Taylor priest

Protein language models reveal evolutionary constraints on synonymous codon choice Evolution has shaped the genetic code, with subtle pressures leading to preferences for some synonymous codons over others. Codons are translated at different speeds by the ribosome, imposing constrai...

This preprint from Helen Sakharova is one of the coolest things to come out of my lab: “Protein language models reveal evolutionary constraints on synonymous codon choice.” Codon choice is a big puzzle in how information is encoded in genomes, and we have a new angle. www.biorxiv.org/content/10.1...

📣 New paper alert! Just out in Cell Reports! pubmed.ncbi.nlm.nih.gov/40644298/
Thrilled to share that we have discovered a brand-new anti-phage defense system! Bacteria have evolved various defense strategies (CRISPR etc) to counter phage attacks. We found a new one - fascinating and dramatic
⚔️🦠❄️🔬

PHACE: Phylogeny-Aware Detection of Molecular Coevolution Abstract. The coevolution trends of amino acids within or between genes offer key insights into protein structure and function. Existing tools for uncoveri

PHACE: phylogeny-aware coevolution algorithm that maps amino acid substitutions onto a phylogenetic tree to detect molecular coevolution academic.oup.com/mbe/article/...

Matthias Wietz (@matthiaswietz.bsky.social) marine biologist & polar researcher | music, scuba diving & SciComm | sounds: https://spti.fi/16bmvbl & http://instagr.am/the.arcwatchers

Special shoutout to first author Alyzza Calayag (not yet on Bluesky)! This was a strong collaboration between @geomarkiel.bsky.social and @awi.de especially @taylorpriest.bsky.social and @matthiaswietz.bsky.social — and others not on bluesky

Very excited to host the GRS Marine Microbes next year, which we are centering on three key themes: diversification, adaptation and resilience! Applications are now open - www.grc.org/marine-micro...

Quantitative metagenomics for marine prokaryotes and photosynthetic eukaryotes Abstract. High-throughput sequencing has provided unprecedented insights into microbial biodiversity in marine and other ecosystems. However, most sequenci

Quantitative metagenomics for marine prokaryotes and photosynthetic eukaryotes #USC_MEB #jcampubs 🌊 academic.oup.com/ismecommun/a...

Biodiversity conservation requires integration of species-centric and process-based strategies | PNAS Conservation science and policy are geared primarily toward the preservation of species and habitats, with priority often given to the rarest, most...

A very nice perspective piece on the need to move beyond species-centric views of #biodiversity and #conservation efforts towards strategies that integrate information on processes www.pnas.org/doi/10.1073/...

Occurrence and temporal dynamics of denitrifying protist endosymbionts in the wastewater microbiome Effective wastewater treatment is of critical importance for preserving public health and protecting natural environments. Key processes in wastewater treatment, such as denitrification, are performed...

Occurrence and temporal dynamics of denitrifying protist endosymbionts in the wastewater microbiome.

Very excited to see the preprint of this story online and big congrats to @louison-nicolas.bsky.social at @mpimarinemicrobio.bsky.social!

www.biorxiv.org/content/10.1...

Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats - Nature Microbiology Nanopore sequencing of Danish soils and sediments yields genomes from over 15,000 microbial species, expanding the phylogenetic diversity of prokaryotes by 8%.

Great showcase of the power of long-read metagenomes for MAG recovery from soil samples - www.nature.com/articles/s41...

Horizon Europe 2028 - 2034: twice bigger, simpler, faster and more impactful Research and innovation news alert: As part of the next long-term EU budget 2028-2034, the Commission is proposing to double the budget of the research and innovation framework programme to €175 billi...

Very promising and uplifting news - #HorizonEurope funding is not only going to become simpler and faster but the budget is DOUBLING in size from 2028!

research-and-innovation.ec.europa.eu/news/all-res...

A dinoflagellate-infecting giant virus with a micron-length tail Viral infection is a ubiquitous source of marine plankton mortality, but relatively few viruses that infect phytoplankton have been characterized. Here we describe a virus, PelV-1, with unusual morpho...

Excited that this is out as a preprint! ❇️

We are introducing a novel dinoflagellate giant virus that holds so many mysteries!

www.biorxiv.org/content/10.1...

🎒 Getting ready for #ESEB2025?
📨 Check your inbox! We have sent out key updates and logistical details. 
𝐂𝐮𝐫𝐢𝐨𝐮𝐬 𝐚𝐛𝐨𝐮𝐭 𝐭𝐡𝐞 𝐟𝐮𝐥𝐥 𝐩𝐫𝐨𝐠𝐫𝐚𝐦𝐦𝐞? The entire scientific schedule is online. 
👉 Explore the agenda: https://lnkd.in/d6MSyPPa

We (with Clement Coclet, not on Bsky) had the chance to work on a broad "state of viromics" review. We tried to use this to give an overview of how the field changed over the last ~ 15 years, and also what we think are some of the major remaining challenges. Full-text access at -> rdcu.be/excHt

Tetranucleotide frequencies differentiate genomic boundaries and metabolic strategies across environmental microbiomes | mSystems Microbes adapt to diverse environments influenced by factors like temperature, acidity, and nutrient availability. We developed a new tool to analyze and visualize the genetic makeup of over 12,000 mi...

