Stacy

This is pretty hilarious and tangentially relevant to this course:

http://www.phdcomics.com/comics.php?f=1312

We’ve learned a lot in this class about evolution through beneficial DNA mutations. Lately, I’ve been thinking about what else is happening in the prokaryotic genome. What about DNA modifications such as methylation? What impact do they have on prokaryotic gene regulation? Are they heritable? Are they acted on by natural selection?

My search has only turned up these two pieces of literature (both of which I don’t have full access to):

http://www.ncbi.nlm.nih.gov/pubmed/9628352
http://cshmonographs.org/index.php/monographs/article/viewArticle/4528

If anyone knows more about this or finds some relevant links, let me know! I’d love to learn more about prokaryotic epigenetics.

Also, breaking news: A New Hampshire farmer might make it into the Guinness Book of World Records. While this is unrelated to the course, it’s a really neat story (cute animal videos included), especially if you have some NH pride! Try not to get to emotional about it though – it might make you a little hoarse.

I really enjoyed the Science Friday podcast. I wish more non-scientists would listen to broadcasts like these. It seems that so much of the scientific knowledge that the average person has in our country comes from the media. It’s nice to hear science being explained by a scientist in a way that many people can understand.

This got me thinking about a conversation I had with my friend the other day. She recently was on antibiotics, and was taking probiotics at the same time (as prescribed by health services). I asked her what the point of taking them concurrently was, and she told me that health services said that the antibiotic didn’t target the bacteria she was taking. I started thinking, what’s the point of replacing a bacteria that isn’t even targeted by the antibiotics you are taking to begin with?

I found in my searches that there many, many species of Lactobacillus (the most common probiotic). Apparently they vary a lot in their antibiotic resistance from species to species. So, in theory, health professionals could prescribe lactobacillus and antibiotics that do not impact one another. I have no idea whether or not they are actually doing this successfully. I would imagine, based on our discussion in class today, that different people have different probiotic species anyway, so how would you predict what treatment is needed?

In a society where we can get probiotic fruit snacks, these are important questions to address.

Mmmmmm! Lactobacillus flavored!

That brings me back to one of the key things I got out of the podcast. We don’t know very much about gut microflora, and what we do know about community composition varies substantially from person to person. Should we be messing with our microbiota before we know the whole story? Many scientists are addressing that right now by simply testing the effect of probiotic treatments for various diseases. Most of the studies I looked at found at least some benefit of using probiotics as a treatment for diseases affecting the human gut. But it seems like there is a lot of variability in the effectiveness of the treatments from person to person.

Something else interesting is that some scientists are addressing the gut microflora question using gutless protozoans as subjects. For instance, as we learned in class, you can exchange the gut microflora of two mice, or in Latin, a paramecium.

Honeybees and other social insects offer a very interesting system in which to study the evolution of virulence. In order to explore this topic further, I read this fascinating article about honeybee evolutionary epidemiology by Ingemar Fries and Scott Camazine. It’s an excellent review of the major diseases effecting commercial honeybee populations, how they are transmitted, and how their mode of transmittance might impact the evolution of their virulence. It really is a whole-package article (if you are looking for something to read), as it addresses evolutionary theory, case studies, and commercial solutions to all types of honeybee pathogens.

Before I really get into the article, I wanted to share a passage from it that really helped me to understand how and why virulence might evolve:

“Virulence is adaptive for the parasite only insofar as it promotes its own fitness, for example by promoting transmission of parasites to new hosts; often virulence is an unavoidable consequence of the parasite’s reproduction. However, here is a trade off for the parasite. If the parasite’s reproduction is too high, the infection may be so virulent that the host dies before sufficient numbers of propagules can be transmitted to new hosts. On the other hand, if parasite reproduction is too low, the parasite loses opportunities for transmission.”

This makes a lot of sense to me, especially in the context of many parasites competing for one host. How does a parasite ensure it is transmitted more readily than other parasites without killing its host? The article goes on to address this question from one particle angle: mode of transmission.

