Field of Science

Social Evolution in Bacteria - SGM series

This is the fourth post in my latest SGM series.
The social behaviour of bacteria is something that I get very excited about. From the wolf-pack hunting strategies of Myxococcus xanthus to the terminal differentiation of cyanobacteria, it's something that I never get tired of writing about. As well as providing interesting quirks of bacterial behaviour, living within a colony also gives new scope for exploring the evolution of bacteria; not just as single entities but as a fully functioning social group.

One of the differences of living within a social colony as opposed to alone means that altruistic-type behaviour has to be adopted. Bacteria living within a biofilm need to excrete the sticky goo that holds the biofilm together, which is problematic because synthesising and secreting goo takes up a lot of energy. So within this colony, there will be 'cheaters' - those bacteria that live in the surrounding goo produced by others, while making none themselves.

A bacterial biofilm, showing individual bacteria in green. Image taken from the FEI website, shown there courtesy of Paul Gunning, Smith & Nephew

As with all colonies, cheating might benefit the individual but has no benefit for the colony as a whole. Too many cheaters and there won't be any biofilm. And recently an even more subtle form of cheating has been shown within the biofilms of the bacteria Pseudomonas aeruginosa, with bacteria that don't just refuse to make vital sticky chemicals, but also abstain from the entire process of forming a biofilm.

Bacteria use a complex communication system called quorum sensing in order to determine how many other bacteria they are surrounded by. Once enough bacteria are present, all signalling their existence, the biofilm will start to form. However some bacteria isolated from the biofilm were shown not to be taking part in any quorum sensing at all. Quorum sensing appears to be quite a burden for a growing cell - cells with the quorum sensing genes knocked out tend to grow a lot faster that the socially conscious cells that allow biofilms to form.

The paper that goes through this (reference one) highlights it as a form of social cheating, with bacteria avoiding quorum sensing to benefit themselves while mooching off the quorum sensing behaviour of others. I'm not entirely certain that this is the case though. It may just be an good example of job allocation within the bacterial society. Clearly not all bacteria are required to be continually quorum sensing, so why should they all have to? Would it not be more sensible to have some exempt from that task, so that they can concentrate on growing, dividing, and spreading the colony? This may be more a case of tax-breaks than of benefit-cheats.

Social evolution doesn't just take place within species, but also between them, and like every other organism bacteria are in a constant state of coevolution with both their 'prey' and their predators. Most predator-prey interactions take long periods of time to study, but the beauty of bacteria is that you can go through several generations in the course of one week's growth. Studies of the bacteria Pseudomonas fluorescens and its bacteriophage parasite showed that both the bacteria and the bacteriophage evolved far quicker when interacting together than they did when competing against a non-changing opponent.

Bacteriophage surrounding a bacteria. Image from wikimedia commons

'Evolve' here means that the bacteria and the bacteriophage showed a greater change in their genetic makeup, and a greater genetic divergence from bacteria not pitted against the phages. Unsurprisingly, the genes that changed the most were those involved in host-phage interaction. This study (reference 2) is also a great example of the usefulness of whole genome sequencing. Whole populations of bacteria and phage were allowed to evolve both together and separately and then just sent away for sequencing with the results analysed at the end.

You really can't be an anti-evolutionist while studying bacteria. They just do it so damn quickly and often you can see it happening.

Sandoz, K., Mitzimberg, S., & Schuster, M. (2007). From the Cover: Social cheating in Pseudomonas aeruginosa quorum sensing Proceedings of the National Academy of Sciences, 104 (40), 15876-15881 DOI: 10.1073/pnas.0705653104

Paterson S, Vogwill T, Buckling A, Benmayor R, Spiers AJ, Thomson NR, Quail M, Smith F, Walker D, Libberton B, Fenton A, Hall N, & Brockhurst MA (2010). Antagonistic coevolution accelerates molecular evolution. Nature, 464 (7286), 275-8 PMID: 20182425

Follow me on Twitter!

The Carnival of Evolution - coming soon.

In one weeks time, the Carnival of Evolution is coming to Lab Rat! Like most of the bloggy carnivals floating around, it's a travelling one and I am very excited to be hosting it.

If you're a blog reader, I hope you'll enjoy looking through a variety of posts from a couple of different people, all on the topic of evolution. If you're a bloggy writer then write me a post! Blog carnivals are a great way to get your blog noticed, and to get more exposure for your writing. Also it's fun to read other people's thoughts on a topic as well as sharing your own.

You can submit articles and blog-posts here. There's still one week left, so plenty of time to get a nice post written!

[And I am aware that the SGM series is going a little slower this time around. I'm really enjoying doing it and I will get through it, I'm just taking my time, as there's a lot of other stuff going on in my life at the moment.]

Life at zero growth rate - SGM series

This is the third post in my latest SGM series.
One of the first topics that I learnt in Biology was that there are two types of things; living things, and dead things. Living things are given a whole host of distinguishing characteristics (growth, reproduction and, my favourite, irritability) where as dead things are defined as everything else. Biology was usually defined as the study of living things.

