Question

What type of methods are used in microbial systematics? Why are multiple methods used to characterize and classify microbial species? Be sure to define the methods and describe the general strengths and weaknesses of each type

Answer 1

Various methods used in microbial systematics are :

1. Phenotypic methods

2. Genotypic methods

3. Phylogenetic methods

Systematics is the study of diversity . Microbial diversity is not easy to understood owing to small size, requirement of processing before their actual observation . Various methods of taxonomy change with change in type of organism.

In phenotypic method only phenotypic characteristics of cell are used to find the correct position of organism in classification system .

Organisms are classified with the help cell wall features, types of flagella , presence of nucleus , types of fatty acids found (FAME analysis ) , cytochrome types etc .

In case of genotypic analysis DNA profiling , DNA -DNA hybridisation method is used .

In phylogenetics method 16 S RNA, RFLP (Restriction fragment length polymorphism ) , AFLP (Amplified fragment length polymorphism ) is used to establish evolutionary history of organisms to others .

Use of different methods becomes necessary because each organism of one type not necessarily show characteristics of its own species like all bacteria do not possess flagella , all bacteria do not get stained with same Crystal violet , all unicellular algae have same chlorophyll pigment . Variations in similar types of molecules in a group causes scientists to look for other avenues of comparison .

Microbes also show vast genetic differences in terms of genes for example only certain bacteria possess nif genes for nitrogen fixation .

Prokaryotic genomes lack Exon introns (split genes ) so prokaryotic microbes are not analysed with the help of those methods which involves study of Exons or introns .

Study involving histones do not apply to bacteria which lack histones .

Bacteria themselves are of different types eubacteria, cyanobacteria and archaebacteria . Only archaebacteria can survive extreme conditions .

All methods are not equally useful as they make use of study of certain molecules like protein or DNA which differ from microbe to microbe .

Like Gram staining methods fails in case of archaebacteria but work well with eubacteria.

Study of microbes with 16sRNA provides in-depth evolutionary relation ship among microbes but study itself is time consuming as ribosomal genes are not easy to isolate and study .But this technique can be applied to any bacteria having 70s Ribosomes.

DNA DNA hybridisation provide more accuracy in establishing evolutionary lineage but it involves tedious DNA isolation and hybridisation involving preparation of autoradiography or flourescent microscopy .

RFLP involves use of restriction enzymes which are costly to prepare , require cloning process and DNA binding techniques .

Phenotypic methods involving cellular features are much easier than genetic methods requiring less microscopy work but results may be far away from accuracy as they are more error prone during analysis like fatty acid analysis .