General Microbiology

The Phylogenetic Tree (Microbial Diversity)

Written by MicroDok

The phylogenetic tree for microbial classification and/or microbial taxonomy comprises Eubacteria, Archaea and Bacteria. It shows in simpler terms how the different families or groups of microorganisms originated from a common ancestor; and how they are distributed and classified under a specific group or family, usually based on some shared morphological and/or physiological features. Eubacteria or Eukarya, Archaea and Bacteria are the three primary groups of microorganisms and macroorganisms, and these are generally referred to as domains- which show the ancestry of these organisms according to phylogeny. Phylogeny is the branch of science that studies the evolutionary correlation amongst organisms using the genetic information encoded in their nucleic acids (i.e. DNA and RNA). However, microbial phylogeny (i.e. the study of the evolutionary relationship between microbes) can be best deduced and studied by using the ribonucleic acid (RNA) component of an organisms nucleic acid and this is because all microbial cells contain ribosomes (the cell structure or component that is composed of RNAs) with the exception of viruses. Ribosomes are the machinery responsible for the synthesis of proteins in a cell; and they are found in all microbial cells except viruses.

Viruses contain either DNA or RNA unlike other microbial cells such as bacteria and fungi that contain both DNA and RNA in their genome. Thus, the RNA macromolecule especially the ribosomal RNA (rRNA) is the best tool for deciphering the evolutionary relationships of microbial cells excluding viruses. The phylogenetic relationship of viruses is determined is determined based on epidemiological, immunological, and evolutionary data or processes that are peculiar to viruses; and these information help biologists to form viral phylogenies – since they cannot be placed in the usual phylogenetic tree of life like other microbial cells. Viruses cannot be included in the phylogenetic tree of life as is applicable to other microbes such as bacteria because viruses do not share characteristics with other microbial cells, and no single gene is shared by all viruses or viral lineages. Thus, viruses are polyphyletic. It is noteworthy that in a phylogenetic tree, the characteristics of members of taxa are inherited from previous ancestors of organisms in those taxa (Figure 1).

Viruses are practically not alive like bacteria, fungi, protozoa and algae especially when they are outside a living host; and the generally lack any form of energy and carbon metabolism that keep living cells going. Viruses cannot replicate or evolve like other microbial cells; and they are reproduced only within living host cells including those of bacteria, plant and animal cells. Without these living host cells (which provide the reproductive machinery for the replication of viruses), viruses are generally inanimate complex organic matter. While cellular life has a single, common origin, viruses are polyphyletic. This implies that viruses have many evolutionary origins. Therefore, viruses (unlike other microorganisms) are in the polyphyletic group, because they have many evolutionary origins. A polyphyletic group is defined as a group of organisms that are derived from more than one common evolutionary ancestor or ancestral group. Such organisms derived from more than one common evolutionary ancestor or ancestral group are usually not suitable for placing in the same taxon. Viruses are typical examples of organisms classiffied under the polyphyletic group. The term “polyphyletic group” is often used to describe groups of microbes that share characteristics that appear to be similar but have not been inherited from a common ancestor.

The phylogenetic tree which elucidates the three domains of microbial life (Eukarya, Archaea and Bacteria), and some other forms of life is constructed based on the application of the comparative sequencing of the rRNAs of different organisms (Figure 1). Eubacteria, Archaea and Bacteria are morphologically and genetically distinct organisms. The prokaryotes are only in two domains: Bacteria and Archaea while the eukaryotes are in the domain Eukarya. All organisms in these domains especially the prokaryotes have a wide range of physiological and genetic diversity that distinguishes them from each other. It is noteworthy that all microbial cells (bacteria, fungi, algae, protozoa and viruses) evolve with time; and thus newer species and diversities of organisms will continue to appear on the face of the earth due to natural selection and mutation and other prevailing environmental and non-environmental factors.

Figure 1: The phylogenetic tree based on comparative rRNA gene sequencing.


Archaea bacteria generally inhabit terrestrial and aquatic environments where the condition of living is extremely harsh and unfavourable for other microbial cells. Habitats occupied by Archaea have very high temperature and salinity. Archaea are known to live in hostile environments including hot springs and areas with high salt concentration. They are not known to cause any disease as their prokaryotic relatives, bacteria. Both Archaea and bacteria differ greatly in their morphological structures, physiology and metabolic activities (Figure 1). Various forms of the Archaea bacteria are known to exist and they include the hyper or extreme thermophiles, the methanogens, the extreme halophiles and the sulphate-reducing Archaea (e.g. Archaeoglobus species). Some Archaea bacteria such as the extreme or hyper-thermophilc organisms (e.g. Sulfolobus acidocaldarius) are highly adapted to living at very high temperature above 100oC.

Thermus aquaticus is an Archaea but not an extreme thermophile; instead T. aquaticus is a thermophile or thermophilic bacterium that lives in habitats with temperature below 100oC. T. aquaticus is the source of the enzyme Taq polymerase which is used in the polymerase chain reaction (PCR), an important laboratory technique in molecular biology. Other examples of thermophilic Archaea bacteria include Thermoplasma species, bacteria without cell walls. Methanogens such are Archaea that produce methane (CH4) gas; and they also occur in the stomach of ruminant animals (e.g. cow). The methanogens that exist in the stomach of animals are known as animal methanogens while those that occur in the natural environment i.e. in harsh terrestrial and aquatic habitats are generally referred to as symbiotic methanogens. The metabolic activities of methanogens are responsible for the world’s reserve of natural gases which are tapped all over the globe for various industrial and economic purposes. Examples of methanogens include Haloferax volcanni and Methanosarcina barkeri.

