World Ocean Database 2023: A Foundational Data Resource for and by the Global Ocean and Coastal Communities - Scientific Data Scientific Data - World Ocean Database 2023: A Foundational Data Resource for and by the Global Ocean and Coastal Communities

World Ocean Database 2023: A Foundational Data Resource for and by the Global Ocean and Coastal Communities www.nature.com/articles/s41... #jcampubs 🌊

The Microbiology and Geochemistry of the Shallow‐Water Hydrothermal Vents of the Gulf of Naples, Italy This study investigated the interplay between fluid geochemistry and microbial diversity in the shallow-water hydrothermal vents of the gulf of Naples, Italy. We found that hydrothermal fluid chemist...

The Microbiology and Geochemistry of the Shallow‐Water Hydrothermal Vents of the Gulf of Naples, Italy enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs 🌊

"A data-conscious checklist for the reviewers of 'omics studies who champion open science", a Comment Iva Veseli and I wrote is now online at metaRxiv:

doi.org/10.31222/osf...

Please read it and consider sharing it with your friends, colleagues, trainees, or editors of your favorite journals.

I have access and can send the PDF to you. Message me with the best way to share it with you.

Carbon monoxide metabolism in freshwater anaerobic methanotrophic archaea - Nature Communications Anaerobic methane-oxidizing archaea mitigate methane emissions in anoxic environments. Here, Egas et al. show that these microbes can also oxidize carbon monoxide, prompting re-evaluation of their cla...

Grab a coffee and enjoy reading up on CO metabolism in methanotrophs!

Freshwater ANME (own work):
www.nature.com/articles/s41...
Marine ANME (@Orphan lab):
www.nature.com/articles/s41...

Big thanks to our collaborators at QUT!
@sjmcilroy.bsky.social (Heyu/Andy/Gene!) @cuwelte.bsky.social

🧬🖥️🦠

Check out our latest preprint that showcases a connection between complex polysaccharide degradation and methanogenesis in an anoxic lake sediment - www.biorxiv.org/content/10.6...

Cultivation‐Based Detection of a Novel High‐GC Nitrospira Derived From the Argentinian Copahue Volcano Area In this cultivation-based study, two novel moderately thermophilic Nitrospira enrichments were obtained from the geothermal field Las Máquinas in the Neuquén Province, Argentina. Both nitrite oxidize...

Cultivation-Based Detection of a Novel High-GC Nitrospira Derived From the Argentinian Copahue Volcano Area
#microbiology #bacteria #volcano #MicroSky
doi.org/10.1111/1462...

Environmental distribution, physiology and genomic adaptations of arctic ammonia-oxidizing archaea
#microbiology #archaea #microbes #ammonia #MicroSky #ArchaeaSky
doi.org/10.3389/fmic...

Ammonia oxidizers offset acidification stress via adaptive substrate affinity in aquatic ecosystems
#microbiology #microbes #ammonia #MicroSky
@natcomms.nature.com
doi.org/10.1038/s414...

The microbiome of marine mat-forming cyanobacteria—a microcosm of taxonomic novelty and phototrophic diversity academic.oup.com/ismecommun/a...

MBARI technology provides new insight into hidden ocean chemistry • MBARI New research led by the University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science has found that nitrogen cycling in marine oxygen-deficient zones is far more dynamic than previo...

New research led by the University of Miami Rosenstiel School of Marine, Atmospheric, and Earth Science with @globaloceanbgc.bsky.social has found that nitrogen cycling in marine oxygen-deficient zones is far more dynamic than previously thought. 🌊🧪 Learn more: www.mbari.org/news/mbari-t...

Extracellular matrix chemistry tunes bacterial biofilm metabolism and optimizes fitness | PNAS Chemically complex extracellular matrices define cellular microenvironments and shape cell behavior across all domains of life. But how has evoluti...

Extracellular matrix chemistry tunes bacterial biofilm metabolism and optimizes fitness

#PNAS from Dianne Newman
with Matt Parsek, Courtney Reichhardt

www.pnas.org/doi/10.1073/...

Very impressive to see all the diversity hidden and generally missed by common approaches!

Oxygen scavenging enables microoxic survival of the marine anammox bacterium Scalindua sp. academic.oup.com/ismej/advanc... #jcampubs 🌊

Hypoxia Decreases Nitrogen Removal in Coastal Marine Sediments Hypoxia impacts sediment nitrogen (N) cycling, yet its effects remain poorly constrained and exhibit strong cross-system inconsistency. We investigate these mechanisms through observations and mass-ba...

#Hypoxia Decreases #Nitrogen Removal in #Coastal Marine Sediments pubs.acs.org/doi/10.1021/...

Converting Relative Amplicon Abundances to Absolute Abundances via Flow Cytometry: Metagenomic Validation and Application to Long Ocean Transects Abstract. With microbes critical for ocean ecological and biogeochemical processes, we need to understand their abundance and diversity distributions. Whil

Want to convert old relative abundance ocean amplicon data into absolute abundances? Williams et al. show a flow cytometry "anchor" can provide reasonable absolute abundances, validated by internal-standard corrected metagenomics with single copy genes, and amplicons academic.oup.com/ismecommun/a...

Cool new paper just dropped from the @nanditagarud.bsky.social & @ctropini.bsky.social labs!

