In April 2010, the state of Wisconsin declared Lactococcus lactis its official microbe. This makes perfect sense because the bacterium is crucial to cheese making, one of Wisconsin's signature enterprises. The announcement prompted Lauren Schenkman (2010) to ask researchers in other states what they might name as their "microbe mascots." The answers included Bradyrhizobium japonium, a symbiont in soybean roots that fixes nitrogen, thus saving Iowa farmers a lot on fertilizer, and Nesiotobacter exalbescens for Hawaii because it is only found in a single lagoon on one of the state's atolls, Laysan. Some researchers took another tack, suggesting bacteria that are more notorious than useful: Salmonella typhimurium for North Carolina, where hog farmers have to be constantly on the lookout for it; and Acidithiobacillus ferrooxidans, a new visitor to Louisiana that arrived in Chinese-made drywall for rebuilding New Orleans and spews out foul sulfurous compounds.
Because this month's ABT theme is microbes, I decided to begin my column with this new way to "honor" them. I had pulled out my "microbes" folder and sorted the articles. First, I separated out those dealing with bacteria because I have to admit they are my favorite microbes. I am enchanted by their versatility. Then I further sorted into two piles: those that dealt with disease-causing organisms, and those that covered odd topics, like the one I've just mentioned, or some of bacteria's more intriguing adaptations. Obviously, pathogenic organisms are important research subjects, but I felt like being more positive; and in fact, I discovered as I studied the articles on adaptations that many of these are related to how microbiologists may finally control some of those dangerous bugs.
But before I get to that, I have to cover a couple of "gee-whiz" topics, such as one about a biofilm found in a mine in Queensland, Australia (Reith et al., 2010). The biofilm – that is, a slimy-coated bacterial community – can dissolve gold, releasing gold ions that are toxic to the bacteria. However, in true bacterial fashion, the microbes have a way of dealing with the problem: converting the ions into metallic gold nanoparticles that form lacelike crystals. These are a much purer form of gold, one that miners seek out. It might be possible to engineer the bacteria to fluoresce when they are purifying gold, and then they could be used to detect the presence of the metal in ore.
In another intriguing piece of research, bacteria are being used not in metal detection but in hunting criminals (Fierer et al., 2010). No matter what the surface, bacteria live there, and microbiologists are finding that the microbes live there in very complex communities. One of the most fertile surfaces is the human skin. With new genetic techniques, researchers have discovered that there are many more microbes living on the skin than previously thought, and that the particular types vary from person to person. The variation is great enough that microbiologists at the University of Colorado, Boulder, decided to find out if they could use the bacterial communities left on fingerprint traces to differentiate between individuals. They found that the amount of material remaining on a computer key was enough to test, even when the key hadn't been touched in two weeks. This means that if there is only a partial fingerprint or a smudged one, there might be enough bacterial evidence to match it to a suspect. I have to admit that I am not a fan of criminal-investigation shows (too many autopsies), but this is fascinating stuff. Once again, bacteria come through with a solution for a detection problem.
In case a criminal is thinking of washing away all those bacteria, that's hardly a possibility, and in fact, a shower can actually expose a person to more bacteria. This is one of those research findings you may not want to read about. The reason once again has to do with biofilms, this time on the showerhead. Microbiologists found a hundred times more non-tuberculosis mycobacteria in these biofilms than in the water supply (Feazel et al., 2009). I'm writing this on Saturday, my housecleaning day, so one response to such results might be to give that showerhead a good scrub. The researchers have already tried that, using bleach, and all that did was select for a particular mycobacterium, M. gordonae. Non-TB mycobacteria can cause serious infections in immune-compromised patients, but also infect healthy individuals. The incidence of such infections is rising in wealthier nations, and our commitment to showering as opposed to taking a bath may be a factor. However, I suspect there are probably some interesting biofilms in that ring around the bathtub, too.
While I'm on the subject of skin, the same kind of research that reveals the variation in bacterial growth between people also indicates that there are great differences in the composition of bacterial populations on different skin surfaces: the arm and the torso don't necessarily harbor the same communities, or the same level of diversity (Pennisi, 2008). I don't know what to make of this, but I find it interesting that there is much less microbial variety in the area between the toes than in the navel. The nose, not surprisingly, is also a rich breeding ground, as is the inside of the elbow. This information may seem to border on the trivial, but an exploration of the skin's surface could be quite useful in trying to determine the limits of normal microbial communities, as a prelude to detecting the differences in the communities on those suffering from various skin infections.
