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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Linking Manganese Fractions and Organic Carbon in Soils of Contrasting Land Use Systems

Manganese (Mn) is an essential micronutrient that influences carbon (C) cycling by binding or oxidizing soil organic matter. Mn fractions in soil and their plant availability depend largely on soil pH, which is commonly altered by agricultural practices. Fractions of Mn in soils range from readily available (e.g., bioavailable Mn, exchangeable Mn) to stabilized (e.g., Mn-oxide minerals, Mn contained in silicates). Furthermore, the distribution of soil Mn with depth was assessed in contrasting land use systems (organic agriculture, conventional agriculture, and unmanaged forest) using a sequential extraction method that targets Mn fractions ranging in bioavailability. Both agricultural sites had similar amounts of total Mn but had available Mn (1–7% of total Mn) lower than that of the unmanaged forested site (15% of total Mn). Manganese and organic C were generally positively correlated, but this relationship depended on soil depth, Mn fractions, and concentrations, while land management change had little influence.

Crops↗
DOE OSTI2025

Reproductive and leaf litterfall fluxes in forest ecosystem sites globally (1950-2022)

Forest allocation of net primary productivity (NPP) to reproduction is poorly quantified globally, despite its critical role in forest regeneration and a well-supported trade-off with allocation to growth. Although field measurements of total NPP are rare, our work finds that a proxy for reproductive carbon allocation constructed from leaf (L) and reproductive (R) litterfall fluxes, R/(R+L), is strongly correlated with R/NPP, facilitating analysis across a wide range of sites where biometric estimates of NPP are not available (R² = 0.85; Hanbury-Brown et al., 2022, Ward et al., in prep). To investigate relationships between ecosystem-scale reproductive allocation (RA) and climate, soil fertility, and stand age gradients, we conducted a literature search and synthesized 824 observations of annual average leaf and reproductive litterfall fluxes across forest sites globally. The zip file includes 1) a folder Data/ containing the litterfall data ("GlobalForestRA_data.csv") and metadata ("GlobalForestRA_metadata.doc") files. The data file includes geographic coordinates, long-term mean annual temperature and precipitation (1970-2000, extracted from WorldClim2.1), leaf and reproductive litterfall fluxes, sampling interval and protocols, forest characteristics (dominant leaf morphology, information pertaining to forest age and successional stage, and disturbance history) and soil properties (% sand, %silt, %clay, total phosphorus (P), nitrogen (N), cation exchange capacity (CEC) and pH) extracted from SoilGrids250 and from on-site measurements, where available. The metadata file contains information about each variable reported in the data file, including data sources, processing methods, and all references. The Data folder contains two additional files used to create Figure 1; these are described in greater detail in the README.2) R scripts GloalForestRA_analysis.r and GlobalForestRA_SI.r and a folder /Functions used to produce results, figures, and tables in the manuscript Ward et al. (in press)3) a README file describing how the data and R scripts can be used to reproduce statistical results, figures, and tables found in the manuscript. Ward et al. (in press)This repository can also be found at: https://github.com/r-ward/Global_Analysis_ForestRA.Ward, R.E., Zhang-Zheng, H. Aernethy, K., Adu-Bredu, S., Arroyo, L., Bailey, A. et al. (in press). Forest age rivals climate to explain reproductive allocation patterns in forest ecosystems globally. Ecology Letters. Hanbury-Brown, A.R., Ward, R.E. & Kueppers, L.M. (2022). Forest regeneration within Earth system models: current process representations and ways forward. New Phytol., 235, 20–40.Ward et al. (2025), Forest age rivals climate to explain reproductive allocation patterns in forest ecosystems globally, in prep.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

An approach for broad molecular imaging of the root-soil interface via indirect matrix-assisted laser desorption/ionization mass spectrometry

Understanding of rhizospheric processes is limited by the need for imaging complex molecular transformations at relevant spatial scales within the root soil continuum. In this work, we demonstrate a method to enable this analysis by first extracting organic compounds from the rhizosphere onto a PVDF membrane while maintaining their 2D distribution. We then image the distribution of chemical compounds using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). This approach permitted us to visualize and identify compounds on the root surface and presumed root exudates in the rhizosphere. Within a 1.8 cm x 0.6 cm sampling area of a switchgrass rhizosphere, we could observe at least four chemically distinct zones. Using high performance Fourier transform ion cyclotron MS, we were able to accurately annotate numerous molecules co-localized to each of these zones.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Phosphorus and cover crop management practices affect phosphorus speciation in soils and eroded sediments

