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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Synthetic Soil Aggregates: Bioprinted Habitats for High-Throughput Microbial Metaphenomics

The dynamics of microbial processes are difficult to study in natural soil, owing to the small spatial scales on which microorganisms operate and to the opacity and chemical complexity of the soil habitat. To circumvent these challenges, we have created a 3D-bioprinted habitat that mimics aspects of natural soil aggregates while providing a chemically defined and translucent alternative culturing method for soil microorganisms. Our Synthetic Soil Aggregates (SSAs) retain the porosity, permeability, and patchy resource distribution of natural soil aggregates—parameters that are expected to influence emergent microbial community interactions. We demonstrate the printability and viability of several different microorganisms within SSAs and show how the SSAs can be integrated into a multi-omics workflow for single SSA resolution genomics, metabolomics, proteomics, lipidomics, and biogeochemical assays. We study the impact of the structured habitat on the distribution of a model co-culture microbial community and find that it is significantly different from the spatial organization of the same community in liquid culture, indicating a potential for SSAs to reproduce naturally occurring emergent community phenotypes. The SSAs have the potential as a tool to help researchers quantify microbial scale processes in situ and achieve high-resolution data from the interplay between environmental properties and microbial ecology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A critical review of 25 years of glomalin research: a better mechanical understanding and robust quantification techniques are required

Arbuscular mycorrhizal fungi (AMF) are important contributors to both plant and soil health. Twenty-five years ago, researchers discovered ‘glomalin’, a soil component potentially produced by AMF, which was unconventionally extracted from soil and bound by a monoclonal antibody raised against Rhizophagus irregularis spores. ‘Glomalin’ can resist boiling, strong acids and bases, and protease treatment. Researchers proposed that ‘glomalin’ is a 60 kDa heat shock protein produced by AMF, while others suggested that it is a mixture of soil organic materials that are not unique to AMF. Despite disagreements on the nature of ‘glomalin’, it has been consistently associated with a long list of plant and soil health benefits, including soil aggregation, soil carbon storage and enhancing growth under abiotic stress. The benefits attributed to ‘glomalin’ have caused much excitement in the plant and soil health community; however, the mechanism(s) for these benefits have yet to be established. This review provides insights into the current understanding of the identity of ‘glomalin’, ‘glomalin’ quantification, and the associated benefits of ‘glomalin’. We invite the community to think more critically about how glomalin-associated benefits are generated. We suggest a series of experiments to test hypotheses regarding the nature of ‘glomalin’ and associated health benefits.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Partial substitution of rice husks for manure in greenhouse vegetable fields: Insight from soil carbon stock and aggregate stability

Abstract Soil aggregate stability and C stock are key factors in greenhouse vegetable production, which are influenced by the application of different organic materials. However, the responses of soil aggregate stability and C stock to organic amendment in greenhouse vegetable fields are not well understood. A 5‐year study was carried out in greenhouse vegetable fields to investigate the effect of partial substitution of rice husks for manure on soil aggregate stability, C compositions, and their relationships. Four treatments included: (a) no organic fertilization (control), (b) 30 t ha −1 chicken manure (CM), (c) 30 t ha −1 rice husks (RH), and (d) 10 t ha −1 chicken manure plus 20 t ha −1 rice husks (MR). Rice husks addition significantly increased the proportion of >2 mm aggregates and mean weight diameter (MWD), while manure addition showed no difference with control. Polysaccharide and humin (HM) were increased with rice husks addition (RH and MR) compared with that in CM treatment. Polysaccharide and HM caused 86.03% variation of soil aggregate, in which polysaccharide and HM contributed 76.3 and 9.7%, respectively. The soil C stock in CM, RH, and MR treatments was increased by 146, 175, and 164% compared with control, respectively. Aliphatic‐C and amorphous Fe‐oxides (Fe‐ox) content were as higher in MR added soil than those in RH treatment. Partial substitution of rice husk for manure improved soil aggregation stability and thus enhanced C stock by suppling more polysaccharide, HM and liberated soil minerals, which was conducive to the sustainable development in greenhouse vegetable production.

