Jump to content


Photo

BioGeoChemistry, Meiobenthology & Microbial Ecology of the Sandbed.


  • Please log in to reply
40 replies to this topic

#1
bitts

bitts

    Yes. I'm blasting Wagner. While chanting KILL Da NOOB.

  • Members
  • 6,333 posts
  • Joined 30 Dec 2006
  • Denver, boulder, loveland, fort collins.....

BioGeoChemistry, Meiobenthology & Microbial Ecology
of the Sandbed.
A Primer for Sandbed Filtration & Bacterioplanktonic System's



version 1.04
INTRO


For the most part, I assume that by the time you've been doing this long enough to be reading this, you have a pretty good idea of the different schools of thought. Dividing things up into the two major opposing methodologies, e.g., Bare Bottom (Berlin) and Deep Sand Bed (DSB) including the Jaubert methodology. Thus I'm skipping all of the history, and just getting started. I obviously have a bias towards sand beds or I wouldn't put all the time into this, but the bare bottom methodology also has some merit to it & is the reference point, where all other should begin from.

Bare Bottom is mostly about water chemistry. Think of it like this - fish, despite everything you know, everything you've been told, are really just water. They look like they’re a solid. You've eaten them as if they where a solid, but no. It was a lie, they’re just water. Therefore, a bare bottom or Berlin type system, allowing for superb water quality, makes for extremely healthy fish and corals. The downside is that it only allows for a limited biologic filter to develop in the set-up.

This division of dsb vs Berlin really breaks down as an ecologic/ecosystem set-up vs. water chemistry with a minimalistic nitrogen cycle. Again, chemistry has its place and provides us a solid foundation to build from, with out which we would not be able to move forward. It is this understanding of reef chemistry that enables the use a sediment layer within the system.

But, this is about using biology & the necessary understanding to have a system that recreates the natural environment to a greater degree. So with this in mind, it’s important to keep in mind that eventually. We're trying to utilize these natural processes for the removal or more accurately the conversion of Nutrients.

Posted Image

Part I:Chemistry & Cycles

  • Biogeochemistry
  • BioGeoChemistry combines elements of chemistry, biology, geology, & physics to study the chemical cycles of certain elements within an environment; the cycling of said elements interact with each other & thus affect the biologic processes of the ecology. Again Major focus is placed upon the cycles of Carbon, Nitrogen, Phosphorus, Oxygen, Hydrogen & sulfur.

    While there are several cycles that take place with in the aquarium. There will be 4 BioGeoChemical cycles to focus on. Due to their relative size & effect on our tanks.


Posted Image

Nitrogen
Let us begin with the Nitrogen cycle, which is the BioGeoChemical cycle that most of us are aware of & is most commonly referred to in the hobby. This can be achieved through an understanding of the roles mineralization, nitrification, dissimulation, & assimilation take through out this cycle. It is useful to think of nitrification as the movement of nitrogenous compounds to states of greater oxidation - from ammonia (NH3) or ammonium (NH4) to nitrite (NO2) then to nitrate (NO3) & finally to nitrogen gas (N2). until in this form they can leave the water column entering the atmosphere.

Now these transformation are, as are all the others that we will talk about, enabled & provided energy from two possible sources. Being either light or chemical. Those reactions which are of a chemical nature involve a “redox” reaction. This is a chemical reaction in which the chemicals Oxidation state is changed by either the loss or gain of electrons. thus resulting in an increase or decrease in the oxidation state respectively.

First there is mineralization, this will occur in the sand bed or on the rock & is Oxidation transforming the organic compounds to their bass inorganic constituents. Basiclly decomp, allowing for them to be assessable to bacteria & the higher trophic levels. most commonly this will be in the form of ammonium. Then moving to Nitrification, which is a purely chemical reaction, we find the biologic Oxidation of Ammonium & Ammonia, into Nitrite & its subsequent Oxidation into Nitrate. By Bacteria in the genus Nitrosomonas & Nitrobacter respectively. On a side note this can cause a drop in ph as alkalinity is used to or more specifically hydrogen ions are released during the process. Actually limiting the rate of Nitrification. Another limiting factor is the presence of or concentration of dissolved O2. as the Oxygen is depleted the Bacteria are forced to use either nitrite or nitrate for respiration. Causing stratification's with in the sediment & bio films. Then the other factors that we want to focus on due to their limiting effects are temperature & available carbon. provided through the, you guessed it, carbon cycle.

Now before we move on, it is important to understand why these reactions happen in such an order. this is a result of the amount of effort & resulting energy created by the reaction.
Though I have been trying to avoid adding much in the way of equations & such, these may be beneficial for some. So for those whom it is simple unneeded, just skip ahead.
  • Reaction Schematic chemistry Proportional Energy Production
  • Aerobic respiration 1/4 CH2O + 1/2 O2 → 1/4 CO2 + 1/4 H2O 1.00
  • Denitrification 1/4 CH2O + 1/5 NO3 + 1/5 H+ → 1/4 CO2 + 1/10 N2 + 7/20 H2O 0.95
  • Nitrate reduction 1/4 CH2O + 1/8 NO3 +1/4 H+ → 1/4 CO2 + 1/8 NH4 + 1/8 H2O 0.66
  • Fermentation CH2O + 1/2 H2O → 1/2 HCOO- + 1/3 CH3OH + H+ 0.21
  • Sulphate reduction 1/4 CH2O + 1/8 SO42 + 1/8 H+ → 1/4 CO2 +1/8 HS- +1/4 H2O 0.20
  • Methane production 1/4 CH2O → 1/8 CO2 + 1/8 CH4 0.19

Posted Image

As you can see the order of the cycle is determined by the energy produced which will be crucial, in the understanding of the sediments stratification. It is also important to see how these energy levels effect the growth rate of the corresponding bacteria. With each level down from the heterotrophic bacteria having a greater demand for the energy to be directed away from reproduction. Where the bacteria on the upper end of this curve (heterotrophic) could, given optimum conditions reach the maximum population levels in the tank in 20 minutes. Those on the lower end, most notably Nitrosomonas & Nitrobacter, will realistically have a doubling rate between 15-20 hours.

Carbon
Entering the water column in one of two forms (gas or solid). The carbon cycle is crucial in regulating the consumption & utilization of N & P though out the system. Combining with both during photosynthesis allowing for the growth of primary producers. Such as phytoplankton & other forms of algae, thus establishing the basis of the ecology.

