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DOE OSTI2023

Summary Data for paper titled: Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry

Climate change is causing an increase in drought in many soil ecosystems and a loss of soil organic carbon. Calcareous soils may partially mitigate these losses via carbon capture and storage. Here, we aimed to determine how irrigation-supplied soil moisture and perennial plants impact biotic and abiotic soil properties that underpin deep soil carbon chemistry in an unfertilized calcareous soil. Soil was sampled up to one meter in depth from irrigated and planted field treatments and analyzed using a suite of omics and chemical analyses. Carbon cycling processes in the surface soil were dominated by plant-microbe interactions that drive organic carbon cycling, whereas inorganic carbon chemistry dominated in deeper soil layers. Both irrigation and plant cover impacted organic and inorganic carbon pools in the soil profiles. This study reveals the complex interactions between water, plants, minerals, and microorganisms that govern organic and inorganic pools of soil carbon at different depths.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Data for Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry: Summary Data

Naasko, Katherine I↗

DOE OSTI2023

Data for Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry: Sequence Data

Naasko, Katherine I↗

NASA NTRS2020

The GGCMI Phase 2 Experiment: Global Gridded Crop Model Simulations Under Uniform Changes in CO2, Temperature, Water, and Nitrogen Levels (Protocol Version 1.0)

Concerns about food security under climate change motivate efforts to better understand future changes in crop yields. Process-based crop models, which represent plant physiological and soil processes, are necessary tools for this purpose since they allow representing future climate and management conditions not sampled in the historical record and new locations to which cultivation may shift. However, process-based crop models differ in many critical details, and their responses to different interacting factors remain only poorly understood. The Global Gridded Crop Model Intercomparison (GGCMI) Phase 2 experiment, an activity of the Agricultural Model Intercomparison and Improvement Project (AgMIP), is designed to provide a systematic parameter sweep focused on climate change factors and their interaction with overall soil fertility, to allow both evaluating model behavior and emulating model responses in impact assessment tools. In this paper we describe the GGCMI Phase 2 experimental protocol and its simulation data archive. A total of 12 crop models simulate five crops with systematic uniform perturbations of historical climate, varying CO2, temperature, water supply, and applied nitrogen (“CTWN”) for rainfed and irrigated agriculture, and a second set of simulations represents a type of adaptation by allowing the adjustment of growing season length. We present some crop yield results to illustrate general characteristics of the simulations and potential uses of the GGCMI Phase 2 archive. For example, in cases without adaptation, modeled yields show robust decreases to warmer temperatures in almost all regions, with a nonlinear dependence that means yields in warmer baseline locations have greater temperature sensitivity. Inter-model uncertainty is qualitatively similar across all the four input dimensions but is largest in high-latitude regions where crops may be grown in the future.

GGCMI↗

DOE OSTI2022

Soil physical and thermal properties from soil samples at multiple locations at Teller Road Site, Seward Peninsula, Alaska, 2019

This dataset contains results of the laboratory analysis of soil samples collected across the watershed located at miles #27 along the Teller road, near Nome, AK. The dataset includes 124 soil samples retrieved from 52 locations during the first week of August 2019. The soil samples were collected in the top 1.2 m of soil with volume known samples, analyzed with a thermal analyser to infer thermal parameters (thermal conductivity, volumetric heat capacity and thermal diffusivity), and then processed in a lab for estimation of their bulk density, water content, carbon and nitrogen content, soil texture, and elemental fractions. This dataset has one csv file and one pdf file.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2018

Soil pH mediates the balance between stochastic and deterministic assembly of bacteria

Little is known about the factors affecting the relative influence of stochastic and deterministic processes that governs the assembly of microbial communities in successional soils. Here, we conducted a meta-analysis of bacterial communities using six different successional soils data sets, scattered across different regions, with different pH conditions in early and late successional soils. We found that soil pH was the best predictor of bacterial community assembly and the relative importance of stochastic and deterministic processes along successional soils. Extreme acidic or alkaline pH conditions lead to assembly of phylogenetically more clustered bacterial communities through deterministic processes, whereas pH conditions close to neutral lead to phylogenetically less clustered bacterial communities with more stochasticity. We suggest that the influence of pH, rather than successional age, is the main driving force in producing trends in phylogenetic assembly of bacteria, and that pH also influences the relative balance of stochastic and deterministic processes along successional soils. Given that pH had a much stronger association with community assembly than did successional age, we evaluated whether the inferred influence of pH was maintained when studying globally-distributed samples collected without regard for successional age. This dataset confirmed the strong influence of pH, suggesting that the influence of soil pH on community assembly processes occurs globally. Extreme pH conditions likely exert more stringent limits on survival and fitness, imposing strong selective pressures through ecological and evolutionary time. Taken together, these findings suggest that the degree to which stochastic vs. deterministic processes shape soil bacterial community assembly is a consequence of soil pH rather than successional age.