Abstract Agricultural runoff often contains P in dissolved and sediment‐bound forms, decreasing surface water quality. No‐till and cover cropping conservation practices have been recommended for reducing erosion and nutrient loss from cropping systems. The overall aims of this study were to characterize and evaluate the effects of fertilizer (placement and source) and cover crop management on P speciation in surface runoff sediments and source soil. In 2014, a field‐scale experiment was established in a no‐till, corn (Zea maysL.)–soybean (Glycine maxL.) cropping system with two cover crop treatments (with and without a winter crop; winter wheat [Triticum aestivumL.], rapeseed [Brassica napusL.], hairy vetch [Vicia villosaRoth], winter triticale [×Triticosecale Wittm.], and cereal rye [Secale cerealeL.]) and three P fertilizer management treatments (no P, fall broadcast diammonium phosphate, and spring subsurface injected ammonium polyphosphate). Phosphorus fractionation in the source soil collected in the fall of 2019 and sediment samples collected throughout 2020 were analyzed using a modified sequential P extraction method to evaluate the cumulative effects of imposing the treatment factors over 5 years. The direct P speciation was done using X‐ray absorption near edge structure spectroscopy. The indirect P speciation (fractionation) results showed that the management practices affected the exchangeable, organic matter‐associated, and Fe‐bound P fractions in sediments and the exchangeable and residual fractions in source soil. Direct P speciation results showed a depletion of Fe‐associated P in soil and sediment from cover crop treatment, suggesting that Fe‐associated P species were affected by cover crops. Changes in soil and runoff sediment P speciation would change the proportions and forms of soluble and particulate P in runoff sediments and may influence P bioavailability in aquatic ecosystems. Developing P fertilizer and cropping system management options with an understanding of soil P transformations helps maintain environmental sustainability.

Environmental Sciences & Ecology↗
DOE OSTI2023

Influence of clay mineral weathering on green rust formation at iron-reducing conditions

Green rusts (GR) are important drivers for trace metal and nutrient cycling in suboxic environments. We investigated whether green rusts would incorporate aluminum (Al) or other elements from naturally-formed clay minerals containing easily-weatherable clay minerals (e.g. mica, interlayered clays). We isolated the clay minerals from a Matapeake silt loam soil by removal of silt and sand, organic matter, and reducible oxides to study mechanisms of interaction between Fe(II) and soil-sourced clay minerals. We conducted batch Fe(II) sorption experiments at multiple near-neutral pHs (6.5–7.5) and reaction times (2h–365 days). Mineral transformations were characterized by selective extractions, X-ray diffraction (XRD), and Fe X-ray absorption spectroscopy (XAS) analyzed by shell-fitting and linear combination fitting (LCF) with natural and synthetic standards. Clay mineral fraction contained a mixture of quartz, kaolinite, interlayered vermiculite, mica, and chlorite with significant structural Fe (2.6% wt). Uptake of Fe(II) increased with pH and kinetics were rapid until 5 days, followed by slow continuous Fe(II) uptake. Citrate-bicarbonate desorption kinetics from Fe(II) sorbed clay released more Al and silicon (Si) compared with unreacted soil clay fraction whereas magnesium (Mg) and potassium (K) were unaffected. Citrate-bicarbonate extracted Fe contained more Fe(II) than an ideal GR with an Fe(II)/Fe(III) molar ratio of 5.50. Analysis of the Fe EXAFS by both LCF and shell fitting was best modeled as a combination of Fe(III)-clay reduction to Fe(II) and precipitation of GR and Fe(II)-Al LDH. After 7 days of Fe(II) sorption, LCF identified 55.2% total Fe in clay, 33.4% GR(Cl) and 11.4% Fe(II)-Al LDH. Further, these results provide novel evidence of Fe(II)-Al LDHs precipitating on naturally-formed soil clay minerals as a minor phase to GR. The geochemical implications are that GRs formed in soils and sediments should be considered to have Al and Si as well as Mg substitutions affecting their structure and reactivity.