Phosphorus
Unlike most of the other major cycles, Phosphorus does not cycle through the atmosphere. Forming a gas only in specialized situations. Within the water column the rate of flux can be quite extreme, while in the sediment & rock this will in fact be the slowest of all the cycles. Actually occurring on a geologic scale. Our interest will come from the its effect on microbial growth, more specifically algae growth & the following bacterial consumption. Mostly though in relation to its cause of algae blooms from an over abundance. Resulting in sudden drops in the level of O2. While a lack may restrict microbial growth resulting in an unnecessary accumulation of nitrogen & carbon in the water column. This can result in what is referred to as phosphate block, characterized by a build up of nitrite due to a lack of P for the Nitrobacter. easily remedied by feeding or introducing any other source of P.

Sulfur
These are some of the things to contemplate about it & we will go into greater depth later. Under what conditions do sulfides form in our tanks? What does sulfide formation mean for us/what are the dangers? How can sulfide formation be dealt with/prevented? relationship between redox & sulfur in the sediment bed. What is microbial sulfate reduction (MSR) & how does it relate to anaerobic oxidation of methane. How redox at x depth may not reflect the amount of O2 present. Adding or preventing the development of sulfides. The change of iron, a.k.a., ferric iron to ferrous iron & how this relates to sediment color. How this change in color relates to the redox potential discontinuity layer. How bioturbation affects the rate sulfides are released into the water column. How the pore water can be oxic or sulfidic regardless of the coloration of the surrounding sediment.

Redox
The redox reaction or reduction-oxidation equations involve the transfer of electrons. As opposed to most other reactions that will be encountered being acid based. The most notable deference between this two types of equations for us will be the speed of the reaction. The redox equations can be divided between those which involve organic carbon in the form of fat & carbohydrates. Or those which are based on proteins.
Fats + Carbohydrates + O2 —> H2O + CO2
Proteins + O2 —> H2O + CO2 + NH3

Calvin cycle
Posted Image



Part II: The Water Column

  • Microbial ecology
  • In simplest terms, Microbial ecology is the study of interactions & relationships between the microorganisms within a specific Environment, to both each other & said Environment.
Now from there lets start with the “dissolved organic”. Because if we’re going to talk about the water, we will need to know whats in the water. Be it Matter, Compounds, Carbon, Colored Dissolved Organic Matter (chromophoric dissolved organic matter caused by the detritus breaking down), dissolved inorganic carbon, dissolved organic Phosphorus, dissolved inorganic Phosphorus, Detritus & Particulate Organic Matter, what ever. There most commonly refered to by their letters. Basically allowing for a more specific way of describing which type of nutrient, & over time the short hand will become more familiar. Of course, in our tanks when we say nutrients we’re mostly referring to Carbon, Phosphorus, Nitrogen, & sulfur. Their build up is referred to as Eutrophication, possibly leading to large scale algae outbreaks & or depleted levels of available O2 from the decomposition of the organics. This begs the question of why is it called Eutrophication. This mostly refers back to the ecosystem’s “trophic” levels, used to describe the movement of food or really energy & matter through the multiple layers of the ecosystem, from the primary producers, up through to the apex consumers. It’s the build up of these nutrients within the lowest trophic layer that we’re concerned with.

  • Microbial Loop.
  • The Microbial loop or as it is more often referred to now, the microbial food web. Is the link between the classical food web comprised of high order trophic levels & 90-95% of the DOC. It mainly follows the Organic carbon from the state of dissolved particle matter or particulate detritus to increasingly higher tropic levels. Until it can finally be brought back into the classical web. When it is Consumed by zooplankton. The most common order in this path is picoplanton, which is then consumed by either nanoplankton or microplankton. Which is intern consumed by the mesoplankton, finally reaching a point in which it can be utilized by the zooplankton or filter feeders.

Posted Image


Energy Creation & Utilization.
But Since we’re now looking at the movement of energy through the system, we should look at how the energy is formed by either chemosynthesis or photosynthesis. These would be the formation or creation of energy through chemical or photo-based processes, respectively. This then brings us to Autotroph & Heterotroph. Yeah more buzz words. Alright then autotrophic is the use of photosynthesis or non organic compounds for nutrition, while heterotrophic is the use of chemosynthesis or the metabolization of organic compounds.

So the way that we’re, well, I’m going to look at this. Is from the standpoint of the water column. From the top, down through the sediment layer. After all, it’s supposed to be an inclusive ecology that we’re creating or replicating. now since we’re talking about carbon anyway. lets talk carbon cycle or to put it another way, what the hell do you mean, you want me to put vodka in the tank! Somewhere along the way you’ve probably heard of some quack getting his fish drunk. or at least what seemed like that could be the only thing he was doing wasting perfectly good vodka on his fish tank. So the first thing we need to get straight is that vodka is for fish & scotch is for us. Ok you can drink some of the vodka but everyone will think your stupid instead of drunk. Anyway. what the hell is this carbon cycle & how does it relate to my wadka.

Going back to our BioGeoChemistry everything is about cycles & if there’s not enough of some thing cycling through the system. Then things become limited by its lack. while there always seems to be an over abundance of Nitrogen, Carbon is capable of a much greater flux. since we’re lookin from the top down though we should start with Carbon fixation through the transformation of CO2 from a gaseous form in to a solid by the phytoplankton, AKA organic carbon. they do this in the same way as any of the other autotrophs that we’re use to thinking about, such as trees & flowers would, Through assimilation. By using photosynthesis to create the energy that they need to live or basically creating it them selves. now this phytoplankton makes up only a part of the primary producers, while the rest is composed mainly by bacteria, including Cyano, & then viruses. which as scary as it may be are actually the most numerous thing by volume in seawater.

This other component of the phytoplankton the heterotrophic bacterias are responsible for most of the assimilation of DOM. believe it or not, this is actually due to their size. Most measuring in at a micron or less. Now by being the smallest consumer, ok they are larger than the viruses but we’re ignoring those, they are able to have a greater surface to volume ratio enabling them to out compete the others. much like in the competition for the best skimmer. Things seems to be coming down to who can make the smallest bubble. Because its all about the surface area being maximised within a finite area. This organic carbon which may have or not been created by the phyto & now been absorbed by the bacteria. will be respired by the bacteria as CO2 gas which can leave the water column. the important point here though is to note that the source of the organic carbon is irrelevant, it will still flow through the cycle just the same. now in some situations where the phyto population is low. The bacteria concentration becomes a limiting factor on itself due to its own rate of consumption. Through a localized reduction in the available DOM & specifically DOC.

