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    Maize can produce a cocktail of antibiotics with a handful of enzymes. (Sam Fentress, CC BY-SA 2.0)
    How Maize Makes An Antibiotic Cocktail
    Zealexins are produced in every corn variety and protect maize by fending off fungal and microbial infections using surprisingly few enzymes.

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    The genome of the common fiber vase or Thelephora terrestris was among those used in the study. (Francis Martin)
    From Competition to Cooperation
    By comparing 135 fungal sequenced genomes, researchers were able to carry out a broader analysis than had ever been done before to look at how saprotrophs have transitioned to the symbiotic lifestyle.

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    Miscanthus grasses. (Roy Kaltschmidt/Berkeley Lab)
    A Grass Model to Help Improve Giant Miscanthus
    The reference genome for M. sinensis, and the associated genomic tools, allows Miscanthus to both inform and benefit from breeding programs of related candidate bioenergy feedstock crops such as sugarcane and sorghum.

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    Poplar (Populus trichocarpa and P. deltoides) grow in the Advanced Plant Phenotyping Laboratory (APPL) at Oak Ridge National Laboratory in Tennessee. Poplar is an important biofuel feedstock, and Populus trichocarpa is the first tree species to have its genome sequenced — a feat accomplished by JGI. (Image courtesy of Oak Ridge National Laboratory, U.S. Dept. of Energy)
    Podcast: Xiaohan Yang on A Plantiful Future
    Building off plant genomics collaborations between the JGI and Oak Ridge National Laboratory, Xiaohan Yang envisions customizing plants for the benefit of human society.

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    Expansin complex with cell wall in background. (Courtesy of Daniel Cosgrove)
    Synthesizing Microbial Expansins with Unusual Activities
    Expansin proteins from diverse microbes have potential uses in deconstructing lignocellulosic biomass for conversion to renewable biofuels, nanocellulosic fibers, and commodity biochemicals.

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    High oleic pennycress. (Courtesy of Ratan Chopra)
    Pennycress – A Solution for Global Food Security, Renewable Energy and Ecosystem Benefits
    Pennycress (Thlaspi arvense) is under development as a winter annual oilseed bioenergy crop. It could produce up to 3 billion gallons of seed oil annually while reducing soil erosion and fertilizer runoff.

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    Artistic interpretation of CheckV assessing virus genome sequences from environmental samples. (Rendered by Zosia Rostomian​, Berkeley Lab)
    An Automated Tool for Assessing Virus Data Quality
    CheckV can be broadly utilized by the research community to gauge virus data quality and will help researchers to follow best practices and guidelines for providing the minimum amount of information for an uncultivated virus genome.

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    Unicellular algae in the Chlorella genus, magnified 1300x. (Andrei Savitsky)
    A One-Stop Shop for Analyzing Algal Genomes
    The PhycoCosm data portal is an interactive browser that allows algal scientists and enthusiasts to look deep into more than 100 algal genomes, compare them, and visualize supporting experimental data.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Podcast: A Primer on Genome Mining
    In Natural Prodcast: the basics of genome mining, and how JGI researchers conducted it in IMG/ABC on thousands of metagenome-derived genomes for a Nature Biotechnology paper.

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    Scanning electron micrographs of diverse diatoms. (Credits: Diana Sarno, Marina Montresor, Nicole Poulsen, Gerhard Dieckmann)
    Learn About the Approved 2021 Large-Scale CSP Proposals
    A total of 27 proposals have been approved through JGI's annual Community Science Program (CSP) call. For the first time, 63 percent of the accepted proposals come from researchers who have not previously been a principal investigator on an approved JGI proposal.

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    MiddleGaylor Michael Beman UC Merced
    How to Successfully Apply for a CSP Proposal
    Reach out to JGI staff for feedback before submitting a proposal. Be sure to describe in detail what you will do with the data.

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    Click on the image or go here to watch the video "Enriching target populations for genomic analyses using HCR-FISH" from the journal Microbiome describing the research.
    How to Target a Microbial Needle within a Community Haystack
    Enabled by the JGI’s Emerging Technologies Opportunity Program, researchers have developed, tested and deployed a pipeline to first target cells from communities of uncultivated microbes, and then efficiently retrieve and characterize their genomes.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Uncovering Novel Genomes from Earth’s Microbiomes
    A public repository of 52,515 microbial draft genomes generated from environmental samples around the world, expanding the known diversity of bacteria and archaea by 44%, is now available .

