Multispecies contaminant transport in undisturbed columns of weathered fractured saprolite

Laboratory-scale tracer experiments were conducted to investigate the geochemical and hydrological processes that govern the fate and transport of organically-chelated radionuclides in clay-rich residual soils. Undisturbed columns (8.5 cm diameter x 15 cm length) of weathered, fractured shale saprolite were obtained from a proposed waste disposal site at the Oak Ridge National Laboratory. Single and multispecies saturated transport experiments were conducted to determine the rates and mechanisms governing the transport of 57.58Co(ΙΙ)EDTA2-, 57Co(ΙΙΙ)EDTA-, 109CdEDTA2-, and H51Cr04-. The transport of reactive contaminants through undisturbed, heterogeneous materials was affected by nonequilibrium conditions, as a result of physical processes, such as multi-region flow, or chemical processes, such as ratelimited sorption or transformation reactions. Geochemical reactions between soil mineral surfaces and chelated contaminants resulted in redox reactions and chelate dissociation, coupled with dissolution of soil minerals. Co(ΙΙ)EDTA2- was oxidized to Co(ΙΙΙ)EDTA-, and a pulse of aqueous Mn suggested that surficial Mn(ΙV) oxides may have catalyzed the redox reaction. Subsurface Fe and A1 oxides dissociated the CdEDTA2- chelate, resulting in the formation of Fe(ΙΙΙ)EDTA-, Al(ΙΙΙ)EDTA-, and uncomplexed Cd. The divalent Cd2+ was transported as a reactive cation, where stabilization may occur by adsorption to soil surfaces. The transport of Cr(VΙ) was governed by the reduction to Cr(ΙΙΙ) in the presence of soil organic matter, followed by irreversible sorption and/or precipitation of the trivalent cation Cr3+. Both Cr(VΙ) and Cr(ΙΙΙ) were irreversibly sorbed, but the proportion of trivalent Cr was greater in a column amended with organic matter, which suggested that oxidation of organics catalyzed the reduction of Cr(VΙ). Nonequilibrium conditions during transport were identified using flow interruption, which allowed ratelimited processes to approach equilibrium. Results were modeled with a version of the convective dispersive equation where flow was segregated into mobile and immobile flow regions. Optimization of the model was completed on the flow interruption, to estimate the rate of diffusive mass transfer between the two regions. Retardation coefficients were obtained by fitting to the breakthrough curves. The results indicated that physical nonequilibrium was significant during column transport studies, and that some geochemical reactions between soil and contaminants were rate-limited, which has implications for predictions of contaminant migration

Representation of Dormant and Active Microbial Dynamics for Ecosystem Modeling

Dormancy is an essential strategy for microorganisms to cope with environmental stress. However, global ecosystem models typically ignore microbial dormancy, resulting in major model uncertainties. To facilitate the consideration of dormancy in these large-scale models, we propose a new microbial physiology component that works for a wide range of substrate availabilities. This new model is based on microbial physiological states and is majorly parameterized with the maximum specific growth and maintenance rates of active microbes and the ratio of dormant to active maintenance rates. A major improvement of our model over extant models is that it can explain the low active microbial fractions commonly observed in undisturbed soils. Our new model shows that the exponentially-increasing respiration from substrate-induced respiration experiments can only be used to determine the maximum specific growth rate and initial active microbial biomass, while the respiration data representing both exponentially-increasing and non-exponentially-increasing phases can robustly determine a range of key parameters including the initial total live biomass, initial active fraction, the maximum specific growth and maintenance rates, and the half-saturation constant. Our new model can be incorporated into existing ecosystem models to account for dormancy in microbially-mediated processes and to provide improved estimates of microbial activities.Comment: 38 pages, 2 Tables, 4 Figure

Response patterns of simulated corn yield and soil nitrous oxide emission to precipitation change

