Following are the approved user proposals for Annual Community Science Program (CSP), FICUS JGI-EMSL, CSP Functional Genomics and CSP New Investigator calls.
FY 2024 Annual CSP Proposals
|Proposer||Affiliation||Proposal Title||Proposal Description|
|Ahern, Olivia||Marine Biological Laboratory||Linking genes to models: Unraveling microbial food web connectivity through multi-substrate RNA stable isotope probing, omics, and metabolic models||Earth’s biogeochemical cycles result from interactions of individual microscopic organisms, but the exact mechanisms driving organic matter cycling in most ecosystems are still poorly characterized. This project focuses on tracking bacteria, viruses, and predators in actual ecosystems by using heavy isotopes of carbon. We can identify the bacteria that consume these heavy carbon isotopes by detecting it in their RNA. In turn, we can detect this heavy RNA from the predators that ate these bacteria. We can therefore understand how carbon is transferred between trophic levels within a real microbial ecosystem. Our proposed collaboration with the JGI aims to sequence the RNA from those tracking experiments and develop ecosystem models derived from the genomes of the organisms involved. Overall, this comprehensive approach combining multiple scientific disciplines will allow researchers to explore various aspects of microbial ecology, biogeochemistry, and ecological modeling at the intersection of these fields.|
|Corrales, Adriana||Society for the Protection of Underground Networks||Ectomycorrhizal functioning in under-explored ecosystems: using fungal genomes and soil metatranscriptomes to discover new mycorrhizal connections with nutrient cycling and climate stress in tropical and Mediterranean biomes||Underground, plant roots form symbiotic associations with mycorrhizal fungi – an important class of soil fungi that provide critical nutrients to plants across the world’s terrestrial ecosystems. There are a growing number of datasets that demonstrate the importance of ectomycorrhizal fungi to carbon sequestration and nutrient cycling. However, these datasets have been largely focused on the Northern Hemisphere. There is an urgent need for data from more diverse mycorrhizal lineages and under-sampled locations in the global south to understand how mycorrhizal communities shape biogeochemical cycles across the Earth. Unlike plants and animals, much of the living part of mycorrhizal fungi is hidden around ground, making it hard to identify species. Working with a new class of machine learning models, we are developing maps that can help predict the hotspots of ectomycorrhizal fungal across the globe. A number of these biodiversity hotspots are understudied tropical and Mediterranean ecosystems. These ecosystems are of extreme interest because the availability and cycling of phosphorus and nitrogen differ to those catalogued in well-studied temperate forests.|
|Cross, Hugh||National Ecological Observatory Network||Continental-scale metagenomics: leveraging the NSF National Ecological Observatory Network to advance understanding of terrestrial and aquatic microbial communities in response to land use and climate change||Our project aims to produce freely available metagenomics data of unprecedented scope to enable novel analyses and insights into microbial communities. We will leverage and combine resources from three entities: the continental scale, long-term ecological data from the National Science Foundation’s National Ecological Observatory Network (NEON), the unmatched sequencing capabilities of the DOE Joint Genome Institute (JGI), and the microbiome database and cutting edge data analysis pipelines of the National Microbiome Data Collaborative (NMDC). We propose to send DNA extracts from NEON soil and water samples to the JGI for sequencing. Then, genomic data will be shared with NMDC who will apply advanced bioinformatics techniques to determine the composition and function of microbes in NEON samples. The raw and processed data will be made available as soon as possible to enable new research and scientific insights. Microbial communities in the soil and water provide the machinery that runs terrestrial and aquatic nutrient cycles and are key to maintaining the flow of energy and materials through the ecosystem. By acquiring high quality genomic data from these communities and linking them with the wealth of NEON measurements from the surrounding ecosystems, this project will provide unmatched opportunities for researchers to explore the fundamental drivers of ecological change from local to continental scales.|
