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    Serpula lacrymans var. lacrymans, an aggressive decomposer of the built environment, attacking this dresser. (Inger Skrede)
    The fungus that made itself at home
    Due to its aggressive capacity to damage the wood in homes, bioenergy researchers have been interested in harnessing the brown rot Serpula lacrymans towards breaking down plant mass for conversion to sustainable, alternative biofuels and bioproducts. In The ISME Journal, insights on how the fungus has responded to manmade changes in its ecological habitat, adapting to thrive in built environments.

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    Sexual reproduction in Rhizopus microspores: (a) Successful mating between fungi harboring bacteria; (b) Lack of sex between mates cured of endobacteria. (Stephen Mondo)
    An Addiction Crucial to a Fungus’ Reproduction
    In the absence of the Burkholderia endobacteria, the Rhizopus fungus cannot act as a plant pathogen, and researchers have now discovered that endobacteria also regulate its sexual reproduction. The work sheds light on a poorly understood group of oleaginous or oil-producing fungi, and the impact this mutualistic interaction has on these potential large-scale biodiesel producing fungi.

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    In Nature Communications, researchers sequenced and analyzed the genome of Kalanchoe fedtschenkoi (lavender scallops) to better understand how this plant transitioned from C3 to CAM photosynthesis. (Forest and Kim Starr, Flickr CC BY 2.0)
    Succulent Genes for Water Use Efficiency
    To understand how many plant lineages have independently transitioned from C3 to CAM photosynthesis, researchers sequenced and analyzed the genome of Kalanchoë fedtschenkoi (lavender scallops). As the first CAM eudicot to have its genome sequenced, Kalanchoë offers researchers a reference to trace the evolution of CAM photosynthesis in this group.

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    Morphological diversity of Xylariaceous endophytes. (J.M. U'Ren)
    Comparative and Population Genomics of Xylariaceae
    A genomic survey of the Xylariaceae, one of the largest and most diverse families of fungi made up of endophytic, pathogenic, and saprotrophic (including wood degrading) species.

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    Virus-infected Brachypodium (Courtesy of Kranthi Mandadi)
    Gene Atlases of Grass-Microbe Interactions
    This proposal seeks to build comprehensive gene atlas maps for diverse bioenergy grass-microbe interactions, including pathogenic and beneficial interactions in two grass models, Brachypodium and Setaria.

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    Yellowstone National Park, Octopus hot spring biofilms (Courtesy of Devaki Bhaya)
    Quantifying Cyanobacteria Interactions
    The long term objective is to quantify dynamic interactions between phototrophs and their virus predators. This will help to build quantitative, dynamic and predictive models of host-viral interactions and the effect on carbon and nutrient cycling.

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    DOE JGI BOOST logo
    New Software Tools Streamline DNA Sequence Design-and-Build Process
    Researchers from the U.S. Department of Energy Joint Genome Institute (DOE JGI) have developed a suite of build-optimization software tools (BOOST) to streamline the design-build transition in synthetic biology engineering workflows.

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    This graphic depicts the geographic distribution of GOLD biosamples and organisms. Organism location of isolation is marked in pink while Biosample location of collection is denoted with blue dots. Updates to the Genomes OnLine Database (GOLD) are reported in the upcoming Database issue of Nucleic Acids Research. (Image from Supratim Mukherjee et al. Nucl. Acids Res. 2016;nar.gkw992)
    DOE JGI Database of DNA viruses and retroviruses debuts on IMG platform
    In a series of four articles published in the Database issue of the Nucleic Acids Research journal, DOE JGI researchers report on the latest updates to several publicly accessible databases and computational tools that benefit the global community of microbial researchers.

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    Sakinaw Lake UBC
    Benchmark Study for Improving Microbial Community Profiling
    Researchers used synthetic and natural microbial lake communities to compare the microbial community profiles generated from high throughput short-read sequencing and high throughput long-read sequencing approaches.

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    Tobias Erb, MPI Marburg (Courtesy of Tobias Erb)
    Meet a JGI User: Tobias Erb
    "The JGI has been crucial for our research because it has provided the scientific community with a tremendous amount of gene sequences over the last couple of years. These gene sequences have become a true treasure grove for synthetic biologists like us."

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    Colleen Hansel, WHOI
    Meet a JGI User: Colleen Hansel
    "We have been working on genomic and transcriptome studies of a unique group of manganese (Mn) oxidizing Ascomycete fungi that were isolated from coal mine drainage treatment systems and metal-laden freshwater ponds. The staff and facilities at the JGI were critical for conducting this research. "

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    J. Chris Pires, University of Missouri
    Meet a JGI User: J. Chris Pires
    "My mission is to train the next generation of scientists by doing high impact, interdisciplinary science in a collaborative atmosphere. JGI is an important partner in this team science effort in cross-training students and postdoctoral researchers."

