Metagenomics of bacterial communities from the rhizosphere of switchgrass

Jesus, E. da C., Susilawati, E., Chai, B., Wang, Q., Rodrigues, J. L. M., Tiedje, J. M.

Presented at the GLBRC Sustainability Retreat (2010-02-10 to 2010-02-12 )

We are studying bacterial communities in the rhizosphere of switchgrass through a metagenomic approach, which allows us to assess the taxonomic and functional composition of bacterial communities. Additionally, we aimed to validate the application of metagenomics to study the rhizosphere of switchgrass. Roots of the cultivar Cave-in-Rock were sampled at the MSU experimental farm and the rhizosphere soil was used for total DNA extraction. Sequencing was done by 454-Titanium pyrosequencing at JGI, generating 291 Mb of sequence in 642441 reads. The final dataset without potential artificial duplicates contains 487,660 reads totaling 237,422,518 base pairs with an average fragment length of 486.86 bp. Sixty-three percent of the sequences could be matched to proteins in SEED subsystems in the MG-RAST pipeline. Most of the reads were assigned to essential functions for cell maintenance such as amino acids and carbohydrate metabolism. Reads were assigned mainly to Proteobacteria (74%), followed by Acidobacteria (4%), Actinobacteria (3%) and Bacteroidetes (2%). Pseudomonadaceae assignments accounted for 54% of all reads. Functions commonly associated with Pseudomonas such as stress resistance and iron scavenging were found. This genus was also found in large numbers by cultivation from the same rhizosphere sample, providing cultured models for further study.

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