Substrate depth

Isn't it bad to have gravel that deep?

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absolutely. anaerobic pockets will develop anyplace where oxygen cannot penetrate (and it won't get down 5 inches, trust me). this in turn will lead to the development of bacterial pathogens which are a serious problem for fish.

liv2padl said:

absolutely. anaerobic pockets will develop anyplace where oxygen cannot penetrate (and it won't get down 5 inches, trust me). this in turn will lead to the development of bacterial pathogens which are a serious problem for fish.

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Thats true but I have at least 5 to 6 inches of gravel in my tank but I also have a undergravel filter which get gets oxygen to those hard to reach spots and I have had no problems for some time now.

First, anaerobic bacteria that thrive in the substrate are not pathogenic. They produce toxins as waste, but the bacteria don't do anything to the fish. Second, without something actively pulling the wastes into the substrate, like an unfiltered UGF or RUGF, or a actively digging fish, there simply isn't much waste deep in the gravel to cause any problem, much less support a huge bacteria colony. If you do have a UGF, the gravel layers won't turn anaerobic, though of course, that thick gravel will reduce the circulation significantly and could have a few small pockets within it. BUT, and this is a crucial bit, anaerobes that are undisturbed are seldom a problem. They are confined to the low flow areas. Layers build up around them of bacteria that process the wastes, and you seldom have a problem, especially with a gravel substrate (larger particle sizes are less efficient in supporting anaerobes than smaller particles like sand).

If you have diggers, or feel the need to clean all the way to the bottom of the tank, there's no problem. If you do have either, then you have to make sure you're consistant and regular in cleaning and turning it over. I'd rather just leave it alone--clean the waste from the surface, and call it good.

anaerobic bacteria that thrive in the substrate are not pathogenic

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i believe you're wrong here. certain species of Pseudomonas - A genus of gram-negative, anaerobic bacteria have been found pathogenic to vertebrates, plants and invertebrates. Sutton et al (1988).

Aeromonad organisms such as Aeromonas salmonicida are facultative anaerobic, Gram-negative rods, and are known to produce septicemia in fish. The species most commonly isolated is A. hydrophilia.

Renibacterium salmoninarum is known to cause bacterial kidney disease in fish.

you might find this paper interesting. http://www.eela.fi/linked/fi/julkaisut/200504vaitosHirvelaKoski.pdf

Never said anaerobic bacteria aren't pathogenic--but the ones that thrive in the substrate tend to be nitrifiers or live in a layer outside the anaerobes to consume wastes (ie, sulfur), which don't go after fish. BKD is prominent in coldwater fish--specifically, salmonids, not tropicals--and it would have to be introduced to the tank. Sorry--just because some anaerobes are pathogens does not mean that all of them are.

If a bacteria is living in an anaerobic (no oxygen) environment (ie the deep gravel), how does it get to the fish w/o first entering an aerobic (has oxygen) environment it is not meant to live in and survive?

Pathogenic anaerobes have a number of survival methods--they can often encyst, or they come in imbedded within a biofilm that protects them. But they still must be introduced to the system--they will not spontaneously form within any anaerobic area within the tank, and those that do show up are highly unlikely to be pathogenic. Also, there are a number of pathogenic aenarobes that are NOT obligate anaerobes--meaning, like our muscle cells, they can survive under anaerobic conditions, but it's not their preferred state, or the flip--they prefer anaerobic conditions, but can readily survive aerobic conditions as well.