It was realized by the biologists during recent past (1970s-80s) that the classification based on genetic characteristics (rather than phenotypic ones) with respect to evolutionary relatedness (phylogeny) of organisms may prove more stable and predictable.
In 1987, Carl Woese of University of Illinois (USA) summarized ten years of work and proposed a phylogenetic classification system for prokaryotic species based on the nucleotide sequence of 16S rRNA molecules, the RNA of small subunit of prokaryotic ribosome.
He concluded that 16S rRNA molecule sequences could not only be used for comparative analysis between different species of prokaryotes but also between prokaryotic and eukaryotic species to provide a tree of relatedness based on common ancestry or genealogy because both prokaryotic and eukaryotic cells contain small subunit rRNA (SSU rRNA).
Ribosomal RNA (rRNA) is considered to act as a good genetic indicator of evolution of one organism from the other because it is functionally constant, universally distributed, and moderately well conserved in sequence across broad phylogenetic distances.
Also, because the number of different possible sequences of ribosomal RNA is so large that the similarity in two sequences always indicates some phylogenetic relationship. However, it is the degree of similarity in ribosomal RNA sequences between two organisms that indicates their relative evolutionary relatedness.
The studies of Carl Woese and his colleagues based on comparative sequencing of 16S (prokaryotic) and 18S (eukaryotic) ribosomal RNA have resulted in the proposal of a universal phylogenetic tree of life on earth (Fig. 2.9).
The universal phylogenetic tree of life strongly suggested that there are three phylogenetically distinct group of cells (lineages) diverged from a common ancestral organism, the “universal ancestor”, early in the history of life on earth.
Also, the innovative nature of the universal phylogenetic tree became clear as both prokaryotic and eukaryotic species could be analysed together to provide:
(i) A picture of the comparative genetic diversity of all cellular life, and
(ii) A true view of the range of diversity accounted for by the prokaryotes.
However, the three phylogenetically distinct lineages or group of cells are called domains and represent the Bacteria, the Archaea, and the Eukarya. The domain Bacteria consists of prokaryotic cells possessing primarily diacyl glycerol diaster lipids in their membranes and bacterial rRNA.
The prokaryotic cells having isoprenoid glycerol diether or diglycerol tetra-ether lipids in their membranes and archacal rRNA constitutes the domain Archaea.
The domain Eukarya represents the eukaryotic organisms possessing primarily glycerol fatty acyl diaster membrane lipids and eukaryotic rRNA. However, the domains are given rank above the kingdom or phylum levels and differ markedly from one another (Table 2.3).
Domain-Bacteria:
The domain Bacteria, as said earlier, consists of enormous variety of prokaryotes that possess primarily diacyl glycerol diaster lipids in their membranes and bacterial rRNA.
Among Bacteria, many phylogenetic lineages or groups have been discovered; the major lineages or groups of this domain shown in Fig. 2.10 and are as follows:
(i) The Proteobacteria is the largest group or lineage within which occur many chemo- organotrophic, several phototrophic and chemolithotrophic bacteria. Several soil and water inhabiting, and parasitic bacteria are the members of Proteobacteria.
(ii) The Gram-positive lineage of bacteria contains endospore-forming Bacillus and Clostridium, and related spore-forming prokaryotes such as the antibiotic- producing Streptomyces. It also includes lactic acid bacteria (e.g.. Streptococcus, Lactobacillus) and the mycoplasmas.
(iii) The Cyanobacteria lineage contains those that are oxygenic phototrophs and phylogenetically related to gram-positive bacteria. These were the first oxygenic phototrophs that appeared on Earth and their production of oxygen paved the way for the evolution of aerobic prokaryotes, the evolution of “higher organisms” such as plants and animals followed from this.
(iv) Planctomyces lineage contains the bacterial cells with a distinct stalk which helps organisms to attach to a solid substratum.
(v) Spirochaetes group of bacteria are helical in morphology.
