Alex Chase 🧬🌋🌊
@microbomics.bsky.social
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Assist Prof of Earth Sciences at SMU Microbial ecologist 🔬🦠 English bulldog enthusiast 🐶🐾
Started off as a reading group and led to a nice mini-review of microbiome evolution in natural communities. Complete credit to Abby for leading this fun collab!
#mevosky
Investigating bacterial evolution in nature with metagenomics
doi.org/10.1016/j.mi...
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Redirecting
https://doi.org/10.1016/j.mib.2025.102654
about 2 months ago
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Alex Chase 🧬🌋🌊
Chris Greening
2 months ago
Our article showing energy production from air alone is in PNAS today. This paper provides an ultimate biochemical proof that microbes can survive simply by 'making' energy from air (making two ATP per molecule atmospheric H2 consumed) and has biotech applications.
www.pnas.org/doi/10.1073/...
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ATP synthesis driven by atmospheric hydrogen concentrations | PNAS
All cells require a continuous supply of the universal energy currency, adenosine triphosphate (ATP), to drive countless cellular reactions. The un...
https://www.pnas.org/doi/10.1073/pnas.2506353122
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Geoff Zahn
3 months ago
Fungal spores reveal a global climate footprint on microbes' traits! Incorporating microbial traits improves predictions of biogeographic shifts. Fun project w
@balachaudhary.bsky.social
@smriti-pehim-limbu.bsky.social
@sturmer.bsky.social
@aguilart.bsky.social
www.pnas.org/doi/10.1073/...
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Climate-linked biogeography of mycorrhizal fungal spore traits | PNAS
Climate-driven variation in traits is crucial for predicting ecological responses to environmental change, yet global patterns and drivers of micro...
https://www.pnas.org/doi/10.1073/pnas.2505059122
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New work led by the amazing
@aprillukowski.bsky.social
lab. Love working on these interdisciplinary projects discovering new chemical diversity in nature. Microbes are the best chemists!
pubs.acs.org/doi/10.1021/...
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Metagenomic Identification of Brominated Indole Biosynthetic Machinery from Cyanobacteria
Halogenated indole natural products have been isolated from a variety of organisms, including plants, marine algae, marine invertebrates, and bacteria. Aquatic cyanobacteria, in particular, are rich producers of brominated indoles, but their cognate biosynthetic enzymes have only been successfully linked in a limited number of natural products, such as the eagle-killing toxin aetokthonotoxin (AETX). The biosynthetic pathway for AETX involves five enzymes, two of which were previously undescribed due to incomplete annotations as hypothetical proteins. Our recent elucidation of AETX biosynthesis established functions of the two previously unknown proteins as enzymes responsible for tryptophan halogenation (AetF) and nitrile synthesis (AetD). Given their sequence novelty, we queried metagenomic data sets for these two enzymes and identified two new cyanobacterial haloindole biosynthetic gene clusters (BGCs) from marine sediment in Moorea, French Polynesia, and soil-derived samples in Maunawili Falls, Hawaii. We characterized the recovered BGCs by biochemically validating a new AetF homologue that exclusively halogenates free indole, rather than tryptophan as observed in AETX biosynthesis, and a new AetD homologue that harbors distinct substrate preferences, expanding the scope of nitrile biosynthesis. Additional characterization of core and accessory enzymes within these AETX-like BGCs highlights the breadth and diversity of haloindole biosynthetic machinery in cyanobacteria.
https://pubs.acs.org/doi/10.1021/acs.jnatprod.5c00492
3 months ago
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En route to ASM Microbe. Excited to be back in CA. Let me know if you’re also going and want to grab a coffee to discuss some science 🙌🏻
4 months ago
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Alex Chase 🧬🌋🌊
Alex Crits-Christoph
4 months ago
There is so, so much good science being shared and discussed on bsky right now. The news of its demise is quite backwards. If you are having trouble finding it among all of the very important political news, use the papersky feed that filters posts you follow to just papers:
bsky.app/profile/pape...
add a skeleton here at some point
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Cameron Thrash
5 months ago
Unearthing Vertical Stratified Archaeal Community and Associated Methane Metabolism in Thermokarst Sediments
enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
#jcampubs
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Unearthing Vertical Stratified Archaeal Community and Associated Methane Metabolism in Thermokarst Sediments
Vertical stratification in thermokarst lake sediments drives archaeal community assembly, with declining diversity, deterministic selection, and modular networks at depth. Taxa shifts (e.g., rising T....
https://enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.70110?af=R
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Alex Chase 🧬🌋🌊
Rike Stelkens
5 months ago
Just out in PNAS!
www.pnas.org/doi/10.1073/...
