AUTHOR=Berry David , Gutierrez Tony 

TITLE=Evaluating the Detection of Hydrocarbon-Degrading Bacteria in 16S rRNA Gene Sequencing Surveys

JOURNAL=Frontiers in Microbiology

VOLUME=8

YEAR=2017

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2017.00896

DOI=10.3389/fmicb.2017.00896

ISSN=1664-302X

ABSTRACT=<p>Hydrocarbonoclastic bacteria (HCB) play a key role in the biodegradation of oil hydrocarbons in marine and other environments. A small number of taxa have been identified as obligate HCB, notably the Gammaproteobacterial genera <italic>Alcanivorax, Cycloclasticus, Marinobacter, Neptumonas, Oleiphilus, Oleispira</italic>, and <italic>Thalassolituus</italic>, as well as the Alphaproteobacterial genus <italic>Thalassospira</italic>. Detection of HCB in amplicon-based sequencing surveys relies on high coverage by PCR primers and accurate taxonomic classification. In this study, we performed a phylogenetic analysis to identify 16S rRNA gene sequence regions that represent the breadth of sequence diversity within these taxa. Using validated sequences, we evaluated 449 universal 16S rRNA gene-targeted bacterial PCR primer pairs for their coverage of these taxa. The results of this analysis provide a practical framework for selection of suitable primer sets for optimal detection of HCB in sequencing surveys.</p>