fresh plant litter to produce oxidative Mn(3+) species at sites of active decay, with Mn eventually accumulating as insoluble Mn(3+/4+) oxides. Formation of reactive Mn(3+) species coincided with the generation of aromatic oxidation products, providing direct proof of the previously posited role of Mn(3+)-based oxidizers in the breakdown of litter. Our results suggest that the litter-decomposing machinery at our coniferous forest site depends on the ability of plants and microbes to supply, accumulate, and regenerate short-lived Mn(3+) species in the litter layer. This observation indicates that biogeochemical constraints on bioavailability, mobility, and reactivity of Mn in the plant-soil system may have a profound impact on litter decomposition rates.

3D spectral imaging with synchrotron Fourier transform infrared spectro-microtomography.

We report Fourier transform infrared spectro-microtomography, a nondestructive three-dimensional imaging approach that reveals the distribution of distinctive chemical compositions throughout an intact biological or materials sample. The method combines mid-infrared absorption contrast with computed tomographic data acquisition and reconstruction to enhance chemical and morphological localization by determining a complete infrared spectrum for every voxel (millions of spectra determined per sample).

Redox properties of plant biomass-derived black carbon (biochar).

Soils and sediments worldwide contain appreciable amounts of thermally altered organic matter (chars). Chars contain electroactive quinoid functional groups and polycondensed aromatic sheets that were recently shown to be of biogeochemical and envirotechnical relevance. However, so far no systematic investigation of the redox properties of chars formed under different pyrolysis conditions has been performed. Here, using mediated electrochemical analysis, we show that chars made from different feedstock and over a range of pyrolysis conditions are redox-active and reversibly accept and donate up to 2 mmol electrons per gram of char. The analysis of two thermosequences revealed that chars produced at intermediate to high heat treatment temperatures (HTTs) (400-700 °C) show the highest capacities to accept and donate electrons. Combined electrochemical, elemental, and spectroscopic analyses of the thermosequence chars provide evidence that the pool of redox-active moieties is dominated by electron-donating, phenolic moieties in the low-HTT chars, by newly formed electron accepting quinone moieties in intermediate-HTT chars, and by electron accepting quinones and possibly condensed aromatics in the high-HTT chars. We propose to consider chars in environmental engineering applications that require controlled electron transfer reactions. Electroactive char components may also contribute to the redox properties of traditionally defined "humic substances".

Synchrotron-based mass spectrometry to investigate the molecular properties of mineral-organic associations.

Soil organic matter (SOM) is important because its decay drives life processes in the biosphere. Analysis of organic compounds in geological systems is difficult because of their intimate association with mineral surfaces. To date there is no procedure capable of quantitatively separating organic from mineral phases without creating artifacts or mass loss. Therefore, analytical techniques that can (a) generate information about both organic and mineral phases simultaneously and (b) allow the examination of predetermined high-interest regions of the sample as opposed to conventional bulk analytical techniques are valuable. Laser desorption synchrotron postionization (synchrotron-LDPI) mass spectrometry is introduced as a novel analytical tool to characterize the molecular properties of organic compounds in mineral-organic samples from terrestrial systems, and it is demonstrated that, when combined with secondary ion mass spectrometry (SIMS), it can provide complementary information on mineral composition. Mass spectrometry along a decomposition gradient in density fractions verifies the consistency of our results with bulk analytical techniques. We further demonstrate that, by changing laser and photoionization energies, variations in molecular stability of organic compounds associated with mineral surfaces can be determined. The combination of synchrotron-LDPI and SIMS shows that the energetic conditions involved in desorption and ionization of organic matter may be a greater determinant of mass spectral signatures than the inherent molecular structure of the organic compounds investigated. The latter has implications for molecular models of natural organic matter that are based on mass spectrometric information.

Consider the Anoxic Microsite: Acknowledging and Appreciating Spatiotemporal Redox Heterogeneity in Soils and Sediments.

