Small Things Considered

Microbial Matchmakers

A mating pair of Drosophila melanogaster. Source.

by Merry

Back in 1983, researchers at Yale borrowed a microbiological tactic to study evolution at a "single gene locus" in a multicellular animal—the use of altered growth media to select for nutritional mutants. They confronted populations of Drosophila pseudoobscura with a growth medium containing either maltose or starch as the sole carbohydrate source and observed inherited changes to the α-amylase allozyme frequencies and the enzyme's location within the gut in the "starch flies." Interesting, useful, but not revolutionary.

A few years later a Yale Ph.D. student working with the same flies reported something unexpected. Looking at populations that had been reared on the maltose or starch medium for a year, she found that starch flies preferred to mate with starch flies rather than maltose flies, and likewise the maltose flies preferred maltose mates. In her paper she concluded that the new behavior was a pleiotropic by-product of the adaption to the different media.

And so the matter rested for about two decades until revisited by a group of five researchers from Israel and one from Maine, with some most intriguing—and microbial—insights. (You knew that there had to be a microbe lurking somewhere. Otherwise I wouldn’t be writing about fly mating behavior here.) In their recent PNAS paper they present evidence that the flies raised on different food sources harbor different populations of bacterial commensals, and that it’s these microbes that are the matchmakers.

The Flying Cow

Hoatzin adult and chick. Notice the claws on
the wings of the chick. Source.

by Elio

Here’s a bird that thinks it’s a ruminant. Or, speaking science, ruminants may have coevolved their singular way to digest plant material with a bird. I am talking about the hoatzin, a tropical pheasant-sized or, in honor of the day, turkey-sized bird of Central and South America that ferments in its crop the leaves it eats. Opisthocomus hoazin, to give his full name, is unique. No other bird—and there are some 9000 species—is known to carry out a pre-gastric (ruminal) fermentation (although a few do something similar in the cecum). Hoatzins are almost exclusively leaf-eaters, so they benefit greatly from having a microbiome that can handle such food, just as cows do. To accommodate this activity, they have an unusually distended crop and a large esophagus.

Physical Virology

by Manuel Sánchez

We reprint here an article from the Spanish blog Curiosidades de al Microbiologia. This post was written by blog host Manuel Sánchez and is reprinted in translation with his permission.

Source.

Physical Virology. Such is the title of the article that appeared in Nature Physics. This is the name for a new discipline that is under development. Its focus is the study of viruses from a physical perspective. Seen this way, viruses are natural nanoparticles with distinct mechanical and thermodynamic properties

Professors W. Roos and G.J.L Wuite of the Foundation For Fundamental Research On Matter of the University of Amsterdam and R. Bruinsma of the Physics Department at UCLA summarize in that article the possible implications of this new discipline, especially for medicine.

Viruses are able to spontaneously assemble into icosahedra that enclose their genetic material, and do so in an environment, such as the cytoplasm of the host cells, that is loaded with similar molecules. This process takes place without an external source of energy, that is it follows the thermodynamic laws of reversible self-assembly. But there is one fundamental difference: once assembled, the capsid does not disassemble. For this reason, viruses are a good model for studying the formation of nanostructures that require only minimal energy expenditure.

Talmudic Question #68

by Mike Rust

Why have the bacterial signaling systems based on histidine and aspartate phosphorylation been abandoned (with some exceptions) in favor of serine/threonine and tyrosine phosphorylation in eukaryotes?  Is this just a "frozen accident" or is there a deep biochemical reason?”

Siblings Strike Again

Cain Killing Abel, Italian School. Source.

by S. Marvin Friedman

Bacteria capable of sporulation go out of their way to grow rather than sporulate. They will therefore try to obtain needed nutrients, even at the cost of killing their neighbors. When starved for nutrients, cells of Bacillus subtilis engage in cannibalism, that is they lyse their siblings and use the nutrients thus obtained to postpone their own sporulation. A similar phenomenon, termed fratricide, has been reported in Streptococcus pneumoniae where the killing of siblings is linked to the induction of competence and the release of DNA from lysed cells. The antimicrobial agents secreted within the same colony by either cannibalism or fratricide belong to the family of bacteriocins. Be’er and his colleagues now report a third unique situation where bacterial stress leads to sibling death.

Panebacillus dendritiformis (T-morphotype) forms branched colonies on low-nutrient, hard agar plates. When two neighboring colonies are produced by inoculation from the same culture, their growth is inhibited at the zone of closest contact. All the cells at the interface of the inhibited region are killed. Death occurs even at relatively high nutrient levels, thus ruling out cannibalism (killing to obtain nutrients) as the mechanism that operates here.

Of Terms in Biology: Bacterial Ploidy

Deinococcus radiodurans. Source.

by Elio

Ploidy is not a term that has much currency in bacteriology, but it does make an appearance once in a while. Ploidy, as per the dictionary, is the number of chromosomes per cell. It’s a term widely used for cells that are generally uninucleated, such as our gametes and our somatic cells. The problem here is that bacteria are not consistently uninucleated. In some bacterial species, the cells always contain more than one nucleoid, while in others the number is variable, depending on their circumstances. Due to such vagaries, there are several ways to define ploidy in bacteria.

