03-08-2013, 04:44 PM
Metagenomics in plant- microbe interaction
ABSTRACT
Saffron (Crocus sativus L) is an autumn-flowering perennial sterile plant; reproduce vegetatively by corms (underground bulb-like organs). Fascinated by the interesting corm root life cycle of saffron, the bacterial diversity associated with roots and corms of saffron was studied using cultivation independent and dependent techniques. There are no reports on the rhizosphere of saffron by cultivation dependent or independent method so far. Though lot of work has been done on the rhizosphere ecology of many economically important plants but no such work has been reported from the cormosphere of corm bearing plants.
In the present study the bacterial diversity of rhizosphere, cormosphere and bulk soil of saffron is studied by cultivation independent / metagenomic and cultivation dependent approach. Using culture dependent approach, 100 bacteria were isolated from the bulk & rhizosphere of Saffron which were identified into five different genera. As only 1% of the bacterial population can be cultivated by routine techniques, researchers resort to alternative metagenomic methods to retrieve information regarding 99% of yet to be cultivated bacteria. Metagenomics is a rapidly growing area of the genome sciences that aids to define the features of intact microbial communities in their native environment. Metagenomics approach was applied to study the bacterial diversity of rhizosphere, cormosphere and bulk soil of Saffron for which the metagenomic DNA was isolated from them and 16S rDNA was amplified by PCR amplification using universal bacterial primers, cloned, sequenced and analysed. 22 genera were obtained along with five unclassified groups.
Cultivation based method were able to isolate only Bacillus, Pseudomonas, chryseobacteria, acinetobacter and arthrobacter genera whereas cultivation independent method obtained different genera namely Bacillus, Pseudomonas, Acidobacteria GP3, GP4, GP5,GP6,GP7, GP17, sphingomonas, Gemmatimonas, Herbaspirillum, Ralastonia, Planctomyces, Serratia, Pantoea, Enterobacter, Serpens, Massila, Shigella, Salmonella, Stenotrophomonas and Staphylococcus were the various bacterial genera which could not be isolated using cultivation dependent techniques. Proteobacteria and firmicutes were the common phylum between obtained from Bulk, rhizosphere and cormosphere using both the techiniques. Bacillus and pseudomonas were the common genera between bulk soil and rhizosphere using cultivation approach whereas Bacillus, Pseudomonas and Acidobacteria GP6 were found common using cultivation independent approach. However cormosphere when compared with rhizosphere obtained Pantoea and enterobacter genera in common but none of the genera were common between bulk soil and cormosphere using metagenomic analysis. Out of total 22 genera, 10 were unique to bulk soil, 4 to cormosphere and 6 to rhizosphere. This is the first report on the bacteria associated with rhizosphere and cormosphere of saffron by cultivation independent method.