Phenotypic and genomic survey on organic acid utilization profile of Pseudomonas mendocina strain S5.2, a vineyard soil isolate
Root exudates are chemical compounds that are released from living plant roots and provide significant energy, carbon, nitrogen and phosphorus sources for microbes inhabiting the rhizosphere. The exudates shape the microflora associated with the plant, as well as influences the plant health and prod...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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SpringerOpen
2017
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| Online Access: | http://eprints.um.edu.my/17539/1/ChongTM_%282017%29.pdf |
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| author | Chong, T.M. Chen, J.W. See-Too, W.S. Yu, C.Y. Ang, G.Y. Lim, Y.L. Yin, Wai Fong Grandclément, C. Faure, D. Dessaux, Y. Chan, Kok Gan |
| author_facet | Chong, T.M. Chen, J.W. See-Too, W.S. Yu, C.Y. Ang, G.Y. Lim, Y.L. Yin, Wai Fong Grandclément, C. Faure, D. Dessaux, Y. Chan, Kok Gan |
| author_sort | Chong, T.M. |
| collection | UM |
| description | Root exudates are chemical compounds that are released from living plant roots and provide significant energy, carbon, nitrogen and phosphorus sources for microbes inhabiting the rhizosphere. The exudates shape the microflora associated with the plant, as well as influences the plant health and productivity. Therefore, a better understanding of the trophic link that is established between the plant and the associated bacteria is necessary. In this study, a comprehensive survey on the utilization of grapevine and rootstock related organic acids were conducted on a vineyard soil isolate which is Pseudomonas mendocina strain S5.2. Phenotype microarray analysis has demonstrated that this strain can utilize several organic acids including lactic acid, succinic acid, malic acid, citric acid and fumaric acid as sole growth substrates. Complete genome analysis using single molecule real-time technology revealed that the genome consists of a 5,120,146 bp circular chromosome and a 252,328 bp megaplasmid. A series of genetic determinants associated with the carbon utilization signature of the strain were subsequently identified in the chromosome. Of note, the coexistence of genes encoding several iron–sulfur cluster independent isoenzymes in the genome indicated the importance of these enzymes in the events of iron deficiency. Synteny and comparative analysis have also unraveled the unique features of d-lactate dehydrogenase of strain S5.2 in the study. Collective information of this work has provided insights on the metabolic role of this strain in vineyard soil rhizosphere. |
| first_indexed | 2024-03-06T05:42:48Z |
| format | Article |
| id | um.eprints-17539 |
| institution | Universiti Malaya |
| language | English |
| last_indexed | 2024-03-06T05:42:48Z |
| publishDate | 2017 |
| publisher | SpringerOpen |
| record_format | dspace |
| spelling | um.eprints-175392019-12-23T06:22:01Z http://eprints.um.edu.my/17539/ Phenotypic and genomic survey on organic acid utilization profile of Pseudomonas mendocina strain S5.2, a vineyard soil isolate Chong, T.M. Chen, J.W. See-Too, W.S. Yu, C.Y. Ang, G.Y. Lim, Y.L. Yin, Wai Fong Grandclément, C. Faure, D. Dessaux, Y. Chan, Kok Gan Q Science (General) QH Natural history Root exudates are chemical compounds that are released from living plant roots and provide significant energy, carbon, nitrogen and phosphorus sources for microbes inhabiting the rhizosphere. The exudates shape the microflora associated with the plant, as well as influences the plant health and productivity. Therefore, a better understanding of the trophic link that is established between the plant and the associated bacteria is necessary. In this study, a comprehensive survey on the utilization of grapevine and rootstock related organic acids were conducted on a vineyard soil isolate which is Pseudomonas mendocina strain S5.2. Phenotype microarray analysis has demonstrated that this strain can utilize several organic acids including lactic acid, succinic acid, malic acid, citric acid and fumaric acid as sole growth substrates. Complete genome analysis using single molecule real-time technology revealed that the genome consists of a 5,120,146 bp circular chromosome and a 252,328 bp megaplasmid. A series of genetic determinants associated with the carbon utilization signature of the strain were subsequently identified in the chromosome. Of note, the coexistence of genes encoding several iron–sulfur cluster independent isoenzymes in the genome indicated the importance of these enzymes in the events of iron deficiency. Synteny and comparative analysis have also unraveled the unique features of d-lactate dehydrogenase of strain S5.2 in the study. Collective information of this work has provided insights on the metabolic role of this strain in vineyard soil rhizosphere. SpringerOpen 2017 Article PeerReviewed application/pdf en http://eprints.um.edu.my/17539/1/ChongTM_%282017%29.pdf Chong, T.M. and Chen, J.W. and See-Too, W.S. and Yu, C.Y. and Ang, G.Y. and Lim, Y.L. and Yin, Wai Fong and Grandclément, C. and Faure, D. and Dessaux, Y. and Chan, Kok Gan (2017) Phenotypic and genomic survey on organic acid utilization profile of Pseudomonas mendocina strain S5.2, a vineyard soil isolate. AMB Express, 7 (1). pp. 1-8. ISSN 2191-0855, DOI https://doi.org/10.1186/s13568-017-0437-7 <https://doi.org/10.1186/s13568-017-0437-7>. https://amb-express.springeropen.com/articles/10.1186/s13568-017-0437-7 DOI: 10.1186/s13568-017-0437-7 |
| spellingShingle | Q Science (General) QH Natural history Chong, T.M. Chen, J.W. See-Too, W.S. Yu, C.Y. Ang, G.Y. Lim, Y.L. Yin, Wai Fong Grandclément, C. Faure, D. Dessaux, Y. Chan, Kok Gan Phenotypic and genomic survey on organic acid utilization profile of Pseudomonas mendocina strain S5.2, a vineyard soil isolate |
| title | Phenotypic and genomic survey on organic acid utilization profile of Pseudomonas mendocina strain S5.2, a vineyard soil isolate |
| title_full | Phenotypic and genomic survey on organic acid utilization profile of Pseudomonas mendocina strain S5.2, a vineyard soil isolate |
| title_fullStr | Phenotypic and genomic survey on organic acid utilization profile of Pseudomonas mendocina strain S5.2, a vineyard soil isolate |
| title_full_unstemmed | Phenotypic and genomic survey on organic acid utilization profile of Pseudomonas mendocina strain S5.2, a vineyard soil isolate |
| title_short | Phenotypic and genomic survey on organic acid utilization profile of Pseudomonas mendocina strain S5.2, a vineyard soil isolate |
| title_sort | phenotypic and genomic survey on organic acid utilization profile of pseudomonas mendocina strain s5 2 a vineyard soil isolate |
| topic | Q Science (General) QH Natural history |
| url | http://eprints.um.edu.my/17539/1/ChongTM_%282017%29.pdf |
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