Bacteria have dominated the world’s biodiversity since life first evolved on planet earth between 3.5 – 4 billion years ago (DeLong & Pace, 2001), and Bacteria and Archaea had the planet to themselves for around 3 billion years (Schopf, 1994). To put this colossal time frame in a perspective the human mind can comprehend, hold your arms out as wide as you can, imagine the origin of life at the finger tips of your left hand, and the present day at the fingertips of your right hand. From your left fingertip to your right shoulder consists of nothing but bacterial life and, on this scale, multicellular life appears around your right elbow (developed from Dawkins (1998)).

After such an ancient evolutionary heritage it is no wonder bacteria are the most diverse groups of organisms that inhabit almost every possible niche found on earth (Dykhuizen, 1998). The study of this immense biological diversity and its interactions with the environment is microbial ecology and it’s a young and rapidly evolving science. Before the application of modern molecular methods, all environmental microbial studies relied on classical culture based techniques, which led to a large underestimation of both microbial diversity and microbial abundances (Hugenholtz et al., 1998). This is because 99.5-99.99% of bacterial taxa are uncultivable in laboratory conditions (Torsvik et al., 1990). In the early 1990s molecular techniques were first applied to soil samples and these produced extraordinary results (Tiedje et al., 1999). It was observed that microbial diversity in soils was orders of magnitude higher than what was predicted by culture based techniques. These molecular based methods proved that microorganisms are the most diverse (Figure 1‑2) and abundant forms of life on planet earth, with estimates of bacterial abundances of around 4-6 x 1030 individual cells worldwide (Whitman et al., 1998). A gram of soil contains over 109 bacteria cells; a handful of soil contains more bacteria than all the humans that have lived their lives out on planet earth since the evolutionary dawn of our species (Davis et al., 2005, Curtin, 2007). As well as dominating in terms of diversity and numbers, bacterial cells play an important role in the cycling and transformation of many biologically important elements. Estimates of global carbon content stored within these microorganisms vary between 350–550 Pg of C (1 Pg = 5 x 1015g); the upper end of that estimate is the carbon equivalent of 58 billion blue whales[1]. If all these bacterial cells were lined up end to end, they would stretch over 1.27 billion light years, or across our milky way 12,000 times[2]. We live on a microbial planet.

Figure 1‑1 Unrooted phylogenetic tree of life showing the huge diversity of bacteria (blue) compared to eukaryotes (red). Each branch represents a kingdom (for the eukaryotes) and phyla (for the bacteria), and the closer two branches are together, the more closely related they are. This means that Humans are more closely related to fungi than plants and more closely related to archaea than bacteria. Each colour represents a different domain. Blue: Bacteria; Green: Archaea; Red: Eukarya (simplified version based on Letunic & Bork (2007))

