Concern about Anaerobic spots

If you push down to the egg crate, and you have gravel and not sand, you are getting anything trapped within the cells of the egg crate. You're probably doing fine.
good luck

1.If you didn't stir up the gravel, nothing biodegradable would get down there, would it?

2. All the substrate is anoxic, under the topmost layer. Diffusion of oxygen is a very slow process and affects onlt very small areas.

Yes, if you do not stir the gravel the fine mulm will still sift down. If nothing else brownian motion wll move it slowly.

But the technique suggested by famman should handle the issue nicely.

Well, maybe not brownian motion, RTR...

The jiggling movement of brownian motion caused by molecular jostling of microscopic specks as small as a single pollen grains is random, so it couldn't actually contribute to settling, even of particles that are small enough. A good action java applet that demonstrates brownian motion: www.phys.virginia.edu/classes/109N/more_stuff/ Applets/brownian/brownian.html (hope this works)

I've been reading a densely-technical but perfectly readable 19-page handbook "Prokaryotes and their habitats" by Hans G. Schlegel and Holger W. Jannasch at: http://microimm.queensu.ca/micr433/Prokaryotic_Habitats .pdf
It's helping me get a better picture of how forces like diffusion work on these microscales.

Microecology is still pretty mysterious for me. My general (and amateur) impression of anaerobic bactrial communities in the substrate is that they're everywhere, that they're highly self-organizing if we don't disturb them, that they're mostly beneficial, and that only under very specialized conditions does enough hydrogen sulfide get produced to kill surrounding mictobes and initiate a noxious sulfuretum.

H2S is a very vivid smell. I think the vaguely stale and gassy smells we get in some tanks are more likely to be phenols and thiols than hydrogen sulfide. Not to say there's no H2S-- it's everywhere in anoxic microzones throughout the aquarium, constantly being oxidized to sulfate by its aerobic neighbors.

This is one area where I actually agree with St. Diana. Anaerobic areas are not dangerous in undisturbed substrates. But how may folk can keep from disturbing their substrate? Move a rock, bump a plastic plant or driftwood, and you can disturb the substrate sufficiently to release toxic gases which would be otherwise harmless or oxidized to harmlessness as they moved upward on their own. Ms Waldstad may never disturb hers, but I don't know anyone else who doesn't . I don't like timebombs in my tanks which I could unintentinally trigger. Avoidable problems should be avoided.

But microbial action alone is insufficient to account for fine silt settlement through particle beds, whether from molecular level vibrations or whatever, silt/mulm does settle over time. At least one of my 'undisturbed' (quibble) plenums (which is the only one with a visible bottom glass) has visible silt spotted over the bottom. Strangely enought - to me at least - that is heaviest around the margins, where gravel comes down to the bottom glass. Out in the plenum space itself, the "coverage" is very low percentage.

Wetman/RTR:

I've always wanted to get your guy's opinion on this and this thread seems to be a good spot to ask. I'm sure you're both familiar with the DSB technique in saltwater, and you both acknowledge that H2S IS present throughout anaerobic bed environments. I agree that if left alone to work itself up through gradually more aerobic upper layers it will be oxidized to much less toxic gasses. However, Dr. Ron Shimek has repeatedly stated many many times that sandbeds usually cannot produce enough H2S to become lethal. His argurment is that by the time it reached threatening levels you would be barely able to breathe. The odor is a warning that the gas is harmful, but you would all but suffocate at lethal levels. I have yet to see any evidence that this is false, but of course the story has been around for so long. Just curious of what you guys, or anyone else really, thinks of this.

I've never done DSB, only plenums, so no direct experience. I have never had fish death that I could blame on H2S, but I have had fish deaths from bad substrate (years ago, before I learned to renew my planted tank substrates periodically). The symptoms were close to septicemia, so the problems appeared bacterial. Tank breakdown after the problems showed multiple areas of ppt'd iron and H2S stench. Related but not necessarily direct causal relationship. But I have only seen such in sour-substrate tanks.

I know that RobertH and cathyh have had similar problems, I assume Karen Randall has as well, as I learned from her the technique of renewing the substrate before it is sour.

RTR's the one with the saltwater experience and the freshwater plenum... I feel like the Fool in the tarot deck, sauntering off the precipice. I never disturb substrates, beyond a little cautious slow uprooting and careful replanting-- though, what with one thing or another my tanks do tend to get rebuilt after six or seven years or so. Maybe I just never reach that stage. I've never noticed hydrogen sulfide in substrates (I know it from a rotten egg I once broke, and a rotted Aponogeton bulb), but it's a rich stinky mud odor that I'd attribute to thiols and iron bacteria and sulfur bacteria.

I don't put any organic enrichment into my lower substrate mix (sand/gravel, Flourite, cat litter, spent peat usually) except what'sgetting recycled after a couple of brisk rinsings. Silty colloidal substrate is what counts, IMO, not decaying organics.

But then I don't disturb the substrate myself-- more like Diana Walstad. If I shift a rock it's a major deal, done with a siphon in the other hand. The wastewater is black --but not rotten-egg H2S smelling.

But then I have undemanding plants on the whole, and a good deal of algae, currently, to be truthful. Not very many fish per tank. All quite simple.

My "aim" when setting a tank is for a 10-year life. Many do not last that long because I get bored and want to try something else. Some few tanks go 15 years or more.

My experiments with DIY substrates were mostly short and ugly - vermiculite, kitty litter, top or subsoil, etc never lasted as I had issues with each. Decades ago my substrates were gravel + mulm. It worked, but developed slowly and painfully. Then Dupla and laterite came along and that worked great. Then we lost access in the US and I tried some of the layered substrates with peat, soils, etc and always had problems within a greater or lesser period. Now we have easy access to laterites and SeaChem's substrates (I've only used the standard Flourite). Life is easy again.

Wetman - perhaps the difference is in the plants we use. I'm big on Vals, Crypts, and swords - all of which burn up their substrate fast and produce massive quantities of roots which will eventually become H2S sites after they become inactive. Without major division and replanting at some interval, all these can have problems. The swords tend to 'walk' very slowly, so it is easier to clear out some of the dead mass every couple of years. The Crypts get crowded, the Vals lose vigor. My other standards - Anubias (require only pruning rarely), Crinums (which I never disturb if I can avoid it), Apon (which largely offer dormancy and an easy window for moving or substrate re-build) or don't involve the substrate (Java Moss, Java Fern, Bolbitis). I do not do stem plants, I'm too lazy.

I do have very little algae - the 29 I can see from here last had its glass cleaned last summer when I pruned the Anubias back. It is time to prune again to even up the carpet and reduce its height, so I'm sure I'll do the glass at the same time. The 55s have to be front glass scraped every few weeks. (they are my highest light tanks). The other are in between those extremes.