The vast majority of individuals in a honeybee colony are clones of the queen. It has been shown many times that homogeneous populations (ie. populations of clones) are far more susceptible to parasites (see my previous blog post on Poeciliopsis and the Red Queen hypothesis. The bees compensate for this by including antibacterial substances in the colony walls, exhibiting hygienic behaviors, and having physiological immune reactions to disease. However, one interesting advantage of bee clonality is that “reproduction” for these organisms can be seen as the creation of new colonies (that is how the genes of the colony persist). Therefore, one can think of a bee colony as an individual, with new colonies that are formed as being its offspring. This means that a parasite must not only successfully infect multiple members of a colony, but it must also infect a new colony to survive. As a result, most pathogens are not very virulent at the colony level, even if they are very virulent among individuals (especially larvae).

Horizontal disease transmission occurs when the parasite is transfered to from one individual (or colony) to another within the same generation. Vertical transmission refers to the passing of a parasite from the parent to the next generation, requiring that the host reproduces. Because vertical transmission requires the health of the host more than horizontal, one can expect that vertical transmission would select for a less virulent parasite. According to Fries and Camazine, this has been demonstrated to hold true experimentally in many types of organisms (from bacteria to wasps).

The main message of this paper (besides offering management solutions to commercial honeybee pathogens) is basically this: The evolution of virulence can be driven by the proportion of vertical to horizontal transmission methods used by a parasites. A pathogen that relies on vertical transmission (from parent to offspring) has a strong selective pressure to preserve the reproductive health of the host. Also, if a pathogen is particularly virulent, it must utilize some amount of horizontal transmission in order to survive. The authors say that the evolution of virulence of a parasite is controlled by the balance of these mechanisms, which is also subject to selective pressure. The result is that in order to understand a how a pathogen will effect a honeybee colony, you must know how it is transmitted, not only from individual to individual but from colony to colony as well.

The authors suggest that raising colonies of honeybees commercially promotes horizontal pathogen transmission over vertical. Based on the evolutionary theory presented in this article, this means that over time more and more virulent pathogens will be selected for. They suggest that it is important to improve practices of beekeepers to ensure that disease is not being transferred between colonies. Also, they recommend selecting for bees that demonstrate disease resistance when beginning a new colony. I find this really interesting, because these recommendations are direct commercial applications of an evolutionary theory, which supports the need for evolutionary questions to be addressed through research.

While the paper offers ideas for beekeepers, I was curious to know what the bees themselves can do to prevent the spread of disease. I decided to interview a healthy bee to find out. When I asked him how he remained so healthy and avoided horizontal disease transmission, he simply replied “I don’t know. I just mind my own beeswax.”

Anyone who has played games like Halo and World of Warcraft can tell you the fundamental advantages of cooperation and selfishness. These games both have two types of game play: player-versus-player and co-op (cooperating to defeat enemies). In PVP, you compete with and kill each other to gain points (honor points, tokens, better stats, etc.). In co-op situation, you are working together with your teammates to defeat a common enemy to gain phat lootz (gear, special items, weapons, etc). Cooperation tends to take more time and organization with a higher payout, and PVP takes less organizational effort but with less (or arguably, just a different) payout. (Note: This metaphor is more or less disregarding the prisoners’ dilemma).

When you’re choosing which mode to play in, the decision often comes down to this: which reward is more worth the effort put in? Because cooperation is biologically expensive, it only evolves when the payout of working together exceeds the relative payout of selfishness. Myxococcus xanthus bacteria really want those phat lootz, and so they will opt to cooperate by any means necessary. Gregory J. Velicer and Yuen-tsu N. Yu (2003) showed that even when the gene that allowed it to cooperate was removed, it evolved another method of cooperation.

Essentially, Velicer and Yu created a population of Myxococcus xanthus mutants that did not have the pili necessary for swarming behavior on soft surfaces, making all of ancestral bacteria (the baseline for their experiment) individual swimmers. Because it is very difficult for them to swarm on soft surfaces without pili and swarming is necessary for these bacteria (to get the phat lootz), they evolved new ways to increase their swarming ability aside from pili. The primary technique they observed was enhancing their extracellular matrix (the structural support of the colony).

