Jackson Tsuji
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jacksontsuji.bsky.social
Jackson Tsuji
@jacksontsuji.bsky.social
Microbial ecologist exploring life in Earth's oceans & aquatic ecosystems from prehistoric to present-day 🔬🦠 Special focus on photosynthesis and the iron cycle ☀️⚡🪨 Young Research Fellow at JAMSTEC, Japan
Reposted by Jackson Tsuji
Diving through the purple sulfur bacteria layer of Fayetteville Green Lake with our ROV last month. This is the most intense density of PSB that I've seen in many years!
November 8, 2025 at 6:30 PM
Reposted by Jackson Tsuji
Metabolic diversity of the Ferrovales and potential contributions to iron oxidation www.biorxiv.org/content/10.1... #jcampubs
November 4, 2025 at 1:53 PM
Reposted by Jackson Tsuji
Metabolic controls on the carbon isotope fractionations of bacterial fermentation www.pnas.org/doi/abs/10.1... #jcampubs
Metabolic controls on the carbon isotope fractionations of bacterial fermentation | PNAS
Microbial fermentation facilitates the initial breakdown of organic matter into small molecules and is thought to be the rate-limiting step of anox...
www.pnas.org
October 10, 2025 at 9:19 PM
Reposted by Jackson Tsuji
Have you ever looked at the night sky and wondered if there’s a chlorophyll f in the reaction centre of Photosystem I from far-red light adapted cyanobacteria? 🦠

Well, we did (don’t judge) and the work that followed is now out as a First Release in @science.org

www.science.org/doi/10.1126/...
Locating the missing chlorophylls f in far-red photosystem I
The discovery of chlorophyll f-containing photosystems, with their long-wavelength photochemistry, represented a distinct, low-energy paradigm for oxygenic photosynthesis. Structural studies on chloro...
www.science.org
October 11, 2025 at 10:37 AM
Reposted by Jackson Tsuji
Diverse bacteriohemerythrin genes of Methylomonas denitrificans FJG1 provide insight into the survival and activity of methanotrophs in low oxygen ecosystems journals.asm.org/doi/full/10.... #jcampubs
September 26, 2025 at 2:43 PM
Reposted by Jackson Tsuji
Our paper reporting a new light-harvesting system in H⁺ & Cl⁻-pumping rhodopsins of marine bacteria is now out in Nature Microbiology! So excited!!!
Key discoveries (using isolated cultures from the research cruise Mirai MR10-01 — personally, this is super exciting🔥):
www.nature.com/articles/s41...
Carotenoids bind rhodopsins and act as photocycle-accelerating pigments in marine Bacteroidota - Nature Microbiology
In marine bacteria, carotenoids enhance rhodopsin function by acting as light-harvesting antennae and photocycle-accelerating pigments, a dual mechanism that enhances light energy capture and expands ...
www.nature.com
September 4, 2025 at 11:27 AM
Reposted by Jackson Tsuji
andez, et al.: Single-cell metabolic flux analysis reveals coexisting optimal sub-groups, cross-feeding, and mixotrophy in a cyanobacterial population https://arxiv.org/abs/2506.05916 https://arxiv.org/pdf/2506.05916 https://arxiv.org/html/2506.05916
June 9, 2025 at 6:16 AM
Reposted by Jackson Tsuji
I'm happy to announce the latest release of the GlobDB, available at globdb.org.

The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.
home | GlobDB
globdb.org
June 10, 2025 at 11:20 AM
Reposted by Jackson Tsuji
🧪Nature, about open-minded science:
“In research, planning is indispensable, but detailed plans are useless”
Contrary to popular belief, what is important in science is as much its spirit as its product: it is as much the openmindedness, the primacy of criticism, the submission to the unforeseen, however upsetting, as the result, however new that may be. – Francois Jacob
www.nature.com/articles/s41...
April 14, 2025 at 3:23 PM
Reposted by Jackson Tsuji
This was another good paleobiology read

Cyanobacteria developed phycobilisomes to absorb green light 2.4B yrs ago, as iron-rich Archaean oceans filtered sunlight. Phycoerythrobilin gave them a competitive edge, fueling oxygenation/biodiversity. Green light adaptation may mark life on exoplanets
🧪⚒️
Archaean green-light environments drove the evolution of cyanobacteria’s light-harvesting system - Nature Ecology & Evolution
Cyanobacteria use both chlorophylls and phycobilins to absorb light energy, and authors here use cultivation experiments, numerical simulations and protein phylogenetics to argue that cyanobacteria ev...
www.nature.com
April 13, 2025 at 5:47 PM
Reposted by Jackson Tsuji
Reposted by Jackson Tsuji
Not really my announcement to make--I am but a lesser co-author--but IQ-TREE 3 has just been released!

(Most credit to Minh Bui and @roblanfear.bsky.social and their labs)

ecoevorxiv.org/repository/v...
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models
ecoevorxiv.org
April 10, 2025 at 2:13 PM
Reposted by Jackson Tsuji
The halophilic #archaea Halorhabdus sp. and Haloferax volcanii, along with its DPANN ectosymbiont Ca. Nanohalococcus occultus, join forces to degrade xylan.
@cellpress.bsky.social
#microbiology #extreme #science
www.cell.com/iscience/ful...
March 5, 2025 at 11:55 AM
Reposted by Jackson Tsuji
New preprint is out!
We investigate how well you can call variants directly from genome assemblies compared to traditional read-based variant calling.

