Comparison of different protocols for the extraction of microbial DNA from reef corals

Santos, Henrique F.; Leite, D. L.; Jesus, Hugo Emiliano de; Maalouf, Pedro De Carvalho; Almeida, Carlos Eduardo; Soriano, Adriana U.; Altomari, D.; Suhett, L.; Vólaro, V.; Valoni, Érika; Francisco, Moisés; Vieira, Jose Costa; Rocha, Rui; Sardinha, B.L.; Mendes, Leonardo Brantes Bacellar; João, R.R.; Lacava, B.; Jesus, Romalde; Sebastian, G.V.; Pessoa, Adalberto; Elsas, Jan Dirk van; Rezende, Rachel Passos; Pires, Débora O.; Duarte, Gabriela; Castro, Clovis B.; Rosado, Alexandre Soares; Peixoto, Raquel S.

doi:10.1590/s1517-83822012000200012

Cited by 21 publications

(21 citation statements)

References 25 publications

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“…Total community DNA extraction was performed using the ZR Soil Microbe DNA Kit (Zymo Research, Irvine, CA, USA) (Santos et al, 2012). The DNA quality and concentration was evaluated using a Qubit fluorometer (Invitrogen, Carlsbad, CA, USA).…”

Section: Community Dna Extractionmentioning

confidence: 99%

Climate change affects key nitrogen-fixing bacterial populations on coral reefs

Santos

Carmo

Duarte³

et al. 2014

The ISME Journal

121

106

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Coral reefs are at serious risk due to events associated with global climate change. Elevated ocean temperatures have unpredictable consequences for the ocean's biogeochemical cycles. The nitrogen cycle is driven by complex microbial transformations, including nitrogen fixation. This study investigated the effects of increased seawater temperature on bacteria able to fix nitrogen (diazotrophs) that live in association with the mussid coral Mussismilia harttii. Consistent increases in diazotroph abundances and diversities were found at increased temperatures. Moreover, gradual shifts in the dominance of particular diazotroph populations occurred as temperature increased, indicating a potential future scenario of climate change. The temperature-sensitive diazotrophs may provide useful bioindicators of the effects of thermal stress on coral reef health, allowing the impact of thermal anomalies to be monitored. In addition, our findings support the development of research on different strategies to improve the fitness of corals during events of thermal stress, such as augmentation with specific diazotrophs.

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Section: Community Dna Extractionmentioning

confidence: 99%

Climate change affects key nitrogen-fixing bacterial populations on coral reefs

Santos

Carmo

Duarte³

et al. 2014

The ISME Journal

121

106

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“…Using a mortar and pestle, 0.5 g of dried material from each coral sample was macerated. A total community DNA extraction was performed using the ZR Soil Microbe DNA Kit (Zymo Research, Irvine, CA) (Santos et al 2012). DNA quality and concentration were evaluated using a Qubit fluorometer (Invitrogen, Carlsbad, CA).…”

Section: Biological Validationmentioning

confidence: 99%

A novel marine mesocosm facility to study global warming, water quality, and ocean acidification

Duarte

Calderón²,

Pereira³

et al. 2015

Ecology and Evolution

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We describe a completely randomizable flow‐through outdoor mesocosm for climate change and ecotoxicology studies that was built with inexpensive materials. The 16 raceway tanks allow up to 6× water renewal per hour, avoiding changes in natural abiotic seawater conditions. We use an open‐source hardware board (Arduino) that was adapted to control heaters and an innovative CO 2 injection system. This system reduced seawater pH up to −0.9 units and increased temperature up to +6°C in three treatments and a control. Treatments can be continuously compared with the control and vary according to diel fluctuations, thus following the diel range observed in the sea. The mesocosm facility also includes an integrated secondary system of 48 aquaria for ecotoxicology studies. We validated the reproducibility and relevance of our experimental system by analyzing the variation of the total DNA of the microbial community extracted from corals in three elevated temperature scenarios during a 40‐day experiment. We also present data from temperature, acidification, and copper contamination trials, which allowed continuous, reliable, and consistent treatment manipulations.

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“…Fingerprinting techniques, which combine target gene amplification with amplicon separation by DGGE can provide important information about changes in the microbial community in response to environmental changes (Ovreas et al , 1997; Nakatsu et al , 2007). The success of molecular tools, including PCR-DGGE, is strongly affected by the DNA or RNA extraction method used (Santos et al , 2012). DNA isolation methods involving insufficient cell lysis or too much DNA degradation may result in underestimates (Holland et al , 2000; McOrist et al , 2002).…”

Section: Introductionmentioning

confidence: 99%

Comparison of DNA extraction protocols for microbial communities from soil treated with biochar

Leite

Balieiro

Pires

et al. 2014

Braz. J. Microbiol.

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Many studies have evaluated the effects of biochar application on soil structure and plant growth. However, there are very few studies describing the effect of biochar on native soil microbial communities. Microbial analysis of environmental samples requires accurate and reproducible methods for the extraction of DNA from samples. Because of the variety among microbial species and the strong adsorption of the phosphate backbone of the DNA molecule to biochar, extracting and purifying high quality microbial DNA from biochar-amended soil is not a trivial process and can be considerably more difficult than the extraction of DNA from other environmental samples. The aim of this study was to compare the relative efficacies of three commercial DNA extraction kits, the FastDNA® SPIN Kit for Soil (FD kit), the PowerSoil® DNA Isolation Kit (PS kit) and the ZR Soil Microbe DNA Kit Miniprep™ (ZR kit), for extracting microbial genomic DNA from sand treated with different types of biochar. The methods were evaluated by comparing the DNA yields and purity and by analysing the bacterial and fungal community profiles generated by PCR-DGGE. Our results showed that the PCR-DGGE profiles for bacterial and fungal communities were highly affected by the purity and yield of the different DNA extracts. Among the tested kits, the PS kit was the most efficient with respect to the amount and purity of recovered DNA and considering the complexity of the generated DGGE microbial fingerprint from the sand-biochar samples.

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Comparison of different protocols for the extraction of microbial DNA from reef corals

Cited by 21 publications

References 25 publications

Climate change affects key nitrogen-fixing bacterial populations on coral reefs

Climate change affects key nitrogen-fixing bacterial populations on coral reefs

A novel marine mesocosm facility to study global warming, water quality, and ocean acidification

Comparison of DNA extraction protocols for microbial communities from soil treated with biochar

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