Research Article: Characterization of novel hydrocarbon-degrading Gordonia paraffinivorans and Gordonia sihwensis strains isolated from composting

Date Published: April 18, 2019

Publisher: Public Library of Science

Author(s): Natalia Maria Silva, Aline Márcia Silva Araújo de Oliveira, Stefania Pegorin, Camila Escandura Giusti, Vitor Batista Ferrari, Deibs Barbosa, Layla Farage Martins, Carlos Morais, João Carlos Setubal, Suzan Pantaroto Vasconcellos, Aline Maria da Silva, Julio Cezar Franco de Oliveira, Renata Castiglioni Pascon, Cristina Viana-Niero, Andrea Franzetti.


Hydrocarbons are important environmental pollutants, and the isolation and characterization of new microorganisms with the ability to degrade these compounds are important for effective biodegradation. In this work we isolated and characterized several bacterial isolates from compost, a substrate rich in microbial diversity. The isolates were obtained from selective culture medium containing n-hexadecane, aiming to recover alkane-degraders. Six isolates identified as Gordonia by MALDI-TOF and 16S rRNA sequencing had the ability to degrade n-hexadecane in three days. Two isolates were selected for genomic and functional characterization, Gordonia paraffinivorans (MTZ052) and Gordonia sihwensis (MTZ096). The CG-MS results showed distinct n-hexadecane degradation rates for MTZ052 and MTZ096 (86% and 100% respectively). The genome sequence showed that MTZ052 encodes only one alkane degrading gene cluster, the CYP153 system, while MTZ096 harbors both the Alkane Hydroxylase (AH) and the CYP153 systems. qPCR showed that both gene clusters are induced by the presence of n-hexadecane in the growth medium, suggesting that G. paraffinivorans and G. sihwensis use these systems for degradation. Altogether, our results indicate that these Gordonia isolates have a good potential for biotransformation of hydrocarbons.

Partial Text

Crude oil and waste of petroleum derivatives are made of hydrocarbons and considered pollutants, which are difficult to treat and remove from the environment [1,2]. Aliphatic hydrocarbons (alkanes) are the major components of crude oil and can be subject to oxidative degradation by bacterial metabolism as a carbon source [3]. To circumvent the inertia of alkanes, some bacteria can activate these molecules through oxidation of their terminal methyl group, converting it into the corresponding primary alcohol. In the subsequent metabolic steps the methyl group is converted to an aldehyde and then to a fatty acid derivative, which enters the β-oxidation pathway to generate the central metabolite acetyl CoA [4,5]. The bacterial enzymatic systems that enable the activation and conversion of alkanes to harmless metabolic molecules comprise terminal monooxygenases such as the membrane-anchored AlkB family of alkane hydroxylases or soluble cytochrome CYP153A enzymes [6].

The assumption that composting could be a source of microorganisms with capacity to degrade hydrocarbons was based on previous observations that composting harbors a great diversity of biodegraders carrying metabolic pathways to degrade a plethora of complex organic compounds [16,17,21–27,54,55]. With this rationale we succeeded in the isolation of two Gordonia strains from compost that have the ability to degrade n-hexadecane. Gordonia spp. are known for their broad capability to degrade recalcitrant organic compounds, including hydrocarbons [10,11].