Tetranucleotide frequencies differentiate genomic boundaries and metabolic strategies across environmental microbiomes - journals.asm.org/doi/10.1128/...

Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper - Nature Biotechnology Novel microbial species in metagenomes are identified using conserved regions within universal marker genes.

A tool for species-level taxonomic profiling of microbes in metagenomes, along with a website containing ~250,000 already profiled samples - www.nature.com/articles/s41...

Arctic Ocean virus communities and their seasonality, bipolarity, and prokaryotic associations - Nature Communications Based on bulk DNA time-series sequencing of the surface Arctic Ocean, Calayag et al. show that planktonic viruses are strongly seasonal in abundance and community composition, and are correlated stron...

Arctic Ocean virus communities and their seasonality, bipolarity, and prokaryotic associations www.nature.com/articles/s41... #jcampubs 🌊

two sentences from the abstract of a paper that resonate with us way more than you can imagine...

A bacterial host factor confines phage localization for excluding the infected compartment through cell division Viruses frequently induce the formation of specialized subcellular compartments to facilitate their replication and assembly. Here, we describe a “hos…

A bacterial host factor confines phage localization for excluding the infected compartment through cell division
www.sciencedirect.com/science/arti...

Arctic Ocean virus communities and their seasonality, bipolarity, and prokaryotic associations - Nature Communications Based on bulk DNA time-series sequencing of the surface Arctic Ocean, Calayag et al. show that planktonic viruses are strongly seasonal in abundance and community composition, and are correlated stron...

🚨Our newest publication on the Fram Strait and #ArcticOcean is out 🚨

We explored the diversity, temporal dynamics and host-associations of Arctic #viruses over a four year time-series using long-read #metagenomics (and their global prevalence and distribution).

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

A new type of rhodopsins (called cryorhodopsins) have been found in actinobacteria inhabiting snow- and ice-dominated environments. They act as sensors of UV irradiation - www.science.org/doi/10.1126/...

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...

Targeted genome mining with GATOR-GC maps the evolutionary landscape of biosynthetic diversity Abstract. Gene clusters, groups of physically adjacent genes that work collectively, are pivotal to bacterial fitness and valuable in biotechnology and med

GATOR-GC is out at @narjournal.bsky.social!! Check out our new targeted genome mining tool featuring a novel similarity metric to efficiently compare and deduplicate gene clusters.

We uncover biosynthetic diversity missed by other genome mining tools

academic.oup.com/nar/article/...

Evidence of the smallest #archaea genome yet identified, with a size of only 238 kbp, has been identified in association with marine dinoflagellates and detected across ocean ecosystems. www.biorxiv.org/content/10.1...

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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EMBL Hamburg scientists have discovered a group of microbial cold-loving molecules, ‘cryorhodopsins’, with extraordinary abilities.

They are the first observed molecules that can act as both on and off switches for electrical activity in cells.
www.embl.org/news/science...

Global declines in net primary production in the ocean color era Nature Communications - This study shows primary production has significantly decreased in nearly half of the ocean. The authors demonstrate that decadal shifts in ocean color are driven by...

Global declines in net primary production observed through long-term assessment of satellite-based ocean colour - www.nature.com/artic...

Characterizing organisms from three domains of life with universal primers from throughout the global ocean - Scientific Data Scientific Data - Characterizing organisms from three domains of life with universal primers from throughout the global ocean

So excited to announce the GRUMP paper is published! This global dataset provides relative abundances for plankton spanning Archaea to Zooplankton from unfractionated (>0.2µm) water samples using 3-domain universal primers that amplify 16S and 18S in one PCR reaction.

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

A control theory framework and in situ experimental platform for informing restoration of coral reefs - Nature Ecology & Evolution Control theory provides a practical framework for managing system states and targeting interventions, such as in agriculture or forestry. This Perspective discusses the application of control theory t...

A control theory framework and experimental set up to inform #coralreef ecosystem restoration - www.nature.com/articles/s41...

Distinguishing among evolutionary and ecological processes shaping microbiome dynamics Abstract. Evolution is defined as the change in allele frequency over time as a result of either neutral processes, such as genetic drift, or as an adaptiv

Distinguishing among evolutionary and ecological processes shaping microbiome dynamics

#ISMEJournal review by Tiffany N Batarseh and @bkoskella.bsky.social

academic.oup.com/ismej/advanc...