Tripathi, Binu M.↗

NASA NTRS2015

Volatile and Isotopic Imprints of Ancient Mars

The science investigations enabled by Curiosity rover's instruments focus on identifying and exploring the habitability of the Martian environment. Measurements of noble gases, organic and inorganic compounds, and the isotopes of light elements permit the study of the physical and chemical processes that have transformed Mars throughout its history. Samples of the atmosphere, volatiles released from soils, and rocks from the floor of Gale Crater have provided a wealth of new data and a window into conditions on ancient Mars.

Ancients↗

DOE OSTI2025

Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils

Arctic soils are climate-critical areas, where microorganisms play crucial roles in nutrient cycling processes. Acidobacteriota are phylogenetically and physiologically diverse bacteria that are abundant and active in Arctic tundra soils. Still, surprisingly little is known about acidobacterial viruses in general and those residing in the Arctic in particular. Here, we applied both culture-dependent and -independent methods to study the virome of Acidobacteriota in Arctic soils. Five virus isolates, Tunturi 1–5, were obtained from Arctic tundra soils, Kilpisjärvi, Finland (69°N), using Tunturiibacter spp. strains originating from the same area as hosts. The new virus isolates have tailed particles with podo- (Tunturi 1, 2, 3), sipho- (Tunturi 4), or myovirus-like (Tunturi 5) morphologies. The dsDNA genomes of the viral isolates are 63–98 kbp long, except Tunturi 5, which is a jumbo phage with a 309-kbp genome. Tunturi 1 and Tunturi 2 share 88% overall nucleotide identity, while the other three are not related to one another. For over half of the open reading frames in Tunturi genomes, no functions could be predicted. To further assess the Acidobacteriota-associated viral diversity in Kilpisjärvi soils, bulk metagenomes from the same soils were explored and a total of 1881 viral operational taxonomic units (vOTUs) were bioinformatically predicted. Almost all vOTUs (98%) were assigned to the class Caudoviricetes. For 125 vOTUs, including five (near-)complete ones, Acidobacteriota hosts were predicted. Acidobacteriota-linked vOTUs were abundant across sites, especially in fens. Terriglobia-associated proviruses were observed in Kilpisjärvi soils, being related to proviruses from distant soils and other biomes. Approximately genus- or higher-level similarities were found between the Tunturi viruses, Kilpisjärvi vOTUs, and other soil vOTUs, suggesting some shared groups of Acidobacteriota viruses across soils. This study provides acidobacterial virus isolates as laboratory models for future research and adds insights into the diversity of viral communities associated with Acidobacteriota in tundra soils. Predicted virus-host links and viral gene functions suggest various interactions between viruses and their host microorganisms. Largely unknown sequences in the isolates and metagenome-assembled viral genomes highlight a need for more extensive sampling of Arctic soils to better understand viral functions and contributions to ecosystem-wide cycling processes in the Arctic.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Predicting measures of soil health using the microbiome and supervised machine learning

