Biomolecular characterization of diazotrophs isolated from the tropical soil in Malaysia
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 taxonom...
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| Format: | Article |
| Language: | English |
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MDPI AG
2013
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| Online Access: | http://psasir.upm.edu.my/id/eprint/29382/ http://psasir.upm.edu.my/id/eprint/29382/1/29382.pdf |
| _version_ | 1848846384456794112 |
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| author | Naher, Umme Aminun Othman, Radziah Latif, Mohammad Abdul Panhwar, Qurban Ali Megat Amaddin, Puteri Aminatulhawa Shamsuddin, Zulkifli |
| author_facet | Naher, Umme Aminun Othman, Radziah Latif, Mohammad Abdul Panhwar, Qurban Ali Megat Amaddin, Puteri Aminatulhawa Shamsuddin, Zulkifli |
| author_sort | Naher, Umme Aminun |
| building | UPM Institutional Repository |
| collection | Online Access |
| description | 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. |
| first_indexed | 2025-11-15T09:01:51Z |
| format | Article |
| id | upm-29382 |
| institution | Universiti Putra Malaysia |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T09:01:51Z |
| publishDate | 2013 |
| publisher | MDPI AG |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | upm-293822016-07-13T01:42:53Z http://psasir.upm.edu.my/id/eprint/29382/ Biomolecular characterization of diazotrophs isolated from the tropical soil in Malaysia Naher, Umme Aminun Othman, Radziah Latif, Mohammad Abdul Panhwar, Qurban Ali Megat Amaddin, Puteri Aminatulhawa Shamsuddin, Zulkifli 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. MDPI AG 2013 Article PeerReviewed application/pdf en http://psasir.upm.edu.my/id/eprint/29382/1/29382.pdf 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 http://www.mdpi.com/1422-0067/14/9/17812 10.3390/ijms140917812 |
| spellingShingle | Naher, Umme Aminun Othman, Radziah Latif, Mohammad Abdul Panhwar, Qurban Ali Megat Amaddin, Puteri Aminatulhawa Shamsuddin, Zulkifli Biomolecular characterization of diazotrophs isolated from the tropical soil in Malaysia |
| title | Biomolecular characterization of diazotrophs isolated from the tropical soil in Malaysia |
| title_full | Biomolecular characterization of diazotrophs isolated from the tropical soil in Malaysia |
| title_fullStr | Biomolecular characterization of diazotrophs isolated from the tropical soil in Malaysia |
| title_full_unstemmed | Biomolecular characterization of diazotrophs isolated from the tropical soil in Malaysia |
| title_short | Biomolecular characterization of diazotrophs isolated from the tropical soil in Malaysia |
| title_sort | biomolecular characterization of diazotrophs isolated from the tropical soil in malaysia |
| url | http://psasir.upm.edu.my/id/eprint/29382/ http://psasir.upm.edu.my/id/eprint/29382/ http://psasir.upm.edu.my/id/eprint/29382/ http://psasir.upm.edu.my/id/eprint/29382/1/29382.pdf |