Mar 04, 2026
Extraction of surface-community DNA from macroalgal thalli
- Torsten Thomas1
- 1University of New South Wales, Sydney, Australia
Protocol Citation: Torsten Thomas 2026. Extraction of surface-community DNA from macroalgal thalli. protocols.io https://dx.doi.org/10.17504/protocols.io.8epv55p54v1b/v1
Manuscript citation:
Burke, C., Kjelleberg, S. and Thomas, T., 2009. Selective extraction of bacterial DNA from the surfaces of macroalgae. Applied and environmental microbiology, 75(1), pp.252-256.
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: March 04, 2026
Last Modified: March 04, 2026
Protocol Integer ID: 245805
Keywords: selective extraction of bacterial dna, community dna from macroalgal thalli, microbial dna, microscopic check of the macroalgal surface, precipitation of the microbial dna, macroalgal surface, direct lysis of the microbial community, surfaces of macroalgae, bacterial dna, microbial community, extraction of surface, organic extraction, macroalgal thalli, environmental microbiology, extraction, macroalgae, community dna, selective extraction, delisea pulchra, removal of basal part
Funders Acknowledgements:
Australian Research Council
Abstract
This method performs a direct lysis of the microbial community on an macroalgal surface followed by an organic extraction and precipitation of the microbial DNA. The method has been applied to Ulva sp. and Delisea pulchra and has not been found to damage the tissue. Microscopic check of the macroalgal surface before treatment and removal of basal parts (old and most likely covered by secondary colonisers) is necessary to ensure efficiency. The method has been published in Burke, C., Kjelleberg, S. and Thomas, T., 2009. Selective extraction of bacterial DNA from the surfaces of macroalgae. Applied and environmental microbiology, 75 (1), pp.252-256.
Troubleshooting
Method
Collect several marcoalgal thalli (e.g Ulva sp.) and transfer into bag/container with seawater. T
Chop the remaining thalli into piece of roughly 2-4 cm length/width
Wash the thalli 3 times for 1-2 min with CMFSW; make sure smaller bits and non-algal material get wash away
Using a balance, weigh out 10-20 g of wet-weight (drip dry) into a petri dish
Transfer thallus material into a sterile 50 ml Falcon tube with 30 ml of CMFSW and 300 μl of 3M Multi Enzyme Cleaner (article number 70500).
Shake gently to make sure the thalli surface is covered with the CMFSW/ cleaner mix and incubate at room temperature. Typically 30-180 min of incubations is enough.
Check removal of microbial cells and integrity of macroalgal surface by microscopy. If macroalgal surface, then consider using higher dilutions (e.g. 30 or 3 μl f 3M Multi Enzyme Cleaner in 30 ml of CMFSW). If microbial cells are not removed, then increase incubation time.
Transfer liquid into 1 or 2 new 50 ml Falcon tubes. Fill tubes with no more than 20 ml and make sure no thalli material is being transferred. Optionally the liquid can be filtered through a sterile 125 μm sieve or a 0.8 μm filter
Add an equal volume of phenol/ chloroform/ isoamylalcohol (25:24:1) to the supernatant and shake gently but thoroughly
Centrifuge for 5 min at 2,000 x g
Transfer aqueous phase into a sterile SS-34 tubes (or equivalent)
Add 1/10 volume of 3M sodium acetate and 3 volumes of 95% ethanol
Shake gently but thoroughly. A white precipitate may become visible
Incubate at −20°C for at least 2 hours
Centrifuge for 30 min at 20,000 x g
Remove supernatant
Add 10 ml of ice-cold 70% ethanol to pellet
Centrifuge for 5 min at 20,000 x g
Remove supernatant and air-dry pellet
Resuspend pellet in 0.5 ml sterile water and transfer into 2 ml microcentrifuge tube
Add 1/10 volume of 3M sodium acetate and 3 volumes of 95% ethanol
Shake gently but thoroughly. A white precipitate may become visible
Incubate at −20°C for at least 2 hours
Centrifuge for 30 min at 20,000 x g
Remove supernatant
Add 1 ml of ice-cold 70% ethanol to pellet
Centrifuge for 5 min at 20,000 x g
Remove supernatant and air-dry pellet
Resuspend pellet into 50-100μl TE-buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0)
Check appr. 1 μl of extracted DNA on agarose gel