The extreme halophiles are Archaea that live in habitats with high salt concentration. Extreme halophiles will not grow at low salt concentrations because they are organisms that require high salt concentration for growth. Examples of halophiles include Halobacterium salinarium and Halobacterium halobium. Archaea bacteria differ greatly from eukaryotic cells and bacteria; and they only exist in extreme and harsh environments due to specialized structures as well as their metabolic adaptations which allow them to inhabit such environments. They are mostly Gram-negative anaerobic bacteria but some are Gram-positive (e.g., Methanobacterium formicicum); and Archaea bacteria differ from other organisms in their physiology, morphology, ecology and reproduction.

Eukarya domain mainly contains all eukaryotic microorganisms such as fungi and algae; and plants, lichens and animals which are known as macro-organisms. Slime moulds and diatoms as well as other protists or protozoa and ciliates are also in the Eukarya domain. The Eukarya domain is unique and it contains several eukaryotic microorganisms (i.e. cells with membrane-bound nucleus and other membrane-bound organelles) that are distinct from the Archaea and Bacteria domains (Figure 1). They also contain organisms that are pathogenic in man and animals; and several of the eukaryotic microorganisms and macroorganisms are non-pathogenic and beneficial to man and his environment. Eukaryotic cells are distinct from prokaryotic cells- which do not have a membrane-bound nucleus as well as other membrane bound organelles.

Bacteria are microbial cells that are neither members of the Eukarya or Archaea domain (Figure 1), but they are basically prokaryotic cells (i.e. organisms without a true nucleus). They are all prokaryotic organisms, and are ubiquitously found in the environment. Bacteria domain includes both pathogenic and beneficial or non-pathogenic bacteria species. Some recognized major phyla of the Bacteria domain which represents different genera of bacteria include Proteobacteria, Green filamentous bacteria, Spirochaetes, Actinobacteria, Fusobacteria, Cyanobacteria, Acidobacteria, Verrucomicrobia, Planctomycetes, Aquifex, Chlamydia and Deinococcus phylum (which contains D. radiodurans– that survives high radiation) et cetera. The Proteobacteria is the largest phylum of the Bacteria domain; and this division contains several genera of bacteria including chemolithotrophic bacteria, phototrophic bacteria as well as numerous species of bacteria that are pathogenic and non-pathogenic in nature.

Five (5) classes of the proteobacteria phyla are known, and these are: alpha (α) proteobacteria (e.g. Rhizobium), beta (β) proteobacteria (e.g. Neisseria), gamma (γ) proteobacteria (e.g. Escherichia), delta (δ) proteobacteria (e.g. Myxococcus) and epsilon (ε) proteobacteria (e.g. Helicobacter). Chemolithotrophs are organisms (Archaea and bacteria inclusive) that obtain their energy from the oxidation of inorganic compounds, and such cells are said to be chemolithotrophic in their mode of nutrition. Phototrophs or phototrophic bacteria such as cyanobacteria and green bacteria obtain their energy through the process of photosynthesis, like plants. Based on their cell walls, bacteria are classified as either Gram-positive or Gram-negative. Some bacteria are neither Gram-positive nor Gram-negative, and are generally known as Gram variable bacteria. In terms of oxygen requirement, the organisms in the Bacteria domain are aerobic, anaerobic, micro-aerobic or facultative aerobes or anaerobes.


Abbott, S. L. (2007). Klebsiella, Enterobacter, Citrobacter, Serratia, Plesiomonas, and Other Enterobacteriaceae. In P. R. Murray, E. J. Baron, J. H. Jorgensen, M. L. Landry & M. A. Pfaller (Eds.), Manual of Clinical Microbiology (9th ed., pp. 698-711). Washington, USA: ASM Press.

Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P (2006). Toward automatic reconstruction of a highly resolved tree of life. Science, 311(5765):1283–1287.

Euzéby, J. P. (2010). List of Bacterial Names with Standing in Nomenclature. Int. J. Syst. Bacteriol., 47, 8 July, 2016. Retrieved from

Fauquet C.M, Mayo M.A, Maniloff J, Desselberger U and Ball L.A. (Eds) (2005). Virus Taxonomy. Eight Report of the International Committee on Taxonomy of Viruses. Burlington, M.A. Elsevier Academic Press.

George M. Garrity (2005). Bergey’s manual of systematic bacteriology. 2. Auflage. Springer, New York, 2005, Volume 2: The Proteobacteria, Part B: The Gammaproteobacteria.

Grenfell B.T, Pybus O.G, Gog J.R, Wood J.L, Daly J.M, Mumford J.A and Holmes E.C (2004). Unifying the Epidemiological and Evolutionary Dynamics of Pathogens. Science, 303(5656): 327–332.

Gupta RS (2000). The natural evolutionary relationships among prokaryotes. Crit. Rev. Microbiol, 26 (2):111–131.

Janda, J. M., and Abbott, S. L. (2006). The Genera Klebsiella and Raoultella. The Enterobacteria (2nd ed., pp. 115-129). Washington, USA: ASM Press.

Madigan M.T., Martinko J.M., Dunlap P.V and Clark D.P (2009). Brock Biology of microorganisms. 12th edition. Pearson Benjamin Cummings Publishers. USA. Pp.795-796.

Moreira D and López-García P (2009). Ten reasons to exclude viruses from the tree of life Nature Reviews Microbiology, 7(4):306-311.

Woese C.R, Kandler O, Wheelis M.L (1990). Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Science, 87(12):4576–4579.

Woese CR and Gupta R (1981). Are Archaebacteria merely derived ‘prokaryotes’?. Nature, 289 (5793): 95–96.

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