Another significant finding of this research is that many of the bacteria were not previously thought to be associated with the skin. For example, Pseudomonas and Janthiobacterium, which this research found to be common on the skin, are known as bacteria that flourish in soil and water. And before I finish with this topic, I should note that in their rambles across the skin, microbiologists didn't just sample the surface, they also scraped off the top cells and sampled again. Finally, they took tiny punches of skin, to access deeper layers. They were surprised to find that there were about a million bacteria per square centimeter under the skin compared to about 10,000 in the scraped areas. But why should this be so surprising? There seem to be few things about bacteria that aren't amazing.
Another surface of the human body that's receiving a lot of attention from microbiologists is the gut. I've already written about this earlier in the year (Flannery, 2011), so I don't want to repeat myself, but I'd love to, because there's new information coming out about it all the time. It is definitely a hot topic, just as skin microbes are, because now researchers finally have tools to detect the diversity of organisms living there. One aspect of this subject that I wrote about was the importance of figuring out how infants develop normal intestinal flora, and the problems that arise when this doesn't occur. In an article that came out after I wrote mine, Lizzie Buchen (2010) discusses an odd coalition that has formed between neonatal pediatricians and microbiologists who study toxic mining debris.
Why this pairing? Doctors studying necrotizing enterocolitis, an often fatal disease of the bowels in premature babies, hope that the techniques used to culture bacteria growing under extreme conditions, such as high acidity or mine runoff with arsenic, uranium, and other metals, might help them tackle the microbes they are faced with. One thing both environments have in common is that they each harbor a limited number of species, and researchers in both fields want to find out how these communities change over time. In the case of the infants, doctors would like to know if they could learn to predict which babies are most likely to develop serious cases of enterocolitis. This is a great example of scientists willing to stretch themselves in order to learn more about their own fields. They admitted that they need to look at a problem from a totally different angle in order to come up with a solution.
Another example of developing a different viewpoint involves the study of the organisms that make antibiotics. Because these chemicals kill or at least slow the growth of microorganisms, most researchers assumed that this must be their role in the organisms that produce them. However, some microbiologists have looked in other directions for the functions of these molecules in their native species. Their findings are beginning to have a greater impact on the field (Mlot, 2009). For example, Harvard University's Roberto Kolter found that nystatin, an antifungal drug purified from Streptomyces noursei, triggers this bacterium to form biofilms. It even produces the effect in other bacterial species such as Bacillus subtilis. It accomplishes this by triggering a quick movement of potassium ions out of the bacterial cells; this, in turn, triggers an enzyme to synthesize biofilm material.
Julian Davies of the University of British Columbia has long held that antibiotics are more than just weapons against other microorganisms. In the 1960s he was studying streptomycin, which was the first antibiotic effective against Mycobacterium tuberculosis, the bacterium that causes TB. He discovered that the drug worked by attaching to ribosomes and thus preventing protein synthesis. The link to RNA made Davies suspect that antibiotics like streptomycin might be ancient molecules that had roles early in evolution when there was an "RNA world" in the first cells. This would be a difficult hypothesis to prove, but Davies has had success with some of his other ideas. For example, he was frustrated by the difficulty of finding new antibiotics and reasoned that the standard approach might be wrong. Most antibiotics are only effective in relatively high doses, which are not seen in natural microbial communities.
Davies decided to follow a cue from the phenomenon of hormesis, whereby the same substance that is toxic at high levels may have stimulatory effects at low concentrations. He tested his idea by using small amounts of such antibiotics as erythromycin and rifampicin on Salmonella typhimurium. He and his colleagues found that each antibiotic changed the control of hundreds of genes involved in everything from cellular transport to DNA. This gave support to his suspicion that antibiotics are part of the normal control machinery for the cell and that their effect on other species is, in many cases, just a nice side effect. The consequence of this changed viewpoint is that researchers can begin to look for antibiotics in a different way: not so much by studying the foreign targets of these chemicals, but by examining the biology of the producing microorganisms themselves. For example, looking at the molecules involved in cell signaling might be a good place to begin. Here again, bacteria have come up with more surprises, or perhaps it would be better to say that biologists have finally got the message that they need to think more broadly about microbial possibilities.
