Horizontal gene transfer drives the emergence of nitrogen fixation in a unicellular Synechocystis lineage Nitrogen fixation plays a central role in primary productivity and nitrogen cycling in aquatic ecosystems, yet its distribution among cyanobacterial lineages remains incompletely understood. Biological nitrogen fixation is energetically costly and highly oxygen-sensitive, imposing constraints in oxygenic phototrophs. The unicellular cyanobacterial genus Synechocystis has long been regarded as strictly non-diazotrophic. Here, we report that Synechocystis sp. LKSZ1 possesses a functional nitrogen fixation system. Comparative genomics revealed that LKSZ1 is distinct from other Synechocystis strains and uniquely harbors a complete nif gene. Phylogenetic and structural analyses indicate acquisition via horizontal gene transfer from filamentous cyanobacteria. Physiological assays demonstrated photoautotrophic growth under nitrogen-depleted conditions and nitrogenase activity under microoxic to anaerobic conditions. Disruption of nifK abolished both growth and activity. These findings show that ecological nitrogen limitation and host compatibility can enable functional integration of horizontally acquired nitrogen fixation. ### Competing Interest Statement The authors have declared no competing interest. MEXT/JSPS KAKENHI, 22K06276 COI-NEXT, JPMJPF2102

Horizontal gene transfer drives the emergence of nitrogen fixation in a unicellular Synechocystis lineage | bioRxiv www.biorxiv.org/content/10.64898/2026.04...

You need to make AI guidelines for your lab Here's why you should, and how to start

“first drafts of Results, Discussion, and Introduction should be the trainee’s own work. AI can help with grammar…tightening prose…critiquing the logic of an argument you’ve already made. But the hard part of forming the argument needs to be yours.’ blekhman.substack.com/p/you-need-t...

Figure 1 shows the conceptual workflow of the algorithm. It first loads the configuration file and the input data of one or multiple binned metagenomes, yet evaluates each bin individually. It then iteratively processes each candidate bin in the input, going through the refinement tasks, potentially multiple times. The refinement either stops when the last step or a preset stop task have been reached or an unrecoverable error has been encountered. The algorithm tasks can be configured individually.

🤯 Manual MAG refinement? Still doing it by hand??

We’ve been there... You could just leave those messy, ill-assigned contigs/scaffolds in your data for NCBI to pick up during your submission…

…OR you could add itBins, our new automated MAG refiner by @jmk-ude.bsky.social, to your pipeline!! 🔥

Myloasm, our long-read metagenome assembler, is now published! w/ @mgmarin.bsky.social and @lh3lh3.bsky.social

Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback.

rdcu.be/famFj

Many journals require data and code sharing. Yet code is still rarely shared and datasets are often hard to reuse.

Our new paper introduces the @sortee.bsky.social guidelines for data & code quality control in ecology & evolution, developed by 26 experienced data editors.

📄 doi.org/10.24072/pcj...

What is the question? - Genome Biology Genome Biology -

A great read! link.springer.com/article/10.1...

Stop Citing AI A response to ‘But ChatGPT said…’

"But ChatGPT said..." stopcitingai.com

Scihub stopped uploading new articles. SciDB is a continuing effort which has the entire scihub collection AND new papers.

annas-archive.org/scidb

HMMER is the bedrock of genomic annotation globally, and now its funding is terminated for no reason.

@cryptogenomicon.bsky.social is now on bsky:

Our group photo ❤️. Big thanks to all participants for their contributions.

" (...) it is very hard to interpret big data in ecology in meaningful ways if you do not know anything about who the organisms are and what they do in the environment."

(Jennifer Powers, A place for natural history in the 21st century, Biotropica. 2025;57:e13364. doi.org/10.1111/btp....)

I am guilty of this 😅
Are most 16S primers (I use 515-926) able to capture archaeal diversity? I, for no good reason, thought they were not