Moselio Schaechter

  • The purpose of this blog is to share my appreciation for the width and depth of the microbial activities on this planet. I will emphasize the unusual and the unexpected phenomena for which I have a special fascination... (more)

    For the memoirs of my first 21 years of life, click here.

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November 25, 2013

Fine Reading: Exploring the Microbial Dark Matter

by Merry Youle

Hic sunt dracones

Figure 1. The marine macrobial dark matter. Hic sunt dracones. Source.

We live in a world run by microbes, the vast majority of which we have yet to identify or name. We can only refer to them collectively as the microbial dark matter (MDM). However you define a prokaryotic species, and however you tally them once identified, there is a huge gap between the 12,000 or so validly-named species and the total number on our planet, currently estimated to be in the millions. The only evidence we have for the existence of that uncultured mob is either a small subunit ribosomal RNA (SSU rRNA) sequence or some hazily-classifiable metagenomic reads. As the speed of sequencing goes up and the cost goes down, this sort of evidence accrues ever more rapidly, further widening the gap. The challenge at hand is to find out more about the organisms that make up that dark matter.

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August 19, 2013

A Whiff of Taxonomy – Archaeoglobus fulgidus

by Elio

Cells of A. fulgidus are typically irregular and with a dimple. Bar: 0.5 µm. Source.

Pick an archaeon, any archaeon, and you will find it has a story to tell. Not all archaea are exotic but plenty of them are. These stalwarts live in environments we humans call extreme, where they carry out what to us seem extreme types of metabolic conversions. Most have come rather late into our awareness. To redress their neglect, I picked one almost at random. It’s a hyperthermophile called Archaeoglobus fulgidus (the genus name derives from “ancient sphere,” the species from “shining,” for its UV fluorescent glow under 420 nm light). The genus was proposed by Stetter in 1988.

The family to which this species belongs, the Archaeoglobales, is typically hyperthermophilic. A. fulgidus grows optimally at 83 °C and is at home in hellish environments such as deep sea vents, oil deposits, and hot springs. A chemolithoautotroph, it reduces sulfate to sulfide, specifically to iron sulfide when given steel pipes to 'eat'. Since iron sulfide corrodes metal pipes, it is a nuisance to the humans tapping oil deposits to produce oil and gas. On the other hand, this skill may come in handy for detoxifying metal contaminants at high temperatures.

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July 29, 2013

The Planctomycetes, Tricky Gram-negatives Awaiting Genetic Manipulation

by Marco Allemann

Figure 1. The original interpretation of the G. obscuriglobus cellular organization. Thin section of cryosubstituted bud cell with large nuclear body bounded by a “nuclear envelope” (E) consisting of two membranes between which is a clear electron-transparent space. The nuclear body contains ribosome-like particles as well as a nucleoid. It is surrounded by cytoplasm that contains superficially similar ribosome-like particles and is bounded by a single intracytoplasmic membrane (ICM). Bar: 200 nm. Source.

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.

What Do You See Inside The Planctos?

Under the electron microscope, sectioned Planctomycetes cells reveal that their internal membrane is highly folded into apparent compartment, including a purported membrane-bound nuclear region. It has been suggested that this arrangement, almost unheard of among prokaryotes, is evidence for the planctos being a “missing link” between Bacteria and Eukaryotes. The linchpin for this notion that the planctos may be some kind of remnant of eukaryogenesis has been their “nuclear envelope,” which is thought to totally surround the nucleoid. There are yet other arguments in favor of this notion, e. g., they are able to endocytose and they divide by budding (although so do other bacteria, such as Caulobacter crescentus). In addition, those planctos capable of anammox (anaerobic ammonia oxidation coupled with nitrate reduction) contain an organelle, a membrane-bound structure called the anammoxosome. Yet, the presence of organelles is not unique to this group of bacteria. Of interest is also that planctos do not contain peptidoglycan in their cell wall, something limited to few bacteria. Surprisingly, they carry genes encoding for known outer membrane proteins and peptidoglycan synthesis, although in this regard they may not be all that unique either because chlamydiae and mycoplasmas also lack peptidoglycan, plus the chlamydiae also carry genes for its synthesis.

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February 11, 2013

The Gram Stain: Its Persistence and Its Quirks

by Elio

What is more emblematic of our science than the Gram stain? Since its invention 130 years ago, it has been in frequent and continuous use. It conveniently places most bacteria into one of two groups, the Gram-positives or the Gram-negatives. Gram staining is cheap, effective, quick, and relatively easy to interpret. Its most useful application is in the clinical setting. When examining a smear of, say, pus from an abscess, this stain often allows to include for consideration roughly half the clinically relevant bacterial species while excluding the others. Or consider a patient with meningitis. Here, speed is of the essence because treatment must be initiated right away. A Gram stain of the spinal fluid may reveal within minutes the presence of Gram-positive cocci, (probably pneumococci), Gram-negative cocci (almost certainly meningococci), or Gram-negative slender rods (most likely Haemophilus influenzae). This can make a critical difference in the choice of antibiotics that have to be administered in great haste. However, when it comes to characterizing the bacteria in an environment, its usefulness diminishes, in part because it is not always in step with taxonomy, which I’ll discuss below. And there yet is another side to this story. Quite a few bacterial species that stain positive early in the growth of a culture become Gram-negative later on. Does this detract from the value of Gram’s method? It may, but not in the hands of a person experienced in its use.

