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Biomolecular characterization of diazotrophs isolated from the tropical soil in Malaysia


Naher, Umme Aminun and Othman, Radziah and Latif, Mohammad Abdul and Panhwar, Qurban Ali and Megat Amaddin, Puteri Aminatulhawa and Shamsuddin, Zulkifli (2013) Biomolecular characterization of diazotrophs isolated from the tropical soil in Malaysia. International Journal of Molecular Sciences, 14 (9). pp. 17812-17829. ISSN 1422-0067


This study was conducted to evaluate selected biomolecular characteristics of rice root-associated diazotrophs isolated from the Tanjong Karang rice irrigation project area of Malaysia. Soil and rice plant samples were collected from seven soil series belonging to order Inceptisol (USDA soil taxonomy). A total of 38 diazotrophs were isolated using a nitrogen-free medium. The biochemical properties of the isolated bacteria, such as nitrogenase activity, indoleacetic acid (IAA) production and sugar utilization, were measured. According to a cluster analysis of Jaccard’s similarity coefficients, the genetic similarities among the isolated diazotrophs ranged from 10% to 100%. A dendogram constructed using the unweighted pair-group method with arithmetic mean (UPGMA) showed that the isolated diazotrophs clustered into 12 groups. The genomic DNA rep-PCR data were subjected to a principal component analysis, and the first four principal components (PC) accounted for 52.46% of the total variation among the 38 diazotrophs. The 10 diazotrophs that tested highly positive in the acetylene reduction assay (ARA) were identified as Bacillus spp. (9 diazotrophs) and Burkholderia sp. (Sb16) using the partial 16S rRNA gene sequence analysis. In the analysis of the biochemical characteristics, three principal components were accounted for approximately 85% of the total variation among the identified diazotrophs. The examination of root colonization using scanning electron microscopy (SEM) and transmission electron microscopy (TEM) proved that two of the isolated diazotrophs (Sb16 and Sb26) were able to colonize the surface and interior of rice roots and fixed 22%–24% of the total tissue nitrogen from the atmosphere. In general, the tropical soils (Inceptisols) of the Tanjong Karang rice irrigation project area in Malaysia harbor a diverse group of diazotrophs that exhibit a large variation of biomolecular characteristics.

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Additional Metadata

Item Type: Article
Divisions: Faculty of Agriculture
Institute of Tropical Agriculture
DOI Number: https://doi.org/10.3390/ijms140917812
Publisher: MDPI AG
Keywords: 16S rRNA; Diazotrophs; Indoleacetic acid; Nitrogenase enzyme activity; Scanning electron microscopy; Transmission electron microscopy
Depositing User: Nurul Ainie Mokhtar
Date Deposited: 13 Jul 2016 01:42
Last Modified: 13 Jul 2016 01:42
Altmetrics: http://www.altmetric.com/details.php?domain=psasir.upm.edu.my&doi=10.3390/ijms140917812
URI: http://psasir.upm.edu.my/id/eprint/29382
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