|DeMarche, Megan||University of Georgia||A canary-in-the-coal-mine for arctic and alpine communities under climate change: using genomics to leverage long-term datasets in Silene acaulis||One of the greatest challenges we face today is to understand how biological systems are impacted and will respond to climate change. Altered climate conditions affect how individuals grow, survive, and reproduce, and these changes scale up to affect whether populations are stable or in decline, where species occur, and how groups of species interact to form larger ecosystems. Yet few studies have the appropriate data to link climate effects on individuals to larger-scale outcomes such as population stability or species distributions that are most relevant for conservation and management decisions. This project is designed to meet this need, by creating crucial genomic resources for an ecologically important plant in arctic and alpine tundra communities. Silene acaulis, or moss campion, is a common and widespread tundra plant that has been intensively studied for decades to understand how climate affects individuals and populations across the species’ latitudinal range, from arctic Alaska to central New Mexico. By carefully monitoring the performance of the same set of permanently marked, long-lived plants year after year, we have found that moss campion is strongly affected by climate change. This project will sequence the genomes of many plants from our long-term study so that we can investigate how genomic variation influences individual responses to climate change, and incorporate this information into population models to predict how the species as a whole will be affected across its geographic range. By using genomics to leverage one of the longest and most comprehensive datasets on individual performance, moss campion can serve as a “canary-in-the-coal-mine” for arctic and alpine communities.|
|Emerson, Joanne||University of California, Davis||Scaling wetland viral impacts on methane cycling from single cells to ecosystems||Viruses in terrestrial wetland ecosystems are predicted to have substantial impacts on carbon cycling and biogeochemistry, yet our understanding of wetland viruses is limited to a handful of field sites. Leveraging peatland and other wetland samples from the USA, UK, France, and Denmark, we propose to perform approximately the same suite of DNA and RNA sequencing-based analyses on a cross-continental dataset to make direct comparisons of virus-host dynamics, host metabolic capacity, and gene expression in similar ecosystems across the globe. Just as 20-40% of the C in ocean microbial cells is estimated to cycle through viruses daily, we expect to find quantitative evidence for substantial cycling of terrestrial C through viruses in microbial food webs, as well as viral impacts on microbial metabolic processes underlying global methane emissions.|
|Hudson, Matthew||University of Illinois at Urbana-Champaign||A reference level pangenome of soybean founder lines||Hypocrealean fungi present various modes of life, including parasitism, mutualism, commensalism and saprophytism. The order Hypocreales comprises over a hundred genera, and the diversity of mechanisms underlying these adaptations is of significant importance. Although extensive research has been conducted on the genetic and molecular mechanisms of entomopathogenicity for entomopathogenic fungi (EPF), little is known regarding their potential to colonize plants, living as endophytes. Similarly, there is a lack of research on mycophilic (or fungicolous) fungi (MF) which parasitize mostly basidiomycetes. This proposal aims to address these knowledge gaps by analyzing the genetic mechanisms involved, the gene expression and secondary metabolites produced by these species during their host colonization. This research we will provide insights for (a) the optimal exploitation of endophytic entomopathogenic fungi (eEPF) as biofertilizers and biostimulants for their plant hosts, in addition to their established use as biological control agents against insect pests, and (b) the interaction among the MF and their fungal hosts.|
|Keller, Megan||University of New Mexico||Potential carbon-degrading genes of saprotrophic compared to ectomycorrhizal fungi in a boreal forest may inform assessments of carbon cycling||The warming Arctic is exposing carbon from once-frozen soils to the atmosphere which could accelerate warming trends. The roles of diverse fungi in either slowing or fueling carbon loss to the atmosphere are poorly understood. This study uses a novel “community genomics” approach to infer the relative carbon degrading capabilities of diverse, co-existing fungi in a boreal forest, where a great deal of carbon resides belowground. The number and diversity of carbon-cycling genes within each genome will be used to determine the potential influence that symbiotic fungi have on carbon degradation compared to co-occurring free-living, decomposer fungi.|