These facts are intriguing and fun, but so what? Why does this matter? These microorganisms provide crucial ecosystem services and it would be no exaggeration to say that without bacteria, life as we know it would not exist; even mitochondria, the energy generating factories nested by the thousands inside animal cells, had their origin as free living bacterial cells (Keeling & Archibald, 2008, Reece & Campbell, 2012). Surprisingly little is known about general patterns and ecological rules in the microbial world and there is a lack of ecological theory in microbial ecology (Prosser et al., 2007). Indeed, the science of macroorganism ecology is now a mature and well established field. Scientists had been observing the natural world for hundreds of years. However, it was only after Charles Darwin’s 1859 publication ‘On the Origin of Species by Means of Natural Selection’ that the science of ecology could truly become established (Darwin, 1859). Before then, studies of the biological world were largely exercises in ‘stamp collecting’; taxonomically naming species and collecting samples for museums and private collections. Darwin’s ingenious theory of natural selection completely revolutionised biology and allowed theoretical models to be constructed, transforming ecology from the purely observational, stamp collecting endeavour of the past, into a respected field of study in which many important hypotheses would be both devised and tested. Darwin’s theory of evolution via natural selection continues to stand the test of time, and more than 150 years since the publication of his seminal work, the majority of biologists agree with Theodosius Dobzhansky (1973), that “Nothing in biology makes sense, except in the light of evolution”. Despite this revolution in Darwinism, it could be argued that microbial ecology is little more advanced than macroscopic ecology before Darwin set sail on the Beagle in 1831 (Darwin, 1860). Indeed, while we have mapped the diversity and distribution of macroorganisms across the globe, microbiologists cannot agree how many species of bacteria are likely to exist, even to within 5 or 6 orders of magnitude (Torsvik et al., 2002). Although recent work is beginning to elucidate the biogeographical patterns of bacteria (Dolan, 2005, Martiny et al., 2006, Lear et al., 2013), in comparison to the ecology of macroorganisms our understanding of microbial biogeography has advanced little since Alfred Russel Wallace first identified biogeography as a science per se in 1872, and debates continue over whether bacteria are even restricted by geographic distributions, with some suggesting that they are nothing more than cosmopolitan vagrants, dispersing passively at the mercy of global currents of wind and water (Finlay & Clarke, 1999). “Everything is everywhere; but the environment selects”- Baas Becking, is one of the most quoted hypothesis in microbial ecology, which implies that bacterial taxa are ubiquitous and environmental selection regulates diversity (de Wit & Bouvier, 2006). But this, too, is almost becoming almost cliché in the literature. Despite this current lack of knowledge, it is clear that microbial communities are the most diverse biological assemblages on the planet and that they play key roles in almost every cycle relevant to life on earth. For this reason, it is essential that we develop a better understanding of biodiversity and biogeography of these essential and complex communities, and of the factors that shape them.

The construction of theoretical models that can explain and predict microbial community composition is one of the major goals in microbial ecology. Understanding the mechanisms that regulate and maintain bacterial diversity will be important in understanding how they will respond to climate change, pollution, ocean acidification and many other issues that will become apparent over the next 50 to 100 years (Houghton, 2001, Wootton et al., 2008). The construction and testing of these models has largely been restricted by the resolution in which we can observe the microbial world. With new high-throughput DNA sequencing technologies, the development of these highly sought after theoretical frameworks seem to be on the horizon. This is mainly due to the fact that these technologies allow much higher resolution at the ‘species’[3] level than older molecular techniques such as denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (tRFLP), which are generally only capable of detecting the DNA of microorganisms with abundances of greater than 1% of the total community (Casamayor et al., 2000, Biswas et al., 2013).

With the development of modern molecular techniques, there has been an increased interest in microbial biogeography. It is a vibrant area of science with many scientist holding opposing views and debates continue to revolve around the extent bacteria are dispersal limited, or if ‘everything is everywhere; but the environment selects’ (Finlay & Clarke, 1999, Finlay, 2002, Dolan, 2005, de Wit & Bouvier, 2006, Martiny et al., 2006, Ramette & Tiedje, 2007, Lau et al., 2012, Sul et al., 2013). As well as these reasons to study and understand bacterial community assembly, I believe microbial ecology can enhance macroecology per se. The ability to generate huge datasets in relatively quick periods of time allows rigorous testing of fundamental ecological principles. It takes years to generate such datasets with animals and plants; for example, it took Stephen Hubbell and colleagues many years to generate the tree data needed to develop his neutral model, which will be discussed in section 1.4. Microbial ecologists, however, can collect and process large numbers of environmental samples in a number of days, or even hours.

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© [1] My own calculation based on Hugenholtz et al., 1998 and Williams et al., 2000. [2] Again, my own calculation based on a cell size of 2µm (Kubitschek, 1990) multiplied by 6 x 1030. Milky way= c 100,000 light years in diameter (Arav et al., 1995). [3] An explanation of the species concept in bacteria is given in section 2.11. Work copyrighted to Jack E. Lee