I don't think I could explain it better than this quote:
Quote:
GRAM-NEGATIVE AND GRAM-POSITIVE BACTERIA.
Bacteria can be divided into two groups, either Gram-
negative (G-) or Gram-positive (G+). This classification is
based on if the bacteria stains (+) or not (-) in a special
staining technique - the Gram staining (invented by Christian
Gram). Positive or negative staining reaction reflects a
fundamental difference in the structure of the cell wall of
the bacteria.
ERYTHROMYCIN IS AN ANTIBIOTIC.
Erythromycin is more efficient towards G(+) bacteria
than G(-). It is one of the safest antibiotics, meaning that
it does not affect plants, fish or animals. Blue-green
bacteria belongs to the G(-) bacteria but it is a special case
with respect to sensitivity to antibiotics (i'm on thin ice
here, but I think I am correct). They are more sensitive to
erythromycin than other G(-) bacteria. Fortunately, the
bacteria important for the nitrogen cycle (your biofilter) are
of the G(-) type and are much less sensitive to erythromycin
than the blue-green bacteria. So your biological filter is
"fairly" safe.
The reason that some tanks experience an ammonia peak
after treatment with erythromycin is (probably) not because
the biological filter is non-functional. It is more likely
that it is because of the high content of protein released
from the dead blue-green bacteria which is broken down to
ammonia and/or nitrite by the "good" nitrifying bacteria in
your biofilter. This boost of protein to be broken down upsets
the finely tuned balance of different bacteria in your filter.
(Actually, if you killed of all bacteria in your tank and
filter, you would never get ammonia).
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This quote was written by Tony Clementz, and can be found on The Krib.
In addition to this, you will find that as long as water changes are kept up to remove the dead stuff, along with the plants absorbing any leftover nutrients, you will notice any biofilter issues.