| Name | Affiliation | Proposal Title | Description |
|---|---|---|---|
| Baker, Bill J. | University of South Florida | Cold-adapted Polyketide Megaenzyme synthesis and expression | This project will study how cold-adapted genes and proteins from an Antarctic organism are synthesizing bioactive metabolites. Researchers seek to learn not only how to produce these metabolites in alternative biological systems, but how that synthetic pathway differs from warmer-water synthetic pathways — ultimately to enhance biosynthesis and reduce energy use in bioproducts. |
| Barrick, Jeff | University of Texas, Austin | Tempo and mode of changes in gene expression in the Escherichia coli long-term evolution experiment | This project will analyze E. coli from the frozen "fossil" record of a 25+-year laboratory evolution experiment to understand how mutations have caused changes in gene expression that improved bacterial fitness over time. Specifically, it will characterize how regulation and production of different bacterial genes has changed over 75,000 generations of bacterial evolution, helping to develop new models to understand microbial evolution and diversity. |
| Gilman, Ian | Michigan State University | The genomics of rapidly evolving CAM photosynthesis in Pelargonium | Pelargonium, “wild geraniums” or “Pellies”, are economically important ornamental plants native to arid southern Africa. By comparing the genomes of multiple Pelargonium species, we will describe the genetic elements responsible for crassulacean acid metabolism (CAM), an adaptation that increases drought resilience by enhancing the water use efficiency of photosynthesis. Dissecting the recent emergence of CAM in Pelargonium will, for the first time, illuminate critical steps in CAM evolution and facilitate the genetic engineering of CAM into other systems, while providing a model for the evolution of plant stress responses. |
| Graf, Louis | Sorbonne University (France) | Genomic and transcriptomic diversification in Arctic and Antarctic green algal Chlamydomonadales | The green algae of the order Chlamydomonadales have successfully colonized the polar environments of the Arctic and Antarctic. Through genome sequencing and gene expression analysis of four strains of these algae, this study will identify genetic, biological and physiological adaptations supporting life in the poles and identify new biomarkers for the fragility and resilience of polar algae. |
| Guo, Yuxi | University of Florida | Unraveling physiological mechanisms driving variations in microbial carbon use efficiency: Insights from metagenomic data | This project will reveal how different agricultural management practices and rainfall patterns affect the genetic machinery of soil microbes at a working cattle ranch in Florida, helping to better manage grasslands for both agricultural productivity and carbon-use efficiency in the future. |
| He, Shaomei | University of Wisconsin, Madison | Depth-discrete metagenomics and metatranscriptomics to inform methane and redox cycling in humic lakes | Globally lakes are experiencing concurrent browning and deoxygenation caused by increased organic carbon inputs from catchment areas and decreased oxygen in the water. Humic lakes, also known as brown-water lakes, serve as a model system to study the ecological consequences and response to surface water-browning and deoxygenation. Researchers will investigate the key players, i.e. microorganisms, in such habitats, aiming to understand their functions and their interactions with each other and with the environment. |
| Hill-Maini, Vayu | Stanford University | Building Phanerochaete chrysosporium as a model for synthetic and systems biology in white-rot fungi | White-rot fungi are able to degrade recalcitrant materials such as wood and plastics — and produce sustainable materials, chemicals, and foods. Using Phanerochoate chrysosporium as a model, researchers will characterize the inner workings of these organisms' complex metabolism and build tools that enable the engineering of white rot fungi for bioenergy and bioproducts. |
| Lefler, Forrest | University of Florida | Linking microbial communities to biogeochemical cycles in stormwater treatment ponds | Stormwater ponds are engineered ecosystems in suburban areas which have recently been identified as biogeochemical (e.g., carbon, nitrogen, phosphorus) hotspots. In this study, researchers aim to evaluate the microbial communities present and their influence on biogeochemical cycling and how they relate to the ponds’ ability to store and sequester nutrients. |
