Genome Insider

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
• Find all episode transcripts on our website
• 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

• Find all episode transcripts on our website
• 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:

• Find all episode transcripts on our website
• 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.

• Find all episode transcripts on our website
• 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 

• Find all episode transcripts on our website
• 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 

• Find all episode transcripts on our website
• HudsonAlpha Institute's Tiny Expeditions Podcast
• Guayule: Can genetics create a natural US rubber source?

• 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 

• Find all episode transcripts on our website
• 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

• Find all episode transcripts on our website
• 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.

• Find all episode transcripts on our website
• 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