Shifts in pore connectivity from precipitation versus groundwater rewetting increases soil carbon loss after drought

Colloid mobilization and transport in response to freeze-thaw cycles: Insights into the heavy metal(loid)s migration at a smelting site

Smelting sites often exhibit significant heavy metal(loid)s (HMs) contamination in the soil and groundwater, which are inevitably subjected to environmental disturbances. However, there is limited information available regarding the migration behaviors of HMs in a disturbed scenario. Thus, this work explored the migration of HMs-bearing colloids in response to freeze-thaw treatments by laboratory simulation and pore-scale study. Ultrafiltration results of soil effluents revealed that 61.5 %, 47.6 %, 68.0 %, and 59.2 % of Zn, Cd, Pb, and As were present in colloidal phase, and co-transported during treatments. Nanoparticle tracking analysis (NTA) further confirmed that freeze-thaw cycles were conducive to the generation of colloidal particles and showed the heteroagglomeration among different particles. Pore-network model (PNM) was used to quantify the soil macropore characteristics (macropore diameter, macropore number, coordination number, and Euler value) after treatments. It is evident that freeze-thaw cycles induced the formation of larger macropores while simultaneously enhancing macropore connectivity, thereby establishing an optimal pathway for colloid migration. These findings underscored the importance of environmental disturbances as a trigger for the release and migration of HMs in the smelting site, offering valuable insights for controlling HMs pollution. ENVIRONMENTAL IMPLICATION: The contaminated site has been subjected to prolonged environmental disturbances, causing the exacerbation of pollutants leaching and frequent occurrences of unstable pollution situations. This work explored the migration of HMs-bearing colloids in response to freeze-thaw treatments by laboratory simulation and pore-scale study. The distinct effects of freeze-thaw treatment on colloidal particle number concentration and macropore characteristics may explain the generation and migration of colloid-associated HMs driven by environmental disturbances. This work revealed the underlying mechanisms driving the redistribution of HMs under freeze-thaw cycles, offering valuable insights for risk assessment of soil and groundwater associated with HMs migration.

Composition and metabolism of microbial communities in soil pores

Delineation of microbial habitats within the soil matrix and characterization of their environments and metabolic processes are crucial to understand soil functioning, yet their experimental identification remains persistently limited. We combined single- and triple-energy X-ray computed microtomography with pore specific allocation of 13C labeled glucose and subsequent stable isotope probing to demonstrate how long-term disparities in vegetation history modify spatial distribution patterns of soil pore and particulate organic matter drivers of microbial habitats, and to probe bacterial communities populating such habitats. Here we show striking differences between large (30-150 µm Ø) and small (4-10 µm Ø) soil pores in (i) microbial diversity, composition, and life-strategies, (ii) responses to added substrate, (iii) metabolic pathways, and (iv) the processing and fate of labile C. We propose a microbial habitat classification concept based on biogeochemical mechanisms and localization of soil processes and also suggests interventions to mitigate the environmental consequences of agricultural management.

Field-scale assessment of direct and indirect effects of soil texture on organic matter mineralization during a dry summer

Soil texture plays a crucial role in organic matter (OM) mineralization through both direct interactions with minerals and indirect effects on soil moisture. Separating these effects could enhance the modelling of soil organic carbon (SOC) dynamics under climate change scenarios. However, the attempts have been limited small-scale experiments. Here, we studied the effects of soil texture on added OM mineralization in loamy sand, loam and silt loam soils in nine agricultural fields in Flanders, Belgium. Soil moisture, temperature, groundwater table depth and the mineralization of 13C-labeled ryegrass were monitored in buried mesocosms for approximately three months during a dry summer. Ryegrass-C mineralization was lowest in the loamy sand (39 ± 7 %) followed by silt loam (48 ± 7 %) and loam (63 ± 5 %) soils, challenging the current clay%-based moderation of C-mineralization rates in soil models. Soil temperature was not influenced by soil texture, whereas soil moisture was indeed dependent on soil texture. It appears that capillarity sustained upward water supply from groundwater to the topsoil in loam and silt loam soils but not in loamy sand soil, although this difference in capillary rise could not fully explain the higher moisture content in loam than that in silt loam soils. Additionally, soil texture only impacted remnant added ryegrass pieces (>500 μm) but not the finer ryegrass-derived SOC (<500 μm), which might point at the important indirect control of texture on OM mineralization during prolonged summer drought. However, these effects are only manifested during drought when no other factors (e.g., groundwater depth or subsurface water flows) exert an overriding impact on the soil water balance. Overall, our findings highlight the need to properly incorporate the indirect effects of soil texture on OM mineralization into soil carbon models to accurately predict soil C stocks under future climate change scenarios.

