Genome Insider

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 websiteJGI'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 fungiWebinar: 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 JGIEpisode TranscriptFor more information about Adopt-A-Genome:Rekha Seshadri: rseshadri@lbl.gov Matt Escobar: mescobar@csusm.edu 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 DSM17908Our 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 MeetingEpisode TranscriptPaper: Cynipid wasps systematically reprogram host metabolism and restructure cell walls in developing gallsOur contact info:Twitter: @JGIEmail: jgi-comms at lbl dot govSound 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 MeetingEpisode TranscriptPaper: Manipulating the 3D organization of the largest synthetic yeast chromosomeNYU Release: Researchers Assemble Nine Synthetic Yeast ChromosomesOur 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 MeetingEpisode TranscriptFeature: 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 ecosystemsFeature: 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 environmentFeature: An Inside Look at How Plants and Mycorrhizal Fungi CooperatePaper: Spatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosisOur 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 programEpisode TranscriptPaper: Drought re-routes soil microbial carbon metabolism towards emission of volatile metabolites in an artificial tropical rainforest  https://doi.org/10.1038/s41564-023-01507-7Our 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 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&MEpisode 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 itSubmit 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 TranscriptPaper: Multiple sources of aerobic methane production in aquatic ecosystems include bacterial photosynthesisLearn about the IMG/M systemJGI Webinars: http://jointgeno.me/Webinars    Our contact info:Twitter: @JGIEmail: jgi-comms at lbl dot govSound 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 2022Our 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 depositsOur 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 MeetingEpisode TranscriptPaper: Genome of Paspalum vaginatum and the role of trehalose mediated autophagy in increasing maize biomassPhytozome: Paspalum vaginatum dataOur 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/proposalsOur 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 TranscriptPaper: 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 Break Down CellulosePNNL 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 TranscriptPaper: A global phylogenomic analysis of the shiitake genus LentinulaThe Lentinula genomes are publicly available on JGI's MycoCosm data portalThe JGI website also features a highlight summary of the paper: Tracing the Evolution of Shiitake MushroomsThis 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 TranscriptLinks from this episode: Community Science ProgramWebinars on JGI Product OfferingsPro Tips for Successful CSP ApplicationsAccessing Functional Genomics CapabilitiesJGI Calls for User Proposals CSP Functional Genomics callNew Investigator CSP callAnnual CSP Proposal CallFICUS callData Release PolicyOur contact info:Contact our Project Management Office with any questions about proposalsTwitter: @JGIEmail: 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 TranscriptJGI@25 StoriesScience Highlight: Rumenating on improving biofuel productionPaper: Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow RumenOur contact info:Twitter: @JGIEmail: jgi-comms at lbl dot govGenome 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 TranscriptSubmit a proposal to work with the JGIVirtual tour of the Joint Genome InstituteWebinar: Long-read sequencing for metagenomics and DNA modification detectionOur contact info:Twitter: @JGIEmail: jgi-comms at lbl dot govGenome 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 TranscriptJGI@25 StoriesThe JGI's IMG/M data portal News Release: A Reference Catalog for the Rumen MicrobiomeVideo: More on the AgResearch DNA sequencing of rumen microbesOur contact info:Twitter: @JGIEmail: jgi-comms at lbl dot govGenome 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 TranscriptHow Black Fungi Adapt to ExtremesIntegrated Microbial Genomes and MicrobiomesSubmit a proposal to work with the JGIOur contact info:Twitter: @JGIEmail: jgi-comms at lbl dot govGenome 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©PNRAAll 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 TranscriptJGI@25 StoriesThe original Glycine max sequence: NatureOur contact info:Twitter: @JGIEmail: jgi-comms at lbl dot govGenome 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: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 TrajectoriesBen Cole's DOE Early Career AwardGenome 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)

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 episodeEpisode TranscriptJGI@25: The Little Alga That CouldChlamydomonas reinhardtii on Phytozome and PhycoCosm JGI Blog Post: Green Algae Reveal One mRNA Encodes Many ProteinsJGI News Release: Green Alga Genome Project Catalogs Carbon Capture Machinery and Reveals Identity as Ancient Cousin of Land Plants and AnimalsThe original sequence: ScienceOur contact info:Twitter: @JGIEmail: jgi-comms at lbl dot govGenome Insider is a production of the Joint Genome Institute. 

