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Open AccessArticle

Metagenomic Insights into the Bacterial Functions of a Diesel-Degrading Consortium for the Rhizoremediation of Diesel-Polluted Soil

1
Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
2
Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, Avenida Complutense 40, 28040 Madrid, Spain
*
Author to whom correspondence should be addressed.
Genes 2019, 10(6), 456; https://doi.org/10.3390/genes10060456
Received: 25 March 2019 / Revised: 7 June 2019 / Accepted: 11 June 2019 / Published: 14 June 2019
(This article belongs to the Special Issue Genetics of Biodegradation and Bioremediation)
Diesel is a complex pollutant composed of a mixture of aliphatic and aromatic hydrocarbons. Because of this complexity, diesel bioremediation requires multiple microorganisms, which harbor the catabolic pathways to degrade the mixture. By enrichment cultivation of rhizospheric soil from a diesel-polluted site, we have isolated a bacterial consortium that can grow aerobically with diesel and different alkanes and polycyclic aromatic hydrocarbons (PAHs) as the sole carbon and energy source. Microbiome diversity analyses based on 16S rRNA gene showed that the diesel-degrading consortium consists of 76 amplicon sequence variants (ASVs) and it is dominated by Pseudomonas, Aquabacterium, Chryseobacterium, and Sphingomonadaceae. Changes in microbiome composition were observed when growing on specific hydrocarbons, reflecting that different populations degrade different hydrocarbons. Shotgun metagenome sequence analysis of the consortium growing on diesel has identified redundant genes encoding enzymes implicated in the initial oxidation of alkanes (AlkB, LadA, CYP450) and a variety of hydroxylating and ring-cleavage dioxygenases involved in aromatic and polyaromatic hydrocarbon degradation. The phylogenetic assignment of these enzymes to specific genera allowed us to model the role of specific populations in the diesel-degrading consortium. Rhizoremediation of diesel-polluted soil microcosms using the consortium, resulted in an important enhancement in the reduction of total petroleum hydrocarbons (TPHs), making it suited for rhizoremediation applications. View Full-Text
Keywords: rhizoremediation; diesel; bacteria; consortium; metagenomics; PAHs; TPH rhizoremediation; diesel; bacteria; consortium; metagenomics; PAHs; TPH
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Garrido-Sanz, D.; Redondo-Nieto, M.; Guirado, M.; Pindado Jiménez, O.; Millán, R.; Martin, M.; Rivilla, R. Metagenomic Insights into the Bacterial Functions of a Diesel-Degrading Consortium for the Rhizoremediation of Diesel-Polluted Soil. Genes 2019, 10, 456.

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