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How to form a species (in the world of the Very Small)


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A species is one of those things that is harder to define than it looks. While it’s clear that (for example) a rat is a different species than a dog, the more closely related animals get, the harder it is to properly put them into species. Usual definitions involve the sharing of physical characteristics (although the physical characteristics shared between a Great Dane and a Shih Tzu can be harder to ascertain…) and the fundamental idea of breeding. If two species can interbreed to produce fertile offspring they are usually considered the same species. This still runs into problems; some animals can interbreed but just don’t (for example if they live on opposite sides of a mountain range) some animals can interbreed and produce mostly asterile offspring with the occasional  random fertile quirk, while some animals could potentially interbreed but it’s rather hard to imagine (again, with the Great Dane and the Shih Tzu)

I have no idea what crossing these two dogs would produce. Possibly some kind of war pompom. Image credit below.

When it comes to the world of microorganisms, however, species becomes even more of a murky concept. For bacteria and archaea even the concept of interbreeding doesn’t really exist. Bacteria don’t require all that squishy ‘sex’ stuff to produce more bacteria, they just divide themselves in half and filch random DNA from their mates, nearby bacteria and the general environment. However at the same time it’s still useful to be able to disinguish bacterial species; for example to recognise that S. aureus is a very different creature from an E. coli. All bacteria are not the same; but if they can share genes so easily, why are there such clearly different species? Why are there any differences between them at all?

Work done on archaea, the sadly ignored cousins of bacteria, is starting to give more of an idea about how a ‘species’ in microorganisms form. Studies done on the thermoacidophilic (high-temperature and low-pH loving) archaeon Sulfolobus islandicus gathered from a hot spring in Russia shows some mechanisms that, in these strains at least, leads to separate archaea species forming rather than one homologous population.

A group of archaea. These ones are halobacteria - salt lovers - rather than the thermoacidophiles in the study. Credit for the image is below.

The paper highlights two main theories as to how species form in microorganisms. ‘Species’ in this instance is defined as lineages with discrete clusters of sequence diversity. Theory one is the ‘niche’ theory, the idea that selection is ecological, and “ecotypes” (i.e almost-species) are kept because they’re specialising themselves to fit into a certain niche. If you’re trying to be the best at living in a hot pond, genes to help you cope with ice-crystals aren’t going to be much use.

The second theory is that there are genetic barriers that cause some clusters of micro-organisms to become genetically distinct and species-like. If the mutations within your own genetic material are more likely to be passed on than genes picked up from nearby organisms then it genetic clusters of species will form. This is all to do with the rates of mutation and recombination, and is explained much better (with many more paragraphs) in the reference below for those who are interested. It can also involve things like restriction enzymes, which chop up DNA. If one archaea line contains enzymes that break down the DNA of another line they aren’t going to be successfully sharing DNA any time soon.

It could also be a bit of a mix between they two. If tiny amounts of DNA are being shared, while large changes are made to the chromosome due to niche-specialisation, then the species fits under theory one. If more DNA is being shared with fellow micro-organisms, and each one is not mutating much, then theory two is clearly more relevant. For different species, in different conditions, speciation may occur using different methods.

For the Sulfolobus islandicus however, there’s now a lot more information on how species and clusters form. The researchers looked at two separate lineages within the hot springs, and found that although the archaea were capable of sharing DNA, they were none-the-less starting to become ecologically distinct and evolutionarily independent. Just to be clear, there was no physical barrier stopping them. They were all just swimming around in close proximity in the same warm springs. There weren’t even biochemical barriers stopping them, the DNA was capable of surviving in both strains without being chewed up by enzymes or otherwise harmed.

An unrelated picture of a Sulfolobus archaea. If you look closely, you can see little white viruses stuck to the surface. Which has nothing to do with this article but is still really cool! Credit below.

So are these two separate strains ‘species’? Not really, they still share DNA, but they seem to be on their way to becoming distinct species. Archaea, like bacteria, will always be capable of sharing DNA with each other. What is fascinating here is that sometimes, it appears, they just don’t want to. It may be that species in micro-organisms form less because of barriers that physically prevent gene flow, and more because the organisms themselves simply don’t want to share DNA anymore.

After all, if you’ve spent the last few hundred years specifically evolving to fit one precise little niche, how much help is DNA from someone who hasn’t?

Ref 1:Cadillo-Quiroz H, Didelot X, Held NL, Herrera A, Darling A, Reno ML, Krause DJ, & Whitaker RJ (2012). Patterns of gene flow define species of thermophilic archaea. PLoS biology, 10 (2) PMID: 22363207

Credit for image 1.

Credit for image 2.

Credit for image 3.

S.E. Gould About the Author: A biochemist with a love of microbiology, the Lab Rat enjoys exploring, reading about and writing about bacteria. Having finally managed to tear herself away from university, she now works for a small company in Cambridge where she turns data into manageable words and awesome graphs. Follow on Twitter @labratting.

The views expressed are those of the author and are not necessarily those of Scientific American.





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  1. 1. jehovajah 7:23 am 03/11/2012

    This “wanting to ” is a “proto-will” adduced from their behaviour, but statisitically it presents as a significantly low uptake of the option. Does the viral influence have a statistical significance? In programming terms: does the DNA get used to produce this cell behaviour?

    Link to this
  2. 2. S.E. Gould in reply to S.E. Gould 7:13 am 03/12/2012

    Heh – probably more accurate to say that “wanting to” is a handy metaphor that I use when writing. It isn’t that the bacteria “want to” specialise into a certain niche, it’s that the ones that do are more likely to survive and spread, sharing their behaviour with offspring. If any bacteria that venture outside of a certain environment die, then you could shorthand this by saying that bacteria “want to” stay in the environment.

    I’m not sure about the effect of viruses here (I assume you meet viruses that share bacterial DNA?) the paper did not go into that.

    There is no need to give the bacteria “proto-will” in this scenario, despite my use of language. The bacteria that stick to their guns and don’t accept outside DNA are simply more likely to survive. This behaviour need not be programmed into the DNA either, it is more likely to be caused by the behaviour of proteins and DNA markers that will determine how often the bacteria conjugate.

    Whether bacteria do or do not have a conscious mind is a question for philosophers – it’s not really one that science can answer!

    Link to this

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