Alex Alleman
@alexanderalleman.bsky.social
Assistant Professor, Western Colorado University. Interested in microbiology, metabolism, and community assembly.
Pinned
Led astray by 16S rRNA: phylogenomics reaffirms the monophyly of Methylobacterium and lack of support for Methylorubrum as a genus
Abstract. Although the 16S (and 18S) rRNA gene has been an essential tool in classifying prokaryotes, using a single locus to revise bacteria taxonomy can
academic.oup.com
Spread the word! Methylorubrum is no more! Thread below (1/4):
academic.oup.com/ismej/advanc...
academic.oup.com/ismej/advanc...
Reposted by Alex Alleman
XoxF and the Calvin-Benson cycle mediate lanthanide-dependent growth on methanol in Bradyrhizobium and Sinorhizobium journals.asm.org/doi/10.1128/... #jcampubs
XoxF and the Calvin-Benson cycle mediate lanthanide-dependent growth on methanol in Bradyrhizobium and Sinorhizobium | Applied and Environmental Microbiology
Nitrogen-fixing soil bacteria such as Bradyrhizobium and Sinorhizobium promote plant growth while reducing dependence on artificial, energy-intensive fertilizers.
Numerous studies have attempted to in...
journals.asm.org
February 4, 2026 at 8:10 PM
XoxF and the Calvin-Benson cycle mediate lanthanide-dependent growth on methanol in Bradyrhizobium and Sinorhizobium journals.asm.org/doi/10.1128/... #jcampubs
Reposted by Alex Alleman
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...).
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...
www.nature.com
February 3, 2026 at 10:52 AM
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...).
Reposted by Alex Alleman
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...
doi.org/10.1128/msys...
February 2, 2026 at 2:43 PM
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...
doi.org/10.1128/msys...
Reposted by Alex Alleman
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
www.grc.org
January 29, 2026 at 3:03 PM
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
Reposted by Alex Alleman
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...
ecoevorxiv.org/repository/v...
January 28, 2026 at 8:22 PM
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...
ecoevorxiv.org/repository/v...
Reposted by Alex Alleman
"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...
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...
How MAHA Exploits the Flaws of Modern Science
Opinion | The weaknesses in science’s processes have been weaponized against it. It’s time to confront those flaws and fix them.
undark.org
January 28, 2026 at 1:37 PM
"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...
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...
Reposted by Alex Alleman
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
Apply - Interfolio
{{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
January 20, 2026 at 5:07 PM
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
Reposted by Alex Alleman
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...
www.science.org/eprint/7H9PX...
Bark microbiota modulate climate-active gas fluxes in Australian forests
Recent studies suggest that microbes inhabit tree bark, yet little is known about their identities, functions, and environmental roles. Here we reveal, through gene-centric and genome-resolved metagen...
www.science.org
January 8, 2026 at 8:37 PM
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...
www.science.org/eprint/7H9PX...
Reposted by Alex Alleman
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...
www.nature.com/articles/s41...
Functional regimes define soil microbiome response to environmental change - Nature
Experimental perturbation of soil pH leads to a generalizable model of the soil microcosm comprising three functional regimes with distinct mechanisms linking environmental change to metabolite dynami...
www.nature.com
July 16, 2025 at 3:19 PM
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...
www.nature.com/articles/s41...
Reposted by Alex Alleman
Pathways to sustainability: a quantitative comparison of
aerobic and anaerobic C1 bioconversion routes.
Via @woolston-lab.bsky.social
www.sciencedirect.com/science/arti...
aerobic and anaerobic C1 bioconversion routes.
Via @woolston-lab.bsky.social
www.sciencedirect.com/science/arti...
Pathways to sustainability: a quantitative comparison of aerobic and anaerobic C1 bioconversion routes
One-carbon (C1) substrates are attractive feedstocks for biological upgrading as part of a circular, carbon-negative bioeconomy. Nature has evolved a …
www.sciencedirect.com
May 7, 2025 at 8:05 PM
Pathways to sustainability: a quantitative comparison of
aerobic and anaerobic C1 bioconversion routes.
Via @woolston-lab.bsky.social
www.sciencedirect.com/science/arti...
aerobic and anaerobic C1 bioconversion routes.
Via @woolston-lab.bsky.social
www.sciencedirect.com/science/arti...
Reposted by Alex Alleman
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...
LINK: www.nature.com/articles/s41...
April 16, 2025 at 4:20 PM
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...
LINK: www.nature.com/articles/s41...
Reposted by Alex Alleman
Bradyrhizobium diazoefficiens cultures display phenotypic heterogeneity academic.oup.com/ismecommun/a... #jcampubs
March 31, 2025 at 11:16 AM
Bradyrhizobium diazoefficiens cultures display phenotypic heterogeneity academic.oup.com/ismecommun/a... #jcampubs
Reposted by Alex Alleman
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
Apply now: apply.interfolio.com/165601
March 30, 2025 at 6:07 PM
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
Apply now: apply.interfolio.com/165601
Reposted by Alex Alleman
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/...
#JBacteriol Mini Review by Nicolaus Jakowec and Steven Finkel
journals.asm.org/doi/10.1128/...
March 31, 2025 at 8:51 PM
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/...
#JBacteriol Mini Review by Nicolaus Jakowec and Steven Finkel
journals.asm.org/doi/10.1128/...
Reposted by Alex Alleman
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...
March 14, 2025 at 8:46 PM
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...
Reposted by Alex Alleman
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....
