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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Assessing horizontal gene transfer in the rhizosphere of Brachypodium distachyon using fabricated ecosystems (EcoFABs)

ABSTRACT Horizontal gene transfer (HGT) is a major process by which genes are transferred between microbes in the rhizosphere. However, examining HGT remains challenging due to the complexity of mimicking conditions within the rhizosphere. Fabricated ecosystems (EcoFABs) have been used to investigate several complex processes in plant-associated environments. Here we show that EcoFABs are efficient tools to examine and measure HGT frequency in the rhizosphere. We provide the first demonstration of gene transfer via a triparental conjugation system in the Brachypodium distachyon rhizosphere in an EcoFAB using Pseudomonas putida KT2440 as both donor and recipient bacterial strain with the donor containing a mobilizable and non-self-transmissible plasmid. We observed that the frequency of plasmid transfer in the rhizosphere is potentially dependent on the plant developmental stage and the composition and amount of root exudates. The frequency of plasmid transfer also increased with higher numbers of donor cells. We demonstrate the transfer of plasmid from P. putida to another B. distachyon root colonizer, Burkholderia sp. OAS925, showing HGT within a rhizosphere microbial community. Environmental stresses also influenced the rate and efficiency of HGT in the rhizosphere between different species and genera. This study provides a robust workflow to evaluate transfer of engineered plasmids in the rhizosphere when such plasmids are potentially introduced in a field or other plant-associated environments. IMPORTANCE We report the use of EcoFABs to investigate the HGT process in a rhizosphere environment. It highlights the potential of EcoFABs in recapitulating the dynamic rhizosphere conditions as well as their versatility in studying plant-microbe interactions. This study also emphasizes the importance of studying the parameters impacting the HGT frequency. Several factors such as plant developmental stages, nutrient conditions, number of donor cells, and environmental stresses influence gene transfer within the rhizosphere microbial community. This study paves the way for future investigations into understanding the fate and movement of engineered plasmids in a field environment.

Priya, Shweta↗
DOE OSTI2025

Root size and soil physicochemical properties drive microscale spatial patterns of Fe and As retention in the rice rhizosphere

Background and Aims: Radial oxygen loss from rice roots in flooded soils oxidizes and precipitates dissolved Fe(II), Mn(II), and As(III) into mixed Fe(III), Mn(III/IV), and As(V) as root plaque and in the rhizosphere soil. It is unknown how different soils and root sizes impact the spatial extent of Fe and As retention outside the root. Methods: We imaged cross-sections of 90 roots from 6 different soils using synchrotron μXRF imaging followed by k-means clustering and elliptical averaging to distinguish bulk soil, rhizosphere, plaque, and roots based on As and Fe patterns. Results: We found preferential As retention in the plaque and rhizospheres of most roots except small (< 0.45 mm) roots in silty soils with low P or high As. In contrast, clayey soils had similar As-Fe correlations across plaque, rhizosphere, and bulk soil. Large (> 0.45 mm) roots often had no oxidized rhizosphere region. We obtained an extensive dataset of 256 As and 155 Mn synchrotron μXANES measurements, which revealed that rhizosphere and plaque As was mainly inorganic As(V) and As(III), and Mn oxidation state varied between soils but not between belowground locations. Conclusion: Small roots in coarse-textured soils were less likely to have As retention in the plaque or rhizosphere compared to large roots and fine-textured soils. Furthermore, the unique and extensive data in this study provides new insight into soil and root size impacts on As retention in the rhizosphere. It is essential to investigate a representative number of samples to draw conclusions from XRF imaging.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Metabolic Interactions between Brachypodium and Pseudomonas fluorescens under Controlled Iron-Limited Conditions