Fei, Chao↗
DOE OSTI2020

Soil aggregate-mediated microbial responses to long-term warming

Soil microbial carbon use efficiency (CUE) is a combination of growth and respiration, which may respond differently to climate change depending on physical protection of soil carbon (C) and its availability to microbes. In a mid-latitude hardwood forest in central Massachusetts, 27 years of soil warming (+5 °C) has resulted in C loss and altered soil organic matter (SOM) quality, yet the underlying mechanisms remain unclear. In this work, we hypothesized that long-term warming reduces physical aggregate protection of SOM, microbial CUE, and its temperature sensitivity. Soil was separated into macroaggregate (250–2000 μm) and microaggregate (<250 μm) fractions, and CUE was measured with 18 O enriched water (H 2 18 O) in samples incubated at 15 and 25 °C for 24 h. We found that long-term warming reduced soil C and nitrogen concentrations and extracellular enzyme activity in macroaggregates, but did not affect physical protection of SOM. Long-term warming showed little effect on CUE or microbial biomass turnover time because it reduced both growth and respiration. However, CUE was less temperature sensitive in macroaggregates from the warmed compared to the control plots. Our findings suggest that microbial thermal responses to long-term warming occur mostly in soil compartments where SOM is less physically protected and thus more vulnerable to microbial degradation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Microbial responses to long-term warming differ across soil microenvironments

Soil carbon loss is likely to increase due to climate warming, but microbiomes and microenvironments may dampen this effect. In a 30-year warming experiment, physical protection within soil aggregates affected the thermal responses of soil microbiomes and carbon dynamics. In this study, we combined metagenomic analysis with physical characterization of soil aggregates to explore mechanisms by which microbial communities respond to climate warming across different soil microenvironments. Long-term warming decreased the relative abundances of genes involved in degrading labile compounds (e.g. cellulose), but increased those genes involved in degrading recalcitrant compounds (e.g. lignin) across aggregate sizes. These changes were observed in most phyla of bacteria, especially for Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, and Planctomycetes. Microbial community composition was considerably altered by warming, leading to declined diversity for bacteria and fungi but not for archaea. Microbial functional genes, diversity, and community composition differed between macroaggregates and microaggregates, indicating the essential role of physical protection in controlling microbial community dynamics. Our findings suggest that microbes have the capacity to employ various strategies to acclimate or adapt to climate change (e.g. warming, heat stress) by shifting functional gene abundances and community structures in varying microenvironments, as regulated by soil physical protection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Cover crops and poultry litter impact on soil structural stability in dryland soybean production in southeastern United States

Abstract This study explored the efficacy of soil aggregate indices in quantifying soil structural development, utilizing 5‐year field experiment data from the Southeastern United States. The experiment utilized a split‐plot design with cover crops (native vegetation as control, cereal rye (Secale cerealeL.), winter wheat (Triticum aestivum), hairy vetch (Vicia villosa), and mustard (Brassica rapa) plus cereal rye as the main factor and fertilizer source (no fertilizer as control, inorganic fertilizer with phosphorus, potassium, and elemental sulfur, and poultry litter) as the secondary factor. Aggregate size fractions were determined using the wet‐sieving method, and aggregate stability index (ASI), mean weight diameter (MWD), geometric mean diameter (GMD), and fractal dimension (FD) were calculated to assess soil structural stability. Main effects results indicated that cereal rye (55.11%) and poultry litter (50.97%) exhibited the highest ASI values. The highest MWD, GMD, and FD were observed under mustard plus cereal rye (1.187 mm), cereal rye (0.462 mm), and hairy vetch (2.573), respectively. Principal component analysis revealed that cover crops significantly improved soil aggregate structure and stability, overcoming limitations of sole fertilization practices. Regression analysis suggested that ASI, MWD, and GWD positively correlated with soil organic carbon, whereas FD negatively correlated with MWD, GMD, and ASI. Principal component analysis exhibited that FD decreased with increasing soil organic carbon, ASI, MWD, and GMD, demonstrating that lower FD values indicate enhanced soil aggregation and structure. Assessed indices, FD included, effectively gauged soil structural stability. These metrics should be prioritized in managerial decisions to support soil productivity and health in agricultural systems.