Reduction-oxidation (redox) reactions underlie essentially all biogeochemical cycles. Like most soil properties and processes, redox is spatiotemporally heterogeneous. However, unlike other soil features, redox heterogeneity has yet to be incorporated into mainstream conceptualizations of soil biogeochemistry. Anoxic microsites, the defining feature of redox heterogeneity in bulk oxic soils and sediments, are zones of oxygen depletion in otherwise oxic environments. In this review, we suggest that anoxic microsites represent a critical component of soil function and that appreciating anoxic microsites promises to advance our understanding of soil and sediment biogeochemistry. In sections 1 and 2, we define anoxic microsites and highlight their dynamic properties, specifically anoxic microsite distribution, redox gradient magnitude, and temporality. In section 3, we describe the influence of anoxic microsites on several key elemental cycles, organic carbon, nitrogen, iron, manganese, and sulfur. In section 4, we evaluate methods for identifying and characterizing anoxic microsites, and in section 5, we highlight past and current approaches to modeling anoxic microsites. Finally, in section 6, we suggest steps for incorporating anoxic microsites and redox heterogeneities more broadly into our understanding of soils and sediments.

Solvent-extractable polycyclic aromatic hydrocarbons in biochar: influence of pyrolysis temperature and feedstock.

Despite the increasing agricultural use of biochar as a way of combining the utilization of biomass for energy production with the removal of CO(2) from the atmosphere, it is not known how variations in pyrolysis temperature and feedstock type affect concentration and composition of polycyclic aromatic hydrocarbons (PAHs) that inevitably form and associate with biochar. To close this knowledge gap, we quantified 11 unsubstituted three- to five-ring PAHs as well as alkylated forms of phenanthrene and anthracene in grass and wood chars produced in 100 °C increments across a temperature range (100 to 700 °C). Our results show that solvent-extractable PAH concentrations in biochars produced at heat treatment temperatures (HTTs) of 400 and 500 °C greatly exceed those observed at higher and lower temperature, supporting a low HTT solid-phase formation mechanism operable at temperatures commonly used for industrial biochar production. The maximum extractable yield of 'pyrolytic' unsubstituted PAHs for grass (22 µg g(-1) at HTT = 500 °C) greatly exceeds the value for wood (5.9 µg g(-1)). Moreover, PAH signatures (e.g., total monomethylphenanthrene to phenanthrene ratios, MP/P ~2-3) at intermediate temperatures (400 °C) resemble those of fossil oils rather than that commonly attributed to pyrolytic products. Further research is needed to characterize the PAH evolution in modern pyrolysis reactors and assess the fate of biochar-bound PAHs in soils and sediments. Various commonly applied PAH ratios and indicator compounds show promise as markers for specific feedstock materials and pyrolysis conditions of biochars in environmental systems.

A holistic framework integrating plant-microbe-mineral regulation of soil bioavailable nitrogen.

Soil organic nitrogen (N) is a critical resource for plants and microbes, but the processes that govern its cycle are not well-described. To promote a holistic understanding of soil N dynamics, we need an integrated model that links soil organic matter (SOM) cycling to bioavailable N in both unmanaged and managed landscapes, including agroecosystems. We present a framework that unifies recent conceptual advances in our understanding of three critical steps in bioavailable N cycling: organic N (ON) depolymerization and solubilization; bioavailable N sorption and desorption on mineral surfaces; and microbial ON turnover including assimilation, mineralization, and the recycling of microbial products. Consideration of the balance between these processes provides insight into the sources, sinks, and flux rates of bioavailable N. By accounting for interactions among the biological, physical, and chemical controls over ON and its availability to plants and microbes, our conceptual model unifies complex mechanisms of ON transformation in a concrete conceptual framework that is amenable to experimental testing and translates into ideas for new management practices. This framework will allow researchers and practitioners to use common measurements of particulate organic matter (POM) and mineral-associated organic matter (MAOM) to design strategic organic N-cycle interventions that optimize ecosystem productivity and minimize environmental N loss. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10533-021-00793-9.

Soil exchange rates of COS and CO18O differ with the diversity of microbial communities and their carbonic anhydrase enzymes.

