By Bob Goemans
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Nature’s Pathways, Part I

Authored by: Bob Goemans

In recent years there has been an increased desire to maintain what is loosely called “natural marine aquariums,” where methods used to maintain them are more inline with the natural processes that occur in the wild, than what high tech equipment can provide. However, it’s a challenge because the desire to have one more pretty specimen in the aquarium often tips the scales in favor of a pending disaster, or, not enough is known about Mother Nature’s energy paths in aquaria. There’s not much I can do about overcrowding, except to say it’s a commonsense issue. But where energy paths are concerned, a ‘Key’ word is ‘Balance,’ and that does not mean X-amount of fish per gallon! Nor does it mean other visible substances, such as specific coral types and fish that would depict an area in the wild. In my opinion, it relates to an intricate network of physical, biological and chemical energy processes that finally enable creatures so tiny they can only be seen with a microscope, i.e., bacteria, to accomplish processes that ‘enhance’ our ability to keep these ‘natural’ systems functioning efficiently.

Keep in mind their (bacteria) success hinge on the efficient usage of energy, whether that is light or chemical energy. And, that all depends upon the quality and quantity of that energy and the pathways it must travel. In fact, I think of these pathways as the streets and roads that transport the ‘energy’ that link the entire maze of metabolic and chemical functions that are occurring in aquariums. All aspects of the journey are important and interconnected because fundamentally they finally affect the bacterium health and ability to function/reproduce. It’s they who actually control the wellbeing of the system!

To help bring about a better understanding of these pathways, we first need to look at light, then water, and finally the pathways in the substrate/sandbed, as they all are the main highways that lead to a ‘healthy and well-balanced’ aquarium environment.


There are various parameters of importance when it comes to selecting lamps to light our aquaria, especially reef aquariums, and I highly recommend reading my articles titled “Let There Be Light” in the November and December 06 issues of FAMA for specifics. However, for the sake of this article, it should suffice to say there must be adequate quantity (intensity) and quality (spectrum) of light energy to traverse the difficult path before it, i.e., pass through seawater and adequately reach the targeted organisms.

And since light (energy) has an electromagnetic force, its passage through water can affect orientation and structure of the dissolved constituents that make seawater so complex. Or, itself changed to less effective wavelengths/spectrum. In fact, I see those molecules of substances in aquarium water as a structure embedded in a cloud of electrons having positive and negative charges with the movement of those electrons generating an electric field. In freshwater the passage of light past its trivial amount of elements and compounds when compared to that of seawater is a fairly easy task, yet, not so in seawater. The seemingly endless array of elements and compounds in seawater, often increasing their quantities/complexity as aquarists apply different additives, makes the travel of light sometimes extremely difficult. Therefore, it’s a must to begin with sufficient light energy (spectrum and intensity) to accomplish the purpose of the aquarium system, whatever its goals (fish-only or reef aquarium).


Water plays several rolls; basically it’s a solvent and a transport medium that is vital to biological functions. It’s just not something for fish to swim in! Water also has light absorption and refraction capabilities, the magnitude of which depends somewhat upon its suspended amount of elements and compounds. The greater it’s reflectance, the less transmittance and lengthening of its useful wavelengths to less useful red band wavelengths.

Yet, one would think all of light’s energy/spectrums would easily penetrate the aquariums shallow depth. That would be correct if there were a constant flow of natural seawater and that light energy from aquarium lamps approached that of natural sunlight. However, there is far less light energy from aquarium lamps ‘and’ usually skewed mineral levels in aquaria that can inhibit the travel of blue-green light, which are the most important wavelengths. In fact, water does not have to be ‘yellow’ looking to inhibit light transmission, as clear water also contains dissolved nutrients such as nitrate, which in closed systems almost always exceed what is found in the wild. And it’s these nutrients ‘and’ the over use of certain mineral additives that create transmission problems for light energy.

Because of that the parameters of aquarium seawater, where feasible, should be very similar to that in the wild where coral reefs exist. It simply doesn’t make sense to create a more complex gauntlet of compounds and elements for light energy to pass through. Keep nitrate-nitrogen levels low, below 10 mg/l and various mineral levels near that of what is found surrounding the reefs in the wild.


Substrate is usually regarded as the bed of material/sediment that covers the aquarium bottom. Nevertheless, rock can also be considered substrate. In fact, anything that bacterium grows on or where infauna exist can be considered substrate, which is ‘thought’ to be the aquariums primary filtration medium.