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December 13, 2012

A Whiff of Taxonomy – Verrucomicrobia, The Bacterial Warthogs

by Elio

"We occasionally post very brief taxonomic pieces on selected bacterial groups. Be warned that we may not be fully attentive to the taxon level and may mix up genera and higher taxa."

A Verrucomicrobium. Source.

Unlike warthogs, likely to be considered beautiful only by their mother, the Verrucomicrobia  (verruca means “wart, thus the warty bacteria; more about this later) have considerable appeal, be it morphological, physiological, or ecological. This is yet another phylum that owes its recognition to nucleic acid technology. Although few of its members have been cultivated, 16S rRNA studies have confirmed that they are widely distributed in many environments, such as fresh water, oceans, soils, and even vertebrate feces.  Some are host-associated, their hosts including humans and, just because you need to know it, their proportion in the gut of ground squirrels increases as they hibernate. There are no known pathogens in this group although suspicion has arisen.  

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November 12, 2012

Why Listeria Is Competent to Be Virulent

by S. Marvin Friedman

A listeriosis outbreak of 2011 caused 147 cases of illness and 33 deaths in 28 states in the US. The source was cantaloupes grown at one Colorado farm. Source.

It is downright scandalous that in our hi-tech world food-borne infections should be so prevalent (some 48 million cases a year in the US alone, with about 3000 deaths). The tools to take care of these problems are hardly mysterious, requiring mainly safe food production and preservation. High on the list of bacterial offenders is Listeria monocytogenes, a Gram-positive facultative intracellular pathogen that is acquired through ingestion of contaminated food or fluids. Listeria is found in uncooked meats, vegetables, fruits such as cantaloupes, unpasteurized milk and milk products, and some processed foods. Although pasteurization and sufficient cooking will kill Listeria, contamination often occurs after cooking and before packaging. Listeriosis is a disease primarily affecting pregnant women, newborns, adults with compromised immune systems, and the elderly. The two most common life-threatening symptoms are sepsis and meningitis. This is a serious disease with a relatively high mortality that can reach 25%.

L. monocytogenes is an intracellular parasite of epithelial cells and macrophages. It initially resides in a membrane-bound vacuole, the phagosomal vesicle, which is a dangerous site for many bacteria. In order to carry out a successful infection, it escapes into the host cell’s cytoplasm by lysing the vacuolar membrane via a pore-forming hemolysin, listeriolysin and two phospholipases. However, the precise mechanism of this escape is not fully understood. Once within the host cell cytoplasm, the bacteria replicate and use the host’s actin filament network to propel themselves within the cell and from cell to cell.

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November 05, 2012

The Excitement of Clinical Microbiology

by Elio

Members of the San Diego VA Clinical Microbiology lab: (L to R) Romelia Quinonez, Raymond Samson, Carlo Basallo, Monica Beach, Icela Gonzalez, Dr. Joshua Fierer, Juan Ybarra, Jasmine Estrada, Tracey Grosser, Laura Gomez.

Clinical microbiology, one of the major branches of microbiology, goes largely unnoticed by academics, in part perhaps because the diagnostic activities of microbiologists are pursued separately, in hospital and commercial labs. I’d venture to guess that many academic microbiology researchers have never set foot in one of these labs. Their loss, as it would be an exciting and rewarding experience.

This rift casts aside the historical roots of our field. At its beginning, soon after bacteria were found to be the cause of infection, there was a huge rush to develop methods for determining the identity of agents responsible for a patient’s illness. Ingenious laboratory media were designed to favor the growth of certain organisms and to reveal their distinguishing properties, and serological techniques were developed alongside. In those days, there was no significant distinction between diagnostic microbiology and the rest. In time, as research in other fields of microbiology matured, these diverged more and more from this point of origin.

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October 22, 2012

A Kick in the Midgut

by S. Marvin Friedman

Malaria is one of the most devastating infectious diseases in the world today. About 400 million people are infected each year and of those 1.2 million die. Efforts to control malaria have been held back by the lack of an effective vaccine, the alarming rapidity with which Plasmodium, the protozoan parasite, develops drug resistance, plus the failure to eradicate the Anopheles mosquito vector. Fresh approaches to fight malaria are urgently needed, to be used singly or perhaps in combination. One novel approach to a vaccine was recently discussed in this blog.

