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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 quickly. But there's a catch: SIP labwork and analysis can be very demanding.  The JGI offers SIP analysis to make these experiments accessible to more researchers. Ultimately, the goal is to generate SIP data that can be useful to multiple teams and analyses. This episode, Rex Malmstrom (JGI), and Roli Wilhelm (Purdue University), share a few different ways they're working to make this technique, SIP, more standardized -- more reproducible, more reusable, and more insightful, for the future of studying microbial communities. Links from this episode: Submit your own proposal to work with the JGIFind all episode transcripts on our website JGI’s Micro-Scale Applications GroupMISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experimentHT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi Webinar: Metagenome quantitative SIP at the JGI: https://www.youtube.com/watch?v=5OgLDTw7eYA  Genome Insider: Party in the Rhizosphere Genome Insider: A Powerful Technique to Study Microbes, Now Easier  Simulating metagenomic stable isotope probing datasets with MetaSIPSim  Microbes Persist: Systems Biology of the Soil Microbiome Science Focus Area (SFA), led by Dr. Jennifer Pett-Ridge at Lawrence Livermore National Laboratory (LLNL)Our contact info:X: @JGIEmail: jgi-comms at lbl dot gov

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 for future research.  Hear from Rekha Seshadri (JGI) and Matt Escobar (California State San Marcos) about how the Adopt-A-Genome project got started. Plus, Kalyani Maitra (California State Fresno) and two students, Angela and Mark Soghomonian share what it was like to take on one of these genomes. Links from this episode: Submit your own proposal to work with the JGIFind all episode transcripts on our website For more information about Adopt-A-Genome:Rekha Seshadri: [email protected] Matt Escobar: [email protected]  Adopt-A-Genome Papers: Draft genome sequence of Nitrobacter vulgaris DSM 10236TDraft genome sequences of Butyrivibrio hungatei DSM 14810 (JK 615T) and Butyrivibrio fibrisolvens DSM 3071 (D1T)Genome sequences of key bacterial symbionts of entomopathogenic nematodes: Xenorhabdus cabanillasii DSM17905, Xenorhabdus ehlersii DSM16337, Xenorhabdus japonica DSM16522, Xenorhabdus koppenhoeferii DSM18168, and Xenorhabdus mauleonii DSM17908 Our contact info:X: @JGIEmail: jgi-comms at lbl dot gov

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 episode, hear from Kasey and Patrick about how this project unfolded, and how they worked with the JGI's metabolomics program to find out more about these weird little pods. Links from this episode: Submit your own proposal to work with the JGIJoin us at the 2024 JGI User Meeting Find all episode transcripts on our websitePaper: Cynipid wasps systematically reprogram host metabolism and restructure cell walls in developing galls Our contact info:Twitter: @JGIEmail: jgi-comms at lbl dot gov Sound effects credits: oars.wav by hazureParma Park Bird Song with Stream.WAV by muneio

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. This project has turned out to be an international collaboration, with some artistic endeavors along the way. Eventually, the goal is to create an entirely human-generated yeast genome. Links from this episode: Submit your own proposal to work with the JGIJoin us at the 2024 JGI User Meeting Find all episode transcripts on our websitePaper: Manipulating the 3D organization of the largest synthetic yeast chromosomeNYU Release: Researchers Assemble Nine Synthetic Yeast Chromosomes Our contact info:X: @JGIEmail: jgi-comms at lbl dot gov

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 with insights from Adam Healey and Xiao Ma. And Karen Serrano and Benjamin Cole explain their research on the symbiotic relationship between mycorrhizal fungi and plant roots.  Links from this episode: Submit your own proposal to work with the JGIJoin us at the 2024 JGI User MeetingFind all episode transcripts on our website Feature: Getting to the Bottom of Fungal Functions Across Earth’s ForestsPaper: Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems Feature: Eelgrass proves to be much younger than we thoughtPaper: Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina)Paper: Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment Paper: Spatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosis Our contact info:Twitter: @JGIEmail: jgi-comms at lbl dot gov

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 rainforest hits a drought. Tag along with their experiments in a fully enclosed, human-made ecosystem: Biosphere 2.  Links from this episode: Submit your own proposal to work with the JGIJoin us at the 2024 JGI User MeetingFICUS program Find all episode transcripts on our websitePaper: Drought re-routes soil microbial carbon metabolism towards emission of volatile metabolites in an artificial tropical rainforest  https://doi.org/10.1038/s41564-023-01507-7 Our contact info:Twitter: @JGIEmail: jgi-comms at lbl dot gov

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 JGIFind all episode transcripts on our websiteRelated 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 JGIFind all episode transcripts on our websiteRobert 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 JGIFind all episode transcripts on our websiteThe 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 Find all episode transcripts on our websiteOur 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: Find all episode transcripts on our websitePublication: 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. Find all episode transcripts on our websitePublication: 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  Find all episode transcripts on our websitePublication: 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  Find all episode transcripts on our websiteHudsonAlpha Institute's Tiny Expeditions PodcastGuayule: Can genetics create a natural US rubber source? 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  Find all episode transcripts on our websitePaper: 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