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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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    (PXFuel)
    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

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    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

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    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

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    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

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    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

    Read more

    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

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    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

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    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

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    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

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    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

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User Programs
Home › User Programs › User Program Info › Closed Calls › CSP Small-scale

CSP Small-scale

(status: CLOSED)

About This Program

The Small-scale Microbial/Metagenome program seeks to target specific project types listed in the call, with an emphasis on providing pilot data to enable future large-scale proposal submission.  Projects from first-time JGI investigators are strongly encouraged.  Proposals may include up samples from up to three project types.  The number of samples proposed must adhere to call guidelines for the proposal to be considered for scientific review.

Proposals for this call may be submitted at any time as brief white papers and will be reviewed every six months.  Applicants may submit up to two proposals per cycle (but may be listed as co-PI on an unlimited number of proposals).

All proposals will undergo an internal pre-review to ensure technical feasibility and alignment with JGI and DOE missions.  Screened proposals will then be reviewed for scientific merit, DOE relevance, proposed data usage by the applicant/community, and track record of the applicant. After proposal approval, and at an established time (roughly two months after approval), the proposer will be asked to provide DNA/RNA meeting JGI’s sample requirements. Samples that are not available at that time, or are of insufficient quality or quantity, will delay or potentially defer approval for sequencing.

For questions about the appropriateness of projects, program specifics or application process, please contact us.

Current Call (status: CLOSED)

Bacterial and archaeal isolates and single cells

Proposed organisms should broaden phylogenetic representation among sequenced representatives or participate in processes directly relevant to DOE missions. Type strains, including proposed strains prior to publication, are highly encouraged. For single-cell sequencing projects, MDA products of single amplified genomes should either be in hand at the time of proposal submission or samples can be sent directly to JGI for single-cell sorting and amplification. Single cells from candidate phyla are encouraged. Between 48 and 92 isolates or single-cell genomes may be proposed. For projects with >92 genomes, please refer to the CSP Annual Call.

Bacterial and archaeal resequencing

The JGI seeks proposals centered on resequencing of bacterial and archaeal isolates for which a reference genome exists. Projects may focus on bacterial community structure, understanding gene function in bacteria under selective pressure or in mutagenized strains. We will also consider collections of highly related strains from nature that display differences in phenotypes related to DOE missions, e.g. lignocellulose decomposition, fermentation of sugar substrates or degradation of environmental toxins. Between 36 and 72 samples may be proposed. For projects with >72 samples, please refer to the CSP Annual Call.

Bacterial and archaeal RNA sequencing

The JGI solicits smaller scale RNA sequencing projects for bacterial and archaeal isolates, for which a reference genome is available. RNA-seq data may be used for improvement of genome annotation or for transcript counting applications (e.g. gene expression profiling during growth on an array of cellulosic substrates to decipher degradation pathways). Projects should be directly relevant to DOE missions. Between 36 and 54 samples (including replicates) may be proposed. For projects with >54 samples, please refer to the CSP Annual Call.

Bacterial and archaeal epigenomes

DNA base modifications (6mA, 5mC, 4mC and others) are known to be important in host defense (as part of restriction systems), but may have additional functional roles that have previously been difficult to detect. New technologies now allow direct sequencing of DNA base modifications, providing a first opportunity for genome-wide exploration of bacterial epigenomes. JGI is seeking proposals to examine the possible regulatory roles of DNA base modification in Bacteria and Archaea. Up to 12 samples may be proposed. For projects with >12 samples, please refer to the CSP Annual Call.

Metagenomes and metatranscriptomes **

Most microbes live in complex communities in oftentimes dynamic environments where the impact of changing environmental parameters on community structure and function are largely unknown. JGI is accepting proposals that include up to 24 metagenomes or metatranscriptomes (in any combination). Up to 184 samples may also be proposed for 16S, 18S or ITS2 tag sequencing on the Illumina MiSeq (itags), although itag-only proposals will not be considered. Each proposal will have a sequencing allocation of up to 360 Gb. Proposals must show clear DOE mission relevance in areas such as bioenergy-related plant-microbe interactions, carbon/nitrogen cycling and/or carbon sequestration processes in soils and sediments, and biogeochemical processes contributing to contaminant biotransformation and/or immobilization. For projects that fall outside these criteria, please refer to the CSP Annual Call.

Proposal Schedule

Proposals are accepted on a continuous basis and will be reviewed twice a year. Letters of intent are not required. Deadline for submission is 60 days prior to the review date.

Submission deadlines (review dates in parentheses):

  •  February 24, 2017 (April 24 2017)
  •  September 4, 2017 (October 2017)
  •  March 1, 2018 (April 2018)
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