while i AM looking forward to (someday) trivially assembling single contig MAGs from long-read data... picking out coherent contig clusters in #anvio will always be very satisfying!

HANDS OFF OUR UC! Join us for a rally tomorrow, Sept 16, 2p at UCSF outside the Regents meeting. @uaw4811.bsky.social @calnurses.bsky.social @teamsterslocal2010.bsky.social @uptecwa.bsky.social @aaup.org @ucaftbayarea.bsky.social @afscme3299.bsky.social

My department (ecology and evolution) is hiring a core bioinformatics/comp bio person (not TT but the last person retired after 25+ years). It's a great place to work!: stonybrooku.taleo.net/careersectio...

ONT has a temporary bioinformatics position (8 months) open while I'm on maternity leave. Focus will be on microbial genomics but with opportunities to work on projects across the breadth of genomics! ejnh.fa.em2.oraclecloud.com/hcmUI/Candid...

The Xue lab at UC Irvine is looking for a staff scientist to support our work investigating how microbes interact and evolve in the gut microbiome! Open to a wide range of previous experience levels, see ad for more. recruit.ap.uci.edu/JPF09601

Staff scientist position (computational): I am looking for a computational scientist to join my genomics lab at Stanford. They should have an outstanding skillset in ML/statistical methods for genomic applications, postdoc experience and a strong publication record. #sciencejobs

Funded postdoc + PhD opportunities in marine microbial ecology! Please share with folks that might be interested. Start date is flexible (fall 2025 to summer 2026) More about the lab + applying (Postdoc rolling, PhD apps due Oct/Jan): sites.google.com/uncc.edu/mic...

over a year later, this one out today! link.springer.com/article/10.1...

an important piece of work, beyond just the marine realm - showing that long read tech not only can mean better genomes but more diverse and possibly previously unresolvable ones!

🚨 ACTION ITEMS to stop the FDA from limiting Covid vaccine access: 1. Submit a public comment to the FDA www.regulations.gov/commenton/FD... 2. Contact your elected officials www.usa.gov/elected-offi...

Marine community metabolomes in the eastern tropical North Pacific Oxygen Deficient Zone reveal glycine betaine as a metabolic link between Prochlorococcus and SAR11 www.biorxiv.org/content/10.1... #jcampubs 🌊

As many of you know, it's been really hard for journal editors to find willing manuscript reviewers. If you are interested in reviewing for ASM's mSphere, please fill out this gform! I'm especially excited to work with early career researchers. forms.gle/53vxpbvF3Lrk...

WHERE WILL YOU BE ON MARCH 7TH!? Head to www.standupforscience2025.org/local-event-information/ or the link in our bio to find your closest event—or add one if you're hosting one! #standupforscience2025

amidst the horrors, a rejuvenating day in the field with @mlmlsci.bsky.social . thanks to the crew of the r/v jh martin!

ACTION THIS WEDNESDAY: Researchers from New York universities are holding a rally to protest the funding cuts at Washington Square Park at 4 pm. This will be part of a national day of action, with rallies at HHS in DC and all around the country. RSVP HERE: docs.google.com/forms/d/e/1F...

Is your NSF grant on this list? Reach out if so! Ted Cruz released a list of grants flagged for DEI or "neo-Marxist class warfare propaganda" from his Oct. report. NSF is using keywords from that report for their review, though Cruz's list is likely larger. www.commerce.senate.gov/2025/2/cruz-...

a first try at something new - tips/tricks/superstitions, especially from those working with environmental samples, very welcome ! @nanoporetech.com

Hey, if you work for the University of California, and you are worried about public access to your research data that are currently hosted on federal sites - follow directions here to get them up on Dryad. 📈 osc.universityofcalifornia.edu/for-authors/... @datadryad.bsky.social @ucdavis.bsky.social

Fellow UC professors, what can we do to advocate for the NSF postdoc fellows (and potentially additional fellows next) who cannot withdraw their paychecks? Contact the UC Federal Relations lawyers?

Our most recent paper on methane seeps is out: bg.copernicus.org/articles/22/.... Two seeps in Monterey Canyon have virtually no ANME (methane oxidizers), suggesting an unabated methane flux at these and similar seeps. The microbiological methane filter in sediments is not ubiquitous.

i have relied heavily on coverm for years; you should too!

wonderful to see this tremendous piece work finally out, from @prywes.bsky.social et al. www.nature.com/articles/s41...

calling all western geobiologists, broadly construed! come join us for the third iteration of this great little symposium, by and for early career scientists

Wetting dry soil rapidly stimulates microbial activity and has important consequences for biogeochemical cycling. In our paper out today, we show that part of that response can be explained by how bacterial genomes are written (i.e. codon usage, nucleotide freq., genome size) doi.org/10.1073/pnas...

this one out today! cc @annedekas.bsky.social academic.oup.com/ismej/articl...