Agriculture↗
DOE OSTI2021

Development of energetic and enzymatic limitations on microbial carbon cycling in soils

Soil organic carbon (SOC) constitutes an important reservoir in the global carbon cycle that is vulnerable to transformation and loss from land use and climate change. Anoxic conditions protect SOC from microbial degradation through limiting the energetics of respiration and inhibiting extracellular oxidative enzymes. Given growing evidence of prevalent anaerobic microsites in upland soils, we designed an experiment testing the development of dissolved organic carbon (DOC) signatures of energetic and enzymatic limitations on microbial carbon utilization across simulated soil aggregates or peds. Reactors comprised a soil column “aggregate” underlying an advective “macropore” channel. Soils received downward diffusive inputs of aerated porewater media with added nitrate, sulfate, or no amendment—where native ferrihydrite served as dominant anaerobic terminal electron acceptor (TEA). After 40 days, added nitrate resulted in highest bulk respiration and DOC production while sulfate did not differ from the control. Nominal oxidation state of carbon (NOSC) was higher (more favorable) with added TEAs at soil surfaces and decreased with depth, while NOSC in the non-amended soil remained lower and constant with depth. DOC generally increased with depth, which along with decreasing NOSC values indicates joint electron-donor and acceptor control over respiration energetics. Of all organic compound classes, only the relative abundance of phenolics increased between 0 and 0.5 cm depth, which aligns with the oxic-anoxic transition and suggests oxidative enzyme inhibition. Furthermore, our results suggest that oxygen limitation within upland soil aggregates may preserve SOC via both energetic and enzymatic C protection mechanisms, which are vulnerable upon exposure to oxygen.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Long‐term changes in soil carbon and nitrogen fractions in switchgrass, native grasses, and no‐till corn bioenergy production systems

Cellulosic bioenergy is a primary land-based climate mitigation strategy, with soil carbon (C) storage and nitrogen (N) conservation as important mitigation elements. Here, we present 13 years of soil C and N change under three cellulosic cropping systems: monoculture switchgrass (Panicum virgatum L.), a five native grasses polyculture, and no-till corn (Zea mays L.). Soil C and N fractions were measured four times over 12 years. Bulk soil C in the 0–25 cm depth at the end of the study period ranged from 28.4 (± 1.4 se) Mg C ha −1 in no-till corn, to 30.8 (± 1.4) Mg C ha −1 in switchgrass, and to 34.8 (± 1.4) Mg C ha −1 in native grasses. Mineral-associated organic matter (MAOM) ranged from 60% to 90% and particulate organic matter (POM) from 10% to 40% of total soil C. Over 12 years, total C as well as both C fractions persisted under no-till corn and switchgrass and increased under native grasses. In contrast, POM N stocks decreased 33% to 45% across systems, whereas MAOM N decreased only in no-till corn and by less than 13%. Declining POM N stocks likely reflect pre-establishment land use, which included alfalfa and manure in earlier rotations. Root production and large soil aggregate formation explained 69% (p < 0.001) and 36% (p = 0.024) of total soil C change, respectively, and 60% (p = 0.020) and 41% (p = 0.023) of soil N change, demonstrating the importance of belowground productivity and soil aggregates for producing and protecting soil C and conserving soil N. Differences between switchgrass and native grasses also indicate a dependence on plant diversity. Soil C and N benefits of bioenergy crops depend strongly on root productivity and pre-establishment land use.

