7 Mwajita et al. Int. J. Biosci. 2014 RESEARCH PAPER OPEN ACCESS Molecular characterization of bacteria and fungi from rice growing regions in Kenya Mwashasha Rashid Mwajita 1* , Hunja Murage 2 , Akio Tani 3 , Esther M. Kahangi 2 , Huxley Mae Makonde 4 1 Kenya Agricultural Research Institute, Nairobi, Kenya 2 Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya 3 Institute of plant science and resources Okayama University, Chuo, Kurashiki Okayama ,Japan 4 Technical University of Mombasa, Mombasa, Kenya Key words: 16S rRNA, 18S rRNA, Mutualism, Phylogeny. http://dx.doi.org/10.12692/ijb/5.3.7-14 Article published on August 02, 2014 Abstract The rice ecosystem provides a conducive habitat for various beneficial micro-organisms. The aim of this study was to characterize and identify soil micro-organisms from rice growing regions of Kenya using molecular approach. A total of 130 and 120 pure bacterial and fungal isolates, respectively, were used. Genomic deoxyribonucleic acid (DNA) was extracted and purified from the bacterial and fungal isolates. Universal primers were used to amplify the 16S rRNA and 18S rRNA gene regions of the bacterial and fungal isolates, respectively. Isolates sequences were identified by blastn analysis on the National Center for Biotechnology Information (NCBI) website. The known and closest match nucleotide sequences were retrieved from the GenBank database and used together with the isolates’ sequences to construct phylogenetic trees. Phylogenetic analysis was constructed using MEGA v 5.1 software. Sequence analysis of 16S rRNA gene indicated a high diversity of bacterial community belonging to the phyla Firmicutes, Proteobacteria and Actinobacteria. Majority of the isolates were closely affiliated with the genus Bacillus. All members of the fungal community belonged to the phylum Ascomycota, which was dominated by the genera Penicillium and Aspergillus. Thus, the Kenyan rice growing regions contain a relative diversity of bacteria and fungi that play important roles to the ecological health of the soil ecosystem. * Corresponding Author: Mwashasha Rashid Mwajita  rashmwa.mwajita585@gmail.com International Journal of Biosciences | IJB | ISSN: 2220-6655 (Print) 2222-5234 (Online) http://www.innspub.net Vol. 5, No. 3, p. 7-14, 2014