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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 Mendota – Part 1: Many, Many MersThe Megadata of Lake Mendota – Part 2: Souped Up ComputingRelated papers: Species invasions shift microbial phenology in a two-decade freshwater time seriesTerabase-Scale Coassembly of a Tropical Soil MicrobiomeOur contact info:Twitter: @JGIEmail: jgi-comms at lbl dot gov

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 called Dori is also capable of running smaller assemblies — so we head there for a sense of what this supercomputing looks like. Links from this episode: Submit your own proposal to work with the JGIEpisode TranscriptRobert Riley at the 2016 DOE JGI Genomics of Energy & Environment MeetingMetaHipMerThe ExaBiome ProjectOur contact info:Twitter: @JGIEmail: jgi-comms at lbl dot gov

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 possible. Links from this episode: Submit your own proposal to work with the JGIEpisode TranscriptThe JGI’s Metagenome ProgramMetaHipMerThe ExaBiome ProjectPaper: Hofmeyr, S., Egan, R., Georganas, E. et al. Terabase-scale metagenome coassembly with MetaHipMer. Sci Rep 10, 10689 (2020). https://doi.org/10.1038/s41598-020-67416-5  Our contact info:Twitter: @JGIEmail: jgi-comms at lbl dot gov

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 EcoFABsConnect with Ying Wang about her lab at Texas A&M Episode TranscriptOur contact info:Twitter: @JGIEmail: jgi-comms at lbl dot gov

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 past The ISME Journal. (2023). doi: 10.1038/s41396-023-01405-0  Our contact info:Twitter: @JGIEmail: jgi-comms at lbl dot gov

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 you can't hideLearn more about geNomad and download it Submit your own proposal to work with the JGIExplore IMG/VR and IMG/PROur contact info:Twitter: @JGIEmail: jgi-comms at lbl dot gov

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 http://jointgeno.me/JGI2023  Episode TranscriptPublication: Perez-Coronel, E., Michael Beman, J. Multiple sources of aerobic methane production in aquatic ecosystems include bacterial photosynthesis. Nat Commun 13, 6454 (2022). doi: 10.1038/s41467-022-34105-yLearn about the IMG/M systemJGI Webinars: http://jointgeno.me/Webinars     Our contact info:Twitter: @JGIEmail: jgi-comms at lbl dot gov Sound Effects Credits: Marmot sound courtesy of slunali, freesound.org

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 at the 2023 JGI User Meeting: http://jointgeno.me/JGI2023  Episode TranscriptHudsonAlpha Institute's Tiny Expeditions PodcastGuayule: Can genetics create a natural US rubber source?Guayule Project in the JGI’s Approved Proposals of 2022 Our contact info:Twitter: @JGIEmail: jgi-comms at lbl dot gov

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: http://jointgeno.me/proposals Join us at the 2023 JGI User Meeting: http://jointgeno.me/JGI2023  Episode TranscriptPaper: Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits Our contact info:Twitter: @JGIEmail: jgi-comms at lbl dot gov

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 the JGIJoin us at the 2023 JGI User Meeting Episode TranscriptPublication: Sun, G., Wase, N., Shu, S. et al. Genome of Paspalum vaginatum and the role of trehalose mediated autophagy in increasing maize biomass. Nat Commun 13, 7731 (2022). doi: 10.1038/s41467-022-35507-8Phytozome: Paspalum vaginatum data Our contact info:Twitter: @JGIEmail: jgi-comms at lbl dot gov

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 Publication: Lankiewicz, T.S., Choudhary, H., Gao, Y. et al. Lignin deconstruction by anaerobic fungi. Nat Microbiol 8, 596–610 (2023). doi: 10.1038/s41564-023-01336-8Science Highlight: Busting the Unbreakable LigninJGI Feature: JGI at 25: Following Fungi that Pry Apart Plant PolymersJGI Release: Fungal Enzymes Team Up to More Efficiently Break Down CellulosePNNL Release: Biofuel Tech Straight from the Farm