New publication out @natcomms.nature.com! We identify novel viruses that actively infect highly productive chemoautotrophs, and reveal key trophic interactions and virus-host dynamics that impact microbial carbon cycling in aphotic environments.
www.nature.com/articles/s41...
Divergent successional patterns and infection dynamics in virion and transcriptionally active soil viral communities following phosphorus amendment and wet-up
Huge effort by Grant Gogul!
www.biorxiv.org/content/10.6...
The Microbiology and Geochemistry of the Shallow‐Water Hydrothermal Vents of the Gulf of Naples, Italy enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs 🌊
13C-Labeled Single-Cell Raman Sorting Reveals Sulfur-Driven Dark Carbon Fixation in Coastal Sediments academic.oup.com/ismecommun/a... #jcampubs
Illuminating the newly produced viruses within the virosphere with BONCAT and single virus genomic sequencing technologies academic.oup.com/ismecommun/a... #jcampubs
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
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.
#Ecology & #Microbiology
Some microbes use atmospheric trace gases as energy and carbon sources, sustaining primary production in caves
@greening.bsky.social
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).
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
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...
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.