In normal environments this is difficult to achieve due to the rate of bacterial growth normally being comparable to that of the phyto. But in the closed systems we maintain the rates can be affected by the inherent limitations of the system. Such as differences in the rate one is removed be protein skimming. this can be compensated for by the controlled dosing of organic carbon & cultured Phyto. unfortunately there is no way to directly monitor the size of these populations. suffice it to say that the goal should be to maintain as large a population of both as possible with out it turning the water green or consuming all of the dissolved Oxygen.

Posted Image

Detritus & Dissolved Particulates
Detritus can be defined as any dissolved particulate matter, regardless of the trophic layer it originated from. Normally this is dead planktonic matter which has combined with mucous secretions or other binders (sugars, amino’s...) to congeal into larger forms, called flocculent matter or more commonly snow. This then allows it to settle out of the water column. Resulting in an increase in the diversity & abundance of the fauna present. Through the improved availability of organic matter. How ever this benefit will only be realized so long as the accumulation & decomposition of the detritus does not cause the level of dissolved oxygen to be negatively effected. Where detritus is composed from mostly planktonic source’s DOM is comprised mainly of bacterial waste, with the remainder being from decaying plants & animals. The prevalence of DOM can in fact be 20-30 times that of POM. With concentrations in the pore water reaching an order of magnitude greater than that of the water column.

Part III:The Sediment. Its Biogeochemistry & Meiobenthology.

Posted Image


  • Meiobenthology
  • The study of benthic invertebrates able to pass through an area from 40 um up to about a mm in size. While exact divisions in size between macro, meio, & micro depend on the text, this should give an idea. As depth increases, pressure will rise at about one atmosphere for every ten meters. While the amount of light penetration is inversely proportional. Forcing adaptation in structure & energy sources.

The benthic habitat, despite the automatic assumption that this environment would be dictated by the sedimentary geology, is in fact based on the composition of the flocculent organic matter. With consideration given to the available organic material, pore water, void space, bioirrigation & others as primary factors. Oceanic sediment beds are for the hole an anoxic environment, with only a Minuit fraction being characterised as zones of oxic stratification. This zone between the sediment water boundary interface & the redox potential discontinuity layer, Comprising the Biogenic mixing depth (BMD), is in fact that which is attempting to be recreated. By the addition of a deep sand bed within a system. This area can not simply be characterised by its grain size, both size or shape, or any of the other standard means which they are discussed in the community. But instead by such aspects as the gelatinous ooze which the pore water becomes; the amount of biological reworking & Bioirrigation of the sediment; the percentage & composition of organic material within the bed, both dissolved & structural.

Limitations of the sand bed are: toxins; amount of dissolved oxygen; specific gravity;
concentration of nitrogen generated by the system itself; rate of nitrogen generated by the livestock; rate of nitrogen conversion by the bacteria; size of bacteria population present; size or amount of media provided to the bacteria (surface area in sand & rock); flow rate through the sand bed, rock, media; amount of bacterial film present; amount of nutrients introduced to the tank as food (uneaten); environmental crap like temp, gravity, o2... These are but some of the factors.

The argument against sand tends to be one of laziness & misunderstanding. dsb's are the most efficient biologic filter available. However, their limitations are normally quickly exceeded by the average hobbyist, resulting in the classics. It’s a nutrient sink or they’re ticking time bombs, man. In a natural sediment bed it takes around 3 years for the bioturbation to completely turn over the top 10 cm. if you keep this in mind, you can see why most without an understanding of their function could have them become problematic. Now, this brings us to the sand bed’s, well the tank’s, carrying capacity. Okay, so there are some really nifty differential equations and some calculus that can be done to figure this out exactly, but, and this is a dusey of a but, they involve the previously mentioned variables plus a few others that you can’t actually know realistically. In the field they would be found through the use of oxygen microsensors which will hopefully become available to the hobby in the next decade or two. So, really, it’s all just a guessing game. Suffice it to say that the things that matter are the size of the bed, well depth and surface area within it, combined with the rate of water flow through the bed & the bacterial colony that has developed.

Now, also keep in mind that getting the water to flow through the sand by itself is never going to happen, diffusive transport alone just doesn’t cut it here. so there needs to either be a pump forcing water through it, simulating the effect of the tidal pressures from wave action on the sediment layer, which is why under gravel filters work, or, and this is really the key to modern sand beds, the presence of life within the sand, churning the grains and gradually turning the bed over for you through bioturbation. This allows the bed to function without constant maintenance being done by you. So the only real things you have control over are the size of your filter and protecting the bugs that make it go...

Now there is a finite limit to the bioload of any system. This will be met when the use of the available media has been met by the bacteria, combined with the flow through the media having been maximized. All that really matters is that the rate of nitrogen being produced is equal or less than that which is capable of being processed. other things to keep in mind are the total livestock biomass vs the biomass of the individual livestock. Then as the biomass is redistributed from a single animal to several, the amount of waste produced will increase. Assuming that each piece of livestock needs an equal percentage of their biomass as food, but of that this will have an amount which is not capable of being used. As the number of animals increase so does the rate of waste compared to that of a single animal. hopefully that isn't to confusing. Basically the effectiveness of consumption decreases with each addition of animals. Now from here the things to consider in this would be. yep, you guessed it, more buzz word bingo.

Permeability, Porosity, pore water flow, Bioturbation, Grain Size, & the effects Hydrodynamics.
Permeability refers to the speed with which water may flow through the sediment, supplying O2, dissolved, & particulate nutrients throughout. Thus it largely controls the conditions for the fauna. While Porosity is the total pore volume of a sediment, this void ratio being affected by the sorting and mixing of grains. Combins with their shapes to determine the density of the sediment layers & its compaction. The shape and texture of the grain will also affect the velocity of water flow. Therefore, pore water flow is not simply dependent on hydrodynamics forcing the water through, but also upon other variables, such as the development of bacterial films upon the sediment itself. Which can in fact have its own vertical stratification of O2 within itself, even allowing for the effective use of shallow sand beds. These are then affected by bioturbation by the benthic fauna rearranging how the sediment fits together. This biotubation can extend up to 20cm below the sediment’s surface, in some truly active areas. but will normally result in the anoxic zones forming around 10-15cm below the surface. keep in mind that this bioturbation can increase the transport of solutes, due to microbial mineralization. Up to three times, compared to molecular diffusion, turning over the pore water in roughly one to two years. While both bioturbation and bioirrigation can result in the release of phosphates and ammonium, resulting in increased eutrophication.

