As you all may know, I wrote a series of blog entries on microbial species concepts back when I first moved over to Seed, which had previously been on my older blog [links at end]. This then became a talk and later a paper, now in review. My argument was that there was a principle by which we could tell if microbes were a single species or not, depending on how regularly it exchanged its genetic material.
Now the American Academy of Microbiology has caught up with me <insert smiley here>...
A report by the AAM entitled Reconciling Microbial Systematics and Genomics raises the issues of what, if anything is to count as a microbial species, in the light of modern genomics. Moselio Schaechter at Small Things Considered asks, somewhat rhetorically, "In our bewilderment we wonder, for example, if the concept of species will - Cheshire Cat-like - fade from view". I think it unlikely.
Problems that microbiologists face is that there is not necessarily a correlation between the specific identification methods of the past - mostly morphology of colonial growth and cell shape, some chemistry, and more recently, DNA hybridisation techniques - and the modern genomics approach known as the "Pan-species genome", in which the use of many genomes to generate a kind of cluster map is what is important.
Partly this is a matter of technical necessity - we cannot culture more than about 10% of all microbes in order to sequence them, so we have to sequence large communities instead in a process known as metagenomics, and look for clusters of genes that might identify different species within that community. Many microbes, of quite distant phylogenetic position, require other organisms in which to form "biofilms" necessary for their survival.
Partly, though, it is the problem that organisms that do not have near-obligate sexual reproduction are not easily distinguished from each other except by morphology and genetics, and there is no hard line between them most of the time. Even so, biologists still identify units or groups, and these are more than mere conveniences, because they do correlate to important biological processes like host adaptation or disease etiology.
Oh, and what is my view? Basically a microbial species is a disjunct of properties: either a MS is a sexual or gene exchanging cluster of organisms or it is a cluster of genomes that track a local environmental fitness peak. Or both. A leading (and my preferred) definition of species for sexual organisms is Alan Templeton's Cluster Conception in which a species is a conjunct of sexual exchange of genes and genomes that track environmental niches. The difference with microbes is that it is a disjunct because sex is not obligate. Read the posts or I can send you the paper on request.
Anyway, here are the links:
AAM Report PDF
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Great post. The ongoing discussion of the species concept is really an excellent example of that whole "philosophy of biology is at least as interesting as politics or sport and twice as important"-thing you've been going at.
One thing I've noticed about this debate is the relative dearth of extremist progressives. I've read a good amount of research by conservative taxonomists and even more by pragmatic researchers (like yourself). In the range of available literature, I can't really find too many people pushing full adoption of some species-less concept. Maybe it's only my own biased perspective, but I think that some in the field are trying to demonize research that takes an alternative viewpoint of the species concept. I find it hard to believe that anyone is looking to entirely disregard the old concepts. What seems more likely to me is that work with a particular goal in mind will use the most useful concept to match their goal.
I guess I'm saying these discussions are interesting and necessary, but I think there is a danger in taking a dogmatic view that treats the species concept as anything other than a means to an end. Obviously, the definitions you put forward here have some great utility and should be employed, but I have to wonder if we should be trying to choose one concept and close the door on others. It just feels to me a bit like the behavior of politicians or clergy, not of scientists.
There are a number of species deniers, as I call them:
Pleijel, Frederik, and G. W. Rouse. 2000. Least-inclusive taxonomic unit: a new taxonomic concept for biology. Proceedings of the Royal Society of London - Series B: Biological Sciences 267 (1443):627-630.
Vrana, P., and Ward Wheeler. 1992. Individual organisms as terminal entities: Laying the species problem to rest. Cladistics 8:67-72.
and of course the Sokal and Sneath OTU was a replacement for species that was rankless. Originally, "deme", by Gilmour, was also a rankless taxon notion designed to replace species. There are a number of pre-Synthesis ones, too.