Small Things Considered

Fine Reading: Arboreal Matters

by Elio

Tree of Life, by Gustav Klimt (1909).

The Tree of Life vies with the Origin of Life for a position of highest significance among biological concerns. Those who write about it (bioarborists?) have much to say about its anatomy. Does it consist of simple branches, as per Darwin’s sketch, or is it anastomosed into a bramble of connected branches? This matters. By one scheme, ancestry can be directly discerned, by the other, much extra information is required. Genealogists know how hard it is to trace family trees when some DNA found its way into the lineage by, shall we say, a supplementary route.

But here is food for those who want to be enlightened. A special issue of the journal Biology and Philosophy is entitled The Tree of Life. Edited by the British biophilosopher (is there such a term?) Maureen O’Malley, it consists of fifteen chapters written by experts in the field. Microbiologists will find this to be an important addition to their long list of things to read, being that some 90% of evolution took place while life was solely microbial.

Commuting to Work

by Elio

A tube core (8 cm diameter) collected from a Thioploca
bacterial mat. The mat is approximately 1 cm thick.
Photo by Lisa Levin. Source.

An underwater microbial mat has been found in fairly shallow waters off the coast of Chile and, according to headlines (click here and here), it’s the size of Greece, or about 132,000 km² (or for us norte-americanos, about the size of Alabama). These communities of sulfide-oxidizing bacteria have been known for some time, but their attention has been highlighted by the recent version of the Census of Marine Life. In fact, they were discovered in 1963 by the oceanographer and microbiologist Victor Gallardo of Chile’s University of Concepción. Scientists may not have known much about these huge mats much earlier on, but the local fishermen sure did and called them estopa, Spanish for burlap or unwashed wool or flax.

What the mats look like on close-up (swaying in the
current?). Source.

Aficionados of the giant sulfur-oxidizing bacterium Thiomargarita namibiensis and other bacterial gargantuas likely include Thioploca, the occupants of these mats, in their catalog of microbial marvels. This is a genus of gliding, filamentous bacteria that live in aquatic sediments where they face the same problem as Thiomargarita, namely how to hook up their fuel (sulfides) with their final electron acceptors (nitrates). (For details of their metabolism, see a recent paper.)

Talmudic Question #66

What if someone found an organism whose genes assignation is 1/3 bacterial, 1/3 archaeal, and 1/3 unknown?

We jumped the gun and posed this question to our friend Ramy Aziz. He responded with answers that reflect various phylogenetic points of view.

• Scientist A thinks this organism is whatever its ribosomal DNA tells us it is.
• Scientist B believes it's whatever its recA gene tells us it is.
• Scientist C proposes that this is proof that there is no tree of life, but rather a reticulum.
• Scientist D declares that, whatever it is, it’s certainly not a prokaryote (as there is no such thing).
• Scientist E tells us that it's an unknown organism that ate both a bacterium and an archaeon.
• Scientist F puts forth that that proves there is a fourth domain of life, or—just wait a while—that it's a synthetic, biologically-created hybrid.
• Scientist G says that it's proof of a viral origin of life.

And yours?

Marine Snow: Dead Organisms and Poop as Manna in the Ocean

by Hannah Waters

Editors' Note: Let’s face up to the fact that important ecological phenomena involving microbes are not always known to many microbiologists. Marine snow, a major factor in the biology of the oceans, is an example. We found an illuminating and well-written description of the subject in the blog Culturing Science and are reproducing it by permission of the blogger.

Rattail swimming out of a cloud of marine snow
near the bottom of the northern trench of the
Charlie-Gibbs Fracture Zone (4400 m, June 2003).
Photo taken as part of MAR-ECO project
through CFML.

When I think of the floor of the deep sea...I see always the steady, unremitting, downward drift of materials from above, flake upon flake, layer upon layer...the most stupendous “snowfall” the earth has ever seen.
                                Rachel Carson,
                                The Sea Around Us (1951)

Marine snow: does the phrase make you think of fish wearing ice skates, seahorses in knit caps, and crabs building snow-fish? If so, I can’t entirely blame you: the stuff looks like snow, hence its name. But marine snow is not composed of frozen water, each flake unique and beautiful. It is, in fact, made up entirely of dead organisms, poop, and random junk floating in the ocean. (Still fancy a marine snowball fight?)