Background Precipitation plays an important role in crop production and soil greenhouse gas emissions. However, how crop yield and soil nitrous oxide (N2O) emission respond to precipitation change, particularly with different background precipitations (dry, normal, and wet years), has not been well investigated. In this study, we examined the impacts of precipitation changes on corn yield and soil N2O emission using a long-term (1981–2020, 40 years) climate dataset as well as seven manipulated precipitation treatments with different background precipitations using the DeNitrification-DeComposition (DNDC) model. Results Results showed large variations of corn yield and precipitation but small variation of soil N2O emission among 40 years. Both corn yield and soil N2O emission showed near linear relationships with precipitation based on the long-term precipitation data, but with different response patters of corn yield and soil N2O emission to precipitation manipulations. Corn yield showed a positive linear response to precipitation manipulations in the dry year, but no response to increases in precipitation in the normal year, and a trend of decrease in the wet year. The extreme drought treatments reduced corn yield sharply in both normal and wet years. In contrast, soil N2O emission mostly responded linearly to precipitation manipulations. Decreases in precipitation in the dry year reduced more soil N2O emission than those in the normal and wet years, while increases in precipitation increased more soil N2O emission in the normal and wet years than in the dry year. Conclusions This study revealed different response patterns of corn yield and soil N2O emission to precipitation and highlights that mitigation strategy for soil N2O emission reduction should consider different background climate conditions

Multi-year incubation experiments boost confidence in model projections of long-term soil carbon dynamics

Global soil organic carbon (SOC) stocks may decline with a warmer climate. However, model projections of changes in SOC due to climate warming depend on microbially-driven processes that are usually parameterized based on laboratory incubations. To assess how lab-scale incubation datasets inform model projections over decades, we optimized five microbially-relevant parameters in the Microbial-ENzyme Decomposition (MEND) model using 16 short-term glucose (6-day), 16 short-term cellulose (30-day) and 16 long-term cellulose (729-day) incubation datasets with soils from forests and grasslands across contrasting soil types. Our analysis identified consistently higher parameter estimates given the short-term versus long-term datasets. Implementing the short-term and long-term parameters, respectively, resulted in SOC loss (–8.2 ± 5.1% or –3.9 ± 2.8%), and minor SOC gain (1.8 ± 1.0%) in response to 5 °C warming, while only the latter is consistent with a meta-analysis of 149 field warming observations (1.6 ± 4.0%). Comparing multiple subsets of cellulose incubations (i.e., 6, 30, 90, 180, 360, 480 and 729-day) revealed comparable projections to the observed long-term SOC changes under warming only on 480- and 729-day. Integrating multi-year datasets of soil incubations (e.g., \u3e 1.5 years) with microbial models can thus achieve more reasonable parameterization of key microbial processes and subsequently boost the accuracy and confidence of long-term SOC projections

Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using 13CO2 and 13C-Methanol.

Stable isotope probing (SIP) enables tracking the nutrient flows from isotopically labeled substrates to specific microorganisms in microbial communities. In proteomic SIP, labeled proteins synthesized by the microbial consumers of labeled substrates are identified with a shotgun proteomics approach. Here, proteomic SIP was combined with targeted metagenomic binning to reconstruct metagenome-assembled genomes (MAGs) of the microorganisms producing labeled proteins. This approach was used to track carbon flows from 13CO2 to the rhizosphere communities of Zea mays, Triticum aestivum, and Arabidopsis thaliana. Rhizosphere microorganisms that assimilated plant-derived 13C were capable of metabolic and signaling interactions with their plant hosts, as shown by their MAGs containing genes for phytohormone modulation, quorum sensing, and transport and metabolism of nutrients typical of those found in root exudates. XoxF-type methanol dehydrogenases were among the most abundant proteins identified in the rhizosphere metaproteomes. 13C-methanol proteomic SIP was used to test the hypothesis that XoxF was used to metabolize and assimilate methanol in the rhizosphere. We detected 7 13C-labeled XoxF proteins and identified methylotrophic pathways in the MAGs of 8 13C-labeled microorganisms, which supported the hypothesis. These two studies demonstrated the capability of proteomic SIP for functional characterization of active microorganisms in complex microbial communities

Differential effects of warming and nitrogen fertilization on soil respiration and microbial dynamics in switchgrass croplands

