Hi, prankster705,
as far as the plastic goes, I'm simply passing on what I have happen to have read.
As mentioned, I'm going by studies and comments I've encountered and the stated slick, non-porous properties of certain types of plastic, together with the fact that I've also read that beneficial bacteria doesn't grow well on glass and plastic surfaces - I'm certainly not criticizing the people who do use plastic as a filtration material and if it works well for you, then that's just ducky.
If you do happen to have a link handy to any studies, I'd be interested - Lord knows that lots of things labeled 'obvious', 'common-sense' or 'everybody knows' facts have been proven mistaken or misleading, and I do know many people swear by the scrubbies in their large filtration systems.
Also, there are so many variables involved - one interesting example:
http
/www.cdc.gov/ncidod/eid/vol8no9/02-0063.htm
... The solid surface may have several characteristics that are important in the attachment process. Characklis et al. (6) noted that the extent of microbial colonization appears to increase as the surface roughness increases. This is because shear forces are diminished, and surface area is higher on rougher surfaces. The physicochemical properties of the surface may also exert a strong influence on the rate and extent of attachment. Most investigators have found that microorganisms attach more rapidly to hydrophobic, nonpolar surfaces such as Teflon and other plastics than to hydrophilic materials such as glass or metals (7–9). Even though results of these studies have at times been contradictory because no standardized methods exist for determining surface hydrophobicity, some kind of hydrophobic interaction apparently occurs between the cell surface and the substratum that would enable the cell to overcome the repulsive forces active within a certain distance from the substratum surface and irreversibly attach.
Conditioning Films
A material surface exposed in an aqueous medium will inevitably and almost immediately become conditioned or coated by polymers from that medium, and the resulting chemical modification will affect the rate and extent of microbial attachment. Loeb and Neihof (10) were the first to report the formation of these conditioning films on surfaces exposed in seawater. These researchers found that films were organic in nature, formed within minutes of exposure, and continued to grow for several hours. The nature of conditioning films may be quite different for surfaces exposed in the human host. A prime example may be the proteinaceous conditioning film called “acquired pellicle,” which develops on tooth enamel surfaces in the oral cavity. Pellicle comprises albumin, lysozyme, glycoproteins, phosphoproteins, lipids, and gingival crevice fluid (11); bacteria from the oral cavity colonize pellicle-conditioned surfaces within hours of exposure to these surfaces. Mittelman noted that a number of host-produced conditioning films such as blood, tears, urine, saliva, intervascular fluid, and respiratory secretions influence the attachment of bacteria to biomaterials (12). Ofek and Doyle (13) also noted that the surface energy of the suspending medium may affect hydrodynamic interactions of microbial cells with surfaces by altering the substratum characteristics. ...
... Other characteristics of the aqueous medium, such as pH, nutrient levels, ionic strength, and temperature, may play a role in the rate of microbial attachment to a substratum. Several studies have shown a seasonal effect on bacterial attachment and biofilm formation in different aqueous systems (17,18). This effect may be due to water temperature or to other unmeasured, seasonally affected parameters. Fletcher (19,20) found that an increase in the concentration of several cations (sodium, calcium, lanthanum, ferric iron) affected the attachment of Pseudomonas fluorescens to glass surfaces, presumably by reducing the repulsive forces between the negatively charged bacterial cells and the glass surfaces. Cowan et al. (21) showed in a laboratory study that an increase in nutrient concentration correlated with an increase in the number of attached bacterial cells. ...
... Tolker-Nielsen and Molin noted that every microbial biofilm community is unique (43) although some structural attributes can generally be considered universal. The term biofilm is in some ways a misnomer, since biofilms are not a continuous monolayer surface deposit. Rather, biofilms are very heterogeneous, containing microcolonies of bacterial cells encased in an EPS matrix and separated from other microcolonies by interstitial voids (water channels) (44). ...
Please note, however, that while that while '... Most investigators have found that microorganisms attach more rapidly to hydrophobic, nonpolar surfaces such as Teflon and other plastics than to hydrophilic materials such as glass or metals ...'. no comparison is made to the relative speed of attachment to/propagation on other materials - and the biofilms would appear to reduce many differences.
Since large industry uses plastic in their biological treatment of sewage and other such applications, it evidently works well enough.
But, if such things are mentioned, it gives those interested an option of looking into it for themselves and forming an opinion otherwise never tested.
One of the things I've been finding is that I, and others, tend to have difficulty thinking 'outside the box' which is hardly surprising, as we obviously are restricted by our own experience and available knowledge - my personal transition into a less-commonly used method of aquarium-keeping has shown how difficult it may be for us to alter often life-long assumptions and habits of thought.
I, for example, have not yet succeeded in taking any of my Walstads off the weekly water change rotation, even though I know it's bad for the tank/plants - and even though my water use is a VERY sore daily point in the household.