| Leung, Pok Man (Bob) | Monash University | Unveiling unique soil microbial adaptations and biogeochemical processes across drylands in seven continents | The diversity of soil microbes and their role in carbon and nutrient cycling in “dryland” ecosystems, which are characterised by a lack of water, is not well-understood. Through an in-depth study of genomic data of soil microbes and their nutrient cycling processes across time and space within major drylands from all seven continents, this project will substantially expand available genomic data of dryland soil microbes to uncover their unique ecosystem roles and adaptations. |
| Li, Huang | University of Nebraska, Lincoln | Transcriptomic profiling of mitochondrial respiratory mutants in Chlamydomonas and Camelina for bioenergetic research | By analyzing the gene expression level and network in modified green algae and oilseed crops that differ in the use of these pathways, researchers seek to identify promising genetic targets and components to improve their respiration and energy efficiency at the cellular level. Ultimately, our insights could lead to breakthroughs in optimizing biofuel crops, increasing their growth rates and yields while reducing energy loss and resource inputs. |
| Maurice, Sundy | University of Oslo | FunDecompo: Processes underlying the assembly of fungal communities and impact on wood decomposition | This project aims to untangle the genetic basis of assembly history and co-occurrences of species in dead wood. Understanding the interplay of saprotrophic fungi using transcriptomics approaches, is a first step toward untangling the decomposition process and consequently the ecosystem functioning. |
| McGivern, Bridget | University of Wisconsin, Eau Claire | Linking microbial gene expression to variations in rumen methane emissions | Through the livestock enteric fermentation process, specialized communities of microorganisms living in rumen convert organic matter from feed into hydrogen gas and smaller organic compounds that are used by the animal for energy. This process generates methane as a byproduct, which is then released into the atmosphere. In this project, researchers aim to understand the rumen microbial mechanisms underlying variable methane emissions in cattle by first building a census of microbial genomes inhabiting cattle rumen, and then examining the gene expression of those genomes related to the carbon cycle. |
| McRose, Darcy | Massachusetts Institute of Technology | Identifying microbial secondary metabolites that solubilize phosphorus in the rhizospheres of native grasses | This proposal focuses on specific types of secondary metabolites, those with redox activity, which can help make the critical nutrient phosphorus more available in soils. We isolated bacteria from the roots of native grasses collected across the US and used newly developed high-throughput chemical screens to identify bacteria that are making secondary metabolites of interest. This work will help us understand how plants and microbes interact and provide tools to help manipulate plant microbiomes for enhanced crop yields. |
| Murali, Ranjani | University of Nevada, Las Vegas | Investigating novel denitrification pathways in hot and cold springs | By mining the large sequence datasets that became available after the genomics sequencing revolution, novel nitrogen-cycling enzymes were identified. In this study, researchers aim to understand the impact of these novel pathways on nitrogen cycling in hot and cold springs, using sequencing technologies, laboratory cultures and biochemical analyses. The results from this study will provide insight into how microbial adaptation to extreme environments can lead to the development of biochemical novelty. |
| Osburn, Ernie | University of Kentucky | Exploring the role of viruses in soil carbon cycling through stable isotope probing | This research focuses on how viruses found in soil ecosystems contribute to carbon cycling, which is essential for maintaining soil health and addressing climate change. To accomplish this goal, researchers aim to develop a new method where "heavy" labelled carbon sources are traced into the DNA of soil viruses, which will allow the identification and characterization of the viruses by sequencing their genomes. |
| Patel, Ravikumar | The Connecticut Agricultural Experiment Station | The role of phytohormones in bacteria, protist, and plant interactions in the rhizosphere | This project explores how plants, protists, and bacteria interact through signaling molecules like plant hormones to shape the rhizosphere ecosystem. By uncovering these interactions, researchers aim to reveal new mechanisms that promote plant growth and soil health, with potential applications in sustainable agriculture. |
| Polturak, Guy | Hebrew University of Jerusalem | Discovery of defense-related biosynthetic gene clusters in sugarcane | This study seeks to explore chemical defense mechanisms in sugarcane, a major biofuel and food crop. By investigating the genes and associated metabolites that are induced in sugarcane in response to biotic stress, researchers aim to provide insights into how sugarcane naturally combats pests and pathogens by producing specialized defense molecules. |