Nitrate with enriched heavy oxygen isotope linked to changes in nitrogen source and transformation as groundwater table rises

Nitrate is a significant constituent of the total nitrogen pool in shallow aquifers and poses an escalating threat to groundwater resources, making it crucial to comprehend the source, conversion, and elimination of nitrogen using appropriate techniques. Although dual-isotope dynamics in nitrate have been widely used, uncertainties remain regarding the asynchronously temporal changes in δ¹⁸O-NO₃^- and δ¹⁵N-NO₃^- observed in hypoxic aquifers. This study aimed to investigate changes in nitrogen sources and transformations using temporal changes in field-based NO₃^- isotopic composition, hydro-chemical variables, and environmental DNA profiling, as the groundwater table varied. The results showed that the larger enrichment in δ¹⁸O-NO₃^- (+13‰) compared with δ¹⁵N-NO₃^- (-2‰) on average during groundwater table rise was due to a combination of factors, including high ¹⁸O-based atmospheric N deposition, canopies nitrification, and soil nitrification transported vertically by rainfalls, and ¹⁸O-enriched O₂ produced through microbial and root respiration within denitrification. The strong association between functional gene abundance and nitrogen-related indicators suggests that anammox was actively processed with nitrification but in small bacterial population during groundwater table rise. Furthermore, bacterial species associated with nitrogen-associated gradients provided insight into subsurface nitrogen transformation, with Burkholderiaceae species and Pseudorhodobacter potentially serving as bioindicators of denitrification, while Candidatus Nitrotogn represents soil nitrification. Fluctuating groundwater tables can cause shifts in hydro-chemical and isotopic composition, which in turn can indicate changes in nitrogen sources and transformations. These changes can be used to improve input sources for mixture models and aid in microbial remediation of nitrate.

Molecular characteristics of natural organic matter in the groundwater system with geogenic iodine contamination in the Datong Basin, Northern China

Natural organic matter (NOM) plays an important role in the iodine mobilization in the groundwater system. In this study, the groundwater and sediments from iodine affected aquifers in the Datong Basin were collected to perform chemistry analysis and molecular characteristics of NOM by Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR-MS). Total iodine concentrations in groundwater and sediments ranged from 1.97 to 926.1 μg/L and 0.001-2.86 μg/g, respectively. A positive correlation was observed between DOC/NOM and groundwater/sediment iodine. FT-ICR-MS results showed that the DOM in the high-iodine groundwater system is characterized by less aliphatic and more aromatic compounds with higher NOSC, indicating the features of more unsaturated larger molecule structures and more bioavailability. Aromatic compounds could be the main carriers of sediment iodine and were easily absorbed on amorphous iron oxides to form the NOM-Fe-I complex. More aliphatic compounds, especially those containing N/S, experienced a higher degree of biodegradation, which further mediated the reductive dissolution of amorphous iron oxides and the transformation of iodine species, thereby causing the release of iodine into groundwater. The findings of this study provide some new insights into the mechanisms of high-iodine groundwater.

Microbial Drivers of Plant Performance during Drought Depend upon Community Composition and the Greater Soil Environment

The increasing occurrence of drought is a global challenge that threatens food security through direct impacts to both plants and their interacting soil microorganisms. Plant growth promoting microbes are increasingly being harnessed to improve plant performance under stress. However, the magnitude of microbiome impacts on both structural and physiological plant traits under water limited and water replete conditions are not well-characterized. Using two microbiomes sourced from a ponderosa pine forest and an agricultural field, we performed a greenhouse experiment that used a crossed design to test the individual and combined effects of the water availability and the soil microbiome composition on plant performance. Specifically, we studied the structural and leaf functional traits of maize that are relevant to drought tolerance. We further examined how microbial relationships with plant phenotypes varied under different combinations of microbial composition and water availability. We found that water availability and microbial composition affected plant structural traits. Surprisingly, they did not alter leaf function. Maize grown in the forest-soil microbiome produced larger plants under well-watered and water-limited conditions, compared to an agricultural soil community. Although leaf functional traits were not significantly different between the watering and microbiome treatments, the bacterial composition and abundance explained significant variability in both plant structure and leaf function within individual treatments, especially water-limited plants. Our results suggest that bacteria-plant interactions that promote plant performance under stress depend upon the greater community composition and the abiotic environment. IMPORTANCE Globally, drought is an increasingly common and severe stress that causes significant damage to agricultural and wild plants, thereby threatening food security. Despite growing evidence of the potential benefits of soil microorganisms on plant performance under stress, decoupling the effects of the microbiome composition versus the water availability on plant growth and performance remains a challenge. We used a highly controlled and replicated greenhouse experiment to understand the impacts of microbial community composition and water limitation on corn growth and drought-relevant functions. We found that both factors affected corn growth, and, interestingly, that individual microbial relationships with corn growth and leaf function were unique to specific watering/microbiome treatment combinations. This finding may help explain the inconsistent success of previously identified microbial inocula in improving plant performance in the face of drought, outside controlled environments.

Moisture-dependent response of soil carbon mineralization to temperature increases in a karst wetland on the Yunnan-Guizhou Plateau

Wetlands are facing gradual drying, leading to large carbon loss due to the transformation from anaerobic to aerobic conditions, but the temperature and drought effects from the temperature and moisture fluctuation on soil organic carbon (SOC) mineralization remain uncertain. An incubation study with three moisture levels (100%, 60%, and 40% WHC, marked as W100, W60, and W40, respectively) and four temperature levels (5, 10, 15, 20 °C, marked as T5, T10, T15, and T20, respectively) was conducted to determine the effect of temperature and moisture interactions on SOC mineralization in the karst wetland of the Yunnan-Guizhou Plateau. Compared with T5, the cumulative mineralization CO₂ in T20 increased by 83.18% (W40), 154.63% (W60), and 148.16% (W100), respectively. The mineralized CO₂ at W60 and W40 significantly decreased compared to that at W100 at the four temperature levels. Temperature, moisture and their interactions had significant positive effects on SOC mineralization rates and cumulative mineralized CO₂. The temperature sensitivity of SOC mineralization rates (Q₁₀) under W40 and W60 increased by 22.03% and 24.52%, respectively, compared to that under W100. The cumulative mineralized CO₂ was positively related to soil urease activity and negatively related to soil pH, N-NH₄⁺, SOM, and catalase activity. Temperature and moisture fluctuation and soil properties explained 85.40% of the variation in SOC mineralization, among which temperature and moisture fluctuation, soil properties, and their interactions explained 19.71%, 4.81%, and 60.88%, respectively. Our results indicated that SOC mineralization is influenced by the joint effect of temperature and drought, as well as their induced changes in soil properties, in which higher temperatures can increase soil CO₂ emissions by enhancing the SOC mineralization rate, but the positive effect may be weakened from the drying wetland.