Vertical Stratification of the Sediment.
Posted Image

Light penetration of the bed can reach up to 2cm, referred to as the microphytobenthos, allowing for autotrophic activity through out this area. Mostly by cyano bacteria, but also by many forms of phyto. This is an important consideration in understanding the emergence of cyano mats. Despite its apparent onset being incredibly sudden, the slow incremental development has occurred below the surface. thus great importance should be given to the amount of algae between the sediment & glass. Also this upper most portion of the bed will be enriched with a majority of the free amino acids present in the sediment. Combining with the sediments organic build up & content from detritus, will thus promote bacteria growth within the substrate. resulting in its population being a degree of magnitude greater than that in the water column. This bacterial load of the bed will usually account for 4% of the available organic carbon. It is this bacterial film that is thus feed upon by the detritivores. Bacterial growth will intensify at the interfaces between the oxygen level stratification. Particularly between the oxic/anoxic interface of decomposing particulates. normally there is an inversely proportional relationship between the sediment grain size & the level of organic matter. For example the fine silty mud of a seagrass bed can be 5 times more biologically active than a near by surf zone. While at the same time being comprised of nearlly 40% from organic matter. Other considerations to be made in regards to the bacterial population would be, selective bacterivory by the meiofauna. Resulting in zonation & possible elimination of the bacterial strain. Due to the combination of predation & competition from other bacterial strains. Resulting in a lose of biodiversity.

Through the sediments vertical stratification, the ph can have fluctuations between readings of 6 & 9. Due to assimilation by microalgae near the surface & the presence hydrogen sulfides at lower levels of dissolved oxygen. This fluctuation is how ph & O2 levels allow for a dsb to help maintain calc levels. But this will be dependent primarily on the beds depth being great enough combined with the grain size allowing for the rpd to develop. But also in the lower portions of the void system. Where pore water becomes a gelatinous ooze of bacterial film the oxic state of the pore water & that of which the sediment is coated in can be greatly divergent. Allowing for great dichotomy between the resulting color of said sediment & the pore waters actual oxic state. Again, yellowing of the sediment reflects the oxidation of Iron & not the rpd.

Sulfur & the sediment.
Redox potential discontinuity layer (rpd): layer between positive & negative redox values, Eh.
color will only correspond to the rpd when there is a dramatic shift in color, from light to dark gray/black. normally the color shift should be gradual from that of light white sand to varying shades of yellow, then moving to gray & black. it is also important to consider the measurement of redox values, while this approach is quite prevalent, it may not be the most accurate representation of dissolved oxygen within the bed. These measurements can in fact be quite deceptive due to the limitations & effects of considerable number of other variables. The creation of Hydrogen Sulfide comes from sulphate reduction in the anoxic zones of the sediment. Also allowing for the mineralization of heavy metals.

As the bed develops there may form anoxic zones noticable by there a destint black or gray coloring. Most importantly don't disturb these do to the possible release of hydrogen-sulfide gas. Over time, the black spots should remove themselves as the bacteria & other microbes fill this area, extending the anaerobic areas deeper, helping to displace the aoxic zones. The sand bed should for the most part take care of itself, as to stirring & turn over, through the microbial population in the bed itself. the black spots indicate that this population has not yet developed adequately to process the nutrients at the rate they are being produced by the tank & then permeating the sand bed, causing a build up directly above these blackened areas, essentially suffocating this portion of the bed. the most important thing to remember with a sand bed is that you are trying to recreate the natural environment of microbial ecology in oceanic sediment beds up through the water column to the surface. The four greatest resources in achieving this are: reducing the nutrient load entering the bed through increasing the water column’s phytoplankton & bacteria load, while reducing their input from things such as unnecessary food; and strong protein skimming to remove dom/doc & decaying microbial waste ( dead bacteria) from the water column, combined with providing a healthy starting colony of appropriate life in the sand through the addition of a small amount of live rock to the bed’s surface. this can later be removed or minimized to prevent surface areas which are not actively turned by the "bugs".
  • this list of factors has been used above for the limitations of the sand bed, but I will repeat it here for simplicity & easier reference. again keep in mind that these are but some of the factors.
  • concentration nitrogen generated by the system its self.
  • rate of nitrogen by the livestock.
  • rate of nitrogen conversion by the bacteria.
  • size of bacteria population present.
  • size or amount of media provided to the bacteria. (surface area in sand & rock)
  • flow rate through the sand bed, rock, media.
  • amount of bacterial film present.
  • environmental crap like temp, gravity, o2...
  • amount introduced to the tank as food. (uneaten)

Remember the amount of o2 will determine the amount of nitrogen to be moved through the mineralization/denitrification processes since its really just the oxidation of nitrogen by the bacteria population. Of course it also has to be moved though the different zones of o2 concentration as well. Did you notice that the amount of Oxygen goes down with each step.

Having the tank dependent on water changes (WC) would indicate that the tank’s ecology is out of balance. Doing large WC to manipulate the chemistry has always seemed a little strange to me, when compared to the idea of replenishing the balance through dosing. As in allowing the levels of calc & alk to drop, then reestablishing them through a WC. Or having any one of the nutrients not completely cycling, resulting in a build up at any stage within said cycle. Most commonly in the form of trates. However, the argument that it’s the only way to combat the build up of certain elements & nutrients (besides nitrogen) appears to have some validity to it, Since it has been found that skimming only removes about a third of the organic waste. still from my own experience, through heavy skimming & strong biology. DOM/DOC can be controlled without WC. also coral warfare is best controlled through skimming. At one point I decided to attempt going 6 months without a WC, maintaining healthy levels in all aspects, despite a medium to heavy bioload. As well as for not feeding the fish for a pirod of 9-10 months allowing them to feed only on the fauna generated by the tank. One thing I think we've skipped is what is safe to add, as far as larger life. skip anything that feeds off the meio, micro, or in, type faunas. they can cause the bed to collapse due to eliminating the needed biodiversity & it will eventually starve. This would include sand sifting cucumbers & stars, hermits, and so on. Snails are a great help though, with certh & nass being excellent examples. While the removal of detritus is essential to proper health for the tank, it is best to not stir the bed itself - just swirl the water above the bed before the water change. The reason for this is due to the amount of time required to reestablish the bacterial biomass within the bed, after any form of disturbance. This population can infact require up to, two or three months to form. Try to instead, increase the flow over the bed’s surface to prevent things from settling out. this will also help to reduce the boundary layer allowing for better nutrient transfer. by not stirring or disturbing the bed, it becomes easier to judge how well the bed is adding in calcification, enabled by the decreased ph in the lower parts of the bed. If the bed is functioning correctly, the sediment will lose about an inch to half inch per year & will need this loss to be replaced slowly in small sections. When establishing the bed live rock can be used to seed the desired fauna. The live rock won’t have to stay in the, well, on, the sand bed for long. It just needs to be there to introduce the "seed" fauna for the bed. If it’s not already active. Just look to see if there are bugs, such as copepods, worms, amphipods & so on.