Fattening Up Microbial Geological Biomarkers

by Paula Welander

First Evolved! Last Extinct! This prokaryotic pride motto was coined by my undergraduate advisor (and good friend) Prof. Mark Martin. As a microbiologist, I love this motto for many reasons, but especially because it alludes to one of the underlying principles of my current research. Microbes were indeed the first to evolve and the metabolic inventions of ancient microbes greatly influenced the ancient Earth’s environment and the evolution of life. The interaction between the Earth and microbes has been recorded in sedimentary rocks that are billions of years old.

Figure 1. The biomarker principle involves the burial and preservation of bacterial lipids such as
hopanoids in the sedimentary rock over billions of years. Diagenesis describes the chemical,
physical, or biological changes undergone by sediment after its initial deposition. Bacteria
present in the water column die and are deposited and buried in the sediment where they undergo
degradation. Hopanoid molecules lose the majority of their functional groups but the basic hopane
structure is preserved over billions of years. Geochemists are then able to extract and detect these
lipids in ancient sediments. Credit: Paula Welander.

Accessing this microbial record continues to be one of the challenges of geomicrobiology. One powerful strategy for understanding the microbial signatures in the rock record is the use of “molecular fossils” or biomarkers, organic compounds that are produced by select groups of microorganisms and, amazingly, are preserved in both modern and ancient sediments. Geochemists are able to extract these molecules from very old rocks and, based on their distribution in modern organisms, link specific groups of bacteria to ancient environments (Figure 1).

Figure 2. Structure of a 2-methylhopanoid. Credit: Paula
Welander.

As Tanja Bosak described in her earlier contribution to this blog, both eukaryotic and bacterial lipids are preserved in old rocks, thus both have the potential to be “molecular fossils.” One example of such is the use of 2-methylhopanoids as biomarkers for cyanobacteria and oxygenic photosynthesis. Hopanoids are pentacyclic triterpenoid lipids produced mainly by bacteria that are structurally similar to eukaryotic sterols (Figure 2). As the name implies, 2-methylhopanoids are methylated at the C-2 position. Although seemingly a minor modification, this chemical alteration endures in ancient rocks. Studies with modern bacteria showed that cyanobacteria are the predominant producers of 2-methylhopanoids. On this basis, 2-methylhopanoids have been used as biomarkers not only for cyanobacteria but also for oxygenic photosynthesis . The presence of these molecules in rocks provided evidence for the antiquity of oxygenic photosynthesis and for the role of cyanobacteria in the ancient past (click here, here, and here).

One Symbiont Is Good, Two Are Better: The Forever Fascinating Story of the Leaf-Cutting Ants and Their Bacteria

by Elio

Leaf- cutting ants returning to their nest. Source.

Now here’s a question you’ve been asking all along about the interaction between the leaf cutting (Attine) ants, the fungi they cultivate, and the bacteria that make antifungals against unwanted fungal species. Have these bacteria evolved along with the ants to protect their gardens from unwanted "weeds," or do the ants pick up such bacteria from their environment? New data suggest both things happen.

To remind you, leaf-cutting ants practice fungiculture, and have been doing this for about 50 million years. The bits of leaves and flowers that they bring to the nest get chewed up, fertilized, placed in suitable “gardens” within the nest, and seeded with fungal material from previous gardens. Obviously, fungal gardens can be overrun by unwanted species, with disastrous results for the colony. To keep this from happening, the ants depend on selective antifungals made by actinomycetes. We have visited this topic in the past (click here and here).

Tales of Death

by Merry

Another tail of death. Source.

Bacteriophages are expert killers, having been delivering death to bacteria for several billion years. We are not the first organisms to recognize their skill. Bacteria themselves have borrowed the tail of a phage and fashioned from it a targeted bacterial killer for their own use.

We first became aware of this in 1925 when André Gratia observed that E. coli produced a proteinaceous agent that efficiently killed other E. coli, but not unrelated bacteria. Being proteinaceous and selective is what distinguishes these agents, the bacteriocins, from other antibiotics. Many are now known, made by both Gram-negatives and Gram-positives. Initially they were classified and named for who produced them. Thus colicin for that first one, monocin made by Gram-positive Listeria monocytogenes and pyocin for those made by Pseudomonas aeruginosa (formerly pyocynia).

As the list grew, it became evident that the bacteriocins are a heterogeneous bunch. Some of them, including colicin, are trypsin-sensitive proteins, typically encoded on plasmids. (For more information about this group, click here.) Others are trypsin-resistant particles that can be purified by the same techniques that are used to purify viruses. Under the electron microscope, they look exactly like phage tails. Some resemble the contractile tails of the Myoviridae complete with sheath, core, base plate, and tail fibers, others the flexible but non-contractile tails of the Siphoviridae. These headless phage particles contain no DNA.