To undergo photosynthesis, marine phytoplankton (the “wandering plants” in Greek) can only live in the sunlit areas (the photic zone) of the ocean, which rarely reaches a depth greater than 200 meters. The phytoplankton do their thing, you know, generate nearly half of the planet’s primary production (no big deal?!), until they are either eaten or die. And when you’re living at the top of a miles-deep ocean, the only way to go is down. And thus we have marine snow.

Good Writing Beats Bad Writing, Most Any Day

by Elio

Tree of Good Writing, by Hiroshige, circa 1846. Source.

There isn't any thought or idea that can't be expressed in a fairly simple declarative sentence.....
                            E.B. White, Fro-Joy

Just when some people believe that the world is going to hell in a hand basket, here I am, ready to make a cheerful personal statement: Scientific writing is improving! Of course I base this on reading the microbiological literature, but assume that it’s generally true. What makes me say so? Well, more often than not, current research papers and reviews contain a fair share of simple declarative sentences. In my earlier days, typical statements were often in the passive form: “The effect of X on Y has been studied.” The first person form is now accepted, much to everyone’s relief. And titles of articles tend to informative. Gone is Studies on the metabolism of Escherichia coli: Part XIV. And, although I couldn’t swear to it, I believe that the language in graduate student papers has also improved. Nowadays, even humor is permissible. It has even permeated this blog, as exemplified by the wicked sense of humor of my co-blogger, Merry, who has come up with titles such as The Bacterium That Doesn’t Know How Tie Its Own Shoelaces, Coxiella Escapes From Cell, and A Holin One.

What has happened? Have scientists turned into Hemingways overnight? Good question. I would guess that changes in culture (sensu lato) are the big factor. We seem to be more factual in communication and less prone to circumlocutions and Victorian adornments of speech. So, this may well be part of a general development, but what about its roots? What caused these cultural changes? I am no wiser.

Bacterial Physiology and Virulence: The Cultures Converge

Close up view of the ppGpp binding site of the
RNAP/DksA/ppGpp complex. Source.

by Fred Neidhardt

Growth dominates the attention of many bacteriologists. It has done so for over a century, inspiring explorations into the complex biochemistry and physiology that produce new cells able to grow, survive harsh environments, and live to grow another day.

Likewise, since the earliest days of microbiology, virulence has been a central focus. In fact, studies of how bacteria cause disease have in sheer number dominated the field for the simple reason that more than intellectual curiosity has been involved: human health has demanded that one learn to cure infectious diseases and protect against them.

Until recently, researchers in these two arenas of microbial exploration shared precious little beyond basic technology and a knowledge of bacterial cell structure and function. Separate scientific cultures developed, as is so often the case in human endeavors. Not uncommonly, investigations of infectious disease proceeded largely in medical school departments of internal medicine or pediatrics, while explorations of the intricacies of microbial growth processes were pursued at the same schools in basic science microbiology departments. That situation has been changing in the past couple of decades, and finally the frontiers of bacterial physiology and of virulence (molecular pathogenesis) have virtually fused. An international symposium (Metabolism Meets Virulence) held in Höhenkammer (Germany) in April, 2009 helped signal this watershed. A scan of the topics covered [Ref 1] reveals some of the subjects in which these two areas of research have become intertwined. Today, each subject benefits from attention to the other.

Many examples could be used to illustrate this sea-change, but none is more fully documented than the intimate involvement of the bacterial stringent control system in Legionnaire’s disease of humans. The central player in the stringent control system is ppGpp (guanosine 5’diphosphate, 3’diphosphate), a nucleotide long known as a major governor of bacterial growth processes. A recent review [LINK] co-authored by Michael Cashel (who in Jonathan Gallant’s laboratory discovered this “magic spot” [LINK and LINK]) brings the ppGpp story up to date. This nucleotide alarmone (as it is frequently dubbed) and its helper protein, DskA, have now been shown to orchestrate the complex alternation between two differentiated intracellular forms of the bacterium Legionella pneumophila, a process required for its pathogenicity.