Quantifying nitrous oxide production rates from nitrification and denitrification under various moisture conditions in agricultural soils: Laboratory study and literature synthesis

Biogenic nitrous oxide (N2O) from nitrification and denitrification in agricultural soils is a major source of N2O in the atmosphere, and its flux changes significantly with soil moisture condition. However, the quantitative relationship between N2O production from different pathways (i.e., nitrification vs. denitrification) and soil moisture content remains elusive, limiting our ability of predicting future agricultural N2O emissions under changing environment. This study quantified N2O production rates from nitrification and denitrification under various soil moisture conditions using laboratory incubation combined with literature synthesis. 15N labeling approach was used to differentiate the N2O production from nitrification and denitrification under eight different soil moisture contents ranging from 40 to 120% water-filled pore space (WFPS) in the laboratory study, while 80 groups of data from 17 studies across global agricultural soils were collected in the literature synthesis. Results showed that as soil moisture increased, N2O production rates of nitrification and denitrification first increased and then decreased, with the peak rates occurring between 80 and 95% WFPS. By contrast, the dominant N2O production pathway switched from nitrification to denitrification between 60 and 70% WFPS. Furthermore, the synthetic data elucidated that moisture content was the major driver controlling the relative contributions of nitrification and denitrification to N2O production, while NH4 + and NO3 - concentrations mainly determined the N2O production rates from each pathway. The moisture treatments with broad contents and narrow gradient were required to capture the comprehensive response of soil N2O production rate to moisture change, and the response is essential for accurately predicting N2O emission from agricultural soils under climate change scenarios.

Microbial community mediates hydroxyl radical production in soil slurries by iron redox transformation

The generation of reactive oxygen species (ROS) mediated by minerals and/or microorganisms plays a vital but underappreciated role in affecting carbon and nutrient cycles at soil-water interfaces. It is currently unknown which interactions between microbial communities and iron (Fe) minerals produce hydroxyl radical (HO^•), which is the strongest oxidant among ROS. Using a series of well-controlled anoxic incubations of soil slurries, we demonstrated that interactions between microbial communities and Fe minerals synergistically drove HO^• production (up to ∼100 nM after 21-day incubation). Microorganisms drove HO^• generation in anoxic environments predominantly by modulating iron redox transformation that was more prominent than direct production of ROS by microorganisms. Among the microbial communities, Geobacter, Paucimonas, Rhodocyclaceae_K82, and Desulfotomaculum were the key genera strongly affecting HO^• production. In manured soils, the former two species had higher abundances and were crucial for HO^• production. In contrast, the latter two species were mainly abundant and important in soils with mineral fertilizers. Our study suggests that abundant highly reactive oxidant HO^• can be generated in anoxic environments and the microbial community-mediated redox transformations of iron (oxyhydr)oxides may be responsible for the HO^• production. These findings shed light on the microbial generation of HO^• in fluctuating redox environments and on consequences for global C and nutrient cycling.

Warming and humidification mediated changes of DOM composition in an Alfisol

Dissolved organic matter (DOM) represents the most mobile and reactive pool of soil organic matter (SOM). Climate changes, such as global warming and altered precipitation exert considerable influences on the quality and quantity of soil DOM. However, rare reports have focused on the interactive effects of soil warming and increased precipitation. In the present study, we conducted a 90-day incubation experiment to investigate how the concentration, source and chemical composition of DOM from an Alfisol respond to the variations of temperatures (15, 30 and 45 °C) and moistures (40%, 60%, and 80% of saturated soil water content). Four DOM components were identified through fluorescence excitation emission matrix (EEM)-parallel factor analysis (PARAFAC). Increased temperature alone aggravated the decomposition of plant-derived aromatic components (C2 and C4) but promoted the accumulation of microbial-derived aliphatic carbon (C1) and tryptophan-like component (C3). Increased fungi/bacteria ratio with warming was responsible for the decomposition of plant-derived components. Warming-induced disassociation of Ca-bearing mineral to colloidal Ca facilitated the accrual of microbial-derived aliphatic DOM. Humidification alone and humidification + warming significantly increased the concentration of DOM and the percentage of plant-derived aromatic carbon (C2, C4), which was attributed to the release of Fe-bearing mineral-OC. Based on the above findings along with the results of two-way ANOVA and Variation partition analysis, we infer that moisture will play a dominant role in regulating the chemical composition of DOM in Alfisols under both warming and humidification which in turn impact global C cycling and the ultimate climate.

