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Chong TM, Chen JW, See-Too WS, et al. Phenotypic and genomic survey on organic acid utilization profile of Pseudomonas mendocina strain S5.2, a vineyard soil isolate. AMB Express. 2017;7(1):138doi: 10.1186/s13568-017-0437-7.
Chong, T. M., Chen, J. W., See-Too, W. S., Yu, C. Y., Ang, G. Y., Lim, Y. L., Yin, W. F., Grandclément, C., Faure, D., Dessaux, Y., & Chan, K. G. (2017). Phenotypic and genomic survey on organic acid utilization profile of Pseudomonas mendocina strain S5.2, a vineyard soil isolate. AMB Express, 7(1), 138. https://doi.org/10.1186/s13568-017-0437-7
Chong, Teik Min, et al. "Phenotypic and genomic survey on organic acid utilization profile of Pseudomonas mendocina strain S5.2, a vineyard soil isolate." AMB Express vol. 7,1 (2017): 138. doi: https://doi.org/10.1186/s13568-017-0437-7
Chong TM, Chen JW, See-Too WS, Yu CY, Ang GY, Lim YL, Yin WF, Grandclément C, Faure D, Dessaux Y, Chan KG. Phenotypic and genomic survey on organic acid utilization profile of Pseudomonas mendocina strain S5.2, a vineyard soil isolate. AMB Express. 2017 Dec;7(1):138. doi: 10.1186/s13568-017-0437-7. Epub 2017 Jun 26. PMID: 28655216; PMCID: PMC5484659.
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AMB Express. 2017 Dec;7(1):138. doi: 10.1186/s13568-017-0437-7. Epub 2017 Jun 26.

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

AMB Express

Teik Min Chong, Jian-Woon Chen, Wah-Seng See-Too, Choo-Yee Yu, Geik-Yong Ang, Yan Lue Lim, Wai-Fong Yin, Catherine Grandclément, Denis Faure, Yves Dessaux, Kok-Gan Chan

Affiliations

  1. Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
  2. UM Omics Centre, University of Malaya, 50603, Kuala Lumpur, Malaysia.
  3. Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, 40450, Shah Alam, Selangor, Malaysia.
  4. Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-Sur-Yvette, France.
  5. Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia. [email protected].
  6. UM Omics Centre, University of Malaya, 50603, Kuala Lumpur, Malaysia. [email protected].

PMID: 28655216 PMCID: PMC5484659 DOI: 10.1186/s13568-017-0437-7

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.

Keywords: Carbon utilization enzymes; Grapevine exudates; Organic acids; Pseudomonas mendocina; Single molecule real-time (SMRT) sequencing; Vineyard soil

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