by Christoph
Keeping with tradition, here is a lightly annotated list of our forty-five posts from the last half year.
Symbioses
Life After CPR (once again...) by Christoph
As true aficionadas y aficionados around the world do, Steve Petrovski's lab at La Trobe University in Melbourne, Australia went on the hunt for bacteriophages in the wild. Which they didn't find, but their booty was a predatory bacterium, and...
How to Be a Lichen by Nastassja Noell
Lichens are symbiotic organisms – algae, fungi, cyanobacteria, bacteria and yeasts – that form miniature ecosystems that you can hold in the palm of your hand. They live on trees and rocks throughout the Southern Appalachians, and are also found in the Arctic, the Antarctic, rainforests, alpine tundra and especially in the desert...
In one step from commensal to mutualist (almost), part 1|2 by Christoph
It is as true as it is, well, boring to keep saying that Escherichia coli is the best understood unicellular organism, and the most-studied with ~41,000 tagged entries in PubMed since 1932. But then, every five years or so, comes a surprise of what unexpected feats this unassuming bacterium is capable of.
In one step from commensal to mutualist (almost), part 2|2 by Christoph
I had concluded the first part by saying that I would now discuss what mutations Koga et al. (2022) found in two mutator E. coli lineages that allowed the bacteria to successfully "take over" from Pantoea sp. as symbionts in Plautia stali stinkbugs (termed "improved" lineages.) Here we go...
Ecology
Lichen in Roth. ©2021 Christoph Weigel
The Ugliest of Mushrooms by Elio
If beauty is in the eyes of the beholder, then, faith and begorra as the Irishmen may say, so does ugliness. It is widely stated in the mycophile literature that the ugliest of mushrooms is one called Pisolithus arhizus (once tinctorius, for reasons I'll explain soon)...
Diazomania I ─ A Bird's-Eye View of the Nitrogen Cycle by Roberto
Here's a good way to get friends or relatives interested in microbiology – if they aren't already. Tell them to take a deep breath and to let it out. Then ask them these questions: "Mostly, what went into your lungs?", and "What happened to it while in your lungs?" Regardless of...
Diazomania II ─ Trichodesmium by Roberto
When it comes to expansive oligotrophic environments replete with microbial life, the surfaces of Earth's oceans are hard to beat. Therein, most of the primary production comes from a rich diversity of photosynthetic microbes. There's plenty of light and CO2, so growth is therefore limited by something else.
Diazomania III ─ Nitrous Oxide, Please Don't Laugh About It by Roberto
If you bike a lot, particularly if you race, you learn to always carry along a spare inner tube and a CO2 canister to help you rapidly change a flat. So, when I started noticing empty gas canisters while riding along a few of the ubiquitous Copenhagen bike lanes, the first thing...
Bacterial Range Expansion by guest author Davide Ciccarese
This image I captured of a result of mine reminds me of how important it is to keep one's mind open and let the results speak for themselves, even after making a mistake. As part of my research I was conducting during my PhD with David Johnson and Dani Or, I was interested in studying...
C. elegans' Microbiome by Roberto
Not long after participating in the discovery of mRNA and the triplet code, Sydney Brenner set out to study "how genes might specify the complex structures found in higher organisms." Those are the words in the opening sentence of his 1974 foundational paper, which established the nematode C. elegans...
Physiology & Genetics
Lichen in Roth. ©2021 Christoph Weigel
A Game of Dice by Christoph
When on the 3rd day of creation − or the 5th, the Old Testament isn't quite clear here − the Bacteria and Archaea were summoned to choose their shapes, there was at once a frantic run on rods and cocci; spirillae were also immediately sold out. The Alphaproteobacteria frolicked and...
A New Model for the Formation of an Endodontic Biofilm by Elio and Roberto
As we speak, biofilms are the rage in microbiology. And why not, being that most bacteria in nature are not free-swimming but are attached to some surface. Model systems for biofilms are therefore sorely needed. Researchers from two institutions in Bogotá, Colombia...
When it's too cold to grow by Roberto
I began thinking about the cold weather in Boston while I swam in an open water competition off the coast of Cartagena de Indias in Colombia's Caribbean coast last weekend. Then my thoughts drifted to bacteria swimming in colder and colder waters. And then the question...
Fine Reading: A Brief History of Plasmids by Roberto
That plasmids are autonomous replicating elements and that they can serve as excellent cloning vectors are facts most certainly well-known to STC readers. However, I venture to guess that the same cannot be said about the historical details of the when, how, and why...