Noise & Dormancy
Besides being able to investigate bacterial metabolism more easily and to census the types of organisms on the skin or in a gold mine, researchers are now even able to figure out what is going on in individual cells. I hesitate to say that the results are surprising, since I've already overused that word, so I'll use "unexpected" instead. In essence, what microbiologists have been doing up until now is measuring chemical processes in a large population of microbes, and even if they are using pure strains, this approach masks a great deal of variability among the cells. To get at this diversity, researchers tagged gene products, both mRNA and protein, with fluorescent labels and put the cells through an automated system that counted the number of tagged molecules in each cell (Tyagi, 2010). This sounds simple but involved a great deal of trial and error in setting up the fluorescent tags and creating measurement standards. However, the results were worth the work. In E. coli, for example, a gene was found to produce from 0.1 to 10,000 copies of each protein studied, and 0.05 to 5 copies of each type of mRNA. And remember, this is in a genetically pure colony with all these cells grown together under the same conditions. Microbiologists refer to this diversity as "noise." Similar studies done with yeast find them to be less "noisy," whereas mammalian cells seem to be more so than their unicellular eukaryotic counterparts. It will take a great deal more research to figure out what all this noise means, if anything. It may just be a function of how molecules get around in a cell and, thus, how promoters get attached to genes. Alternatively, there may be some harmony under the noise. Perhaps there is an advantage to this cacophony in that cells with different protein levels may be able to respond more quickly to particular environmental changes. Microbiologists are planning to tackle questions about whether bacterial noise varies with the age of a colony or the conditions under which they grow, or with the species involved.
In an article on what may be a related topic, Slava Epstein (2009) discusses microbial dormancy. He doesn't deal with microbes that create spores that can survive for centuries at least; rather, he focuses on non-sporulating species. They have long been suspected of having a dormant state, but it's been difficult to nail down evidence for it. Epstein speculates that "perhaps these microorganisms have a different mechanism of revival than those we are used to. Rather than awakening to environmental cues...these microbes may wake stochastically—randomly" (p. 1083). He thinks that microbial populations may be composed of a mix of active and dormant cells, the ratio dependent on conditions: when things are bad, there are more dormant cells and in good times more cells are activated.
This hypothesis would explain the observation that although there are a great many cells in a sample, when the sample is plated out on agar only a relatively small number of colonies develop. It might be that the other cells are lurking on the plate but are dormant and not dividing, not making their presence known. Here's another reminder that, especially in the tiny microbial world, just because a researcher can't detect something, that doesn't mean it's not happening. This cryptic dormancy might also account for disease recurrence in cases of infections like tuberculosis. There may be a small number of dormant cells and a few of what Epstein calls "scouts," cells that become active to, in a sense, test the waters and find out if conditions are right for growth. Whether or not the activity of these scouts leads to a flare-up of the infection may depend on the immune system's ability to eliminate them. But all Epstein's ideas are based on speculation. He doesn't have much hard evidence that such a form of dormancy exists, and even he admits that it would be hard to detect these cells because they don't divide. Microbiologists are used to finding organisms by growing them in culture, and only lately are other methods, like the search for genetic ensembles, being used. So it may be that the validity of Epstein's hypothesis can be verified in the next few years.
There are some forms of life that are especially diverse and intriguing. One is the bacterium and another is the insect, so when they get together, it's not surprising that they can do some amazing things. The complexity of one particular case, the symbiosis between the pea aphid Acyrthosiphon pisum and the bacterium Buchnera aphidicola, came to light after the genomes of both organisms were deciphered (Pennisi, 2009). The genetic evidence is that this is a long-standing relationship with accommodations on both sides. The aphid is a pest of legume crops and, as aphids do, it bores into the stem to suck up sugary sap. Since this material is low in protein, the insect relies on B. aphidicola to provide essential amino acids. The microbe has a very small genome with only about 640 genes, but it can supply the insect with nine different amino acids. Interestingly, the bacteria can't do it alone; some of the necessary enzymes for synthesis of these molecules are in the aphid. The aphid's acceptance of this bug has been enhanced by the loss of a number of genes that would otherwise slow down Gram-negative bacteria like this one. This is a beautiful example of symbiosis, of what might be considered a molecular negotiation between two species. In addition, there are 11 bacterial genes that have been incorporated into the aphid genome. These include two that are needed for the production of the bacterium's cell wall. However, to make things even more intricate, these genes didn't originate in B. aphidicola but in a different microbe, an alpha protobacterium. This is another good example of how genomics can reveal the intricate interplay among species over vast periods.
