Jesse McNichol

“The Party told you to reject the evidence of your eyes and ears. It was their final, most essential command.”

― George Orwell, 1984

Expansion of aerobic methanotrophy to the phylum of Actinomycetota and its environmental implications | Applied and Environmental Microbiology The climate crisis is one of the most imminent threats to humanity and all life on our planet. Methane is not only the second most potent greenhouse gas (GHG) and is responsible for approximately 31% of GHG-induced global warming since the start of the industrial revolution (1) but is also the most rapid increasing GHG in the atmosphere (2). The latter is likely caused by increased microbiological production of methane from, e.g., wetlands (2). This fact stresses the importance of methanotrophic microbes that can degrade methane with and without oxygen (3, 4) and thereby fulfill a crucial role in our global climate.

Wow, our AEM paper on a new methane-oxidizing bacterium just got a Commentary! 🎉
Congrats Kambara-san—so happy to see the work getting recognized!
journals.asm.org/doi/10.1128/...

I’m excited to share our effort to obtain one of the first estimates of the net rate, in physical time, of lateral gene transfer (LGT) – nature’s own genetic engineering - across a complex, global microbiome:
doi.org/10.1093/isme...

'I just want to learn': Students in limbo as many Dalhousie classes cancelled amid strike | CBC News Classes at Dalhousie University are supposed to start on Tuesday, but most have been cancelled due to a strike.

Not just classes are cancelled. DFA members have been locked out by the admin since August 20th: we can't sign students in from waitlists, can't advise them, can't share syllabi, can't help them with scholarship applications, etc. etc.

#KeepDalStrong

www.cbc.ca/news/canada/...

Paris said au revoir to cars. Air pollution maps reveal a dramatic change. Air pollution fell substantially as the city restricted car traffic and made way for parks and bike lanes.

Wow. Check this out.
Politicians actually trying to solve problems can achieve a lot!
www.washingtonpost.com/climate-solu...

Hip-Hop as a Contemplative Practice Jessica Angima talks with Buddhist teacher and rapper Born I about Lyrical Dharma, the limits of language, and how we all contain the seeds of our ancestors.

“Suffering is not a death sentence; it can be confronted, it can be overcome. And we can be creative in how we address the human condition.” —Ofosu Jones-Quartey

‘Challenges and uncertainty:’ Dalhousie University faculty lockout leaves students worried The lockout of Dalhousie University faculty is inching closer to the start of the school year, and it's fuelling concerns among students.

I am increasingly frustrated, even angry, about the hypocrisy—tempted to say disinformation—from @dalhousie.bsky.social’s administration. How can you say “the university’s priority is working with the DFA to reach a resolution” when they have not even tried to return to the table? #KeepDalStrong

Chris Algar, Assoc Prof, Oceanography @dalhousieu.bsky.social Lessons in solidarity from the picket lines. This isn’t just a fight to #KeepDalStrong; it’s a fight against employer greed. @ansut.bsky.social @caut.bsky.social

Sequestration by the biological carbon pump: Do we really know what we are talking about? aslopubs.onlinelibrary.wiley.com/doi/10.1002/... #jcampubs 🌊

Detergent-based separation of microbes from marine particles Marine particles, typically composed of organic detritus and cellular debris, harbor microbial communities that are distinct from the planktonic, or free-living, communities in the pelagic ocean. Howe...

Our latest, and the second paper led by Jordan Coelho this year. Want to remove bacteria from POM for single-cell microbiology/culturing/'omics applications? We've got some data:

Detergent-based separation of microbes from marine particles www.biorxiv.org/content/10.1... #jcampubs 🌊

Logo for the Sandpiper website

Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵

GRUMP Presentation 2025 CBIOMES 2025, GRUMP

For a handy summary of what GRUMP is, feel free to view and share the following presentation from the CBIOMES 2025 annual meeting: slides.com/jcmcnch/cbio...

GRUMP Presentation 2025 CBIOMES 2025, GRUMP

For a handy summary of what GRUMP is, feel free to view and share the following presentation from the CBIOMES 2025 annual meeting: slides.com/jcmcnch/cbio...

Characterizing organisms from three domains of life with universal primers from throughout the global ocean - Scientific Data Scientific Data - Characterizing organisms from three domains of life with universal primers from throughout the global ocean

You might try BLASTing against GRUMP ASVs: www.nature.com/articles/s41... We don't have a web tool but pros of GRUMP are good coverage of the ocean, unfractionated samples (>0.2 μm), and you can access the data through CMAP here: simonscmap.com/catalog/data...

