Diversity of the Bacterial Community in the Rice Rhizosphere Managed Under Conventional and No-tillage Practices

Zubair Aslam; Muhammad Yasir; Hwan Sik Yoon; Che Ok Jeon; Young Ryun Chung

doi:10.1007/s12275-013-2528-8

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Diversity of the Bacterial Community in the Rice Rhizosphere Managed Under Conventional and No-tillage Practices: Zubair Aslam ^1,2, Muhammad Yasir ³, Hwan Sik Yoon ¹, Che Ok Jeon ⁴, Young Ryun Chung ¹; Journal of Microbiology 2013;51(6):747-756.
DOI: https://doi.org/10.1007/s12275-013-2528-8
Published online: December 19, 2013

¹Division of Applied Life Science (BK 21), Plant Molecular Biology & Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea, ²Department of Agronomy, University of Agriculture, Faisalabad 38040, Pakistan, ³King Fahd Medical Research Center, King Abdulaziz University, Jeddah, 21589, Saudi Arabia, ⁴School of Biological Sciences, Research Center for Biomolecules & Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea¹Division of Applied Life Science (BK 21), Plant Molecular Biology & Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea, ²Department of Agronomy, University of Agriculture, Faisalabad 38040, Pakistan, ³King Fahd Medical Research Center, King Abdulaziz University, Jeddah, 21589, Saudi Arabia, ⁴School of Biological Sciences, Research Center for Biomolecules & Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea

Corresponding author: Young Ryun Chung , Tel: +82-55-772-1326,

Received: 28 September 2012 • Accepted: 22 May 2013

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Abstract

Bacterial diversity in the rice rhizosphere at different rice growth stages, managed under conventional and no-tillage practices, was explored using a culture-based approach. Actinobacteria are among the bacterial phyla abundant in the rice rhizosphere. Their diversity was further examined by constructing metagenomic libraries based on the 16S rRNA gene, using actinobacterial- and streptomycete-specific polymerase chain reaction (PCR) primers. The study included 132 culturable strains and 125 clones from the 16S rRNA gene libraries. In conventional tillage, there were 38% Proteobacteria, 22% Actinobacteria, 33% Firmicutes, 5% Bacteroidetes, and 2% Acidobacteria, whereas with no-tillage management there were 63% Proteobacteria, 24% Actinobacteria, 6% Firmicutes, and 8% Bacteroidetes as estimated using the culturedependent
method
during the four stages of rice cultivation. Principal coordinates analysis was used to cluster the bacterial communities along axes of maximal variance. The different growth stages of rice appeared to influence the rhizosphere bacterial profile for both cultivation practices. Novel clones with low similarities (89–97%) to Actinobacteria and Streptomyces were retrieved from both rice fields by screening the 16S rRNA gene libraries using actinobacterial- and streptomycete-specific primers. By comparing the actinobacterial community retrieved by culture-dependent and molecular methods, it was clear that a more comprehensive assessment of microbial diversity in the rice rhizosphere can be obtained using a combination of both techniques than by using either method alone. We also succeeded in culturing a number of bacteria that were previously described as unculturable. These were in a phylogenetically deep lineage when compared with related cultivable genera.

Keywords: rice;no-tillage;diversity;phylogeny;actinobacteria

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Diversity of the Bacterial Community in the Rice Rhizosphere Managed Under Conventional and No-tillage Practices

J. Microbiol. 2013;51(6):747-756. Published online December 19, 2013

DOI: https://doi.org/10.1007/s12275-013-2528-8

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