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. Links from this episode:Sequencing the Amazonian Stinkbird's MicrobiomeAcronym Action: EPICON projectSubmit a proposal to work with the JGI!Find out more about the FICUS program between JGI and EMSLGenome Insider is a production of the Joint Genome Institute. --Sound Effects Credits:"Splash, Small, A.wav" by InspectorJ (www.jshaw.co.uk) of Freesound.org“Water movements big splashes and waves” by KyleS of Freesound.org“Fishing-rod” by KirstenBrooks3232 of Freesound.org“By a Pond Ambience” by Cueckermann of Freesound.org“Splash, edited” by MRicken1 of Freesound.org“Fishing Rod Whip” by TyroneW of Freesound.org

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 https://jgi.doe.gov/genome-insider-s2-episode-9-creating-an-energy-market-for-miscanthus/.

Every summer, the JGI invites undergraduate and graduate students from the University of California, Merced to participate in the flagship JGI-UC Merced Internship Program and engage in real, impactful research projects with JGI mentors. In this episode, hear two interns from the 2021 cohort describe their deep dives into genomics, computational tools, and big data. Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2-episode-8-uc-merced-intern-dispatches/.

The US Department of Energy's favorite tree is poplar. They're the fastest growing trees in the Northern Hemisphere, making them tantalizing plants to harness for bioenergy. In this episode, hear from Oak Ridge National Laboratory scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials. Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2-ep-7-the-bioenergy-tree/.

You might know sorghum as an edible grain. But there are some sorghum varieties, grown on marginal land with little water, which were developed specifically to turn their biomass into sustainable biofuel and bioproducts. John Mullet, a biologist at Texas A&M University, tells us how sorghum's historical — and literal — roots could play a big role in our energy future.Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2-ep-6-back-to-the-future-a-sorghum-story.

Lawrence Livermore National Lab biologist Jennifer Pett-Ridge collaborated with JGI scientists on an ambitious project: to bring in robots to help process experiments that measure microbial activity in soil. Now, the researchers and robots have made these experiments easier for scientists everywhere.Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2-ep5-a-powerful-technique-to-study-microbes-now-easier 

There’s a party in the soil, and microbes are the VIPs. They’re feasting on the compounds that plants secrete through their roots, creating a lively zone called the rhizosphere. In this episode, biologist Jennifer Pett-Ridge of Lawrence Livermore National Laboratory has your backstage pass.Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2ep4-party-in-the-rhizosphere

Biofuels and bioproducts are a way to kick our addiction to fossil fuels. In this episode, we get a peek into how scientists Aindrila Mukhopadhyay and Steve Singer are harnessing the versatile bacterium Pseudomonas putida to break down biomass and help bring about a more sustainable, bio-based economy. They conduct research at the Joint BioEnergy Institute (JBEI), a JGI partner and one of the four US Department of Energy Bioenergy Research Centers. Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2ep3-better-living-through-bioenergy/

Diatoms, a group of tiny algae, are also known as “living opals” because of the strange, beautiful properties of their silica shells. But what genes are responsible for such mesmerizing exteriors? Setsuko Wakao and Kris Niyogi, biologists at UC Berkeley and Lawrence Berkeley National Laboratory, aim to find out. Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2ep2-cracking-the-secrets-of-the-diatoms-shell/.