As I grew older, I found that there were many complications to this neat little classification. Viruses - which are neither fully living, nor properly dead. A whole organism can be dead, despite the fact that many of its cells are still alive (how alive is a freshly killed animal? Or the flowers in a vase?). And of course what is for me the most intriguing case, that of dormant bacteria.

Dormancy is an odd state to be in. A dormant organism shows none of the signs of being alive. It does not eat, grow or divide (although some very basic metabolic processes may still continue). It shows no response to any outside stimulus, and can often be placed in conditions that would
lead the living organism to perish, such as extremes of temperature and pressure. Yet somehow just one simple stimulus can cause this previously dead looking organism to spring magically back into life.

Bacteria are not the only things that can go dormant. Some
animals can as well, the most famous example being tardigrades -the thing shown on the right that looks a bit like a plushie made by Tim Burton (image from wikimedia commons). Yeast are well-known for forming dormant spores, and it can be argued that a seed is technically a dormant plant, just waiting for water to be added to bring it back to life.

One of the most medically important dormant bacteria is Mycobacterium tuberculosis which infects humans and leads to TB. One of the reasons for its pathogenicity is that they can go dormant, both outside the body (which makes them hard to shift from a hospital) and inside the body, after the primary infection (which makes them even harder to shift from inside a human body).

Although the latent cells can remain within the body for many years, sometimes never coming back from dormancy at all, ideally there should be some signal to bring them back to life. These signals are known as "resuscitation-promoting factors" or RFPs. These RFPs are required for virulence, and to bring the bacteria back from dormancy, but are not necessary for the growth and proliferation of cultures in the lab.

Within human tissues, and throughout the cycle of the disease, you can track these RFPs to try and get an insight into what the bacteria is up too, and when it may move from latent periods to periods of active growth. As well as being useful for tracking the course of infection, this might also have therapeutic implications. If you can convince the bacteria not to come out of dormancy then you have an infection state that might not be completely curable but is at least controllable.

How organisms survive in a state of dormancy, and indeed how they ever come out of it, is a subject I find really fascinating. I'm unlikely to ever get to do much research on it (because as fascinating as it might be screwing around with my little bugs till they do what I want is endlessly more fun) but I'll probably have a good few more posts writing about it and exploring how it works.

Kana BD, Gordhan BG, Downing KJ, Sung N, Vostroktunova G, Machowski EE, Tsenova L, Young M, Kaprelyants A, Kaplan G, & Mizrahi V (2008). The resuscitation-promoting factors of Mycobacterium tuberculosis are required for virulence and resuscitation from dormancy but are collectively dispensable for growth in vitro. Molecular microbiology, 67 (3), 672-84 PMID: 18186793

Davies AP, Dhillon AP, Young M, Henderson B, McHugh TD, & Gillespie SH (2008). Resuscitation-promoting factors are expressed in Mycobacterium tuberculosis-infected human tissue. Tuberculosis (Edinburgh, Scotland), 88 (5), 462-8 PMID: 18440866

Insect Symbiosis - SGM series

This is the second post from my latest SGM series.

ResearchBlogging.orgIt's a pretty well known fact now that the human body contains lots of bacteria. Bacteria live on your skin and in your throat and gut, for the most part completely harmlessly, protecting your body from more dangerous invaders.

But something that doesn't get mentioned quite so often is that humans are not the only animals with a corresponding posse of bacteria. Other animals have them as well, including insects. From a bacterial point of view both your body and an insect's body are merely new lands to be colonised, and if they can colonise those lands without totally destroying them, then so much the better.

Like human bacteria, some bacteria that live within insencts have formed a symbiotic relationship, where the insect relies on the bacteria for survival. The pea aphid (shown to the right - photo by Marlin E. Rice) contains a symbiotic bacteria, Buchnera aphidicola that is required to produce one of the major amino-acids used to make important proteins. Completely sequencing the genome of the aphid shows that it does not contain the gene for argenine; it requires the Buchnera to make it. Likewise the sequenced bacterial genome lacks the genes for animo-acid deregulation, and several other minor amino acids. It gets these from its insect host. The bacteria lives within the host, in specialised little cells, and is passed down from mother aphid to daughter as without it the aphids will not survive.

This raises important questions about the control of the genetic activity of both the bacteria and the insect. If the insect needs more argenine, it must have a way of telling the bacterial genome to produce it, likewise if the bacteria requires more of the non-essential amino-acids it needs to be able to push the insect to make them. Modeling flux pathways for the creation and degredation of some of these amino acids helps to build up a picture of how this control can function, at a metabolic level if not a genomic one. The flux analysis also shows how important this symbiotic relationship is, for both the bacteria and the insects.

Leaf cutter ants (shown on the left - image from Wikimedia commons) have what is possibly the most complex and fascinating of interactions with microorganisms. For a start, they harvest fungi growing it in little gardens and feeding it with mashed up plants. This fungi can be susceptible to infections, so the ants also need to provide pesticides to keep their crops alive. As ants have not quite reached the level of large scale chemical manufacture, they have to rely on symbiotic bacteria to produce the antibacterial and antifungal compounds they need. The bacteria they use are species of Pseudonocardia and Streptomyces which produce a large number of secondary metabolites that can be used to destroy the fungal-infectors. The ants excrete these secondary metabolites in their waste, which can then be moved into the fungal garden. The bacteria also showed some anti-fungal activity against the fungus growing in the gardens, so could be used to control how far the crop spreads.

