Alex Chase 🧬🌋🌊

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...

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...

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/...

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...

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/...

GitHub - gamcil/clinker: Gene cluster comparison figure generator Gene cluster comparison figure generator. Contribute to gamcil/clinker development by creating an account on GitHub.

If you want something very simple but does a great job visualizing. Just need input genbank files:

github.com/gamcil/clinker

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.

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/...

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 🙌🏻

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...

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....

Unearthing Vertical Stratified Archaeal Community and Associated Methane Metabolism in Thermokarst Sediments enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs

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

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,...

When is microbial cross-feeding evolutionarily stable?
www.biorxiv.org/content/10.1...

so is it like even worth starting to prepare a CAREER grant??? 🤷‍♂️

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...

New opinion paper from the lab!

www.cell.com/trends/micro...

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...

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 🧵

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...

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...

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
🌎🌱🛰️🍃♻️💡

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.

If anyone is teaching environmental science #Envsci I highly recommend showing students this interactive world map of the ocean-atmosphere interactions 🌎 🌊 🌬️
classic.nullschool.net

Large-scale biosynthetic analysis of human microbiomes reveals diverse protective ribosomal peptides - Nature Communications Here, by analyzing 306481 microbial genomes from human-associated microbiomes, the authors reveal a largely unexplored biosynthetic landscape of ribosomal peptides (RiPPs), identifying protective pept...

and another recent one giving some ecological context to RiPPs in the human gut: five AIPs effectively inhibit the biofilm formation of disease-associated pathogens
www.nature.com/articles/s41...

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...

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...

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.

www.nature.com/articles/s41...

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...

“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/...

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...

🚨New paper from NSF EMERGE BII: A framework for integrating genomics, microbial traits, and ecosystem biogeochemistry. Read here: www.nature.com/articles/s41...

Feel free to share your favorites! Always need new papers to read and discuss, especially anything microbial evolution related

Maintenance of Sympatric and Allopatric Populations in Free-Living Terrestrial Bacteria | mBio Due to the promiscuous exchange of genetic material and asexual reproduction, delineating microbial species (and, by extension, populations) remains challenging. Because of this, the vast majority of microbial studies assessing population structure often ...

All of these (+ so many more) influenced a lot of our ongoing work.

Maintenance of Sympatric and Allopatric Populations in Free-Living Terrestrial Bacteria
doi.org/10.1128/mbio...

Adaptive differentiation and rapid evolution of a soil bacterium along a climate gradient
www.pnas.org/doi/10.1073/...

12. And one for the human microbiome fans out there!

Elevated rates of horizontal gene transfer in the industrialized human microbiome
doi.org/10.1016/j.ce...

11. One of the more influential papers for me as a graduate student. Always nice for a re-read!

Horizontal gene transfer and the evolution of bacterial and archaeal population structure
doi.org/10.1016/j.ti...

Emergence of trait variability through the lens of nitrogen assimilation in Prochlorococcus In the context of an organism's ecology, physiology, and macroevolutionary history, inheritance and gene loss can yield emergent patterns of trait variability that give the appearance of gene acquisit...

10. Another fav of mine looking at past evolution driving trait divergence

Emergence of trait variability through the lens of nitrogen assimilation in Prochlorococcus
elifesciences.org/articles/41043

A Reverse Ecology Approach Based on a Biological Definition of Microbial Populations Defining bacterial populations by examining recent horizontal gene transfer events illuminates ecologically meaningful interspecies relationships in the environment and in the human microbiome.

9. Framework for understanding how ecology influences bacterial populations

A Reverse Ecology Approach Based on a Biological Definition of Microbial Populations
www.cell.com/cell/fulltex...

8. Probably my fav story link gen2phen

Population Genomics of Early Events in the Ecological Differentiation of Bacteria
doi.org/10.1126/scie...

Competition–dispersal tradeoff ecologically differentiates recently speciated marine bacterioplankton populations
www.pnas.org/doi/full/10....

Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow - The ISME Journal The ISME Journal - Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow

7. And for those interested in soil systems, fear not!

Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow
www.nature.com/articles/s41...

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations AbstractMultiple models describe the formation and evolution of distinct microbial phylogenetic groups. These evolutionary models make different prediction

6. One of my personal favorites using MAGs and env. data to understand spatiotemporal dynamics

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations
academic.oup.com/ismej/articl...