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 every part of this project depends on lakewater samples — so this episode is a look at how researchers get these specialized snapshots of a freshwater ecosystem. Links from this episode: Submit your own proposal to work with the JGIEpisode TranscriptThe Megadata of Lake...

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 National Lab is home to two supercomputers — Summit and Frontier — that process terabytes of data with MetaHipMer2. And the National Energy Research Scientific Computing (NERSC) has another supercomputer, Perlmutter that works at large scale. But nearby the JGI, a cluster...

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 years ago, when they set out to analyze 500 metagenomes, it was the biggest project the JGI had ever put together.  The next 3 episodes are the story behind that giant assembly from Lake Mendota. In this episode: the software evolution that made metagenome assemblies like this...

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 compare their work consistently. And EcoFABs also work well in the classroom. This episode, we visit Los Medanos College to see EcoFABs in action in Jill Bouchard’s BIO 21 lab course.  Links from this episode: Submit your own proposal to work with the JGIFind out more about...

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 a new way of moving: a tail-like flagella.  Submit your own proposal to work with the JGIJoin us at the 2023 JGI User MeetingLinks from this episode: Episode TranscriptPublication: Palmer, M, et al.Thermophilic Dehalococcoidia with unusual traits shed light on an unexpected...

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 affect how microbes cycle nutrients and adapt to climate change. Episode TranscriptPublication: Camargo, A.P., et al. “Identification of mobile genetic elements with geNomad,” Nature Biotechnology. (2023). doi: 10.1038/s41587-023-01953-yScience Highlight: You can move, but...

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. They’re a great way to see how climate change affects freshwater ecosystems, and how those ecosystems work.  Links from this episode: Submit your own proposal to work with the JGI http://jointgeno.me/proposals Join us at the 2023 JGI User Meeting...

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 desert shrub that’s native to North America: guayule.  This episode was made in collaboration with our friends at the HudsonAlpha Institute for Biotechnology. Links from this episode: Submit your own proposal to work with the JGI : http://jointgeno.me/proposals  Join us...

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 researchers Anna-Louise Reysenbach, Emily St. John, Gilberto Flores, and Peter Girguis about sampling these communities, and understanding how they’ve adapted to this extreme environment.   Links from this episode: Submit your own proposal to work with the JGI:...

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, Guangchao Sun and Vladimir Torrres have looked into traits that could transfer from grasses into other crops.  One grass they studied just happened to be the same species that covered World Cup pitches in 2022. Links from this episode: Submit your own proposal to work with...

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 viruses — to power a more sustainable future. Stick around for a snippet of the next episode. Join us at our User Meeting: jointgeno.me/JGI2023 Find out how to become a JGI user here: jointgeno.me/proposals Our contact info: Twitter: @JGIEmail: jgi-comms at lbl dot gov

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 explore for efficient biofuel production. Episode Transcript Paper: Lignin deconstruction by anaerobic fungiScience Highlight: Busting the Unbreakable LigninJGI Feature: JGI at 25: Following Fungi that Pry Apart Plant PolymersJGI Release: Fungal Enzymes Team Up to More Efficiently...

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. Episode Transcript Paper: A global phylogenomic analysis of the shiitake genus Lentinula The Lentinula genomes are publicly available on JGI’s MycoCosm data portal The JGI website also features a highlight summary of the paper: Tracing the Evolution of Shiitake Mushrooms This work was...

The JGI’s Community Science Program gives researchers access to all kinds of sequencing, ‘omics and bioinformatics capabilities — and it’s open to scientists at any career stage, anywhere in the world, for free. We accept new projects related to energy and the environment several times a year. A few proposal calls have deadlines coming up – in January, March, and later on in the spring. In this episode, hear proposal tips from Tanja Woyke, who runs user programs at the JGI, and project...

