Alex Chase 🧬🌋🌊

Alex Chase 🧬🌋🌊

@microbomics.bsky.social

Assist Prof of Earth Sciences at SMU Microbial ecologist 🔬🦠 English bulldog enthusiast 🐶🐾

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Alex Chase 🧬🌋🌊
@microbomics.bsky.social

🧫 Graduate students wanted - microbial edition The Chase Lab at SMU Earth Sciences is looking for microbial humans: adaptive, collaborative, and occasionally anaerobic. If you get excited about connecting sequence data to actual biology, come join the experiment. 🌍 Dallas, TX 🔗 microbomics.com

Alex Chase 🧬🌋🌊
@microbomics.bsky.social

New paper out today in ES&T! 🎉 This one started with me sitting in a seminar about gas transport thinking: okay, but what about the microbes? A few years, some confusing metagenomes, unexpected methanotrophs, and a crash course in stable-isotope geochemistry later... pubs.acs.org/esthag/artic...

pubs.acs.orgA Diffusion-Driven CH4–O2 Boundary Structures Methane Oxidation and Carbon Transformation in Upland SoilsAbstract. Although extensive work has characterized high-affinity atmospheric methane oxidation in upland soils and sustained oxidation in chronically meth

Alex Chase 🧬🌋🌊 reposted

Elsa Abs
@elsa-abs.bsky.social

I'm excited to share our new perspective in Biogeosciences: omics to connect microbial cells to planetary biogeochemistry. Entry points for soil, ocean, air, ice, paleo-archives, plus a cross-ecosystem table of omics resources: coverage, limits, standards. doi.org/10.5194/bg-2...

doi.orgIdeas and perspectives: Using meta-omics to unravel biogeochemical changes from cell to planetary scalesAbstract. Increased human impacts on Earth systems are radically altering biogeochemical cycles. While long-term environmental observatories and Earth System Models (ESMs) provide valuable insights in...
Alex Chase 🧬🌋🌊
@microbomics.bsky.social

I’m excited to launch Microbial Planet, a new editorial-style section of the Chase Lab website for short research dispatches on microbial ecology, evolution, environmental genomics, biogeochemistry, and microbial chemical ecology.

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Alex Chase 🧬🌋🌊
@microbomics.bsky.social

The launch also re-releases two earlier essays: - Reconstructing Microbial Life from Metagenomes: MAGs as reconstructed genomic hyp, not direct observations of organisms - BGCs and the Evolution of Microbial Chemistry: links between molecular innovation, ecological interactions, and diversification

Alex Chase 🧬🌋🌊
@microbomics.bsky.social

I’m excited to launch Microbial Planet, a new editorial-style section of the Chase Lab website for short research dispatches on microbial ecology, evolution, environmental genomics, biogeochemistry, and microbial chemical ecology.

Alex Chase 🧬🌋🌊
@microbomics.bsky.social

The first issue asks a deceptively simple question: what is the scale of microbial adaptation? The Scale of Microbial Adaptation discusses two recent human gut microbiome studies showing contrasting selective sweeps: some localized to genes, others extending across genomic backgrounds.

Alex Chase 🧬🌋🌊
@microbomics.bsky.social

man sometimes I absolutely love this job, but the other side really bums me out... after 9mo review on career, I get: "we know that it does! We have know this for decades!" "intellectual novelty...is non-existent" "PI isn't corr author...calls to question prior exp. as claimed" "low productivity"

Alex Chase 🧬🌋🌊
@microbomics.bsky.social

like I get critiquing the science, totally fine addressing or even responding to valid ideas/comments - that's how things get better and why peer review is so important! I'm not asking for favors, just treat people with respect and be a decent human being...

