The Mobilome in the Mire
For years, researchers have known that many datasets miss a key part of microbial genomes: the mobile genetic elements, or MGEs, that can move between organisms. But now, deep sequencing and new analysis methods are brin...
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SIPs with Standards
Stable Isotope Probing (SIP) is a powerful technique for studying microbial communities. These experiments can show which microbes are handling specific nutrients, or what they're doing with those nutrients, and even how...
Adopt-A-Genome
In this episode, undergraduates adopt genomes that the JGI sequenced, but never published in the literature. These students analyze the genomes, write reports, and publish first-author papers, making the data available f...
Gotta Catch 'Em Gall
Kasey Markel and Patrick Shih (UC Berkeley and the Joint BioEnergy Institute) are looking for new ways to engineer plants. So they’ve looked into wasps that program oak trees to grow structures called galls.In this episo...
A Redesign for Yeast’s Genome, Chromosome by Chromosome - Jef Boeke, Weimin Zhang & Leslie Mitchell
To engineer yeast to do more, and understand genomes in general, Jef Boeke, Weimin Zhang (NYU Langone Health) and Leslie Mitchell (Neochromosome) have worked to replace yeast’s native chromosomes with synthetic versions....
Forest Fungi, Seagrass, and a New View of Symbiosis
Three stories of JGI-supported research, connected to nutrient cycles. Francis Martin and Lucas Auer discuss their work on communities of forest floor fungi. Allison Joy looks into seagrass meadows' carbon sequestration ...
What Happens To a Rainforest When You Dial Up Drought? - Linnea Honeker and Malak Tfaily
Rainforests store a big fraction of all the carbon on Earth, and soil microbes play a key role in pulling that carbon out of the atmosphere. This episode, researchers take a look at what happens to that storage when a ra...
The Megadata of Lake Mendota - Part 3: Boating Out to David Buoy
This is the third and final episode of our series on a giant metagenome assembly from Wisconsin’s Lake Mendota. In the last two episodes, we’ve covered the specialized software and supercomputers behind this project. But...
The Megadata of Lake Mendota - Part 2: Souped Up Computing
This series is the story of a giant metagenome assembly from Wisconsin’s Lake Mendota. In this episode: a look at the supercomputing that stitches together large datasets with the assembler program MetaHipMer2.Oak Ridge ...
The Megadata of Lake Mendota - Part 1: Many, Many Mers
Lake Mendota sits right next to the University of Wisconsin, Madison. And Trina McMahon's lab has been sampling the microbes of that lake for over 20 years, to understand how the freshwater ecosystem works. So a few year...
Experimenting with EcoFABs for Student Labs - Jill Bouchard & Ying Wang
To set up flexible, repeatable experiments on plants and microbes, Trent Northen’s group at Berkeley Lab created a fabricated ecosystem – an EcoFAB. These small plastic growth chambers let researchers around the world co...
JGIota: A Surprise for Chloroflexota — The First Flagella!
To understand how organisms adapt to extreme environments, Marike Palmer and Brian Hedlund study organisms living in hot springs. Hear how their recent work revealed more about the history of the Chloroflexota phylum and...
JGIota: A Tool to Find the Nomadic Genes that Help Microbes Adapt - geNomad
A quick snippet on Antonio Camargo and Simon Roux, a few of the JGI researchers behind software that finds plasmids and viruses within microbial genomes. As mobile genetic elements like viruses spread their DNA, they can...
Methane Makers in Yosemite's Lakes - Mike Beman and Elisabet Perez Coronel
Meet researchers who have hiked, rafted and met local wildlife (a marmot!) as they’ve sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains. These lakes are isolated, but varied...
A Shrubbier Version of Rubber - Andrew Nelson and Colleen McMahan
Right now, our natural rubber comes from just one tree species: Hevea brasiliensis. It’s great at producing latex that becomes rubber, but it’s vulnerable to disease and climate shifts. So researchers are looking into a ...
The Busy World of Deep Sea Eruptions - Anna-Louise Reysenbach and Emily St. John
The ocean depths are vast and dark. But there are hotspots on the ocean floor — underwater volcanoes and hydrothermal vents — where lively microbial communities thrive, and even support entire ecosystems. Hear from resea...
Crops as Tough as World Cup Turf - James Schnable and Guangchao Sun
In our warming world, we’ll need corn, sorghum and other crops to grow well in worse conditions: with more heat, less water and less fertilizer. Grasses do better in these conditions, so plant biologists James Schable, G...
Season 4 Trailer (and sneak peek!)
On June 8th, Genome Insider is back! We've got a batch of 4 new episodes where researchers discover the expertise encoded in our environment — in the genomes of plants, fungi, bacteria, archaea, algae, and environmental ...
JGIota: A Biofuel Breakthrough in Anaerobic Fungi with Michelle O'Malley and Tom Lankiewicz
Michelle O'Malley and Tom Lankiewicz of UC-Santa Barbara discuss the importance of studying anaerobic fungi, as well as a recent discovery that turns scientific presumption on its head and opens up a new avenue to explor...
JGIota: Sequencing Shiitakes with David Hibbett
David Hibbett (Clark University) fills us in on the kind of decay that makes shiitake mushrooms special. This week, he 39 collaborators published a paper tracing how these mushrooms have evolved.Find all episode transcri...