Bacteria and the tree of life

Microbial phylogeny: a mouthful to say, let alone consider. I have been doing quite a lot of work on it and get increasingly sucked in to the fascinating complexity and speculations which exist within it. Phylogeny is the study of the tree of life, how all living organisms relate to all others. The only illustration in Darwin's "On the Origin of the Species by Means of Natural Selection," the tree of life has been our starting point for evolutionary theory ever since.

 Phylogenetic tree by Haeckel

Originally, bacteria and other microbes were thought to le outside the tree, to be primitive ,left over life forms. They leave no fossil record and, within living memory, were thought not to have genes as they were already understood in higher organisms. In 1942, in his book, Evolution, the Modern Synthesis, the famous evolutionary theorist, Julian Huxley, excluded bacteria from the evolutionary synthesis because they had no genes as then understood.
It has become clear in the half century since the discovery of DNA, with the explosion of molecular technology which followed it, that microbes have an evolutionary story at least as complex and a great deal more ancient than the "higher" organisms. The whole concept of a tree may be completely irrelevant on a whole organism scale, as most microbes are capable of lateral gene transfer between species, genera and even kingdoms.
One of the (many) problems in dealing with microbial phylogeny is simply the speed with which the accepted wisdom in the field changes. When I was at school (less than 20 years ago), bacteria were part of the kingdom known as Monera; by the time I got to University, they were a kingdom of their own. Now it seems ,they are greater than that ,a domain, or (sounding like something out of science fiction), an Urkingdom!
A lot of this is simply semantics, something in which microbial taxonomists (those responsible for naming and classifying) excel.
Does it matter? Well, yes. Firstly , if we don't understand the simple spread of genes through generations, how can we ever get a handle on how collections of genes, coding for antibiotic resistance, or the lethal factors which turn a fairly nasty but local germ into a worldwide pandemic, spread.
Secondly, bacterial evolution is vital for human evolution. It is now widely accepted that the energy powerhouses of all our cells, mitochondria, are simply intracellular bacteria gone native. An amazing survival strategy for that germ. Microbial evolution drives changes in our food crops, our pests (it is estimated that one genus of bacteria, Wolbachia ,lives inside up to 70% of insect cells) and, of course, the diseases which threaten us daily.
Thirdly, it is becoming clear that the amazing adaptibility of microbes may have a lot to teach us about cliimate change and responses to it. There have been several mass extinctions in geological history; is it possible that somewhere within the genetic history of microbial life there is a molecular "signature" which could tell us what actually happened? There are bacteria which have evolved to deal with almost all possible extreme conditions, but a sudden spread in, for instance, sulphur-metabolising bacteria, 65million years ago, might support the theory that massive volcanic activity killed off the dinosaurs.