58 GEOSCIENCES↗
DOE OSTI2020

Soil microbial function and fungal community data along an ectomycorrhizal basal area gradient, Vermont, May 2019

Mycorrhizal fungi can affect soil organic matter cycling through several mechanisms including priming, nutrient competition, and direct enzyme production. Differences in nutrient foraging strategies between ectomycorrhizal (EcM) and arbuscular mycorrhizal (AM) fungi produce divergent belowground dynamics: where EcM can take up organic nitrogen and directly break down SOM by producing enzymes, AM fungi are limited to scavenging mineral N. EcM-associated tree species also have leaf litter with relatively higher ratios of carbon to nitrogen (C:N), and belowground saprotrophic communities more dominated by fungi. Consequently, free-living microbes in EcM-dominated soils should experience nitrogen limitation, with subsequent increases in enzyme production and decreased carbon use efficiency (CUE). However, the relative importance of the effects of substrate quality and fungal community composition on enzyme production and CUE are unclear. To assess this distinction, we sampled the organic horizon and 10 cm of the mineral horizon in northern temperate forest soils along a gradient of EcM dominance (see SCxTS_DBH.csv for full tree species information). We characterized fungal community composition by measuring EcM relative abundances from extracted fungal DNA (To run raw ASV data through R code, use SCxTS_ASV_taxonomy.csv, and R code ITS_processing.Rmd; to see processed data with EcM relative abundance, use file SCxTS_sum_afitch_Feb18.20.csv) and the fungal to bacterial ratios (see data file SCxTS_plfa.csv) from phospholipid fatty acid analysis. Soil microbial functions were measured as potential activities of five hydrolytic and two oxidative enzymes ( To run raw data through R code us SCxTS_metadata.csv, hydrolytic_oxidative_raw.csv, MUBraw.csv, Enzyme_soilweight.csv, and incubationtime.csv, and R code SCxTS_enzymes.Rmd; to use Enzyme data ready to run through statistics code, use file Enzyme.data.csv) and microbial carbon use efficiency (see file SCxTS_CUE.csv and for full calculations file 18O_CUEcalcs_SCxTS_2019.xlsx). We assessed soil substrate quality as the soil carbon:nitrogen ratio (See file Organic_CN.csv). Statistical analysis can be run using R code from file SCxTS_analysis.Rmd.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

1000 Soils Pilot Dataset, version 8, May 2025

This record hosts data generated by the 1000 Soils Pilot. Data will be updated as more become available. Please see the most recent data upload for current data. A beta visualization tool is available for some data types at https://shinyproxy.emsl.pnnl.gov/app/1000soils. Please submit any suggestions or comments through the 'contact' tab. We are actively working to improve visualizations and value all feedback. Data completed include: Geochemistry, texture, respiration, and enzyme activities FTICR-MS organic matter chemistry Microbial biomass C and N TOC/TDN of water-extractable OM X-ray computed tomography (derived metrics available here, raw data available upon request) Metagenomes; a variety of data formats are available upon request Soil hydraulic properties Data in progress: LC-MS/MS in development, timeline TBD, inquire for status 1000S_processed_BGC_summary.csv contains all available biogeochemical data; microbial biomass C and N; and TOC/TDN of water-extractable OM; and 1000S_Tomography.xslx contains a summary of data generated via X-ray computed tomography. icr_v2_corems2.csv contains FTICR-MS data processed by CoreMS version 2. These data are merged by formula across instrument runs to enable cross-sample comparisons. Technical replicates are merged by retaining peaks present in 2 out of 3 replicates. 1000Soils_Metadata_Site_Mastersheet_v1.csv contains site information. Soil Hydraulics_corrected_02042025.xlsx contains soil hydraulics information. Readme File_v4.xlsx is the readme file. Please contact the MONet project (monet.emsl@pnnl.gov) or Emily Graham (emily.graham@pnnl.gov) with questions. The following file and all raw data are available upon request: icr_by_mass_for_single_sample_analysis_only.csv contains FTICR-MS data processed by CoreMS and is intended for usage in the calculation of biochemical transformations within samples only. These data are not acceptable for cross-sample comparison of masses because they are from multiple instrument runs. For more information, please see: https://www.emsl.pnnl.gov/monet and https://sc-data.emsl.pnnl.gov/monet Acknowledgment: Soil data were provided by the Molecular Observation Network (MONet) at the Environmental Molecular Sciences Laboratory (https://ror.org/04rc0xn13), a DOE Office of Science user facility sponsored by the Biological and Environmental Research program under Contract No. DE-AC05-76RL01830. The work (proposal: 10.46936/10.25585/60008970) conducted by the U.S. Department of Energy, Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science user facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231. The Molecular Observation Network (MONet) database is an open, FAIR, and publicly available compilation of the molecular and microstructural properties of soil. Data in the MONet open science database can be found at https://sc-data.emsl.pnnl.gov/.

