In situ visualization of bacterial populations in coral tissues: pitfalls and solutions.
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.
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.
Naohisa
N
Wada
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.
Frederic J
FJ
Pollock
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.
Bette L
BL
Willis
ARC Centre of Excellence for Coral Reef Studies, James Cook University of North Queensland , Townsville , Queensland , Australia.
Tracy
T
Ainsworth
Department of Marine Science and Resources, College of Bioresource Science, Nihon University , Fujisawa , Kanagawa , Japan.
Nobuhiro
N
Mano
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.
David G
DG
Bourne
Bacteria; Coral; Fluorescence in situ hybridization; Holobiont; In situ visualization
Lett Appl Microbiol. 2002;34(5):359-64
11967059
Appl Environ Microbiol. 2007 Feb;73(3):981-92
17158622
Appl Environ Microbiol. 2004 Feb;70(2):1213-21
14766608
Science. 2004 Aug 13;305(5686):997-1000
15310901
ISME J. 2011 Mar;5(3):559-64
20811471
Dis Aquat Organ. 2006 Jun 12;70(1-2):155-60
16875402
Nature. 2000 Dec 14;408(6814):850-3
11130722
ISME J. 2015 Oct;9(10):2261-74
25885563
ISME J. 2009 Jun;3(6):685-99
19242535
Nat Rev Microbiol. 2007 May;5(5):355-62
17384666
J Microsc. 2008 Nov;232(2):197-9
19017217
PLoS Pathog. 2011 Oct;7(10):e1002183
22028646
ISME J. 2017 Jan;11(1):186-200
27392086
Syst Appl Microbiol. 1999 Sep;22(3):434-44
10553296
Trends Microbiol. 2009 Dec;17(12):554-62
19822428
Appl Environ Microbiol. 2013 Aug;79(15):4759-62
23709513
Appl Environ Microbiol. 2006 Apr;72(4):3016-20
16598010
Microb Ecol. 1999 Feb;37(2):77-85
9929396
Cytometry. 1993;14(2):136-43
7679962
J Cell Sci. 2003 Jul 15;116(Pt 14):2833-8
12808017
Appl Environ Microbiol. 2002 Jun;68(6):3094-101
12039771
Appl Environ Microbiol. 1997 Mar;63(3):867-73
16535553
J Microbiol Methods. 2003 Jun;53(3):327-34
12689710
J Microbiol Methods. 2000 Jul;41(2):85-112
10991623