Natsuko Hamamura

Chromosomal capture of beneficial genes drives plasmids towards ecological redundancy Abstract. Plasmids are a ubiquitous feature of bacterial genomes, but the forces driving genes and phenotypes to become associated with plasmids are poorly

Chromosomal capture of beneficial genes drives plasmids towards ecological redundancy | The ISME Journal | Oxford Academic https://academic.oup.com/ismej/advance-article/doi/10.1093/ismejo/wraf091/8128477?rss=1&login=false

Hunting extreme microbes that redefine the limits of life An adventurous survey of inhospitable habitats unearths extraordinary organisms that pose challenging research questions.

Hunting extreme microbes that redefine the limits of life

book by @karenlloyd.bsky.social #usc_earth #usc_meb
www.nature.com/articles/d41...

Bacterial nitrite production oxidizes Fe(II) bioremediating acidic abandoned coal mine drainage journals.asm.org/doi/full/10.... #jcampubs

Enrichment and characterization of anaerobic ammonium oxidation coupled with iron reduction (Feammox) by anaerobic digestion and conventional activated sludges Anaerobic ammonium oxidation coupled to iron reduction (Feammox) plays a key role in nitrogen cycling, yet its potential for wastewater treatment rema…

Enrichment and characterization of anaerobic ammonium oxidation coupled with #iron reduction ( #Feammox ) by anaerobic digestion and conventional activated sludges #anammoxhttps://www.sciencedirect.com/science/article/pii/S2213343725013351

A geological timescale for bacterial evolution and oxygen adaptation Microbial life has dominated Earth’s history but left a sparse fossil record, greatly hindering our understanding of evolution in deep time. However, bacterial metabolism has left signatures in the ge...

A geological timescale for bacterial evolution and oxygen adaptation www.science.org/doi/abs/10.1... #jcampubs

AI for research: the ultimate guide to choosing the right tool Curious about using artificial intelligence to boost your research? Here are the programs you shouldn’t miss.

AI for research: the ultimate guide to choosing the right tool www.nature.com/articles/d41...

Extracellular electron transfer proteins contribute to reduction of ferric minerals by Geobacter biofilms journals.asm.org/doi/full/10.... #jcampubs

Most bacterial gene families are biased toward specific chromosomal positions The arrangement of genes along bacterial chromosomes influences their expression through growth rate–dependent gene copy number changes during DNA replication. Although translation- and transcription-...

Most bacterial gene families are biased toward specific chromosomal positions www.science.org/doi/abs/10.1... #jcampubs

Credit: Margot Riggi (@margotriggi.bsky.social), Max-Planck Institute of Biochemistry (@mpibiochem.bsky.social)

Asgard archaea have actin - but what about microtubules? Where do they come from? 🧐 Our new paper www.cell.com/cell/fulltex... by @xujwet.bsky.social & @florianwollweber.bsky.social, in collaboration with the Schleper & Wieczorek labs, describes tiny Asgard microtubules! #TeamTomo #ArchaeaSky 1/6

Nitrate-driven dark oxygen production by diverse deep-sea microorganisms To date, only three biotic pathways for light-independent oxygen (i.e. dark oxygen) production: chlorate dismutation, nitric oxide dismutation, and methanobactin-dependent lysis of water. Oxygen has b...

Just noticed this preprint about #dark_oxygen production by nitrate reducing bacteria. I thought the case of the Deferribacterota is pretty convincing. For the orther bacteria, more work needs to be done. If this is true, dark oxygen turns out te be very prevalent! www.biorxiv.org/content/10.1...

Enhanced Ammonium Oxidation and Iron Cycle of Feammox Under Micro-Oxygen Condition Autotrophic anaerobic ammonium oxidation coupled to Fe(III) reduction (Feammox) is a promising technology for treating low C/N wastewater. However, Fe…

Enhanced Ammonium Oxidation and Iron Cycle of #Feammox Under Micro-Oxygen Condition
www.sciencedirect.com/science/arti...

Visited Río Clarillo National Park in Chile with our collaborator Nacho Iganacio’a group. Hope our set up works! Thank you for a great team effort yesterday!

Meet the Microbiologist: Manuel Martinez Garcia, Ph.D., a professor of microbiology at the University of Alicante in Spain, analyzes genomic signatures of microorganisms frozen in ice cores collected from the Filchner–Ronne Ice Shelf in the Antarctic. asm.org/Podcasts/MTM...

Large Filamentous Bacteria Isolated From Sulphidic Sediments Reveal Novel Species and Distinct Energy and Defence Mechanisms for Survival In this study, we used micromanipulation and omics to analyse 15 large filamentous bacteria collected from sulphidic sediments off Chile. We discovered novel species from various phyla, and diverse m...

