In situ visualization of bacterial populations in coral tissues: pitfalls and solutions

Naohisa Wada; Frederic J Pollock; Bette L Willis; Tracy Ainsworth; Nobuhiro Mano; David G Bourne

doi:10.7717/peerj.2424

In situ visualization of bacterial populations in coral tissues: pitfalls and solutions

PeerJ. 2016 Sep 20:4:e2424. doi: 10.7717/peerj.2424. eCollection 2016.

Authors

Naohisa Wada¹, Frederic J Pollock², Bette L Willis³, Tracy Ainsworth⁴, Nobuhiro Mano⁵, David G Bourne⁶

Affiliations

¹ Department of Marine Science and Resources, College of Bioresource Science, Nihon University, Fujisawa, Kanagawa, Japan; Australian Institute of Marine Science, Townsville, Queensland, Australia; AIMS@JCU, Townsville, Queensland, Australia.
² Australian Institute of Marine Science, Townsville, Queensland, Australia; AIMS@JCU, Townsville, Queensland, Australia; Department of Biology, Eberly College of Science, Pennsylvania State University, University Park, PA, United States; ARC Centre of Excellence for Coral Reef Studies, James Cook University of North Queensland, Townsville, Queensland, Australia; College of Science and Engineering, James Cook University of North Queensland, Townsville, Queensland, Australia.
³ AIMS@JCU, Townsville, Queensland, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University of North Queensland, Townsville, Queensland, Australia; College of Science and Engineering, James Cook University of North Queensland, Townsville, Queensland, Australia.
⁴ ARC Centre of Excellence for Coral Reef Studies, James Cook University of North Queensland , Townsville , Queensland , Australia.
⁵ Department of Marine Science and Resources, College of Bioresource Science, Nihon University , Fujisawa , Kanagawa , Japan.
⁶ Australian Institute of Marine Science, Townsville, Queensland, Australia; AIMS@JCU, Townsville, Queensland, Australia; College of Science and Engineering, James Cook University of North Queensland, Townsville, Queensland, Australia.

Abstract

In situ visualization of microbial communities within their natural habitats provides a powerful approach to explore complex interactions between microorganisms and their macroscopic hosts. Specifically, the application of fluorescence in situ hybridization (FISH) to simultaneously identify and visualize diverse microbial taxa associated with coral hosts, including symbiotic algae (Symbiodinium), Bacteria, Archaea, Fungi and protists, could help untangle the structure and function of these diverse taxa within the coral holobiont. However, the application of FISH approaches to coral samples is constrained by non-specific binding of targeted rRNA probes to cellular structures within the coral animal tissues (including nematocysts, spirocysts, granular gland cells within the gastrodermis and cnidoglandular bands of mesenterial filaments). This issue, combined with high auto-fluorescence of both host tissues and endosymbiotic dinoflagellates (Symbiodinium), make FISH approaches for analyses of coral tissues challenging. Here we outline the major pitfalls associated with applying FISH to coral samples and describe approaches to overcome these challenges.

Keywords: Bacteria; Coral; Fluorescence in situ hybridization; Holobiont; In situ visualization.

Grants and funding

This work was funded through internal funding from the Australian Institute of Marine Science and the Australian Research Council Discovery Award DP130101421. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.