The mechanistic understanding of warming and nitrogen (N) fertilization, alone or in combination, on microbially mediated decomposition is limited. In this study, soil samples were collected from previously harvested switchgrass (Panicum virgatum L.) plots that had been treated with high N fertilizer (HN: 67 kg N ha−1) and those that had received no N fertilizer (NN) over a 3-year period. The samples were incubated for 180 days at 15 °C and 20 °C, during which heterotrophic respiration, δ13C of CO2, microbial biomass (MB), specific soil respiration rate (Rs: respiration per unit of microbial biomass), and exoenzyme activities were quantified at 10 different collections time. Employing switchgrass tissues (referred to as litter) with naturally abundant 13C allowed us to partition CO2 respiration derived from soil and amended litter. Cumulative soil respiration increased significantly by 16.4% and 4.2% under warming and N fertilization, respectively. Respiration derived from soil was elevated significantly with warming, while oxidase, the agent for recalcitrant soil substrate decomposition, was not significantly affected by warming. Warming, however, significantly enhanced MB and Rs indicating a decrease in microbial growth efficiency (MGE). On the contrary, respiration derived from amended litter was elevated with N fertilization, which was consistent with the significantly elevated hydrolase. N fertilization, however, had little effect on MB and Rs, suggesting little change in microbial physiology. Temperature and N fertilization showed minimal interactive effects likely due to little differences in soil N availability between NN and HN samples, which is partly attributable to switchgrass biomass N accumulation (equivalent to ~53% of fertilizer N). Overall, the differential individual effects of warming and N fertilization may be driven by physiological adaptation and stimulated exoenzyme kinetics, respectively. The study shed insights on distinct microbial acquisition of different substrates under global temperature increase and N enrichment

Soil extracellular enzyme activities, soil carbon and nitrogen storage under nitrogen fertilization: A meta-analysis

Nitrogen (N) fertilization affects the rate of soil organic carbon (SOC) decomposition by regulating extracellular enzyme activities (EEA). Extracellular enzymes have not been represented in global biogeochemical models. Understanding the relationships among EEA and SOC, soil N (TN), and soil microbial biomass carbon (MBC) under N fertilization would enable modeling of the influence of EEA on SOC decomposition. Based on 65 published studies, we synthesized the activities of α-1,4-glucosidase (AG), β-1,4-glucosidase (BG), β-d-cellobiosidase (CBH), β-1,4-xylosidase (BX), β-1,4-N-acetyl-glucosaminidase (NAG), leucine amino peptidase (LAP), urease (UREA), acid phosphatase (AP), phenol oxidase (PHO), and peroxidase (PEO) in response to N fertilization. The proxy variables for hydrolytic C acquisition enzymes (C-acq), N acquisition (N-acq), and oxidative decomposition (OX) were calculated as the sum of AG, BG, CBH and BX; AG and LAP; PHO and PEO, respectively. The relationships between response ratios (RRs) of EEA and SOC, TN, or MBC were explored when they were reported simultaneously. Results showed that N fertilization significantly increased CBH, C-acq, AP, BX, BG, AG, and UREA activities by 6.4, 9.1, 10.6, 11.0, 11.2, 12.0, and 18.6%, but decreased PEO, OX and PHO by 6.1, 7.9 and 11.1%, respectively. N fertilization enhanced SOC and TN by 7.6% and 15.3%, respectively, but inhibited MBC by 9.5%. Significant positive correlations were found only between the RRs of C-acq and MBC, suggesting that changes in combined hydrolase activities might act as a proxy for MBC under N fertilization. In contrast with other variables, the RRs of AP, MBC, and TN showed unidirectional trends under different edaphic, environmental, and physiological conditions. Our results provide the first comprehensive set of evidence of how hydrolase and oxidase activities respond to N fertilization in various ecosystems. Future large-scale model projections could incorporate the observed relationship between hydrolases and microbial biomass as a proxy for C acquisition under global N enrichment scenarios in different ecosystems

Differential Organic Carbon Mineralization Responses to Soil Moisture in Three Different Soil Orders Under Mixed Forested System

Soil microbial respiration is one of the largest sources of carbon (C) emissions to the atmosphere in terrestrial ecosystems, which is strongly dependent on multiple environmental variables including soil moisture. Soil moisture content is strongly dependent on soil texture, and the combined effects of texture and moisture on microbial respiration are complex and less explored. Therefore, this study examines the effects of soil moisture on the mineralization of soil organic C Soil organic carbon in three different soils, Ultisol, Alfisol and Vertisol, collected from mixed forests of Georgia, Missouri, and Texas, United States , respectively. A laboratory microcosm experiment was conducted for 90 days under different moisture regimes. Soil respiration was measured weekly, and destructive harvests were conducted at 1, 15, 60, and 90 days after incubation to determine extractable organic C (EOC), phospholipid fatty acid based microbial community, and C-acquiring hydrolytic extracellular enzyme activities (EEA). The highest cumulative respiration in Ultisol was observed at 50% water holding capacity (WHC), in Alfisol at 100% water holding capacity, and in Vertisol at 175% WHC. The trends in Extractable Organic Carbon were opposite to that of cumulative microbial respiration as the moisture levels showing the highest respiration showed the lowest EOC concentration in all soil types. Also, extracellular enzyme activities increased with increase in soil moisture in all soils, however, respiration and EEA showed a decoupled relationship in Ultisol and Alfisol soils. Soil moisture differences did not influence microbial community composition

