Osama Alian

GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities Abstract. Fluorescence in situ hybridisation (FISH) is a powerful tool for visualising the spatial organisation of microbial communities. However, traditio

Very excited to share the first paper out of my Postdoc @CMR:

GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities.
@sjmcilroy.bsky.social @jamesvolmer.bsky.social @benjwoodcroft.bsky.social

doi.org/10.1093/isme...

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Guidelines for preventing and reporting contamination in low-biomass microbiome studies - Nature Microbiology In this Consensus Statement, the authors outline strategies for processing, analysing and interpreting low-biomass microbiome samples, and provide recommendations to minimize contaminants.

New Consensus Statement in Nature Microbiology!
Working with low-biomass microbiome samples? From deep subsurface rocks to human lungs, contamination is a major challenge. We offer field-to-data analysis guidelines to help keep your results clean.
📖 doi.org/10.1038/s415...

Defining ultra-slow-growing extremophilic microorganisms as aeonophiles - Nature Microbiology In environments like the deep subsurface, microorganisms with long doubling times can remain metabolically active for millions of years — we propose referring to this class of extremophile as aeonophi...

Defining ultra-slow-growing extremophilic microorganisms as aeonophiles #USC_earth #USC_MEB #jcampubs www.nature.com/articles/s41...

This, by Michael Lynch.

I'd include AI techbros as well.

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

Functional biogeography of marine microbial heterotrophs Heterotrophic bacteria and archaea (“heteroprokaryotes”) drive global carbon cycling, but how to quantitatively organize their functional complexity remains unclear. We generated a global-scale unders...

Out in Science! Zakem et al. mechanistically modeled global marine prokaryotic functional diversity, grounded with field data. Shifts in community composition drive respiration and thus biological C storage. This facilitates C cycle projections in a warming ocean
www.science.org/doi/10.1126/...

Exciting! We have successfully deployed our in situ mass spectrometer, developed together with @marumunibremen.bsky.social, on their brand new #ROV #MARUM-QUEST 5000. It provides real-time in­form­a­tion on gas con­cen­tra­tions in wa­ter 400°C hot and 4000m deep.

mpi-bremen.de/en/Diving-ro...

Diel partitioning in microbial phosphorus acquisition in the Sargasso Sea | PNAS The daily cycle of photosynthetic primary production at the base of marine food webs is often limited by the availability of scarce nutrients. Micr...

In the phosphorus-limited Sargasso Sea, microbes partition phosphorus uptake by time of day—bacteria in the morning, phytoplankton by day, and cyanobacteria at dusk—revealing a temporal niche strategy. www.pnas.org/doi/10.1073/...

New paper out!
We discovered a tiny archaeon with the smallest known archaeal genome — only 238 kbp!
Candidatus Sukunaarchaeum mirabile has almost no recognizable metabolic pathways and may rely heavily on a host to survive.
It also represents a novel, deep-branching lineage in the archaeal tree.

The crown of a crinoid sits just within smooth grey rock, its arms gently folded over one another as it lays on its side. A partial stalk extends from the bottom of the crinoid's crown (the calyx), appearing as if it's just been separated from the rest of its body.

A cropped image with a closer view of the crinoid's long, tendril-like arms and rounded calyx. Small, feather-like extensions (pinnules) hang from the arms and gently drape over one another.

Happy #FossilFriday, check out this beautifully preserved crinoid! These animals have inhabited the oceans for 480 million years, and they're relatives of sea urchins and sea stars. This specimen is long fossilized, but looks like it just died and fell into the seabed's embrace. (1/3)
#paleontology

40 years ago all of Genbank was published in print form by NAR. The same format today would require over 4 light seconds of shelf space. To a year of progress in 2025.

A figure from the preprint manuscript showing a phylogenetic tree with the three clases of molybdenum-dependent nitrogenases and their predicted structures

A screenshot of the preprint title "Nitrogenase structural evolution across Earth's history" by authors Bruno Cuevas-Zuviria, F Detemple, K Amirtkar, AK Garcia, LC Seedfeld, and B Kaçar

🧪🦠🌍 Nitrogenases are one of the most ecologically important enzymes on Earth. They're ancient too.

In this PREPRINT, Cuevas-Zuviría & Co. analyze how their structures tell the story of planetary-wide ecological changes
doi.org/10.1101/2024...

Flipping FLIP ship saved from scrapyard at last minute The US Navy and Scripps Institution of Oceanography's unique FLoating Instrument Platform (FLIP) has been saved at the last minute from the breaker's yard. Scheduled to be scrapped in Mexico, it was p...

I am so happy that FLIP will live on!

newatlas.com/marine/flipp...

Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection - Scientific Reports Scientific Reports - Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection

Useful benchmarking study

'Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection'

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

Now that we've had a migration of twitter people here, I figured it's a good time to re-share our most recent work, measuring the growth rates of individual microbial cells with Raman. Super cool technique if you're curious about quantifying microbial activity in/on minerals, plants, etc!

Life finds a way

Histogram peaked at 3 minutes and 2 weeks since sent

When I will respond to your email

If you are not aware, Giant Squid eyes are huge. #marinelife

Metabolomics folks / mass spectrometrists, are you looking for a cool postdoc opportunity? Dr. Anitra Ingalls @ the Univ. of Washington is hiring a postdoc to work with an international team (including yours truly) on the metabolites of marine critters. Come work with us!
apply.interfolio.com/150110

It's so nice to find the science tribe again 🥲