Emil Ruff

Emil Ruff

@emilruff.bsky.social

Microbial ecology and ecophysiology. Associate Scientist at The Marine Biological Laboratory, Woods Hole. https://rufflab.org/ Science, music, art, graphics, comics.

869 followers469 following105 posts

Emil Ruff
@emilruff.bsky.social

Chlorobi paper hattrick! Chlorobi use broad metabolic strategies to support stable blooms www.biorxiv.org/content/10.6... Bloom-forming bacteria heavily invest in anti-phage defense www.biorxiv.org/content/10.6... A 3000-year record of a temperate estuary www.sciencedirect.com/science/arti...

biorxiv.orgAnoxygenic phototrophic Chlorobi use broad metabolic and resource acquisition strategies to support stable near-clonal bloomsAnoxygenic phototrophic green sulfur bacteria (GSB; Chlorobiia) are important primary producers in anoxic and sulfidic environments, whose significance in aquatic ecosystems will expand with coastal deoxygenation. Here, we employed a uniquely comprehensive analytical approach to investigate the formation, maintenance, and collapse of a GSB bloom. We combined multi-omics—V4V5 and synthetic long read 16S rRNA amplicon sequencing, metagenomics, and metaproteomics—with total and GSB-specific cell counts, biogeochemical measurements, and isotopic analysis. The GSB bloom exceeded 109 cells ml-1, among the highest environmental cell densities reported to date, with up to 96 % of the bloom consisting of a single strain-level Prosthecochloris lineage (GSB-TRL01). Extreme sulfide concentrations (> 17 mM) coincided with peaking cell density and a shift in isotopic composition. Bloom persistence is supported by tightly coupled sulfur cycling, high rates of nitrogen fixation, mechanisms to tolerate oxidative stress and maintain redox balance, and nutrient acquisition through outer membrane transport systems. A shift in sulfur oxidizing enzymes towards enzymes with higher sulfide affinity proceeded bloom demise. Prosthecochloris GSB-TRL01 differs from closely related lineages in several outer membrane transport systems, including porins to transport phosphate and tonB-dependent transporters. Collectively, these findings identify physiological and metabolic strategies that may enable near-clonal Prosthecochloris populations to attain extraordinary biomass while coupling the sulfur, carbon, and nitrogen cycles in coastal euxinic environments. ### Competing Interest Statement The authors have declared no competing interest. U.S. National Science Foundation, https://ror.org/021nxhr62, 2205993, 2426305, BIO220128 Simons Foundation, 824763

Emil Ruff reposted

Roland Hatzenpichler
@environmicrobio.bsky.social

Join us at the "2027 Applied and Environmental GRC: Mechanistic Microbiology for a Complex World" July 18-23, 2027 and GRS "Mechanistic Microbiology Beyond the Model Organism" July 17-18. Applications are open! @thuls.bsky.social and I put together an awesome schedule! www.grc.org/applied-and-...

grc.org2027 Applied and Environmental Microbiology Conference GRCThe 2027 Gordon Research Conference on Applied and Environmental Microbiology will be held in South Hadley, Massachusetts. Apply today to reserve your spot.

Emil Ruff reposted

Manuel Kleiner
@manuelkleiner.bsky.social

We are looking to hire a microbiology laboratory research technician here at NC State in Raleigh, NC. If you have experience in microbiology and/or LC-MS/MS please consider applying. Please repost! jobs.ncsu.edu/postings/234...

jobs.ncsu.eduMicrobiology Laboratory Research TechnicianThe Kleiner Lab at North Carolina State University is seeking a Research Technician to support research focused on complex microbial communities, microbial symbioses, and metaproteomics. Reporting to ...
Emil Ruff
@emilruff.bsky.social

This years ISSM is in Vienna from Aug 30 - Sept 4, the early bird deadline is 15 June. As a premier conference in subsurface microbiology, the ISSM features exciting sessions and excellent keynote speakers. Spread the word, see you there. issm2026.univie.ac.at #deeplife #microbiome #subsurface

issm2026.univie.ac.atissm conference 2026 vienna 12th issm conference12th ISSM COnference Vienna: Subsurface microbiology plays a critical role in shaping Earth's ecosystems, driving biogeochemical processes, and addressing critical environmental challenges. ISSM provi...