|Kelliher, Julia||Los Alamos National Laboratory||Elucidating the molecular mechanisms underlying the novel phenomenon of fungal internalization of plant- and algal-derived chloroplasts||Fungi are capable of harboring a diverse microbiome within their cells, yet knowledge on how the fungal microbiome impacts the fungal host and its interactions with other organisms in complex communities remains limited. Previous studies conducted by our team have revealed that phylogenetically diverse fungi can frequently harbor chloroplasts, and that fungi are capable of internalizing chloroplasts at a surprisingly fast rate. This proposed work expands upon our previous work to investigate the genetic mechanisms underlying the internalization of chloroplasts in select fungi. Through comparative transcriptomic experiments, this work will examine how both fungal and chloroplast gene expression are altered when they are co-cultured together, and the temporal dynamics of their interactions over the course of several hours.|
|Kouvelis, Vassili||University of Athens (Greece)||Deciphering the genetic and metabolic plasticity of endophytic entomopathogens and fungicolous fungi of the order Hypocreales||Hypocrealean fungi present various modes of life, including parasitism, mutualism, commensalism and saprophytism. The order Hypocreales comprises over a hundred genera, and the diversity of mechanisms underlying these adaptations is of significant importance. Although extensive research has been conducted on the genetic and molecular mechanisms of entomopathogenicity for entomopathogenic fungi (EPF), little is known regarding their potential to colonize plants, living as endophytes.
This proposal aims to address these knowledge gaps by analyzing the genetic mechanisms involved, the gene expression and secondary metabolites produced by these species during their host colonization. This research we will provide insights for (a) the optimal exploitation of endophytic entomopathogenic fungi (eEPF) as biofertilizers and biostimulants for their plant hosts, in addition to their established use as biological control agents against insect pests, and (b) the interaction among the MF and their fungal hosts.
To achieve these objectives, a holistic approach integrating comparative genomics, transcriptomics and metabolomics will be employed. This will enable us to decipher the genes and mechanisms involved in endophytic and mycophilic modes of life. Thus, fundamental questions in the evolution of nutritional plasticity in economically important fungi will be addressed, developing the resources needed to understand the complexity between inter- and intra-kingdom interactions.
|Kuehn, Seppe||University of Chicago||Understanding denitrifying soil microbiome response to environmental change||Researchers are increasingly discovering the fascinating potential of the microbiome in solving problems in the environment and agriculture. For example, microbial communities play significant roles in regulating global carbon and nitrogen cycles related to climate change, enhancing crop health for sustainable agriculture. Recent advances in DNA sequencing allow researchers to relate the microbiome’s genomic composition (structure) to the metabolic activities (function) of these communities. To effectively manipulate the microbial communities toward beneficial metabolic functions, we need to infer design principles and strategies from these observed structure-function relationships. However, much of the successes in mapping structure to function mostly come from simplified systems or synthetic communities, rather than the fully complex natural communities such as soils. In the context of natural communities, efforts have sought to connect taxonomic or genomic composition to key process rates in soils, but these predictions remain poor. Therefore, With metagenomics data, we will bridge this gap by understanding the underlying microbial genetic components and their interactions that dictate soil microbiota’s metabolic response (function) to environmental change. Ultimately, this will enable us to predict and control microbial metabolism in soils in changing environments.|
|Mengiste, Tesfaye||Purdue University||Sorghum anthracnose genomics and elucidation of virulence genes||This project will provide the foundational knowledge and blueprint for future progress. Understanding the genetic makeup and DNA sequences of important fungal species is critical for the protection of biofuel crops from devastating fungal diseases. These will provide ways to build genetic resistance and avoid chemical disease control, thus reduce pesticide use and help maintain public safety and environmental quality.|