Looks like the gut is a (well) mixed bag! Strain frequencies were invariant throughout the gut, even if species abundances differ along the length of the (mouse) gut.

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

Hi‐C Links Reveal Viral Activity and Infection Within the Free‐Living Microbial Community of a Secondary Chlorophyll Maximum in the Eastern Tropical North Pacific Hi-C sequencing was used to link viral sequences with microbial metagenome assembled genomes in the largely uncultivated waters of an oxygen-deficient zone's secondary chlorophyll maximum within the ...

Hi‐C Links Reveal Viral Activity and Infection Within the Free‐Living Microbial Community of a Secondary Chlorophyll Maximum in the Eastern Tropical North Pacific enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs 🌊

Conserved pathway for homarine catabolism in environmental bacteria - Nature Microbiology Homarine is a ubiquitous, phytoplankton-derived metabolite that is broken down by widely distributed and diverse marine bacteria containing a conserved homABCDER operon.

Conserved pathway for homarine catabolism in environmental bacteria www.nature.com/articles/s41... #jcampubs 🌊

Quantification of anaerobic #methanotrophic archaea Candidatus #Methanoperedens of the ANME-2d cluster using new PCR primers www.sciencedirect.com/science/arti...

Sulfur disproportionation occurs globally across anoxic habitats and has multiple mechanisms of independent evolutionary origin Abstract. Microbial sulfur disproportionation is a unique and enigmatic pathway of energy metabolism in bacteria where a single intermediate sulfur species

Sulfur disproportionation occurs globally across anoxic habitats and has multiple mechanisms of independent evolutionary origin
#microbiology #sulfur #MicroSky
@isme-microbes.bsky.social
doi.org/10.1093/isme...

Sulfoquinovose degradation by cow rumen microbiota Abstract. Sulfoquinovose, a sulfonated sugar derived from the thylakoid membrane lipid sulfoquinovosyl diacylglycerol, is abundant in photosynthetic organi

📢 New paper 🚨

☘️🌿🌱🐄💨🦠🔬🧫🧬

#sulfoquinovose #microbiome

#microsky #microbiomesky

academic.oup.com/ismej/articl...

GitHub - bluenote-1577/myloasm: A new high-resolution long-read metagenome assembler for even noisy reads A new high-resolution long-read metagenome assembler for even noisy reads - bluenote-1577/myloasm

Myloasm - long-read metagenomics assembler 🦠

Open preprint: www.biorxiv.org/content/10.1...

Publication: www.nature.com/articles/s41...

GitHub: github.com/bluenote-157...

Drought Reduces Formation, but Enhances Persistence, of Mineral‐Associated Organic Matter in a Grassland Soil We used a 13C-CO2 labeling study to track the formation and persistence of mineral-associated soil carbon derived from living root and decaying root inputs under normal moisture and droughted conditi...

Drought Reduces Formation, but Enhances Persistence, of Mineral-Associated Organic Matter in a Grassland Soil、Global Change Biology, #stableisotopes onlinelibrary.wiley.com/doi/full/10....

Fluctuations in Ammonia-Oxidizing Bacteria Biomass Density as a Potential Driver of Seasonal Variations in N2O Emissions from Activated Sludge Nitrification Wastewater treatment plants (WWTPs) exhibit marked seasonality in N2O emissions. This study aimed at investigating whether the temperature response of the wastewater nitrifying community contributes t...

Fluctuations in Ammonia-Oxidizing Bacteria Biomass Density as a Potential Driver of Seasonal Variations in N2O Emissions from Activated Sludge Nitrification

doi.org/10.1021/acs....

Congratulations on the publication @jonaswickman.bsky.social!!!

Happy to announce new paper with @chrisklausmeier.bsky.social and @elenalitchman.bsky.social in @asn-amnat.bsky.social in their new Inspiring Perspectives category! (1/4)

www.journals.uchicago.edu/doi/10.1086/...

SypC, a symbiont outer membrane vesicle protein, impacts the development of the squid–vibrio partnership | PNAS Bacterial outer membrane vesicles (OMVs) and the cargo they carry are increasingly recognized as a means of communication between microbial symbion...

#SymbioSky #MicroSky

Comparative physiological and genomic characterization of a novel Nitrobacter vulgaris strain from a nitrate-contaminated subsurface | Applied and Environmental Microbiology Nitrobacter species play a key role in nitrogen cycling; however, their physiological adaptations and genomic diversity remain largely underexplored. This study characterizes Nitrobacter vulgaris strain MLSD-S22, isolated from a nitrate- and heavy-metal-contaminated subsurface, revealing unexpected genomic and metabolic traits. Higher nitrite and oxygen affinities compared to previous reports indicate that some Nitrobacter are more competitive in low-substrate environments than previously believed. The presence of a complete nitrous oxide (N2O) reduction operon highlights the genomic potential related to N2O reduction within this genus; however, we did not observe N2O reduction under the conditions tested. By expanding Nitrobacter ecophysiology, this work provides a foundation for future research on the metabolic flexibility of Nitrobacter and their contributions to nitrogen transformations in diverse environments.

Our paper describing a novel Nitrobacter strain is out in AEM journals.asm.org/doi/10.1128/... #mevosky #microsky