Research
In our research we explore the biogeochemical processes occurring at the soil-water-plant interface (a.k.a. the Rhizosphere) and how these interactions influence ecosystem level processes in both agronomic and native environments (figure below). Below are descriptions of the various past and current rhizolab projects (select the + sign for expanded content).
PROJECTS:
- SOIL P AND CROP PRODUCTIVITY -
Rhizosphere priming effects on legacy organic phosphorus
(Po) in managed agroecosystems.
Sponsor: USDA-AFRI, Microbial communities program
(Po) in managed agroecosystems.
Sponsor: USDA-AFRI, Microbial communities program
High-quality mineral P fertilizers are essential for sustainable crop production, however, P is a finite resource with an estimated 80-100 years of reserves remaining. Decreasing supplies of available Pi in the future could impose significant economic burden on development and society at large; threatening food security and social stability. Organic P can account for 30% to 80% of the total P in soils but often receives little consideration when making soil fertility recommendations because there are few analytical methods to directly measure Po bioavailability. A better understanding of the contribution of organic phosphorus (Po) to the total P needs of crop plants could significantly reduce Pi fertilizer inputs simultaneously improving the economic sustainability of agronomic crop production systems and preserving vital ecosystem services. The primary goals of this proposal are to quantify how much of the fixed organic P (Po) in the roots of a previous winter wheat (WW) cover crop is available to successive crops in minimal-till systems, uncover the mechanisms involved in this process, and ultimately develop management practices to maximize Po utilization. The proposed study will be unique compared to other studies on this topic in that it will integrate plant phenotyping with advanced analytical, molecular genetic techniques, and classical soil chemical methods to identify the primary physical and biogeochemical processes affecting the transformation, movement and storage of Po in managed agroecosystems
Related publications
- McGrail, R.K., D.A. VanSanford, and D.H. McNear Jr. 2020. Trait-based root phenotyping as a necessary tool fro crop selection and improvement. Agronomy, 10:1328
- PLANT MICROBE SYMBIOSIS -
Understanding endophyte effects on soil processes in tall fescue pastures: from rhizosphere to regional scales. Sponsor: USDA-NRI, Soil Processes Program.
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Tall fescue (TF) covers greater than 15 million hectares within the United States and is considered one of the most desirable forage species for grazing livestock. Because of animal toxicity issues associated with common toxic endophyte-TF varieties, novel endophyte infected TF varieties are gaining popularity. Only anecdotal evidence exists which specifically addresses the role of the endophyte in dictating root exudate composition or the role that these exudates may play in altering soil microbial composition or nutrient cycling. This research provide important and novel data on how the soil chemical environment, soil microbial communities, and soil C and N dynamics are altered by shoot-specific common and novel fungal endophyte symbioses with tall fescue. The studies were unique from other studies on this topic in that they integrated advanced analytical and molecular genetics techniques with classical soil chemical methods to identify root exudates specific to the fungal-TF symbiosis and elucidate their effects on rhizosphere and bulk soil microbial composition, and carbon and nitrogen pools in field soils. The goals were accomplished by combining methodical pure culture, bioactivity guided assays of root exudates from endophyte infected and endophyte free tall fescue varieties with lab and field-based observations to verify the validity of our results. This researched provided basic knowledge on how an agriculturally-important, widely occurring plant-fungal symbiosis impacts soil microbial communities, chemical properties and nutrient cycling.
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Related publications
- Guo, J., R.L. McCulley, T. Phillips, and D.H. McNear Jr. (2016) Fungal endophyte and tall fescue cultivar interact to differentially effect bulk and rhizosphere soil processes governing C and N cycling. Soil Biology & Biochem 101:165-174
- Guo J, McCulley RL and McNear Jr. DH. (2015) Tall fescue cultivar and fungal endophyte combinations influence plant growth and root exudate composition. Front. Plant Sci. 6:183. doi: 10.3389/fpls.2015.00183
- Rojas, X., J.W. Leff, D.H. McNear Jr., and R.L. McCulley. (2016) Infection with a shoot-specific fungal endophyte (Epichloë) alters tall fescue rhizosphere microbial communities. Microbial Ecology 72(1):197-205 (IF=4.82)
Influence of tall fescue cultivar and endophyte genotype combinations on root system architecture, exudate composition and soil biogeochemical processes.
Sponsor: USDA NIFA-AFRI Microbial Communities Program
Sponsor: USDA NIFA-AFRI Microbial Communities Program
PROJECT SUMMARY
The primary goals of this project are to determine what influence different shoot-specific fungal endophyte genotypes and tall fescue cultivar combinations have on root morphological traits, root exudate chemical composition and the edaphic factors controlling their persistence and ability to assist in nutrient acquisition. We are specifically interested in the role that the fungal endosymbiont plays in helping tall fescue access phosphorous from soils.
