#small things considered

[nakedgeometry]

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by Marcia Stone Viruses are supposed to be small and simple-not even alive, just mobile genetic material after all. So what do we make of giant double-stranded DNA (dsDNA) viruses, one of which-the newly discovered Pandoravirus salinus-has an even larger genome than a hunky parasitic eukaryote called Encephalitozoon? The recent identification of P. salinus adds evidence to growing speculation that it and other mammoth viruses evolved from cellular ancestors and represent domains of life that likely existed on Earth before the last universal common ancestor (LUCA). Increasing numbers of scientists are coming around to this point of view; some of whom like Gustavo Caetano-Anollés at the University of Illinois at Urbana-Champaign go even further, asserting in Microbe magazine that “giant viruses not only existed at the same time as the LUCA of cellular life, they’re direct descendants of the lineage that gave rise to it. ”Caetano-Anollés does not say this lightly-he has protein data to substantiate the claim.

[therewillcomesoftraines]

by Monika Buczek As humans we live our lives in 24-hour increments—waking, eating, and sleeping at specific times dictated to us not solely by our discerning willpower, but also by the greater underlying persuasion of our circadian rhythm. Based on the earth’s rotation from day into night, we have internalized a deeply rooted clock that drives how we behave in response to our genetic expression patterns. It’s not hard to imagine that several other organisms respond to an internal sense of time. Sure enough, the 24-hour circadian rhythm is a highly conserved behavior—from complex mammals down to plants, fungi, and cyanobacteria. Interestingly, there are also examples of different temporal rhythm patterns—ranging from years and seasons to minutes and seconds. A curious example is that of the bacterium Paenibacillus dendritiformis, which seems to have its own internal clock of a mere 20 seconds.

[therewillcomesoftraines]

Microbiology, we will agree, is a vast subject where many important aspects are likely to evade one’s sight. Here’s an example—the formation of vesicles from the outer membrane of Gram-negative bacteria. This phenomenon, known as vesiculation, is widespread and noteworthy for enhancing our understanding of bacterial capabilities and for its potential applications. My guess is that many microbiologists, like myself until recently, have only a hazy notion of it. Let me set this in context. Bacteria have evolved a panoply of tactics for communicating both socially and antisocially with most anyone, be they other bacteria or cells of their host. For this they deploy small molecules (active only above a critical threshold concentration, hence quorum sensing), they construct pili to translocate DNA, and they export proteins via more than a half dozen secretory systems. Each of these tactics requires its own mechanics and makes its own demand for energy. Secreting proteins freely into the environment is particularly wasteful of resources because few of the molecules are likely to reach their intended target. To improve the odds, some bacteria depend on making direct contact between donors and recipients before exporting. Others parcel out the molecules inside specialized delivery structures—the subject of this post.

Outer Membrane Vesicles on E. coli. Picture by Amanda McBroom

[therewillcomesoftraines]

Members of the bacterial phylum Planctomycetes (click here and here) inhabit a wide variety of environments throughout the world. What makes them special is that in the mind of some investigators they possess a mix of eukaryotic and prokaryotic structural attributes. Now that is something pretty unique and worth contemplating. This group of organisms has been previously described in this blog by previous graduate students. So this serves as an update, which is timely because there is critical news on the plancto front.

[therewillcomesoftraines]

This is the title my friend Fred Neidhardt recently used for a talk, and a good question it is. I suppose that most microbiologists and the readers of this blog would split the answer down the middle, the biomass of this planet and the chemical transactions therein being about half microbial, half everything else. However, it’s safe to say that most people, many scientists included, are unaware of the colossal importance of the microbial half, not only in biology and medicine but in geology, meteorology, and in our Earth’s habitability. This state of affairs should not be unexpected, given that we have only became aware of much of this during the last few decades. I lived roughly the first half of my life carrying only a vague notion of the global importance of the microbial world. But now we know, and the word needs to go out. A measure of microbial literacy is required for anyone to understand the workings of our living planet. Through the years, many influential writers have endeavored to convey the global influence of microbes to scientists and non-scientists alike. We can now add to these efforts a new contribution that speaks to scientists of all spheres, but especially to other biologists. It was recently published as a Perspective in PNAS, a most appropriate venue. Entitled Animals in a bacterial world, a new imperative for the life sciences, it is authored by 26 scientists whose names are bracketed by those of Margaret McFall-Ngai and Jennifer Wernergreen. It deals specifically with the role of microbes in the lives of animals. While interactions with plants and the inanimate environment are not included, this seems a fitting focus given the anthropocentric interest of most readers. The other stories are for another day, to include the viruses, the most numerous of all players and which interact with all other living things.

Microbes rule the world! It is only relatively recently that their importance is being recognized.