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    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

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    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    A panoramic view of a lake reflecting a granite mountain.
    Genome Insider: Methane Makers in Yosemite’s Lakes
    Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work.

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    A light green shrub with spiny leaves, up close.
    Genome Insider: A Shrubbier Version of Rubber
    Hear from the consortium working on understanding the guayule plant's genome, which could lead to an improved natural rubber plant.

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    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

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  • Data & Tools
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    iPHoP image (Simon Roux)
    iPHoP: A Matchmaker for Phages and their Hosts
    Building on existing virus-host prediction approaches, a new tool combines and evaluates multiple predictions to reliably match viruses with their archaea and bacteria hosts.

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    Abstract image of gold lights and squares against a black backdrop
    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

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    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

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    Green plant matter grows from the top, with the area just beneath the surface also visible as soil, root systems and a fuzzy white substance surrounding them.
    Supercharging SIP in the Fungal Hyphosphere
    Applying high-throughput stable isotope probing to the study of a particular fungi, researchers identified novel interactions between bacteria and the fungi.

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    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

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    croppe image of the JGI helix sculpture
    Tips for a Winning Community Science Program Proposal
    In the Genome Insider podcast, tips to successfully avail of the JGI's proposal calls, many through the Community Science Program.

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    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

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    image from gif that shows where in the globe JGI fungal collaborators are located.
    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

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    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

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Our Projects
Home › CSP Plans
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October 1, 2019

Gene Atlas of a Nitrogen-Fixing Legume Symbiont

A transmission electron micrograph of Sinorhizobium meliloti strain 1021. The scale bar represents 2 microns. (George diCenzo)We will use a high-throughput approach to help fill-in gaps in knowledge of the functional properties of microbes and their genes, laying a solid foundation for researchers hoping to engineer bacteria with improved or novel traits. [Read More]

October 1, 2019

How Beneficial Fungi Regulate Effector Gene Expression

In this study, we will perform a fine-graded comparative analysis of transcription factor activities and functions in relation to beneficial fungal-associations with model plant hosts and measure how outcomes are altered by encounters with pathogenic fungi and selected root-associated bacteria. Improved knowledge of fungal gene regulation during confrontation with other microbes and in different plant hosts will help engineering more resilient fungal strains with enhanced root colonization and growth promotion capacities and provide fresh leads to plant-protection strategies. [Read More]

October 1, 2019

Virus-Host Interactions in Model Systems

Microbes and their viruses are recently found to be profoundly impacting in virtually any ecosystem studied – from the oceans and soils to humans and bioreactors. While our knowledge of viral diversity is growing, we often observe genomes without knowing which host cell the virus infects. This proposal seeks to leverage ecosystem modeling and high-resolution time series datasets to scalably identify which viruses infect which hosts in experimental model systems and complex communities. Should it be successful, the new analytic will be powerful context for studying viruses in any ecosystem. [Read More]

October 1, 2019

Inter-organismal Interactions in the Rumen Ecosystem

We propose to generate data that would provide us with a better understanding of the role of different microorganisms involved methanogenesis in the rumen ecosystem and the foundation to develop new strategies for methane mitigation from ruminants. Ruminant animals are one of major anthropogenic sources of the highly potent greenhouse gas methane and advanced methane mitigation strategies would have a significant impact on the global methane emission and the therefore on climate change. This aligns fully with DOE’s mission to reduce the anthropogenic carbon footprint. [Read More]

October 1, 2019

Microbial Genomes Across the World’s Rivers

This proposal seeks to create a global census of microbial genomes across 250 of the world’s rivers, from the Amazon to the Mississippi. Our goal is to create a Genome Resolved Open Watershed (GROW) database- which will be an open access resource to advance knowledge of aquatic microbiology for the entire scientific community. [Read More]

October 1, 2019

International Arctic Ice Drift Experiment MOSAiC

The MOSAiC drift experiment will provide sequence data to study for the first time how microbial communities change over a complete seasonal cycle in the Arctic Ocean in terms of their diversity and gene activity. These results will be instrumental to study climate processes they drive. [Read More]

October 1, 2019

Diversity of Parasitic and Commensal Chytrids

Chytrids are basal fungi. Despite the chytrids major negative impact on algal phytoplankton productivity and as a major pest in microalgal biofuels production facilities, extremely little is known about the biology of these organisms. We expect that the genomic data provided from this CSP will shed light on the “blackbox” of unknown molecular events at various stages of infections in the inter-organismal chytrid/algal systems. This work is highly relevant to the DOE mission in the context of organic carbon cycling in aquatic plankton communities and due to the microalgae being feedstock for biofuels applications. [Read More]

October 1, 2019

Cross-Domain Interactions in Microalgae Communities

Algae–prokaryote associations in phototrophic high pH–high alkalinity cultures containing Chlorella sorokiniana strain SLA-04. a: algal cells, b: bacterial cells; s: algal sheath. (Images courtesy of Dr. Huyen Bui, Center of Biofilm Engineering, Montana State University)We will characterize algal communities from some of the most productive ecosystems in the world to understand the interactions between the microbial community members involved. Our goal is to develop strategies for establishing stable and highly productive photosynthetic communities suitable for biofuel and high-value product generation on an industrial scale. [Read More]

October 1, 2019

Characterizing Viruses in Antarctica

Characterizing viruses in extreme environments may facilitate a better understanding of the role that viruses play in the dynamics and evolution of complex microbial communities. [Read More]

October 1, 2019

Role of Fungal Endosymbionts in Host Reproduction

Transmission electron microscopy of Mycoavidus cysteinexigens (arrows) aggregated around lipid bodies (lb) inside hyphae of Mortierella elongata isolate NVP64. Scale bar 1 um. (Alessandro Desiro)Some beneficial plant associated fungi house bacteria inside their cells which impact fungal and plant health. Recent studies show that some fungal endosymbionts manipulate reproduction of their hosts, and may influence plant ecosystems. This project focuses on endosymbionts and fungal reproduction, expanding knowledge on the complexities of microbiome interactions. These fungi are industrially important because they produce valuable lipid products. Our goal is to learn about optimal conditions for fungal health and apply that knowledge to increase crop health and produce alternative energies. [Read More]
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