I have periphyton samples that also contain sediment/sand. Some of the samples have green clumps made up of sand and algae (greens, cyanobacteria and diatoms) all held together by pectin. These clumps do not sufficiently break during vigorous hand agitation. I am considering sonicating the samples to break up these clumps. I know that this will have some breakage of the filamentous green algae and I'll have to still be able to identify that individual cells SHOULD have been part of a filament. If you have done this with similar samples, how badly does it damage the cells? Were they still easily identifiable? Did it only break up the filamentous or were the diatom frustules broken by this process? I do not need to identify to species but need to be able to identify broad groups which will be difficult if the cells are badly damaged.
I just spoke with the professor who has the sonicator and he didn't say which type of sonicator it was, but that he agreed it would completely obliterate my cells beyond identification. Thanks for your answers to my question. I think I'll be moving to plan B (mashing these clumps by placing with water between two plates of glass and sliding back and forth, then sieving).
I use frequently sonication to separate episammic diatoms and sediment grain, without damage frustule.
I have often used sonication and I helps a lot to break up clumps and does not damage the cells. You can also blend the sample in a blender prior to sonication but this does Break up filaments into
smaller pieces so be sure to keep part of the sample untouched for Identification.
I have sonicated marine sediment samples with diatoms and dinoflagellate cysts. I have not worked with samples with presence of filamentous green algae and cyanobacteria. Diatoms and dinoflagellate cysts are not damaged by sonication.
I have experiance with bacterial biofilms. It realy depend on the type of sonication device you use and duration of the treatment. waterbath devices bring less ultrasonic energy and ussualy do not demage bacteria when applied for 2 minutes. probe devices bring much more energy into the samples and damage bacterial cells. see our paper in Water Res. 2004 Nov;38(18):3971-9.
I agree with Viviana and Aleksandra. A sonic bath (jeweller's ultrasonic cleaner) will do the job with no cell damage. I attachan old paper of mine which migh help,
Cheers
Thank you Domenico and Aleksandra! Your papers were a big help!
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