Alex Alleman
@alexanderalleman.bsky.social
Post-Doc Univeristy of Idaho, Marx Lab. 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
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
Reposted by Alex Alleman
Check out Kyle Crocker and Abby Skwara's amazing paper from our lab about how rapid and slow environmental fluctuations elicit different response from distinct functional guilds!!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Microbial functional guilds respond cohesively to rapidly fluctuating environments
Microbial communities experience environmental fluctuations across timescales from rapid changes in moisture, temperature, or light levels to long-term seasonal or climactic variations. Understanding ...
www.biorxiv.org
February 4, 2025 at 1:55 AM
Check out Kyle Crocker and Abby Skwara's amazing paper from our lab about how rapid and slow environmental fluctuations elicit different response from distinct functional guilds!!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Alex Alleman
Our study on #lichen #symbiosis is out in @currentbiology.bsky.social! How can multiple microbes create a large, 3D, and structurally complex organism? To answer this question, we used #metagenomics, #metatranscriptomics, and a bit of protein structure modeling 🧵1/7
🧬 🖥️ 🧪 🦠 🧫 #SymbioSky
🧬 🖥️ 🧪 🦠 🧫 #SymbioSky
January 31, 2025 at 4:35 PM
Our study on #lichen #symbiosis is out in @currentbiology.bsky.social! How can multiple microbes create a large, 3D, and structurally complex organism? To answer this question, we used #metagenomics, #metatranscriptomics, and a bit of protein structure modeling 🧵1/7
🧬 🖥️ 🧪 🦠 🧫 #SymbioSky
🧬 🖥️ 🧪 🦠 🧫 #SymbioSky
Reposted by Alex Alleman
Emergence and evolution of heterocyte glycolipid biosynthesis enabled specialized nitrogen fixation in cyanobacteria www.pnas.org/doi/abs/10.1... #jcampubs
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
www.pnas.org
January 28, 2025 at 2:28 PM
Emergence and evolution of heterocyte glycolipid biosynthesis enabled specialized nitrogen fixation in cyanobacteria www.pnas.org/doi/abs/10.1... #jcampubs
Reposted by Alex Alleman
Bioenergetic trade-offs can reveal the path to superior microbial CO2 fixation pathways journals.asm.org/doi/full/10.... #jcampubs
January 28, 2025 at 3:08 PM
Bioenergetic trade-offs can reveal the path to superior microbial CO2 fixation pathways journals.asm.org/doi/full/10.... #jcampubs
Reposted by Alex Alleman
Nitrogenase loss-of-function mutants are more likely to arise if they can escape their competitive ancestor rather than reaping a fitness advantage from cross-fed ammonium. Proud of all the hard work from grad student @ofsheff.bsky.social. and other collaborators. www.biorxiv.org/content/10.1...
Microbial cross-feeding is stabilized when a dependent mutant is segregated from its independent ancestor
Microbial gene loss is hypothesized to be beneficial when gene function is costly, and the gene product can be replaced via cross-feeding from a neighbor. However, cross-fed metabolites are often only...
www.biorxiv.org
January 25, 2025 at 3:22 PM
Nitrogenase loss-of-function mutants are more likely to arise if they can escape their competitive ancestor rather than reaping a fitness advantage from cross-fed ammonium. Proud of all the hard work from grad student @ofsheff.bsky.social. and other collaborators. www.biorxiv.org/content/10.1...
Reposted by Alex Alleman
Excited to share our team's first paper! In this study, we present two CO oxidisers from volcanic deposits, including a Cupriavidus - the first CO oxidiser identified from this genus. Hope you enjoy reading it!
rdcu.be/d7CCx
rdcu.be/d7CCx
Carbon monoxide-oxidising Pseudomonadota on volcanic deposits - Environmental Microbiome
Carbon monoxide (CO) oxidising microorganisms are present in volcanic deposits throughout succession, with levels of vegetation and soil influencing the communities present. Carboxydovores are a subse...
eur01.safelinks.protection.outlook.com
January 27, 2025 at 6:55 AM
Excited to share our team's first paper! In this study, we present two CO oxidisers from volcanic deposits, including a Cupriavidus - the first CO oxidiser identified from this genus. Hope you enjoy reading it!
rdcu.be/d7CCx
rdcu.be/d7CCx
Reposted by Alex Alleman
New pre-print!!! What types of genes end up on plasmids and why? The take home message of this paper is that beneficial genes move from plasmids to chromosome, causing the ecological value of plasmids to decay over time.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Chromosomal capture of beneficial genes drives plasmids towards ecological redundancy
Plasmids are a ubiquitous feature of bacterial genomes, but the evolutionary forces driving genes to become associated with plasmids are poorly understood. To address this problem, we compared the fit...
www.biorxiv.org
January 24, 2025 at 11:10 PM
New pre-print!!! What types of genes end up on plasmids and why? The take home message of this paper is that beneficial genes move from plasmids to chromosome, causing the ecological value of plasmids to decay over time.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...