Retrospective, December 2018

by Elio
 

Photo Credit: Unhindered by Talent

For your convenience, we present a lightly annotated list that includes most of the posts of the past half year, with suitably links. Note in passing that we are observing the twelfth year of this blog's existence.
 

Gastronomic Microbiology

Replay: A Close Encounter of the Enological Kind   We reprinted a classic piece by John Ingra­ham wherein he describes the path to the discovery of Oenococcus oenii, a bacterium that con­verts the undesirable malic acid into the softer-to-the-palate lactic acid (known as the malolactic fer­men­­tation). The story has some fascinating twists and turns, narrated by one of its main original protagonists.

The Secrets of Ancient Beer   Ex-UCSD grad student Gillian Belk ponders about the finding of te­tracycline in old bones. Might it come from antibiotic-producing streptomycetes that were seren­dipitously introduced into the fermentation process of an­cient beer? Sounds plausible.

Tainted   Next time you open a bottle of wine and turn up your nose because it tastes musky, meaning that it's 'corked', think of this post by Vivienne Baillie Gerritsen. She tells us that the off-taste is due to compounds known as chloroanisoles, made by the fungus Trichoderma longi­bra­chi­atum from trichlorphenols. The story is actually quite intricate, ergo worth reading.

The Microbial Ecology of Chocolate   Making chocolate requires a complex fermentation by a succession of yeasts, lactic acid-, acetic acid-bacteria, and others. Roberto suggests that this is "an ideal system for experimen­tal ecology that has scarcely been exploited." Chocolate lovers, here's your chance…

It Comes With The Terroir   Roberto makes the dubious claim that he is no wine connoisseur. Never mind that, he tells of two studies on the changes in the microbiome during stages in wine making, one carried out in California, the other in Sardinia. Both suggest that there is a particular ‘microbiological terroir.' Terroir, by the way, is a somewhat mythical term that only Frenchmen are comfortable with, that denotes what is special in any given wine-making site.
 

The Fungi

State of the World's Fungi   Roberto introduces a fascinating and comprehensive report on this subject, by folks at London's Kew Garden. No small thing, the fungal world!

Fungi, Toxins, and Fungal Viruses (A Snippet)   Some polychetide toxins made by some molds (ochratoxins, relatives of aflatoxins) are synthesized under the control of a mycovirus. This has implications for the control of contaminated food as well as for understanding the regulation of these compounds' biosynthesis.

Psilocybin (A Snippet)   Why do some unrelated mushrooms make hallucinogens? Nobody knows, according to Elio, but the subject is not without fascination.
 

Symbiosis

Symbiosis   A quartet of intrepid would-be philosophers (Elio, guest Tony, Roberto, and Christoph) muse about what symbiosis means to them.

Rounding up the Honey Bees (1) and (2)   In a two-part post, Christoph deals with a serious en­vi­ronmental problem. The widely used agricultural insecticide, Roundup (glyphosate), was thought to be innocuous to bees. Far from it, as it affects the bees' intestinal microbiome in a serious way.

How Bacteria on our Skin Might Prevent Skin Cancer   UCSD graduate students Jammal Abu-khazneh and Chih-Kai Yang discuss work from the Richard Gallo lab indicating that skin-dwelling strains of Staphylococcus epidermidis make a chemical (6-N-hydroxyaminopurine) that is active against other bacteria as well as some tumors.

What To Do When You Run Out of a Cherished Symbiont?   The answer, Elio says, is to pick up another one. This is what happens to cicadas, which depended on two bacterial endosymbionts for some of their food. When they lost one of these two, they replaced it with a yeast that makes up for the loss.

Friend & Foe   Christoph recently introduced the term 'defensive symbioses', where symbiotic bacteria produce a cocktail of antibiotics that protect their eukaryotic host against an ar­ray of op­portunistic bacterial and fungal pathogens. Here, he introduces the interesting case of a South American beetle and its symbiotic bacterium, Burkholderia gladioli.

Snacking on thistles (1st bite, 2nd bite)   In a two-part story, Christoph describes the problems faced by insects that live on plant sap or on the contents of cells, namely how to get across the plant cells' pectin-containing cell walls. Some acquire a pectinase gene, others hire a symbiotic bacterium that has this gene. Here, the symbiont does not provide nutrients directly but rather the tools to obtain them.
 

Pathogenesis

Shining a light on Vibrio DNA uptake   Rachel Diner, a grad student at UCSD, shines a light on the process of natural transformation in the cholera bacillus and how its pilus is involved in the appropriations of extracellular DNA. The paper she discusses is a thing of fluorescent microscopy and genetic beauty.

Vaccines and the Fight Against Antibiotic Resistance   Roberto hails the renewed emphasis that vaccines are enjoying in an era of increased bacterial resistance to antibiotics. Popular is be­coming "reverse vaccinology", using whole genome sequences and bioinformatics to predict ef­fective antigens from pathogens to use in vaccine development.

Cultivating the Uncultivable   True, you can't yet cultivate the agent of syphilis all by itself in ar­ti­ficial media, but it grows fine if co-cultured with epithelial cells. But whether the fungus Pneum­o­cys­tis (of AIDS fame) can be grown in co-culture is up for debate.

Fast Is Good...   Michael Schmidt introduces a new way of determining antibiotic sensitivity in hours instead of days, by looking at effects on the growth of bacteria in microfluidic chambers. Could be useful to decide at the bedside what drug to use.