| Reich, Marlis | University of Bremen | Decoding the genetic mechanisms of fungal roles in carbon transformation within the aquatic microbial carbon pump | This project aims to unravel the intricate mechanisms through which aquatic fungi contribute to carbon transformation processes, both in present conditions and under future climate scenarios. By employing advanced transcriptomic and meta-transcriptomic analyses, the project aims to uncover how fungi, through their degradation activity and interactions with other microbes, shape the overall carbon transformation processes within the microbial community. |
| RoyChowdhury, Taniya | Woodwell Climate Research Center | Pathways of carbon metabolism under cover crops | This study will use a highly-resolved metabolomics approach to quantifying the chemically diverse carbon substrates available for microbial uptake in the cover crop rhizosphere, using data mining techniques to predict the impacts of such chemical diversity on the active soil microbiome by using metatranscriptomics. |
| Schmidt, Mar | Cornell University | Decoding the metabolic network that sustains Lake Ontario | Microbes are essential to the health of the Great Lakes, which harbor roughly 2 octillion microbial genes — an immense genetic potential currently underexplored, with their diversity and role in the ecosystem largely unknown. This study will explore how microbial communities in Lake Ontario — a vital drinking water source for ~9 million people — adapt and influence water quality, helping to understand how microbial communities regulate nutrient cycling in this vital freshwater ecosystem. |
| Spiegel, Cody | University of California, San Diego | Integrating metatranscriptomics and metabolomics to reveal key microbial metabolic traits underlying aquatic ecosystem function | This study explores how the mixing of terrestrial and aquatic microbial communities influences leaf litter decomposition in river systems, by linking bacterial gene expression to changes in litter chemistry. Researchers aim to better understand how these microbes interact and adapt to environmental shifts, contributing to ecosystem resilience in the face of climate and land-use change. |
| Tan, James | Ohio State University | Integrating ecogenomics, a novel viral-host linkage method, and functional genomics to study biogeochemically critical phage-host interactions in a coastal time-series | To understand how coastal microbiomes, particularly viral communities, support ecosystem health and biogeochemical processes in the Gulf of the Naples, researchers will sequence viral and bacterial communities across a comprehensive monthly time-series. In conjunction with novel single-cell techniques and functional genomics, they will explore how viruses impact their host metabolisms, providing insight into how they modulate coastal biogeochemistry. |
| Timmins-Schiffman, Emma | University of Washington | Antarctic Sea ice and snow metagenomes to reveal community biogeochemical function in a changing environment | Antarctic sea ice is home to diverse micro-organisms, including bacteria and algae. The goal of this project is to understand how these microbes impact the movement of chemical compounds and nutrients in their ice habitat that connects the seawater below with the atmosphere above. |
| Venturini, Andressa M. | American University | Amazonian forest degradation: Impacts on soil microorganisms | The Amazon rainforest is rapidly changing: 20% has been cleared, and nearly 40% of what remains is degraded by fires, timber extraction, droughts, and/or habitat fragmentation; yet the impact on soil microbes — key regulators of nutrient and greenhouse gas cycling — remains poorly understood. This research will investigate how Amazonian land-use change and forest degradation affect microbial diversity and function, providing insights to inform environmental policies in the region and its implication for bioenergy production. |
| Waschulin, Valentin | University of Vienna | Understanding the effect of recurrent drought on growth and function of a grassland soil microbial community | This project is focused on understanding the effect of drought on soil bacteria. Droughts are big stress events for all soil organisms, including bacteria, and recurrent drought significantly changes which bacteria found in a soil. Using a 17-year data set from an experimental site in the Austrian Alps, researchers will analyse the genes of the bacteria that are present in the different plots — which range from no drought treatment to 17 years of drought treatment — to find out how some bacteria continue to thrive when others quite literally “dry up.” |