As for the word ‘filtration,’ I see that process in the context of what protein skimmers and activated carbon provide. They ‘remove’ or ‘export’ elements and compounds from the water. On the other hand, bacteria use a process called ‘metabolism’ to accomplish environmental changes by transforming elements and compounds into something different. Without a doubt, various microbial processes are the foundation of every aquarium system. Healthy longevity of which is based upon how well they (bacteria) function. How well they function is in turn dependent upon your knowledge of their existence, their requirements and the results one can expect from them! In my opinion, they are the heart and soul of the system.

Nevertheless, infauna also need to be taken into consideration, as they and bacteria are part of every sandbed, and the only difference between them is the percentage of each that encompasses that quantity of substrate. And to better understand them, there are several terms that need defining, e.g., diffusion, bioturbation, porewater and oxygen, which are useful when it comes to establishing a sandbed in the so-called ‘natural aquarium.’


It’s the all-encompassing way nature moves molecules from one place to another. It could also be said it’s the movement of a fluid down a gradient from an area of higher concentration to an area of lower concentration, and it can be considered ‘Natures’ fundamental transport process. It exists in the majority of aquarium sandbeds where it is responsible for most nutrient transport and encompasses how molecules collide and react, how food molecules approach cells, and how wastes leave local environments. It’s a very dynamic process that facilitates many biological functions.


This is the disturbing and/or altering of a surface or substrate by the physical activity of organisms such as worms/crustaceans (infauna). In the wild it generally occurs in fine sand and mud-like substrates and in deeper beds where diffusion is not possible and/or where infauna is present. It would be fair to say that relatively simple alterations to this type bioactivity transport structure can result in dramatic changes. Whether these are good or not for the equilibrium/balance of closed systems, depend on many factors. For example, infauna tunneling may release ammonium or cause increased nitrification rather than nitrate reduction because of elevated oxygen levels. Orthophosphate may also be released.

It should also be said that many models of bioturbation have shown both advantages and disadvantages resulting from a best-fit application, i.e., each model is appropriate for particular circumstances, particular use, and/or explanation of basic phenomena. Therefore the interactions between reactions, organic matter decomposition pathways, transport regime, pore-filling secretions, and the complex structures formed by individual burrows or burrow groupings in the wild remain a largely unexplored area of both modern sedimentary bio-geochemistry and the study of the evolution of biogeochemical cycles. Therefore, those individual model results shouldn’t be over generalized for the purpose of answering questions relating to the majority of aquarium sandbeds. Our closed systems are just that, a world by itself where the aquarist is God-like, and who needs to understand ‘its’ parameters and limitations!


This refers to the minute water-filled area around each sand particle. It’s an active region of diffusion for all elemental components of energy flow and nutrient cycling. And, the smaller the sediment particles, the closer each particle is to each other thereby reducing the amount of space/water between them. This then relates to the word ‘permeability’ which in turn defines the physical shape and distribution of the sediment (sand). Fine-grained sediments have low permeability, thus restricting porewater flow (B. Bourdreau, 2002). Courser sediments, i.e., above .5 mm, have more useful permeability and diffusion is usually the main form of transportation for foodstuffs to microbial colonies. In finer sand/mud, infauna may provide for the mixing and distribution of foodstuffs. They also consume some of the nutrients and also generate similar nutrients.


Another word that sometimes causes confusion is the word ‘oxygen.’ It’s sometimes written as dissolved oxygen or molecular oxygen, and sometimes simply as oxygen. Oxygen exists either in the gaseous form (molecular oxygen (O2)) or in water as dissolved oxygen, also as O2. Oxic bacteria at the upper most segment of the sediment are about the only users of oxygen dissolved in the water (dissolved oxygen). It’s also what’s measured when one takes a water sample from the aquarium for the purpose of testing its oxygen level. As for its presence in the upper most portion of the sediment, even that is a varying subject because of the interaction between autotrophs and heterotrophs and diurnal cycles (oxygen used versus oxygen produced at what time of day). As you travel downward into the sediment, the word ‘oxygen’ is mostly associated with the complex reactions taking place. And when it comes to our sandbeds, the element oxygen (O) is tied to all kinds of things; however, the real issue is oxygen flux from the bed’s surface/bulk water interface area on down to the anaerobic zone.

Now that you’re armed with some of the terminology basics, their importance in different type sand/depth beds and how it can affect system overall balance is what Part II is all about.

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