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....
Evolving a plant-beneficial bacterium in soil vs. nutrient-rich liquid culture has contrasting effects on in-soil fitness | Applied and Environmental Microbiology
Innovative solutions are needed to address emerging challenges in agriculture while
reducing its environmental footprint. Management of soil microbiomes could contribute
to this effort, as plant growt...
journals.asm.org
March 14, 2025 at 7:40 AM
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....
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....
Reposted by Alex Alleman
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...
novonordiskfonden.dk/en/news/pion...
Pioneering plant microbiome research: Julia Vorholt receives 2025 Novonesis Biotechnology Prize - Novo Nordisk Fonden
novonordiskfonden.dk
March 13, 2025 at 7:47 PM
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...
novonordiskfonden.dk/en/news/pion...
Reposted by Alex Alleman
Reposted by Alex Alleman
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/...
journals.plos.org/plosbiology/...
March 4, 2025 at 1:45 PM
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/...
journals.plos.org/plosbiology/...
Reposted by Alex Alleman
Super excited to see my main PhD project finally out in @naturemicrobiol.bsky.social www.nature.com/articles/s41.... We show for the first time that a synthetic and engineered pathway can indeed exceed nature at one-carbon fixation.
One-carbon fixation via the synthetic reductive glycine pathway exceeds yield of the Calvin cycle - Nature Microbiology
An engineered one-carbon-fixation pathway increases biomass yields of Cupriavidus necator compared with the Calvin cycle and can support future, sustainable bio-based production.
www.nature.com
February 27, 2025 at 10:34 AM
Super excited to see my main PhD project finally out in @naturemicrobiol.bsky.social www.nature.com/articles/s41.... We show for the first time that a synthetic and engineered pathway can indeed exceed nature at one-carbon fixation.
Reposted by Alex Alleman
Happy 37th birthday to the LTEE!
the-ltee.org/history/
the-ltee.org/history/
History – The Long-Term Evolution Experiment
the-ltee.org
February 24, 2025 at 3:39 PM
Happy 37th birthday to the LTEE!
the-ltee.org/history/
the-ltee.org/history/
Reposted by Alex Alleman
Super intriguing paper from Rainey's Lab. It is possible to experimentally evolve *evolvabiliy*. But could we evolve bacteria also towards non-evolvability or non-evolution 🤔 www.science.org/doi/10.1126/...
Experimental evolution of evolvability
Evolvability—the capacity to generate adaptive variation—is a trait that can itself evolve through natural selection. However, the idea that mutation can become biased toward adaptive outcomes remains...
www.science.org
February 21, 2025 at 2:02 PM
Super intriguing paper from Rainey's Lab. It is possible to experimentally evolve *evolvabiliy*. But could we evolve bacteria also towards non-evolvability or non-evolution 🤔 www.science.org/doi/10.1126/...
Reposted by Alex Alleman
After an extensive search, the Danforth Center has named Giles Oldroyd, PhD, its next President.
@gilesoldroyd.bsky.social is a renowned plant geneticist & one of only a few hundred scientists elected to both the UK @royalsociety.org & the US @nasonline.org.
www.danforthcenter.org/news/interna...
@gilesoldroyd.bsky.social is a renowned plant geneticist & one of only a few hundred scientists elected to both the UK @royalsociety.org & the US @nasonline.org.
www.danforthcenter.org/news/interna...
Internationally recognized plant scientist named next President of the Danforth Plant Science Center - Danforth Plant Science Center
After an extensive international search, the Donald Danforth Plant Science Center has named Giles Oldroyd, PhD, as its next President.
www.danforthcenter.org
February 18, 2025 at 3:40 PM
After an extensive search, the Danforth Center has named Giles Oldroyd, PhD, its next President.
@gilesoldroyd.bsky.social is a renowned plant geneticist & one of only a few hundred scientists elected to both the UK @royalsociety.org & the US @nasonline.org.
www.danforthcenter.org/news/interna...
@gilesoldroyd.bsky.social is a renowned plant geneticist & one of only a few hundred scientists elected to both the UK @royalsociety.org & the US @nasonline.org.
www.danforthcenter.org/news/interna...
Reposted by Alex Alleman
That's a beautiful symbiosis. Plants give carbon in exchange from nitrogen from insect cadavers. https://onlinelibrary.wiley.com/doi/full/10.1002/npp2.23
Metarhizium fungi as plant symbionts
Metarhizium species are entomopathogenic and plant mutualistic fungi that mainly colonize the rhizosphere and rhizoplane with root epidermal cells being sporadically occupied. These fungi utilize pla...
onlinelibrary.wiley.com
February 13, 2025 at 2:58 PM
That's a beautiful symbiosis. Plants give carbon in exchange from nitrogen from insect cadavers. https://onlinelibrary.wiley.com/doi/full/10.1002/npp2.23
Reposted by Alex Alleman
Setting new boundaries of 16S rRNA gene identity for prokaryotic taxonomy www.biorxiv.org/content/10.1... #jcampubs
Setting new boundaries of 16S rRNA gene identity for prokaryotic taxonomy
The 16S ribosomal RNA (rRNA) gene is frequently sequenced to classify prokaryotes and identify new taxa. If sequences from two strains share less than ~99% identity, the strains are usually classified...
www.biorxiv.org
February 5, 2025 at 2:33 PM
Setting new boundaries of 16S rRNA gene identity for prokaryotic taxonomy www.biorxiv.org/content/10.1... #jcampubs