Britt Abrahamson

I think this paper will be a game-changer for studying microbiome function. Matthew Schmitt and I found that a simple neural network, when trained on paired sequencing and functional data, can infer functional group structure directly from data. Pls read our preprint! www.biorxiv.org/content/10.6...

Biological nitrite oxidation in the presence of MnO2 under anoxic conditions Biological nitrogen transformation driven by manganese redox reactions in anaerobic environments is receiving increasing attention. In particular, mic…

Biological nitrite oxidation in the presence of MnO2 under anoxic conditions
www.sciencedirect.com/science/arti...

Ocean warming enhances iron use efficiencies of marine ammonia-oxidizing archaea #USC_MEB www.pnas.org/doi/abs/10.1... #jcampubs

The molecular mechanism and activity of Kuenenia stuttgartiensis #hydrazine synthase #microbiology @ribesresearch.bsky.social @robertsjansen.bsky.social et al www.biorxiv.org/content/10.6....

Kinetic Plasticity of Nitrite-Oxidizing Bacteria Containing Cytoplasmic Nitrite Oxidoreductase academic.oup.com/ismej/advanc... #jcampubs

A novel North Sea ammonia-oxidizing archaeon Nitrosarchaeum marinum leverages a high abundance of transport systems to grow over a wide salinity range Isolation and characterization of a novel North Sea ammonia oxidizing archaeon, Nitrosarchaeum marinum T12, reveals an adaptation to a broad salinity under

novel North Sea ammonia-oxidizing archaeon Nitrosarchaeum marinum leverages a high abundance of transport systems to grow over a wide salinity range | FEMS Microbiology Ecology | Oxford Academic https://academic.oup.com/femsec/article/102/3/fiag013/8499647?login=false

Quantitative metagenomics using a portable protocol | Applied and Environmental Microbiology Rapid and real-time monitoring of microbial communities is critical for a vast array of applications in environmental microbiology and biotechnology. While recent developments in portable sequencing t...

Quantitative metagenomics using a portable protocol | Applied Environmental Microbiology

Article: journals.asm.org/doi/10.1128/...
GitHub: github.com/Harper19/wf-...

See our newest manuscript dissecting emergent functions in a multispecies biofilm (metabolite cross-feeding, siderophore induction and cross-species utilization) that translates to plant growth promotion
Great work by @jiyuxie.bsky.social and Xinli Sun
www.biorxiv.org/content/10.6...

Elevated Temperature Simulating Heatwaves Restructures Active Nitrifying Communities and Associated Viruses in Tidal Flats and Agricultural Soils Abstract. Global heatwave intensification under climate change will impact the nitrogen cycle, yet its effect on active nitrifier groups or their interacti

Elevated Temperature Simulating Heatwaves Restructures Active Nitrifying Communities and Associated Viruses in Tidal Flats and Agricultural Soils | @isme-microbes.bsky.social

doi.org/10.1093/isme...

Beyond thrilled to share that our study has been published!
This project encompasses years of work, including my thesis research on Asgard archaea in the @archaeal.bsky.social lab at @utmsi.bsky.social and
@texasscience.bsky.social!!!
#MicroSky #ArchaeaSky 1/12

Finally out in @nature.com: a new piece of the puzzle of how complex life evolved. Lead by @archaeal.bsky.social & @katyappler.bsky.social. Great collab with @greening.bsky.social and @kassipan.bsky.social. More pieces to follow soon! www.nature.com/articles/s41...

Excited to see @cdiener.com's community-scale metabolic models tools getting a shout-out in this @natbiotech.nature.com editorial.

Specifically, mentioning Nick Quinn-Bohmann's recent paper on predicting personalized SCFA production (for precision nutrition): www.nature.com/articles/s41...

Coincidental and exciting! Anaerobic methanotrophic archaea (ANME) do like carbon monoxide - two independent studies showcasing CO metabolism across freshwater and marine ANME (ANME-2d and -2b).

ANME-2d: doi.org/10.1101/2025... (Welte lab)
ANME-2b: reposted (Orphan lab)

Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning - Nature Biotechnology PlasMAAG uses cross-sample information to improve plasmid reconstruction from metagenomic samples.

Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... #jcampubs

Growth of methanogenic culture under different stress conditions

New preprint: “Proteomic stress response by a novel methanogen enriched from the Great Salt Lake”, first author William Christian. TLDR: we enriched a novel, euryarchaeotal, methyl-dismutating methanogen that grows at 16% salinity. biorxiv.org/content/10.64898/2026.01.29.702513v2 🧵 🦠 #microsky

Incredibly helpful annotation tool!

Thank you @pierresimongarcia.bsky.social
@sgribaldo.bsky.social @archaeal.bsky.social @valdeanda.bsky.social and G. Borrel!

Evolution and diversity of oxidoreductases involved in redox balance and energy conservation - Nature Ecology & Evolution HORBEC are protein complexes involved in the regulation of redox balance and energy conservation. The authors develop a bioinformatic tool for HORBEC annotation in bacterial and archaeal genomes and r...

Passioned by #bioenergetics? Do not miss our new article on the evolutionary history of oxidoreductases with G. Borrel and @sgribaldo.bsky.social @archaeal.bsky.social @valdeanda.bsky.social @pasteur.fr @cnrs.fr @cnrsbiologie.bsky.social @natecoevo.nature.com (www.nature.com/articles/s41...).