Bacterial adaptability to difficult conditions must have its limits, but it's difficult to find them. Even when researchers cripple the reproductive mechanisms of Bacillus subtilis, it still finds a way to divide (Leaver et al., 2009). L-form strains are ones that lack cell walls, and these have been used in research for years. Recent work on B. subtilis, which is an especially easy-to-manipulate species, has generated an L-form in which a single point mutation predisposes the cells to grow without cell walls. In addition, this strain doesn't use the normal mechanism for cell division, in which the key protein in cytokinesis is called FtsZ, a homologue of tubulin, which forms a ring that attracts other proteins. Even without FtsZ, the L-form mutant still divides using a recently discovered alternative system in which pseudopodium-like protrusions form and eventually separate from the cell. Researchers speculate that a system like this may have functioned in early microbes, since it seems to be less complex than the FtsZ system. They are now searching for organisms that might use such an alternative system, including some that don't have FtsZ. This is a great example of how a model organism can shed light on a process that can then be tracked down in other species. It also shows that models continue to be useful even when they've been used in research for a long time: there always seem to be new layers to explore.
Now comes the point in a column when I begin to run out of space before I run out of ideas to discuss; this is a particular problem when writing about bacteria. After all, they are the most abundant form of life on earth and, I might also say, the most interesting. So I'll finish by quickly reporting on some other notable items. For example, there are bacteria that oxidize methane aerobically and others that do it anaerobically. Now microbiologists have identified a new species, Methylomirabilis oxyfera, which does things in still another way (Oremland, 2010). It begins the process by oxidizing methane anaerobically, and then there's a twist, thanks to the enzyme nitric oxide (NO) dismutase, which produces N2 and oxygen. The intracellular oxygen is then used in an aerobic methane pathway. So this is a bug that, thanks to a novel enzyme, appears to have the best of both worlds.
While there must be some challenges that bacteria can't meet, they seem to be able to rise to almost any occasion. For example, some species live inside cells, thus hiding from the host's immune system. They are, however, faced with the problem of moving on to new cells. To study how this transfer takes place, microbiologists are studying the infectious microbe Mycobacterium marinum, which uses an actin-containing structure called an "ejectosome." In the amoeba Dictyostelium discoideum, M. marinum triggers the formation of a barrel-shaped structure that contains actin and that surrounds the bacterium as it crosses the host's cell membrane on leaving that cell (Carlsson & Brown, 2009). In multicellular organisms, the ejected cell would be close to other host cells and would likely be quickly taken up by one of them and the cycle could continue. Since a similar system seems to exist in the tuberculosis-causing M. tuberculosis, this discovery could have therapeutic implications if a way to thwart ejectosomes could be found.
Finally, there is the surprising, perhaps too surprising, finding that there is a bacterium that can use arsenic rather than phosphorus in building its DNA (Pennisi, 2010). This rather startling discovery was announced in late 2010, and since then there have been questions about whether or not these results are valid. After all, it is pretty startling, although if you look at a periodic table, you'll see that arsenic is located right beneath phosphorus in the same column, so it does have similar chemical properties. Also in support of this discovery is the fact that the organism in question, a strain of the Halomonadaceae called GFAJ-1, was isolated from the arsenic-rich muds of Lake Mono in California. Felisa Wolfe-Simon of the U.S. Geological Survey and her colleagues published evidence that the DNA in GFAJ-1 does in fact contain arsenic in place of phosphorus, but a number of other researchers are not ready to accept this report. However, Wolfe-Simon's team has already published a second paper in Science, the journal that published the first one (Pennisi, 2011). This describes the microbe in more detail and provides evidence for arsenate not only in nucleic acids but in proteins as well. This is the kind of result that I root for: something totally outside the biological norm. And it's risky even putting it in this column because by the time you read it, the whole issue may very well be settled, one way or another. I can't wait.
She earned a B.S. in biology from Marymount Manhattan College; an M.S., also in biology, from Boston College; and a Ph.D. in science education from New York University. Her major interests are in communicating science to the nonscientist and in the relationship between biology and art.