New preprint on the limits of detecting higher-order interactions in microbial communities.
www.biorxiv.org/content/10.6...
We find that the dominance of additive and pairwise interactions on community function may not reflect biological simplicity, but fundamental limits of statistical detection.
Reposting for the microbial evolution community
#microSky #evoSky #mevoSky
Once again, selection has led to interesting outcomes that challenge our understanding of metabolism and adaptation to stressful substrates. In my new lab at WCU, I am currently investigating some of the biochemistry of this novel aromatic pathway and am open to collaborations!
The mutations led to counterintuitive trade-offs and "trade-ups" between VA and PCA metabolism. And a loss of fitness on the native organic acid succinate. Showing that antigonistic pleiotropy within mutations in the TCA cycle and substrate transport.
As always, evolution provided very interesting results: When grown on aromatics the ancestor produced a large amount of PHB even under low C:N ratios, most likely due to an overflow of C2 intermediates. Evolved strains all reduced PHB accumulation using different mutations to relieve this overflow.
We set off to see how a naive Methylobacterium could adapt to a novel aromatic catabolic pathway. @nkrumahgrant.bsky.social started an evo experiment growing an engineered Methylo on vanillate and protocatechuate. The strains evolved for ~72 generations, showing a major improvement in growth.
Members of the genus Methylobacterium have recently been shown to consume methoxylated aromatics produced from lignin. With Methylobacterium's natural C1 metabolism, the toxic formaldhyde produced is not a limiting factor as seen in other species. See Koko's paper journals.asm.org/doi/full/10....
Proud to announce a new preprint from my Post Doc with Chris Marx. Great collaboration with Akorede Seriki, @nkrumahgrant.bsky.social, and others.
Evolutionary Integration of a Foreign Aromatic Catabolic Pathway Drives Metabolic Trade-offs in M. extorquens
www.biorxiv.org/content/10.6...
A new preprint with Matthew Schmitt, @kiseokmicro.bsky.social and Vincenzo Vitelli makes a huge step forward in learning functional groups of components in complex biological systems. It's dimension reduction that speaks to biological function. www.biorxiv.org/content/10.6...
Why are most metabolites barely detectable in wild-type cells — biology or technology?
A new study from the Link lab shows it's biology: cells actively maintain minimal metabolite pools to avoid unwanted effects.
www.cmfi.uni-tuebingen.de/en/news-even...
Excited to share this new Preprint from our lab led by PhD Candidate Carl Stone (defending Tuesday).
Here we present a framework for longitudinal rbTn-Seq and apply it to the Microbial extended growth curve to resolve the fitness seascape through growth, death, and long-term stationary phase!
XoxF and the Calvin-Benson cycle mediate lanthanide-dependent growth on methanol in Bradyrhizobium and Sinorhizobium journals.asm.org/doi/10.1128/... #jcampubs
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...).
Glad to have this out in mSystems! We emphasize how this work is informative of the extent that temporal patterns can be gleaned given ~1d sampling. The Q of how measurement shapes the dynamics we can observe is an area of active interest, so feel free to reach out!
doi.org/10.1128/msys...
Registration is open for the inaugural GRC conference in the Function of Evolving Systems. Aug 9-14, 2026, Waterville Valley. Truly stellar speaker lineup. Student/postdoc fellowships are available! Please come join us! www.grc.org/function-of-... @joybergelson.bsky.social
Happy to share my solo-authored Perspective "An Interpretation, Survey, and Outlook of Microbial Macroecology"! Making time these last few months to take stock of the patterns us microbial ecologists examine + models we invoke has been invaluable. Feedback welcome!
ecoevorxiv.org/repository/v...
"Take away college football tomorrow & watch college towns descend into chaos. But when they came for our pipettes & microscopes, almost nothing happened. "
New thoughts on the War on Science, 1 yr later, for @undark.org:
'How MAHA Exploits the Flaws of Modern Science '
undark.org/2026/01/28/o...
The Abreu lab at NYU is hiring another postdoc! We study microbial ecology and evolution, using yeast/bacteria microcosms, DNA barcoding for evolutionary lineage tracking, and simple mathematical modeling. Apply here: apply.interfolio.com/179949
In this week’s @science.org cover article, we discover tree bark is a hidden habitat for abundant, diverse, and specialized microbial life that actively regulate our climate 🦠. Bark isn't just an inert armor of tree but an active interface for climate and biodiversity
www.science.org/eprint/7H9PX...
Published in Nature today! Here, we sought to systematically ask how natural community's metabolism changes with the environment. A simple consumer-resource model can predict N-cycle metabolism (nitrate use) and, more importantly, the mechanism behind its change.
www.nature.com/articles/s41...
Pathways to sustainability: a quantitative comparison of
aerobic and anaerobic C1 bioconversion routes.
Via @woolston-lab.bsky.social
www.sciencedirect.com/science/arti...
I'm truly excited to announce our new publication in @nature.com unraveling a central picture of the Methyl-coenzyme M reductase (MCR) activation machinery and it's strong ATP dependency - kudos to @rnfr2d2.bsky.social for the fantastic illustration!
LINK: www.nature.com/articles/s41...
Bradyrhizobium diazoefficiens cultures display phenotypic heterogeneity academic.oup.com/ismecommun/a... #jcampubs
Controlled burn: interconnections between energy-spilling pathways and metabolic signaling in bacteria
#JBacteriol Mini Review by Nicolaus Jakowec and Steven Finkel
journals.asm.org/doi/10.1128/...
Excited about microbiomes and want to study them at the single-cell level? Join our team to pioneer research using microfluidics paired with automated timelapse microscopy. We're hiring motivated postdocs to push the boundaries of microbial ecology!
Apply now: apply.interfolio.com/165601
5 relative abundance plots arranged to have increasing compositional variability (variability across relative abundance samples, here vertical bars)
1/ Hey y'all, I'm excited to share my latest paper, which is out now in PNAS! We introduce FAVA, a statistical framework to measure compositional variability across microbiome samples. If you want to measure variability across a stacked bar plot, FAVA is for you! Paper: doi.org/10.1073/pnas...
Evolving a plant-beneficial bacterium in soil vs. nutrient-rich liquid culture has contrasting effects on in-soil fitness
i.e. Priestia megaterium [note: no plant experiment in paper]
#ApplEnvironMicrobiol by Laura Kaminsky et al from Terrence Bell
journals.asm.org/doi/full/10....
Glad to see Julia Vorholt as winner of the @novonesis.com #Biotechnology Prize 2025 for her research on the plant #microbiome — among other achievements (e.g. synthetic C1 assimilation). Amazing and inspiring colleague #WomenInScience @eth-dbiol.bsky.social
novonordiskfonden.dk/en/news/pion...
Sorghum aerial roots producing mucilage and hosting bacteria that fix nitrogen from the air
Our latest article on biological nitrogen fixation on the aerial roots of sorghum has been published in @plosbiology.org. We thank the @energygov.bsky.social for supporting this exciting project.
journals.plos.org/plosbiology/...