Soil health encompasses a range of biological, chemical, and physical soil properties that sustain the commercial and ecological value of agroecosystems. Monitoring soil health requires a comprehensive set of diagnostics that can be cost-prohibitive for routine analyses. The soil microbiome provides a rich source of information about soil properties, which can be assayed in a high-throughput, cost-effective way. We evaluated the accuracy of random forest (RF) and support vector machine (SVM) regression and classification models in predicting 12 measures of soil health, tillage status, and soil texture from 16S rRNA gene amplicon data with an operationally relevant sample set. We validated the efficacy of the best performing models against independent datasets and also tested best practices for processing microbiome data for use in machine learning. Soil health metrics could be predicted from microbiome data with the best models achieving a Kappa value of ~0.65, for categorical assessments, and a R2 value of ~0.8, for numerical scores. Biological health ratings were better predicted than chemical or physical ratings. Validation with independent datasets revealed that models had general predictive value for soil properties, including yield. The ecological profiles of several taxa important for model accuracy matched the observed relationships with soil health, including Pyrinomonadaceae, Nitrososphaeraceae, and Candidatus Udeaobacter. Models trained at the highest taxonomic resolution proved most accurate, with losses in accuracy resulting from rarefying, sparsity filtering, and aggregating at higher taxonomic ranks. Furthermore, our study provides the groundwork for developing scalable technology to use microbiome-based diagnostics for the assessment of soil health.

16S rRNA gene↗

DOE OSTI2018

Investigation of Polypropylene-Montmorillonite Clay Nanocomposite Films Containing a Pro-degradant Additive

This paper investigates the performance of polypropylene (PP) incorporated with montmorillonite (MMT) nanoclay, maleic anhydride grafted PP (PP-g-MAH), and pro-degradant additive (TDPA®), which provides additional benefits of increasing biodegradability. A twin-screw extruder was used to compound PP, MMT, PP-g-MAH, and TDPA, and the extruded nanocomposite films were collected for testing, and their mechanical, thermal, barrier, oxo-biodegradability, and morphological properties were evaluated. Tensile test, differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), oxygen permeability test, soil burial test, X-ray diffraction (XRD), transmission electron microscopy (TEM), and scanning electron microscope (SEM) analysis were used to investigate these properties. Increasing MMT content from 1 to 3 phr increases tensile strength and Young’s modulus of the neat PP samples up to ca.45% and 27% respectively. Improvement of thermal properties for neat PP samples was observed by increasing MMT content from 1 to 3 phr. However, at 4 phr MMT content, both mechanical and thermal properties of nanocomposites dropped slightly. For soil buried samples, DSC and TGA results revealed significant changes in the thermal properties for PP samples containing TDPE additive compared to neat PP, clearly confirming the effectiveness of this TDPA additive in promoting oxo-biodegradation process of PP. Similarly weight loss evaluation result shows that about 4% weight loss for sample (PP/TD), which is PP and TDPA blend only, compared to neat PP. However, increasing MMT content from 1 to 4 phr slightly reduced weight loss of PP from 3.5 to 1.5%, respectively, for 6 month soil exposure period, which indicates that increasing MMT content was detrimental to the degradation process. For higher MMT content, the oxygen permeability of PP nanocomposites was decreased by 46% of the corresponding values for neat PP. The XRD and TEM results confirmed the exfoliation structure of the nanocomposites. The morphological change after soil burial test was studied using scanning electron microscopy (SEM).

77 NANOSCIENCE AND NANOTECHNOLOGY↗

NASA NTRS1989

Summary of activities

Four space projects' activities are summarized. Design work on the Mars Penetrator Project, in cooperation with the NASA Ames Research Center, is being continued. Efforts are focused on the drilling mechanism which must penetrate the martian subsurface soil to collect and retrieve an uncontaminated sample. The new design consists of a rotary-percussive drill mechanism. This mechanism is optimum for dry drilling, necessary to avoid contamination of the soil sample, in many different soil types. The need for a small, relatively inexpensive device to study the chemical structure of this martian soil was also established. The egg design was chosen for its low cost compared to other systems and potential for a large number of eggs to be deployed on the martian surface. The design process included analysis of the dynamics of reentry, dissipation of heat during reentry, impact with the surface, access to undisturbed soil samples, and ability to gather samples from the soil at three depths. The egg consists of the reentry systems, soil probe lifting system, soil probe package, gas chromatograph, transmitter, and battery power supply. The egg must function only once, but is designed to withstand one martian year. The Mars Mole is designed as a rover-based device which penetrates the martian soil to a depth of up to 10 m, obtains a sample of soil, and returns it to the surface for analysis. The mole was designed to meet the following specifications: (1) weight less than 10 kg; (2) size less than 20 x 20 x 30 cm; (3) power less than 100 W; (4) ability to obtain a sample of at least 5 cc; (5) ability to penetrate fine, loose sand; and (6) need to obtain at least one sample. The space station umbilical connector project is a device which provides the translational motion of the connectors on the Space Station Freedom to allow engagement for power and data transfer. The design is capable of delivering a 20 lb force within the necessary tolerances and will operate reliably in the space environment.

