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Amy Grunden

William Neal Reynolds Distinguished Professor; University Faculty Scholar

Assistant Director, NCARS


My research program is focused on the study of microorganisms called extremophiles, which are capable of thriving in diverse extreme environmental conditions such as high or low temperatures, high salinity, acidic or alkaline environments.  The goals of the extremophile research conducted in my laboratory are first to understand the adaptive mechanisms extremophiles use to survive in harsh environmental conditions and second to exploit these adaptations for biotechnological applications.  Research projects currently underway involve using selected extremophile enzymes and synthetic biology approaches to (1) decontaminate toxic organophosphorus-based nerve agents found in some pesticides and chemical warfare agents, (2) generate transgenic plants with increased tolerance to harsh environmental conditions for the purpose of developing plants that can survive in marginal environments, and (3) use extremophile genes to optimize fatty acid production in microalgae for biofuel production and (4) develop a synthetic carbon fixation cycle using archaeal and bacterial enzymes to augment the Calvin-Benson cycle in plant systems.  Research in my laboratory has been funded by DOD, DOE, NASA, NCBC, NSF, and the USDA.

Courses Taught:

  • MB 351- General Microbiology
  • MB 714- Metabolic Regulation


Ph.D. Microbiology University of Florida, Gainesville 1996

B.S. Microbiology University of Florida, Gainesville 1993

Area(s) of Expertise

Microbial physiology and Microbial biotechnology


View all publications 


Date: 09/01/22 - 8/31/27
Amount: $6,641,853.00
Funding Agencies: Novo Nordisk Foundation

This fundamental research is motivated by three major global challenges that directly involve the transformation of gas molecules: carbon dioxide (CO2) capture for greenhouse gas mitigation, CO2 conversion to fuels and chemicals, and nitrogen (N2) gas conversion to biologically available ammonia to meet growing fertilizer demand. The research focuses on creating and investigating multi-functional interfaces that durably immobilize enzymes near their gaseous substrates while simultaneously delivering essential chemical and electrical reducing equivalents and removing reaction products to achieve maximum catalytic rates. Biocatalytic systems to be explored are: conversion of CO2 to bicarbonate catalyzed by carbonic anhydrase, reduction of CO2 to formate catalyzed by formate dehydrogenase, and reduction of N2 to ammonia catalyzed by nitrogenase. We envision that minimization of reaction barriers near immobilized biocatalyst interfaces involving gas molecule conversions will lead to transformative innovations that help overcome global sustainability challenges.

Date: 10/01/19 - 12/31/25
Amount: $1,862,709.00
Funding Agencies: Novo Nordisk Foundation

Our Vision is to provide a science-based platform for new agricultural practices enabling plant producers to manage their production ecosystems in a resource-efficient way with limited environmental footprint based on an in-depth understanding of key ecological functions in the soilplant interphase (rhizosphere). Our Motivation is to address the major research gaps in deciphering the complexity of microbemicrobe and microbe-plant interactions in the rhizosphere, and thereby provide new conceptual understanding on how these interactions influence plant performance. This motivation is timely due to recent developments in methodology and will enable us to provide the knowledge-base for unlocking the potential of the soil rhizobiota (microbes living on in the rhizosphere) as the key to development of sustainable and resilient plant production systems. Our Focus is to identify and quantify main determinants of microbial interactions and networks in the rhizosphere leading toward a resilient ecological unit, and thus reveal the importance and potential of microbial interactions and functions in the rhizosphere. The proposed research will take advantage of a multi-faceted, integrative and cross-disciplinary approach, which is fundamental for 1) achieving a deep understanding of the chemical and biological factors that control microbe-microbe and plantmicrobe interactions and functions under natural soil conditions, 2) establishing improved predictive models for microbial interactions in soil and 3) exploiting the microbial potential in plant-soil production systems for the benefit of plant growth and resilience. INTERACT will decode these important, yet often transient, microbial interactions in the complex soil matrix, in relation to soil biogeochemical status, water stress as well as pathogen attack, and the impact of these interactions on plant performance. We will challenge the currently accepted view among scientists that plants are the primary drivers for rhizobiome assembly. Hence, we will determine whether in fact soil microbes, largely through chemical communication and signaling, play a greater role in rhizobiome development and function than has been previously appreciated. INTERACT will provide critical insight into the rhizosphere ecology, as a basis for actively influencing the assembly of effective rhizosphere communities to support plant health and productivity, either through biotechnological or agronomic approaches.

