ARS | Publication request: The Phylogeny of Fluorescent Pseudomonads in an Unflooded Rice Paddy Soil

Submitted to: Annals of Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 18, 2007
Publication Date: September 15, 2007
Citation: Weon, H., Dungan, R.S., Kwon, S., Kim, J. 2007. The Phylogeny of Fluorescent Pseudomonads in an Unflooded Rice Paddy Soil. Annals of Microbiology. 57:299-306.

Interpretive Summary: Rice is one of the world’s most important agronomic crops and the study of microbial communities in flooded rice paddy soils is an interesting topic. In particular, fluorescent pseudomonads are an ecologically important group of soil bacteria due to the ability of some species to produce iron-binding siderophores, antibiotics, and plant-growth regulators. In this study, pseudomonas isolates from unflooded rice paddy soils were studied using molecular techniques and matching their DNA sequences. Phylogenetic analysis revealed that fluorescent pseudomonads from unflooded rice paddy soils clustered into taxonomic groups that were similar to those found in upland agricultural soils. These results improve our understanding of the ecology of fluorescent pseudomonads and may ultimately offer important insights into the management of paddy soils.

Technical Abstract: The purpose of this research was to determine the diversity and distribution of fluorescent pseudomonads in an unflooded rice paddy soil. A region of the 16S ribosomal RNA gene from isolates was amplified using PCR and subsequently analyzed by sequence analysis for bacterial identification and phylogenetic classification. A total of 117 fluorescent pseudomonads, representing between 10 and 21 species, were isolated from two sampling sites within the same paddy (designated as soils C and S). The isolates were found to be ' 96% homologous with known sequences, and were most closely related to the following pseudomonas species: P. antarctica, P. costantini, P. extremorientalis, P. frederiksbergensis, P. kilonensis, P. koreensis, P. lini, P. mandelii, P. poae, P. rhodesiae, and P. veronii. Of these matches, the bulk of the isolates (49%) were affiliated with P. mandelii. In soils C and S, phylogenetic analysis revealed that 35 and 82 isolates co-clustered with 39% and 59% of 66 fluorescent pseudomonad type strains, respectively.