biogeochemistry↗
DOE OSTI2021

First report of Seville root-knot nematode, Meloidogyne hispanica (Nematoda: Meloidogynidae) in the USA and North America

A high number of second stage juveniles of the root-knot nematode were recovered from soil samples collected from a corn field, located in Pickens County, South Carolina, USA in 2019. Extracted nematodes were examined morphologically and molecularly for species identification which indicated that the specimens of root knot juveniles were Meloidogyne hispanica. The morphological examination and morphometric details from second-stage juveniles were consistent with the original description and redescriptions of this species. The ITS rRNA, D2-D3 expansion segments of 28S rRNA, intergenic COII-16S region, nad5 and COI gene sequences were obtained from the South Carolina population of M. hispanica. Phylogenetic analysis of the intergenic COII-16S region of mtDNA gene sequence alignment using statistical parsimony showed that the South Carolina population clustered with Meloidogyne hispanica from Portugal and Australia. To our best knowledge, this finding represents the first report of Meloidogyne hispanica in the USA and North America.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

SPRUCE Soil Metabolome Responses to Whole Ecosystem Warming in SPRUCE Experimental Plots Beginning in 2016

This dataset reports a suite of complementary environmental geochemical analyses of peat extracts and porewater samples from SPRUCE experimental plots across a range of whole ecosystem warming (WEW) temperature treatments beginning in 2016. Results of peat extract analyses include NMR and GC-MS analyses of central metabolites, liquid chromatography mass spectra (LC-MS) analyses of lipids, and quantitative proteomics. Porewater was analyzed by FTICR-MS for secondary metabolites, and for carbon dioxide (CO2), methane (CH4) concentrations, stable isotope composition, and the differential solubility corrected CO2:CH4 ratio. This dataset contains six files in comma separated (*.csv) format.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Microbial Biomass in Soils Receiving Varying Levels of Organic Inputs - A Data Compilation

This dataset contains soil microbial biomass data compiled from published laboratory studies and field manipulations of organic inputs to soils. Each study included at least three levels of a given type of organic input applied to a given type of soil. Studies were selected from the literature that had experimentally manipulated organic input rates to soils using unburned, non-synthetic material (e.g. plant litters, manures, and composts). Fifty-five (55) studies, conducted from 1997 to October 2019, were chosen and compiled into a dataset with 358 observations from 96 combinations of a given organic material applied to a given soil in agricultural systems, laboratory incubations, forests, or grasslands. • Studies were selected when biomass measurements used the chloroform fumigation-extraction procedure followed by carbon analysis, or, in two instances, studies estimated microbial biomass using phospholipid fatty acid analysis. • Studies that used fewer than three input rates or characterized microbial biomass via substrate induced respiration were excluded. • The temporal and spatial aspects of the laboratory and field studies were not essential to the analyses (Craig et al., 2021) and were not included with the measurement data. These data were used to assess the relationship between organic input amounts and microbial biomass. Complete reference citations are provided if additional information is needed. The compiled data are provided in two .csv files: (1) soil treatments and microbial biomass data and (2) literature citations. The “Study” field is the cross reference between files. Also provided is the R code for reproducing the results in the related publication.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Soil resistance and recovery during neotropical forest succession

The recovery of soil conditions is crucial for successful ecosystem restoration and, hence, for achieving the goals of the UN Decade on Ecosystem Restoration. Here, we assess how soils resist forest conversion and agricultural land use, and how soils recover during subsequent tropical forest succession on abandoned agricultural fields. Our overarching question is how soil resistance and recovery depend on local conditions such as climate, soil type and land-use history. For 300 plots in 21 sites across the Neotropics, we used a chronosequence approach in which we sampled soils from two depths in old-growth forests, agricultural fields (i.e. crop fields and pastures), and secondary forests that differ in age (1–95 years) since abandonment. We measured six soil properties using a standardized sampling design and laboratory analyses. Soil resistance strongly depended on local conditions. Croplands and sites on high-activity clay (i.e. high fertility) show strong increases in bulk density and decreases in pH, carbon (C) and nitrogen (N) during deforestation and subsequent agricultural use. Resistance is lower in such sites probably because of a sharp decline in fine root biomass in croplands in the upper soil layers, and a decline in litter input from formerly productive old-growth forest (on high-activity clays). Soil recovery also strongly depended on local conditions. During forest succession, high-activity clays and croplands decreased most strongly in bulk density and increased in C and N, possibly because of strongly compacted soils with low C and N after cropland abandonment, and because of rapid vegetation recovery in high-activity clays leading to greater fine root growth and litter input. Furthermore, sites at low precipitation decreased in pH, whereas sites at high precipitation increased in N and decreased in C : N ratio. Extractable phosphorus (P) did not recover during succession, suggesting increased P limitation as forests age. These results indicate that no single solution exists for effective soil restoration and that local site conditions should determine the restoration strategies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Soil metagenomics umbrella narrative