I'm always wary of ants, I certainly got bitten by them enough times as a kid. With their little societies and gardens and wars and multistory-housing compexes they are scarily human for a tiny piece of exoskeleton with legs.

Wilson AC, Ashton PD, Calevro F, Charles H, Colella S, Febvay G, Jander G, Kushlan PF, Macdonald SJ, Schwartz JF, Thomas GH, & Douglas AE (2010). Genomic insight into the amino acid relations of the pea aphid, Acyrthosiphon pisum, with its symbiotic bacterium Buchnera aphidicola. Insect molecular biology, 19 Suppl 2, 249-58 PMID: 20482655

Thomas GH, Zucker J, Macdonald SJ, Sorokin A, Goryanin I, & Douglas AE (2009). A fragile metabolic network adapted for cooperation in the symbiotic bacterium Buchnera aphidicola. BMC systems biology, 3 PMID: 19232131

Schoenian I, Spiteller M, Ghaste M, Wirth R, Herz H, & Spiteller D (2011). Chemical basis of the synergism and antagonism in microbial communities in the nests of leaf-cutting ants. Proceedings of the National Academy of Sciences of the United States of America, 108 (5), 1955-60 PMID: 21245311

Follow me on Twitter!

Guarding Microbial diversity - SGM series

This is the first of the Spring 2011 SGM series; where I steal random topics from the Society for General Microbiology Spring Conference and write about them in my blog. It should be noted that I am in no way affiliated to the Society, I'm just currently not rich or scientific enough to go to their conferences. (next year...)

I was quite intrigued when I saw this topic, as microbial diversity has always seemed to me to be a little bit like rats. Interesting to the people that study them, irritating and potentially hazardous to those who don't, but not really in need of any special protection. Bacteria evolve quickly, and share DNA easily, forming many, many diverse species capable of occupying a wide variety of niches.

However while bacteria are indeed very diverse and happy to remain so, the challenge comes in cataloguing all of that diversity. New bacteria need to be examined, named, placed in a taxonomic group, and preferably stored so that if anyone has a particular urge to work on (say) a specific type of hydrogen-eating swamp bacteria, they can find a sample of it and do that work.

What I hadn't realised was that there are quite a few places that are designed to store bacterial cultures. One such place is the DSMZ collection in Germany which boasts over 20,000 cultures of assorted microorganisms. These are stored as dried samples, not alive yet easily able to resuscitate. For a small fee, you can order a sample from them, together with instructions as to how to bring it back to life and culture it within a laboratory. Without storage facilities such as these, it's easy to see how interesting new bacteria would simply get lost, due to freezer melt-downs in labs, or people discarding the wrong samples.

It's not just the finding and the storing of bacteria that are vital in order to maintain scientific knowledge of their diversity, you've also got to name the things. After all, an unlabelled catalogue is no use at all. And with the name comes characterisation - a whole list of the properties and behaviour of the bacteria down to as much biochemical information as is feasible. The speed and accuracy of full-genome sequencing does make this a lot easier, but there are still many properties that depend on more than just the genes. A bacterium might possess the gene for (say) iron metabolism, but that doesn't mean it uses it all the time, or indeed at all. Knowing the genome sequence also makes it a lot easier to quickly place a bacterium into an existing group or species. Although bacteria do share DNA between each other, recently acquired DNA can usually be distinguished from the core genes that mark the species.

UK strains can be acquired through the Health Protection Agency, which is an aggregation of four previously separate culture collections. The bacterial arm of it has around 5000 different bacterial cultures. I did do a quick check as to whether I could get a small sample of S. erythraea using my Debit Card, but you need to be officially registered before they start handing out the bacteria!

It's quite strange to think that these talks are actually taking place up in the north of the country while I'm writing this. Next year though, I'm aiming not just to turn up, but actually bring a poster with me, to show off some of my own work.

New SGM series!

The Society for General Microbiology runs regular conferences that concentrate exclusively on the world of the very small. Although I am currently not a member :( I have been in the past, and plan to be again next year!

The conferences are always very good, and last august I bemoaned not being able to make one. This spring I am also not able to attend as I've only just come back from my honeymoon, and in the general scheme of work-life balance it would be a very sad and hardcore worker who would put an actual wedding second to marriage.

The last SGM conference that I missed, I decided to do a nerdy little one-women conference of my own, here at Lab Rat. And it worked so well that this time I'm going to try and do it again. One post every two days, covering the following topics in no particular order:

Seeing the cell through the “eyes” of the virus
Guarding microbial diversity
Insect symbiosis
Life at Zero Growth Rate
Maths & microbes - heh that'll be fun!
Social evolution in micro-organisms

Seven topics, which should take me two weeks to get through. It'll be a good way to get my self back into blogging and back into the exciting world of bacteria. It should be an interesting fortnight!