Plant iron (Fe) nutritional status has a significant impact on rhizosphere microbial communities. While this effect has been attributed to alterations in the composition of root exudates, the underlying mechanisms are not known. Here, we investigated the effect of Fe deficiency on the interactions between the grass Brachypodium distachyon and the common soil bacteria Pseudomonas fluorescens SBW25. Increased phytosiderophore production was the most significant response of Brachypodium root exudation to Fe deficiency. We observed upregulated expression of phytosiderophore biosynthesis genes but lower accumulated exudate concentrations in the presence of Pseudomonas, indicating that the bacteria degrade these phytosiderophores. Pseudomonas did not produce endogenous siderophores under the low Fe conditions. Rather, the bacterial transcriptome revealed upregulation of four genes in response to Fe deficiency that contain motifs associated with cellular uptake of small molecules. Collectively, these results suggest that rhizosphere Pseudomonas fluorescens may take up phytosiderophores produced by grasses in response to Fe deficiency, and we propose target genes that may be involved. Our findings provide insight into the molecular basis for the exchange of C, N, and Fe between plants and bacteria under Fe deficient conditions. These interactions may contribute to differences in the rhizosphere microbial community structure across soil pH regimes.

Boiteau, Rene M.↗
DOE OSTI2025

Phosphorus budgets of intensively managed row crops at a long–term agroecosystem research site in the upper US Midwest

Phosphorus (P) budgets for cropping systems provide insights for keeping soil P at optimal levels for crops while avoiding excess inputs. We quantified 12 years of P inputs (fertilizer and atmospheric deposition) and outputs (harvest and leaching losses) for replicated maize (Zea mays L.)—soybean (Glycine max L.)—wheat (Triticum aestivum) crop rotations under conventional, no-till, reduced input, and biologically based (organic without compost or manure) management systems at the Kellogg Biological Station LTAR site in southwest Michigan. Conventional, no-till, and reduced input systems were fertilized between 13 and 50 kg P ha –1 depending on year. Soil test phosphorus (STP) was measured at 0- to 25-cm depth every autumn. Leached P was measured as dissolved P in the soil solution sampled beneath the rooting depth and combined with modeled percolation. Fertilization and harvest were the predominant P fluxes in the fertilized systems, whereas only harvest dominated P flux in the unfertilized organic system. Leaching losses were minor terms in the budgets, but leachate concentrations were nevertheless close to the range of concern for downstream eutrophication. Over the 12-year study period, the organic system exhibited a negative P balance (–82.0 kg P ha –1 ), coinciding with suboptimal STP levels, suggesting a need for P supplementation. In contrast, the fertilized systems showed positive P balances (mean: 70.1 kg P ha –1 ) with STP levels well above agronomic optima. Results underscore the importance of tailored P management strategies to sustain crop productivity while mitigating environmental impacts.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Selection and development of aptamers for pyoverdine

The rhizosphere is a small region surrounding plant roots that is enriched in biochemicals from root exudates and populated with fungi, nematode, and bacteria. Interaction of rhizosphere organisms with plants is mainly promoted by exudates from the roots. Root exudates contain biochemicals that come from primary and secondary metabolisms of plants. These biochemicals attract microbes, which influence plant nutrition. The rhizosphere bacteria (microbiome) are vital to plant nutrient uptake and influence biotic and abiotic stress and pathogenesis. Pseudomonas is a genus of gammaproteobacteria known for its ubiquitous presence in natural habitats and its striking ecological, metabolic, and biochemical diversity. Within the genus, members of the Pseudomonas fluorescens group are common inhabitants of soil and plant surfaces, and certain strains function in the biological control of plant disease, protecting plants from infection by soilborne and aerial plant pathogens. The soil bacterium Pseudomonas protegens Pf-5 (also known as Pseudomonas fluorescensPf-5) is a well-characterized biological strain, which is distinguished by its prolific production of the secondary metabolite, pyoverdine. Knowledge of the distribution of P. fluorescens secretory activity around plant roots is very important for understanding the interaction between P. fluorescens and plants and can be achieved by real time tracking of pyoverdine. To achieve the capability of real-time tracking in soil, we have used a structure-switching SELEX strategy to select high affinity ssDNA and 2’ F-Y-RNA aptamers with specificity for pyoverdine over other siderophores. Pyoverdines from various strains possess a conserved chromophore along with strain-specific peptide chain. Some of the isolated aptamers bind to chromophore of pyoverdine. These will identify pyoverdines from a variety of pseudomonads. Identification of aptamers that selectively bind the peptide portion of pyoverdine Pf-5 is underway. The identified aptamers that are broadly and narrowly specific for pyoverdines or Pf-5 will be optimized for integration into an electrochemical biosensor to track, in real time, P fluorescens activity and other pseudomonads in and around the rhizosphere.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

