For years, researchers have known that many datasets miss a key part of microbial genomes: the mobile genetic elements, or MGEs, that can move between organisms. But now, deep sequencing and new analysis methods are bringing this mobilome into light, and opening up new options for engineering these microbes in the future. Join Sarah Bagby (Case Western Reserve University) and Simon Roux (JGI) as they talk about their recent work on a time series from Sweden’s Stordalen Mire. Nature Mi...

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 episo...

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...

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 Meetin...

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 20...

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 U...

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 ...

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 websiteR...

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 cal...

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 ...