Source record↗

NASA NTRS2005

Mars Geochemical Instrument (MarGI): An instrument for the analysis of the Martian surface and the search for evidence of life

The Mars Geochemical Instrument, MarGI, was developed to provide a comprehensive analysis of the rocks and surface material on Mars. The instrument combines Differential Thermal Analysis (DTA) with miniature Gas Chromatography-Ion Mobility Spectrometry (GC-IMS) to identify minerals, the presence and state of water, and organic compounds. Miniature pyrolysis ovens are used to both, conduct DTA analysis of soil or crushed rocks samples, and pyrolyze the samples at temperatures up to 1000 degrees C for GC-IMS analysis of the released gases. This combination of analytical processes and techniques, which can characterize the mineralogy of the rocks and soil, and identify and quantify volatiles released during pyrolysis, has applications across a wide range of target sites including comets, planets, asteroids, and moons such as Titan and Europa. The MarGI analytical approach evolved from the Cometary Ice and Dust Experiment (CIDEX) selected to fly on the Comet Rendezvous Asteroid Flyby Mission (CRAF).

Kojiro, Daniel R.↗

NASA NTRS1984

Tropospheric sources of NO(x) - Lightning and biology

Laboratory tests were performed to quantify the expected NO(x) production by lightning and biological processes. Attention was focused on energy deposition by lightning and the oxygen partial pressure of soil, and one-dimensional photochemical models were defined for the tropospheric distributions of NO and HNO3 for various NO source strengths. The Lightning Facility data were compared with air samples of N2O production gathered during over 2 yr of flights through storms. Soil NO(x) productions were studied in terms of nitrification processes involving Nitrosomonas europaea and Alcaligenes faecalis bacteria, which change ammonium to nitrite and release NO and N2O as byproducts. The results indicate that atmospheric NO(x) is generated at two tropospheric levels, with lightning and soil bacteria being significant contributors.

Levine, J. S.↗

DOE OSTI2022

Morphological and Molecular Characterization of Punctodera stonei Brzeski, 1998 (Nematoda: Heteroderidae) from Virginia, USA

In August of 2021, several cysts with juveniles and eggs were discovered during a vegetation survey conducted at the Arlington National Cemetery, Virginia. Eight soil samples were collected from the rhizosphere region of the common grass (Festuca arundinacea L.) and processed at the Mycology and Nematology Genetic Diversity and Biology Laboratory (MNGDBL). Cysts were light to dark brown in color, and oval to pear-shaped without bullae in young cysts but present in older cysts and with prominent vulval cone. The juveniles had slightly concave stylet knobs projecting sometimes anteriorly, tail tapering gradually to a narrowly rounded terminus, and hyaline tail terminus conspicuous at least twice the length of stylet. The molecular analysis included the analysis of three gene sequence fragments: D2–D3 of 28S rRNA, ITS rRNA, and COI. The nematode species was identified by both morphological and molecular means as Stone's cyst nematode, Punctodera stonei. Detection of P. stonei in Virginia represents a new record of this species in the United States, and a second report after Canada in North America.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1975

Microwave resonance thermomagnetic analysis - A new method for characterizing fine-grained ferromagnetic constituents in lunar materials

Microwave resonance thermomagnetic analysis (MRTA) is the name given to a newly evolved technique for inferring the natures of fine-grained ferromagnetic constituents in lunar materials. Based on standard ferromagnetic resonance (FMR) procedures, the method makes use of the microwave skin effect for diagnosing the presence of metallic iron. Modelling experiments carried out on well-characterized iron and magnetitelike precipitates produced independently in simulated lunar glasses, coupled with published data for magnetite, provide a potential basis for detecting and discriminating between iron metal and ferric iron spinel, even when both are present in an unknown sample. Application of the technique to the lunar samples indicates the possible existence of magnetitelike phases in amounts up to about 0.3 wt% in soils from seven samples regions of the moon. These findings do not require any special geologic processes for their explanation, although some evidence supports the suggestion that fumarolic activity may have occurred in the lunar highlands.

