A. Murat Eren (Meren)

As of this week, I have begun a new part-time role as a Professor at Aalborg University in Denmark. I’m very excited to join AAU’s Center for Microbial Communities’ ambitious team while continuing my research programs and serving as SCGC director at Bigelow Laboratory for Ocean Sciences in the US.

POSTDOC POSITION --- Bernd Blasius has just opened a PostDoc position to model viral evolution. The project is a collaboration with me Dirk Brockmann and famous virologist Christian Drosten, among others. uol.de/en/job/postd...

» A new simplification in modeling enables us to predict system failures before they begin. « (@mhab.bsky.social)
How? ➡️ Read in our latest newsletter: 241806.seu2.cleverreach.com/m/16915050

Also news about Red Sea coral reef protection, BBNJ, a new working group and... a special cemetery 😱

𝐖𝐡𝐚𝐭 𝐩𝐫𝐨𝐜𝐞𝐬𝐬𝐞𝐬 𝐠𝐨𝐯𝐞𝐫𝐧 𝐩𝐡𝐨𝐭𝐨𝐬𝐲𝐦𝐛𝐢𝐨𝐬𝐢𝐬 𝐞𝐬𝐭𝐚𝐛𝐥𝐢𝐬𝐡𝐦𝐞𝐧𝐭 𝐚𝐧𝐝 𝐛𝐫𝐞𝐚𝐤𝐝𝐨𝐰𝐧? 🪸

Join us for a 3-year #Postdoc and help us find out! Our ERC-funded project at @hifmb.de offers excellent facilities and an international collaborative work environment.

Apply by April 1st: jobs.awi.de/Vacancies/21...

#ScienceJobs

Rossella Alba, our new colleague at @hifmb.de leading the Marine Policy and Management working group, offers two fully funded PhD positions here: jobs.awi.de/Vacancies/21... apply until March 18, and feel free to make potential applicants aware. 🧪 @icbm-uol.bsky.social

Resurrected nitrogenases recapitulate canonical N-isotope biosignatures over two billion years - Nature Communications The study shows that nitrogenase enzymes have maintained stable isotope signatures over billions of years, revealing how ancient microbes shaped Earth’s nitrogen cycle and offering a new experimental ...

Our new paper, out today! We resurrected ancient nitrogenases first used by life on Earth 3 billion years ago. We combined synthetic biology and geology & validated their chemical #biosignature in rocks that helps reveal ancient life on Earth!(and beyond!)

Link: www.nature.com/articles/s41...

With the release of anvi'o v9, the 300k+ contigs databases available for download on the GlobDB website are now compatible with both the development version and the latest stable release (v9) of anvi'o.

More info:
globdb.org/news

Thanks #anvio team!
🖥️🧬🦠

Yes, many plans :) We are still working on it, and we wish that branch to reach a level of maturity before we merge it for anvio-dev. But it is accessible to those who don't mind switching branches in their anvio-dev setup, and any help would be most welcome. We would love to collaborate.

Some more:

anvi-script-find-misassemblies: anvio.org/m/anvi-scrip...

anvi-display-codon-frequencies: anvio.org/m/anvi-displ...

anvi-reorient-genomes: anvio.org/m/anvi-reori...

Some of the new programs in this release:

anvi-compute-rarefaction-curves: anvio.org/m/anvi-compu...

anvi-draw-kegg-pathways: anvio.org/m/anvi-draw-...

anvi-predict-metabolic-exchanges: anvio.org/m/anvi-predi...

We just released #anvio v9, "eunice" 🎉

This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176.

Read the release notes:

github.com/merenlab/anv...

Visit our up-to-date web page:

anvio.org

Now published in Nature Biotechnology:
go.nature.com/44P7nSm
If you missed it, the TL;DR is in my April thread below

Troubleshooting common errors in assemblies of long-read metagenomes - Nature Biotechnology Long-read sequence assemblies from metagenomes contain frequent errors.