Effects of nitrogen fertilization and bioenergy crop type on topsoil organic carbon and total Nitrogen contents in middle Tennessee USA

Nitrogen (N) fertilization affects bioenergy crop growth and productivity and consequently carbon (C) and N contents in soil, it however remains unclear whether N fertilization and crop type individually or interactively influence soil organic carbon (SOC) and total N (TN). In a three-year long fertilization experiment in switchgrass (SG: Panicum virgatum L.) and gamagrass (GG: Tripsacum dactyloides L.) croplands in Middle Tennessee USA, soil samples (0–15cm) were collected in plots with no N input (NN), low N input (LN: 84 kg N ha-1 yr-1 in urea) and high N input (HN: 168 kg N ha-1 yr-1 in urea). Besides SOC and TN, the aboveground plant biomass was also quantified. In addition to a summary of published root morphology data based on a separated mesocosm experiment, the root leachable dissolved organic matter (DOM) of both crops was also measured using archived samples. Results showed no significant interaction of N fertilization and crop type on SOC, TN or plant aboveground biomass (ABG). Relative to NN, HN (not LN) significantly increased SOC and TN in both crops. Though SG showed a 15–68% significantly higher ABG than GG, GG showed a 9.3–12% significantly higher SOC and TN than SG. The positive linear relationships of SOC or TN with ABG were identified for SG. However, GG showed structurally more complex and less readily decomposed root DOM, a larger root volume, total root length and surface area than SG. Collectively, these suggested that intensive N fertilization could increase C and N stocks in bioenergy cropland soils but these effects may be more likely mediated by the aboveground biomass in SG and root chemistry and morphology in GG. Future studies are expected to examine the root characteristics in different bioenergy croplands under the field fertilization experiment

Nitrogen Fertilization Restructured Spatial Patterns of Soil Organic Carbon and Total Nitrogen in Switchgrass and Gamagrass Croplands in Tennessee USA

Nitrogen (N) fertilizers can potentially alter spatial distribution of soil organic carbon (SOC) and total nitrogen (TN) concentrations in croplands such as switchgrass (SG: Panicum virgatum L.) and gamagrass (GG: Tripsacum dactyloides L.), but it remains unclear whether these effects are the same between crops and under different rates of fertilization. 13C and 15N are two important proxy measures of soil biogeochemistry, but they were rarely examined as to their spatial distributions in soil. Based on a three-year long fertilization experiment in Middle Tennessee, USA, the top mineral horizon soils (0–15 cm) were collected using a spatially explicit design within two 15-m2 plots under three fertilization treatments in SG and GG croplands. A total of 288 samples were collected based on 12 plots and 24 samples in each plot. The fertilization treatments were no N input (NN), low N input (LN: 84 kg N ha−1 in urea) and high N input (HN: 168 kg N ha−1 in urea). The SOC, TN, SOC/TN (C: N), δ13C and δ15N were quantified and their within-plot variations and spatial distributions were achieved via descriptive and geostatistical methods. Results showed that SG generally displayed 10~120% higher plot-level variations in all variables than GG, and the plot-level variations were 20~77% higher in NN plots than LN and HN plots in SG but they were comparable in unfertilized and fertilized plots in GG. Relative to NN, LN and HN showed more significant surface trends and spatial structures in SOC and TN in both croplands, and the fertilization effect appeared more pronounced in SG. Spatial patterns in C: N, δ13C and δ15N were comparable among different fertilization treatments in both croplands. The descending within-plot variations were also identified among variables (SOC \u3e TN \u3e δ15N \u3e C: N \u3e δ13C). This study demonstrated that N fertilizations generally reduced the plot-level variance and simultaneously re-established spatial structures of SOC and TN in bioenergy croplands, which little varied with fertilization rate but was more responsive in switchgrass cropland