Then once the bed has the needed life just give it time. At this point, the vodka or carbon methodology is actually beneficial/complementary to the dsb, by helping in completing the ecosystem that is started by having the dsb. within the water column there are phyto & bacteria which utilize it to help consume other nutrients. Then through this, most of the carbon is released back out as co2, while the nutrients are bound as waste (dom), enabling them to be removed by the skimmer, and helping to prevent them from entering or reentering the bed. the main thing to remember is that the sand bed methodology differs from bare bottom in that the entire water column & sand bed is used as the biologic filter. nutrients flow down through the water column’s phyto & bacteria loads, into & through the sediment layer being processed by the fauna. This then move back up though these layers to be released as gases or consumed by the enclosed ecosystem.

System Design
As to system design. My first step is to find the “everything I want” list & start weeding things out. The most important aspects here are territory & interaction. this is not just fish, this is everything - coral, inverts, cleanup crew, fish, everything. Once the list is reduced to those which will be good together & fits in the available space together. Not the “I want it & I don't care if they get along” list (again this would include corals). you can move on to the filtration. Now here's going to be the part that everybody will find funky - again doing water changes means that you scerwed up. water should only come in & out of the tank for the purposes of water chemistry, a.k.a., to get that really nice salt you picked up into the tank. If you’re doing these to fix things like nitrates then you’re pushing beyond the system’s carrying capacity. Now there are other things to think about as well, like what’s in the water you’re taking out of the tank, and how much of the biofilter was in that water you just pulled. if 30% of the system’s filter is in the water & you do a 20, 30, 50% water change due to trates, then how will that affect the tank over the next couple of days? will the bacteria & phyto that was making the tank go be replaced? Sure, possibly even quickly, but what effect will it have? will it add stress to the tank? now, not all tanks will have the water acting as the majority of the biofilter. but all tanks include the water in the biofilter. this is why WC should not be considered part of the filtration. So now we're thinking filtration, what can we do to improve it? Maximize the level of beneficial bacteria & phyto in the system. The next thing is to pick a skimmer. Again, I'm out there a little with some of my thoughts & very biased. But, no matter what, run a skimmer. Sure there's plenty of ways to set up a tank, but no matter what skimmers are necessary. Can the tank be set up with out it? Sure. That’s just not what I think works best. But besides waste, the skimmer will pull phyto & bacteria, so the tank will need to be able to supply this at the same rate as it’s pulled, or, if not. Then, it needs to be added back in. Where the bacteria should be able to easily match this rate of exchange, phyto may be more difficult. Leading many to culture it themselves . One other benefit of the skimmer is in additional levels of O2 helping to maintain a constant state of Oxygen saturation. If this level of O2 drops its effect can be seen as a drop in the ph level. So long as the calc & alk levels are constant. But remember that solubility is better in cooler water. That’s the actual problem with tanks overheating in the summer, your fish suffocate. By volume the ecosystem you have setup in that little box has nothing to do with fish or corals. They just happen to live in it & poop all over the place. But by volume your ecosystem is plankton, bacteria, & bugs. If there populations are stable & healthy than the bioload is correct.

CONCLUSION
Taking your time & doing the research is smart. as to feeding. not quite more than they will eat. But, but learn to control the level of nutrients produced by the fish through feeding them. most tanks are underfeed to prevent build ups in nitrates & phosphates, but in some ways this is what feeds the tank. if you've learned to keep the trates at 0. than the next step is to learn to bring them up & down by feeding the fish, with out losing control of them or relying on water
Changes. so somewhere between 0 & 5. your standard test kit wont be calibrated for this so you have to use the tank & its livestock to do this. things like lps polyp extension, red slime algae between the sand & glass, algae growth, how quickly the glass forms a film you need to scrape off, consumption of alk by denitrification, growth rate of corals, fish, inverts, & so forth. maybe feed that extra pellet you've always felt guilty about not letting them have, or even adding a meal. possibly adding more phyto when you dose. just go back to basics, after all its all just one big cycle. the better you become at manipulating & understanding the interactions. the greater your tank will respond. just remember that first cycle the tank went through only finishes if the tank crashes. you can’t control it, just interact with it. Like any other living thing.





Disclaimer:
I have no degree in marine bio or for that matter, have ever even taken a class in it. I have simply read some on the subject & kept a tank. this is simply my ramblings on the subject matter & should not be taken as more. I shall edit this over time adding to it as I have time & feel the whim. this is of course colored by my bias in all aspects. There are bound to be topics overlooked & possibly even gross inaccuracies caused by them. Remember these are simply the ravings of a maniacal noob.

Edited by bitts, 26 April 2011 - 09:09 AM.


#2
spanko

spanko

    Somewhere there is a place where we belong.

  • Members
  • 8,270 posts
  • Joined 01 Feb 2007
  • Michigan
Nicely done.
It might be a good idea to list your references at the end.

#3
keydiver

keydiver

    dedicated macro man

  • Members
  • 2,535 posts
  • Joined 14 Aug 2010
  • miami, FL
wow, great job jp! It's going to take me a awhile to read this whole thread, but im going to bookmark it.

Thanks!
Posted Image
 
57g Rimless Reef
29 biocube (Decommissioned- Moved into 57g rimless)
20 gal macro tank (Decommissioned- Absorbed by 40g rimless lagoon tank)
40g rimless high tech planted FW tank (Now the 40g lagoon tank)
Keydivers Exo Terra PDF vivarium

#4
Deleted User 6

Deleted User 6

    Nano Reefer

  • Members
  • 30,988 posts
  • Joined 19 Mar 2008
tl;dr




































:P

hutthutt!