Magnificently long : Thiomargarita magnifica by Christoph
Microbiologists study microbes with microscopes because they are not visible to the naked eye. Unless they are. This was exactly the case for "Candidatus Thiomargarita magnifica", described in a recent BioRχiv preprint by Vollard et al. (2022): "A centimeter-long bacterium with DNA compart..." (more about the second part of the title...
On drums: Escherichia coli by Christoph
"Light funky groove with a rolling snare pattern and occasional fills, syncopated wood block and percussive hand‑drum and rolling conga pattern" describes a particular drum pattern (#15) by acclaimed Nigerian master drummer Tony Allen. But don't worry, you didn't stumble into the drums section of a music magazine by accident. This is still Small Things Considered. Mind you, I'm a fan...
Pictures Considered
...and Many Images of Microbiology by George O'Toole
Roberto Kolter, after over 20 years of service, has decided to step away as the cover editor at the Journal of Bacteriology (JB), and I want to take this opportunity to both thank him and to reflect. When Roberto started as cover editor, the front of JB...
Pictures Considered #57: Coloring a Cell by Christoph
Our ability to visually perceive and discriminate is always slighly overwhelmed by black-and-white images. Especially, of course, when the objects depicted are outside our trained, familiar size spectrum, such as bacterial cells and their innards. Take for example Figure 1, the cryo-ET image of a tiny bacterial cell (Scale bar: 100 nm!) that I had shown...
The RNA World
Lichen in Roth. ©2021 Christoph Weigel
How to Fine‑Tune a Riboswitch by Janie
It has the inklings of a lame biology joke, but actuality it has profound implications among microbial communities: What's the similarity between male moths and RNA? The answer is the ability to detect extremely specific compounds. Like male moths that can detect a single pheromone molecule...
Nailing the twists of a twisted nails puzzle, part 1|2 by Christoph
I recently mentioned in passing that "...one is poking a wasps' nest when studying cAMP·CRP regulated genes." Are you ready to do some poking with me? Well, in a back corner of said wasp's nest lies a twisted nails puzzle, the solution to which I will reveal here. You would be right...
Nailing the twists of a twisted nails puzzle, part 2|2 by Christoph
I had almost solved the twisted nails puzzle in the first part. I had untwisted the function of the first nail, spot 42 RNA, as well as the function of the second nail, the open reading frame contained within this 'dual‑function RNA' that is translated as the SpfP protein. Here now are two more twists…
Viruses and Phages
The Phage Treaty by Roberto
In 1938, after developing a keen interest in genes, Max Delbrück arrived at Caltech set to work on Drosophila genetics with Thomas Morgan. But, as someone trained in theoretical physics, the pace of working with fruit flies proved too slow. Fortunately for the history of molecular biology, Delbrück met...
Of Terms in Biology: The Polony Method by Christoph
If there is one venerable laboratory technique in virology, it is the plaque assay for the detection and quantification of bacteriophages. It was pioneered by Felix d'Herelle already around 1917, and in the early 1950s, plaque assays were also established for eukaryotic viruses...
Odds & Ends
Lichen in Berlin. ©2021 Christoph Weigel
Bench to Nature, A Call to Molecular Biologists by Roberto
Along several decades my curiosity drove me from the comfort of purified enzymes to the complexity of plant root microbial communities, along the way passing through stationary phase physiology, biofilms, interspecies interactions, to mention but a few. All along, somewhere hidden...
Celebrated Women in Microbiology by Roberto
...This provided the perfect opportunity to dive into the life of this noted microbiologist. Alice Evans (1881–1975) made some of most important contributions to microbiology in the early 20th century. In 1917 she presented her work showing that a bacterium found in raw milk – Bacillus abortus, now Brucella abortus – and the...
Staying in Science Past Retirement by Elio, Linc Sonenshein, and Roberto
As their years in the profession pass, practicing scientists might ponder on a question regarding their future. When I retire, how can I remain in science? In the United States mandatory retirement was abolished in 1986. In many other countries, mandatory retirement still prevails. Regardless of whether mandated or voluntary, retirement is likely to be...
Of Terms for Biologists: Wanderjahre by Roberto
Hope you noticed the not-so-subtle twist from our usual "Of Terms in Biology" to "Of Terms for Biologists." Indeed, Wanderjahre is certainly not a term in biology. It is, however, a term I hope many biologists-in-training will embrace and put into practice. I'll come forth and admit it; for me, it is...
Science Poetry: The Universe in Verse by Janie
What do you get when you mix together scientists, poets, musicians, authors, historians, Nobel laureates, comedians, science writers, artists, actors, entrepreneurs, and Grammy winners?