I’m at a loss as to tie a joke in with this material, so I think I’ll tell you a little about my weekend – I went to a wedding for two antennae. The wedding itself was a bit boring, but the reception was great.

If you are having difficultly wrapping your mind around the implications of The Red Queen hypothesis (I know I was), then I would strongly recommend reading this passage:

“The Read Queen hypothesis for the maintenance of biparental sexual reproduction suggests that, for species locked in coevolutionary struggles with biological enemies, the production of variable progeny compensates for the genetic or ecological disadvantages of sex. The advantage of sex and recombination under this hypothesis stems from the production of rare phenotypes, which are expected to be more likely to escape infection or predation by coevolved biological enemies.”

In short, this means that in parasite-host relationships, it’s much better to be a rare phenotype than a common one, as parasites will typically be evolved to prey on the most common phenotype. The advantage of sex under this hypothesis is that sex results in variable offspring and therefore more rare phenotypes. My understanding is that the “Red Queen” aspect of this hypothesis is that if only the rare phenotypes don’t get parasitized, you will never have an entire population of resistant hosts, due to coevolution of the parasite.

What a pain in the genome!

The passage above is from this article entitled “Red Queen hypothesis supported by parasitism in sexual and clonal fish” by Lively et al. It’s an eloquent experiment demonstrating the plausibility of some of the assumptions behind the Red Queen hypothesis. I would strongly suggest reading it (it’s only 2.5 pages!). But if you aren’t inclined to do so, I’ve summarized the experiment and results to the best of my ability.

Lively and his colleagues set out to demonstrate that parasites will attack the most common phenotype disproportionately more often than other phenotypes (which is a major assumption of The Red Queen hypothesis). They examined topminnows in three natural rock pools in Mexico. The rock pools all had a type of sexually reproducing topminnows (Poeciliopsis monacha) as well as at least one type of hybrid clone of P. monacha and P. lucida that was not sexually reproducing. These fish are all susceptible to infection by a trematode larvae that encysts in the skin by burrowing into the body wall.

Let me quickly explain the advantages of this fantastic system. First, you have isolated groups of fish co-evolving (presumably) with a parasite. Then, you have sexual and non-sexual individuals with very similar phylogeny coexisting in the same natural conditions. And as icing on the cake, the parasites burrow into the body wall of their hosts and encyst, leaving visible (and therefore easily countable) indications of infection. This makes this system pretty much the ideal place to study the Red Queen hypothesis in situ.

What they found was that the commonly found hybrid clones were parasitized by significantly more trematodes (greater # parasites per individual) than were the smaller and more variable sexual populations. There was one exception to this, however, and that was a situation in which an extinction event followed by a reintroduction by humans caused the sexual population to become extremely inbred. In this situation, the inbred sexual fish were more parasitized than the more common clonal fish, which the authors suggest is a result of inbreeding depression.

Basically, the authors were able to show that the parasites opted for the more common, uniform genotype (the clones), while the more variable sexual fish were infected with far fewer trematodes. This, they say, offers support for the plausibility of the assumptions of the Red Queen hypothesis.

This experiment was very clear and fascinating, and I think the authors did an excellent job of using their empirical evidence to support the validity of the assumptions behind this evolutionary hypothesis. Of course, they were limited by the fact that there are very few study sites in the world like this, but the experiment still brings up many interesting ideas and questions that can further be addressed in the lab. At the very least, the article gave me a much better understanding of what the Red Queen hypothesis implies for parasite-host evolutionary relationships.

And now for an extremely relevant joke…

A trematode larvae swam up to a P. monacha-lucida hybrid and said “Excuse me, but I need to burrow into your body wall in order to advance to the next stage in my life-cycle.”

The hybrid responded, “No way! Go burrow in one of the members of the sexual subpopulation!”

The trematode, getting irritated, replied, “I’m sorry, but I must encyst!”

Can we use microbial experimentation to study macroevolution?

On some levels, microbial evolution is influenced by many of the same factors as macroevolution (eg. habitat diversity, competition for space and resources, and abiotic disasters), and therefore microbes can be used to model some of the basic ideas of evolution.  However, microbes are very different from “macrobes” (plants and animals), and any correlations between their evolutionary processes should be taken with a grain of salt.