#5
jeremai

jeremai

    an island of reality in an ocean of diarrhea

  • Premium Members
  • 27,121 posts
  • Joined 08 Nov 2005
  • Las Vegas
The science was solid, but the application was... interesting.

Having the tank dependent on water changes (WC) would indicate that the tank’s ecology is out of balance. Doing large WC to manipulate the chemistry has always seemed a little strange to me, when compared to the idea of replenishing the balance through dosing

To my knowledge, no one with any experience would ever advocate water changes as a way of changing the water chemistry. In contrast, most people advocate having the water as chemically similar to what's in the tank as possible - same pH, temp, salinity, etc. Water changes are meant to remove dissolved organic compounds from the water before they can be processed into harmful substances, with chemical replenishment being a bonus. Which leads me to...

Now there are other things to think about as well, like what’s in the water you’re taking out of the tank, and how much of the biofilter was in that water you just pulled. if 30% of the system’s filter is in the water & you do a 20, 30, 50% water change due to trates, then how will that affect the tank over the next couple of days? will the bacteria & phyto that was making the tank go be replaced? Sure, possibly even quickly, but what effect will it have? will it add stress to the tank? now, not all tanks will have the water acting as the majority of the biofilter. but all tanks include the water in the biofilter. this is why WC should not be considered part of the filtration.

Do you have a specific reference for the part in bold? I would have guessed it at much lower, less than 5% even. Whatever bacteria or phytoplankton exist in the water column is negligible compared to the biofiltration capacity of a system's live rock. Nitrifying bacteria are benthic by nature, not pelagic.

I like this write-up, but I think there may be a bit of information overload happening here. We need an abridged version. Sandbeds for Dummies. ;)

pretty sure jer was referring to the length

 
reef information and articles
photography, writing, etc.
 

#6
bitts

bitts

    Yes. I'm blasting Wagner. While chanting KILL Da NOOB.

  • Members
  • 6,333 posts
  • Joined 30 Dec 2006
  • Denver, boulder, loveland, fort collins.....
Luv ya 2 cankle monster. :lol:

#7
bitts

bitts

    Yes. I'm blasting Wagner. While chanting KILL Da NOOB.

  • Members
  • 6,333 posts
  • Joined 30 Dec 2006
  • Denver, boulder, loveland, fort collins.....
Hey Jer.
Thanks for catching that. There are I'm sure, just like this, several places were what I wrote does not reflect what was passing through my head. Thus not something I will catch my self. I meant for it to be an example based on some of the more extreme bare bottom tanks I have seen recently. Such as those by Jake Adams, Leonardo & others using very little to no rock in the system.
The number is my best guess at to the portion of the bioload which would be carried by the water column, in such cases. assuming that the coral skeleton in these tanks is acting as a medium for a bacterial population to develop. Which needs to be made clearer. will edit it to reflect this. Again I would expect the bacteria to repopulate within a matter of hours under good conditions. Assuming that all parameters for a proper wc are met. But If those are not met than it could be point of significant stress.

As to the population of bacteria with in the sand vs that which is present in the water column. Well lets just put it as, with a fine grain. The usable surface area could be in the sq kilometers per cubic meter of sediment. But I have not yet seen a way to measure the amount in the water column its self. So again any number is an educated guess.

But this is a good question & I'll see if I have some info on it that I've missed.

Edited by bitts, 25 January 2011 - 07:26 PM.


#8
jeremai

jeremai

    an island of reality in an ocean of diarrhea

  • Premium Members
  • 27,121 posts
  • Joined 08 Nov 2005
  • Las Vegas
Oh, I see. I agree that a barebottom tank will have less inherent filtration ability than a tank with a DSB, but that is usually made up for with oversized skimmers or refugiums (which also provide substrate for bacterial populations, in addition to their intended filtration abilities), and frequent large water changes. Again, I believe that water changes should absolutely be considered part of the filtration regime.

What are your thoughts on shallow sand beds? Most tanks on this site are too small to employ a satisfactory DSB, and many people (myself included) dislike the look of barebottom tanks.

pretty sure jer was referring to the length

 
reef information and articles
photography, writing, etc.
 

#9
gutterguy

gutterguy

    21 & OVER PLEASE

  • Members
  • 1,270 posts
  • Joined 10 Feb 2010
  • Somewhere between Cleveland and Akron

Sandbeds for Dummies. ;)

+1
The smokin reefer... just add pork!
Posted Image

Or you could have kept your mouth shut and not dicked up his thread.


#10
bitts

bitts

    Yes. I'm blasting Wagner. While chanting KILL Da NOOB.

  • Members
  • 6,333 posts
  • Joined 30 Dec 2006
  • Denver, boulder, loveland, fort collins.....
One of the most surprising aspect to all of this is that the grains them selves become a microcosm of the sediment layer. Generating an oxic stratification in the Biofilm surrounding each grain. thus each being capable of denitrification in their own right. Although on a very limited scale when compared to that reached in the anoxic zones of a true dsb. as far as how that effects us. I would see it as suggesting guidelines in grain size & proper maintenance of the bed. But that there would be a definite benefit to running even a shallow bed.

Edited by bitts, 25 January 2011 - 09:55 PM.


#11
bitts

bitts

    Yes. I'm blasting Wagner. While chanting KILL Da NOOB.

  • Members
  • 6,333 posts
  • Joined 30 Dec 2006
  • Denver, boulder, loveland, fort collins.....
Jer. One thing I forgot to mention before, as to the maintenance of the shallow sandbed. Is the doubling rate of the bacterial population should be taken into consideration, when planning to clean the sediment. If you figure that the doubling rate of the two needed bacteria for denitrification is 20 hours or so. You should be able to find the needed time for repopulating before, again disturbing the bed. Also even in a shallow bed, a useful population of both can begin to form. Since both prefer an oxygen saturation of around 80% with temp in the range of 78-80 degree's. Only the top 2-3 mm of the bed will be at a fully oxic state. Now it will of course depend on the grain size & the amount of organic sedimentation present. But this should be achievable within a 2-3 cm layer.

#12
bitts

bitts

    Yes. I'm blasting Wagner. While chanting KILL Da NOOB.

