Question for #microbiology #sequencing folks:

I see lots of 3rd party ONT sequencing services around, but not as many PacBio based sequencing service providers. Is there any? Who are your go-to providers for PacBio specific outsourcing, say on SMRT flowcell?

Very nice study from Henshaw et al shows that #marine heterotrophic bacteria can sense and move towards cyanobacteria when the latter are infected with #viruses.

Presumably the signatures of early infection are a sign that nutrients from a lysed cell will be available soon.

This is a nice study that has implications for understanding the role of viruses in the #ocean.

Article here:
https://www.nature.com/articles/s41564-024-01843-2

And we wrote a commentary here:
https://www.nature.com/articles/s41564-024-01867-8

#microbiology

Metabolites from intact phage-infected Synechococcus chemotactically attract heterotrophic marine bacteria - Nature Microbiology

The authors use time-resolved metabolomics and microfluidics to characterize enhanced heterotroph chemoattraction to metabolites released from cyanobacteria during early stages of phage infection.

^Nature

Ran my way back from work at 3AM to streak out Archaea cells from a very generous collaborator. First round of plates are already cooking in the incubator - once we have data we'll know something about conserved genomic architecture dating back 250 million years. Exciting.

#microbiology #archaea

Thanks for a wonderful 1st day of the #IUMS2024. It's been busy at our booth yesterday 😎 Take your chance and visit us today to learn about the DSMZ 🦠🧫🧬🔬

#florence #conference #microbiology #dsmzdigitaldiversity

The coevolution of fungus-ant agriculture

https://www.science.org/doi/10.1126/science.adn7179

#symbiosis #microbiology #ants #insects

Hunting down giant viruses that attack tiny algae
https://phys.org/news/2024-09-giant-viruses-tiny-algae.html

#viruses #algae #microbiology

Hunting down giant viruses that attack tiny algae

They were said to come from outer space, and there were even claims that they were actually bacteria and that they undermined the very definition of viruses.

^{Weizmann Institute of Science (Phys.org)}

Profile and Binomica Labs registered on archaea.bio!

I'll be doing a lot more Halobacteria & Halococcus work in the near future, looking forward to sharing some interesting notes

https://www.archaea.bio/profiles/sung-won-lim

#microbiology #archaea #bioinformatics

Sung won Lim

Independent researcher at Binomica Labs (Queens, NYC), and a remote adjunct researcher in Kyle lab at University of New Hampshire. 

^{Sung won Lim (archaea.bio)}

A newly discovered bacterium, Uabimicrobium helgolandensis, eats other bacteria and is a kind of 'bacteria of prey,' that should not even exist based on previous concepts about microbial cells. It could be a kind of microbial missing link, researchers suggest.

#biology #nature #life #cell #microbiology #science #research

https://www.labroots.com/trending/microbiology/27762/incomprehensible-cell-parasitic-prokaryote-discovered

We found a really big active endogenous virus

https://www.biorxiv.org/content/10.1101/2024.09.03.611062v1

#viruses #algae #microbiology

Latent infection of an active giant endogenous virus in a unicellular green alga

Latency is a common strategy in a wide range of viral lineages, but its prevalence in giant viruses remains unknown.

^bioRxiv

Terrabacteria: redefining bacterial envelope diversity, biogenesis and evolution

https://www.nature.com/articles/s41579-024-01088-0

#microbiology #evolution #science

Terrabacteria: redefining bacterial envelope diversity, biogenesis and evolution - Nature Reviews Microbiology

In this Review, Gribaldo and co-workers explore the diversity and evolution of Terrabacteria and highlight their unique cell envelopes that deviate from Gram-positive and Gram-negative classifications, challenging traditional views on the bacterial c…

^Nature

Do you know MediaDive, the world’s largest collection of cultivation media for microorganisms 🧫? It contains detailed introductions how to prepare the medium you need for your strain. In addition to the provision of all media used at the DSMZ, you can also create your own media or search for a medium suitable for your strain. Give it a try 😉
https://mediadive.dsmz.de/

#database #microbiology #research #DSMZDigitalDiversity #bacteria #fungi

The diel disconnect between cell growth and division in Aureococcus is interrupted by giant virus infection

https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1426193/full

#viruses #algae #microbiology

Frontiers | The diel disconnect between cell growth and division in Aureococcus is interrupted by giant virus infection

Viruses of eukaryotic algae have become an important research focus due to their role(s) in nutrient cycling and top-down control of algal blooms. Omics-base...