RELATED PUBLICATIONS
- Ding, N., Kupper, K and McNear Jr., D.H. 2015. Phosphate Source Interacts with Endophyte Strain to Influence Biomass and Root System Architecture in Tall Fescue. Agronomy Journal. 107(2)662-670. (IF= 1.6)
- Ding, N., H. Guo, J.V. Kupper and D.H. McNear Jr. 2016. Shoot specific fungal endophytes alter soil phosphorus (P) fractions and potential acid phophotase activity but do not increase P uptake in tall fescue. Plant and Soil, 401(1):291-305 (IF=2.64)
Plant-Microbe communication in the Medicago truncatula rhizosphere: functional metagenomics, biochemistry and community analysis.
Sponsor: USDA NIFA AFRI, Microbial Communities Program
Sponsor: USDA NIFA AFRI, Microbial Communities Program
Project Summary:
The long-term goal of this collaborative effort is to understand how plant genetic diversity affects rhizosphere microbial diversity, and to further discern the principles governing plant microbe interactions at the plant root-soil interface.We hypothesize that genetic diversity within a plant species leads to alterations in plant root biochemistry that, in turn, alters both the taxonomic and functional diversity of the associated rhizosphere microbial community. Ultimately, alterations in the taxonomic and functional diversity of the rhizosphere microbial community affect plants by virtue of the myriad biochemical processes carried out by the rhizosphere microbial community, including enhancing nutrient acquisition and suppressing plant pathogens. The proposed work aims to develop a system whereby mutants of the legume Medicago truncatula that are shown to have altered root phenotypes are used to determine the effects of mutations on the taxonomic diversity of the associated rhizosphere microbial community (using T-RFLP of 16S rRNA genes) as well as on the functional diversity of the community (using a functional metagenomic “operon-trap” method). This work will result in characterization of novel plant-microbe communication mechanisms and will introduce a method by which gene expression in a soil metagenome in response to changes in environmental conditions can be probed.
related publications
- Szoboszlay, M., Lambers, J., Chappell, J., Kupper, J.V., Moe, L., McNear Jr., D.H. 2014. Comparison of root system architecture and rhizosphere microbial communties of Balsas teosinte and domesticated corn cultivars. Soil Biology and Biochemistry. 80:34-44(IF=4.41)
NANOPARTICLES, METALS, AND PHYTOREMEDIATION
Transatlantic initiative for nanotechnology and the environment (TINE). Sponsor: Joint U.S. EPA- United Kingdom ENI
Project Summary
Examining the major pathways of nanomaterial release to the environment via a life cycle perspective has pointed towards land application of biosolids as a major vector for the introduction and mass loading (over time) of several important classes (e.g., Ag, TiO2, and ZnO) of manufactured nanomaterials to the environment (vide infra). Soil is also an important repository for other widely used MNMs, either from atmospheric inputs (e.g., carbon-based and CeO2) or from subsurface disposal of consumer goods containing MNMs in landfills (e.g., carbon-based). While much of the environmental fate and effects research dealing with MNMs to date has focused on ecological receptors from aquatic systems, there are compelling arguments to focus attention on terrestrial ecosystems from the standpoint of environmental effects and ultimately, risks to human health and welfare from important classes of MNMs (e.g., Ag, TiO2, ZnO, CeO2). The soil resource forms the base of the ecosystem services pyramid which ultimately controls the function of natural and managed ecosystems, delivering food, feed, fiber, and renewable fuels as well as sufficient high quality water. Thus, this research aims to examine the potential impacts of MNMs to terrestrial ecosystem function via their introduction to soil as well as potential terrestrial-based pathways for human exposure.