So I'm forced to the realization that it's important to consider things often unmentioned or unconsidered - and I'm trying to introduce a wider-range viewpoint not only in myself, but in anyone willing to wade through some of my lengthier posts, lol.
The main point I'd like to make actually goes beyond this particular example provided by the OP - that not everybody uses the identical methods providing identical conditions and that different actions can produce vastly different results in different tanks.
You, for example, use a wet dry filter in your example - your system has BIG strong filtration and the bacterial processing dependency in your tank is heavily filter-oriented.
That suits your purpose and your aims - you're a high-tech kinda guy.
The nice chappy checking in for advice on his low-stocked 20 gallon with an Aqua Clear and some plants has more bacterial input likely from other sources; a far higher proportion, comparatively speaking, of bacterial processing is likely to be provided by that on the plants, rock and gravel in his tank than would be in yours, with your very large, powerful filtration system.
In his case, the removal of that gravel could very well cause a spike.
Something that may not appreciably affect your type of high-tech/filtered tank could very well affect another's - not necessarily the OP's, but others.
And forum lurkers with tanks which might be affected by this type of substrate substitution are very likely to read this and decide it's perfectly safe for them, no need to monitor closely for potential results - or even be advised that it is necessarily so.
If you think about the fact that not only MTS but Khuli loaches can survive for long periods burrowing under and through the gravel in various tanks, it becomes evident that there is, indeed, clearly sufficient oxygen and food (ammonia from poop, for example) to support itty-bitty beneficial bacteria in that gravel as well.
The information released by equipment manufacturers naturally places emphasis on the actions of their filter and there's no funding for promoting free methods, so commerce likely both directly and indirectly provides a main source of official information in this area.
This works well for people interested in high-tech.
But the vast majority of people with fish tanks not only cannot afford high tech, but typically have different aims.
I notice that your immediate response to the mention of nitrifying bacteria in gravel pertains to the use of artificial (undergravel) filtration, which is typical of a great many of us.
But what I'm actually referring to isn't what's directly artificially supported within a mechanical filtration system but what naturally exists on surfaces within the average tank - and that's what I mean by thinking outside the box.
A high-tech system is managed in every area - dosing is precisely calculated, filtration is as strong as poss., plants are sculpted into elegantly designed and maintained underwater gardens - of course the proponents think only of what is done TO the tank by human intervention in tweaking everything to maintained perfection.
But in the average tank, typically, stuff happens and is encouraged or discouraged to varying degrees.
And some of us are attempting to support a balanced, more natural type of system, and learning (I hope, lol) to consider the complexity of life working together within our tanks - and some of us (me! anyway, lol) have the new convert's tendency to share our delight.
As you've probably noticed, people like Tom Barr, who's commented on the El Natural forum as well as here, often consider/experiment with new things, even though they have their own highly successful methods, because they're generally interested in seeing what works, even where the method differs entirely from their own.
And I thought I'd have a peek over there in finding an illustration of what I mean by different circumstances - got lucky pretty much off the hop and found the perfect example among commenters on a thread.
http/www.barrreport.com/general-plant-to...e+ammonia+spike
The OP:
... I want to do a major scape change and replace/remove some of my substrate. ...
My concern is basically losing bacterial filtration with the loss of the existing substrate and the effect on it's overall health and it's inhabitants.
I do not know how much of the beneficial bacteria exist in the substrate as opposed to the rest of the tank/filters/etc, but due to it's size in AREA (72X24), I suspect it is substantial.
Will this in effect cause a new tank cycle or even a partial spike? ...
From one commenter:
... I don't have all the answers to your questions but I can guarantee you that you will have an ammonia/nitrite spike and a mini cycle. I had this happen to me in my non planted 10G tank when I removed the top layer of substrate. In your case given the large surface area and also add to it the fact that you will move plants around causing them to pause with plant growth while they re-establish themselves in their new environment, I'd expect a pretty big "mini" cycle. I would think that you'd need to do daily water changes and dose ferts. You might still have algae issues due to the spiking ammonia levels. I would definitely take Tom's advice, or someone else with experience who has done this before.
...
From another commenter:
By the way when I changed out the substrate in my 10g tank...I did 100% at once (not too hard in a 10g) and had no ammonia or nitrite spike at all. I think it has to do with how fully loaded the tank is fishwise and how good your filtration is. With better filtration, more of the bacteria will be in the filter than the substrate so the chances of a minicycle drop somewhat. In my case, getting rid of my substrate which was caked with living or dead bga and other algae of various sorts, and hiding a lot of yucky stuff which got removed when the substrate came out, actually reduced the bioload of the tank and possibly offset any minicycle I might have had otherwise.
...
