Microbial ecology examines the diversity and activity of microorganism in Earth's biosphere. Microorganisms have been integral to the history and function of life on Earth. They have played important and central roles in Earth's climate, geological, geochemical and biological evolution. The applications of genomics tools have revolutionized microbial ecological studies. The word 'genomics' have become a trendy term widely used by the scientific community and the general public. The term was used to describe a specific discipline on genetics that deals with mapping, sequencing and anlysing genomes. A genome refers the complete set of genes and chromosomes in an organism.
The most significant technical advance in genomics is the development of efficient, high throughput DNA-sequencing techniques and instruments. High throughput DNA sequencing such as pyrosequencing are faster and cheaper methods which could sequence 25 millions bases in a four-hour run.
Polymerase chain reaction (PCR) allows highly selective amplification of target DNA from minute amount of DNA amplification by PCR and analysis of the nuclear small ribosomal RNA gene from environmental samples have been used for the study of natural microbial diversities. DNA cloning systems allow the separation and amplification of individual DNA sequences from unknown but heterogeneous gene pools. A large variety of such system is now available to accommodate different types and size of DNA fragments. Vectors with large insert capacities such as cosmid, bacterial artificial chromosomes (BAC), yeast artificial chromosomes (YAC) are ideal for studying genome organization of uncultureable microorganisms in the environment.
Hybridization techniques such as DNA re-association kinetics analysis, fluorescent in situ hybridization (FISH) and microarray technique are used in microbial ecology studies. The analysis of DNA re-association kinetics can be used to provide estimate on the diversity of microbial genomes in environmental DNA samples. Using fluorescently tagged specific probes, FISH allows the direct observation and estimation of microorganisms from specific species, general, family or phyla in a given environment samples. DNA microarrays are glass surface to which arrays of specific DNA fragments of various lengths have been attached at discrete locations. These fragments serve as probes for hybridization. This DNA microarray technology is used to analysis the distribution of genes and species in natural microbial world.
Representational difference analysis (RDA) is used to study variation among strains in species with sequenced representative. In fact, in this analysis only one of two strains will be completely sequenced as large-scale DNA sequencing is still an expensive for most species. This analysis includes various molecular techniques such as cloning, selective PCR, DNA-DNA re-association kinetics and DNA sequencing. This is used for genome size and gene content comparison among strains in microbial species.
The tools such as the high throughput microarray technology, 2-D gel electrophoresis, mass spectrometry and gas chromatography are used for the analysis of the messenger RNA, proteins and metabolites of the microbial community as well as interaction among these cellular constituents. Bioinformatics refers to the use of computer to seek specific pattern in the observed biological data obtained from all the methods mentioned above and to propose mechanism for such pattern in microbial ecological research.
About Author / Additional Info:
Dr. Suresh Kaushik
Molecular Biology and Biotechnology