"The evolution of thermal performance curves in response to rising temperatures across the model genus yeast". Beautiful work using experimental evolution forecasting climate impacts on biodiversity by Jennifer Molinet
@jennifermolinet.bsky.social
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When is microbial cross-feeding evolutionarily stable?
www.biorxiv.org/content/10.1...
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When is microbial cross-feeding evolutionarily stable?
Cross-feeding, a phenomenon in which organisms share metabolites, is frequently observed in microbial communities across the natural world. One of the most common forms is waste-product cross-feeding,...
https://www.biorxiv.org/content/10.1101/2025.05.16.654511v2
5 months ago
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so is it like even worth starting to prepare a CAREER grant??? 🤷♂️
5 months ago
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Alex Chase 🧬🌋🌊
Alvaro San Millan
5 months ago
New opinion paper from the lab!
www.cell.com/trends/micro...
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Plasmid–bacteria associations in the clinical context
Antimicrobial resistance (AMR) is one of the most pressing global health problems, with plasmids playing a central role in its evolution and dissemination. Over the past decades, many studies have inv...
https://www.cell.com/trends/microbiology/abstract/S0966-842X(25)00122-2?dgcid=raven_jbs_aip_email
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Alex Chase 🧬🌋🌊
Florian Trigodet
5 months ago
I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers,
www.biorxiv.org/content/10.1...
and tell you just a little bit about it in the following 🧵
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Assemblies of long-read metagenomes suffer from diverse errors
Genomes from metagenomes have revolutionised our understanding of microbial diversity, ecology, and evolution, propelling advances in basic science, biomedicine, and biotechnology. Assembly algorithms...
https://www.biorxiv.org/content/10.1101/2025.04.22.649783v2
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Love this title! My ecology class reads the original Hutchinson paper to start the semester every year.
#niches
Paradox of the Sub-Plankton: Plausible Mechanisms andOpen Problems Underlying Strain-Level Diversity inMicrobial Communities
doi.org/10.1111/1462...
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Paradox of the Sub‐Plankton: Plausible Mechanisms and Open Problems Underlying Strain‐Level Diversity in Microbial Communities
“Paradox of the sub-plankton: Plausible mechanisms and open problems underlying strain-level diversity in microbial communities” by Akshit Goyal* and Griffin Chure*. This work highlights the limitati...
https://doi.org/10.1111/1462-2920.70094
5 months ago
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If you're in DFW next week, come join us for our 3rd Annual SMU Energy, Environment, and Natural Resources (EENR) Colloquium. Exciting invited speakers and panels addressing science, industry, and law about pressing
#envsci
issues 📍 SMU 📅 Friday May 2 🌎🌱🛰️🍃♻️💡
5 months ago
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If anyone is teaching environmental science
#Envsci
I highly recommend showing students this interactive world map of the ocean-atmosphere interactions 🌎 🌊 🌬️
classic.nullschool.net
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earth :: a global map of wind, weather, and ocean conditions
See current wind, weather, ocean, and pollution conditions, as forecast by supercomputers, on an interactive animated map. Updated every three hours.
https://classic.nullschool.net/
6 months ago
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really cool paper on RiPPs that binds to a new ribosomal site, inhibits translation elongation and induces miscoding in G+ and G-
www.nature.com/articles/s41...
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A broad-spectrum lasso peptide antibiotic targeting the bacterial ribosome - Nature
A new lasso peptide antibiotic exhibits broad-spectrum activity against Gram-negative and Gram-positive bacteria by interfering with bacterial protein synthesis, is unaffected by common resistanc...
https://www.nature.com/articles/s41586-025-08723-7
6 months ago
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www.nature.com/articles/s41...
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A polyene macrolide targeting phospholipids in the fungal cell membrane - Nature
Mandimycin, a polyene macrolide, exhibits strong antifungal activity and possesses a mode of action that is distinct from other compounds of this class.
https://www.nature.com/articles/s41586-025-08678-9
7 months ago
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“species composition and functional properties of tropical American forests (and possibly all tropical forests) are increasingly out of equilibrium with local climate”
www.science.org/doi/10.1126/...
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Tropical forests in the Americas are changing too slowly to track climate change
Understanding the capacity of forests to adapt to climate change is of pivotal importance for conservation science, yet this is still widely unknown. This knowledge gap is particularly acute in high-b...
https://www.science.org/doi/10.1126/science.adl5414
7 months ago
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Alex Chase 🧬🌋🌊
Sullivan Lab at OSU
7 months ago
🚨New paper from NSF EMERGE BII: A framework for integrating genomics, microbial traits, and ecosystem biogeochemistry. Read here:
www.nature.com/articles/s41...