The History and Politics Surrounding our Attempts to Harness and Control Germs   Daniel reviews two recent books, The Vaccine Race: Science, Politics, and the Human Costs of Defeating Dis­ease by Meredith Wadman and Germ Wars: The Politics of Microbes and America's Landscape of Fear by Melanie Armstrong.
 

Ecology

How Much Does Biology Weigh?   At Israel's Weizmann Institute and at Caltech, numbers count. More specifically, how much do all the plants, animals, and microbes weigh? The total, should you wonder, comes to ca. 550 gigatons of carbon. Read on to find out how this figure breaks out in ways that may surprise you.

Take a Deep Breath of... Methane   The bacterium Rhodopseudomonas palustris makes methane (a process called biomethanation) and does it in a novel way, using for this purpose its nitroge­na­se, a promiscuous enzyme. So do some cyanobacteria. Putting it all together, biomethanation con­tributes to the global carbon cycle, ergo to climate change.

Needles in a Metagenomic Haystack: Hunting for Molecular Plastic-Chewers   Janie Kim, a so­phomore at Princeton, writes about one of our major ecological problem, the accumulation of plastics, and how genes for enzymes that degrade a major one, PET, can be overexpressed in bac­teria to yield maximal activities. A new algorithm plus a streamlined lab workflow will help 'winnow out the proverbial grain from the chaff.'

Mono Lake (a Snippet)   This lake, much enjoyed by Elio on a trip to the eastern slope of Califor­nia's Sierra Nevada, is known for its limestone columns protruding from the water. Microbes were involved in their formation, probably because their biofilms provided sites for calcite nucleation.

More Respect For the Silicon Cycle, Please   Elio points out that the silica (or silicon) cycle deals with all-important aspects of the global carbon cycle, such as the transformation of silicate rocks into carbonate rocks and back. Some large protists that belong to the Rhizaria contribute to the making of silicate rocks, with the release of CO₂.

Of Mountains and Microbes…   San Diego State's David Lipson brings up the topic of C4 photo­synthesis (as opposed to the more common one, which is called C3 because the main product is the 3-carbon phosphoglycerate). C4 photosynthesizing plants (making the C4 compound oxalo­ace­tate) appeared more recently. David discusses their role in ecology and evolution.

Small (and Large) Numbers Considered   Roberto has fun with numbers, such as the size of ty­pical bacteria, their number in the human body, the number of their species, and other very large and very small figures. His post elicited quite a response regarding how many mitochondria there are per cell.

Occasionally, Microbiologists use Macroscopes...   Christoph points out that microbial blooms can be so huge that micro­biologists have to turn to "macroscopes", that is, satellite ima­gery, to see them in their full glory.

To The Bottom of the Sea   The lowest part of the oceans, the Mariana Trench has not escaped the grasp of metagenomicists. Not a place for yet undiscovered monsters of the deep, these sites are rich in life, the largest animal there being a shrimp-like amphipod whose gut microbiome is do­minated by a Psychromonas with a reduced genome and other fun attributes.
 

Evolution

Why, oh why, can't life be less complicated?   Regarding papers on ploidy in bacteria, Christoph says: "Pro­bably the most intriguing of their observations was the fluctuation of ploidy numbers with growth stage and growth conditions. Also, ploidies weren't fixed for one species. Rather, they varied among strains of a species, and also among closely related genera."

The Truth Is In The Outcome   Extinct New Zealand giant moas ate mushrooms. How do we know? Elio tells about fungal DNA being found in 7000-year-old moa coprolites – fossil poop, that is.

Ancient Microbial DNA: Paleomicrobiology   Daniel reviews Paleomicrobiology of Humans, a mo­nograph edited by M. Drancourt and D. Raoult. He liked it, asking for elaborations in some parts.

The Human Story, as Told by Our Genomes   Jamie reviews the book Who We Are and How We Got Here by David Reich. She liked it.

How To Turn An E. coli  Into An Archaeon (Sort Of)   Elio reports on the successful cloning of genes for typical archaeal lipid enzymes into E. coli. These don't mind, especially because they now become archaea-like, more resistant to temperature stresses, both higher and lower.

On your marks, get set, go!   Christoph explains that all codons, not just the 'dedicated ones' can work in initiation of translation, just that most of them don't do it very well. A fine review of your biochemistry plus unexpected conclusions.
 

Outreach

From the Classroom   A student of Melanie Armstrong at Western Colorado University asks: if wooly mammoths are to be reintroduced, where will their gut microbiome come from?

"May I ask you a question?"   Elio recounts his experience with his first lecture to medical stu­dents. Please read to the end.

The Microbial Life Exhibition at the Harvard Museum of Natural History   Scott was guest cu­rator to a major microbiological exhibit called Microbial Life: A Universe at the Edge of Sight. It in­cluded an interactive, volunteer staffed microscopy station.

How to Build a Giant Winogradsky Column   Scott elaborates on one of the most popular ex­hibits at microbiologically-themed museum shows, Harvard's included.

Why You Must  Plot Your Growth Data On Semi-log Graph Paper   Elio gets impatient with people who plot growth data linearly, as if bacterial growth were linear instead of exponential.

Microbe 2018   Elio attended Microbe, the 2018 big meeting of the ASM in Atlanta (where they kindly provided him with an electric wheelchair) and returned thinking that some of the most fas­cinating papers were on the 3-D world of microbes.

Apuleius's Ass   A small opening on the ways the STC team operates, revealed in a discussion of possible encounters with the truth.