The Turbulent Pressure Spectrum Within the Roughness Sublayer of a Subarctic Forest Canopy

The turbulent static pressure spectrum E pp (k x ) as a function of longitudinal wavenumber k x in the roughness sublayer of forested canopies is of interest to a plethora of problems such as pressure transport in the turbulent kinetic energy budget, pressure pumping from snow or forest floor, and coupling between flow within and above canopies. Long term static pressure measurements above a sub-arctic forested canopy for near-neutral conditions during the winter and spring were collected and analyzed for three snow cover conditions: trees and ground covered with snow, trees are snow free but the ground is covered with snow, and snow free cover. In all three cases, it is shown that E pp (k x ) obeys the attached eddy hypothesis at low wavenumbers (1/δ < k x < 1/z) —with E pp (k x ) ∝ u$^4_*$k$^{-1}_x$ and Kolmogorov scaling in the inertial subrange at higher wavenumbers—with E pp (k x ) ∝ ϵ 4/3 k x -7/3 , where u * is the friction velocity at the canopy top, is the mean turbulent kinetic energy dissipation rate, z is the distance from the snow top, and is the boundary layer depth. The implications of these two scaling laws to the normalized root-mean squared pressure C p = o p /u$^2_*$ and its newly proposed logarithmic scaling with normalized wall-normal distance z/δ are discussed for snow covered and snow free vegetation conditions. The work here also shows that k$^{-1}_x$ the in the E pp (k x ) appears more extensive and robust than its longitudinal velocity counterpart.

Aslan, Toprak [Finnish Meteorological Inst., Helsi↗
DOE OSTI2022

Soil phosphorus drawdown by perennial bioenergy cropping systems in the Midwestern US

Abstract Without fertilization, harvest of perennial bioenergy cropping systems diminishes soil nutrient stocks, yet the time course of nutrient drawdown has not often been investigated. We analyzed phosphorus (P) inputs (fertilization and atmospheric deposition) and outputs (harvest and leaching losses) over 7 years in three representative biomass crops—switchgrass ( Panicum virgatum L.), miscanthus ( Miscanthus × giganteus ) and hybrid poplar trees ( Populus nigra × P. maximowiczii )—as well as in no‐till corn (maize; Zea mays L.) for comparison, all planted on former cropland in SW Michigan, USA. Only corn received P fertilizer. Corn (grain and stover), switchgrass, and miscanthus were harvested annually, while poplar was harvested after 6 years. Soil test P (STP; Bray‐1 method) was measured in the upper 25 cm of soil annually. Harvest P removal was calculated from tissue P concentration and harvest yield (or annual woody biomass accrual in poplar). Leaching was estimated as total dissolved P concentration in soil solutions sampled beneath the rooting depth (1.25 m), combined with hydrological modeling. Fertilization and harvest were by far the dominant P budget terms for corn, and harvest P removal dominated the P budgets in switchgrass, miscanthus, and poplar, while atmospheric deposition and leaching losses were comparatively insignificant. Because of significant P removal by harvest, the P balances of switchgrass, miscanthus, and poplar were negative and corresponded with decreasing STP, whereas P fertilization compensated for the harvest P removal in corn, resulting in a positive P balance. Results indicate that perennial crop harvest without P fertilization removed legacy P from soils, and continued harvest will soon draw P down to limiting levels, even in soils once heavily P‐fertilized. Widespread cultivation of bioenergy crops may, therefore, alter P balances in agricultural landscapes, eventually requiring P fertilization, which could be supplied by P recovery from harvested biomass.

