Phenotypic and genomic survey on organic acid utilization profile of Pseudomonas mendocina strain S5.2, a vineyard soil isolate

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.

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Abstract

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.

Item Type:	Article
Funders:	University of Malaya. HIR Grants awarded to KGC (UM-MOHE HIR Grant UM C/625/1/HIR/MOHE/CHAN/14/1, No. H-50001-A000027; UM-MOHE HIR Grant UM C/625/1/HIR/MOHE/CHAN/01, No. A000001-50001), Postgraduate Research Fund (PPP) (Grant No. PG080-2015B) awarded to TMC
Uncontrolled Keywords:	Pseudomonas mendocina; Single molecule real-time (SMRT) sequencing; Vineyard soil; Grapevine exudates; Organic acids; Carbon utilization enzymes
Subjects:	Q Science > Q Science (General) Q Science > QH Natural history
Divisions:	Faculty of Science > Institute of Biological Sciences
Depositing User:	Ms. Juhaida Abd Rahim
Date Deposited:	20 Jul 2017 04:43
Last Modified:	23 Dec 2019 06:22
URI:	http://eprints.um.edu.my/id/eprint/17539

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