^Frontiers

The Last Universal Common Ancestor of Ribosome-Encoding Organisms: Portrait of LUCA

https://link.springer.com/article/10.1007/s00239-024-10186-9

#evolution #microbiology #science #microbes

The Last Universal Common Ancestor of Ribosome-Encoding Organisms: Portrait of LUCA - Journal of Molecular Evolution

The existence of LUCA in the distant past is the logical consequence of the binary mechanism of cell division.

^SpringerLink

Ancient microbes offer clues to how complex life evolved

https://phys.org/news/2024-07-ancient-microbes-clues-complex-life.html

#evolution #microbiology

Ancient microbes offer clues to how complex life evolved

A new study published in Science Advances reveals a surprising twist in the evolutionary history of complex life.

^{Science X (Phys.org)}

How Viruses Shape Microbial Plankton Microdiversity

https://doi.org/10.1146/annurev-marine-040623-090847

#microbiology #plankton #viruses #ocean

Stochasticity, determinism, and contingency shape genome evolution of endosymbiotic bacteria

https://www.nature.com/articles/s41467-024-48784-2

#evolution #microbiology #genomics

Stochasticity, determinism, and contingency shape genome evolution of endosymbiotic bacteria - Nature Communications

Endosymbionts often have small genomes that maintain minimal functions required to serve their hosts. This study examines cases of new endosymbiont acquisition and finds genome degeneration involves both stochastic and deterministic processes that sh…

^Nature

Distinct life cycle stages of an ectosymbiotic DPANN archaeon

https://academic.oup.com/ismej/article/18/1/wrae076/7660939

#archaea #symbiosis #microbiology

Distinct life cycle stages of an ectosymbiotic DPANN archaeon

Abstract. DPANN archaea are a diverse group of microorganisms that are thought to rely on an ectosymbiotic lifestyle; however, the cell biology of these ce

^{Gaisin, Vasil A (Oxford University Press)}

Mesmerising microbes: bacteria as you’ve never seen it before – in pictures

“As a side hustle he manipulates and photographs the microbial world; his images are collected in a book, Beautiful Bacteria. Taking bacteria from substances such as wastewater, dental plaque or kimchi, Danino lets them multiply in a petri dish, adding dyes. The results are artworks differing from the digital enhancements often made in scientific photography to make images more informative.”

https://www.theguardian.com/artanddesign/gallery/2024/may/18/beautiful-bacteria-encounters-in-the-microuniverse-tal-danino

#News #Photography #Photo #Photos #Image #Images #Microbiology #Biology #Science #STEM #Bacteria #Microbes #Microbes @science @biology @microbiology

Mesmerising microbes: bacteria as you’ve never seen it before – in pictures

Scientist Tal Danino’s incredible images of the microbial world

^{The Guardian}

Never a Dull Enzyme

by Roberto — The tricarboxylic acid enzyme citrate synthase from Synechococcus elongatus has the remarkable feature that it self-assembles into multimeric fractal shapes, specifically Sierpiński triangles. As Arthur Kornberg would have said: "Never a dull enzyme!"...

Read more > https://tinyurl.com/m4zyt2h
#microbiology

Systematic identification of cargo-mobilizing genetic elements reveals new dimensions of eukaryotic diversity

https://doi.org/10.1093/nar/gkae327

#genomics #microbiology

A giant virus infecting the amoeboflagellate Naegleria

https://www.nature.com/articles/s41467-024-47308-2

#viruses #giantViruses #microbiology

A giant virus infecting the amoeboflagellate Naegleria - Nature Communications

This is the first report on a virus infecting the amoeboflagellate Naegleria, including the lethal human pathogen N. fowleri.

^Nature

Fascinating - I'll have to make time to dig into this one later.

"Many purported pseudogenes in bacterial genomes are bona-fide genes"

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-024-10137-0

#microbiology #pseudogenes

Many purported pseudogenes in bacterial genomes are bona fide genes - BMC Genomics

Background Microbial genomes are largely comprised of protein coding sequences, yet some genomes contain many pseudogenes caused by frameshifts or internal stop codons.

^{BioMed Central}

Nitrogen-fixing organelle in a marine alga

https://www.science.org/doi/10.1126/science.adk1075

#oceanography #microbiology

Who are giant viruses infecting in the ocean?