For those interested in the direction of current microbiological research, this tale of ppGpp in disease is enthralling. Here we shall concentrate on Legionella virulence, but readers are directed to a recent review [LINK] that presents in scholarly detail the known involvement of ppGpp in many infectious diseases—and suggests the likely extension to many others.

The following account is a brief summary by one who has been a student of growth and ppGpp regulatory effects for four decades. To ease this author’s conscience for not mentioning all the talented researchers who have explored the stringent system or pioneered studies of Legionella virulence, I express my regret at not paying due respect to these fellow adventurers. Their work is the basis of our story, and I trust that the two recent comprehensive reviews [LINK and LINK] of these areas will be consulted to learn their names and their contributions to this community effort.

Making it Personal

by Amy Cheng Vollmer

Here we are looking at the beginning of another academic year! Like many faculty members, my teaching load includes courses in my area of expertise (microbiology) and also some outside of my true comfort zone (introductory biology). Over the years, my attitude toward teaching introductory biology has shifted from dread to resignation to acceptance and finally, nowadays, to excitement.

At Swarthmore, we offer only one tier of introductory biology—not one geared for majors and another for people satisfying their science ‘general education’ requirement. In fact, students here are required to take two courses in the Division of Natural Sciences and Engineering, one of which must have a lab (or ‘practicum’ to distinguish it from language labs, for example.) Hence our Biology 001 (Cellular and Molecular Biology) and 002 (Organismal and Population Biology) courses are popular choices. The enrollment is between 90 and 120 each term. Seated in the lecture hall is an audience with great diversity: ethnic, high school experience, interest, motivation, aptitude, and attitude. Many times we end up with ‘converts’ to Biology, while also discouraging a few students who simply want to memorize.

Listeria's Visiting Card

by Elio

Listeria monocytogenes (Scanning EM). Source.

During infection, host and parasite carry out repeated and intense conversations that often rise to the level of shouting matches. The language they use is chemical, the words and sentences eloquent and forceful. Eavesdropping on the conversation between Listeria monocytogenes and immune cells of its host, Portnoy and colleagues discovered an intriguing linguistic use for a novel “second messenger,” cyclic-di-AMP (c-di-AMP).

It has been known that Listeria, like many intracellular pathogens, promotes the making of an interferon (IFN-β), which in turn signals cells of the immune system, thus activates them. But what sets this in motion? What are the signals emitted by Listeria and how are they “heard” by the host cells? The answer is that the bacteria excrete c-di-AMP, which activates the so-called cytosolic surveillance pathway. One aspect of this is the making of interferon. The immune response is now off and running; mobilized killer lymphocytes and other host defenses ward off the invading organisms.

Talmudic Question #65

What is it about the cyclic nature of nucleotides, both monomers and dimers, that makes them such favorites for signaling purposes?

Dr. Rous’s Prize-Winning Chicken

by Welkin Johnson

If one were to apply contemporary principles of evaluation to the work of Peyton Rous in his time and without the benefit of hindsight, this work would certainly be assigned a low priority, not fundable, and probably also not publishable in the trendsetting journals that today alone can confer recognition and prestige. Even in 1966, the year of the [Nobel] prize, it was impossible to guess at the full significance of the Rous sarcoma virus for human medicine and biology…The urgent lesson from the Rous experience, then, should be that it is the quality of the science that counts, not its compliance with a fashionable trend and not its perceived future value, which cannot be predicted.
                                 Peter K. Vogt (1996. The FASEB Journal 10:1559-1562.)

Peyton Rous. Source.

One hundred years ago today, Peyton Rous published the first in a series of papers describing experiments that began with work on a sarcoma from a single Plymouth Rock hen. In that initial paper, Rous showed that bits of the tumor could establish new tumors when injected into healthy chickens. A year later, in 1911, Rous published what has become a classic in the annals of virology—A Sarcoma of the Fowl Transmissible by an Agent Separable from the Tumor Cells—reporting that the tumors were transmissible from one chicken to another by injection of a cell-free, filtered homogenate of the tumor tissue. The conclusion, since confirmed a thousand times over, was that a virus caused the tumors. The virus, now known as Rous sarcoma virus (RSV), went on to play a starring role in 20^th century biomedical research.