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Substrate would cause the barbels to deteriorate. When I was more naive, I purchased flourite and eco-complete and my cories barbels suffered greatly and they were not thriving. I replaced it with Fluval Planted substrate (soft, circular granules) and they've grown back in two weeks.
The degredation of the barbels in combination with other factors (slightly unclean water, high nitrates, stressed fish as a result) may have caused a bacterial infection leading to lesions and rot. Can you take a picture of the injured cories?
Ultimately, I would put them in a medi-tank while you add the new substrate. Adding it while they're in the tank will be VERY stressful for them and they may be injured in the process. Use water from your tank to fill the smaller tank, then perhaps treat some of the water you usually add after a WC and fill the rest.
without more visuals I wouldn't feel comfortable diagnosing them. But there are antibiotics and antifungal medications available in chain stores (petco, petsmart).
Tetracycline and Maradin are antibiotics that will treat a wide spectrum of bacterial infections including rot.
API has a "Fungus Cure" that treats fungal infections + some secondary bacterial.
Look up beforehand which medications use copper, as Cories are very sensitive to it and could die if misused.
Googled an article and found this to be pretty helpful:
"Corydoras paleatus are very hardy and disease is not usually a problem in a well maintained aquarium. There is no guarantee that you won't have to deal with health problems or disease, but cory catfish are very resilient.
High nitrate levels can cause Peppered Cory catfish to develop infected barbels; this makes it difficult for them to navigate and eat normally. Maintain nitrate levels below 20 ppm through regular water changes. Because they are a scaleless fish, catfish can be treated with pimafix or melafix but should not be treated with potassium permanganate or copper based medications. Malachite green or formalin can be used at one half to one fourth the recommended dosage. All medications should be used with caution.
The best way to proactively prevent disease is to give your fish the proper environment and give them a well balanced diet. The closer to their natural habitat the less stress the fish will have, making them healthier and happy. A stressed fish will is more likely to acquire disease. Anything you add to your tank can bring disease with it. Not only other fish but plants, substrate, and decorations can harbor bacteria. Take great care and make sure to properly clean or quarantine anything that you add to an established tank so as not to add new diseases to the tank. For information about fish diseases and illnesses, see Aquarium Fish Diseases and Treatments."
Link is here: http://animal-world.com/encyclo/fresh/catfish/PepperedCorydoras.php
Hope this helps!
The degredation of the barbels in combination with other factors (slightly unclean water, high nitrates, stressed fish as a result) may have caused a bacterial infection leading to lesions and rot. Can you take a picture of the injured cories?
Ultimately, I would put them in a medi-tank while you add the new substrate. Adding it while they're in the tank will be VERY stressful for them and they may be injured in the process. Use water from your tank to fill the smaller tank, then perhaps treat some of the water you usually add after a WC and fill the rest.
without more visuals I wouldn't feel comfortable diagnosing them. But there are antibiotics and antifungal medications available in chain stores (petco, petsmart).
Tetracycline and Maradin are antibiotics that will treat a wide spectrum of bacterial infections including rot.
API has a "Fungus Cure" that treats fungal infections + some secondary bacterial.
Look up beforehand which medications use copper, as Cories are very sensitive to it and could die if misused.
Googled an article and found this to be pretty helpful:
"Corydoras paleatus are very hardy and disease is not usually a problem in a well maintained aquarium. There is no guarantee that you won't have to deal with health problems or disease, but cory catfish are very resilient.
High nitrate levels can cause Peppered Cory catfish to develop infected barbels; this makes it difficult for them to navigate and eat normally. Maintain nitrate levels below 20 ppm through regular water changes. Because they are a scaleless fish, catfish can be treated with pimafix or melafix but should not be treated with potassium permanganate or copper based medications. Malachite green or formalin can be used at one half to one fourth the recommended dosage. All medications should be used with caution.
The best way to proactively prevent disease is to give your fish the proper environment and give them a well balanced diet. The closer to their natural habitat the less stress the fish will have, making them healthier and happy. A stressed fish will is more likely to acquire disease. Anything you add to your tank can bring disease with it. Not only other fish but plants, substrate, and decorations can harbor bacteria. Take great care and make sure to properly clean or quarantine anything that you add to an established tank so as not to add new diseases to the tank. For information about fish diseases and illnesses, see Aquarium Fish Diseases and Treatments."
Link is here: http://animal-world.com/encyclo/fresh/catfish/PepperedCorydoras.php
Hope this helps!