Size Matters

Physics textbooks will tell you that the size of an object or organism has an enormous impact on how it interacts with its environment.  Many processes and characteristics of microbes do not “scale up,” which is why we do not have giant E. coli cells sauntering around Durham.  Microbes are microscopic and unicellular, and therefore they have a higher surface area to volume ratio, different ways of transporting material, and different forms of movement than macro organisms.  As physicists put it, they function at a much lower Reynold’s number.   This places them in a situation that is different from plants and animals.  Their evolution primarily comes from changes in metabolic processes and cellular composition, as opposed to both changes in physiology and morphology.   In my opinion, these types of changes are just too different to draw conclusive parallels between micro- and macrooganismal evolution.

While body size effects evolution greatly, genome size is also incredibly important to consider.  Prokaryotes typically have only one circular chromosome, while eukaryotes typically have multiple chromosomes and much larger genomes.  Genome size and arrangement have a strong influence on how genes are passed on.   The frequency and nature of genome variation events influences evolutionary mechanisms and rate, making it extremely difficult to make comparisons between the organisms.

More Cells, More Problems

It goes without saying that most multicellular organisms have vastly different experiences than microbes.  Multiple cells means that the organism must spend more energy on transport of organic and inorganic material, as well as cellular differentiation.  Organisms with many cells must coordinate the functions of all cells at the cost of energy.  With the addition of more complex body plans to facilitate that coordination, multicellular organisms lose plasticity.

The Bacillus and the Bees

While some multicellular organisms are asexual, most reproduce by the fusion of gametes from two different individuals, promoting frequent recombination.  Microbes are more prone to insertions of foreign DNA, due to the increased frequency of gene transfer events.   While these things result in comparable rates of evolution in microbes and macrobes, I am hesitant to compare their genetic evolution given the difference in the mechanisms for the changes.

Why can’t we all just get along?

I want to throw this out there quickly: I think one really interesting way to compare microbe and macrobe evolution is to study systems of co-evolving microbes and animals.   If we can observe evolution of a microbial species caused by an adaptation made by its animal host, we can compare % change in neucleotide sequences as well as evolutionary rate to draw conclusions are to how comparable these types of organisms are when evolving on the same time scale.

Instead of doing a pun this week, I thought I would try my hand at embedding a video, while attempting to educate.  I know that microbiologists deal primarily with asexual reproduction, so I’m including a brief refresher on fertilization.  Watch it if you have the time (sorry, did I say there would be no puns?)

Assessments of biodiversity are critical to understanding how ecosystems and communities function.  In extreme conditions in which we know little about the community structures, microbial diversity can be a valuable character to use to examine a system.   In order to assess diversity in microbes using genetic techniques, we must have parameters for how we define a microbial species.

A report published in 2007 by Huber et. al. examined the microbial community structure of two neighboring hydrothermal vents in the northeast Pacific Ocean.  Their objective was to compile an exhaustive picture of bacterial and archaeal diversity at the sites and compare them.  They were successful in characterizing all or most of the archaeal diversity.  However, when it came to the bacteria, they struggled with a familiar problem – more sequencing led to an increasing number of taxa identified, resulting in steep rarefaction curves.  This led the researchers to conclude that the majority of the bacterial inhabitants were “rare, divergent taxa.”

The interesting aspect of the project to me was the comparison between the two sites.  You can see here that the different sites consisted of different community structures (FS312 and FS396 each represent a vent) even though they were a part of the same vent system.  I believe that comparison between ecological sites (whether on hydrothermal vents or on our own bodies) is one of the most important applications for the microbial species question.  We know from the MLST study of Neisseria that microbes with very different phenotypes (here, virulence) can be highly genetically similar.   That leads one to believe that simply sampling microbes with the resolution of 16S rRNA sequences, as Huber et al. did, gives us only a snapshot of the microbial community structure that isn’t even close to the whole picture.

