Gareth (Gary) Trubl

We said goodbye to Buddy. We will cherish the 15yrs he shared with us. Buddy was here for many milestones: engagement, college graduations, wedding, bringing our kids home, cross-country moves, buying a house. He lived with us in 4 different states & 9 different homes. I miss him terribly.

New preprint! We propose "anergiobiosis" to describe microbial life at thermodynamic limits as a way of separating the physiological state from questions about aeonophilic extremophile specialization. ecoevorxiv.org/repository/v...
#Microbiology #Extremophiles #SubsurfaceMicrobiology #MicroSky

FDA agrees to review Moderna mRNA flu vaccine in dramatic reversal After initially rejecting Moderna’s application for review, the FDA will now consider the mRNA flu shot

After initially rejecting Moderna’s application for review, the FDA will now consider the mRNA flu shot

One on left is a black dog and above it the words “Reality”. Below it is “I chased a squirrel” One the right is a black dog and above it says “LinkedIn”. Below it says, Proud to announce that I effectively executed a rapid-response squirrel displacement strategy to mitigate potential yard intrusions. Humbled by the unwavering support of my family and local stakeholders. This experience reinforced the importance of vigilance, ownership, and continuous improvement. Looking forward to scaling this impact in future engagements.

😂

The closet genes that I am aware of are in Simon (2016) & Consuelo's (2020) papers, but I am not up-to-date with marine virus work. There have been some recent soil virus papers on N (mostly N2O), but when I think N & soil viruses I look to Christina Hazard & Graeme Nicol. That is the best I can do.

>90% of viral genes are unknown, so that makes sense. Viruses move genes and have bycatch all the time. We are finding more and more genes that viruses carry. Viruses drive genetic mutation and they tend to hold onto genes that are efficient, or so we think.

Super cool! I'd love to include viruses in this work.

Microbial aerotrophy enables continuous primary production in diverse cave ecosystems - Nature Communications Metabolic strategies of cave microorganisms are poorly studied. Here, the authors show that cave microbes use atmospheric trace gases hydrogen, carbon monoxide and methane as energy and carbon sources, sustaining primary production and revealing how life can thrive in oligotrophic and dark ecosystems.

#Ecology & #Microbiology

Some microbes use atmospheric trace gases as energy and carbon sources, sustaining primary production in caves

@greening.bsky.social

Unearthing the Viral Secrets of a Changing Landscape Thawing permafrost is reshaping landscapes and releasing carbon—and soil viruses may play a hidden role. By uncovering ~10,000 new Arctic soil viruses, we reveal unseen players shaping microbes and ca...

Read the behind the paper communities.springernature.com/posts/uneart...

ssDNA viruses spanned multiple major phyla, dominated by Cressdnaviricota, with representatives of Microviridae, Parvoviridae, and Inoviridae. They were strongly enriched in fully thawed fen habitats, revealing peatland soils as a vast, largely unexplored viral reservoir.

We compared two quantitative library prep methods: one targeting dsDNA only & one capturing both ssDNA & dsDNA. Both recovered similar dsDNA viral communities, but only the latter revealed the hidden diversity of ssDNA viruses in soil. Both library prep methods are available @jgi.doe.gov

Viral genomes encoded 811 putative auxiliary metabolic genes (AMGs), nearly half linked to carbon processing. Both viral diversity & the abundance & diversity of virus-encoded AMGs increased along the permafrost thaw gradient, suggesting expanding potential for viruses to modulate host metabolism.

We predicted microbial hosts for 38% of viral populations, largely dsDNA viruses, spanning 9 archaeal & 36 bacterial phyla, including key carbon-cycling taxa. The ssDNA viruses were predicted to infect bacteria & microbial eukaryotes.

Across a natural permafrost thaw gradient, we used optimized soil viromics to quantitatively recover ~10,000 mostly novel ssDNA and dsDNA soil viruses. Viral communities were highly habitat specific, with most viruses endemic to a single thaw stage (palsa, bog, or fen).

Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient - Nature Communications The potential roles of viruses in microbial-induced permafrost thaw, which is accelerated by climate change, are unclear. Here, Trubl et al. sample a permafrost thaw gradient and identify thousands of...

