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 JGI Episode Transcript The Megadata of Lake Mendota – Part 1: Many, Many Mers The Megadata of Lake Mendota – Part 2: Souped Up Computing Related papers: Species invasions shift microbial phenology in a two-decade freshwater time series Terabase-Scale Coassembly of a Tropical Soil Microbiome Our contact info: Twitter: @JGI Email: 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 JGI Episode Transcript Robert Riley at the 2016 DOE JGI Genomics of Energy & Environment Meeting MetaHipMer The ExaBiome Project Our contact info: Twitter: @JGI Email: 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 JGI Episode Transcript The JGI’s Metagenome Program MetaHipMer The ExaBiome Project Paper: 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: @JGI Email: 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 JGI Find out more about EcoFABs Connect with Ying Wang about her lab at Texas A&M Episode Transcript Our contact info: Twitter: @JGI Email: 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 JGI Join us at the 2023 JGI User Meeting Links from this episode: Episode Transcript Publication: 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: @JGI Email: 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 Transcript Publication: Camargo, A.P., et al. “Identification of mobile genetic elements with geNomad,” Nature Biotechnology. (2023). doi: 10.1038/s41587-023-01953-y Science Highlight: You can move, but you can't hide Learn more about geNomad and download it Submit your own proposal to work with the JGI Explore IMG/VR and IMG/PR Our contact info: Twitter: @JGI Email: 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 Transcript Publication: 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-y Learn about the IMG/M system JGI Webinars: http://jointgeno.me/Webinars Our contact info: Twitter: @JGI Email: 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 Transcript HudsonAlpha Institute's Tiny Expeditions Podcast Guayule: Can genetics create a natural US rubber source? Guayule Project in the JGI’s Approved Proposals of 2022 Our contact info: Twitter: @JGI Email: 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 Transcript Paper: Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits Our contact info: Twitter: @JGI Email: 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 JGI Join us at the 2023 JGI User Meeting Episode Transcript Publication: 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/s41467-022-35507-8 Phytozome: Paspalum vaginatum data Our contact info: Twitter: @JGI Email: 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: @JGI Email: 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/s41564-023-01336-8 Science Highlight: Busting the Unbreakable Lignin JGI Feature: JGI at 25: Following Fungi that Pry Apart Plant Polymers JGI Release: Fungal Enzymes Team Up to More Efficiently Break Down Cellulose PNNL Release: Biofuel Tech Straight from the Farm

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 Publication: Sierra-Patev S et al. A global phylogenomic analysis of the shiitake genus Lentinula. Proc Natl Acad Sci U S A. 2023 Mar 7;120(10):e2214076120. doi: 10.1073/pnas.2214076120. 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 supported by the JGI’s Community Science Program. Find out how to become a JGI User here: https://jgi.doe.gov/user-programs/

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 manager Miranda Harmon-Smith, who helps shepherd CSP projects along. Find more information about proposal calls and capabilities on the JGI website, jgi.doe.gov. Episode Transcript Links from this episode: Community Science Program Webinars on JGI Product Offerings Pro Tips for Successful CSP Applications Accessing Functional Genomics Capabilities JGI Calls for User Proposals CSP Functional Genomics call New Investigator CSP call Annual CSP Proposal Call FICUS call Data Release Policy Our contact info: Contact our Project Management Office with any questions about proposals Twitter: @JGI Email: jgi-comms at lbl dot gov

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 chair of the JGI User Executive Committee, on how that study went from the lab to the classroom. Links from this episode: Episode Transcript JGI@25 Stories Science Highlight: Rumenating on improving biofuel production Paper: Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen Our contact info: Twitter: @JGI Email: jgi-comms at lbl dot gov Genome Insider is a production of the Joint Genome Institute.

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 Transcript Submit a proposal to work with the JGI Virtual tour of the Joint Genome Institute Webinar: Long-read sequencing for metagenomics and DNA modification detection Our contact info: Twitter: @JGI Email: jgi-comms at lbl dot gov Genome Insider is a production of the Joint Genome Institute. Sound Effects Credits: George Hopkins “Mechanical keyboard typing”

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 Greenhouse Gas Research Centre) and Bill Kelly (AgResearch). Links from this episode: Episode Transcript JGI@25 Stories The JGI’s IMG/M data portal News Release: A Reference Catalog for the Rumen Microbiome Video: More on the AgResearch DNA sequencing of rumen microbes Our contact info: Twitter: @JGI Email: jgi-comms at lbl dot gov Genome Insider is a production of the Joint Genome Institute.

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 Transcript How Black Fungi Adapt to Extremes Integrated Microbial Genomes and Microbiomes Submit a proposal to work with the JGI Our contact info: Twitter: @JGI Email: jgi-comms at lbl dot gov Genome Insider is a production of the Joint Genome Institute. Some audio in the opening scene comes from an expedition Laura took to Antarctica. Laura.Selbmann©PNRA All the sampling activities in Antarctica have been performed in the frame of italian expeditions of the Italian National Program for Antarctic Researches (PNRA), funded by the Italian Ministry of University and Research; all specimens collected and fungi isolated are preserved in the Culture Collection of Fungi from Extreme Environment, the Italian National Antarctic Museum (MNA-CCFEE)

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 episode: Episode Transcript JGI@25 Stories The original Glycine max sequence: Nature Our contact info: Twitter: @JGI Email: jgi-comms at lbl dot gov Genome Insider is a production of the Joint Genome Institute.

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: Episode transcript 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 SLAM talk The JGI’s Genomics of Plant-Microbial Interactions group Plant Single-cell Solutions for Energy and the Environment (Workshop report) JGI Blog: A Plant Root Atlas for Tracking Developmental Trajectories Ben Cole’s DOE Early Career Award Genome Insider is a production of the Joint Genome Institute. This episode uses two pieces of music from Free Music Archive: Sad French Accordion by Dana Boulé (CC BY-NC 4.0) Sonata No. 20 in G Major, Op. 49 No. 2 - I. Allegro ma non troppo by Daniel Veesey (Public Domain)