Hydrocarbon metabolism and petroleum seepage as ecological and evolutionary drivers for Cycloclasticus academic.oup.com/ismej/advanc... #jcampubs

Hello bluesky world! Happy to be here and looking forward to connecting/re-connecting with you all. I'm excited to share a paper just out today, led by postdoc @alexjaf.bsky.social. Prochlorococcus with two forms of rubisco! www.pnas.org/doi/10.1073/....

published today: www.pnas.org/doi/full/10....

I am super excited to share our new preprint "Contribution of ammonia oxidizers to inorganic carbon fixation in the dark ocean". This has been my absolute favorite project from my Postdoc at the Santoro Lab (UCSB) and @dome-vienna.bsky.social 🌊🦠 biorxiv.org/cgi/content/...

Super excited to share our new review article on the diversity and ecology of microbial sulfur metabolism. Please share widely. www.nature.com/articles/s41...

Modern microbiology: Embracing complexity through integration across scales A review from @merenbey.bsky.social and Jill Banfield www.cell.com/cell/abstrac...

cyanobacteria can have multiple distinct forms of rubisco! check out our new preprint to learn about the unusual carbon fixation machinery of an low O2 prochlorococcus and what we think it might mean for physiology and ecosystem biogeochem

a nice survey of chemoautotrophy in extreme environments (here, cold) + an elegant biochemical modeling approach for rubisco led by Kaitlin Harrison

this out today exploring the role of urea in the interconnected deep sea nitrogen and carbon cycles! a fun opportunity to consider how best to merge single-cell (nanosims) and bulk community (metagenomics) analyses. #MicroSky

it's preprint day! happy to share my first piece of postdoc work as well as my first in the marine space, this time, exploring the biology of bacteria and archaea fixing carbon with rubisco in the deep water column more to come soon..

Selective lipid recruitment by an archaeal DPANN symbiont from its host www.nature.com/articles/s41... #jcampubs

Nice genome-resolved metagenomics of 90 fermented foods - including a lot of fungal genomes www.biorxiv.org/content/10.1...

mobile genetic elements within mobile genetic elements ? 🤯 congrats to @luisvalentin.bsky.social et al on this exciting set of findings in a novel lineage of asgardarchaea

New resource from Cultivarium: models to predict oxygen tolerance, temperature, salinity, and pH optima from a genome - without using pesky gene annotations. They work for incomplete MAGs, so we could predict growth conditions across all bacteria and archaea, cultivated or not. Data available.

"Individual actions can be distilled into three key components: showing respect to trans colleagues and students without singling them out, educating oneself and others, and utilizing one’s privilege and influence to advocate for institutional and political change." www.cell.com/cell/fulltex...

exciting work from @deemteam.bsky.social shedding light on the interactions btwn cpr bacteria, host, and phage! really looking forward to seeing what other insights come from this system #microsky

This year, the STAMPS course on microbial ecology and microbiome analysis will be held from July 17-July 27th, 2024. This is a great course with lots of hands-on training! Deadline: March 11th. @amydwillis.bsky.social and I are the Course Directors and would be happy to answer questions!

western geobiologists (broadly construed), join us at this year's Northern California Geobiology Symposium at stanford in early april! free, great ECR talks, and sunny weather - submit abstracts by mar 1 here: norcalgeobiology.stanford.edu

exciting work from (yet-to-be-on-bluesky) alexa nicolas, and colleagues - worth a read for a creative and emerging lens on microbial community structuring... twit thread here: twitter.com/AlexaMNicola...

happy to share this 'quick guide' to the Candidate Phyla Radiation bacteria out today in @currentbiology.bsky.social! its purpose is to be a plain language summary of all the great recent work in this space, with a few key papers for reference. www.cell.com/current-biol...

Nearly 20 years ago, Jill Banfield, Gene Tyson & team transformed #microbiology with their seminal paper on genome-resolved metagenomics. Their innovative approach in reconstructing microbial genomes opened new frontiers in understanding ecosystem dynamics! paper here: www.nature.com/articles/nat...

a big congrats to @luisvalentin.bsky.social who carried a longtime lab project over the finish line and in doing so added so much rich biological insight (and gorgeous data viz)

On Monday, the faculty of the CSU go on strike. Here's why this matters to me, and why it's important that we win. #highered

ecologists, is there a metric that describes how cosmopolitan/provincial a species is, while taking into account unequal sampling density? like occupancy, with distance between samples considered?

Open-access review of life in the deep-sea water-column, by me and Anela Choy... Come learn how animals survive and thrive down in the depths of the ocean, how scientists study them, and what's to come. 🦑 🧪 🌊 www.annualreviews.org/doi/abs/10.1...