Characterizing organisms from three domains of life with universal primers from throughout the global ocean - Scientific Data Scientific Data - Characterizing organisms from three domains of life with universal primers from throughout the global ocean

Please Re-Post. Our global GRUMP microbial ocean database is out in Scientific Data! Unfractionated, single universal PCR, with Archaea, Bacteria, and Eukaryotes all on the same scale with the same denominator. Pole to pole, depths to 6000m. Lots of metadata. www.nature.com/articles/s41...

It was great to have you guys on board! Cheers from Nova Scotia!

Thanks Augustus! Will be great to see your study and glad you find the 3-domain primers useful to your research 😀

Thanks for carrying the baton across the finish line gentlemen. Keep an eye out in the next few years for papers from Yubin and Lexi Jones-Kellett, a new-and-improved bioinformatic pipeline (snakemake!), as well as GRUMP 2.0 (now with internal standards!).

This was a huge team effort - many thanks to our collaborators, especially "early adopters" including Craig/Ellie (UCSB), Paul/‪@stevenbiller.bsky.social‬ (MIT/Wellesley), Wade/Joe (USF) as well as my "partners in crime" Nathan Williams and Yubin Raut!

The GRUMP project began in 2018 when I started as a postdoc in @jedfuhrman.bsky.social's lab and was funded by the @simonsfoundation.org as part of the CBIOMES collaboration.

Characterizing organisms from three domains of life with universal primers from throughout the global ocean - Scientific Data Scientific Data - Characterizing organisms from three domains of life with universal primers from throughout the global ocean

So excited to announce the GRUMP paper is published! This global dataset provides relative abundances for plankton spanning Archaea to Zooplankton from unfractionated (>0.2µm) water samples using 3-domain universal primers that amplify 16S and 18S in one PCR reaction.

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

Protect transgender scientists Transgender and gender nonconforming (TGnC) people are a primary target of the Trump administration. Multiple executive orders seek to erase TGnC protections; mandate denial of gender identity; and ba...

"Institutions must support transgender and gender nonconforming and other marginalized scientists by securing their safety and privacy; their access to legal aid and health care; and their opportunities in education, employment, and society," argues a new #LetterToScience. scim.ag/4kQCMtr

quote that reads "This study is a great example of a clinically relevant finding that stems from very fundamental, basic science"

A healthy diet outperforms fecal transplants in restoring and protecting the gut microbiome, according to new research from the Simons Foundation’s Joy Bergelson and collaborators: www.simonsfoundation.org/2025/05/13/t... #science

US science is being wrecked, and its leadership is fighting the last war Facing an extreme budget, the National Academies hosted an event that ignored it.

NSF: "Biology, engineering, and education will all be slashed by over 70 percent..."
"The fleet of research ships [UNOLS] will essentially become someone else's problem"

Contact your representatives, even in blue states, as these cuts can still be stopped!

arstechnica.com/science/2025...

Very grateful to #MarcGarneau for his kindness and support when we fought to protect environmental laws attacked by Harper administration. We have lost a truly great Canadian.. and far too soon. #RIP

I am honored to have been named a 2025 Howes Scholar by the Computational Science Graduate Fellowship committee!

www.krellinst.org/csgf/about-d...

Excellent, exhaustive, and frightening summary of the attacks by the Trump regime.

So happy to see this paper finally out! A fun project with collaborators Emily Zakem, @jlw-ecoevo.bsky.social and Yubin Raut!

Improved maximum growth rate prediction from microbial genomes by integrating phylogenetic information - Nature Communications Microbial maximum growth rates vary widely across species, and their measurement is challenging, especially for uncultivated organisms. Here, Xu, Zakem & Weissman present Phydon, a framework for g...

Our newest on using genomic and phylogenetic information to predict microbial maximum growth rates www.nature.com/articles/s41... with @liangxu.bsky.social

Risk–reward trade-off during carbon starvation generates dichotomy in motility endurance among marine bacteria - Nature Microbiology Marine bacteria opt for divergent foraging strategies when faced with carbon starvation—either cease motility entirely, or convert biomass to energy to retain motility.

Very cool study - motility in marine bacteria represents a risk-reward trade off under carbon starvation: some keep swimming at the expense of biomass while others stop swimming #MicroEco - www.nature.com/articles/s41...