09 BIOMASS FUELS↗
DOE OSTI2021

Physical protection regulates microbial thermal responses to chronic soil warming

Climate warming can affect the temperature sensitivity of microbial activity and growth efficiency, possibly explained by changes to microbially unavailable carbon (C) protected within in soil aggregates. Here, we assessed physical protection by crushing macroaggregates (250–2000 μm) and microaggregates (<250 μm) isolated from mineral soils exposed to 27 years of experimental warming (+5 °C). We hypothesized that removal of physical protection would increase microbial activity and reduce C use efficiency (CUE). We found that crushing increased microbial respiration and biomass turnover rate, but did not affect CUE. We also hypothesized that long-term warming would reduce the effect of physical protection on microbial activity, and that physical protection would attenuate microbial temperature sensitivity in heated compared to control soils. We found that long-term warming was associated with a smaller effect of physical protection for microbial respiration but with a larger effect for biomass turnover rate in macroaggregates. Physical protection reduced the temperature sensitivity of respiration but enhanced the temperature sensitivity of microbial biomass turnover rate in heated compared to control soils. Our work shows that long-term warming has contrasting effects on how microbial respiration, biomass turnover rate, and their thermal responses are mediated by physical protection within soil aggregates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Organic carbon enables the biotic engineering of beneficial soil structure in Profundihumic and Haplic Ferralsols

We investigated how organic matter may, directly and indirectly, modify the porosity of Ferralsols, that is, deeply weathered soils of the tropics and subtropics. Although empirical and anecdotal evidence suggests that organic matter accumulation may increase porosity, a mechanistic understanding of the processes underlying this beneficial effect is lacking, especially so for Ferralsols. To achieve our end, we leveraged the fact that the Profundihumic qualifier of Ferralsols (PF) is distinguished from Haplic Ferralsols (HF) by both a much larger average carbon content in the first 1 m of soil depth (19 kg C m -3 in PF vs. 10 kg C m -3 in HF) and a significantly lower bulk density (1.05 ± 0.08 kg L -1 in PF vs. 1.21 ± 0.05 kg L -1 in HF). Through exhaustive modelling of carbon – bulk density relationships, we demonstrate that the lower bulk density of PF cannot be satisfactorily explained by a simple dilution effect. Rather, we found that bulk density correlated with carbon content when combined with carbon: nitrogen ratio (r 2 = 0.51), black carbon content (r 2 = 0.75), and Δ 14 C (r 2 =0.81). Total pore space was greater in PF (61± 3%) than in HF (55 ± 2%), but x-ray computed tomography revealed that pore space inside soil aggregates of 4–5 mm diameter does not vary between the studied Ferralsols. We further observed nearly twice as many roots and burrows in PF compared with HF. We thus infer that the mechanism responsible for the increase in porosity is most likely an enhancement of resource availability (e.g., energy, carbon, and nutrients) for the organisms (earthworms, ants, termites, etc.) that physically displace soil particles and promote soil aggregation. As a result of increased resource availability, soil organisms can create especially the mesoscale structural soil features necessary for unrestricted water flow and rapid gas exchange. In conclusion, this insight paves the way for the development of land management technologies to optimize the physical shape and capacity of the soil bioreactor.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1984

Aggregating available soil water holding capacity data for crop yield models

The total amount of water available to plants that is held against gravity in a soil is usually estimated as the amount present at -0.03 MPa average water potential minus the amount present at -1.5 MPa water potential. This value, designated available water-holding capacity (AWHC), is a very important soil characteristic that is strongly and positively correlated to the inherent productivity of soils. In various applications, including assessing soil moisture status over large areas, it is necessary to group soil types or series as to their productivity. Current methods to classify AWHC of soils consider only total capacity of soil profiles and thus may group together soils which differ greatly in AWHC as a function of depth in the profile. A general approach for evaluating quantitatively the multidimensional nature of AWHC in soils is described. Data for 902 soil profiles, representing 184 soil series, in Indiana were obtained from the Soil Characterization Laboratory at Purdue University. The AWHC for each of ten 150-mm layers in each soil was established, based on soil texture and parent material. A multivariate clustering procedure was used to classify each soil profile into one of 4, 8, or 12 classes based upon ten-dimensional AWHC values. The optimum number of classes depends on the range of AWHC in the population of oil profiles analyzed and on the sensitivity of a crop to differences in distribution of water within the soil profile.