Emil Ruff reposted

Mya Breitbart
@viromegirl.bsky.social

Lots of people have reached out asking how they can support us after the devastating fire in the MSL building, the heart of @cmarinescience.bsky.social Here’s one way, a GoFundMe organized by our graduate students - gofund.me/4373c6ff3. Please share widely, and thanks for helping our community!

gofund.meDonate to USF Marine Science: Fire Recovery Support, organized by Bella IannottaOn Saturday, May 2nd the University of South Florida Marine Science Lab (MSL)… Bella Iannotta needs your support for USF Marine Science: Fire Recovery Support
Emil Ruff
@emilruff.bsky.social

The International Symposium on Subsurface Microbiology (ISSM) is in Vienna this year. Aug 30th - Sept 4th I am so excited! Early Bird deadline is April 30th. issmvienna2026.univie.ac.at #deeplife 🧪⚒️ #subsurface

issmvienna2026.univie.ac.atissm conference 2026, viennaSubsurface microbiology plays a critical role in shaping Earth's ecosystems, driving biogeochemical processes, and addressing critical environmental challenges. ISSM provides a unique forum for researchers to explore the complex interactions between subsurface microorganisms and their environments.

Emil Ruff reposted

Amelia Rotaru
@ameliarotaru.bsky.social

In addition to the 2 postdoc jobs posted yesterday, we’re recruiting 2 PhD students (environmental microbiology/ molecular ecology) to join us from April. The projects will map microbial populations across niches in bioelectrochemical systems relevant to biomethanation & link them to performance.

fa-eosd-saasfaprod1.fa.ocs.oraclecloud.comTwo fully funded PhD candidate positions in Electromicrobiology (3 years)Application deadline: 4 March 2026 at 23:59 hours local Danish time
Emil Ruff
@emilruff.bsky.social

Come work with us on #darkoxygen as part of the NASA Postdoctoral Fellowship Program. It is an amazing opportunity to get up to 3 years of funding. Deadlines are March 1. and November 1. Happy to discuss your ideas! Details here: zintellect.com/Opportunity/... @mblscience.bsky.social #astrobiology

zintellect.comZintellect - National Aeronautics and Space Administration (NASA) - ICAR - OxyMoRon: Understanding dioxygen production and consumption in apparently anoxic environments - 0042-NPP-MAR26-ABProg-Astrobi...About the NASA Postdoctoral Program The NASA Postdoctoral Program (NPP) offers unique research opportunities to highly-talented scientists to engage in ong
Emil Ruff
@emilruff.bsky.social

Meet "OxyMoRon" our 5-year NASA ICAR program to study dark oxygen production in Earth's hidden ecosystems. We have multiple positions and are happy about collabs. Co-PIs:@valdeanda.bsky.social @microbiaki.bsky.social @valiergaly.bsky.social Ranjani Murali, Scott Wankel www.mbl.edu/news/emil-ru...

mbl.eduEmil Ruff Leads Team to Explore Dark Oxygen Through NASA Collaborative Award | Marine Biological LaboratoryFor more than a century, textbooks asserted that molecular oxygen (O2) on Earth is produced almost entirely by photosynthesis, through plants and microbes. But discoveries over the past decade have ov...
Emil Ruff
@emilruff.bsky.social

If you work on Dark Oxygen --> come to #AbSciCon2026 this year. 17-22 May, Madison Join our session on ""Dark Oxygen" Production: where does it happen, how does it work, and what does it mean for astrobiology?" Submit your abstract until January 14 More info here: agu.confex.com/agu/abscicon...

agu.confex.com2026 Astrobiology Science ConferenceMolecular oxygen (O₂) is often regarded as a strong biosignature in the search for life. Traditionally the production of O2 has been linked to photosynthesis, yet non-photosynthetic (“dark”) pathways ...

Emil Ruff reposted

Emeline Vidal
@emvidal.bsky.social

Thrilled to share our new paper: Subsurface Life on Earth as a Key to Unlock Extraterrestrial Mysteries. 🧪 @melroselane.bsky.social, @drbradbrad.bsky.social , @geobiomaggie.bsky.social, @emilruff.bsky.social @mblscience.bsky.social enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

enviromicro-journals.onlinelibrary.wiley.comSubsurface Life on Earth as a Key to Unlock Extraterrestrial MysteriesThis paper discusses current research on subsurface microbiology. Exploring Earth's deep and extreme subsurface environments provides critical insights into life's limits and adaptability. Subsurface...
Emil Ruff
@emilruff.bsky.social

👇🥂🎊🥳

The Probst Lab@probstlab.bsky.social

We are excited to share @probstlab.bsky.social's latest publication on the diversity of CRISPR-Cas spacers, led by @katharinasures.bsky.social !! 🧬 Have a read!! ➡️ doi.org/10.1093/gbe/... @emilruff.bsky.social @alexjaffe.bsky.social @geomicrosoares.bsky.social & others not in Bluesky!

doi.orgAcquisition of Spacers from Foreign Prokaryotic Genomes by CRISPR-Cas Systems in Natural EnvironmentsAbstract. Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems of bacteria and archaea provide immunities

Emil Ruff reposted

Beate Kraft
@beatekraft.bsky.social

Please apply if you are interested in marine biogeochemistry and microbial dark oxygen production. Deadline: November 17th.