If there's enough beneficial bacteria present within the substrate in a filtered tank for its removal to cause an ammonia spike, it's part of the system - whole-tank nitrification is involved.
And please note that the respondent with the spike and mini-cycle had this occur in a NON-planted tank therefore lacking any assistance in ammonia/ammonium reduction.
As you see, there may or may not be a problem, depending on circumstances such as tank/filtration types - showing how different tanks can respond VERY differently to similar alterations - something to bear in mind, and worthy of mention and concern, as with the shut-down of a filter for any extended period.
The quoted material I used '... One final tip for maintaining helpful bacteria is to not turn the filter off, except for maintenance, especially with a canister filter. ...' had no concerns over shut-down for maintenance, and the concern was not actually with a short duration of shut-down but with that of a lengthier period.
The examples of problems I mentioned having encountered on my travels through various fish-related sites generally involved power outages and unnoticed disconnections ranging from overnight to several days - I had no intention of implying that a brief shutdown of a couple of hours would be likely to produce problems, merely that an extended shutdown formed a legitimate subject of concern and was worthy of mention/consideration, rather than casual dismissal.
If you noticed, what I stated specified an 'extended filter shut down' (which I'd consider, correctly or not, implied more than a few hours, in context with the quote) as a 'potential hazard', and one where I stated I had NO IDEA of the actual percentage of risk:
... There may only be an immediate serious problem apparent in one of a hundred or even a thousand cases of extended filter shut down - I've no idea of the percentage.
I only know it's occurred, and that I, personally, wouldn't risk my fish on the assumption that it wouldn't 'this time'.
There may be more gradual problems introduced which are not immediately noticeable in only one of a hundred or even a thousand cases of extended filter shutdown - there's no way even of establishing accurate attribution in many cases.
However, the probability of this occurring at some point in some tanks is a virtual certainty by any standards reasonably exercised.
Such issues, while not invariably occurring, are nonetheless potential and should be taken into consideration - there is always that aspect of Russian Roulette involved in merely reconnecting and running a filter after such a period of disuse, which cannot be negated by focusing on and dismissing only one of the myriad potential hazards which could result. ...
So if one of my tanks was disconnected or if (heaven forfend) a power outage occurred which resulted in one or more filters being inactive for, say, a period of 8-12 hours, I wouldn't use the media - if this happened to you, you might.
Problems might or might not result in either case - I personally don't feel that either choice is ridiculous, it merely boils down to an individual concept of risk assessment.
But the potential degree of risk is something to be borne in mind.
The OP might not have been considering a longer duration than several hours of filter shutdown, however, the concern voiced regarding potential problems with filters left stagnant for any period of time was worth consideration, and I quoted a pertinent section in response, offered as something to think about.
Discussion is nice, isn't it?
P.S. - respect to anyone who can be bothered to read my lengthy replies, lol.
And just in case of any interest - and, of course, 'if not essential' means precisely that it likely is:
(Please also note from below: ... All surfaces in the aquarium offer a potential home to the community of aerobic bacterial that metabolize ammonia finally to nitrate. The uppermost surfaces of the substrate are a prime location for these populations, as you know. ...
And from excerpt from linked article following this: ... The nitrifying bacteria will become fixed in any location where theres a good supply of oxygen (since the main process of the cycle is aerobic, i.e., in the presence of oxygen). However, the colonies will prosper in places where there isn't too much light, and where the water current doesn't disturb them too much. ...)
http/www.skepticalaquarist.com/docs/nutrient/nitcyc.shtml
... Competition for ammonium. In a well-planted aquarium, ammonium is also quite likely to be scavenged by plants before the nitrifying bacteria even get a chance at it. Aquatic plants use ammonium in preference to nitrate, if they can get it. So in planted tanks like mine, plants and nitrifying bacteria are direct competitors in scavenging any available ammonium. Diana Walstad has recently been teaching us that aquatic plants prefer ammonium (NH4) and its toxic (to animals) counterpart ammonia (NH3) to nitrate. She points out, "Nitrifying bacteria are helpful, if not essential, in tanks without plants. However, in planted tanks they compete with plants for ammonia. The energy nitrifying bacteria gain from oxidising ammonium to nitrate is an equivalent energy loss to plants." (The Ecology of the Planted Aquarium, p 63) The "if not" construction is always ambiguous, but I think she meant "helpful, even essential" rather than "helpful, though not essential."
I had always assumed that aquarium plants were assimilating nitrate, as I "knew" garden plants do. But no. It seems that when both ammonium and nitrate are available, tests show that aquatic plants don't take up appreciable quantities of nitrate until the ammonium is gone. The presence of some ammonium actually inhibits the uptake of bacterially-produced nitrate, not just in plants but in a range of other nitrate-users--— algae and fungi too. Algae it now appears don't assimilate nitrate if the NH4 concentration is higher that about 0.02 mg/L. I don't have a hobbyist test kit that could even register that level of ammonium.