Implementing accessible, authentic research experiences in introductory courses is challenging, particularly at institutions serving diverse student populations. To address this gap, we developed and deployed a Course-based Undergraduate Research Experience (CURE) focused on plant-microbe interactions in General Biology II at Northeastern Illinois University (NEIU), a minority-serving institution with a diverse student body. Students grew sugar beets (Beta vulgaris), extracted DNA from the rhizoplane, and used the Department of Energy Systems Biology Knowledgebase (KBase) for bioinformatic analysis to compare microbial relative abundance in fertilized versus unfertilized soil. Over five semesters, the CURE engaged 103 students and leveraged the intuitive KBase platform to make complex sequencing data accessible. Pre/post-course survey data revealed significant increases in student self-assessed research skills, including the ability to explain results and determine the types of data to collect. Furthermore, students reported significant gains in confidence related to experimental design and hypothesis development, alongside a strong increase in familiarity with KBase. Informal faculty feedback indicated high student engagement and appreciation for the real-world connections (e.g. food systems, agriculture, and health). This scalable, low-cost model effectively integrates data science tools into the foundational curriculum, demonstrating a potent strategy for boosting research skills and broadening participation in authentic scientific inquiry among diverse undergraduate students.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Manganese: The overlooked contaminant in the world largest mine tailings dam collapse

Manganese (Mn) is an abundant element in terrestrial and coastal ecosystems and an essential micronutrient in the metabolic processes of plants and animals. Mn is generally not considered a potentially toxic element due to its low content in both soil and water. However, in coastal ecosystems, the Mn dynamic (commonly associated with the Fe cycle) is mostly controlled by redox processes. Here, we assessed the potential contamination of the Rio Doce estuary (SE Brazil) by Mn after the world’s largest mine tailings dam collapse, potentially resulting in chronic exposure to local wildlife and humans. Estuarine soils, water, and fish were collected and analyzed seven days after the arrival of the tailings in 2015 and again two years after the dam collapse in 2017. Using a suite of solid-phase analyses including X-ray absorption spectroscopy and sequential extractions, our results indicated that a large quantity of Mn II arrived in the estuary in 2015 bound to Fe oxyhydroxides. Over time, dissolved Mn and Fe were released from soils when Fe III oxyhydroxides underwent reductive dissolution. Due to seasonal redox oscillations, both Fe and Mn were then re-oxidized to Fe III , Mn III , and Mn IV and re-precipitated as poorly crystalline Fe oxyhydroxides and poorly crystalline Mn oxides. In 2017, redox conditions (Eh: -47 ± 83 mV; pH: 6.7 ± 0.5) favorable to both Fe and Mn reduction led to an increase (~880%) of dissolved Mn (average for 2015: 66 ± 130 μg L -1 ; 2017: 582 ± 626 μg L -1 ) in water and a decrease (~75%, 2015: 547 ± 498 mg kg -1 ; 2017: 135 ± 80 mg kg -1 ) in the total Mn content in soils. The crystalline Fe oxyhydroxides content significantly decreased while the fraction of poorly ordered Fe oxides increased in the soils limiting the role of Fe in Mn retention. The high concentration of dissolved Mn found within the estuary two years after the arrival of mine tailings indicates a possible chronic contamination scenario, which is supported by the high levels of Mn in two species of fish living in the estuary. Our work suggests a high risk to estuarine biota and human health due to the rapid Fe and Mn biogeochemical dynamic within the impacted estuary.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Soil organic carbon cycling in response to simulated soil moisture variation under field conditions