Beate Kraft @beatekraft.bsky.social

📣Postdoc opportunity @nordcee.bsky.social , University of Southern Denmark! 📣 Join us and work with Bo Thamdrup and me on microbial dark oxygen production in marine oxygen minimum zones! Please share widely! Deadline: 17 November More information can be found here: tinyurl.com/2vuur3wh

fa-eosd-saasfaprod1.fa.ocs.oraclecloud.comPostdoc on microbial oxygen production in marine oxygen minimum zonesApplication deadline: 17 November 2025 at 23:59 hours local Danish time
Emil Ruff
@emilruff.bsky.social

Looking for a cutting-edge and fun conference in 2026? How about: GRC Geobiology in Ventura, CA - January 11-16, 2026 www.grc.org/geobiology-c... AbSciCon in Madison, WI - May 17-22, 2026 www.agu.org/abscicon 🤩The Ruff Lab will be there with sessions and presentations on Dark Oxygen Production 🥳

grc.org2026 Geobiology Conference GRCThe 2026 Gordon Research Conference on Geobiology will be held in Ventura, California. Apply today to reserve your spot.
Emil Ruff
@emilruff.bsky.social

Spend the summer at the Marine Biological Laboratory in Woods Hole, Massachusetts, conducting your own original research. Applications open now. grassfoundation.org/application-... @mblscience.bsky.social

grassfoundation.orgApply for the Grass Fellowship – The Grass FoundationPriority Deadline: October 15, 2025 Applicants who apply by this date will have the opportunity to receive technical feedback and update their proposal accordingly prior to the final deadline. Letters of reference must be received by December 15, 2025.

Emil Ruff reposted

Nichole Ginnan 🦠
@botanichole.bsky.social

Great publication from Maggie Wagner (KU) and Manuel Kleiner (NCS) on how to design microbiome (+ other Omic) projects with downstream statistics in mind! A must read for trainees! www.nature.com/articles/s41...

nature.comHow thoughtful experimental design can empower biologists in the omics era - Nature CommunicationsHere, the authors discuss principles of experimental design that are relevant for all biology research, along with special considerations for projects using -omics approaches, highlighting common expe...

Emil Ruff reposted

Riikka Kietäväinen
@riikkakie.bsky.social

Excited to present our DODGE project (#Safer2028) results on dark oxygen in the deep continental biosphere today at the #Goldschmidt2025 conference in Prague. It's session 9e in the Small Hall - see you there if you are around!

Emil Ruff
@emilruff.bsky.social

For ANME enthusiasts & for those who wonder how a methanogen turns into a methanotroph 👇New work by Orphanlab Identification of key steps in the evolution of anaerobic methanotrophy in Candidatus Methanovorans (ANME-3) archaea www.science.org/doi/10.1126/... @caltech.edu @mblscience.bsky.social

science.orgIdentification of key steps in the evolution of anaerobic methanotrophy in Candidatus Methanovorans (ANME-3) archaeaModification of core carbon and energy metabolism aided a recent evolution of anaerobic methanotrophy in archaea.
Emil Ruff
@emilruff.bsky.social

This week: Holden Thorp, Editor-in-Chief, Science Magazine talking about “Staying True to the Indispensable Values of Science”. Don't miss MBL Friday evening lectures. Like every year the line-up is excellent. In person & virtual. www.mbl.edu/events/frida... @mblscience.bsky.social @science.org

mbl.edu2025 Friday Evening Lectures | Marine Biological LaboratoryJoin us for these venerable MBL events bringing our local and global communities together live.

Emil Ruff reposted

Dr. Lucky Tran
@luckytran.com

"We are speaking on behalf of hundreds of NIH staff who are standing up together to say: WE DISSENT. I am so scared about doing this but I am trying to be brave for my kids because it's only gonna get harder to speak up." Thank you to Dr. Jenna Norton and NIH scientists for your courage!