|Schwartz, Egbert||Northern Arizona University||High temporal resolution of transcripts and metabolites to analyze rapid responses of soil microbial communities to C and N addition||Carbon dioxide concentration in the atmosphere is increasing rapidly because humans are burning extremely large quantities of fossil fuels. Carbon dioxide is a greenhouse gas and traps heat in the atmosphere resulting in climate change. To limit climate change, and associated damage to human infrastructures, we must figure out how to take carbon out of the atmosphere and store it underground, including into soil organic matter. Our research has shown that many of the processes that lead to soil organic matter formation, including microbial growth and predation, are occurring much faster, on the time scale of hours, than previously thought. Yet all of the collected data sets are on a time scale of days, weeks, or even months. Here we propose to sample soils amended with a carbon source, on an hourly time scale so that we can elucidate microbial processes that lead to soil organic matter formation.|
|Shulman, Hannah||University of Tennessee at Knoxville||Impact of climate change on the plant-microbe N cycling network across time and space in montane ecosystems||Climate change is causing significant changes in mountain ecosystems. Warmer and drier conditions are affecting where plants grow and how they function. Our ongoing research in these high elevation areas has shown that nitrogen, an essential nutrient for plants, is influenced by different types of microbes that cycle nitrogen in specific seasons. Nitrogen availability also changes with increasing elevation, and this affects the ability of plants to expand their range in the mountains. We want to understand how climate change affects nitrogen over time and in different locations by studying genes, ecosystems, and the relationships between microbes and plants. To do this, we need to collect detailed information about plants, microorganisms, and the cycling of nutrients in different environments and under different climate change conditions.|
|Stone, Bram||Pacific Northwest National Laboratory||The role of microbial predation and cooperation on soil carbon turnover and sequestration measured through multi-omics networks||The aim of our research is to quantify how interactions between soil microorganisms affect the way that carbon is stored, lost, or transformed in the soil. Soils represent the largest global reservoir of terrestrial carbon and soil microorganisms (bacteria, fungi, protists) are the key agents of carbon recycling because they control decomposition. Our work proposes to extensively sequence which genes soil microbes use when interacting with other microbes. These data will be combined with concurrent stable isotope tracing experiments which track the movement of important elements (carbon and oxygen) into microbial cells.|
|Voriskova, Jana||Czech Academy of Sciences||Response of soil microbial communities to changing climate in Arctic tundra||The Arctic represents one of the most vulnerable ecosystems to climate change. Microbes are known to play key roles in determining the stability of soil carbon and its possible release into the atmosphere as carbon dioxide and methane. In our project we aim to comprehensively explore the response of microbial communities to predicted climate warming in tundra soil. Our goal will be achieved by combining long-term soil, vegetation and CO2 emissions data from climate manipulation experiment located in Greenland with sequencing data enabling detailed characterization of soil microbes.|
|Proposer||Affiliation||Proposal Title||Proposal Description|
|de Vries, Ronald||Westerdijk Fungal Biodiversity Institute (Netherlands)||Expanding synthetic biology tools by deeper understanding of Aspergillus niger primary metabolism||A deep understanding of metabolism is crucial for efficient and effective metabolic engineering strategies to develop novel or improved fungal cell factories for a range of biotechnological applications. In this project, researchers will use EMSL and JGI capabilities to discover and characterize novel enzymes and to obtain a new level of understanding of primary carbon metabolism in fungi.|
|Ernakovich, Jessica||University of New Hampshire||A high-resolution view of the plant-microbe-mineral interactions affecting C-cycling in thawed permafrost soils||Researchers aim to determine how plants, microbial activity, and organo-mineral associations influence permafrost soil carbon balance. Findings will be integrated into a modeling framework to resolve the interactions among plants, microbes, and minerals, which are critical to advancing fundamental understanding of biogeochemical processes in a warming and thawing Arctic.|
|Hatzenpichler, Roland||Montana State University||(Eco)Physiology of methanogens of the phylum Thermoproteota||In this project, scientists will study the physiology of newly discovered methanogens both in culture and in their native habitat. The team will address how these cells vary their gene expression and metabolomes under changing physiochemical and thermodynamic conditions.|