09 BIOMASS FUELS↗
DOE OSTI2020

Serendipita bescii promotes winter wheat growth and modulates the host root transcriptome under phosphorus and nitrogen starvation

Summary Serendipita vermifera ssp. bescii , hereafter referred to as S. bescii , is a root‐associated fungus that promotes plant growth in both its native switchgrass host and a variety of monocots and dicots. Winter wheat ( Triticum aestivum L.), a dual‐purpose crop, used for both forage and grain production, significantly contributes to the agricultural economies of the Southern Great Plains, USA. In this study, we investigated the influence of S. bescii on growth and transcriptome regulation of nitrogen (N) and phosphorus (P) metabolism in winter wheat. Serendipita bescii significantly improved lateral root growth and forage biomass under a limited N or P regime. Further, S. bescii activated sets of host genes regulating N and P starvation responses. These genes include, root‐specific auxin transport, strigolactone and gibberellin biosynthesis, degradation of phospholipids and biosynthesis of glycerolipid, downregulation of ammonium transport and nitrate assimilation, restriction of protein degradation by autophagy and subsequent N remobilization. All these genes are hypothesized to regulate acquisition, assimilation and remobilization of N and P. Based on transcriptional level gene regulation and physiological responses to N or P limitation, we suggest S. bescii plays a critical role in modulating stress imposed by limitation of these two critical nutrients in winter wheat.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Specific modulation of the root immune system by a community of commensal bacteria

Significance In natural environments, plants establish intimate interactions with a wide diversity of microbes. It is unknown, however, how microbiota composed of commensal bacteria colonize roots in the face of a sophisticated plant immune system that evolved to recognize microbial-associated molecular patterns. We investigate the interaction between plant immune system function and the root microbiota. We report that root-associated commensal bacteria actively suppress the host immune response in the context of a community. Suppressors and nonsuppressors co-occur in the root microbiome and the presence of the former can enhance the colonization ability of the latter. We highlight the role of a specific sector of the plant immune system and its suppression in gating microbial access to the roots.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Microbial seasonality promotes soil respiratory carbon emission in natural ecosystems: A modeling study

Seasonality is a key feature of the biosphere and the seasonal dynamics of soil carbon (C) emissions represent a fundamental mechanism regulating the terrestrial–climate interaction. We applied a microbial explicit model—CLM-Microbe—to evaluate the impacts of microbial seasonality on soil C cycling in terrestrial ecosystems. Additionally, the CLM-Microbe model was validated in simulating belowground respiratory fluxes, that is, microbial respiration, root respiration, and soil respiration at the site level. On average, the CLM-Microbe model explained 72% (n = 19, p < 0.0001), 65% (n = 19, p < 0.0001), and 71% (n = 18, p < 0.0001) of the variation in microbial respiration, root respiration, and soil respiration, respectively. We then compared the model simulations of soil respiratory fluxes and soil organic C content in top 1 m between the CLM-Microbe model with (CLM-Microbe) and without (CLM-Microbe_wos) seasonal dynamics of soil microbial biomass in natural biomes. Removing soil microbial seasonality reduced model performance in simulating microbial respiration and soil respiration, but led to slight differences in simulating root respiration. Compared with the CLM-Microbe, the CLM-Microbe_wos underestimated the annual flux of microbial respiration by 0.6%–32% and annual flux of soil respiration by 0.4%–29% in natural biomes. Correspondingly, the CLM-Microbe_wos estimated higher soil organic C content in top 1 m (0.2%–7%) except for the sites in Arctic and boreal regions. Our findings suggest that soil microbial seasonality enhances soil respiratory C emissions, leading to a decline in SOC storage. An explicit representation of soil microbial seasonality represents a critical improvement for projecting soil C decomposition and reducing the uncertainties in global C cycle projection under the changing climate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

ACORN Review: NPK fertilizer use in loblolly pine plantations: Who are we really feeding?