  • Members
  • 6,333 posts
  • Joined 30 Dec 2006
  • Denver, boulder, loveland, fort collins.....
Sandbeds for dummy's part 1

Why do we care about the BioGeoChemistry of N, P, & C & why dose carbon.
There will all ways be some carbon added to the system form things like feeding & gas exchange. So long as there is sufficient phyto present to utilize it. It will be turned into organic carbon to feed the cycle. There will of course be one regardless & the 3 will balance them selves out, until one is completely consumed. resulting in the build up of the others if they are not in the correct proportions. So carbon dosing is not needed, but allows for a greater amount of nutrients to be pushed through the system. Thus enabling it to more closely match the natural environment. The normal system is lucky to be able to handle 10% of the feeding you would find in nature. the reason for this is that when your are dosing the carbon you are matching the amount of carbon to the nitrate & phosphate present. While when not dosing you are matching the phosphates & nitrogen from feeding to the amount of carbon that is present.

the reason its easier to reach ultra low levels by dosing carbon is that there is no way to test for carbon but you can for the others. Then increasing or decreasing the amount carbon to match them.

I guess that my point if I have one is. It doesn't really matter if you dose carbon so long as you understand how the nutrients work together with the bacteria & each other. Enabling you to tell whats going on from there. you should still be able to reach low levels of all nutrients. while also realizing that a little of this or that being present doesn't matter all that much so long as they don't steadily increase.

Edited by bitts, 08 February 2011 - 07:44 PM.


#13
bitts

bitts

    Yes. I'm blasting Wagner. While chanting KILL Da NOOB.

  • Members
  • 6,333 posts
  • Joined 30 Dec 2006
  • Denver, boulder, loveland, fort collins.....

"The highest overall death rates were seen in aquaria with shallow coarse sediments over a plenum, and the lowest death rates occurred in aquaria with a sandbed composed of deep coarse sediments" from your second link in "sand bed primer links directory"

That seems to contradict Ron Shimek's recommendations of finer grain or "mud"... Still reading....


Edit:

"For a sand bed to contain the most animals of the most species, it really should have a distribution where sediment sizes span from about 2 mm to 0.063 mm (2 mm to 1/16th mm), and where most of the particles are in the 0.250 mm to 0.125 mm range. This will make a sediment that is acceptable, if not perfect, for most animals. " Ron Shimek How Sandbeds REALLY Work

I think this makes my plan sound like it might work out... Mixing substrates should bring the total to about this recommended average.

2nd Edit:

And another author you linked says DSB's must consist entirely of grains of .025-.2mm. Can't anyone just agree? Hahah



LOL & the Best part is they all have PHd's right! Gotta love it.


One of the most frustrating things for many Trying to learn this from an entry level is that the feild is still realistically young. Thus even the experts can disagree at times.

#14
Trick

Trick

    Nano Reefer

  • Members
  • 1,520 posts
  • Joined 26 Mar 2010
So, if everything is better left undisturbed how are you supposed to transfer tanks without completely Effing everything up? what will happen when you transfer tanks? Also, how large must a deep sand bed be? I plan on having a remote DSB for my next tank and it's going to be tiny compared to the size of the tank, while the tank itself will have a shallow sand bed.

#15
Squared

Squared

    nano reefer

  • Members
  • 12,100 posts
  • Joined 13 Feb 2010
  • SoCal

Squared I don't want to jack the thread so Ask here & I'll answer any Questions you have on sand.
http://www.nano-reef...howtopic=260742


how deep does a DSB need to be to be considered a DSB? also what kind of sand should be used in a DSB?

29g & NC12

 

 

 


#16
TheMac86

TheMac86

    UNLV/CSN BIOLOGY

  • Members
  • 350 posts
  • Joined 28 Dec 2009
  • Las Vegas, Nevada
Very nice indeed.
Aqua Illumination Club
BC29 SPS dominated

SPS- Stability Promotes Success.....

#17
bitts

bitts

    Yes. I'm blasting Wagner. While chanting KILL Da NOOB.

  • Members
  • 6,333 posts
  • Joined 30 Dec 2006
  • Denver, boulder, loveland, fort collins.....

So, if everything is better left undisturbed how are you supposed to transfer tanks without completely Effing everything up? what will happen when you transfer tanks? Also, how large must a deep sand bed be? I plan on having a remote DSB for my next tank and it's going to be tiny compared to the size of the tank, while the tank itself will have a shallow sand bed.


That is the one problem that really has no solution. Possible solutions to this are moving the tank with the sand in it with a little water over it to prevent any air from entering it. although this is only practical in very small tanks & even then not recommended do to the stress it will place on the silicone. eventually resulting in the tank failing. I will admit to having done this with some success with 10's. But when I last did it it nuked the lower have of the bed. creating a 3inch anoxic layer which took months to sort its self out. At this point the only time I would recommend it would be with a remote DSB that can be run separately for a time after the move. Allowing for the nutrients that have been released to go through some form of filtration. this is the other aspect that can present its self, the release of the nutrients in all their many forms back into the water column. Even if the bed is stable during the move the pore water will be disturbed resulting in a massive release from the bed.

Really the best way to handle it is either new sand, or to recycle the current sand. Which is pretty easy to do. First the current sand will be layered into several Levels of O2. which means that the surface layers & there fauna, will be fine if you scoop them out. the benefit of this is that the majority of the fauna will be in this layer about 2 cm deep. then the rest can be removed, rinsed, & again used for the lower layers. most find this to be an incredible pain in the @%$, choosing to skip it for new sand. Then add the surface layer to the bed which will reseed the lower layers. even if there are anoxic zones that form its not the end of the world. one they still process nutrients. two the solution to there presence is the maximize flow across the bed, helping to force water through the sediment due to water pressure. while utilizing a strong cleanup crew focused on snails which aid in the bioturbation (certh & nassi). third unless disturbed most dangers such as the release of hydrogen-sulfide gas is fairly low. just remember that you should wait to do the big 90% water change for a few days after moving the tank as opposed to a bare bottom system where it would be done during the move.

Personally moving sand has never really been that much of a problem. the main ? is how long will the bed be up. Ideally at least a year. To make it worth the extra effort.


how deep does a DSB need to be to be considered a DSB? also what kind of sand should be used in a DSB?


The purpose of a DSB is to recreate the area between the beds surface & the anoxic zone. The buzzword bingo for this would be the biogenic mixing depth & Redox potential discontinuity layer. Now there are several factors that work on this beyond the sand it self which is why now one can give you a straight answer. they would be things like the water flow, nutrient levels, Biodiversity & so on.

