**1. Introduction**

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Microorganisms are actually composed of very different and taxonomically diverse groups of communities: archaea, bacteria, fungi and viruses. The members of these groups or taxa are distinct in terms of their morphology, physiology and phylogeny and fall into both prokaryotic and eukaryotic domains. They constitute a broad group of life system inhabiting the known ecosystems on earth: terrestrial and marine; including geographical locations considered to be extreme or inimical to life. The latter comprise of such areas as habitats with high salinity, alkalinity, acidity, high and low temperatures, high pressure, and high radiation. Considering the adaptability of microorganisms to grow and survive under varied physico-chemical conditions and their contribution in maintaining the balance in ecosystems, it is pertinent to catalogue their diversity as it exists. The inability to visualize them with the naked eye precludes effective classification. As such, using the available tools, microorganisms are broadly classified into prokaryotes and eukaryotes and subsequently into various taxonomical units depending on the resources available and required.

The sustenance of life on earth depends on maintaining the diversity of microorganisms. Human intervention is resulting in depletion of biodiversity and many hotspots are also fast losing their endemic biodiversity. While specific data is hard to come by, it is likely that loss of macro life forms also results in loss of the associated microbial species: symbionts as well as the rhizosphere-colonizing microbes. The significant contribution made by microorganisms in ecosystem sustainability as well as the industrially important biomolecules obtained from them: antibiotics, anti-cancer drugs, enzymes, biofuel and various other compounds, implies that cataloguing them is imperative. However, a simple and effective microbial identification system is still far off. The available tools for classification and identification of microorganisms rely on a number of different technologies. This chapter provides an overview of taxonomy

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tools for understanding prokaryotic and eukaryotic microbial diversity. Taxonomy (or biosystematics) consists of three main parts: *classification* (arrangement of organisms based on similarity), *nomenclature* (naming of the organisms) and *identification* (determining whether an organism belongs to the group under which it is classified and named). Modern biosystematics also includes *phylogeny* as an integral part of the classification process [1].

of which two comprise of bacteria and archaea (prokaryotes) and the third domain is of eukaryotes [6]. It is important to understand evolution in the context of biodiversity. Evolution leading to new ecotypes/species is achieved in many ways. Some species with quick generation times also undergo mutation frequently leading to novel species or strains [3]. Horizontal gene transfer (HGT), via transformation, transduction or conjugation, also accounts for introduction of genes into distantly related organisms, thereby introducing new traits and also impacting on interaction between species and thereby ecosystem processes [7]. It has also been hypothe‐ sized that large population sizes of microbes and their low extinction rates may also play a role in maintaining biodiversity, though measurement of such extinction rates is difficult ([8]

Modern Taxonomy for Microbial Diversity http://dx.doi.org/10.5772/57407 53

The phylogenetic tree representing all living organisms shows that, evolution of current forms of life occurred from a common ancestor (the universal ancestor), depicted by the root (see Figure 1). Two domains are of prokaryotic systems of life: the archaea and Eubacteria; in contrast to previous systems of classification, wherein, the prokaryotes were confined to a single kingdom. However, it is intriguing to note that, genomic studies have shown the archaea to contain unique gene sequences which are not present in bacteria or eukaryotes. Certain

**Figure 1.** The universal phylogenetic tree based on comparative ribosomal RNA sequences (adapted from [6]).

and references therein).

**4. Microbial phylogeny**