Related publications
- Shoults-Wilson, A., O.I. Zurbich, D.H. McNear Jr., O.V. Tsyusko, P.M. Bertsch and J. Unrine. (2011) Evidence for avoidance of Ag nanoparticles by earthworms (Eisenia fetida). Ecotoxicology. 20:385-396 (IF= 3.05)
- Judy, J., D.H. McNear Jr., C. Chen, R.W. Lewis,, O.V. Tsyusko, P.M. Bertsch, W. Rao, J. Stegemeier, G.V. Lowry, S.P. McGrath, M. Durenkamp and J.M. Unrine. (2016) Nanomaterials in biosolids inhibit nodulation, shift microbial community composition, and result in increased metal uptake relative to bulk/dissolved metals. Environ. Sci. Techn. (IF=5.48)
- Chen, C. J.M. Unrine, J.D. Judy, R.W. Lewis, J. Guo, D.H. McNear Jr., and O.V. Tsyusko. (2016) Toxicogenomic responses of the model legume Medicago truncatula to aged biosolids containing a mixture of nanomaterials (TiO2, Ag and ZnO) from a pilot wastewater treatment plant. Environ. Sci. Techno. (IF=5.48)
- Lewis, R. W., Bertsch, P. M., McNear, D. H. 2019. Nanotoxicity of Engineered Nanomaterials (ENMs) to Environmentally Relevant Beneficial Soil Bacteria: A Critical Review, Oxfordshire: Nanotoxicology, (IF=4.92)
- Lewis, R.W., J. Unrine, P.M. Bertsch, and D.H. McNear. 2017. Silver engineered nanomaterials and ions elicit species-specific O2 consumption responses in plant growth promoting rhizobacteria. Biointerphases doi: 10.1116/1.4995605 (IF = 2.0)
Spatiotemporal tradeoffs of Zn and glucosinolates in
leaves of the Zn hyperaccumulator Noccaea caerulescens: Influence on insect feeding behavior
Collaborators: Richard Caprioli and Michelle reyzer, Vanderbilt Mass Spectrometery Center
leaves of the Zn hyperaccumulator Noccaea caerulescens: Influence on insect feeding behavior
Collaborators: Richard Caprioli and Michelle reyzer, Vanderbilt Mass Spectrometery Center
Project Summary
T.ni feeding
Description Coming Soon
related publications
Mechanisms of Mn tolerance and toxicity in the Nickel hyperaccumulator Alyssum murale
Project Summary
Mn spots on
A. murale
Background and Aims: Mechanisms of Mn accumulation and toxicity in and around trichomes on the Ni hyperaccumulator Alyssum murale were investigated. Methods: Plants were grown aeroponically with variable amounts of Mn and Ni. Total metals were determined and electron microprobe analysis (EMPA) and synchrotron-based micro x-ray fluorescence (micro-SXRF) spectroscopy were used to evaluate metal distribution. Synchrotron techniques (-XANES, u-EXAFS) along with infrared spectroscopy (DRIFT) were used to determine Mn speciation. Results: At lower Mn concentrations or when grown together with Ni, Mn is confined to the trichome basal compartment in the +2 oxidation state in a complex with phosphate. At tissue concentrations > 1150 mg g-1 Mn-rich lesions develop around some trichomes in which greater amounts of Mn 3+ is found.
Conclusions: Mn is preferentially stored in trichomes on the plant surface which at higher concentrations enters the cell wall or apoplastic space of neighboring cells resulting in the formation of brown reaction products and oxidized Mn species. We propose a mechanism by which lesion formation and oxidized Mn species around some trichomes is possibly due to induction of the peroxidase system by excess Mn, triggering the accumulation of toxic phenoxy radicals and Mn3+.
Related Publication:
Conclusions: Mn is preferentially stored in trichomes on the plant surface which at higher concentrations enters the cell wall or apoplastic space of neighboring cells resulting in the formation of brown reaction products and oxidized Mn species. We propose a mechanism by which lesion formation and oxidized Mn species around some trichomes is possibly due to induction of the peroxidase system by excess Mn, triggering the accumulation of toxic phenoxy radicals and Mn3+.
Related Publication:
- McNear Jr., D.H. and J.V. Kupper. (2014) Mechanisms of trichome-specific Mn accumulation and toxicity in the Ni hyperaccumulator Alyssum murale. Plant and Soil. DOI 10.1007/s11104-013-2003-7 (IF=2.638)
related publications
- McNear Jr., D.H. and J.V. Kupper. (2014) Mechanisms of trichome-specific Mn accumulation and toxicity in the Ni hyperaccumulator Alyssum murale. Plant and Soil. DOI 10.1007/s11104-013-2003-7 (IF=2.638)
Exploring the structural basis for the Se/Hg antagonism in Allium fistulosum
Collaborators: Joseph Caruso (RIP) and Scott Afton, University of Cincinnati Metalomics Center
Collaborators: Joseph Caruso (RIP) and Scott Afton, University of Cincinnati Metalomics Center
Project Summary
While continuing efforts are devoted to studying the mutually protective effect of mercury and selenium in mammals, few studies have investigated the mercury–selenium antagonism in plants. In this study, we report the metabolic fate of mercury and selenium in Allium fistulosum (green onion) after supplementation with sodium selenite and mercuric chloride. Analysis of homogenized root extracts via capillary reversed phase chromatography coupled with inductively coupled plasma mass spectrometry (capRPLC-ICP-MS) suggests the formation of a mercury–selenium containing compound. Micro-focused synchrotron X-ray fluorescence mapping of freshly excised roots show Hg sequestered on the root surface and outlining individual root cells, while Se is more evenly distributed throughout the root. There are also discrete Hg-only, Se only regions and an overall strong correlation between Hg and Se throughout the root. Analysis of the X-ray absorption near edge structure (XANES) spectra show a ‘‘background’’ of methylselenocysteine within the root with discrete spots of SeO32, Se0 and solid HgSe on the root surface. Mercury outlining individual root cells is possibly binding to sulfhydryl groups or plasma membrane or cell wall proteins, and in some places reacting with reduced selenium in the rhizosphere to form a mercury(II) selenide species. Together with the formation of the root-bound mercury(II) selenide species, we also report on the formation of cinnabar (HgS) and Hg0 in the rhizosphere. The results resented herein shed light on the intricate chemical and biological processes occurring within the rhizosphere that influence Hg and Se bioavailability and will be instrumental in predicting the fate and assisting in the remediation of these metals in the environment and informing whether or not fruit and vegetable food selection from aerial plant compartments or roots from plants grown in Hg contaminated soils, are safe for consumption.