Silly Poem by Elio
No matter how hard I try, / I have little use for poetray. / I cannot produce a decent rhyme / At this or any other time. // I do not think it's swell / To say that a tortoise' shell / Has its own eccentric smell. // Or that a graceful otter / of clams is a great spotter...
A Lasting Memory by Roberto
Almost forty years ago, I arrived in Boston to begin my job as an assistant professor in the micro department at Harvard Medical School. During my post-doc at Stanford, I had very much hoped to get a call from bacteriology at UC Davis. Instead, I got the call from...
Mind the Frame (also on April 1st) by Christoph
As you may know, STC has been on Twitter since August 2018. Mostly, we use this platform to announce our Monday and Thursday posts. Occasionally, we comment on tweets that we find interesting, sometimes directly or by re-tweeting them. Twitter being Twitter, not everything we re-tweet is...
An Exceptional Vintage by Roberto
I had a dream. I believe it was greatly influenced by a paper I read recently. It describes the fungal populations and the metabolomics of Corvina grapes (Vitis vinifera L. cv. Corvina). For those of you not deeply steeped in winemaking, Corvina grapes serve as the staple for...
Book Reviews
Lichen in Berlin. ©2022 Christoph Weigel
Book Review: Life's Edge by Janie
Ask biologists what they study and the answers will quickly home in on living things, on particular lifeforms that they've spent countless hours thinking, scrutinizing, analyzing, and toiling over. Yet one further question – what exactly is a living thing? – is a sure-fire ticket to hesitation...
Book Review: Finding the Mother Tree by Janie
Behind the scenes, underground, fungal networks are essential to the wellbeing of forests. Trees symbiotically associate with mycorrhizal fungi, exchanging plant-produced sugars for fungus-gathered soil nutrients and water. It's an intimate arrangement: the fungal cells thread between...
A Women's-History-Month Read: Her Hidden Genius (Book Review) by Janie
March is Women's History Month. So, it was perfect timing to read a new historical fiction book on the life and work of a preeminent woman in scientific history, Rosalind Franklin. In Her Hidden Genius, author Marie Benedict sculpts a snapshot rendering of Rosalind Franklin from 1947 to 1958...
Otherlands' Tour of Microbes Through Prehistory by Janie
"It is the crucial paradox at the heart of paleontology that practically all our information about life comes only from death." This line from Thomas Halliday's Otherlands, of course, refers to the fossil record. So, it stands to reason that the entire field of paleontology is contingent upon microbes...
A Revisionist History of Science by Janie
Whether read or listened to, a story is essentially a colorless armature made of words, and it's up to each reader/listener to interpret it, imagine it, and people it with appearances, colors, movements, emotions. The process depends upon the individual's own experiences, since all things present grow from all things past...
The Lives of Fungi by Elio
In the beginning of this gorgeous and intellectually fulfilling book, Britt tells us that, due to modern technology, fungi are now known to be "more ubiquitous than we thought" and are "much more important to the environment and, by extension, to ourselves." He proceeds to justify these statements...
A Microbiology Picture Book by Janie
Here's a fun way to get little ones interested in microbiology. In Wonderful World of the Small: A First Book of Microbiology, Lindsey Millar and Vivien Sárkány introduce the diversity of microbes on Earth. They present an anthropomorphized cast of different types of microbes...
In Memoriam
E. O. Wilson (1929−2021) by Roberto
The world lost one of its premier defenders of biodiversity and a pioneering ecologist and evolutionary biologist when E. O. Wilson died on December 26, 2021, at the age of 92. We start the year honoring the memory...
Howard Berg, a Grand Master of Microbial Motility (1934─2021) by guest author Ariane Briegel
Not many scientists become legends, even fewer achieve this status during their own lifetime. However, Howard Berg was certainly one of them. He was undoubtedly an exceptional scientist that inspired a large cohort of students, postdocs, and peers.
Talmudic Questions
#193 contributed by Michael Eisen. Do you consider mitochondrial DNA to be part of a eukaryote's genome?
#194 Imagine that some life forms in other planets resemble Bacteria or Archaea. Would you guess that they are most like the Gram positives, the Gram negatives or the Archaea?
#195 Can you imagine if Schrödinger's cat is hiding somewhere – and if yes: where – in microbiology?
#196 The establishment of an oxygen-respiring bacterium in the cytoplasm of an archeon might have given rise to the eukaryotes. What was the first adaptive trait in the evolution of this symbiosis and why was it selected?
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