my first 'data descriptor'! hoping this one will be useful for folks interested in tracing the distribution of genomes/genes/proteins over physicochemical gradients in the (deep) marine water column.

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 2w ago

Deeply-sequenced metagenomes and over 1000 draft genomes from the epipelagic to bathypelagic Northeast Pacific Ocean https://www.biorxiv.org/content/10.64898/2026.07.18.739368v1

Form I and II Rubiscos Exhibit Temperature Dependent Carbon Kinetic Isotope Effects https://www.biorxiv.org/content/10.64898/2026.06.29.735352v1

A reminder... deadline June 30, 2026 Simons Graduate Fellowships in Ecology and Evolution 👇

Simons Graduate Fellowships in Ecology and Evolution

The purpose of these awards is to provide support for students entering U.S.-based Ph.D. programs with a plan to perform research in ecology and evolution. While we will consider all projects in ecolo...

simonsfoundation.org

Excited to share a preprint from my postdoc research at @ucberkeleyofficial.bsky.social in the @banfieldlab.bsky.social! We surveyed soil microbiomes for autotrophy - and found it nearly everywhere, but most abundant in deep, saturated soils. Check it out below! www.biorxiv.org/content/10.6...

New preprint alert 🚨: Who actually drives methane production in anoxic sediments 🧬🔥? We point to a transcriptionally dominant 🦠 clade: VadinHA17. shorturl.at/Rijc0 @bledinadede.bsky.social @taylorpriest.bsky.social

Again looking for (self)nominations of/by grad students and postdocs to give virtual talks (via zoom) in the fall seminar series of MSU's Thermal Biology Institute. Does >not< need to be on thermophiles. Email me!

🚨 preprint alert! check out our new pub on an unusual summer flu outbreak among shorebirds traced with targeted metagenomic sequencing of wastewater. more like this coming soon from our team at @wastewaterscan.bsky.social !

medRxivpreprint@medrxivpreprint.bsky.social · 4mo ago

Divergent avian strains drive an off-season influenza A peak in municipal wastewater https://www.medrxiv.org/content/10.64898/2026.04.02.26350079v1

marine micro folks: @elliearrington.bsky.social and i are guest editing an issue of JOVE (journal of visualized experiments) focusing on molecular techniques: app.jove.com/methods-coll... we're looking for abstract submissions (by april) exploring best practices in..

🚨 preprint day for a thorough investigation of the genetic potential for chemoautotrophy in the deep northeastern pacific, led by @cometkid001.bsky.social in the @annedekas.bsky.social lab

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 7mo ago

Substantial genetic potential for deep-sea chemoautotrophy extends beyond nitrifiers https://www.biorxiv.org/content/10.64898/2026.01.13.699260v1

Troubleshooting common errors in assemblies of long-read metagenomes www.nature.com/articles/s41... #jcampubs

Troubleshooting common errors in assemblies of long-read metagenomes - Nature Biotechnology

Long-read sequence assemblies from metagenomes contain frequent errors.

nature.com

If you are interested in this work and are looking for a postdoc position, please get in touch -- we are actively looking for someone to join our group at UCLA!

Are you a postdoc or 4-5th year grad student working on any problem in environmental microbiology and are interested in giving a virtual seminar (via zoom) on your hard work to a crowd of interested researchers at Montana State's Thermal Biology Institute in spring? Email/DM me!

excited to see this one with @leahtaylorkearney.bsky.social @prywes.bsky.social et al. out, bringing a truly interdisciplinary (comparative genomics/phylogeny + biochemistry) lens to our favorite enzyme rubisco

bioRxiv Biochemistry@biorxiv-biochem.bsky.social · 9mo ago

Diversity-driven biochemical survey reveals dimeric structural origin of rubisco https://www.biorxiv.org/content/10.1101/2025.11.05.686826v1

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

Junior, Assistant, or Associate Specialist – Xue Lab

University of California, Irvine is hiring. Apply now!

recruit.ap.uci.edu

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...

Luo Lab - Microbial Ecology - join

The Luo Lab is accepting applications for funded Postdoc and PhD opportunities. Details below. Lab members will have access to state-of-the art wet lab, and computing, and sequencing resources, inclu...

sites.google.com

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

Abundant and metabolically flexible bacterial lineages underlie a vast potential for rubisco-mediated carbon fixation in the dark ocean - Genome Biology

Background Rubisco is among the most abundant enzymes on Earth and is a critical conduit for inorganic carbon into the biosphere. Despite this, the full extent of rubisco diversity and the biology of ...

link.springer.com

alex jaffe@alexjaf.bsky.social · 2y ago

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..

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!

Steven Robbins@stevenjrobbins.bsky.social · last yr.

Very excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.biorxiv.org/content/10.1...

🚨 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-...

Cruz-Led Investigation Uncovers $2 Billion in Woke DEI Grants at NSF, Releases Full Database

commerce.senate.gov

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