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organic substrate layers and decomposition by-products

     I've mentioned layering of substrate materials previously but didn't 
     explain why this is so important. The reason is this:
     Almost no oxygen diffuses into the substrate much below an inch with a 
     fine gravel/sand substrate. The roots of aquatic plants mainly grow 
     and spread about an inch or two into the substrate (although many go 
     deeper in quest of mineral nutrients). In nature, virtually all macro 
     nutrients from organic materials are found in the top inch or so of 
     mud. You should maintain all organic materials (IF you use them) 
     within a layer no more than an inch thick and covered by no more than 
     an inch of 2-3 mm gravel or coarse washed sand. The organic material 
     should always be mixed with sand or soil. Ordinary garden soil is a 
     better source of organic material because it is well decomposed and 
     well leached of nutrients. Earthworm castings for example, seem to be 
     very fertile and should be used sparingly IF used. While advertised to 
     be a good source of humus, they are also a good (bad?) source of 
     nutrients and labile organic material.
     When organic materials decay in the substrate below 2 inches or so, 
     the reduction-oxidation (redox) potential becomes very low since 
     oxygen, nitrate and other oxidizing chemicals are used up by the 
     bacteria. At this point, anaerobic bacteria take over using processes 
     such as fermentation which results in small (or large) amounts of 
     somewhat toxic by-products such as alcohols, ketones, esters and 
     aldehydes. Often there will also be various mercator (HS-) compounds 
     which have the distinctive sulfer smell of natural gas and which are 
     easy to identify. The gas bubbles which you get from organic 
     substrates are primarily methane but could also contain ethane as well 
     as nitrogen. The presence of iron in the substrate (iron containing 
     soils, iron oxide, laterite, red clay) helps to bind sulfide radicals 
     and thus reduce their mobility. Certain types of fish are much more 
     likely to be affected by small amounts of these compounds than are 
     plants. Regular water changes and carbon filtration are good 
     precautions. Activated carbon (if changed weekly) will remove most 
     dissolved organic compounds (DOC) such as the ones I mentioned above 
     so I would advise this if you are keeping delicate fish.
     When you have a deeper substrate (3" or more) what you're attempting 
     to do with the lower layers is provide iron and manganese trace 
     elements at the low redox potential there. A shallow substrate can get 
     filled with plant roots to the point where the redox potential is too 
     high to provide enough iron for the plants. I suspect that it also 
     takes many plants like Hygrophila, a long time to develop large enough 
     root systems to get enough iron to satisfy their rapid growth. I've 
     always had to supplement chelated Fe to avoid chlorosis symptoms with 
     this plant in good nutrient/high light conditions. The only organic 
     material you might want at all below 2 inches is possibly a small 
     amount of humus which you can get from outdoor soil (not potting soil 
     or the like). Peat plates may be an exception but these are far less 
     subject to decomposition. Again peat plates should probably be no more 
     than 2-3" deep in the substrate.
     Bottom layer: clay, sand, iron compounds, laterite, micronized iron, 
     iron oxides etc. trace humus.
     Middle layer: (1") sand, silt, soil, peat(10%) or aged compost(<5%)...
     Top layer: sand or fine gravel to keep things from getting stirred up.
     You'll probably only use a single organic material such as peat or if 
     you use a combination, you'll reduce the overall amounts to limit the 
     total organic content. Aged compost or earthworm castings might be 
     better if limited to 2-3% by weight or better yet, leached for a month 
     or two in a bucket of water. The organic components of a substrate can 
     be left out and you can also get good results using a laterite or 
     similar additive in the bottom 1/3 of your substrate for iron.
     Steve P in Vancouver BC where it's summer again...