Alex Chase 🧬🌋🌊 reposted

Dave Baltrus 🦦
@surtlab.bsky.social

Well, that’s a cool study

Cameron Thrash@jcamthrash.bsky.social

The adaptation chip: repurposing the principles of the ichip for guiding in situ experimental evolution academic.oup.com/ismecommun/a... #jcampubs

Alex Chase 🧬🌋🌊
@microbomics.bsky.social

Always love papers blending ecology and evolution, should be a fun read! Emergence of alternative stable states in microbial communities undergoing horizontal gene transfer elifesciences.org/articles/99593

elifesciences.orgEmergence of alternative stable states in microbial communities undergoing horizontal gene transferMathematical models of horizontal gene transfer reveal the determinants underlying multistability of microbial communities, offering key insights for the predictive control and engineering of complex ...
Alex Chase 🧬🌋🌊
@microbomics.bsky.social

🌊🌊🌊 Our PNAS paper on octocoral diterpene evolution is out - a huge interdisciplinary effort led by @immo-burkhardt.bsky.social and the first publication from our @noaa.gov grant on the biopharmaceutical potential of the CCE🪸🤿🧬 www.pnas.org/doi/full/10....

pnas.orgDiversification of diterpene biosynthesis occurred early in octocoral evolution | PNASOctocorals are the major source of marine-derived bioactive terpenoids. However, the vast majority of explored chemistry is known from shallow-wate...
Alex Chase 🧬🌋🌊
@microbomics.bsky.social

We study how microbial lineages evolve and assemble linking genomes, metabolites, and ecological roles. Fieldwork, mass specs, metagenomes, and a bit of chaos. 🧬 PhDs are fully funded (tuition, stipend, the works). Additional competitive fellowships are available through SMU’s grad school.

Alex Chase 🧬🌋🌊 reposted

Chris Greening
@greening.bsky.social

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/...

pnas.orgATP synthesis driven by atmospheric hydrogen concentrations | PNASAll cells require a continuous supply of the universal energy currency, adenosine triphosphate (ATP), to drive countless cellular reactions. The un...

Alex Chase 🧬🌋🌊 reposted

Geoff Zahn
@geoffzahn.bsky.social

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/...

pnas.orgClimate-linked biogeography of mycorrhizal fungal spore traits | PNASClimate-driven variation in traits is crucial for predicting ecological responses to environmental change, yet global patterns and drivers of micro...
Alex Chase 🧬🌋🌊
@microbomics.bsky.social

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/...

pubs.acs.orgMetagenomic Identification of Brominated Indole Biosynthetic Machinery from CyanobacteriaHalogenated 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.

Alex Chase 🧬🌋🌊 reposted

Cameron Thrash
@jcamthrash.bsky.social

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

enviromicro-journals.onlinelibrary.wiley.comUnearthing Vertical Stratified Archaeal Community and Associated Methane Metabolism in Thermokarst SedimentsVertical 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....

Alex Chase 🧬🌋🌊 reposted

Florian Trigodet
@floriantrigodet.bsky.social

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 🧵

biorxiv.orgAssemblies of long-read metagenomes suffer from diverse errorsGenomes from metagenomes have revolutionised our understanding of microbial diversity, ecology, and evolution, propelling advances in basic science, biomedicine, and biotechnology. Assembly algorithms...
Alex Chase 🧬🌋🌊
@microbomics.bsky.social

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...

doi.orgParadox 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...
Alex Chase 🧬🌋🌊
@microbomics.bsky.social

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 🌎🌱🛰️🍃♻️💡

Alex Chase 🧬🌋🌊
@microbomics.bsky.social

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...

nature.comLarge-scale biosynthetic analysis of human microbiomes reveals diverse protective ribosomal peptides - Nature CommunicationsHere, by analyzing 306481 microbial genomes from human-associated microbiomes, the authors reveal a largely unexplored biosynthetic landscape of ribosomal peptides (RiPPs), identifying protective pept...
Alex Chase 🧬🌋🌊
@microbomics.bsky.social

“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/...

science.orgTropical forests in the Americas are changing too slowly to track climate changeUnderstanding 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...

Alex Chase 🧬🌋🌊 reposted

Sullivan Lab at OSU
@sullivan-lab.bsky.social

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

nature.comA framework for integrating genomics, microbial traits, and ecosystem biogeochemistry - Nature CommunicationsMicrobes 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...