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    Freedom and Flexibility: Thinking Outside the Cell for Functional Genomics
    The latest proposal approved through the JGI’s Emerging Technologies Opportunity Program (ETOP) aims to develop an optimized cell-free platform that will enable researchers to speed up the “build” and “test” portion of the design-build-test-analyze cycle in synthetic biology.

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    Depiction of rumen microbiome. (Ella Maru studio, www.scientific-illustrations.com)
    A Reference Catalog for the Rumen Microbiome
    In Nature Biotechnology, an international team presents one of the largest targeted cultivation and sequencing projects to date: a reference catalog of rumen microbial genomes and isolates cultivated and sequenced from the Hungate1000 collection produced through the coordinated efforts of rumen microbiology researchers worldwide.

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    https://jgi.doe.gov/tracking-microbial-diversity-through-terrestrial-subsurface/
    Tracking Microbial Diversity Through the Terrestrial Subsurface
    In Nature Microbiology, JGI researchers collaborated with a team led by longtime collaborator Jill Banfield of the University of California, Berkeley and Cathy Ryan of the University of Calgary in Canada, investigating samples collected at Utah's Crystal Geyser over one of the its complex, five-day eruption cycles.

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Home › Items tagged with: metagenomics

Content Tagged "metagenomics"

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November 8, 2013

New tool helps find gene markers in microorganisms

New tool helps find gene markers in microorganismsResearchers have devised a novel method to exploit relationships between bacteria and archaea for a new set of gene markers The Science The researchers developed a new way to identify gene markers in bacteria and the primitive microorganisms classified in the kingdom known as Archaea. Dubbed, PhyEco (for phylogenetic and phylogenetic ecology) this strategy can… [Read More]

August 30, 2013

Subsurface Sediment Yields Novel Organism

Subsurface Sediment Yields Novel OrganismMetagenomic analysis emphasizes the “extraordinary microbial novelty” of poorly-explored subsurface ecosystems The Science Through metagenomics, researchers reconstructed a dominant organism and member of a new phylum-level lineage from an aquifer sediment in Colorado. The Impact Analysis of the complete microbial genome led to a detailed metabolic model with evidence for multiple new enzymes and pathways…. [Read More]

August 16, 2013

Solving the Secrets of Sedimentary Microbes

Solving the Secrets of Sedimentary MicrobesMicrobes from Phylum Chloroflexi Provide Clues to Carbon Cycling, Respiration in Sediments The Science Through metagenomics, researchers sequenced 86 organisms from the phylum Chloroflexi that represent 15 distinct lineages in order to discover the secrets of microbial life within terrestrial aquifer sediment deposits. The Impact These Chloroflexi microbes were found to have metabolic processes involved… [Read More]

July 22, 2013

Leaf-cutter ants project in Milwaukee Journal Sentinel

“These bacteria and these fungi have evolved for millions of years to deconstruct plant biomass,” said Frank Aylward, a graduate student at the University of Wisconsin-Madison who studies leaf-cutter ants and their fungus gardens. “We should try to learn from them and find out how it occurs in nature.” Read more at JSOnline.com about this… [Read More]

May 24, 2013

Microbial genomes help propose phylum name

Microbial genomes help propose phylum nameMetagenomicsand single-cell genomics are tools helping researchers learn more about the “biological dark matter” that has not been cultivated and studied in the laboratory. In an article published May 14, 2013 in Nature Communications. [Read More]

May 17, 2013

The genetic diversity of the maize microbiome

The genetic diversity of the maize microbiomeThe rhizosphere is the space in, on and around the plant roots where microbes in the plant interact with the microbes in the soil. The DOE JGI did a study with the plant Arabidopsis. [Read More]

May 3, 2013

Marine metagenome offers clues to ocean nitrogen cycle

Marine metagenome offers clues to ocean nitrogen cycleNitrification is the process by which ammonia is converted first into nitrites and then into nitrates, a form of nitrogen that can then be used by plants to grow. However, understanding how the nitrogen cycle works in marine environments is equally crucial. Until 1977, scientists believed that ammonium could only be oxidized by aerobic bacteria…. [Read More]

March 15, 2013

Bacterial sequence to help understand ant fungal gardens

Bacterial sequence to help understand ant fungal gardensLeaf-cutter ant colonies are comprised of millions of ants harvesting hundreds of kilos of leaves annually for use in growing their primary food source, a fungus. The fungal gardens tended by these ants allow them to convert plant biomass on a very large scale. Bioenergy researchers are looking at the microbial composition of the fungal… [Read More]

March 8, 2013

Comparing extremophile isolates from Yellowstone

Comparing extremophile isolates from YellowstoneResearchers isolated and sequenced four species of Hydrogenobaculum. [Read More]

February 22, 2013

Metagenomic study of methane in marine microbial communities

Metagenomic study of methane in marine microbial communitiesMethane is one of the most potent greenhouse gases and previous studies suggested that it is removed from the atmosphere through aerobic and anaerobic processes with the help of bacteria and archaea. Recent evidence suggests, however, that methane can be removed through other pathways involving as-yet unidentified microbes. To learn more about these pathways and… [Read More]
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