Optimizing loblolly pine (Pinus taeda L.) productivity using fertilizers and various site management practices has been a goal of foresters for decades. Nitrogen (N), phosphorus (P), and potassium (K) are the three most operationally applied fertilizers to loblolly pine silviculture and are of primary importance to their total productivity. Fertilizer recommendations for N, P, and K in loblolly pine are primarily made on abiotic factors such as site and soil characteristics, while the biological factors controlling nutrient uptake are typically overlooked in the production and optimization of these stands. Arguably the most important of these biological factors are the diverse ectomycorrhizal fungal (ECM) communities that colonize the fine roots of almost all loblolly pine trees. The mantle formed by ECM fungi on short-root tips presents a barrier for direct apoplastic uptake of N, P, and K from soil solution by pine roots. In well-colonized roots, the tree is dependent on symplastic fungal transport of N, P, and K foraged from the soil by the extraradical hyphal network. This raises the question: Who are we really feeding if the ECM fungi are the ones assimilating most of the tree's total nutritional requirements? Considering multiple species of ECM fungi can inhabit a single root system, many questions remain regarding the drivers of colonization, why some species are more efficient at taking up and exchanging nutrients with their hosts than others, and why certain fertilizers directly affect the morphology of ECM growth. The purposes of this review here are (1) to explore how the most commonly commercially applied macronutrients, N, P, and K, affect the relationship between loblolly pine and ECM communities, and (2) to propose future directions to investigate, preserve, and manipulate these interactions in pine plantations to optimize productivity.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Hole Trapping at Acceptor Impurities and Alloying Elements in AlN

Hole localization is a root cause of difficulties in p-type doping of aluminum nitride. Herein, the stability of localized holes in AlN and their susceptibility to self-trapping within bulk material or in the presence of isovalent elements and acceptor impurities are calculated. It is found that self-trapped holes are metastable in bulk AlN, and also exhibit a very low barrier to detrapping. However, holes become trapped in the presence of acceptor impurities as well as isovalent elements such as B, In, and Sc, and may contribute to the broad luminescence observed in AlN alloys. It is also found that hole trapping contributes to the large ionization energies for acceptors in AlN. Most acceptors can also trap a second hole, becoming positively charged and further exacerbating difficulties in doping aluminum nitride p type. Furthermore, the stability of trapped holes is found to scale with atomic size mismatch to Al.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2023

Hugoniot, sound speed, and phase transitions of single-crystal sapphire for pressures 0.2–2.1 TPa

Sapphire (Al 2 O 3 ) is a major constituent of the Earth's mantle and has significant contributions to the field of high-pressure physics. Constraining its Hugoniot over a wide pressure range and identifying the location of shock-driven phase transitions allows for development of a multiphase equation of state and enables its use as an impedance-matching standard in shock physics experiments. In this paper we present measurements of the principal Hugoniot and sound velocity from direct impact experiments using magnetically launched flyers on the Z machine at Sandia National Laboratories. The Hugoniot was constrained for pressures from 0.2–2.1 TPa and a four-segment piecewise linear shock-velocity–particle-velocity fit was determined. First-principles molecular dynamics simulations were conducted and agree well with the experimental Hugoniot. Sound-speed measurements identified the onset of melt between 450 and 530 GPa, and the Hugoniot fit refined the onset to 525 ± 13 GPa. A phase diagram which incorporates literature diamond-anvil cell data and melting measurements is presented.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Novel 3D Force Sensors for a Cost-Effective 3D Force Plate for Biomechanical Analysis

