Microbial phylogenetics is the study of the manner in which various groups of

microorganism A microorganism, or microbe,, ''mikros'', "small") and ''organism'' from the el, ὀργανισμός, ''organismós'', "organism"). It is usually written as a single word but is sometimes hyphenated (''micro-organism''), especially in olde ...

s are genetically related. This helps to trace their

evolution Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation ...

. To study these relationships biologists rely on

comparative genomics Comparative genomics is a field of biological research in which the genomic features of different organisms are compared. The genomic features may include the DNA sequence, genes, gene order, regulatory sequences, and other genomic structural lan ...

, as

physiology Physiology (; ) is the scientific study of functions and mechanisms in a living system. As a sub-discipline of biology, physiology focuses on how organisms, organ systems, individual organs, cells, and biomolecules carry out the chemical ...

and

comparative anatomy Comparative anatomy is the study of similarities and differences in the anatomy of different species. It is closely related to evolutionary biology and phylogeny (the evolution of species). The science began in the classical era, continuing in t ...

are not possible methods.

History

1960s–1970s

Microbial

phylogenetics In biology, phylogenetics (; from Greek language, Greek wikt:φυλή, φυλή/wikt:φῦλον, φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary his ...

emerged as a field of study in the 1960s, scientists started to create genealogical trees based on differences in the order of

amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha am ...

s of

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...

s and

nucleotide Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules wi ...

s of genes instead of using comparative anatomy and physiology. One of the most important figures in the early stage of this field is

Carl Woese Carl Richard Woese (; July 15, 1928 – December 30, 2012) was an American microbiologist and biophysicist. Woese is famous for defining the Archaea (a new domain of life) in 1977 through a pioneering phylogenetic taxonomy of 16S ribosomal RNA, ...

, who in his researches, focused on

Bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...

, looking at

RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...

instead of proteins. More specifically, he decided to compare the small subunit

ribosomal RNA Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosomal ...

(16rRNA) oligonucleotides. Matching oligonucleotides in different bacteria could be compared to one another to determine how closely the organisms were related. In 1977, after collecting and comparing 16s rRNA fragments for almost 200 species of bacteria,

Woese Carl Richard Woese (; July 15, 1928 – December 30, 2012) was an American microbiologist and biophysicist. Woese is famous for defining the Archaea (a new domain of life) in 1977 through a pioneering phylogenetic taxonomy of 16S ribosomal RNA, a ...

and his team in 1977 concluded that

Archaebacteria Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebact ...

were not part of Bacteria but completely independent organisms.

1980s–1990s

In the 1980s microbial phylogenetics went into its golden age, as the techniques for

sequencing In genetics and biochemistry, sequencing means to determine the primary structure (sometimes incorrectly called the primary sequence) of an unbranched biopolymer. Sequencing results in a symbolic linear depiction known as a sequence which succ ...

RNA and DNA improved greatly. For example, comparison of the

nucleotide sequences A nucleic acid sequence is a succession of bases signified by a series of a set of five different letters that indicate the order of nucleotides forming alleles within a DNA (using GACT) or RNA (GACU) molecule. By convention, sequences are usu ...

of whole

gene In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...

s was facilitated by the development of the means to clone DNA, making possible to create many copies of sequences from minute samples. Of incredible impact for the microbial phylogenetics was the invention of the

polymerase chain reaction The polymerase chain reaction (PCR) is a method widely used to rapidly make millions to billions of copies (complete or partial) of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it (or a part of it) t ...

(PCR). All these new techniques led to the formal proposal of the three domains of life:

Archaea Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebac ...

(Woese himself proposed this name to replace the old nomination of Archaebacteria), and Eukarya, arguably one of the key passage in the history of taxonomy. One of the intrinsic problems of studying microbial organisms was the dependence of the studies from pure culture in a laboratory. Biologists tried to overcome this limitation by sequencing

rRNA Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosoma ...

genes obtained from DNA isolated directly from the environment. This technique made possible to fully appreciate that bacteria, not only to have the greatest diversity but to constitute the greatest

biomass Biomass is plant-based material used as a fuel for heat or electricity production. It can be in the form of wood, wood residues, energy crops, agricultural residues, and waste from industry, farms, and households. Some people use the terms bi ...

on earth. In the late 1990s sequencing of genomes from various microbial organisms started and by 2005, 260 complete genomes had been sequenced resulting in the classification of 33 eucaryotes, 206 eubacteria, and 21 archeons.

2000s

In the early 2000s, scientists started creating phylogenetic trees based not on

, but on other genes with different function (for example the gene for the enzyme RNA polymerase). The resulting

genealogies Genealogy () is the study of families, family history, and the tracing of their lineages. Genealogists use oral interviews, historical records, genetic analysis, and other records to obtain information about a family and to demonstrate kinsh ...

differed greatly from the ones based on the rRNA. These gene histories were so different between them that the only hypothesis that could explain these divergences was a major influence of

horizontal gene transfer Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between Unicellular organism, unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offsprin ...

(HGT), a mechanism which permits a

bacterium Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...

to acquire one or more

s from a completely unrelated organism. HGT explains why similarities and differences in some

s have to be carefully studied before being used as a measure of genealogical relationship for microbial organisms. Studies aimed at understanding the widespread of HGT suggested that the ease with which genes are transferred among

bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...

made impossible to apply ‘the biological species concept’ for them.

Phylogenetic representation

Since Darwin, every phylogeny for every organism has been represented in the form of a tree. Nonetheless, due to the great role that HGT plays for

microbes A microorganism, or microbe,, ''mikros'', "small") and ''organism'' from the el, ὀργανισμός, ''organismós'', "organism"). It is usually written as a single word but is sometimes hyphenated (''micro-organism''), especially in olde ...

some evolutionary microbiologists suggested abandoning this classical view in favor of a representation of genealogies more closely resembling a web, also known as network. However, there are some issues with this network representation, such as the inability to precisely establish the donor organism for a HGT event and the difficulty to determine the correct path across organisms when multiple HGT events happened. Therefore, there is not still a consensus between biologists on which representation is a better fit for the microbial world.

References