Proteomic stress response by a novel methanogen enriched from the Great Salt Lake Methanogenic archaea affect the climate through their production of the greenhouse gas, methane. However, it is unclear how a changing climate and other anthropogenic influences impact methanogen physiology and consequent methane flux. The Great Salt Lake (GSL) is an environment that has been heavily impacted by human activity; more than doubling its salt concentration since the last methanogen was cultured from it in 1985. In this study, we enriched a novel methanogen, for which we propose the name Candidatus Methanohalophilus hillemani, from the GSL at a time when its salinity reached a historical high. Interestingly, Ca. M. hillemani does not increase expression of energy-conservation or osmo-tolerance proteins when challenged with salinity or oxygen. In contrast, Ca. M. hillemani prioritizes trace metal uptake and immune functions in response to the presence of the sulfate-reducing bacterium Desulfovermiculus . 16S rRNA gene amplicon data from GSL shore soils with extremely high and variable methane flux indicated the presence of Ca. M. hillemani. Our results show that Ca. M. hillemani is active when challenged with environmental stressors and contributes to the methane flux emanating from the GSL.

Proteomic stress response by a novel methanogen enriched from the Great Salt Lake | bioRxiv https://www.biorxiv.org/content/10.64898/2026.01.29.702513v1?rss=1

Microbial nitrogen removal and recycling in the redox transition zone of a meromictic lake and its coupling to sulfur cycling | doi.org/10.1002/lno....

Ammonia oxidizers offset acidification stress via adaptive substrate affinity in aquatic ecosystems www.nature.com/articles/s41... #jcampubs 🌊

Microbial BioRemediation Database: A Comprehensive Database of Genes Involved in Microbial Bioremediation Processes We present the Microbial BioRemediation (MBR) database, a curated resource of over 642,000 bacterial protein sequences involved in the degradation of 564 environmental pollutants. By enabling rapid f...

Microbial BioRemediation Database: A Comprehensive Database of Genes Involved in Microbial Bioremediation Processes onlinelibrary.wiley.com/doi/10.1002/... #jcampubs

Genus-specific remodeling of carbon and energy metabolism facilitates acetoclastic methanogenesis in Methanosarcina spp. and Methanothrix spp.
#methanogens #methane #archaea #MicroSky #ArchaeaSky
@asm.org
journals.asm.org/doi/full/10....

Bacterial necromass recycling promotes diversity maintenance in bacterial communities via resource partitioning - Nature Ecology & Evolution In this study, the authors conduct experiments involving 276 soil-derived microcosms to reveal that the ecological process of necromass recycling promotes diversity maintenance in bacterial communitie...

Bacterial necromass recycling promotes diversity maintenance in bacterial communities via resource partitioning www.nature.com/articles/s41... #jcampubs

This study shows that #acidification increases substrate affinity in ammonia-oxidizing #microbes, partly offsetting reduced ammonia availability. Stronger responses in #archaea than #bacteria explain contrasting #ecosystem reactions.

Ammonia oxidizers offset acidification stress via adaptive substrate affinity in aquatic ecosystems | Nature Communications https://www.nature.com/articles/s41467-026-68747-z

Always exciting to see a manuscript about NOB physiology and their interactions with ammonia oxidizers!

doi.org/10.1093/isme...

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 ...

Resurrected nitrogenases recapitulate canonical N-isotope biosignatures over two billion years
#nitrogen #evolution
@natcomms.nature.com
www.nature.com/articles/s41...

Physiology, functional genomics and proteomics of Verruconatronum alginivorum gen. nov., sp. nov., a first haloalkaliphilic representative of the phylum Verrucomicrobiota from soda habitats Despite the successful cultivation of many microbes from rich bacterial communities inhabiting alkaline soda lakes, members of the bacterial phylum Verrucomicrobiota have so far been detected only through metagenomics. Here, we used alginate as a selective substrate to enrich and isolate two strains of haloalkaliphilic Verrucomicrobiota. The isolates share identical 16S rRNA gene sequences representing a new genus lineage, and, together with other metagenome assembled genomes, a new family within Opitutales. Cells of strains AB-alg1T (from soda lakes) and AB-alg4 (from soda solonchak soils) are small and motile cocci forming submerged colonies in soft alginate agar. They are saccharolytic heterotrophs growing aerobically on polysaccharides (alginate, starch and inulin) and sugars (glucose, fructose, mannose, sucrose, melezitose, maltose and cellobiose). They also grow anaerobically by fermentation of alginate and D-mannose and by coupling incomplete denitrification to oxidation of alginate. Both isolates are obligately alkaliphilic and moderately salt-tolerant. The dominant membrane phospholipids include phosphatidylcholines and diphosphatidylglycerols (cardiolipins). The genome of AB-alg1T features polysaccharide lyases of the PL6, 7, 15, 17, 38, and 39 families for depolymerization of alginate. Based on distinct phenotype and phylogeny, we propose classification of strains AB-alg1T (JCM 35393T=UQM 41574T) and AB-alg4 as Verruconatronum alginivorum gen. nov., sp. nov. within a new family Verruconatronumaceae.

Physiology, functional genomics and proteomics of Verruconatronum alginivorum gen. nov., sp. nov., a first haloalkaliphilic representative of the phylum Verrucomicrobiota from soda habitats | bioRxiv https://www.biorxiv.org/content/10.64898/2026.01.22.701064v1?rss=1

Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation - Nature Microbiology Without key cell cycle control genes, SAR11 cells experience aneuploidy and growth inhibition when exposed to changes in nutrients, carbon sources or temperature stress, a vulnerability that may repre...

Our latest. Led by the very talented @ahoiching.bsky.social

Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation www.nature.com/articles/s41... #jcampubs 🌊