Culture-independent metagenomic approach to characterize the surface and subsurface soil bacterial community in the Brahmaputra valley, Assam, North-East India, an Indo-Burma mega-biodiversity hotspot

Soil bacterial communities, which contain the
highest level of prokaryotic diversity of any natural envi
ronment,areimportantforecosystemfunctioning.Aculture
independent metagenomic approach was employed in the
present investigation to characterize the diversity of soil
bacterial community composition in five geochemically and
hydrologically different surface and subsurface soil habitats
of Brahmaputra valley, Assam, North-East India, an Indo
Burma mega-biodiversity hotspot. The diversity of soil
bacterial community was determined through sequence
analysis of 16S–23S intergenic spacer regions (ISR). Poly
merase chain reaction (PCR) universal primers, 1406F
(50-TGYACACACCGCCCGT-30) and 155r (50-GGGTT
BCATTCRG-30) were used for amplification of 16S–23S
ribosomal DNA intergenic spacers of bacteria. Amplifica
tion resulted in an intense array of PCR products approxi
mately ranging in size from 200 to 900 bp. Clear banding
patterns were observed in analysed samples using the primer
set in combination. A clear change in microbial ISR profile
was observed on visual analysis of gel electrophoresis pro
f
iles. Fast alignment database searches of PCR amplicons of
16S–23S ISR sequence data revealed that the isolated
sequences resembled five major phylogenetic groups of bacteria, namely a-, b- and c-subdivisions ofProteobacteria,
Acidobacterium and Comamonadaceae.