Small Things Considered

One If by Land and Two If by Sea

by S. Marvin Friedman

Colonization of wheat roots with Azospirillum lipoferum
labeled with the green fluorescent protein (gfp) reporter
gene. Source.

Is the current preoccupation of the scientific community with sequencing every genome extant merely an exercise in providing databases for GenBank? Certainly not, for this information also reveals very important characteristics of the organism under analysis. For example, we are at the early stages of a medical revolution that will see affordable individual human genome sequences made available to physicians as part of routine annual check-ups. As the role of various genes involved in health issues becomes even more fully elucidated, such a report will allow the physician to compile a profile of the patient’s susceptibilities to a broad range of diseases. In the case of microbiology, many fresh insights have been derived from genome sequences, including one that I have previously blogged in STC, namely genome reduction as one possible consequence of a bacterium’s commitment to an obligate parasitic lifestyle. Another of my blogs showed that the genome of the 14^th century plague bacillus isn’t so different from that of the much less virulent modern strains, indicating that other factors during the medieval era were probably in play. In the paper I am about to discuss, we will see that bacterial genome sequences tell us when and how some bacteria transitioned from aquatic to terrestrial ecosystems.

Lake Vostok: A New Microbial Habitat?

by Elio

The Vostok Station Drilling Apparatus. Source.

You must have heard by now that Lake Vostok, a large deep lake in Antarctica, has been penetrated by a Russian drill. The scientists will have to wait until next polar summer to retrieve any material. A British and American team is trying to do the same thing on another lake. You can bet that microbiologists will be there, Erlenmeyer flasks in hand, ready to receive some of the precious water emerging from the depths. Your job is to figure out what to do with it, perhaps emphasizing the less obvious.

Ovobacter propellens, Not Your Average Boring Bacterium

TEM section through an O. pro-
pellens 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.

Source.

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.

Fine Reading: Houses Made by Protists

by Elio

Euglypha rotunda test showing some 120 extremely
regular, overlapping tiles that, prior to cell division,
become arranged around the newly budding organism.
A further 8 to 14 slightly thicker, toothed tiles
surround the aperture. Source.

If there is a limit to what unicellular organisms can do, you can't prove it by me. As Michael Hansell writes in an article entitled Houses Made by Protists, some single cells can make exceedingly intricate structures. Using a Q&A format, Hansell, who bears the interesting title of Professor of Animal Architecture at the University of Glasgow, discusses examples that defy the imagination.

Take for instance the pyramids of Egypt. They are made of huge limestone blocks of fossil shells of ancient foraminifera (forams). These are true giants among the protists, making shells that reach 10 cm across. That’s some amoeba! (The ancient Greeks thought they were petrified lentils. That’s some lentils!) A lovely account of this gigantism can be seen in a site called Pyramids, forams, and Red Sea reefs: Field notes from Lorraine Casazza. Foraminifera are not the only ones to make houses; the so-called testate amoebas do, too. (“Testate” refers to tests, the name of such shells. A confusing term, that. Try giving a test about protist tests.)

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-
margarita-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.

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.

Talmudic Question #84

Within a group of well-studied DNA-based microbes (phages, bacteria, and eukaryotes), genome sizes are found to vary by almost four orders of magnitude. Their rates of mutation per base pair also vary by about that much, so the net result is that their mutation rates per genome vary less than 10-fold. Why do you think this is?

Peer Pressure Induces Biofilm Production

by S. Marvin Friedman

Diagram illustrating the development of B. subtilis into
matrix-producing cannibals and then spores. At low Spo0A
phosphorylation levels, B. subtilis activates genes required
for the production of matrix and produces two cannibalism
toxins. High phosphorylation levels initiate sporulation.
Source.

Bacteria are expert census takers. Using chemical signals they can recognize when they are in a crowd, and then they respond with appropriate collective behaviors. This census taking, termed quorum sensing, activates such diverse cellular processes as bioluminescence, virulence factor production, biofilm formation, and sporulation. Pathogens often construct biofilms. The CDC (Centers for Disease Control and Prevention) estimates that about 70% of our bacterial Infections involve biofilms, including urinary tract infections, dental caries, catheter infections, middle ear infections, cystic fibrosis, and endocarditis. Furthermore, bacteria ensconced in a biofilm are notoriously more resistant to antibiotics than their free-living or planktonic counterparts.

Biofilm formation is a complex developmental process that, it turns out, can be influenced by chemical signals produced by nearby cells of other species as well. But first, let me characterize the players involved in biofilm formation and the closely linked phenomenon of sporulation in Bacillus subtilis. Sporulation is an extreme measure not to be taken unless absolutely necessary. The decision to take the tentative first step into sporulation is controlled by a master response regulator called Spo0A. This regulator governs the expression of about 120 genes that influence cell competence, motility, and antibiotic resistance, as well as biofilm formation and sporulation. Spo0A itself is regulated via phosphorylation by membrane-bound histidine kinases, enzymes that typically act as cellular receptors for signaling molecules in the environment. Low levels of phosphorylation of Spo0A cause B. subtilis to develop into matrix-producing (i.e., biofilm forming) cells that secrete two toxins: sporulation-delaying protein (SDP) and sporulation killing factor (SKF). They also produce the immunity proteins necessary for their own survival. The toxins kill susceptible cells of B. subtilis and other microbes, thus providing the toxin producers with nutrients that enable them to postpone sporulation. Such cells have been appropriately called cannibals, and they are important biofilm components. When Spo0A phosphorylation levels are high, the genes for matrix production are repressed, sporulation genes are induced, and the cannibals progress on to sporulation.

Fine Reading: Small Wonders

by Merry

The genome of Mycoplasma genitalium, the free-living organism with
the smallest genome, is two to four times as large as the genomes of
five symbionts recently shown to have tiny genomes (that is, smaller
than 300 kb). Gene functions are color-coded: blue = information
processesing; maroon = vitamin or amino acid biosynthesis; green =
ribosomal RNA; grey = other; breaks = non-coding regions. Source.

The bacterial endosymbionts of insects are a perpetual source of wonderment. We wonder, for example, what is driving the paring down of the genomes in the intracellular world? How far can it go? Is the pattern of gene loss similar from one endosymbiont to the next? Are they on the road to becoming organelles? In a recent review, John McCutcheon and Nancy Moran share their best current answers to these questions and more, and even make a prediction or two.