| Winck, Flavia Vischi | Universidade de São Paulo | Omics analysis of the interplay of amino acids in the regulation of the arginine metabolism and lipids accumulation in Chlamydomonas reinhardtii | This project will investigate how specific amino acids can enhance the production of oils in the microalgae Chlamydomonas reinhardtii, a promising organism for biofuel production. Further research will focus on how these amino acids impact the metabolism of C. reinhardtii to identify specific biological mechanisms that control oil production. By uncovering how these pathways work, the study aims to provide insights for developing new methods to increase oil production in algae, making it a more viable source for renewable energy. |
| Wisecaver, Jen | Purdue University | Transcriptional characterization of toxin biosynthesis pathways in Prymnesium parvum, a growing algal threat to freshwater ecosystems | Many algal species produce a diverse array of toxins and other specialized bioproducts. Identifying the genes that make these toxins would enable new investigation into how these toxins are synthesized and open new doors for natural product research. This study aims to create a gene expression atlas for the golden alga Prymnesium parvum, surveying 30 unique culture conditions known to perturb toxin production and other traits associated with toxicity. |
| You, Yaqi | SUNY College of Environmental Science and Forestry | Understanding biochar-induced rhizosphere reprogramming for greenhouse gas mitigation and sustainable bioenergy crop production | Understanding biochar-induced rhizosphere reprogramming for greenhouse gas mitigation and sustainable bioenergy crop production This project will investigate biochar-induced changes in the rhizosphere, with a focus on the microbial mechanisms associated with shifts in plant-microbe interactions, to enhance bioenergy crop production while mitigating human impact through improved microbial interactions and nutrient cycling. |
| Zhang, Yong | Georgia Southern University | Exploring genomic dynamics and gene regulatory networks underlying the biofuel producing capability of Fusarium oxysporum | F. oxysporum is one of the few filamentous fungal species able to break down biomass and convert monosaccharides to ethanol. Although numerous F. oxysporum have been sequenced as pathogens, its bioenergy production potential has not been comprehensively studied using the cutting edge genomic and functional approaches. This proposed work aims to bridge the gap by sequencing of F. oxysporum with inter-species variation in producing bioethanol from plant biomass. These data will be used to understand the genes and regulatory mechanisms that contribute to bioconversion efficacy. |
| Zhong, Zhiping | Ohio State University | Illuminating microbial responses to climate change at decadal-to-millennial scales archived in the largest tropical glacier | This proposal requests sequencing of environmental DNA from glacier materials (snow, firn, and ice) and surrounding soils from the world’s largest tropical glacier. These samples have been characterized by paleoclimatologist members of this team for date, climate proxies, dust, and chemistry. The sequencing will be used to understand the relationship between climate variation and microbial and viral community response. |
Pictured from left: [Top] Bill J. Baker, Jeff Barrick, Ian Gilman, Louis Graf, Yuxi Guo, Shaomei He, Vayu Hill- Maini, Forrest Lefler, Pok Man (Bob) Leung and Huang Li; [middle] Sundy Maurice, Bridget McGivern, Darcy McRose, Ranjani Murali, Ernie Osburn, Ravikumar Patel, Guy Polturak, Marlis Reich, Taniya RoyChowdhury and Mar Schmidt; [bottom] Cody Spiegel, James Tan, Emma Timmins-Schiffman, Andressa M. Venturini, Valentin Waschulin, Flavia Winck Vischi, Jennifer Wisecaver, Yaqi You, Yong Zhang and Zhiping Zhong. (All images courtesy of the researchers)
Each year, the JGI searches for novel research projects from PIs who have not led any previously accepted proposals. The New Investigator call, part of our Community Science Program, allows us to work and share our tools with a widening circle of researchers whose work aligns with DOE missions.
Below find a list of researchers whose proposals were accepted for 2025. Utilizing the JGI’s resources, these researchers will investigate a diverse array of projects, including the genomic dynamics of biofuel-producing fungi, the effects of biochar on rhizosphere microbiomes, and the metabolic pathways of algae. They will harness JGI capabilities such as metatranscriptomics and environmental DNA sequencing to explore microbial and plant interactions across unique ecosystems, from alpine soils to tropical glaciers.
Proposals are accepted year-round for this ongoing call; the next deadline for proposal submission is Sept. 9, 2025, for inclusion in the November 2025 review. You can also find more information about the JGI’s various proposal calls here.
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