The Use of a Combination of alkB Primers to Better Characterize the Distribution of Alkane-Degrading Bacteria

Abstract

The alkane monooxygenase AlkB, which is encoded by the alkB gene, is a key enzyme involved in bacterial alkane degradation. To study the alkB gene within bacterial communities, researchers need to be aware of the variations in alkB nucleotide sequences; a failure to consider the sequence variations results in the low representation of the diversity and richness of alkane-degrading bacteria. To minimize this shortcoming, the use of a combination of three alkB-targeting primers to enhance the detection of the alkB gene in previously isolated alkane-degrading bacteria was proposed. Using this approach, alkB-related PCR products were detected in 79% of the strains tested. Furthermore, the chosen set of primers was used to study alkB richness and diversity in different soils sampled in Carmópolis, Brazil and King George Island, Antarctica. The DNA extracted from the different soils was PCR amplified with each set of alkB-targeting primers, and clone libraries were constructed, sequenced and analyzed. A total of 255 alkB phylotypes were detected. Venn diagram analyses revealed that only low numbers of alkB phylotypes were shared among the different libraries derived from each primer pair. Therefore, the combination of three alkB-targeting primers enhanced the richness of alkB phylotypes detected in the different soils by 45% to 139%, when compared to the use of a single alkB-targeting primer. In addition, a dendrogram analysis and beta diversity comparison of the alkB composition showed that each of the sampling sites studied had a particular set of alkane-degrading bacteria. The use of a combination of alkB primers was an efficient strategy for enhancing the detection of the alkB gene in cultivable bacteria and for better characterizing the distribution of alkane-degrading bacteria in different soil environments.

Biodegradation potential of Serratiamarcescens for diesel/biodiesel blends

“…Alkane-utilizing bacteria are widespread in marine and terrestrial environments. These bacteria generally possess the Alk enzyme system, which is involved in the metabolic pathway for the degradation of alkanes, the main compounds found in petroleum and its derivatives (Jurelevicius et al, 2013). Alkane hydroxylase is a key enzyme in alkane degradation.…”

Secondary successional trajectories of structural and catabolic bacterial communities in oil‐polluted soil planted with hybrid poplar

“…Alkane monooxygenase (AlkB), used as a catabolic marker for alkane degraders in this study, is a membranebound nonhaem diiron monooxygenase and is the first enzyme in the terminal oxidation pathway of alkane (C5-C16) degradation (van Beilen & Funhoff 2007). We used the primer pairs designed by Kloos et al (2006) which have been shown to successfully amplify alkane monooxygenases from a broad range of bacterial phyla in a variety of pristine and polluted ecosystems (Bell et al 2011;P erez-de-Mora et al 2011;Schulz et al 2012;Giebler et al 2013;Jurelevicius et al 2013).…”

Production of rhamnolipids and diesel oil degradation by bacteria isolated from soil contaminated by petroleum

“…The presence of the alkB gene was detected in 16 strains that showed a band of 100 bp corresponding to this gene (Figure ). As in this work, other studies have used this gene successfully as a biomarker to detect hydrocarbon‐degrading bacteria in different environments …”