Date: 10/01/19 - 9/30/25
Amount: $1,404,026.00
Funding Agencies: Novo Nordisk Foundation

In the coming century, agricultural crop production and with it, civilization, will face great challenges. Two billion additional people will need to be fed by 2050, and together with the rise in global disposable income, the demand for food will increase by up to 50%. Despite constant increase in crop productivity since the first green revolution, the current rate of improvement is not sufficient to meet these needs. Filling this critical food security gap requires new approaches and initiatives that we do not currently use, which will lead to the next green revolution. Furthermore, any solutions to this food security challenge must be safe, sustainable and effective in the face of climate change and environmental pressures that will make crops more vulnerable. challenges of a changing world. From the strategic discussions begun at the 2018 Crop Resiliency Workshop and subsequent virtual and in-person project planning meetings held throughout the spring and early summer, three stand-alone, yet highly synergistic projects that aim to transform global agriculture and food security have been developed that will be briefly described in turn: 1) MATRIX, 2) InRoot, and 3) INTERACT (Figure 1). MATRIX (Microbiome Assisted Triticum Resilience In X-dimensions) will develop a scalable system-based strategy to harness the functional potential of plant microbiomes for improving crop resilience by focusing on experimental analyses and deep-learning modelling of the above-ground plant-associated microbial community (phyllosphere microbiome) of wheat (Triticum aestivum), one of the most important cereal food crops worldwide. Genomics, metabolomics, and phenomics will provide foundational data to build mechanistic models. These models will be iteratively tested with theoretical simulations and experimental validation to identify phyllosphere community members that are critical for productivity. Success for MATRIX will be yielding microbiome-assisted wheat culturing practice, resilient to ever-changing environmental stresses and resource limitations. InRoot (Molecular Mechanisms and Dynamics of Plant-Microbe Interactions at the Root-Soil Interface) will provide knowledge and tools for science-based development of new crop varieties and associated microbial interventions that will improve productivity, reduce the need for fertilizers and pesticides, and alleviate negative environmental impact. These critically important advances will be achieved by disentangling the effects of climate and soil type from the impact of root-microbe interactions, identifying key bacterial taxa governing the establishment of host-driven microbial networks in the rhizosphere, defining the plant genetic components that control infection of plant roots by ubiquitous and host-specific endophytes, understanding molecular mechanisms integrating root-microbe interactions into whole-plant physiology, and predicting plant performance as a function of plant and microbiota genotypes by building multiscale models. INTERACT will provide much needed insight into rhizosphere ecology with a goal to provide diagnostic chemical/biological signatures for agro-system stability. With this knowledge, we can rationally and strategically manipulate plant-associated microbial communities to support high plant productivity across challenging climatic and stress scenarios. These critical advances in our understanding of rhizosphere community structure and the chemical landscape that influences its formation and function will be achieved by using genomics, transcriptomics, metabolomics, in-field and greenhouse plant phenotyping, and network analysis/model construction for evaluating rhizosphere interactions for both wheat and the increasingly globally significant food, feed and energy crop, sorghum.

