Scholarly record
PRESENCE AND EXPRESSION OF GENES ENCODING HYDROCARBON DECOMPOSITION ABILITY OF MICROBES IN DIFFERENT SOIL TYPES SAMPLED IN TATARSTAN REPUBLIC (RUSSIA)
Abstract
Large areas of oil contaminated soil are an urgent problem in oil producing regions, such as the Republic of Tatarstan (Russia). One of important factors of soil self-restoration is the presence of members able to decompose hydrocarbons in the microbial community. Different groups of genes are responsible for decomposing different hydrocarbon groups: for example, alkane monooxygenase gene and naphthalene dioxygenase gene are the predominant genes corresponding to first-step hydroxylases involved in the metabolism of alkanes and aromatic hydrocarbons, respectively; genes encoding catechol 2,3-dioxygenase are capable of activating the decomposition of xylene, toluene and other PAHs. In this research, we investigated the presence and expression of genes encoding microbial ability to decompose hydrocarbons in pristine soils using qPCR and reverse transcription qPCR (RT-qPCR), respectively. We evaluated the distribution of the genes of alkane-monooxygenase (alkB, alkM and alkB), genes encoding dioxygenase xylE (Sphingobium-like catechol 2,3-dioxygenase), cat2,3 (catechol 2,3-dioxygenase, related to the genera Pseudomonas, Sphingomonas and Bacillus) and nah (naphthalene dioxygenase). The most abundant group was the alkB and alkB1 genes, associated with the representatives of the genera Pseudomonas (Ps. fluorescens, Ps. aeruginosa), Rhodococcus, Burkholderia and Amycolatopsis. These genes were present in all soil samples and ranged from 2.8?103 to 3.5?106 gene copies number g-1. The alkB genes belonging to the representatives of the species Pseudomonas putida and genus Stenotrophomonas were detected in 20 samples and ranged from 1.6?102 to 2.0?104 gene copies number g-1. The gene alkM, belonging to the genus Acinetobacter was not detected in any of the samples. Genes responsible for the encoding of dioxygenases were detected in only 10 soil samples in insignificant amounts: cat2,3 ? in the range of 1.1?103 to 8.3?103 gene copies number g-1, xylE - 2.0?102 to 4.9?103 gene copies number g-1. The nah gene responsible for the encoding of naphthalene-dioxygenase was detected in 13 samples in the range of 1.6?102 to 1.8?104 gene copies number g-1. The analysis of expression of hydrocarbon degrading genes under investigaion showed negative expression in all the samples. Thus, genes responsible for the degradation of hydrocarbons (alkB and alkB1, xylE, cat2,3) were detected in pristine soils in the Republic of Tatarstan, however, the expression of the identified genes did not occur. The alkM gene was not detected.
Publication Impact Profile
Publication details
References15
Kohno T, Sugimoto Y, Sei K, Mori K. Design of PCR Primers and Gene Probes for General Detection of Alcane-Degrading Bacteria. Microbes Environ., vol. 17, pp 114–121, 2002.
Whyte LG, Smits THM, Labbé D, Witholt B, Greer CW, Van Beilen JB. Gene cloning and characterization of multiple alkane hydroxylase systems in Rhodococcus strains Q15 and NRRL B-16531. Appl Environ Microbiol., vol.68, pp 5933–5942, 2002.
Ratajczak A, Geißdörfer W, Hillen W. Alkane hydroxylase from Acinetobacter sp. strain ADP1 is encoded by alkM and belongs to a new family of bacterial integral-membrane hydrocarbon hydroxylases. Appl Environ Microbiol., vol.64, pp 1175–1179, 1998.
Vázquez S, Nogales B, Ruberto L, Mestre C, Christie-Oleza J, Ferrero M, et al. Characterization of bacterial consortia from diesel-contaminated Antarctic soils: Towards the design of tailored formulas for bioaugmentation. Int Biodeterior Biodegrad., vol.77, pp 22–30, 2013.
Luz AP, Pellizari VH, Whyte LG, Greer CW. A survey of indigenous microbial hydrocarbon degradation genes in soils from Antarctica and Brazil. Can J Microbiol., vol. 50, pp 323–333, 2004.
van Beilen JB, Wubbolts MG, Witholt B. Genetics of alkane oxidation by Pseudomonas oleovorans. Biodegradation., vol. 5, pp 161–174,1994.
Song M, Yang Y, Jiang L, Hong Q, Zhang D, Shen Z, et al. Characterisation of the phenanthrene degradation-related genes and degrading ability of a newly isolated copper-tolerant bacterium. Environ Pollut., vol. 220, pp 1059–1067, 2017.
Liu Q, Tang J, Bai Z, Hecker M, Giesy JP. Distribution of petroleum degrading genes and factor analysis of petroleum contaminated soil from the Dagang Oilfield, China. Sci Rep., vol.5, pp 12, 2015.
Powell SM, Bowman JP, Ferguson SH, Snape I. The importance of soil characteristics to the structure of alkane-degrading bacterial communities on sub-Antarctic Macquarie Island. Soil Biol Biochem., vol. 42, pp 2012–2021, 2010.
Afzal M, Yousaf S, Reichenauer TG, Kuffner M, Sessitsch A. Soil type affects plant colonization, activity and catabolic gene expression of inoculated bacterial strains during phytoremediation of diesel. J Hazard Mater., vol. 186, pp 1568–1575, 2011.
Khan S, Afzal M, Iqbal S, Mirza MS, Khan QM. Inoculum pretreatment affects bacterial survival, activity and catabolic gene expression during phytoremediation of diesel contaminated soil. Chemosphere, vol. 91, pp 663–668, 2013.
Margesin R, Labbé D, Schinner F, Greer CW, Whyte LG. Characterization of hydrocarbon-degrading microbial populations in contaminated and pristine Alpine soils. Appl Environ Microbiol., vol. 69, pp 3085–3092, 2003.
Aislabie J, McLeod M, Fraser R. Potential for biodegradation of hydrocarbons in soil from the Ross Dependency, Antarctica. Appl Microbiol Biotechnol., vol.49, pp 210–214, 1998.
Yang Y, Wang J, Liao J, Xie S, Huang Y. Abundance and diversity of soil petroleum hydrocarbon-degrading microbial communities in oil exploring areas. Appl Microbiol Biotechnol. 2014;99: 1935–1946.
Kuhn E, Bellicanta GS, Pellizari VH. New alk genes detected in Antarctic marine sediments. Environ Microbiol., vol. 11, pp 669–673, 2009.
View or Download full articleAccess options
SWS access login
Login as SWS Scientific CommitteeLogin as SWS Scientific PartnerLogin as SWS AuthorAuthors and approved SWS contributors will read and export their own linked papers after identity matching by SWS profile, email and SGEM GlobalID.
For librarian assistance: [email protected]
Purchase Instant Access
- Article can be downloaded after successful payment.
- Article may be used according to SWS library access terms.
- Article cannot be redistributed.
