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DGGE profiling of bacterial community from Arabian Sea
Advances in genomic analysis are providing new technologies that may be useful for characterizing uncultivated prokaryotes. Large DNA fragments can be recovered from mixed microbial populations using modern genomic techniques. Analysis of these large fragments can yield information on gene organization, structure and content of uncultivated bacteria. To study spatial and temporal variation of microbial communities, multiple sample analysis is essential. Approaches based on cloning and sequencing of the PCR amplified 16S rRNA gene fragments are too labor intensive, costly and time consuming, especially for analysis of large microbial diversity. More appropriate techniques in such cases are the molecular fingerprinting techniques such as denaturing gradient gel electrophoresis (DGGE). DGGE is able to detect differences in the melting behavior of small DNA fragments (200-700 bp) that differ by as little as a single base substitution. By DGGE, the DNA fragments of the same length but with different sequences can be separated. Further, DGGE is useful to separate polymerase chain reaction (PCR)-generated DNA fragments. Using this technique, Scientists at NIO analyzed the bacterial community structure from six locations in the Arabian Sea. Fig 1 depicts the possible number of different bacterial species and station-wise changes. Fig 2 depicts the vertical profile of bacterial community in four samples from surface to 1900m at on location. These analyses suggest both horizontal and depth-wise differences in bacterial community. As each band corresponds to a single bacterial species, as many as 21 bacterial species would be present in the water sample collected at 13?54.26?N 74?18.97?E. Similarly, at 14�00.29'N; 73�29.94'E; 14�00.24'N; 73�13.97'E; 14�00.25'N; 73�08.11'E and, 14�00.30'N; 72�57.22'E the possible number of bacterial species are 17, 15,24 and 22. Many of the bands were common to all the 5 water samples, indicating presence of same bacterial species. Similarly from Fig 2, it can be made out that as many as 28 bacterial species are present in the surface sample. At 250, 1000 and 1900 m the possible numbers of bacterial species are 23, 21 and 22 respectively. If one had to follow conventional (biochemical) identification method, it would have taken very long time to obtain such information. Also, this conventional method would not be useful if many of the ?species? we could count using DGGE technique were non-cultivable. The work was carried out by Dr N Ramaiah and Sanjay Kumar Singh. The students Aditi Thakur and Deepthi Rao from VIT, Vellore also participated in the experiment as a part of their dissertation work.
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