Three-dimensional force plates are important tools for biomechanics discovery and sports performance practice. However, currently, available 3D force plates lack portability and are often cost-prohibitive. To address this, a recently discovered 3D force sensor technology was used in the fabrication of a prototype force plate. Thirteen participants performed bodyweight and weighted lunges and squats on the prototype force plate and a standard 3D force plate positioned in series to compare forces measured by both force plates and validate the technology. For the lunges, there was excellent agreement between the experimental force plate and the standard force plate in the X-, Y-, and Z-axes (r = 0.950–0.999, p < 0.001). For the squats, there was excellent agreement between the force plates in the Z-axis (r = 0.996, p < 0.001). Across axes and movements, root mean square error (RMSE) ranged from 1.17% to 5.36% between force plates. Although the current prototype force plate is limited in sampling rate, the low RMSEs and extremely high agreement in peak forces provide confidence the novel force sensors have utility in constructing cost-effective and versatile use-case 3D force plates.

42 ENGINEERING↗
DOE OSTI2022

Chronic drought differentially alters the belowground microbiome of drought tolerant and drought susceptible genotypes of Populus trichocarpa

Populus trichocarpa is an ecologically important tree species and economically important biofeedstock. Belowground, P. trichocarpa interacts with diverse microorganisms in the rhizosphere and root endosphere. These plant-microbial interactions can bolster a variety of plant processes, ranging from pathogen suppression to drought tolerance, yet we know little about the impact of chronic drought stress on P. trichocarpa’s belowground microbiomes. To investigate the interactive effect of chronic drought on belowground microbial communities across genetically different P. trichocarpa hosts, we assessed archaeal/bacterial and fungal communities within the root endosphere, rhizosphere, and surrounding bulk soil of selected genotypes in a long-term drought experiment in Boardman, OR, USA. We sequenced the 16S rRNA and ITS2 gene region on samples collected from 16 distinct P. trichocarpa genotypes in plots with full or reduced irrigation. Eight of these genotypes have been previously identified as drought tolerant while the other eight genotypes were drought susceptible. While reduced irrigation influenced the composition of every archaeal/bacterial microbiome compartment, fungal communities were only affected in the rhizosphere and bulk soil compartments. Drought-tolerant bacteria, such as Actinobacteria, were differentially abundant in reduced irrigation across all belowground microbiomes. Host drought-tolerance influenced plant-associated microbiome compartments but had little impact on the bulk soil compartment. Drought-tolerant trees were enriched for potential growth-promoting microorganisms in the root endosphere and rhizosphere, including Sphingomonas bacteria and ectomycorrhizal fungi. Overall, associations of growth-promoting microbes in drought resistant P. trichocarpa genotypes can be leveraged to improve biofeedstock productivity in regions prone to periodic drought.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Direct root contact among neighboring plants influences activity of soil extracellular enzymes

Composition and diversity of vegetation systems can influence soil microbial activity and extracellular enzyme (EE) dynamics, which are crucial for soil carbon (C) accrual and nutrient cycling. Yet, the impact of plant interactions and competition on EE activities remains a notable knowledge gap. This study examines how direct root contact and neighboring plant identity affect the activity and spatial distribution of four key soil EEs: β-glucosidase (BGlu), chitinase, acid phosphatase (AcidP), and alkaline phosphatase (AlkP). Using three-compartment rhizoboxes with switchgrass (Panicum virgatum L.) grown alongside bush clover (Lespedeza capitata Michx.), and black-eyed Susan (Rudbeckia hirta L.), we assessed enzyme activities using zymography under conditions that either allowed or restricted direct root contact by root barriers. Results show that root proliferation and species interactions significantly influenced EE activity. While BGlu and AcidP activities were strongly correlated with root biomass, AlkP activity was consistently higher in the absence of root barriers, indicating a pronounced microbial response to plant interactions via direct/close root contacts. Additionally, soil phosphorus availability modulated enzyme activity, with higher phosphatase activities in low-P soils. Furthermore, these findings highlight the importance of root-root interactions and plant species composition in shaping soil biochemical processes.

enyzme activity↗