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 JGI
• Join us at the 2024 JGI User Meeting

• Episode Transcript
• Paper: Manipulating the 3D organization of the largest synthetic yeast chromosome
• NYU Release: Researchers Assemble Nine Synthetic Yeast Chromosomes

• Our contact info:
  • X: @JGI
  • Email: 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 JGI
• Join us at the 2024 JGI User Meeting
• Episode Transcript

• Feature: Getting to the Bottom of Fungal Functions Across Earth’s Forests
• Paper: 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 thought
• Paper: Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina)
• Paper: Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment

• Feature: An Inside Look at How Plants and Mycorrhizal Fungi Cooperate
• Paper: Spatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosis

• Our contact info:
  • Twitter: @JGI
  • Email: 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 JGI
• Join us at the 2024 JGI User Meeting
• FICUS program

• Episode Transcript
• Paper: 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: @JGI
• Email: 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 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