Seubert, C. E.↗
DOE OSTI2022

A workflow for segmenting soil and plant X-ray computed tomography images with deep learning in Google’s Colaboratory

X-ray micro-computed tomography (X-ray μCT) has enabled the characterization of the properties and processes that take place in plants and soils at the micron scale. Despite the widespread use of this advanced technique, major limitations in both hardware and software limit the speed and accuracy of image processing and data analysis. Recent advances in machine learning, specifically the application of convolutional neural networks to image analysis, have enabled rapid and accurate segmentation of image data. Yet, challenges remain in applying convolutional neural networks to the analysis of environmentally and agriculturally relevant images. Specifically, there is a disconnect between the computer scientists and engineers, who build these AI/ML tools, and the potential end users in agricultural research, who may be unsure of how to apply these tools in their work. Additionally, the computing resources required for training and applying deep learning models are unique, more common to computer gaming systems or graphics design work, than to traditional computational systems. To navigate these challenges, we developed a modular workflow for applying convolutional neural networks to X-ray μCT images, using low-cost resources in Google’s Colaboratory web application. Here we present the results of the workflow, illustrating how parameters can be optimized to achieve best results using example scans from walnut leaves, almond flower buds, and a soil aggregate. We expect that this framework will accelerate the adoption and use of emerging deep learning techniques within the plant and soil sciences.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Deciphering exopolysaccharide functional specificity via visualization of chemical motifs that mediate microbial-microenvironment interactions in soil micromodels

Exopolysaccharides (EPS) are carbohydrate-based matrices of microbial biofilms that microbes use to adapt to their surroundings. Microbial EPS also promotes soil aggregate stability and contributes toward soil health by reducing erosion caused by continued land use. The chemical structure of EPS, even within single species biofilms, can vary greatly: from repeating units and branching patterns to the non-carbohydrate decorations. Despite the wealth of knowledge on EPS chemistry, many unresolved questions regarding the biological implications of EPS chemical variations remain. Here, we develop a mass spectrometry imaging toolbox that reveal how EPS chemistry enables microbial adaptation to different microenvironments such as specific moisture, soil-biofilm interfaces, and food source proximity. First, we developed emulated soil micromodels (ESMs), microfluidic channels that simulate the physical properties of soil, for biofilm formation in different microenvironments. Then, in order to map chemical features of EPS in these micromodels, we develop strategies for in-situ releasing of oligosaccharides using specific enzymes. Lastly, we optimized matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging (MSI) to spatially analyze the released compounds in ESMs.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Conservation management decreases surface runoff and soil erosion

Conservation management practices – including agroforestry, cover cropping, no-till, reduced tillage, and residue return – have been applied for decades to control surface runoff and soil erosion, yet results have not been integrated and evaluated across cropping systems. In this study we collected data comparing agricultural production with and without conservation management strategies. We used a bootstrap resampling analysis to explore interactions between practice type, soil texture, surface runoff, and soil erosion. We then used a correlation analysis to relate changes in surface runoff and soil erosion to 13 other soil health and agronomic indicators, including soil organic carbon, soil aggregation, infiltration, porosity, subsurface leaching, and cash crop yield. Across all conservation management practices, surface runoff and erosion had respective mean decreases of 67% and 80% compared with controls. Use of cover cropping provided the largest decreases in erosion and surface runoff, thus emphasizing the importance of maintaining continuous vegetative cover on soils. Coarse- and medium-textured soils had greater decreases in both erosion and runoff than fine-textured soils. Changes in surface runoff and soil erosion under conservation management were highly correlated with soil organic carbon, aggregation, porosity, infiltration, leaching, and yield, showing that conservation practices help drive important interactions between these different facets of soil health. This study offers the first large-scale comparison of how different conservation agriculture practices reduce surface runoff and soil erosion, and at the same time provides new insight into how these interactions influence the improvement or loss of soil health.

