Preservation of corals in salt-saturated DMSO buffer is superior to ethanol for PCR experiments

Gaither, Michelle R.; Szabó, Zoltán; Crepeau, Marc W.; Bird, C. E.; Toonen, Robert J.

doi:10.1007/s00338-010-0687-1

Cited by 68 publications

(70 citation statements)

References 8 publications

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“…For all specimens, DNA extractions were highly fragmented and of low molecular weight, as is often observed for ethanol-preserved specimens (Gaither et al, 2011). As a result, the success of PCR amplification varied from specimen to specimen.…”

Section: Molecular Datamentioning

confidence: 95%

Shallow-water scleractinian corals of Ascension Island, Central South Atlantic

Zibrowius¹,

Wirtz²,

Nunes³

et al. 2014

J. Mar. Biol. Ass.

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The presence of five shallow-water scleractinian species at Ascension Island is confirmed, i.e. Favia gravida, Madracis sp., Siderastrea radians, Polycyathus atlanticus and Rhizosmilia gerdae. The three former are zooxanthellate, the two latter azooxanthellate. A sixth species, Cladocora debilis (azooxanthellate), dredged from moderately deep water is also expected to occur in shallow water. Madracis sp. and P. atlanticus are new records for the island. A previous record of Astrangia solitaria at Ascension is now referred to as P. atlanticus. Favia gravida, S. radians and C. debilis are amphi-Atlantic. Rhizosmilia gerdae is currently known only from Ascension Island and the Western Atlantic. None of the species are endemic to Ascension Island. No member of the family Dendrophylliidae has as yet been found at Ascension, whereas that family is represented at its nearest neighbour, St Helena Island.

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Section: Molecular Datamentioning

confidence: 95%

Shallow-water scleractinian corals of Ascension Island, Central South Atlantic

Zibrowius¹,

Wirtz²,

Nunes³

et al. 2014

J. Mar. Biol. Ass.

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“…Sampled specimens were stored in Ziploc plastic bags upon collection and transported in coolers filled with seawater. Upon returning to shore, samples were transferred into cryotubes, DMSO/NaCl buffer was added (Gaither et al, 2011), and samples were stored at 4°C until DNA extraction.…”

Section: Sample Collection and Environmental Conditionsmentioning

confidence: 99%

Biogeography and molecular diversity of coral symbionts in the genus Symbiodinium around the Arabian Peninsula

Ziegler

Arif

Burt

et al. 2017

Journal of Biogeography

139

130

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AimCoral reefs rely on the symbiosis between scleractinian corals and intracellular, photosynthetic dinoflagellates of the genus Symbiodinium making the assessment of symbiont diversity critical to our understanding of ecological resilience of these ecosystems. This study characterizes Symbiodinium diversity around the Arabian Peninsula, which contains some of the most thermally diverse and understudied reefs on Earth.LocationShallow water coral reefs throughout the Red Sea (RS), Sea of Oman (SO), and Persian/Arabian Gulf (PAG).MethodsNext‐generation sequencing of the ITS2 marker gene was used to assess Symbiodinium community composition and diversity comprising 892 samples from 46 hard and soft coral genera.ResultsCorals were associated with a large diversity of Symbiodinium, which usually consisted of one or two prevalent symbiont types and many types at low abundance. Symbiodinium communities were strongly structured according to geographical region and to a lesser extent by coral host identity. Overall symbiont communities were composed primarily of species from clade A and C in the RS, clade A, C, and D in the SO, and clade C and D in the PAG, representing a gradual shift from C‐ to D‐dominated coral hosts. The analysis of symbiont diversity in an Operational Taxonomic Unit (OTU)‐based framework allowed the identification of differences in symbiont taxon richness over geographical regions and host genera.Main conclusionsOur study represents a comprehensive overview over biogeography and molecular diversity of Symbiodinium in the Arabian Seas, where coral reefs thrive in one of the most extreme environmental settings on the planet. As such our data will serve as a baseline for further exploration into the effects of environmental change on host–symbiont pairings and the identification and ecological significance of Symbiodinium types from regions already experiencing ‘Future Ocean’ conditions.

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“…DESS is a nonproprietary solution that has been used to preserve DNA and has been shown to be superior to ethanol for coral tissue DNA preservation (Gaither et al, 2010). Like DNAgard TM , samples in this solution can be stored long term (up to 24 weeks) at room temperature, though without the need for desiccation (Seutin et al, 1991), and this preservative has been used to preserve bacterial DNA from coral mucus swabs for up to 4.5 months (May et al, 2011).…”

Section: Dmso/edta/saturated Sodium Chloride (Dess)mentioning

confidence: 99%

Comparison of DNA preservation methods for environmental bacterial community samples

Gray

Pratte

Kellogg

2012

FEMS Microbiol Ecol

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Field collections of environmental samples, for example corals, for molecular microbial analyses present distinct challenges. The lack of laboratory facilities in remote locations is common, and preservation of microbial community DNA for later study is critical. A particular challenge is keeping samples frozen in transit. Five nucleic acid preservation methods that do not require cold storage were compared for effectiveness over time and ease of use. Mixed microbial communities of known composition were created and preserved by DNAgard(™), RNAlater(®), DMSO-EDTA-salt (DESS), FTA(®) cards, and FTA Elute(®) cards. Automated ribosomal intergenic spacer analysis and clone libraries were used to detect specific changes in the faux communities over weeks and months of storage. A previously known bias in FTA(®) cards that results in lower recovery of pure cultures of Gram-positive bacteria was also detected in mixed community samples. There appears to be a uniform bias across all five preservation methods against microorganisms with high G + C DNA. Overall, the liquid-based preservatives (DNAgard(™), RNAlater(®), and DESS) outperformed the card-based methods. No single liquid method clearly outperformed the others, leaving method choice to be based on experimental design, field facilities, shipping constraints, and allowable cost.

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Preservation of corals in salt-saturated DMSO buffer is superior to ethanol for PCR experiments

Cited by 68 publications

References 8 publications

Shallow-water scleractinian corals of Ascension Island, Central South Atlantic

Shallow-water scleractinian corals of Ascension Island, Central South Atlantic

Biogeography and molecular diversity of coral symbionts in the genus Symbiodinium around the Arabian Peninsula

Comparison of DNA preservation methods for environmental bacterial community samples

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