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    Green millet (Setaria viridis) plant collected in the wild. (Courtesy of the Kellogg lab)
    Shattering Expectations: Novel Seed Dispersal Gene Found in Green Millet
    In Nature Biotechnology, a very high quality reference Setaria viridis genome was sequenced, and for the first time in wild populations, a gene related to seed dispersal was identified.

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    The Brachypodium distachyon-B. stacei-B. hybridum polyploid model complex. (Illustrations credits: Juan Luis Castillo)
    The More the Merrier: Making the Case for Plant Pan-genomes
    Crop breeders have harnessed polyploidy to increase fruit and flower size, and confer stress tolerance traits. Using a Brachypodium model system, researchers have sought to learn the origins, evolution and development of plant polyploids. The work recently appeared in Nature Communications.

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November 11, 2013

Macondo wellhead metagenomes

The 2010 Deepwater Horizon oil spill presented researchers with an opportunity to employ a variety of approaches to quantify and model the microbial community composition and activity through successive metabolic petroleum hydrocarbon degradation. The Macondo wellhead oil leak, in the Gulf of Mexico, released a complex mixture of hydrocarbons into the water column that stimulated… [Read More]

November 11, 2013

Extremophilic microbial mat communities

Found worldwide, microbial mat communities are often the pioneering species in perturbed environments and can represent the only biota in extreme habitats. These associations are well-adapted to a range of harsh conditions that include extremes of temperature, salinity, high or low oxygen levels, and nutrient deprivation. In many cases, microbial mats are highly productive biochemical… [Read More]

November 11, 2013

NutNet soil metagenomes

Terrestrial ecosystems worldwide are receiving elevated inputs of nitrogen and recent studies suggest that the additional nitrogen is impacting soil carbon sequestration rates. It has been speculated that nitrogen additions alter the microbial processing of organic carbon pools, inhibiting decomposition of certain pools and accelerating soil carbon sequestration. This project focuses on shotgun metagenomic sequencing… [Read More]

November 11, 2013

Single-cell sequencing of iron-oxidizing bacteria

Iron is the fourth most abundant element in the Earth’s crust and is potentially one of the most abundant energy sources on Earth. Deep sea hydrothermal vents deposit iron oxides into the oceans annually. Several decades ago, the first hints of unusual microbial communities associated with iron oxides at seamounts came from samples collected by… [Read More]

November 11, 2013

Bacterial symbionts of gutless marine worms

More than 100 species of gutless worms have been found in marine sediments around the world, and they have formed symbiotic relationships with bacteria that provide them with nutrition and have enabled them to colonize nutrient-poor environments. The symbionts are so efficient at feeding their hosts and recycling their waste compounds that the worms have… [Read More]

November 11, 2013

Carbon-storing bacteria in rhizosphere soils

Microbes are able to store carbon under suboptimal growth conditions in culture, but the extent to which they store carbon in bulk or rhizosphere soil are not well understood. One stress response observed in microbes is the production of carbon storage granules as a means of trapping the needed carbon in the soil. Understanding the… [Read More]

November 11, 2013

Assembling plant microbiomes

The relationships between plants and the microbes in the surrounding soil influences nutrient uptake, disease resistance and stress tolerance. Essentially all land plants grow in intimate association with complex microbial communities both above the ground (phyllosphere) and below the ground on roots and the immediately surrounding area (rhizosphere) and deep inside root intercellular spaces (endophytes)…. [Read More]

November 11, 2013

Fungal plant pathogens and energy feedstocks

The fungal genus Colletotrichum is one of the most common and destructive groups of plant pathogenic fungi, causing disease on plants from nearly every crop and natural ecosystem worldwide. Fourteen species are known pathogens of grasses and cereals, including several candidate bioenergy feedstocks. The impact of Colletotrichum on next-generation bioenergy feedstock production and yield could… [Read More]

November 11, 2013

Microbes in Antarctica’s Dry Valley

The Antarctic Dry Valley system represents one of the harshest and most extreme environments inhabited by microorganisms on Earth. The soils of these valleys contain microbes that must cope with cold temperatures, poor water and nutrient availability, high salinities, exposure to high doses of ultraviolet radiation, and lack of sunlight during polar winters. Such an… [Read More]

November 11, 2013

Boosting biomass of perennial grasses

Switchgrass and prairie cordgrass are candidate bioenergy feedstocks while Brachypodium distachyon is a model grass being used to study related candidate bioenergy feedstocks that was sequenced at the DOE JGI. All three plants have relationships with fungi that lead to benefits such as increased biomass and stress resistance. By studying the transcriptome –the tiny fraction… [Read More]
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