Diana Walstad avers that extensive bio-filtration may slow plant growth. At first I was skeptical, reading this. But soon I recalled a phenomenon I've noticed in a densely-planted 10-gallon tank I use intermittently for quarantine. It's a sturdy, balanced environment, but the bioload represented by fishes varies: it may have a single small Siamese Algae-Eater for a month, lie empty for a week, then receive a dozen tetras. A new load of fishes can trigger a noticable spurt of plant growth. Not unexpectedly. But then plant growth levels off again, I've noticed. Bacteria tend to live at the brink of starvation. When they are presented with new resources, they characteristically increase their population, until they are once again living on the edge, in true Malthusian fashion. Now, in my intermittently-used Q-tank, during the brief period while bacteria are catching up to take advantage of new sources of ammonia, there is a temporary supply of it to fertilize plants, resulting in the spurt of new growth. Soon, however, the system restabilizes in a new dynamic balance, available ammonium drops to zero, and plant growth returns to its previous maintenance level of leaf replacement. So, now I'm convinced that extensive bio-filtration may indeed slow plant growth. Many knowledgeable aquarists would remain more skeptical than I am.
De-nitrification, you remember, is the other "arc" that completes the nitrogen cycle. All surfaces in the aquarium offer a potential home to the community of aerobic bacterial that metabolize ammonia finally to nitrate. The uppermost surfaces of the substrate are a prime location for these populations, as you know. The nitrification process demands a lot of oxygen, more than familiar cellular respiration. Only a few centimeters below the substrate's surface, the diffusion of oxygen can't keep up with demand. As oxygen levels drop, facultative anaerobic bacteria find their niche. "Facultative" in this sense merely means "opportunistic." Many ordinary bacteria are facultative anaerobes; when oxygen is in short supply, these kinds of bacteria are able to switch to a metabolism that doesn't require oxygen. Instead, they use nitrate. The familiar nitrating bacteria provide the nitrate, and their high oxygen demands also tend to exhaust the limited supply. So besides providing the nitrate, a thriving microzone of aerobic nitrifiers provide the low-oxygen conditions too. You can visualize a mutually beneficial exchange between the two types of bacteria across a fluctuating boundary lying not far beneath the surface of the substrate. If there were no other reason not to disturb the substrate in an aquarium, this would be enough for me.
In fact there are two different chemical pathways that provide energy for de-nitrating bacteria. In one, some of them metabolize nitrate to nitrous oxide (N0), harmless, colorless non-reactive "laughing gas." It dissolves in water and finds its way back to the atmosphere, completing the nitrogen cycle. In the other chemical pathway, members of this anaerobic community metabolize some nitrate back to nitrite or ammonia. And if the nitrogen still hasn't been scavenged by the roothairs of plants, eventually still other members of the anaerobe community produce molecules of di-nitrogen (N2). Chemically inert and harmless, dissolved in water and diffused back into the water column, the molecules of nitrogen gas also eventually escape into the atmosphere. You see why this "other arc" of the nitrogen cycle is called "de-nitrification." Diana Walstad says, "for aquarium hobbyists, de-nitrification is a harmless bacterial process that helps prevent nitrate accumulation." (in The Ecology of the Planted Aquarium, 1999, p. 65).
A freshwater plenum. The idea of encouraging this bacterial community and applying to planted freshwater aquaria the reefkeepers' "Jaubert" system, with a low-oxygen area in the lower substrate (the "plenum") where de-nitrification proceeds, seems to have been kicked around first by Australian David Aiken, posting to the Aquatic-Plants Digest in the winter of 1997. His post is worth searching out if you have planted tanks and dare to reduce your sponge filters and bio-wheels, and let the plants handle the ammonia instead. A further less optimistic 1999 post from Roger Miller is also worth reading. To supplement my few thoughts in the filtration pages about a freshwater "plenum" try running "freshwater-plenum" through www.google.com. ...
Article above links to
http/www.aquahobby.com/articles/e_ciclo.php
... The nitrifying bacteria will become fixed in any location where theres a good supply of oxygen (since the main process of the cycle is aerobic, i.e., in the presence of oxygen). However, the colonies will prosper in places where there isn't too much light, and where the water current doesn't disturb them too much. This is the most important part of the Nitrogen Cycle in terms of fishkeeping, but actually it doesn't stop here. As an example, if oxygen runs short in the water, Nitrate can be transformed back into Nitrite or, through a process called denitrifying, it can be transformed by anaerobic bacteria back into nitrogen gas (N2), and the cycle is complete. ...
... Used to be better, always nice to have Andy around 
And I'm glad that my OP managed to spark such a great discussion.
