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Yeah, some algeacides can kill your bacterial colonies. They can also kill your fish. Chemicals are really not recommended except as a last resort.

You might want to consider alternatives to chemicals if you're having algae probs. Some fish eat algae, such as plecs, otos, and siamese algae eaters (chinese do as well, although not for long and become large and aggressive over time). Mechanical removal with a scraper is another option for surfaces such as tank walls. Also consider the reason for the algae; green algae is usually due to too much light, brown algae (diatoms) are usually due to too little, and all algae probs can be traced back to too much nutrients be it phosphate, nitrates or silica.
 
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