Griscom, D. L.↗

NASA NTRS1975

Heavy element affinities in Apollo 17 samples

Pb-204, Bi, Tl, and Zn in samples from the Apollo 17 site exhibit relationships not found in samples from other sites. Pb-204, Tl, and Zn in residues remaining after dilute acid leaching are correlated with one another. Orange soil 74220, which is enriched in Pb-204, Tl, and Zn, is included in these relationships. In addition, the submicron metallic phase generally associated with agglutinate formation is correlated with all three of these elements; this relationship has already been reported for Pb-204 in other samples. Thus, orange soil and agglutinates appear to be involved in concentrating heavy volatile metals. A process other than mixing is required to account for this. As a consequence of the isolation of the landing site by the surrounding massifs, local supply and recycling of volatile trace elements in soils may account for some of the interelement relations.

Allen, R. O., Jr.↗

NASA NTRS2017

Documenting Surface and Sub-surface Volatiles While Drilling in Frozen Lunar Simulant

NASA's Resource Prospector (RP) mission is intended to characterize the three-dimensional nature of volatiles in lunar polar regions and permanently shadowed regions. RP is slated to carry two instruments for prospecting purposes. These include the Neutron Spectrometer System (NSS) and Near-Infrared Volatile Spectrometer System (NIRVSS). A Honybee Robotics drill (HRD) is intended to sample to depths of 1 m, and deliver a sample to a crucible that is processed by the Oxygen Volatile Extraction Node (OVEN) where the soil is heated and evolved gas is delivered to the gas chromatograph / mass spectrometer of the Lunar Advanced Volatile Analysis system (LAVA). For several years, tests of various sub-systems have been undertaken in a large cryo-vacuum chamber facility (VF-13) located at Glenn Research Center. In these tests a large tube (1.2 m high x 25.4 cm diameter) is filled with lunar simulant, NU-LHT-3M, prepared with known abundances of water. There are thermo-couples embedded at different depths, and also across the surface of the soil tube. The soil tube is placed in the chamber and cooled with LN2 as the pressure is reduced to approx.5-6x10(exp -6) Torr. Here we discuss May 2016 tests where two soil tubes were prepared and placed in the chamber. Also located in the chamber were 5 crucibles, an Inficon mass spectrometer, and a trolly permitting x-y translation, where the HRD and NIRVSS, were mounted. The shroud surrounding the soil tube was held at different temperatures for each tube to simulate a warm and cold lunar environment.

Oxygen Volatile Extraction Node↗

DOE OSTI2024

FREDA: A Web Application for the Processing, Analysis, and Visualization of Fourier‐Transform Mass Spectrometry Data

The high-resolution measurement capability of Fourier-transform mass spectrometry (FT-MS) has made it a necessity for exploring the molecular composition of complex organic mixtures, like soil, plant, aquatic, and petroleum samples. This demand has driven a need for informatics tools to explore and analyze FT-MS data in a robust and reproducible manner. FREDA is an interactive web application developed to enable spectrometrists to format, process, and explore their FT-MS data without the need for statistical programming expertise. FREDA was built to explore outputs from a molecular identification tool, like CoreMS, and provide a suite of methods to filter data, compute chemical properties of peaks, statistically compare samples and groups of samples, conduct exploratory data analysis, and download the results with a report detailing all steps conducted. To demonstrate the utility of FREDA, an example analysis was conducted using FT-MS data from a soil microbiology study of samples collected in two different soil depths at the Sphagnum bog forest north of Grand Rapids, Minnesota. Differences between the two depths are observed using Kendrick, Gibbs free energy, and van Krevelen plots. G-tests are used to quantify a significant difference between the groups. All analyses and plotting are conducted using only the FREDA application. FREDA is an open-source and readily available web application that allows users to explore and make statistically valid conclusions about their FT-MS data. The application is available online (https://map.emsl.pnnl.gov/app/freda) with a tutorial web series (https://youtu.be/k5HLE2kNSBY?si=yB6sGoyvzxrFf5MP) and freely accessible code on Github (https://github.com/EMSL-Computing/FREDA).

47 OTHER INSTRUMENTATION↗