Revealing the biotechnological potential of Delftia sp. JD2 by a genomic approach

María A. Morel; Andrés Iriarte; Eugenio Jara; Héctor Musto; Susana Castro-Sowinski; María A. Morel; Andrés Iriarte; Eugenio Jara; Héctor Musto; Susana Castro-Sowinski

doi:10.3934/bioeng.2016.2.156

AIMS Bioengineering

2016, Volume 3, Issue 2: 156-175. doi: 10.3934/bioeng.2016.2.156

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Revealing the biotechnological potential of Delftia sp. JD2 by a genomic approach

1.
Unidad Microbiología Molecular, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE). Av Italia 3318, 11600, Montevideo, Uruguay
2.
Dpto de Bioquímica y Genómica Microbiana and Dpto de Genómica (IIBCE), Av. Italia 3318, 11600, Montevideo, Uruguay
3.
Dpto de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República (UdelaR), Av. Gral. Flores 2125, 11800, Montevideo, Uruguay
4.
Organización y Evolución del Genoma, Facultad de Ciencias, UdelaR, Iguá 4225, 11400, Montevideo, Uruguay
5.
Sección Bioquímica y Biología Molecular, Facultad de Ciencias, UdelaR, Iguá 4225, 11400, Montevideo, Uruguay

Received: 07 March 2016 Accepted: 12 April 2016 Published: 14 April 2016

Delftia sp. JD2 is a chromium-resistant bacterium that reduces Cr(VI) to Cr(III), accumulates Pb(II), produces the phytohormone indole-3-acetic acid and siderophores, and increases the plant growth performance of rhizobia in co-inoculation experiments. We aimed to analyze the biotechnological potential of JD2 using a genomic approach. JD2 has a genome of 6.76Mb, with 6,051 predicted protein coding sequences and 93 RNA genes (tRNA and rRNA). The indole-acetamide pathway was identified as responsible for the synthesis of indole-3-acetic acid. The genetic information involved in chromium resistance (the gene cluster, chrBACF,) was found. At least 40 putative genes encoding for TonB-dependent receptors, probably involved in the utilization of siderophores and biopolymers, and genes for the synthesis, maturation, exportation and uptake of pyoverdine, and acquisition of Fe-pyochelin and Fe-enterobactin were also identified. The information also suggests that JD2 produce polyhydroxybutyrate, a carbon reserve polymer commonly used for manufacturing petrochemical free bioplastics. In addition, JD2 may degrade lignin-derived aromatic compounds to 2-pyrone-4,6-dicarboxylate, a molecule used in the bio-based polymer industry. Finally, a comparative genomic analysis of JD2, Delftia sp. Cs1-4 and Delftia acidovorans SPH-1 is also discussed. The present work provides insights into the physiology and genetics of a microorganism with many potential uses in biotechnology.
- Delftia,
- plant-growth promotion,
- bioremediation,
- comparative genomic,
- plant-microbe interaction
Citation: María A. Morel, Andrés Iriarte, Eugenio Jara, Héctor Musto, Susana Castro-Sowinski. Revealing the biotechnological potential of Delftia sp. JD2 by a genomic approach[J]. AIMS Bioengineering, 2016, 3(2): 156-175. doi: 10.3934/bioeng.2016.2.156

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Abstract

Delftia sp. JD2 is a chromium-resistant bacterium that reduces Cr(VI) to Cr(III), accumulates Pb(II), produces the phytohormone indole-3-acetic acid and siderophores, and increases the plant growth performance of rhizobia in co-inoculation experiments. We aimed to analyze the biotechnological potential of JD2 using a genomic approach. JD2 has a genome of 6.76Mb, with 6,051 predicted protein coding sequences and 93 RNA genes (tRNA and rRNA). The indole-acetamide pathway was identified as responsible for the synthesis of indole-3-acetic acid. The genetic information involved in chromium resistance (the gene cluster, chrBACF,) was found. At least 40 putative genes encoding for TonB-dependent receptors, probably involved in the utilization of siderophores and biopolymers, and genes for the synthesis, maturation, exportation and uptake of pyoverdine, and acquisition of Fe-pyochelin and Fe-enterobactin were also identified. The information also suggests that JD2 produce polyhydroxybutyrate, a carbon reserve polymer commonly used for manufacturing petrochemical free bioplastics. In addition, JD2 may degrade lignin-derived aromatic compounds to 2-pyrone-4,6-dicarboxylate, a molecule used in the bio-based polymer industry. Finally, a comparative genomic analysis of JD2, Delftia sp. Cs1-4 and Delftia acidovorans SPH-1 is also discussed. The present work provides insights into the physiology and genetics of a microorganism with many potential uses in biotechnology.

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