Formation of Plasmodium berghei (a rodent parasite) oocysts in culture. A. Ookinetes. B. Transforming ookinete and C. young oocysts. F. Transformation begins with a small hump on the outer edge of the ookinete. Transforming ookinetes (“tooks”) then take on a snail-like appearance (v). The entire population of ookinetes transform in 12–36 h, depending on nutrient availability. Source.

Plasmodium undergoes an unusually large number of lifestyle changes in its trip from the female mosquito to a human and back. This is one of the most complex life cycles extant, with so many details that it taxes one’s memory. Each one of the dozen or so stages is labeled with a fancy name and ought be a target for intervention but, for a host of reasons, that has proven elusive. However, the parasite is especially vulnerable in one stage, the transition from a cell called the ookinete to one named the oocyst, which occurs in the mosquito’s midgut. Eventually, the oocysts cross the midgut epithelium into the insect’s circulatory space, the hemocoel. But before going across, the ookinetes are detected by recognition components of the mosquito’s immune system. Killing factors from both the midgut and nearby tissues are recruited and the ookinetes targeted for destruction. In some model systems, fewer that 5% of the ookinetes survive. This, then, is a bottleneck in the Plasmodium life cycle and an attractive place to try to intervene for extermination of the parasite.

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February 20, 2012

Ovobacter propellens, Not Your Average Boring Bacterium

Fenchel 3

TEM section through an O. pro-
showing the abundant
flagella and a row of regularly
spaced, electron dense organelles
consisting of stacked membranes.
Bar = 1 μm. Source.

by Elio

I bet most of you have never heard of this one. And you are not alone in this. Look for it by name in PubMed and you find two entries, both from the same lab. This bug deserves better. Found by using a fairly direct enrichment technique from sediments in shallow Danish waters, this organism evinces aspects of both structural and physiological uniqueness. It is seen as an ovoid cell that looks less like a bacterium than like a small ciliate. The evidence that it is a prokaryote relies on morphology alone, as it has not been cultivated nor has its DNA been sequenced.

Fenchel 1 teble

Ovobacter propellens (or, to reluctantly obey one of my least favorite rules of taxonomy, Candidatus O. propellens) appears as large ovoid cells, 4-5 μm in length, each possessing a huge tuft made up of some 400 flagella. Armed with such equipment, it travels at astounding speeds, having been clocked at 1 mm per second. (That’s some 200 body lengths. To equal that, a human would have to swim at over 300 meters per second.) Now for a small digression: by chance I encountered a most informative table of examples of microbial motility. You will notice (see table) that while paramecia outswim all others in terms of velocity, protists and bacteria alike, O. propellens matches them.

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February 13, 2012

The Three Faces of Thiomargarita

by Merry

How inappropriate to call this planet Earth when it is quite clearly Ocean.
            Arthur C. Clarke


Budding is evident on these attached, elongated Thio-
-like bacteria collected near a methane seep off
the coast of Costa Rica. Bar = ~1 mm. Source.

Ahhh, the delicious aroma of hydrogen sulfide. When as kids we encountered  it, we would hold our nose and proclaim “yuck, rotten eggs!” It is indeed produced by something ‘rotting,’ but specifically rotting under anaerobic conditions, such as in swamps and sewers. It is also abundant in coastal marine sediments, produced by the oxygen-consuming heterotrophic decomposition of organic matter. This makes for a layer at the sea bottom that is sulfide rich but oxygen poor. Nevertheless, leaving no potential energy source untapped, some bacteria in these zones use sulfur oxidation as their energy source. They include two remarkably large γ-proteobacteria, Thioploca and Thiomargarita. Thioploca copes with the lack of oxygen by using nitrate as an alternate terminal electron acceptor, but this just exchanges one problem for another. The sulfides are in the sediment, the nitrate in the water column above. So Thioploca commutes between the two zones, as Elio described in an earlier post.

Namibiensis chain

Thiomargarita namibiensis, the “Namibian sulfur pearl.”
Courtesy of the Microbiological Garden. Source.

Non-motile Thiomargarita uses a different tactic. This bacterium was first discovered in 1999 off the Namibian coast, thus was named T. namibiensis. Its cells are large spheres, arranged in chains, each chain enclosed in a mucous sheath. Average cell diameter is 180 μm, with rare individuals reaching 750 μm, which is about as big as bacterial cells get. But they do this by cheating. Most of the ‘cell’ is a large vacuole, with the cytoplasm relegated to a thin surrounding outer layer. Sulfur globules are evident in the cytoplasm. Thus the genus name, Thiomargarita, that was derived from the Greek for ‘sulfur pearl.’ Thiomargarita spp. are widespread in hydrogen sulfide-rich coastal sediments. They, too, use nitrate as their terminal electron acceptor. Their strategy is to take advantage of the occasional events that resuspend the sediment and bring abundant nitrates into the water column. They then hoard nitrate in their huge vacuoles—enough nitrate to see them through even months of scarcity.

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