Date: 03/01/22 - 2/28/25
Amount: $117,736.00
Funding Agencies: National Science Foundation (NSF)

The biology of plant-microbe interactions is an exciting area of research that suffers from an under-representation of scientists from a number of demographic groups. We believe that an approach that focuses on problems that today’s college students are passionate about will attract a greater diversity of students to the discipline. Incorporating research opportunities in plant-microbe interactions that address questions surrounding climate change, global food security, and sustainability will draw in students of varying interests and disciplines and will inspire them to pursue research not only for practical applications, but also to answer basic biological questions in plant and microbial biology. Integrative Microbial and Plant Systems will engage students in cutting-edge research using molecular biology and computational tools, encompassing basic and applied issues in plant and microbial sciences. It will encourage students to examine and understand plant-microbe community systems as a whole using “OMICs” approaches and will go beyond traditional biotechnology by challenging the students to identify key mechanisms underlying plant-microbe interactions and to use this understanding to improve plant growth and development, particularly in response to environmental stressors.

Date: 10/01/19 - 9/30/24
Amount: $638,751.00
Funding Agencies: National Science Foundation (NSF)

When seeking solutions to today's elevated atmospheric CO2 levels, it is critical that we include data from the past, because atmospheric CO2 concentrations have fluctuated throughout Earth history. In fact, CO2 levels have been consistently higher in the past—often significantly higher, at times perhaps as much as 6x pre-industrial values. The biological response of life on Earth to these global conditions, from their onset to their cessation, is recorded in the rock record. Intriguingly, Konservat Lagerstätte (e.g., sedimentary deposits that preserve fossils in extraordinary detail) occur more frequently in the distant past (i.e., deep time) than in more recent depositional environments. Could these be linked? We hypothesize that ancient microorganisms responded to pre-Cenozoic high atmospheric CO2 by sequestering carbon through very rapid precipitation of carbonate minerals in terrestrial, as well as marine settings. This increase in microbial precipitation of carbonates, sometimes as concretions, created conditions favorable to the stabilization of normally labile tissues and the exclusion of exogenous, degradative influences. These factors very likely contributed to exceptional preservation of fossil remains, including persistence of non-biomineralized (i.e., “soft”) tissues. Although microbes have been invoked as agents of preservation as well as destruction, because they act to “seal” sediments surrounding bone to form a relatively closed system, to date, the effect of contemporaneous atmospheric CO2 levels on microbial carbonate precipitation, and its implications for preservation, have not been explored. The convergence research we propose would enable us to design and implement empirical studies that directly test this idea, and characterize the microbial influence in depositional environments producing exceptionally preserved fossils. Thus, we ask the following: 1) Did the elevated CO2 in Mesozoic atmospheres play a role in microbially mediated exceptional preservation? 2) If this can be demonstrated through actualistic experiments and fossil studies, could this mechanism of fossil preservation also shed light on microbial sequestration of atmospheric CO2 in terrestrial environments? 3) Furthermore, can this understanding of microbially mediated CO2 sequestration be harnessed for development of robust, scalable carbon-capture systems? To test these hypotheses, we propose a two-pronged approach. We will conduct empirical tests that involve growing known microbially induced carbonate precipitation (MCIP) strains, as well as microbial communities from relevant environments, under conditions of Mesozoic proxy atmospheres. We will compare the rate and degree of precipitation in organisms grown in enriched CO2 with those of the same strains grown in ambient atmospheres, to characterize the effects of elevated CO2 on precipitation rates. Then, we will examine: 1) the sediments surrounding exceptionally preserved fossils, 2) the composition of concretions that contain fossil material, 3) the morphological and molecular preservation of the fossils themselves, and 4) biomarkers associated with microbes in these fossil materials, using a combination of chemical and molecular techniques. Our interdisciplinary team will work synergistically to examine the role of microbes in both fostering and impeding exceptional preservation, the relationship of exceptional preservation to elevated atmospheric CO2, and potential microbial pathways that can be exploited to accomplish terrestrial carbon sequestration. Such pathways are rarely considered in the dialogue regarding potential solutions to anthropogenic carbon release, but may present a viable, cost-effective mitigation measure

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