Differentiating the contributions of photosynthesis and respiration to the global carbon cycle is critical for improving predictive climate models. Carbonic anhydrase (CA) activity in leaves is responsible for the largest biosphere-atmosphere trace gas fluxes of carbonyl sulfide (COS) and the oxygen-18 isotopologue of carbon dioxide (CO18O) that both reflect gross photosynthetic rates. However, CA activity also occurs in soils and will be a source of uncertainty in the use of COS and CO18O as carbon cycle tracers until process-based constraints are improved. In this study, we measured COS and CO18O exchange rates and estimated the corresponding CA activity in soils from a range of biomes and land use types. Soil CA activity was not uniform for COS and CO2, and patterns of divergence were related to microbial community composition and CA gene expression patterns. In some cases, the same microbial taxa and CA classes catalyzed both COS and CO2 reactions in soil, but in other cases the specificity towards the two substrates differed markedly. CA activity for COS was related to fungal taxa and ß-D-CA expression, whereas CA activity for CO2 was related to algal and bacterial taxa and α-CA expression. This study integrates gas exchange measurements, enzyme activity models, and characterization of soil taxonomic and genetic diversity to build connections between CA activity and the soil microbiome. Importantly, our results identify kinetic parameters to represent soil CA activity during application of COS and CO18O as carbon cycle tracers.

Anaerobic microsites have an unaccounted role in soil carbon stabilization.

Soils represent the largest carbon reservoir within terrestrial ecosystems. The mechanisms controlling the amount of carbon stored and its feedback to the climate system, however, remain poorly resolved. Global carbon models assume that carbon cycling in upland soils is entirely driven by aerobic respiration; the impact of anaerobic microsites prevalent even within well-drained soils is missed within this conception. Here, we show that anaerobic microsites are important regulators of soil carbon persistence, shifting microbial metabolism to less efficient anaerobic respiration, and selectively protecting otherwise bioavailable, reduced organic compounds such as lipids and waxes from decomposition. Further, shifting from anaerobic to aerobic conditions leads to a 10-fold increase in volume-specific mineralization rate, illustrating the sensitivity of anaerobically protected carbon to disturbance. The vulnerability of anaerobically protected carbon to future climate or land use change thus constitutes a yet unrecognized soil carbon-climate feedback that should be incorporated into terrestrial ecosystem models.

Polar and aliphatic domains regulate sorption of phthalic acid esters (PAEs) to biochars.

Molecular variations among different biochar categories translate into differences in their ability to function as sorbents to three phthalic acid esters (PAEs) representing a gradient in hydrophobicity. The sorption capacity (K(OC)) for all three PAEs was the greatest for amorphous biochars (heat treatment temperature HTT=400 °C), followed by biochars produced at 300 °C, and was best explained by the hydrophobicity of the sorbate. Greater alkyl C content and higher polarity of grass chars versus wood chars prepared at similar temperatures explained both (a) the difference in sorbent strength between feedstocks and (b) the maximum in sorbent strength at relatively low HTTs (300-400 °C). Hydrophobic partitioning into 'soft' alkyl carbon and specific H-bonding involving char-bound O and N groups jointly account for high affinities of PAEs for low-HTT biochars. The results highlight the influence of feedstocks and HTTs on PAEs sorption strength and mechanism.

Sorption of fluorinated herbicides to plant biomass-derived biochars as a function of molecular structure.

Biochars produced at different heat treatment temperatures (HTT) are molecularly distinct and thus expected to show variable sorbent characteristics. We investigated the difference in sorption behavior of norflurazon (NORO) and fluridone (FLUN) to biochars from wood and grass feedstocks produced at different HTT. Amorphous biochars (HTT=400°C) exhibited the highest sorption parameter (K(OC)) for the two herbicides, emphasizing the importance of amorphous structural arrangement of aromatic moieties in these chars. Negative correlation between biochar aromaticity and isotherm nonlinearity (n) suggests that the n values were related mainly to total aromatic C content, not to that in the individual phases. Sorption of FLUN and NORO to low-temperature biochars (HTT=400°C) was about 1100 times and 6400 times greater, respectively, than a sediment sample, confirming that applications of low-temperature biochars to arable soils may reduce the mobility of FLUN and NORO, thus preventing unwanted herbicide leaching and subsequent contamination of sensitive water bodies.