(iv) The lineages Green Sulphur Bacteria and the Green Non-sulphur Bacteria are phototrophic and can grow as autotrophs.
(vii) The Dienococcus lineage consists of bacteria with unusual cell walls and are innate resistants to high levels of radiation; Dienococcus radiodurans is a major species in this group.
(viii) The bacteria belonging to Aquifex and Thermotoga, though phylogcnetically distinct from one another, commonly share their property of growth at high temperature (thermophily).
Domain-Archaea:
The domain Archaea (Fig. 2.11), represents those prokaryotic cells that have isoprenoid glycerol diether or diglycerol tetraether lipids in their membranes and archaeal rRNA. The domain Archaea consists of three large phyla, the Crenarchaeota, the Euryachaeota, and a third possible one called the “Korarchaeota”.
(i) Crenarchaeota phylum consists of representatives that live on both ends of Nature’s temperature extremes – boiling and freezing. Most crenarchaeotes are hyperthermophylic having ability to grow at even or above the boiling point of water (e.g., Sulfolobus, Acidianus, Pyrolobus etc.) By contrast with the hyperthermophiles, cold-dwelling crenarchaeotes thrive even in frigid waters such as those of the Antarctic.
(ii) Euryarchaeota comprise a physiologically diverse group of Archaea that inhabit extreme environments of one or the other.
Many of them are extreme halophiles i.e. inhabit very highly saline environments (e.g., Halobacterium, Natronobacterium), others are methane-producing (methanogens; e.g., Methanobacterium, Methanosarcina), and still others are most acidophilic (e.g., Thermoplasma, Ferroplasma and Picrophilus). Methanogenium, an euryarchaeote, has recently been isolated from Ace Lake of Antarctica.
(iii) Konarchaeota group is not yet officially recognized taxonomically. Representatives of this group were originally discovered from a single hot spring, Obsidian Pool, present in Yellowstone National Park (USA). However, mixed laboratory cultures of this group of Archaea clearly indicate that they are hyperthermophilic.
Domain-Eukarya:
The domain Eukarya consists of eukaryotic organisms that possess primarily glycerol fatty acyl diaster membrane lipids and eukaryotic rRNA. The phylogeny of Eukarya (Fig. 2.12) is deduced from comparative sequencing of 18S rRNA obtained from cytoplasmic ribosomes and indicates that they, as a group, are more closely related to Archaea than they are to Bacteria.
The lineages Diplomonas (e.g. Giardia), Microsporidia (e.g. Encephalitozoon) and Trichomonads (e.g., Trichomonas) represent the “early eukaryotes”. They all have a membrane-enclosed nucleus but lack mitochondria.
The microsporidia are considered to be evolutionary enigma as they lack all organelles (including the golgi complex and hydrogenosomes) and contain very small genomes. Indeed, microsporidia have all the characters predicted to be present in an “early eukaryote”.
Protozoa are phylogenetically diverse, appearing in several lineages (Flagellates, Amoebae, Ciliates) on the Eukarya-tree. They are wall-less unicellular eukaryotic micro-organisms generally colourless and motile. The group of slime moulds resemble both Protozoa and Fungi phenotypically. They are more ancient than Fungi and some protozoa (such as ciliates).
All fungi produce spores, lack photosynthetic pigments and are either unicellular or filamentous. They are the major agents of biodegradation in Nature and are major recyclers of organic matter in soils and other ecosystems.
The lineages of algae (green algae, red algae, diatoms, dinoflagellates, and brown algae) contain chlorophyll and carry out oxygenic photosynthesis. Most of the algae are microscopic hence clearly microorganisms, the remaining ones are macroscopic growing upto over 30 m in length (some seaweeds).
Though customarily studied as microorganisms, there are entities beyond cellular organization, viz., viruses, viroids, virusoids, prions whose biological status is enigmatic. It is still not clear with certainty whether they are living or non-living and, therefore, they still have not secured their place in any system of classification (either kingdoms or domains) of cellular living beings.