In conclusion, I feel that microbial diversity in an ecosystem is an important character for comparison.  The methods that we use now to accomplish diversity assessments would benefit greatly from a more stringent definition of what a microbial species is, so that we can get a “whole picture” analysis of the differences in community structure.

So of course, I need to end in a joke.  I’m trying to be selective and somewhat relevant with my puns.  My goal is to entertain while staying somewhat on topic.  For instance, I wouldn’t tell a fish pun just for the halibut.

The discussion section of the Hanage et al. study summarized the primary problem of the bacterial species concept eloquently:

“We have no idea whether large populations of related bacteria can invariably be divided into discrete clusters using suitable molecular methods or, alternatively, whether many groups of related bacteria fall into a genetic continuum where clear divisions do not exist.”

The paper does address this gap in our knowledge by demonstrating that it is possible, to some degree, to resolve clusters of bacteria into groups that can be called species.  However, within this study and presumably with other microbes, the clusters were not discretely organized, suggesting more of a genetic continuum.  In my mind, the question of whether or not microbes always form discrete clusters has a answer – and that is “No, they do not.”  I personally favor an understanding of speciation that incorporates the idea of a continuum of genetic similarity between organisms.

The important question when considering the definition of a bacterial species is: what is the best way to define individual species that is most useful to us?  For example, are we going to be using this information to study bacterial ecology within and across geographical locations?  Will we use it to determine how to treat an infection?  What is the resolution we need for these pursuits and why?   How do we achieve that resolution?

The idea of a genetic continuum befuddles these questions by suggesting that there are no boundaries that will help us to define a species other than phenotypic relationships.  If invariably discrete clusters of bacteria cannot be deciphered from molecular data, how can we define bacterial species?  Hanage et al. begins to address this question using MLST, but there is much more to work to be done.  I believe that future work will enable us to find a way to define borders between species in molecular data that may not be discrete but will still provide useful resolution for classification.

On a side note, there are many differences between microbial and animal speciation, particularly because of the differences in reproduction, dispersal, and genome size.  However, I’ve been reading about animal speciation, and many of the principles (especially some of the mathematical concepts) seem useful for understanding microbial speciation.   This book by Daniel Howard and Stewart Berlocher entitled “Endless Forms” gives a history of how we’ve defined animal species and goes into great depth on our current understanding of the linkage between phenotype and genotype.  So if that’s something that interests you, check it out – much of it is free on Google Books.

On another side note, recently, molecular biologists have discovered a new method of determining the “gender” of a microbe.  When questioned about the method, the PI on the project said “we simply pulled down its genes.”

If we interpret the Baas-Becking hypothesis of “Everything is everywhere, the environment selects” to mean that all microorganisms are everywhere, the phenomenon witnessed by Whitaker et al. negates this hypothesis.  They observed that the extremophile archaea Sulfolobus exists in isolated populations at different geographic locations.  Not only do these populations show significant genetic differentiation from populations at other locations, but they also show an increase in divergence with increased distance (if >50 m) between study sites .  Furthermore, there was no relationship found between geographic conditions and genetic similarity.

Their results strongly suggest that the populations observed were isolated by the barriers of their extreme environment.  The populations appear to have evolved independently of each other since the time of their arrival at their respective geographic locations.  If this is the case, than the conditions of the environment are not the main force shaping the genetics of these communities, but rather it is the gene flow and genetic drift within a location that has the most influence.  If the Baas-Becking hypothesis were true, there would be a strong relationship between environmental conditions and genetic arrangement with a weak relationship between genetic difference and geological distance.  However, this is the opposite of what was shown here.

Whitaker presents a strong start in the direction of disproving the Baas-Becking hypothesis.  The next step for this project would be to try to observe (or not observe) this phenomenon in other microbes inhabiting the same geothermal springs in order to show repeatability in other organisms.  After that, this could be tested in other microbes that are isolated by other types of geographic barriers to demonstrate that this is not limited to geothermal springs.  I would like to know if it would be possible to observe a similar distance/divergence relationship in more ubiquitous microbes, even though the amount of gene flow would be much greater.

Speaking of Yellowstone, I went camping there last weekend.  It was in tents.