Application of microfluidic systems in modelling impacts of environmental structure on stress-sensing by individual microbial cells

Environmental structure describes physical structure that can determine heterogenous spatial distribution of biotic and abiotic (nutrients, stressors etc.) components of a microorganism's microenvironment. This study investigated the impact of micrometre-scale structure on microbial stress sensing, using yeast cells exposed to copper in microfluidic devices comprising either complex soil-like architectures or simplified environmental structures. In the soil micromodels, the responses of individual cells to inflowing medium supplemented with high copper (using cells expressing a copper-responsive pCUP1-reporter fusion) could be described neither by spatial metrics developed to quantify proximity to environmental structures and surrounding space, nor by computational modelling of fluid flow in the systems. In contrast, the proximities of cells to structures did correlate with their responses to elevated copper in microfluidic chambers that contained simplified environmental structure. Here, cells within more open spaces showed the stronger responses to the copper-supplemented inflow. These insights highlight not only the importance of structure for microbial responses to their chemical environment, but also how predictive modelling of these interactions can depend on complexity of the system, even when deploying controlled laboratory conditions and microfluidics.

Soil organic matter and clay zeta potential influence aggregation of a clayey red soil (Ultisol) under long-term fertilization

The effect of soil organic matter (SOM) on aggregation of variably-charged red soils (Ultisol) through clay zeta potential is not fully understood. Therefore, the objectives of this study were to investigate the SOM effect on the clay zeta potential and soil aggregation after fertilization. Soils under 17 years of fertilization (manure, NPK + straw, NPK, and control (CK) were adjusted by KCl solution to reach varying soil pH and concentration in order to determine clay zeta potential, cations, and aggregate size distribution. The SOM content and C-functional groups by ¹³C-NMR analysis were also determined. Results showed that the negative zeta potential displayed a bell-shaped pattern with increasing concentration of KCl, but displayed different amplitude of variation among treatments. Manure had the highest zeta potential value and its degree of variation in relative to the value at KCl concentration of 0.1 mol L^-1 (19%), NPK + straw and NPK treatments were similar, and CK was the least. Greater negative zeta potential for manure treatment was attributed to higher SOM content, aromatic-C functional groups, and their greater concentrations of Ca²⁺ and Mg²⁺ than did the CK. As a result, higher SOM and clay zeta potential yielded in less release of amount of soil particles (< 10 μm) (r = - 0.46*) and enhanced water stable macroaggregates for manure instead of NPK + straw. Long-term manure fertilization would be suggested as a conservation practice for red soil due to its increase in soil aggregate stability and negative zeta potential in subtropical climate.

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.

Pulse Effect of Precipitation: Spatial Patterns and Mechanisms of Soil Carbon Emissions

The rapid and strong release of CO2 caused by precipitation (known as the pulse effect) is a common phenomenon that significantly affects ecosystem C cycling. However, the degree to which the pulse effect occurs overlarge regional scales remains unclear. In this study, we conducted continuous and high-frequency measurements of soil CO2 release rates (Rs) for 48 h after simulated precipitation, along a precipitation gradient of different grassland types (i.e., meadow, typical, and desert) in Inner Mongolia, China. Pulse effects were assessed using the maximum Rs (Rsoil–max) and accumulated CO2 emissions (ARs–soil). Strong precipitation pulse effects were found in all sites; however, the effects differed among grassland types. In addition, an apparent decrease in both Rsoil–max and ARs–soil was observed from the east to west, i.e., along the decreasing precipitation gradient. ARs–soil values followed the order: temperate meadow grassland (0.097 mg C g–1 soil) &gt; typical temperate grassland (0.081 mg C g–1 soil) &gt; temperate desert grassland (0.040 mg C g–1 soil). Furthermore, Rsoil–max and ARs–soil were significantly positively correlated with soil quality (SOC, POC, and N, etc.; P &lt; 0.01). ARs–soil (P &lt; 0.05) and ARs–SOC (P &lt; 0.01) were significantly affected. ARs–soil and ARs–SOC were also positively correlated with soil microbial biomass significantly (P &lt; 0.05). Rsoil–max and ARs–soil had similar spatial variations and controlling mechanisms. These results greatly support the substrate supply hypothesis for the effects of precipitation pulses, and provide valuable information for predicting CO2 emissions. Our findings also verified the significant effect of soil CO2 release from precipitation pulses on the grasslands of arid and semi-arid regions. Our data provide a scientific basis for model simulations to better predict the responses of ecosystem carbon cycles in arid and semi-arid regions under predicted climate change scenarios.

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 organic carbon is not just for soil scientists: measurement recommendations for diverse practitioners

Soil organic carbon (SOC) regulates terrestrial ecosystem functioning, provides diverse energy sources for soil microorganisms, governs soil structure, and regulates the availability of organically bound nutrients. Investigators in increasingly diverse disciplines recognize how quantifying SOC attributes can provide insight about ecological states and processes. Today, multiple research networks collect and provide SOC data, and robust, new technologies are available for managing, sharing, and analyzing large data sets. We advocate that the scientific community capitalize on these developments to augment SOC data sets via standardized protocols. We describe why such efforts are important and the breadth of disciplines for which it will be helpful, and outline a tiered approach for standardized sampling of SOC and ancillary variables that ranges from simple to more complex. We target scientists ranging from those with little to no background in soil science to those with more soil-related expertise, and offer examples of the ways in which the resulting data can be organized, shared, and discoverable.