Troubleshooting common errors in assemblies of long-read metagenomes - @merenbey.bsky.social @banfieldlab.bsky.social go.nature.com/44P7nSm

In my opinion, in theory nothing can be more reliable than the assembly graph. So if the graph says something is circular, I'd take that more seriously than the other way around :)

With ONT and PacBio you do get many many genuinely circular elements. Some of which are excellent, some others are quite questionable, but luckily finding the poop ones and being more careful with them is not that difficult:

anvio.org/help/main/pr...

Here is the boring fact: it depends on the environment, lib prep, & depth of sequencing. Quite a large number of plasmids and viruses will circularize with Illumina.

One can curate Bacterial genomes manually to circularity, but I'd say it would be unlikely to get them assembled circular :/

If a tandem repeat collapses to a single copy of itself during the assembly, it certainly would become indistinguishable from a circular element through RF evidence. Probably that is a very big problem for eukaryotic genomics, but we don't assemble many euks from metagenomes.

Of course tandem repeats can also produce end-localized RF pairs, but I'd say it will be a rare event compared to circular elements in a metagenome. Probably that's why almost all circular elements we capture in metagenomes resolve to plasmids or viruses (at least in human gut metagenomes).

Proper pairs will unlikely map exclusively to contig ends when they originate from tandem repeats. That's why in addition to measuring distance between RF pairs, one needs to track precisely where those proper pairs map on a given contig, their coverage, and the insert size dist in the dataset.

But if you mean one needs to be 'lucky' because most people prepare libraries without proper size selection (which leads to garbage insert size distribution that ruin robust RF statistics), and most assemblies break at low-complexity / repeat regions, then yes, you need to be lucky there :)

A circle does not have an end, but a linear contig that represents a circular molecule after assembly does, in which case the paired-end reads that span the artificial breakpoint will have RF orientation. It works pretty well actually (and I'm not a very lucky person in general .. so, IDK).

What does luck have anything to do with it?

It is pretty simple for all domains of life. You need proper RF reads exclusively at contig ends :)

anvi-report-circularity An anvi'o program. Predict contig circularity from paired-end read alignments in a given BAM file.

anvio.org/help/main/pr...

HIFMB newsletter out now! 🦑
In our top story, Bettina Meyer outlines the Krill Stock Hypothesis, a scientific framework for setting krill catch quotas to protect the ecological balance in the Southern Ocean.
That and more here: 241806.seu2.cleverreach.com/m/16677411

Lost and Found in Modern Microbiology: An Ethnography of Modern Microbiologists A paper on how microbiologists navigate the tension between reductionism and complexity in their everyday practices, and my 2 cents on it.

New blog post for my microbiologist colleagues:

merenlab.org/2025/12/15/r...

In which Meren talks about a paper by Valentina Marcheselli on how microbiologists navigate the tension between reductionism and complexity in their everyday practices.

Towards a broader perspective on marine biodiversity change - Marine Biodiversity Biodiversity decline jeopardizes the foundation of natural ecosystems and human well-being, a concern that prompted major global agreements aiming to bend the curve towards a net positive biodiversity...

More than a year ago researchers from @hifmb.de and @icbm-uol.bsky.social started to write about different perspectives on marine biodiversity change from natural and social science perspectives. This morphed into a review paper that was published online today link.springer.com/article/10.1... 🧪

Ocean_observatories_socials

📝 We need YOUR input!

We're writing a perspective piece to share a vision for a future global observatory for marine microbial 'omics. One aspect of the perspective piece is to synthesize ongoing marine microbiome time-series.

Please review our list and add any we've missed: tinyurl.com/4bmeenp9

Marine Microbial Observatories for the Future: From Samples to Data to Legacy Using Integrated 'Omics Strategies A workshop for the future

What would a marine microbiome observing system meant to last decades look like? 🌊🦠

We explored this at the recent MMOFF Workshop, which brought together diverse partners to envision the future of marine microbiome observations.

merenlab.org/workshops/MM...

A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts - Scientific Data Scientific Data - A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts

I am happy to share that our data descriptor on the Hawaiʻi Diel Sampling is now published! 🌊🦠https://www.nature.com/articles/s41597-025-06166-3

Every 1.5 hours for 48 hours, we collected ocean microbes from within and adjacent to Kāneʻohe Bay, Oʻahu, Hawaiʻi and produced a multi-omics dataset.