related publications
- McNear Jr., D.H., S. Afton, and J. Caruso. 2011. Exploring the structural basis for selenium/mercury antagonism in allium fistulosum. Metallomics. 4:267-276 (IF=3.902)
Elucidating the chromium detoxification pathway in the multi-metal accumulator Silene vulgaris. Collaborators: Ana Pradas del Real, Araceli Perez-Sanz and Carmen M. Lobo, iMiDRA Madrid, Spain
Project Summary
Silene vulgaris
Phytomanagement could be a viable alternative in areas polluted with wastes from chromium-using industries. Cr(III) and Cr(VI) are the two most common oxidation states of Cr but Cr(VI) is much more available and toxic to living organisms than Cr(III). This study investigated the ability of Silene vulgaris to take up Cr(III) and Cr(VI) with special attention on the mechanism used by this species to tolerate high doses of Cr(VI). Plants were grown semi-hydroponically with different concentrations of either Cr(III) or Cr(VI). A combination of synchrotron X-ray spectroscopic techniques, scanning electron and light microscopy and infrared spectroscopy were used to determine the distribution and speciation of Cr and S. vulgaris. S.vulgaris accumulated more Cr when grown with Cr(VI) resulting in an overall reduction in biomass. Starch accumulation in leaves of S. vulgaris at higher Cr(VI) doses may be attributed to an impartment between carbon utilization and assimilation resulting in stunted plant growth but not the complete inhibition of photosynthesis indicating that S. vulgaris possess tolerance mechanisms that allows it to survive in Cr(VI) rich environments. The primary mechanisms implicated in Cr(VI) tolerance are a) the total reduction of Cr(VI) to Cr(III) in the rhizosphere or just after uptake in the fine lateral root tips and b) chelation of Cr(III) to the cell wall both of which reduce metal interference with critical cell functions. These mechanisms make S. vulgaris suitable for in situ remediation of Cr polluted soils.
related publications
Pradas del Real, A.E., Pérez-Sanz, A., Lobo,M.C., McNear Jr., D.H. Accepted. The Chromium Detoxification Pathway in the Multi-metal Accumulator Silene vulgaris. Environmental Science and Technology. 48(19) pp 11479-11486 (IF=5.481
Speciation and spatial distribution of Cr, Cu and As from CCA treated fences across the Kentucky landscape
Project Summary
Soils adjacent to Chromated Copper Arsenate (CCA) treated fence posts along a fence line transecting different soil series, parent material, drainage classes and slope were used to determine which soil properties had the most influence on As spatial distribution and speciation. Metal distribution was evaluated at both macroscopic (total metal concentration contour maps) and microscopic scales (micro synchrotron X-ray fluorescence (µ-SXRF) maps), As speciation was determined using extended x-ray absorption fine structure spectroscopy (EXAFS), and redox status and a myriad of other basic soil properties were elucidated. All geochemical parameters measured point to a condition in which the mobilization of As becomes more favorable moving down the topographic gradient likely resulting through competition (meh-P, SOM), neutral/slightly basic pH, and redox conditions which are favorable for As mobilization (higher Fe(II) and total-Fe concentrations in water extracts). On the landscape scale, with hundreds of kilometers of fence, the arsenic loading into the soil can be substantial (~ 8-12 kg/km). Although a significant amount of the As is stable, extended use of CCA treated wood has resulted in elevate As concentrations in the local environment, increasing the risk of exposure and ecosystem perturbation, and therefore, a move toward arsenic free alternatives in agricultural applications (for which it is currently permitted) should be considered.
related publications
- Schwer III, D.R.* and D.H. McNear Jr. 2011. Chromated copper arsenate treated fence posts in the agronomic landscape: soil properties controllng arsenic speciation and spatial distribution. J. Environ. Qual. 40(4):1172-1181. (IF=2.33)