Former PhD student Alexis Fonseca has just published his paper about filamentous uncultivated bacteria from sediment off the coast of Chile: dx.doi.org/10.1111/1462... @larspeternielsen.bsky.social

Cartoon display of the bioenergetic scenario for Huc using either bd-I oxidase or bcc-aa oxidase as pmf-generating unit, driving ATP synthesis by the F1F o-ATP synthase.

Hydrogenase-driven ATP synthesis from air
www.biorxiv.org/content/10.1...

New work from us where we put the Huc hydrogenase to work to see if it can generate a proton motive force. It can!
cc: @ashleighkropp.bsky.social @rhyswg.bsky.social @greening.bsky.social

The Bacterial Antimonite Oxidase AnoA: Unexpected Diversity and Environmental Widespread Occurrence The bacterial antimonite oxidase AnoA has been identified in various taxa of the Pseudomonadota and Actinomycetota. The anoA gene was suggested to be mainly inherited vertically and was revealed to b....

The Bacterial Antimonite Oxidase AnoA: Unexpected Diversity and Environmental Widespread Occurrence enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs

Unusual ‘soda lakes’ may have kick-started life on Earth by concentrating key compounds Phosphorus leached from volcanic rocks in warm waters could have triggered reactions needed to launch biochemistry

Nice perspective in Science summing up recent advances on the importance of phosphate to the origin of life and featuring my lab's favorite field sites: Lakes Goodenough and Last Chance... (photo is Mono Lake though) www.science.org/content/arti...

Should I stay or should I go: transmission trade-offs in phages and plasmids Mobile genetic elements (MGEs), like temperate bacteriophages and conjugative plasmids, are major vectors of virulence and antibiotic resistance in bacterial populations. For reproductive success, MGE...

Should I stay or should I go: transmission trade-offs in phages and plasmids

@cp-trendsmicrobiol.bsky.social Opinion by @jhuisman.bsky.social, Andrina Bernhard and
@claudiaigler.bsky.social

www.cell.com/trends/micro...

🦠 #OilReservoirs harbor unseen microbial worlds! 🌍🔬 @alexjprobst.bsky.social lab study of a pristine reservoir reveals bacteria & fungi breaking down #hydrocarbons—and a global network of shared genes. But the mystery of plasmid distribution pattern remains! 🧬 #Biodegradation
https://buff.ly/4gwdYUJ

Less than 2-weeks until the deadline for #Goldschmidt2025 session and workshop proposals. Help build the #geochemistry science program, more info⬇️

Distribution of early-branching Cyanobacteriia and the potential habitats that gave rise to the earliest oxygenic phototrophs journals.asm.org/doi/full/10.... #jcampubs

Methanol transfer supports metabolic syntrophy between bacteria and archaea - Nature Zhaonella formicivorans produces methanol, for a novel syntrophic interaction, without requiring methylated compounds as an input.

Methanol transfer supports metabolic syntrophy between bacteria and archaea www.nature.com/articles/s41... #jcampubs

Out now, a comprehensive guide to metagenomics -- from sample collection to data analysis. This primer covers best practices, challenges, and applications in health, agriculture & environment. A roadmap for studying microbial communities 👇

www.nature.com/articles/s43...

Single-cell phenotyping of extracellular electron transfer via microdroplet encapsulation journals.asm.org/doi/full/10.... #jcampubs

Since I hope to find things to "spark microbial joy," what could be better than scaling up a microbial fuel cell? Maybe from these high sulfide mud seeps in Puget Sound. Right, @pgirguis.bsky.social ??

Introducing mGems, mBio’s new review type | mBio journals.asm.org/doi/full/10....

Exciting new msystems webinar

E. coli prepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrients It is widely believed that due to nutrient limitations in natural environments, bacteria spend most of their life in non-growing states. However, very little is known about how bacteria change their p...

What do bacterial cells do when they run out of nutrients? Although most bacterial studies focus on cells in exponentially growing states, in the wild bacteria likely spend most of their time slowly starving to death. 1/n
www.biorxiv.org/content/10.1...

A global comparison of surface and subsurface microbiomes reveals large-scale biodiversity gradients, and a marine-terrestrial divide The microbiomes of Earth’s surface and subsurface environments are different in composition, but similar in diversity.

Deep life is astonishing and diverse, and we have so much more to learn!

So happy that this study is out. Big thanks to co-first author @bellahda.bsky.social and all the collaborators!

www.science.org/doi/10.1126/...
@science.org @mblscience.bsky.social @simonsfoundation.org #deeplife #microbiome