PriME - Principles of Microbial Ecosystems

Bacterial iron acquisition by Escherichia coli is facilitated by amino acid complexation in a rapid-renewal environment | PNAS In natural environments, bacteria often encounter low concentrations of nutrient mixtures that are continuously replenished by physical processes s...

🔥Hot off the press!

❓ How do bacteria get iron when nutrients are scarce and constantly washed away❓

A PriME collective effort reveals—using a new continuous culture device—how bacteria acquire iron under rapid nutrient renewal, beyond #siderophores.

www.pnas.org/doi/10.1073/...

Phosphate deprivation restricts bacterial degradation of the marine polysaccharide fucoidan - Nature Microbiology Limiting phosphate concentrations could be a strategy to protect and sequester carbon dioxide as fucoidan, a polysaccharide produced by marine algae.

❓Does low phosphate help keep carbon locked in fucoidan rather than recycled by bacteria❓

A PriME fellow from the Hehemann lab and his colleagues explored this question in a study just published in Nature Microbiology 🤗⬇️

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

We say goodbye to Jeremy, who joined PriME as a PhD student and leaves as a Postdoc - he has been an active and valued part of our community! He now continues his journey at the University of Maryland, studying viral removal rates in marine ecosystems 🦠🌊

Thank you - and all the best, Jeremy 🤗!

A warm PriME welcome to Richard!🎉

Richard joined the Hwa Lab at UC SanDiego
as a new Postdoc, exploring how physiological variation within bacterial species shapes their evolution 🧫🔬.

We’re excited to have you with us!
primecollaboration.org/profiles/richa

Welcome to the PriME team, Eliane! 🎉

Eliane has just joined the Stocker Lab as a new PhD student, exploring how microbial processes shape the ocean’s carbon cycle 🌊🦠.

We’re thrilled to have you on board!
🔗 primecollaboration.org/profiles/eliane-ballmer

We gathered this week for our Annual Meeting in NYC - three days of inspiring exchange!✨

This year, we introduced group work sessions for review papers🗒️to reflect and synthesize our interdisciplinary work😀

Thank you to all participants and @simonsfoundation.org
for the support!

Congratulations to all authors, including our PriME fellows 🤗

Vitamin auxotrophies shape microbial community assembly on model marine particles Abstract. Microbial community assembly is governed by the flow of carbon sources and other primary metabolites between species. However, central metabolism

❓How do microbes that can’t make their own vitamins survive in the ocean? 🌊🦠

In this new paper, @rachelgregor.bsky.social and fellow PriME members uncover the role of B vitamin auxotrophies in microbial communities.

👇Check it out 😀
academic.oup.com/ismej/advanc...

Exciting work from former and current PriME members 🤗 Looking forward to seeing it published!

Degradation of extracellular polymeric substances shapes microbial community diversity Cross-feeding of small metabolites is known to drive carbon exchange among microbial species, but the role of extracellular polymeric substances (EPS) has been poorly understood. This study shows that...

❓What if microbes share not just small metabolites, but also complex molecules that shape community assembly 🦠?

@sammy-pontrelli.bsky.social and co-authors explored this question in a new collaborative PriME study 😃

Learn more about it 👇
journals.plos.org/plosbiology/...

PriME Dr. #5 in 2025 is Gabriel from Otto Cordero's lab!

He successfully defended his thesis "Shaping Function Through Space: The Role of Spatial Organization in Microbial Communities" 🧑‍🎓🥳

Thank you Gabriel for your collaborative spirit and contribution🦠🤗 All the best for your future!

Fluid flow generates bacterial conjugation hot spots by increasing the rate of shear-driven cell–cell encounters | PNAS Conjugation accelerates bacterial evolution by enabling bacteria to acquire genes horizontally from their neighbors. Plasmid donors must physically...

❓How does fluid flow affect bacterial gene exchange? 🌊🦠❓

In his first publication, PriME member Matti Zbinden and co-authors show that stirring at the right speed can boost conjugation rates by increasing cell encounters without disrupting transfer.

Find out more 😀 👇
www.pnas.org/doi/abs/10.1...

🎉Excited to welcome Melanie Stäubli in our network as a new PostDoc (@Levine's group)!

As a microbial ecologist with a flair for quantitative modeling, she studies how phycosphere interactions shape phytoplankton dynamics and impact marine carbon cycling.

Great to have you on board, Melanie! 🌊🔬

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...

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...

We welcome our new PostDoc member Nittay @nittaym.bsky.social @micsysecolab.bsky.social 😃.

He’ll be investigating how catabolic cascades emerge from species’ proteomic strategies — and how these shape community responses to environmental changes 🌍

Nice to have you aboard, Nittay! 🙌

🎓Congrats to Margot Bligh @marumunibremen.bsky.social on successfully defending her PhD thesis “Environmental and structural drivers of algal glycan persistence in the ocean” 🥳

Thanks for your great contribution to PriME — we’re happy you’ll be collaborating with us a little longer! 😃

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...

New funding opportunity: We are providing support for students entering U.S.-based Ph.D. programs with a plan to perform research in #ecology and #evolution. Deadline is 7/31: www.simonsfoundation.org/grant/simons... #science

Postdoctoral Associate MIT - Postdoctoral Associate - Cambridge MA 02139

‼️I'm looking for a postdoc‼️ Come join effort in using metagenomes to quantify microbial catabolic potential and carbon substrate availability at the ecosystem level. We seek to understand evolutionary forces shaping the carbon cycle. Part of ccomp-stc.org

careers.peopleclick.com/careerscp/cl...

Chemotaxis, growth, and inter-species interactions shape early bacterial community assembly Abstract. From the perspective of a marine copiotrophic bacterium, the surface ocean is a mosaic of exploitable hotspots of organic matter released from li

❓How do #marinebacteria navigate and compete for #phytoplankton -derived organic matter hotspots — and what happens when their microbial neighbors 🦠tag along❓

Check out this exciting PriME collaborative work, just published in @ISMEJournal! 😃👏👇
academic.oup.com/ismej/advanc...

Congratulations Glen 🥳and to all former and current PriME members who contributed to this manuscript 🤗👏

We're excited to welcome Michaela, who recently joined us as a PostDoc at the Cordero's lab (MIT)!

She will explore how changes in cellular function impact #microbialcommunity dynamics, bringing her expertise in metabolic engineering, protein engineering, and synthetic biology 🤗🦠

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.

❓What survival strategies enable #marinebacteria to chase sinking particles for days under starvation — and how might this shape the ocean’s long-term carbon storage ❓

A joint PriME effort just hot off the press 🔥🥳👇
www.nature.com/articles/s41...

We gladly introduce PriME, an international and interdisciplinary collaboration which aims to derive fundamental principles of how microbial ecosystems assemble and function, with a primary focus on #marinemicrobes and #carboncycling 🦠🌊