Back in 2011, JGI-supported researchers published a paper in the journal Science. They’d used metagenomics to sift for microbial genes encoding carbohydrate-chomping enzymes in cow rumen — and found 27,000 candidates. The data from that study is now used across California State University campuses for biotechnology education as part of a course-based undergraduate resource experience. Hear from CSU San Marcos Professor Matt Escobar and UC Davis Associate Professor Matthias Hess, also the...

Every year, the JGI sequences around 35,000 samples — from plants, algae, bacteria, archaea, fungi, viruses — to support scientists around the world. Most of those researchers send their samples in from afar, without ever hearing much about the sequencing lab. So today, Chris Daum walks through the JGI’s sequencing pipeline, where there are freezers with names — but not doors — and robots handle a bunch of benchwork. Links from this episode: Episode TranscriptSubmit a proposal to work with...

We count on livestock for food and fiber, but raising these animals also produces an atmosphere-warming gas: methane. Those emissions mainly come from gut microbes — the bacteria and archaea breaking down plant matter. So since 2010, the JGI has supported researchers studying those microbial methane-makers. Eventually, that could help us dial back their emissions, while still producing things like meat, milk, and wool. Hear more from JGI collaborators Sinead Leahy (New Zealand Agricultural...

Black fungi are microscopic and mighty. They survive everywhere from Antarctica to Joshua Tree National Park, despite extremely harsh conditions. And their survival secrets could one day help other organisms survive hotter, drier climates. So University of Tuscia researchers Laura Selbmann and Claudia Coleine are working with scientists from around the world – and the JGI – to understand them better. Links from this episode: Episode TranscriptHow Black Fungi Adapt to ExtremesIntegrated...

The soybean is a crop that could boost biofuels and fertilize fields. So in 2010, the JGI helped publish the original genome sequence for the soybean, Glycine max. With a full genome sequence, researchers have been able to look into soybean’s strengths – along with a fungus that threatens this important crop. Hear more about that work from researchers Gary Stacey (University of Missouri), Peter van Esse (The Sainsbury Laboratory) and Sebastien Duplessis (INRAE). Links from this...

In this episode, we peer into plant cells. Researchers are using measurements from single cells to understand which genes help plants grow, get nutrients, weather drought, and more. And eventually, their findings could help us grow better crops, with less impact on our planet. Links from this episode: Monet’s Waterloo Bridge at Sunset (1904) Serat’s A Sunday on La Grande Jatte (1884) Submit a proposal to work with the JGI: https://jointgeno.me/proposals  Margot’s 2021 Berkeley Lab...

This shorter episode is about a tiny, single-celled alga – Chlamydomonas reinhardtii – that’s managed to have a big impact. UC Berkeley plant biologist Sabeeha Merchant explains why she works on this alga, how researchers managed to sequence its genome, and what it has to teach us about other organisms – like plants.  Links from this episode Episode TranscriptJGI@25: The Little Alga That CouldChlamydomonas reinhardtii on Phytozome and PhycoCosm JGI Blog Post: Green Algae Reveal One mRNA...

We know all kinds of things about plastic – except, how to break it down for recycling. But some hungry insects can digest plastic. So researchers are taking a look at how these critters process plastic, to improve plastic recycling by following their lead.  Episode Transcript Links from this episode: Sequencing the Amazonian Stinkbird’s Microbiome Acronym Action: EPICON project Submit a proposal to work with the JGI! Find out more about the FICUS program between JGI and...

What if we understood plants and how they adapt to their ever-changing environments better? We could unlock new innovations to drive more productive food, medicine, and bioenergy crops. But most available genomes are from narrow swaths of the plant tree of life. One project aims to change that. Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2-episode-10-filling-in-the-plant-tree-of-life/.

What grass is a prized ornamental and a bioenergy plant? Meet Miscanthus, an attractive addition to your garden and a potential fuel for the future. But, to be competitive in the market, both energy policy and Miscanthus will need some upgrades. In this episode, hear from scientists working on understanding Miscanthus biology and the economic terrain to help make the plant a viable alternative to fossil fuels. Find more info on this episode, including the transcript, at...