Seasonal variations in the response of soil respiration to rainfall events in a riparian poplar plantation

Rainfall events have profound influence on the soil carbon release in different forest ecosystems. However, seasonal variations in soil respiration (RS) response to rainfall events and associated regulatory processes are not well documented in riparian forest ecosystems to date. We continuously measured soil respiration in a riparian plantation ecosystem from 2015 to 2018 to explore the relationships between soil respiration and rainfall events. Across the 4 years, 83 individual rainfall events were identified for spring, summer and autumn. We found that mean RS rate after rain (post-RS) was significantly higher than that before rain (pre-RS) (p < 0.05) in spring, and the relative change in soil respiration (RSrc) increased against rainfall size due to the stimulation by the significant increases in soil moisture content (ΔSM). In contrast, mean post-RS was lower than pre-RS and RSrc was significantly decreased with the increasing rainfall size (p < 0.01) in summer and autumn. Reduced changes in soil temperature (ΔTS) and increased soil moisture content after rain (post-SM) contributed to the decreased RS due to frequently occurring heavy rain events in summer. Increased ΔSM following rainfall events coupled with groundwater level increase suppressed RSrc in autumn, even though increased ΔTS could offset the negative effects of SM on RS to some extent. In addition, we found that higher post-SM after large rainfall events (>10 mm day^-1) changed the response of RS to soil temperature (TS) by reducing the temperature sensitivity (Q₁₀) even in this riparian plantation ecosystem. Our study highlights the importance of integrating seasonal difference in soil respiration response to rainfall events and the impact of large rainfall events on soil C release for estimating forest soil carbon cycling at multiple scales.

From pools to flow: The PROMISE framework for new insights on soil carbon cycling in a changing world

Soils represent the largest terrestrial reservoir of organic carbon, and the balance between soil organic carbon (SOC) formation and loss will drive powerful carbon-climate feedbacks over the coming century. To date, efforts to predict SOC dynamics have rested on pool-based models, which assume classes of SOC with internally homogenous physicochemical properties. However, emerging evidence suggests that soil carbon turnover is not dominantly controlled by the chemistry of carbon inputs, but rather by restrictions on microbial access to organic matter in the spatially heterogeneous soil environment. The dynamic processes that control the physicochemical protection of carbon translate poorly to pool-based SOC models; as a result, we are challenged to mechanistically predict how environmental change will impact movement of carbon between soils and the atmosphere. Here, we propose a novel conceptual framework to explore controls on belowground carbon cycling: Probabilistic Representation of Organic Matter Interactions within the Soil Environment (PROMISE). In contrast to traditional model frameworks, PROMISE does not attempt to define carbon pools united by common thermodynamic or functional attributes. Rather, the PROMISE concept considers how SOC cycling rates are governed by the stochastic processes that influence the proximity between microbial decomposers and organic matter, with emphasis on their physical location in the soil matrix. We illustrate the applications of this framework with a new biogeochemical simulation model that traces the fate of individual carbon atoms as they interact with their environment, undergoing biochemical transformations and moving through the soil pore space. We also discuss how the PROMISE framework reshapes dialogue around issues related to SOC management in a changing world. We intend the PROMISE framework to spur the development of new hypotheses, analytical tools, and model structures across disciplines that will illuminate mechanistic controls on the flow of carbon between plant, soil, and atmospheric pools.

Molecular Evidence of Arsenic Mobility Linked to Biodegradable Organic Matter

Molecular characteristics of natural organic matter (NOM) and their potential connections to arsenic enrichment processes remain poorly understood. Here, we examine dissolved organic matter (DOM) in groundwater and water-soluble organic matter (WSOM) in aquifer sediments being depth-matched with groundwater samples from a typical arid-semiarid basin (Hetao Basin, China) hosting high arsenic groundwater. We used Fourier transform ion cyclotron resonance mass spectrometry to determine molecular characteristics of DOM and WSOM and evaluate potential roles of biodegradable compounds in microbially mediated arsenic mobility at the molecular level. High-arsenic groundwater DOM was generally enriched in recalcitrant molecules (including lignins and aromatic structures). Although potential contribution of recalcitrant compounds to arsenic enrichment cannot be ruled out, preferential degradation of the labile molecules coupled with reduction of Fe(III) (oxyhydr)oxides seemed to dominate arsenic mobilization. Both the number and the intensity of biodegradable compounds (including aliphatic/proteins and carbohydrates) were higher in WSOM than those in DOM in depth-matched high-arsenic groundwater (arsenic >0.67 μmol/L or 50 μg/L). Groundwater arsenic concentration generally increased with the increase in the number and the intensity of unique biodegradable compounds (especially N-containing compounds) in WSOM at matched depths. Anoxic incubations of sediments and deionized water show that more arsenic and Fe(II) were released from aquifer sediments with greater numbers and intensities of consumed biodegradable compounds in WSOM (especially N-containing compounds), with a higher proportion of microbially derived compounds produced. These observations indicate that the biodegradation of aliphatic/proteins and carbohydrates (especially CHON formulas) in WSOM fueling the reductive dissolution of Fe(III) (oxyhydr)oxides predominantly promotes arsenic release from aquifer solids. Our unique data present a better understanding of arsenic mobilization shaped by microbial degradation of labile organic compounds in anoxic aquifers at the molecular level.