The combination of extended dry periods and high intensity rainfall, common in the southeastern US, leads to greater variability in soil moisture and consequently increases uncertainty to microbial processes pertinent to soil carbon (C) mineralization. However, field-based findings on soil moisture sensitivity to soil C cycling are very limited. Therefore, a field experiment was conducted in 2018 and 2019 on a soybean (Glycine max L.) cropland in the southeastern US with three soil moisture treatments: drought (simulated using rainout-shelter from June to October in each year), rainfed (natural precipitation), and irrigated (irrigation and precipitation). Soil respiration was measured weekly from May to November in both years. Soil samples were collected multiple times each year from 0–5, 5–15, and 15–30 cm depths to determine microbial biomass C (MBC), extractable organic C (EOC), hydrolytic enzyme activities, and fungal abundance. The cumulative respiration under drought compared to other treatments was lower by 32% to 33% in 2018 and 38% to 45% in 2019. Increased MBC, EOC, and fungal abundance were observed under drought than other treatments. Specific enzyme activity indicated fewer metabolically active microbes under drought treatment compared to rainfed and irrigated treatments. Also, maintenance of enzyme pool was observed under drought condition. These results provide critical insights on microbial metabolism in response to soil moisture variation and how that influences different pools of soil C under field conditions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics

The study of soil viruses, though not new, has languished relative to the study of marine viruses. This is particularly due to challenges associated with separating virions from harboring soils. Generally, three approaches to analyzing soil viruses have been employed: (1) Isolation, to characterize virus genotypes and phenotypes, the primary method used prior to the start of the 21st century. (2) Metagenomics, which has revealed a vast diversity of viruses while also allowing insights into viral community ecology, although with limitations due to DNA from cellular organisms obscuring viral DNA. (3) Viromics (targeted metagenomics of virus-like-particles), which has provided a more focused development of ‘virus-sequence-to-ecology’ pipelines, a result of separation of presumptive virions from cellular organisms prior to DNA extraction. This separation permits greater sequencing emphasis on virus DNA and thereby more targeted molecular and ecological characterization of viruses. Employing viromics to characterize soil systems presents new challenges, however. Ones that only recently are being addressed. Here we provide a guide to implementing these three approaches to studying environmental viruses, highlighting benefits, difficulties, and potential contamination, all toward fostering greater focus on viruses in the study of soil ecology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Cryo-EM visualization of viruses from partially irrigated soils

Viruses are numerically the most abundant forms on Earth, and most are present in soil. Even though viruses are highly abundant in soil and critical to rhizosphere function, visualizing the diverse morphotypes within soil has been challenging. The difficulty is primarily due to the heterogenous nature of isolated suspensions that typically contain nanometer to micron scale debris which renders protein crystallography for structural studies unfeasible and hinders cryo-electron microscopy due to ice thickness and contrast issues. Here we employed and compared a simple spin filtration method to cleanup solutions of extracted viruses for direct observation with cryo-electron microscopy. The method employs common physical biochemical separation steps to remove large and small debris which dramatically improves image quality and preservation of structural features to permit visualizing morphotypes not typically seen with conventional negative stain approaches. In addition to tailed and non-tailed polyhedral phages, several under reported or novel morphotypes of soil viruses are directly visualized as a particle library with both 2D and 3D information.

cryo-EM↗
DOE OSTI2025

Combining organic amendments with enhanced rock weathering shifts soil carbon storage in croplands

Enhanced rock weathering (ERW) involves applying crushed silicate minerals to cropland soils to remove carbon dioxide and stabilize the global climate. If practiced widely, ERW has the potential to mitigate climate change and improve soil health and crop productivity. However, most ERW studies emphasize inorganic carbon (IC) chemistry, using model-based estimates and short-term mesocosms. Limited field data exist on how ERW interacts with organic amendments to affect organic carbon (C) cycling in soils. In a three-year field study in conventionally managed, irrigated maize fields, we monitored how key soil variables responded to crushed rock-alone, and in combination with compost and/or biochar. We measured weathering indicators (pH, major cations, and IC contents) and organic fractions, including particulate organic matter (POM), mineral-associated organic matter (MAOM), microbial biomass C, and water-extractable organic C. Rock-alone treatments increased weathering proxies (pH and IC) and showed an increasing trend in POM and MAOM, relative to control. In contrast, combining crushed rock with organic amendments resulted in lower soil organic C and nitrogen (N) concentrations (in both POM and MAOM) compared to organic amendments alone, though IC increased in the rock+compost treatment. Combining rock with both compost and biochar (compost/biochar) significantly lowered MAOM-N compared to compost/biochar alone. Overall, co-applying rock with organic inputs may promote weathering and C accrual but slow the accrual rate of organic C and N relative to organic amendments alone. Quantifying these trade-offs over multiple years and scales is critical to integrating ERW with existing soil health practices and climate mitigation strategies.

Biological and medical sciences↗