New paper published in @natcomms.nature.com!

Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient

doi.org/10.1038/s414...

www.nature.com/collections/...

@sullivan-lab.bsky.social

Out now in Nature Communications, from IGI's Jill Banfield (The Banfield Lab) and collaborators: Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses

Read here: https://www.nature.com/articles/s41467-025-65646-7

Research Experience for Undergraduates (REU) | Biofilm Research Center | Binghamton University

Summer REU in biofilms! Pls share.
www.binghamton.edu/centers/biof...

This was a hard read. I strongly disagree with "many of the recommended policies, including lockdowns, social distancing, school closures, wearing masks & vaccine mandates, lacked robust confirmatory evidence and remain the subject of debate about their overall benefits and unintended consequences"

"Seasonal enhancement of the viral shunt catalyzes a subsurface oxygen maximum in the Sargasso Sea" https://www.nature.com/articles/s41467-025-67002-1

Viruses transform microbes, populations, & ecosystems.

In new work jointly led w/@tn-marine-micro.bsky.social + more, we find a link between enhanced viral infection and productivity 50 meters below the surface in the otherwise nutrient limited Sargasso Sea.

a 🧵

www.nature.com/articles/s41...

I am grateful to collaborators, mentors, field assistants, & funding support that made this possible. A special thanks to our editor and reviewers.

Honored that this paper was selected as an Editors’ Highlight.
www.nature.com/ncomms/edito...

Unearthing the Viral Secrets of a Changing Landscape Thawing permafrost is reshaping landscapes and releasing carbon—and soil viruses may play a hidden role. By uncovering ~10,000 new Arctic soil viruses, we reveal unseen players shaping microbes and ca...

I also wrote a Behind the Paper piece reflecting on the fieldwork, the challenges of soil viromics, & the long road from peat cores to viral genomes.

communities.springernature.com/posts/uneart...

Soil viruses are notoriously hard to study, but we used an optimized viromics workflow to explore how viruses change across a natural permafrost thaw gradient.

We quantitatively captured ssDNA + dsDNA viruses, revealing ~10,000 mostly novel viruses & their roles in C cycling.

A big milestone, my final PhD paper is finally out!

Started lab work in 2017 & bioinformatics via a DOE SCGSR fellowship @jgi.doe.gov with @simrouxvirus.bsky.social @sullivan-lab.bsky.social

doi.org/10.1038/s414...

Illustration depicting a bacterium under assault by phage. The bacterium “sees” phage immune evasion proteins and protects itself using a newly described antiphage system called Panoptes, named for the many-eyed mythical giant Argus Panoptes. Credit: Clair Huffine Insight Illustrations LLC

Our work on the Panoptes antiphage system is published! Here we find that Panoptes "watches" the cytosol for phage immune evasion proteins–captured in this illustration by Clair Huffine of Insight Illustrations. A beautiful example of the effector triggered immunity paradigm.

I have a fabulous undergrad who has a lot of experience with QIIME2 & using R to analyze microbiome data. She is looking for a job starting in January. Would love to learn more bench and field skills (will be getting some in her last 2 months). Open to academic, industry, government jobs in the US.

I know. I always support open access, but it was over 4K & we do not currently have the funds for that. I did put a preprint before on Zenodo which is updated doi.org/10.5281/zeno...

Same! Now, let's see if I still get requests to do "16S metagenomics"...ugh.

Clarifying Terminology in Microbial Ecology: A Call for Precision in Scientific Communication The rapid evolution of microbiology as a field of research has led to the introduction of new terminology and the adaptation of existing terms. However, inconsistencies in the use of these terms, inc...

New paper alert with @alexjprobst.bsky.social.

enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

This Is the Greatest Threat to Our Human Future Co-authors Michael Mann and Peter Hotez share 5 key insights from their new book, Science Under Siege: How to Fight the Five Most Powerful Forces that Threaten Our World.

“This Is the Greatest Threat to Our Human Future” | @peterhotezmdphd.bsky.social and I discuss with @nextbigidea.bsky.social about our new book, #ScienceUnderSiege:

nextbigideaclub.com/magazine/gre...

Baker Institute

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