METAGENOMICS ANALYSIS OF EUKARYOTIC COMMUNITY IN SOIL USING 18S AND 28S rRNA GENE HIGH THROUGHPUT SEQUENCING

S. GUPTA¹*, S.K. CHIKARA^2
1Department of Biotechnology, Shri Venkateshwara University, Rajabpur Gajraula - 244 236, UP, India.
²Department of Biotechnology, Shri Venkateshwara University, Rajabpur Gajraula - 244 236, UP, India.
* Corresponding Author : shobit.jhs@gmail.com

Received : 20-06-2015     Accepted : 16-07-2015     Published : 03-09-2015
Volume : 7     Issue : 1       Pages : 161 - 164
Genetics 7.1 (2015):161-164

Keywords : Soil, 18S r RNA and 28S r RNA gene, High throughput sequencing
Academic Editor : Dr K M Singh, Dr. Navin Srivastava, Dr Ashma Richa, Dr. Chetan Jawale, Patwari J.M., Swapnil Prasadrao Deshmukh
Conflict of Interest : None declared
Acknowledgements/Funding : The authors are thankful to Director of Xcelris labs, Ahmedabad, Gujarat, India for providing fund of this work.

The present study applied metagenomics to characterize the diversity and relative occurrence of eukaryotic organisms in the soils of Chandan plant (Santalum album; MS1) and Bamboo plant (Bambussa bambus; MS2). DNA-based methods do not depend on the culturability of microbes, and therefore they offer an effective method for the study of metagenomics profiling. For this purpose, we used PCR primers that allow the specific amplification of 18S-ribosomal-DNA (rDNA) and 28S-ribosomal-DNA sequences. The metagenome samples were subjected to sequencing by Ion torrent PGM which resulted in 431,425 (MS1) and 303,564 (MS2) reads respectively. The taxonomic profile obtained by comparison with SILVA SSU database showed predominance of the phyla: Ascomycota (32.22% in MS2), Streptophyata (31.49% in MS2), Annelida (27.99% in MS 1), Nematoda (16.6% in MS1). At the genus level Enchytraeus (26% in MS1), and Aspergillus (22.4% in MS2) were predominant. The taxonomic assignment based nuclear 18S and 28S ribosomal sequences showed discrepancy with the SSU based assignments possibly due to the absence of most eukaryotic genomes in the public databases. The present study provides a preliminary snapshot of the diversity and relative abundance of the metazoan within the soil samples and expands our knowledge of these multicellular eukaryotes present in the soil ecosystem and these consortiums may be helpful in soil fertility and enhance plant productivity.