|Jakes, Joseph||USDA Forest Service, Forest Products Laboratory||Nanoscale multimodal analysis of brown rot fungal decay mechanisms for improved biomimetic lignocellulosic biorefinery processes||Researchers will use resources at EMSL, JGI, and APS to produce accumulative transcriptomic, chemical, composition, structural, and mechanical data that will be used to identify different decay stages in wood with their associated decay mechanisms and cell wall modifications.|
|Master, Emma||University of Toronto||Functional and structural analysis of microbial expansin-related proteins that loosen in lignocellulosic and chitin fiber networks||This project brings together functional genomics, structural biology, and advanced techniques in material science to evaluate the untapped potential of microbial expansin-related proteins in the production of bio-based chemicals and materials.|
|Saleska, Scott||University of Arizona||Integrating microbial meta-omics, isotopes and methane metabolites to connect belowground microbial processes to aboveground methane emissions in seasonally-inundated Amazonian floodplain forests.||This project builds on the first continuous whole-ecosystem measurements of methane emissions, via eddy covariance methods, from a seasonal inundated floodplain forest in the Amazon. Researchers will use metagenome and metatranscriptome sequencing and metabolomics to mechanistically identify the distribution of methane production and consumption activity in soils and tree stems, and how these components shift between wet and dry season in seasonally inundated forests, and between a floodplain forest and an upland terra firme forest.|
|Smertenko, Andrei||Washington State University||Systems Analysis of Embolism Resiliency in Grasses for Biofuel Production Under Marginal Environments||Water flows from roots to shoots through vessels composed of hollow dead cells. Specialized regions in the cell wall, known as pits, conduct water between vessels. Drought causes embolism of vessels leading to blockage of water movement. Pits contribute to the embolism spread between the vessels. This project aims at developing technology for containing embolism by optimizing pit morphology.|
|Smith, Heidi||Montana State University||Opening the black box of glacial carbon cycling – providing fundamental insight into impacts of a changing climate||In this project, scientists will study the physiology of newly discovered methanogens both in culture and in their native habitat. The team will address how these cells vary their gene expression and metabolomes under changing physiochemical and thermodynamic conditions.
Roughly 104 petagrams of organic carbon are stored within ice worldwide. Glacial carbon originates from new atmospherically deposited material (including black carbon from wildfires) and in situ production by microorganisms. The metabolic strategies of carbon transformation within glacial systems are not well understood, yet critically affect adjacent and downstream aquatic ecosystems. This research will link microbial processing of discrete sources of organic carbon and its concomitant compositional shifts.
|Stone, Bram||Pacific Northwest National Laboratory||The role of microbial predation and cooperation on soil carbon pathways measured through multi-omics||Researchers will conduct labeled isotope tracer incubations to follow the movement of plant and microbial carbon under different moisture and predator manipulations. Data from this experiment will be used to combine soil carbon processing more rigorously with organismal interactions. These data will thus address the critical knowledge gap of how and when microbial interactions accelerate soil carbon cycling.|
|Ziegler, Samantha||National Renewable Energy Laboratory||Structural and biochemical characterization of glycosyltransferase 47 family proteins from Spirodella to enable predictive biology||In this project, researchers are comprehensively studying cell wall synthesis enzymes found in the duckweed Spirodela polyrhiza to create a database that can be used to predict the functionality of similar proteins in other organisms. The data generated from this proposal will be used to create designer plants, with specified cell wall structures for bioproduction.|
|Zimmerman, Amy||Pacific Northwest National Laboratory||Linking multi-organism-environment interactions across lab and field scales to estimate viral contributions to soil C cycling||Researchers will conduct complementary field and laboratory-based experiments to generate the data necessary for baseline estimates of when and how much viruses contribute to soil carbon cycling. The team will generate some of the first quantitative data about rates of viral production in soil, shifts in soil carbon pools as a result of viral predation, and the degree to which natural soil viral communities vary over time.|