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A framework for integrating genomics, microbial traits, and ecosystem biogeochemistry - Nature Communications
Microbes drive the Earth’s biogeochemical cycles. Here, Li et al. present a framework for integrating genome-inferred microbial kinetic traits into ecosystem mechanistic models, and use it to benchmar...
https://www.nature.com/articles/s41467-025-57386-5
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#mevosky
Last semester: reading group on micro evolution - trying to understand in natural communities. Wanted to share! 🧬🦠 1. Start with THE classic paper on MAGs Community structure and metabolism through reconstruction of microbial genomes from the environment
www.nature.com/articles/nat...
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Community structure and metabolism through reconstruction of microbial genomes from the environment - Nature
Nature - Community structure and metabolism through reconstruction of microbial genomes from the environment
https://www.nature.com/articles/nature02340
7 months ago
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Need a reading group or something to catch-up on some amazing papers!! A vast repertoire of secondary metabolites potentially influences community dynamics and biogeochemical processes in cold seeps | Science Advances
www.science.org/doi/full/10....
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A vast repertoire of secondary metabolites potentially influences community dynamics and biogeochemical processes in cold seeps
Cold seep sediments harbor a treasure of undiscovered microbial products, reshaping our understanding of deep-sea ecosystems.
https://www.science.org/doi/full/10.1126/sciadv.adl2281
7 months ago
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Some of my first year grad students in my class are asking for books to read that will get them thinking about what questions to ask and how to know what they should ask. I have a couple of recs but wondering if anyone can help. What inspired you??
7 months ago
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Alex Chase 🧬🌋🌊
Rauf Salamzade
7 months ago
Our minireview on BGC evolution being shaped by genomic & ecological context is now live on mSystems:
journals.asm.org/doi/10.1128/...
#secmet
#MEvoSky
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Context matters: assessing the impacts of genomic background and ecology on microbial biosynthetic gene cluster evolution | mSystems
Microbial secondary metabolites are compounds produced by bacteria and fungi that are not required for their replication and unconditional survival (1, 2). While they are thus not expected to be unive...
https://journals.asm.org/doi/10.1128/msystems.01538-24
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Alex Chase 🧬🌋🌊
Sebastian S. Cocioba
8 months ago
I think the Microbial Evolution feed is working! Simply add the
#MEvoSky
hashtag to your post and it will aggregate to the feed linked below. Feel free to introduce yourself in context of microbial evo and adjacent topics. Experimental and directed evo welcome too!
bsky.app/profile/did:...
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Alex Chase 🧬🌋🌊
Jonathan Eisen
8 months ago
This is worth a read for anybody interested in microbial diversity
www.science.org/doi/10.1126/...
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A metagenomic perspective on the microbial prokaryotic genome census
Microbial sequencing reveals vast diversity, emphasizing metagenome contributions and urgent need for targeted cultivation.
https://www.science.org/doi/10.1126/sciadv.adq2166
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Alex Chase 🧬🌋🌊
Marc Chevrette
10 months ago
Adam Rivers (USDA-ARS) and I are hiring a joint postdoc to on a microfluidics and sequencing based project to better understand synthetic and natural microbiome community dynamics and generate data to build AI/ML models to infer interspp. interactions. Hit me up if interested!
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First ever
#AGU24
was a massive success. Loved hearing about all the soil talks and POM v MAOM mechanisms, both geochemical and microbial mediated. Definitely has me thinking a lot more about soil dynamics.
10 months ago
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Alex Chase 🧬🌋🌊
Elsa Abs
10 months ago
📣 All our sessions about advancing soil carbon predictions is today!
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Today's JC paper on the theme of microbial evolution: Competition–dispersal tradeoff ecologically differentiates recently speciated marine bacterioplankton populations
doi.org/10.1073/pnas...
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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...
https://doi.org/10.1073/pnas.1318943111
10 months ago
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and it's now live! congrats to all involved!
pubs.acs.org/doi/10.1021/...
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11 months ago
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Slipper season is back 🙌🏻
11 months ago
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Giving a lecture today on environmental impacts of livestock. Blows my mind every time I prep for this one. If interested highly recommend the “Cowspiracy” documentary on Netflix 🐑🐓
11 months ago
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Why do I always procrastinate reviewing papers?? 😫
11 months ago
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After yesterday, I couldn’t do it anymore. Had to leave that other platform but excited to join here. Lmk what I need to do to get back to communicating science 🧪🧬🦠
11 months ago
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