58 GEOSCIENCES↗
DOE OSTI2024

Soil properties and root characteristics across four lowland Panamanian forests from 0 - 1 m soil depths

Objectives:Fine roots significantly influence ecosystem-scale cycling of nutrients, carbon (C), and water, yet there is limited understanding of how fine root traits vary across and within tropical forests, some of Earth's most C-rich ecosystems. The biomass of fine roots can impact soil carbon storage, as root mortality is a primary source of new carbon to soils. A positive relationship has been observed between fine root biomass and soil carbon stocks in Panama (Cusack et al 2018). Beyond biomass, root characteristics like specific root length (SRL) could also influence soil carbon, as roots with higher SRL are less dense and thinner, potentially decomposing more easily or promoting soil aggregation. Understanding the effects of root morphology and tissue quality on soil carbon storage and with soil properties in general can improve predictions of landscape-scale carbon patterns. We aggregated new data of root biomass, morphology and nutrient content at 0-10 cm, 10-20 cm, 20-50 cm and 50-100 cm depth increments across four distinct lowland Panamanian forests and paired with already published datasets (Cusack et al 2018; Cusack and Turner 2020) of soil chemistry from the same sites and soil depths to explore relationship between soil carbon stocks and root characteristics.Datasets included:The datasets provided include .csv and .xlsx files for fine root characteristics and soil chemistry from four different forests across 0-10 cm, 10-20 cm, 20-50 cm, and 50-100 cm depth increments. Root characteristics include live fine root biomass, dead fine root biomass, coarse root biomass, specific root length, root diameter, root tissue density, specific root area, root %N, root %C, and root C/N ratio. Soil chemistry data includes total carbon (TC), dissolved organic carbon (DOC), bulk density, total phosphorus (TP), available phosphorus (AEM Pi), and various Mehlich-extractable elements such as aluminum, calcium, iron, potassium, manganese, phosphorus, and zinc. Nitrogen content measures include ammonium, nitrate, total dissolved nitrogen (TDN), dissolved inorganic nitrogen (DIN), and dissolved organic nitrogen (DON). The dataset also includes total exchangeable bases (TEB) and effective cation exchange capacity (ECEC) in both centimoles of charge per kilogram and micromoles of charge per gram. The soil chemistry data was obtained from Cusack et al (2018) and Cusack and Turner (2020) and paired with root characteristics data for the same depth increments and sites. Additionally, a .kml file is provided with coordinates for all 32 plots included in the study across four forests (n = 8 plots per site). Root data was averaged across these 8 plots per site and soil data was collected in one pit in each site. This dataset serves as baseline data before a throughfall exclusion experiment, Panama Rainforest Changes with Experimental Drying (PARCHED), was implemented. No special software is needed to open these files.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Reducing the matrix effect in mass spectral imaging of biofilms using flow-cell culture

The interactions between soil microorganisms and soil minerals play a crucial role in the formation and evolution of minerals and the stability of soil aggregates. Due to the heterogeneity and diversity of the soil environment, the under-standing of the functions of bacterial biofilms in soil minerals at the microscale is limited. A soil mineral-bacterial biofilm system was used as a model in this study, and it was analyzed by time-of-flight secondary ion mass spectrometry (ToF-SIMS) to acquire molecular level information. Static culture in multi-wells and dynamic flow-cell culture in microfluidics of biofilms were investigated. Our results show that more characteristic molecules of biofilms can be observed in SIMS spectra of the flow-cell culture. In contrast, biofilm signature peaks are buried under the mineral components in SIMS spectra in the static culture case. Spectral overlay was used in peak selection prior to performing Principal component analysis (PCA). Comparisons of the PCA results between the static and flow-cell culture show more pronounced molecular features and higher loadings of organic peaks of the dynamic cultured specimens. For example, fatty acids secreted from bacterial biofilm extracellular polymeric substance are likely to be responsible for biofilm dispersal due to mineral treatment up to 48 h. Such findings suggest that the use of microfluidic cells to dynamically culture biofilms be a more suitable method for reducing the matrix effect arisen from the growth medium and minerals as a perturbation fac-tor for improved spectral and multivariate analysis of complex mass spectral data in ToF-SIMS. These results show that the interaction mechanism between biofilms and soil minerals at the molecular level can be better studied using the flow-cell culture and advanced mass spectral imaging techniques like ToF-SIMS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