DNA Extraction Method Plays a Significant Role When Defining Bacterial Community Composition in the Marine Invertebrate Echinometra mathaei

Remi N. Ketchum, Edward G. Smith, Grace O. Vaughan, Britney L. Phippen, Dain McParland, Noura Al-Mansoori, Tyler J. Carrier, John A. Burt, Adam M. Reitzel

Research output: Contribution to journalArticlepeer-review

Abstract

The microbial assemblages of marine organisms play fundamental biological roles in their eukaryotic hosts. Studies aimed at characterizing this diversity have increased over the last decade and with the availability of high-throughput sequencing, we are now able to characterize bacteria that were non-culturable and, therefore, went undetected. With the number of marine microbiome studies growing rapidly, it is increasingly important to develop a set of “best practices” in order to accurately represent the bacterial communities present, and correct for biases. To address this, we sampled the gut communities of the pan-tropical echinoid Echinometra mathaei from two environmentally distinct populations along the Arabian Peninsula. We used three common DNA extraction procedures and compared inferred bacterial diversity from each method through 16S ribosomal RNA (rRNA) gene amplicon sequencing. Our results show that the addition of a bead-beating and lysozyme step more effectively capture traditionally difficult to lyse taxa, such as gram-positive bacteria. Further, DNA extraction method plays an important role in estimates of Shannon diversity, with diversity indices significantly higher in both sites combined when a lysozyme and bead beating step was used. Finally, we conducted a literature synthesis to highlight the current diversity of approaches used to characterize the microbiome of marine invertebrates and found that the inclusion of a lysozyme treatment is uncommon (2% of surveyed studies), despite the importance of this step in recovery of rare OTUs as shown in our study.

Original languageEnglish (US)
Article number255
JournalFrontiers in Marine Science
Volume5
DOIs
StatePublished - Jul 31 2018

Keywords

  • 16S rRNA
  • Arabian Peninsula
  • bead-beating
  • lysozyme
  • microbiome
  • sea urchin

ASJC Scopus subject areas

  • Oceanography
  • Global and Planetary Change
  • Aquatic Science
  • Water Science and Technology
  • Environmental Science (miscellaneous)
  • Ocean Engineering

Fingerprint Dive into the research topics of 'DNA Extraction Method Plays a Significant Role When Defining Bacterial Community Composition in the Marine Invertebrate Echinometra mathaei'. Together they form a unique fingerprint.

Cite this