In a collaborative paper with the Vardi lab, we were able to link many giant virus lineages to protist hosts using #SingleCell #RNASeq. One #protist host (leucocryptos) made up less than 1% of the community, but we could still identify a cryptic viral lineage infecting it, leading to population collapse.

https://www.nature.com/articles/s41564-024-01669-y

#marine #viruses #microbiology

Single-cell RNA-seq of the rare virosphere reveals the native hosts of giant viruses in the marine environment - Nature Microbiology

Active infections of giant viruses in their marine protists hosts are tracked at single-cell resolution, showing that, despite being rare, these viruses still impact microbial population dynamics.

^Nature

Our latest commentary about a cool recent paper on virophage-mediated defense against giant #viruses!

March of the proviruses

https://www.pnas.org/doi/abs/10.1073/pnas.2402541121

#virology #microbiology

There's a new minimap2 release with ONT specific accurate long reads setting. Looking forward to giving it a test run!

https://github.com/lh3/minimap2/releases/tag/v2.27

#bioinformatics #microbiology

Release Minimap2-2.27 (r1193) · lh3/minimap2

Notable changes to minimap2: New feature: added the lr:hq preset for accurate long reads at ~1% error rate. This was suggested by Oxford Nanopore developers (#1127). It is not clear if this prese...

^GitHub

The Simons Foundation has amazing #postdoc #fellowships for anyone interested in #marine microbial #ecology or #evolution.

I'd love to sponsor anyone interested in viral diversity!

Please spread the word!

https://www.simonsfoundation.org/grant/simons-postdoctoral-fellowships-in-marine-microbial-ecology/?mc_cid=3818457af5&mc_eid=0969502559

#viruses #microbiology

Simons Postdoctoral Fellowships in Marine Microbial Ecology | Simons Foundation

The Simons Foundation invites applications for postdoctoral fellowships to support candidates who intend to pursue a career in basic research on fundamental problems in marine microbial ecology, with an emphasis on understanding the role of microorga…

^{Simons Foundation}

Looking for some suggestions - I'm working with Archaeal genomic regions whose optimally fitting model seems to be Tamura-Nei (https://doi.org/10.1093/oxfordjournals.molbev.a040023).

Would it be too much to suspect the Archaeal region is under similar types of evolutionary pressure?

#archaea #microbiology #evolution #phylogenetics #bioinformatics

Cool paper looking at biomass degradation in leaf cutter ant fungus gardens:

Mapping microhabitats of lignocellulose decomposition by a microbial consortium

https://www.nature.com/articles/s41589-023-01536-7

#microbiology #fungi #cellulose

Mapping microhabitats of lignocellulose decomposition by a microbial consortium - Nature Chemical Biology

Metabolome-informed proteome imaging provides a comprehensive view of underlying biological pathways within micrometer-scale microhabitats of the fungal garden, informing the understanding of metabolic fungal pathways in plant matter degradation.

^Nature

French chemist and microbiologist Louis Pasteur was born #OTD in 1822

He is renowned for his discoveries of the principles of vaccination, microbial fermentation, and pasteurization, the last of which was named after him. His research in chemistry led to remarkable breakthroughs in the understanding of the causes & preventions of diseases, which laid down the foundations of hygiene, public health & much of modern medicine.

Louis Pasteur at PG:
https://www.gutenberg.org/ebooks/search/?query=louis+pasteur&submit_search=Go%21

#books #microbiology

Apply for our Phd project on "Discovering and characterising novel defence systems in pathogenic Serratia spp using microbiology and genomics"

#genomics #microbiology #omics

FindAPhD : Pathogens and Host Defences Doctoral Training Partnership PhD Studentships at University of Sussex
https://www.findaphd.com/phds/program/pathogens-and-host-defences-doctoral-training-partnership-phd-studentships/?p6353

FindAPhD : Pathogens and Host Defences Doctoral Training Partnership PhD Studentships at University of Sussex

Apply for a PhD: Pathogens and Host Defences Doctoral Training Partnership PhD Studentships at University of Sussex

^{www.FindAPhD.com}

Happy to share our latest paper, in which we examined the timing at which different microbial groups colonized the ocean!

The first author (Carolina Martinez) is starting her lab at UC Santa Barbara in 2024 and is looking to recruit postdocs and PhD students, so if this looks interesting to you, please reach out to her!

A timeline of bacterial and archaeal diversification in the ocean

https://elifesciences.org/articles/88268

#microbiology #ocean #marine #evolution

A timeline of bacterial and archaeal diversification in the ocean

Phylogenomics reveals the timeline over which marine bacteria and archaea colonized the oceans and shows the geological context of their diversification.

^{Carolina A Martinez-Gutierrez (eLife Sciences Publications, Ltd)}