Chemodiversity of Soil Dissolved Organic Matter

Dissolved organic matter (DOM) plays a key role in many biogeochemical processes, but the drivers controlling the diversity of chemical composition and properties of DOM molecules (chemodiversity) in soils are poorly understood. It has also been debated whether environmental conditions or intrinsic molecular properties control the accumulation and persistence of DOM due to the complexity of both molecular composition of DOM and interactions between DOM and surrounding environments. In this study, soil DOM samples were extracted from 33 soils collected from different regions of China, and we investigated the effects of climate and soil properties on the chemodiversity of DOM across different regions of China, employing a combination of Fourier transform ion cyclotron resonance mass spectrometry, optical spectroscopy, and statistical analyses. Our results indicated that, despite the heterogeneity of soil samples and complex influencing factors, aridity and clay can account for the majority of the variations of DOM chemical composition. The finding implied that DOM chemodiversity is an ecosystem property closely related to the environment, and can be used in developing large-scale soil biogeochemistry models for predicting C cycling in soils.

Representing the function and sensitivity of coastal interfaces in Earth system models

Between the land and ocean, diverse coastal ecosystems transform, store, and transport material. Across these interfaces, the dynamic exchange of energy and matter is driven by hydrological and hydrodynamic processes such as river and groundwater discharge, tides, waves, and storms. These dynamics regulate ecosystem functions and Earth's climate, yet global models lack representation of coastal processes and related feedbacks, impeding their predictions of coastal and global responses to change. Here, we assess existing coastal monitoring networks and regional models, existing challenges in these efforts, and recommend a path towards development of global models that more robustly reflect the coastal interface.

Irrigation and Greenhouse Gas Emissions: A Review of Field-Based Studies

Irrigation practices can greatly influence greenhouse gas (GHG) emissions because of their control on soil microbial activity and substrate supply. However, the effects of different irrigation management practices, such as flood irrigations versus reduced volume methods, including drip and sprinkler irrigation, on GHG emissions are still poorly understood. Therefore, this review was performed to investigate the effects of different irrigation management strategies on the emission of nitrous oxide (N2O), carbon dioxide (CO2), and methane (CH4) by synthesizing existing research that either directly or indirectly examined the effects of at least two irrigation rates on GHG emissions within a single field-based study. Out of thirty-two articles selected for review, reduced irrigation was found to be effective in lowering the rate of CH4 emissions, while flood irrigation had the highest CH4 emission. The rate of CO2 emission increased mostly under low irrigation, and the effect of irrigation strategies on N2O emissions were inconsistent, though a majority of studies reported low N2O emissions in continuously flooded field treatments. The global warming potential (GWP) demonstrated that reduced or water-saving irrigation strategies have the potential to decrease the effect of GHG emissions. In general, GWP was higher for the field that was continuously flooded. The major finding from this review is that optimizing irrigation may help to reduce CH4 emissions and net GWP. However, more field research assessing the effect of varying rates of irrigation on the emission of GHGs from the agricultural field is warranted.

Water repellency reduces soil CO2 efflux upon rewetting

Carbon dioxide (CO₂) efflux from soil represents one of the biggest ecosystem carbon (C) fluxes and high-magnitude pulses caused by rainfall make a substantial contribution to the overall C emissions. It is widely accepted that the drier the soil, the larger the CO₂ pulses will be, but this notion has never been tested for water-repellent soils. Soil water repellency (SWR) is a common feature of many soils and is especially prominent after dry periods or fires. An important unanswered question is to what degree SWR affects common assumptions about soil CO₂ dynamics. To address this, our study investigates, for the first time, the effect of SWR on the CO₂ pulse upon wetting for water-repellent soils from recently burned forest sites. CO₂ efflux measurements in response to simulated wetting were conducted both under laboratory and in situ conditions. Experiments were conducted on severely and extremely water-repellent soils, with a wettable scenario simulated by adding a wetting agent to the water. CO₂ efflux upon rewetting was significantly lower in the water-repellent scenarios. Under laboratory conditions, CO₂ pulse was up to four times lower under the water-repellent scenario as a result of limited wetting, with 70% of applied water draining rapidly via preferential flow paths, leaving much of the soil dry. We suggest that the predominant cause of the lower CO₂ pulse in water-repellent soils was the smaller volume of pores in which the CO₂ was replaced by infiltrating water, compared to wettable soil. This study shows that SWR should be considered as an important factor when measuring or predicting the CO₂ flush upon rewetting of dry soils. Although this study focused mainly on short-term effects of rewetting on CO₂ fluxes, the overall implications of SWR on physical changes in soil conditions can be long lasting, with overall larger consequences for C dynamics.

Variations in Greenhouse Gas Fluxes in Response to Short-Term Changes in Weather Variables at Three Elevation Ranges, Wakiso District, Uganda

Weather conditions are among the major factors leading to the increasing greenhouse gas (GHG) fluxes from the agricultural soils. In this study, variations in the soil GHG fluxes with precipitation and soil temperatures at different elevation ranges in banana–coffee farms, in the Wakiso District, Uganda, were evaluated. The soil GHG fluxes were collected weekly, using the chamber method, and analyzed by using gas chromatography. Parallel soil temperature samples were collected by using a REOTEMP soil thermometer. Daily precipitation was measured with an automated weather station instrument installed on-site. The results showed that CO2, N2O, and CH4 fluxes were significantly different between the sites at different elevation ranges. Daily precipitation and soil temperatures significantly (p < 0.05) affected the soil GHG fluxes. Along an elevation gradient, daily precipitation and soil temperatures positively associated with the soil GHG fluxes. The combined factors of daily precipitation and soil temperatures also influence the soil GHG fluxes, but their effect was less than that of the single effects. Overall, daily precipitation and soil temperatures are key weather factors driving the soil GHG fluxes in time and space. This particular study suggests that agriculture at lower elevation levels would help reduce the magnitudes of the soil GHG fluxes. However, this study did not measure the soil GHG fluxes from the non-cultivated ecosystems. Therefore, future studies should focus on assessing the variations in the soil GHG fluxes from non-cultivated ecosystems relative to agriculture systems, at varying elevation ranges.