Read it here: www.biorxiv.org/content/10.1...
Data & code: github.com/rrwick/Are-r...
(1/8)
Are reads required? High-precision variant calling from bacterial genome assemblies
Accurate nucleotide variant calling is essential in microbial genomics, particularly for outbreak tracking and phylogenetics. This study evaluates variant calls derived from genome assemblies compared...
www.biorxiv.org
March 3, 2025 at 3:24 AM
Reposted by Jackson Tsuji
New isolates from eukaryote's closest archaeal relative: ‘Hodarchaeales’!! Syntrophic microaerotolerant peptide-degrading anaerobic archaea w/ simple cell structure & protrusions. Features conserved across the phylum provide new insight into our ancestor’s biology!
www.biorxiv.org/content/10.1...
Eukaryotes' closest relatives are internally simple syntrophic archaea
Eukaryotes are theorized to have originated from an archaeal phylum Promethearchaeota (formerly 'Asgard' archaea)1,2. The first cultured representatives revealed valuable insight3,4 but are distantly ...
www.biorxiv.org
February 27, 2025 at 4:25 AM
Reposted by Jackson Tsuji
Isolated in just 3 years! (previously, 12 years). We obtained two strains from 'Hodarchaeales', proposed to be closest to our archaeal ancestor. Our analysis suggests the ancestor was an anaerobic, syntrophic, peptidotrophic, archaeon with a simple intracellular structure and possible aerotolerance.
Eukaryotes' closest relatives are internally simple syntrophic archaea
Eukaryotes are theorized to have originated from an archaeal phylum Promethearchaeota (formerly 'Asgard' archaea)1,2. The first cultured representatives revealed valuable insight3,4 but are distantly ...
www.biorxiv.org
February 27, 2025 at 3:58 AM
Reposted by Jackson Tsuji
Excited to share that our paper on locus visualisation tool LoVis4u is out! Entirely driven by fantastic PhD student Artyom Egorov @egorov.bsky.social academic.oup.com/nargab/artic...
LoVis4u: a locus visualization tool for comparative genomics and coverage profiles
Abstract. Comparative genomic analysis often involves visualization of alignments of genomic loci. While several software tools are available for this task
academic.oup.com
February 25, 2025 at 7:27 AM
Reposted by Jackson Tsuji
Our new paper highlights aerobic methane production from methylphosphonates by abundant Methylotenera in Pleistocene era groundwaters. Congrats to @shengjieli.bsky.social, colleagues, and partners at AEPA! academic.oup.com/ismej/advanc...
Proteomic evidence for aerobic methane production in groundwater by methylotrophic Methylotenera
Abstract. Members of Methylotenera are signature denitrifiers and methylotrophs commonly found together with methanotrophic bacteria in lakes and freshwate
academic.oup.com
February 13, 2025 at 6:20 PM
Reposted by Jackson Tsuji
New bacterial phylum Minisyncoccota (formerly Ca. Patescibacteria or CPR) in the kingdom Bacillati.

Congratulations, Kuroda-san, Narihiro-san, and Nobu (@masarunobu.bsky.social)!

www.microbiologyresearch.org/content/jour...
Minisyncoccus archaeiphilus gen. nov., sp. nov., a mesophilic, obligate parasitic bacterium and proposal of Minisyncoccaceae fam. nov., Minisyncoccales ord. nov., Minisyncoccia class. nov. and Minisyn...
In the domain Bacteria, one of the largest, most diverse and environmentally ubiquitous phylogenetic groups, Candidatus Patescibacteria (also known as candidate phyla radiation/CPR), remains poorly ch...
www.microbiologyresearch.org
February 11, 2025 at 11:03 PM
Reposted by Jackson Tsuji
Why did an engineer become a researcher in biological evolution? My esteemed research partner, colleague, and friend, Masaru K. Nobu, is sharing some side stories about strain MK-D1 research.
www.nature.com/articles/s41...
Engineering history with Asgard archaea of the kingdom Promethearchaeati - Nature Microbiology
Multiple histories converge in Masaru Nobu’s story of culturing an archaeon closely related to us eukaryotes.
www.nature.com
November 30, 2024 at 12:30 AM
Reposted by Jackson Tsuji
An opportunity to work at an amazing place with amazing people! 🦠

“GeneLab is seeking a #Bioinformatics #ProgramDeveloper to drive research with #omics data from space biology experiments. Develop workflows and analyze data critical to human space exploration.

🔗 Apply now: tinyurl.com/8psb8uwn
December 18, 2024 at 10:18 AM
Reposted by Jackson Tsuji
MMseqs2 Release 16 Highlights: GPU-accelerated search📄, ORF or new 6-frame translated search modes, contig taxonomy always keeps the longest ORF, bug fixes (reduced memory and higher sensitivity) and relicensed as MIT
📄 biorxiv.org/content/10.1...
💾 mmseqs.com and 🐍Bioconda 🖥️🧬🧶
November 27, 2024 at 9:08 AM
Reposted by Jackson Tsuji
I apologise for HydDB being down. Aarhus University decided to stop hosting it at quite short notice. However, we plan to relaunch first thing next year and are in the midst of creating a much-needed HydDB 2.0. HydDB 1.0 is good for hydrogenase information, but our HMMs best for classification. 1/2
December 19, 2024 at 6:15 AM
Reposted by Jackson Tsuji
Phylogenetics methods announcement: piqtree is out! It exposes selected IQ-TREE2 capabilities within Python, using the cogent3 library as the interface, better enabling pipelines. piqtree is an addition to, not a replacement of, IQ-TREE2.
Full announcement at github.com/iqtree/piqtr...
piqtree: IQ-TREE2 meets Python via cogent3 · iqtree piqtree · Discussion #145
The developers of IQ-TREE2 and cogent3 have joined forces to bring the power of IQ-TREE2 to Python users as piqtree. piqtree exposes selected IQ-TREE2 capabilities within Python, using the cogent3 ...
github.com
December 19, 2024 at 3:49 PM