Now the simple answer is small grains, with an irregular shape. should allow you to do it in about 5-6 inches. large grains will take maybe 8, sometimes 10-11 inches to do this. Small grains are also better for most of the fish since it can pass through the gills with greater ease.

#18
Trick

Trick

    Nano Reefer

  • Members
  • 1,520 posts
  • Joined 26 Mar 2010
So basically if your going to move any sand from one tank to another tank then you basically start the cycle all over. You can't disturb the sand bed or it resets the cycle. That sucks. Ive seen people transfer their stuff from one tank to another though without much problem. maybe a spike in nitrates or something like that.

#19
jeremai

jeremai

    an island of reality in an ocean of diarrhea

  • Premium Members
  • 27,121 posts
  • Joined 08 Nov 2005
  • Las Vegas

Jer. One thing I forgot to mention before, as to the maintenance of the shallow sandbed. Is the doubling rate of the bacterial population should be taken into consideration, when planning to clean the sediment. If you figure that the doubling rate of the two needed bacteria for denitrification is 20 hours or so. You should be able to find the needed time for repopulating before, again disturbing the bed. Also even in a shallow bed, a useful population of both can begin to form. Since both prefer an oxygen saturation of around 80% with temp in the range of 78-80 degree's. Only the top 2-3 mm of the bed will be at a fully oxic state. Now it will of course depend on the grain size & the amount of organic sedimentation present. But this should be achievable within a 2-3 cm layer.

I missed this. Interesting point about the doubling time. I don't generally siphon or otherwise manually clean my sandbeds though, other than what snails and other assorted fauna do. The 2-3cm layer point is good news; my new tank is getting a 2" sandbed. :happy:

So basically if your going to move any sand from one tank to another tank then you basically start the cycle all over. You can't disturb the sand bed or it resets the cycle. That sucks. Ive seen people transfer their stuff from one tank to another though without much problem. maybe a spike in nitrates or something like that.

This is why most people recommend replacing the sandbed for a tank move; better to start all over with sterile sand than to risk complications from disturbing an established sandbed.

pretty sure jer was referring to the length

 
reef information and articles
photography, writing, etc.
 

#20
FishStrings

FishStrings

    Nano Reefer

  • Members
  • 406 posts
  • Joined 31 Jul 2010
You mean the sea doesn't get weekly water changes? ;)
You notice carbon on the cycle too. Therefore it is perfectly safe to use carbon in reefs which is a key point. The carbons they have now will also never leech so its just like you're taking any contaminant directly out of the tank like nature. Good job, but would run this on word and fix all the red and green lines.

#21
bitts

bitts

    Yes. I'm blasting Wagner. While chanting KILL Da NOOB.

  • Members
  • 6,333 posts
  • Joined 30 Dec 2006
  • Denver, boulder, loveland, fort collins.....
First since its the top of the page I thought I should add something meaningful so here are some great article's from POMAKANTHA. Which happens to be a great resource.

uln bacterialplankton systems & biopellets

You mean the sea doesn't get weekly water changes? ;)
You notice carbon on the cycle too. Therefore it is perfectly safe to use carbon in reefs which is a key point. The carbons they have now will also never leech so its just like you're taking any contaminant directly out of the tank like nature. Good job, but would run this on word and fix all the red and green lines.

While it is even at times recommended to run "carbon". The carbon being discussed in terms of Biogeochemistry, would be that moving through the carbon cycle & not that which is used in a reactor to aid in filtration.

Carbon Cycle.

Edited by bitts, 18 February 2011 - 05:46 PM.


#22
FishStrings

FishStrings

    Nano Reefer

  • Members
  • 406 posts
  • Joined 31 Jul 2010
The carbon cycle is actually very much similar to the carbon you put in your reactor. Its just not pelleted, treated and mixed, or in convenient form. It is however, very much the same matter and is a mined resource to my knowledge.

#23
Amphiprion1

Amphiprion1

    Nano Reefer

  • Members
  • 1,149 posts
  • Joined 06 Mar 2010

The carbon cycle is actually very much similar to the carbon you put in your reactor. Its just not pelleted, treated and mixed, or in convenient form. It is however, very much the same matter and is a mined resource to my knowledge.



??? How is the carbon cycle similar? I missed that.

Some carbon is mined, but not all of it.

#24
bitts

bitts

    Yes. I'm blasting Wagner. While chanting KILL Da NOOB.

  • Members
  • 6,333 posts
  • Joined 30 Dec 2006
  • Denver, boulder, loveland, fort collins.....
The Carbon in flux through the cycle being refereed to is sourced from two possible place's. Either as inorganic carbon, such as that in the form of CO2. Utilized by the phyto or other algae in photosynthesis & thus converted to organic carbon to be used through out the tank. Or as organic carbon. Normally dosed in any number of forms, most often vodka, to drive a Bacterialplanktoic ULN system. I agree that the activated carbon used in a reactor is Carbon & there for part of the global carbon cycle. But the separation being made between it & that which is in flux, is in its intended use. Where the carbon in flux moves through several redox reaction as it passes through the system enabling life to thrive. The activated carbon is there to sequester dissolved organic Particulates. Which in this environment may actually be detrimental removing needed nutrients as they move through the tropic levels.

Edited by bitts, 19 February 2011 - 12:36 PM.


#25
Amphiprion1

Amphiprion1

    Nano Reefer

  • Members
  • 1,149 posts
  • Joined 06 Mar 2010

The Carbon in flux through the cycle being refereed to is sourced from two possible place's. Either as inorganic carbon, such as that in the form of CO2. Utilized by the phyto or other algae in photosynthesis & thus converted to organic carbon to be used through out the tank. Or as organic carbon. Normally dosed in any number of forms, most often vodka, to drive a Bacterialplanktoic ULN system. I agree that the activated carbon used in a reactor is Carbon & there for part of the global carbon cycle. But the separation being made between it & that which is in flux, is in its intended use. Where the carbon in flux moves through several redox reaction as it passes through the system enabling life to thrive. The activated carbon is there to sequester dissolved organic Particulates. Which in this environment may actually be detrimental removing needed nutrients as they move through the tropic levels.


I think FishStrings may have confused activated carbon and the carbon cycle itself--which, in turn, completely threw me off. I was failing to see any correlation (real or imagined) between the two...