Wetlands have been referred as nature’s kidneys. Much interest has developed in recent years to study the mechanism and possible impact of wetlands to remove contaminants from water, whether it is effluent from municipal or private waste systems, industrial or agricultural wastewater. Wetland ecosystem is rich in microbial diversity, which have still remained unexplored. Diversity of microbial communities in this natural aquatic systems and their metabolic functions have remained largely unexplored. Besides the conversion of dissolved organic matter into particulate carbon, these microbes synthesize and secret number of enzymes that degrade complex organic matters and release nutrients. Studies of microbial communities in wetland aquatic ecosystems provides important insights into relations between various aspects of ecosystem functioning and changes in biodiversity. In microbial analysis, the species identification of a microorganism is important for proper identification and characterization of both pathogenic and non-pathogenic microbes from environment and clinical cases.
Methods used for discrimination of genera, species, and isolates can be divided into phenotypic and genetic procedures. Phenotypic procedures take advantage of biochemical, physiological, and biological phenomena, whereas genetic procedures aim to detect polymorphisms at the level of nucleic acids or to detect allelic variation at the level of enzymes (Louws et al., 1999). Identification and additional typing can be done on the basis of the their phonotypic characteristics such as i) cultural and biochemical characteristics like growth on a selective or differential medium, general features such as odor and colony form and their action on various substrates, antibiotic susceptibility ii) serological and immunological properties like the recognition of microbial antigens by monoclonal or polyclonal antibodies, susceptibility to infection by bacteriophages. The shortcomings of phenotypically based typing methods have led to the development of typing methods based on the microbial genotype or DNA sequence, like (i) random whole-genome analysis; (ii) specific gene variation and (iii) mobile genetic elements. (i) The use of RAPD, REP-PCR, ERIC-PCR, PFGE and AFLP , minimize the problems with typeability and reproducibility and, in some cases, enable the establishment of large databases of characterized organisms (Olive, and Bean, 1999). These techniques help to analyse the whole genome and provide a skeleton of polymorphic sites with exact genomic positions as whole-genome sequence data become available. Different genes provide different levels of evolutionary information for determining isolate relatedness depending on whether they are highly variable (prone to recombination events and horizontal transfer), housekeeping genes with only a small number of single nucleotide differences between isolates. Comparative analyses of these different gene classes can provide enhanced information about isolate relatedness. Mobile genetic elements such as insertion sequences, transposons, plasmids and bacteriophages integrate into the bacterial genome at specific (e.g. tRNA genes) or non-specific sites to alter band patterns produced by PFGE, RAPD, REP-PCR, ERIC-PCR or AFLP.
Combination of all data, including those gathered by phototypic methods and those by the use of high-resolution molecular techniques, can lead to unequivocal identification and, in some cases, can even discriminate among isolates of a given species. These data can be used for epidemiologic purposes. Determination of unique characteristics of a microorganism allows study of colonization or cross-infection and enables the establishment of phylogenetic relationships (Belkum,1994). In this paper, we have compared some of the common laboratory used phenotypic and genotypic methods for phenotyping and genotypic typing of microbial isolates, especially from wetland ecosystem
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