**4. Microbial phylogeny**

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

The diversity of microbial communities varies within habitats as much as between habitats [2]. This variation can even occur within a few millimetres, suggesting that microbial diversity encompasses more than the documented evidence available. Hence, biogeography is gaining importance as a field of study from microbial diversity point of interest. Many reasons have been postulated to explain this phenomenon. Due to the innately small size of the microor‐ ganisms, environmental complexity plays a major role in determining diversity. Spatial heterogeneity is likely to lead to the formation of many niches within a habitat [3]. Recent tools like metagenomics aid in biogeography studies by providing information on nucleic acid sequence data, thereby directly identifying microorganisms (see Section 9). Therefore the phylogenetic information can be used to compare microbial diversity profile across habitats [2]. Generally, diversity within a particular location and in a community is called alpha diversity. Beta diversity measures the community composition between two or more locations while gamma diversity applies to a region, across continents and biomes and is larger in size than

The evolutionary relationship of microorganisms is called phylogeny. Understanding phylo‐ genetic profiles of microbes becomes a daunting task because of their small size and the lack of particular indicators that could serve as markers. Some proteins and genes are considered as evolutionary chronometers which measure the evolutionary change [5]. Currently, the 16S rDNA sequence is considered to be most reliable for measuring evolutionary relationships in bacteria and archaea (detailed in Section 7.2.1) and the 18S sequence for fungi (see Section 8). However, it is necessary to choose the correct protein or gene for such studies. Such a gene or protein should have certain features which make it most appropriate for deriving evolutionary relationship. The most important criterion is that it should be present in all members of the target group and be functionally homologous in the organisms. The molecule must contain regions of conserved sequences for comparison purposes. The changes in sequence data must be at a slow enough rate to permit measurement so that it may also reflect evolutionary change

In the current system of classification, based on the 16S rDNA sequence, evolutionary relationships form the basis for division and three major domains have been recognized, out

also includes *phylogeny* as an integral part of the classification process [1].

**2. Biogeography of microbial diversity**

52 Biodiversity - The Dynamic Balance of the Planet

that used for measuring alpha diversity [4].

**3. Microbial evolution**

for the entire group [5].

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]).

genes are also shared between all the three domains. The genes required for core cellular functions are the ones which are necessary for survival of a cell and could have arisen from the common ancestor.

here that the nomenclature of a taxon is very important as it serves to maintain effective communication across microbiological disciplines and it is governed by the Bacteriological

Modern Taxonomy for Microbial Diversity http://dx.doi.org/10.5772/57407 55

**Figure 2.** Various techniques used in polyphasic taxonomy for characterization of prokaryotes.

While the species is accepted as the basic unit of taxonomy (see Section 6), sub-species, strains and ecotypes occupy lower distinctive taxonomic levels for certain groups of organisms and are not mandatory for all. When classifying a new taxon, it is essential to describe phenotypic, genotypic and phylogenetic information as accurately as possible. This constitutes the polyphasic approach of taxonomy [1] and is shown in Figure 2. The phenotypic information comes from the colony characteristics, cell type, cell wall-type, pigmentation patterns, proteins and other chemotaxonomic markers while genotypic features are derived from the nucleic acids (DNA / RNA). Phylogenetic information is obtained from studying sequence similarities of the 16S rRNA or 23 S rRNA genes in case of bacteria and 18S rRNA in case of fungi. Many types of molecules are used for delineating and describing a taxon; some are mandatory (16S

**7. Polyphasic taxonomy**

Code [17, 18].

The divergence of the organisms represents the differences in genetic sequences which could have become fixed in each group as they evolved. It is also postulated that earlier, HGT played a key role in transfer of genes between organisms early in the evolutionary history [6]. It occurs as a response to any change in the environment and provides for better adaptation ([9] and references therein). Subsequently, reproductive isolation could have prevented extensive exchange of genes, though it continues to occur amongst prokaryotes.

## **5. The prokaryotic microbes — Bacteria and archaea**

The bacteria and archaea have evolved along different lines though both are essentially prokaryotic. The archaea are considered to be the most primitive and are common inhabitants of the so-called extreme habitats (hot springs, deep sea hydrothermal vents, alkaline and acidic habitats). Though the bacteria and archaea share certain common features, the archaea also share similarities with eukaryotes which are further exemplified by the 16S rDNA-based phylogenetic analyses.

#### **6. The species concept**

An array of diverse definitions have been proposed to describe microbial species. Currently, a polyphasic approach is used to define a microbial species using phenotypic and genotypic properties [1, 10]. Whenever a new taxon is proposed, it is essential that the organism be isolated in pure culture and its characteristic features be tested under standard conditions [11]. Whether an organism constitutes a member of a common species is primarily based on whether its DNA-DNA re-association values are more than 70% and melting temperature (ΔTm) is less than 5ºC, the experiments being performed under standard conditions [12]. All the strains within a species must show similar phenotypes. A designated type strain of a species consti‐ tutes the reference specimen for that species [13]. A species description must preferably be based on the characteristics of more than one type strain. To be assigned a different species name, members must show at least one and is governed by the [12]. If the 16S rDNA sequences of organisms are ≤ 98.7% or ≤ 97% identical, they are members of different species. This is considered even in the absence of DNA-DNA hybridization experiments since this level of divergence in 16S rDNA sequences constitutes less than 70% DNA-DNA similarity [14]. Uncultured microbes cannot be assigned to a definite species since their phenotype is not known; however, they can be assigned a '*Candidatus*' designation provided their 16S rRNA sequence subscribes to the principles of identity with known species [15]. A concept applying to a taxon lower than that of the strain is the ecotype – those microorganisms that occupy an ecological niche and are adapted to the conditions of that niche [16]. It is important to remember here that the nomenclature of a taxon is very important as it serves to maintain effective communication across microbiological disciplines and it is governed by the Bacteriological Code [17, 18].

**Figure 2.** Various techniques used in polyphasic taxonomy for characterization of prokaryotes.
