TABLE 1.
Techniques employed for characterizing microbial biodiversity in studies published from 1975 to 1999
| Techniques based on analysis of: | Specific techniques employeda |
|---|---|
| Metabolic properties | API; BIOLOG; presence of certain enzymes; classical phenotypic tests; sensitivity to phages |
| Resistance to antimicrobial compounds | Profiles of resistance to biocides including antibiotics, bacteriocins, pesticides, heavy metals, and polyaromatic hydrocarbons |
| Pathogenicity, pathogenicity-like processes, | Pathogenicity to plants or animals and type of symptoms; capacity for symbiosis; potential |
| and production of toxins | to infect or presence of markers of virulence including cytotoxicity or toxin production |
| Colony and cellular morphology | Morphotype; colony type; cell type |
| Markers of other specific phenotypic properties | Protein profiles; characterization of lipopolysaccharides, antigens, fatty acids, isozymes, and opines |
| Growth on specific media | Growth on selective, semiselective, or differential media |
| Other diverse phenotypic properties | Ice nucleation activity, vegetative compatibility types, mating types, antagonistic activity, etc. |
| Total DNA | RFLP without probes; RFLP with anonymous probes; rep-PCR; AFLP; DAF; microsatellite analysis; PFGE; DNA-DNA hybridization; ASAP; RAPD |
| Targeted DNA sequences | Plasmid profiles; FISH; RFLP with specific probes; hybridization of specific probes; analysis of sequences of ribosomic genes; PCR polymorphisms; PCR-RFLP; ITS polymorphisms; DGGE; ARDRA |
| Other types of genotypic profiles | Genotyping techniques not listed above |
a
rep-PCR, repetitive-sequence based PCR; AFLP, amplification fragment length polymorphism; DAF, DNA amplification fingerprinting; PFGE, pulsed-field gel electrophoresis; ASAP, arbitrary signature from amplification profiles; RAPD, randomly amplified polymorphic DNA; FISH, fluorescent in situ hybridization; ITS, internal transcribed spacer; DGGE, denaturing gradient gel electrophoresis; ARDRA, amplified R-DNA restriction analysis.