A tall native plant of the North American prairie, switchgrass (Panicum virgatum) has long been a tantalizing potential biofuel feedstock. But switchgrass has a complex genome and, as a species, encompasses dizzying diversity. So, a team of scientists made an ambitious plan to link the plant’s diverse traits — height, biomass, hardiness to cold, etc. — to its genes. The undertaking took shovels, trucks — and more than a decade. With the results just published in the journal Nature, listen to the episode for a romp through their switchgrass story. Find more info on this episode, including the transcript, at https://jgi.doe.gov/genome-insider-s2ep1-exploring-diversity-of-american-prairie-switchgrass/.

Every fall, a mysterious green growth appears on farmers’ fields: a microbial community that might be quietly improving the soil. Penn State researchers Mary Ann Bruns and Terry Bell are digging in to understand how. Find more info on this episode, including the transcript, here.We hope you enjoy this last episode of Season 1! Stay tuned for Season 2, coming in 2021.

Can plants help humans attain a renewable energy future? Can they help lock away more carbon? Xiaohan Yang, a scientist at Oakridge National Laboratory, believes they can. And, what’s more, that using gene editing technology to conscientiously mix traits of different plant species will help us get there. Find more info on this episode, including the transcript, here.

Life as we know it wouldn’t exist without cyanobacteria; they began oxygenating Earth over two billion years ago. A team of researchers set out to Yellowstone National Park to study how cyanobacteria are living, communally, in microbial mats. Along the way, they’ve encountered surprises, adopted new technologies, and made a few discoveries about the microbial mat denizens. Find more info on the episode, including the transcript, here: https://jgi.doe.gov/genome-insider-episode-7-decoding-yellowstone-microbial-mats/

A mini-episode: JGI collaborator Pankaj Trivedi is harnessing microbiome science to make plants more resilient to drought. Find more info on this episode, including the transcript here: jgi.doe.gov/genome-insider-mini-episode-6-how-microbes-can-protect-plants-in-drier-straits/

As waters warm due to climate change, corals are in mortal peril. But corals comprise multiple organisms: a coral host, a photosynthetic microalgae, and a little-characterized microbiome. When warm waters stress corals but before they bleach, a coral’s microbes, including its photosynthetic partner, may be what helps them take the heat. Find more info on this episode, including the transcript, here.

Despite their diminutive stature, “short plants” such as mosses could be uniquely powerful in helping scientists link plant genetic sequences to what they do. But sequencing the genome of one short plant — fire moss — has an unexpected hurdle: ginormous sex chromosomes. Find more info on this episode, including the transcript, here.

Kelly Wrighton and her group at Colorado State University in Fort Collins have a massive undertaking: sequencing the world’s river microbiomes. And they’re using team science to do it. Find more info on this episode, including the transcript here.

Gary Trubl, virologist and postdoc at Lawrence Livermore National Laboratory, has more to share about bacteria-infecting viruses in the arctic. He’s researching how viruses influence the flow of carbon in thawing peatlands — and bioinformatics and isotopes are crucial to the quest. Find more info on this episode, including the transcript here.

Gary Trubl, virologist and postdoc at Lawrence Livermore National Laboratory, has more to share about bacteria-infecting viruses in the arctic. He’s researching how viruses influence the flow of carbon in thawing peatlands — and bioinformatics and isotopes are crucial to the quest. Find more info on this episode, including the transcript here.

Alison Takemura tells you about the podcast, and Ed Hall, microbiologist at Colorado State University, talks about how this is a unique time in human history.Genome Insider is brought to you by the U.S. Department of Energy Joint Genome Institute.

Alison Takemura tells you about the podcast, and Monica Medina, coral biologist at Penn State, talks about going from tiny critters to magnificent coral reefs. Genome Insider is brought to you by the U.S. Department of Energy Joint Genome Institute.

Alison Takemura tells you about the podcast, and Kelly Wrighton, microbiologist at Colorado State University, talks about filters full of microbes. Genome Insider is brought to you by the U.S. Department of Energy Joint Genome Institute.

Alison Takemura tells you about the podcast, and Gary Trubl, virologist at Lawrence Livermore National Lab, weighs in on what a peatland sounds like. Genome Insider is brought to you by the U.S. Department of Energy Joint Genome Institute.