Microbial spatial footprint as a driver of soil carbon stabilization

Increasing the potential of soil to store carbon (C) is an acknowledged and emphasized strategy for capturing atmospheric CO₂. Well-recognized approaches for soil C accretion include reducing soil disturbance, increasing plant biomass inputs, and enhancing plant diversity. Yet experimental evidence often fails to support anticipated C gains, suggesting that our integrated understanding of soil C accretion remains insufficient. Here we use a unique combination of X-ray micro-tomography and micro-scale enzyme mapping to demonstrate for the first time that plant-stimulated soil pore formation appears to be a major, hitherto unrecognized, determinant of whether new C inputs are stored or lost to the atmosphere. Unlike monocultures, diverse plant communities favor the development of 30–150 µm pores. Such pores are the micro-environments associated with higher enzyme activities, and greater abundance of such pores translates into a greater spatial footprint that microorganisms make on the soil and consequently soil C storage capacity.

The processes driving soil carbon accretion remain to be poorly understood. Here the authors combined X-ray micro-tomography and zymography to demonstrate that plant-stimulated soil pore formation is a major, hitherto unrecognized, determinant of whether new C inputs are stored or lost to the atmosphere.

Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales

Soils contain a tangle of minerals, water, nutrients, gases, plant roots, decaying organic matter, and microorganisms which work together to cycle nutrients and support terrestrial plant growth. Most soil microorganisms live in periodically interconnected communities closely associated with soil aggregates, i.e., small (<2 mm), strongly bound clusters of minerals and organic carbon that persist through mechanical disruptions and wetting events. Their spatial structure is important for biogeochemical cycling, and we cannot reliably predict soil biological activities and variability by studying bulk soils alone. To fully understand the biogeochemical processes at work in soils, it is necessary to understand the micrometer-scale interactions that occur between soil particles and their microbial inhabitants. Here, we review the current state of knowledge regarding soil aggregate microbial communities and identify areas of opportunity to study soil ecosystems at a scale relevant to individual cells. We present a framework for understanding aggregate communities as "microbial villages" that are periodically connected through wetting events, allowing for the transfer of genetic material, metabolites, and viruses. We describe both top-down (whole community) and bottom-up (reductionist) strategies for studying these communities. Understanding this requires combining "model system" approaches (e.g., developing mock community artificial aggregates), field observations of natural communities, and broader study of community interactions to include understudied community members, like viruses. Initial studies suggest that aggregate-based approaches are a critical next step for developing a predictive understanding of how geochemical and community interactions govern microbial community structure and nutrient cycling in soil.

Online supercritical fluid extraction mass spectrometry (SFE-LC-FTMS) for sensitive characterization of soil organic matter

We report a novel technical approach for subcritical fluid extraction (SFE) for organic matter characterization in complex matrices such as soil.

Microscale water distribution and its effects on organic carbon decomposition in unsaturated soils

Microscale water distribution in the subsurface is key to many geochemical and biogeochemical reactions. This study investigated microscale water distribution and movement in unsaturated soils using micro-continuum hydrodynamic models, and examined the effect of microscale water distribution on organic carbon (C) decomposition using a micro-continuum biogeochemical reaction model. The micro-continuum hydrodynamic model that relates capillary pressure to porosity captured the measured water imbibition curve at the core scale, and exhibited reasonable water distribution and movement at the microscale. The simulations of organic C decomposition illustrate that microscale water distribution strongly affected the distribution of C decomposition rates by regulating the availability of dissolved organic C and oxygen. Particularly, changes in water distribution altered the location and intensity of reactive hotspots and thereby CO₂ flux from soils. The microscale interactions between water content and organic C decomposition rate provide underlying mechanisms for explaining macroscale phenomenon observed in laboratory and fields. Overall, this study presents a useful tool for explicating hydro-biogeochemical behaviors in the subsurface by integrating micro-continuum hydrodynamic and biogeochemical reaction modeling.

Life in Dry Soils: Effects of Drought on Soil Microbial Communities and Processes

Throughout Earth's history, drought has been a common crisis in terrestrial ecosystems; in human societies, it can cause famine, one of the Four Horsemen of the apocalypse. As the global hydrological cycle intensifies with global warming, deeper droughts and rewetting will alter, and possibly transform, ecosystems. Soil communities, however, seem more tolerant than plants or animals are to water stress—the main effects, in fact, on soil processes appear to be limited diffusion and the limited supply of resources to soil organisms. Thus, the rains that end a drought not only release soil microbes from stress but also create a resource pulse that fuels soil microbial activity. It remains unclear whether the effects of drought on soil processes result from drying or rewetting. It is also unclear whether the flush of activity on rewetting is driven by microbial growth or by the physical/chemical processes that mobilize organic matter. In this review, I discuss how soil water, and the lack of it, regulates microbial life and biogeochemical processes. I first focus on organismal-level responses and then consider how these influence whole-soil organic matter dynamics. A final focus is on how to incorporate these effects into Earth System models that can effectively capture dry–wet cycling.

Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain

Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the bulk, macroscopic parameters (e.g., granulometry, pH, soil organic matter, and biomass contents) commonly used to characterize soils provide insufficient information to describe quantitatively the activity of soil microorganisms and some of its outcomes, like the emission of greenhouse gasses. Clearly, new, more appropriate macroscopic parameters are needed, which reflect better the spatial heterogeneity of soils at the microscale (i.e., the pore scale) that is commensurate with the habitat of many microorganisms. For a long time, spectroscopic and microscopic tools were lacking to quantify processes at that scale, but major technological advances over the last 15 years have made suitable equipment available to researchers. In this context, the objective of the present article is to review progress achieved to date in the significant research program that has ensued. This program can be rationalized as a sequence of steps, namely the quantification and modeling of the physical-, (bio)chemical-, and microbiological properties of soils, the integration of these different perspectives into a unified theory, its upscaling to the macroscopic scale, and, eventually, the development of new approaches to measure macroscopic soil characteristics. At this stage, significant progress has been achieved on the physical front, and to a lesser extent on the (bio)chemical one as well, both in terms of experiments and modeling. With regard to the microbial aspects, although a lot of work has been devoted to the modeling of bacterial and fungal activity in soils at the pore scale, the appropriateness of model assumptions cannot be readily assessed because of the scarcity of relevant experimental data. For significant progress to be made, it is crucial to make sure that research on the microbial components of soil systems does not keep lagging behind the work on the physical and (bio)chemical characteristics. Concerning the subsequent steps in the program, very little integration of the various disciplinary perspectives has occurred so far, and, as a result, researchers have not yet been able to tackle the scaling up to the macroscopic level. Many challenges, some of them daunting, remain on the path ahead. Fortunately, a number of these challenges may be resolved by brand new measuring equipment that will become commercially available in the very near future.

Effects of altered dry season length and plant inputs on soluble soil carbon

Soil moisture controls microbial activity and soil carbon cycling. Because microbial activity decreases as soils dry, decomposition of soil organic matter (SOM) is thought to decrease with increasing drought length. Yet, microbial biomass and a pool of water-extractable organic carbon (WEOC) can increase as soils dry, perhaps implying microbes may continue to break down SOM even if drought stressed. Here, we test the hypothesis that WEOC increases as soils dry because exoenzymes continue to break down litter, while their products accumulate because they cannot diffuse to microbes. To test this hypothesis, we manipulated field plots by cutting off litter inputs and by irrigating and excluding precipitation inputs to extend or shorten the length of the dry season. We expected that the longer the soils would remain dry, the more WEOC would accumulate in the presence of litter, whereas shortening the length of the dry season, or cutting off litter inputs, would reduce WEOC accumulation. Lastly, we incubated grass roots in the laboratory and measured the concentration of reducing sugars and potential hydrolytic enzyme activities, strictly to understand the mechanisms whereby exoenzymes break down litter over the dry season. As expected, extending dry season length increased WEOC concentrations by 30% above the 108 μg C/g measured in untreated plots, whereas keeping soils moist prevented WEOC from accumulating. Contrary to our hypothesis, excluding plant litter inputs actually increased WEOC concentrations by 40% above the 105 μg C/g measured in plots with plants. Reducing sugars did not accumulate in dry senesced roots in our laboratory incubation. Potential rates of reducing sugar production by hydrolytic enzymes ranged from 0.7 to 10 μmol·g^-1 ·h^-1 and far exceeded the rates of reducing sugar accumulation (~0.001 μmol·g^-1 ·h^-1 ). Our observations do not support the hypothesis that exoenzymes continue to break down litter to produce WEOC in dry soils. Instead, we develop the argument that physical processes are more likely to govern short-term WEOC dynamics via slaking of microaggregates that stabilize SOM and through WEOC redistribution when soils wet up, as well as through less understood effects of drought on the soil mineral matrix.

A moisture function of soil heterotrophic respiration that incorporates microscale processes

Soil heterotrophic respiration (HR) is an important source of soil-to-atmosphere CO₂ flux, but its response to changes in soil water content (θ) is poorly understood. Earth system models commonly use empirical moisture functions to describe the HR–θ relationship, introducing significant uncertainty in predicting CO₂ flux from soils. Generalized, mechanistic models that address this uncertainty are thus urgently needed. Here we derive, test, and calibrate a novel moisture function, f_m, that encapsulates primary physicochemical and biological processes controlling soil HR. We validated f_m using simulation results and published experimental data, and established the quantitative relationships between parameters of f_m and measurable soil properties, which enables f_m to predict the HR–θ relationships for different soils across spatial scales. The f_m function predicted comparable HR–θ relationships with laboratory and field measurements, and may reduce the uncertainty in predicting the response of soil organic carbon stocks to climate change compared with the empirical moisture functions currently used in Earth system models.

Empirical moisture functions that describe the relationship between soil heterotrophic respiration and moisture introduce considerable uncertainty in soil CO₂ flux predictions. Here, the authors derive a process-based moisture function by incorporating mechanisms that control soil heterotrophic respiration.