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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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    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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    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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    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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    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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    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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    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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    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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Past Events
Home › Past Events › CSP 2012 PI Workshop

CSP 2012 PI Workshop

Walnut Creek, California

The DOE-JGI is organizing a two-day workshop for Principal Investigators on successful CSP 2012 proposals in the focus areas of “plant-microbe interactions” and “terrestrial greenhouse gas emissions and capture” to be held at the JGI in Walnut Creek, CA, on January 23-24, 2012.

Attendance to this workshop is by invitation only

List of Projects

  • Dangl et al., Plant associated metagenomes–Microbial community diversity and host control of community assembly across model and emerging plant ecological genomics systems.
  • Schadt et al., Defining the Populus Microbiome: Role of Genotype by Environment Interactions in Shaping the Rhizosphere Microbiome of Populus trichocarpa Gross et al., The Agave Microbiome: Exploring the role of microbial communities in plant adaptations to desert environments
  • Bucking et al., Exploring the transcriptome of perennial grasses in association with beneficial microorganisms to increase biomass production and environmental sustainability of bioenergy production
  • Laplaze et al., Transcriptome Analysis of Salt Tolerance in Casuarina trees
  • Fierer et al., Cross-site metagenomic analyses to assess the impacts of experimental nitrogen additions on belowground carbon dynamics
  • Brodie et al., Mediterranean Grassland Soil Metagenome (MGSM): Enabling a systems view of soil carbon and nitrogen biogeochemistry under a changing climate.
  • Pester et al., Targeted metagenomics and metatranscriptomics of a sulfate-reducing rare biosphere member and potentially novel sulfate reducers that impact methane emission from peatlands
  • Rodrigues et al., Profiling metagenomic consequences of Amazon deforestation at different spatial scales
  • Martin et al., Metatranscriptomics of Soil Forest Ecosystems
  • DeAngelis et al., Microbial ecology and genomics of carbon-storing bacteria in rhizosphere soils
  • Mohn et al., Metagenomic and metatranscriptomic analysis of forest soil communities across North America

 

  • 2016 Microbial and Plant Systems Modulated by Secondary Metabolites Meeting
  • NeLLi 2017: From New Lineages of Life To New Functions
  • 2017 Microbial and Plant Systems Modulated by Secondary Metabolites Meeting
  • Program Meetings and Workshops
  • CSP 2012 PI Workshop
  • Bay Area Plant Microbe Interaction Symposium II
  • Microbial Genome Reannotation Workshop
  • Application of High Performance Computing to the DOE Joint Genomic Institute’s Data Challenges

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