Culturing Vital Bacteria for Marine Aquariums

Purple Non-Sulfur Bacteria and Natural Aquarium Filtration

Bacteria are, to say the least, ubiquitous. They are in our guts. They are in just about every breath of air we take. They most certainly should (at least some types) be in our aquarium filtration systems.

Yet, many aquarists remain a wee bit oblivious to the critical roles that bacteria and archaea play in captive ecosystems; from their limited perspective, there are “good” bacteria (a label usually reserved exclusively for the nitrifying bacteria) and the rest are all “germs.” That being said, things have really begun to change in recent years as hobbyists (following the lead from professional aquaculturists) become increasingly aware of beneficial microbes such as the purple non-sulfur bacteria (PNSB).

PNSB will surely to be put into much more common use as aquarists see firsthand what they can do—which is a lot. We will here describe these many uses. We begin by providing an overview of biological filtration techniques; we then summarize ways in which purple non-sulfur bacteria complement each.

Nitrifying Filters

One early and particularly frustrating marine aquarium condition was known as “new tank syndrome.” Put plainly, the usual outcome of this mysterious malady was a speedy death for all inhabitants. Fortunately, very soon after discovering ammonia as the culprit, hobbyists learned how to promote the development of nitrifying microbial communities. These aerobic chemoautotrophs reliably and naturally convert toxic ammonia to relatively nontoxic nitrate. The process of establishing a biological “filter” became commonplace, if not standard, and remains so to this very day. We indeed continue to improve the performance of these nitrifiers, whether through more habitable media or through more effective inoculants.

That being said, a heck of a lot of other things happened in the hobby over the course of the next half-century. Arguably, the most significant of these changes has been the shift from fish-dominated systems towards much more diverse (albeit coral-dominated) reef tanks.

Denitrifying Filters

Sure, eliminating the underlying cause of new tank syndrome made it possible for the hardiest reef animals (mostly fishes) to survive in the conventional recirculating aquarium system. As we made our first earnest efforts to keep corals, however, it became painfully evident that our initial victories amounted to little more than sweeping the problem under the rug. Nitrate tends to accumulate over time, particularly in overfed and under-serviced systems. Not only is nitrate toxic to many aquarium invertebrates at higher concentrations, but it also contributes to the rapid growth of benthic microalgae that overgrow or poison neighboring corals. This latter issue is compounded by the use of intense light required by zooxanthellate corals.

Our response was to promote the growth of denitrifying bacteria. Culturing and maintaining these anaerobic chemoheterotrophic bacteria in your filtration necessitated special reactors known as denitrifying filters. To remain anaerobic, water can pass through them only very slowly. And, because these microbes are heterotrophs, they must be drip fed a source of “food” such as lactose. Nitrate is used in the organisms’ respiratory processes (rather than assimilated) and converted to nitrogen gas (which passes through an opening in the filter).

Denitrifying filters are troublesome to operate. If the flow rate is too high, harmful nitrite is produced; if too much food is added, noxious hydrogen sulfide is produced. Thus, this method of denitrification (while at least sort of natural) never really caught on.

Algal Scrubbers/Refugia

By the early 90s, as denitrifying filters were (already!) falling out of favor, the concept of algae scrubbing came into play. Big, noisy and messy, early scrubbers were quickly superseded by refugia. Part of the refugium’s subsequent rise to popularity certainly owed to its suitability as a refuge for certain small, desirable fauna (especially microcrustaceans such as copepods). Some aquarists liked that they could employ sediment filtration methods here rather than in their main tank (see below). Even so, for nearly all who installed refugia, nutrient-to-plant sequestration has been the primary objective. Planted refugia do seem to work quite well for this purpose (and can even be attractive), though not without some complication.

From the beginning, the foremost complaint from scrubber and refugium keepers alike was the accumulation of various algal secretions (together known as yellowing compounds). At best, they irk users by discoloring the water; at worst, when the bulk of these releases are allelopathic (i.e. produced as a sort of chemical weapon), they are potentially detrimental to corals. Such is the case with some species of the green alga Caulerpa (such as C. racemosa) which were once widely used as marine refugium plants. The Great Caulerpicin Scare caused a general decline of refugium use from approximately 2005-2015.

Oddly, during this time, scrubbers (usually utilizing Chaetomorpha) made a bit of a come-back in the form of algae reactors. Coinciding with a greatly increased selection of macroalgae (especially the more benign red algae), this development led to the greater-than-ever popularity of planted refugia which continues into the present.

Live Rock/Sand Filtration Methods

A heavy reliance on live rock and/or sediment filtration methods (utilizing a plenum, deep sand bed (DSB) or Miracle Mud) came into play during the 90s. In concept, nitrifying bacteria that reside at the oxygenated rock/sand surface layer convert ammonia to nitrate which drifts to deeper, anaerobic zones where it is converted by denitrifiers to nitrogen gas.

The first part of this process is surely limited in the typically well-illuminated reef tank, as it has been repeatedly demonstrated that nitrifiers (especially the ammonia oxidizers) are considerably inhibited by the presence of light. One study does however show that sediment filtration (all methods) is effective at supporting denitrification. Nevertheless, hobbyists have increasingly abandoned this approach due to expense (quality aquarium substrates aren’t cheap), aesthetic concerns (particularly with plenums) and yes, even because of the extra few inches of space they displace from the tank volume.

Particulate/Dissolved Organics Filtration

By definition, these substances are compounds that contain carbon and hydrogen and are biological in origin. However, they might include nutrient, metal or trace element components. They range widely in molecular weight from small, simple sugars to large, complex fatty acids, phenolics, etc. Water-borne organics occur in both particulate and dissolved forms. Particulate organics are produced from the decomposion of dead organisms as well as mucus, feces, etc. In small amounts, these tiny chunks of organic waste provide a valuable and natural source of nutrition for diverse species; filter-feeders consume suspended particles whereas detritivores consume those that have settled to the tank floor. Problems occur when it is produced at a faster rate than it is consumed. In the water column and over the substrate, heavy consumption of these materials by aerobic heterotrophs can deplete the aquarium water of oxygen. As it reaches deep parts of the sand bed, the undersides of live rock, etc., anaerobic sulfate-reducing heterotrophs can proliferate, thereafter generating poisonous hydrogen sulfide.

Many types of fiber- or sponge-based mechanical filter media are effective at removing particulate organics. What is most important is that these media are cleaned often—before the entrapped particles break down into dissolve organics!

Dissolved organics cause all of the problems created by particulate organics; they are, however, a lot more difficult to remove! High-quality granular activated carbon (GAC) does a fairly impressive job at removing these compounds but can get expensive to use on a regular basis; moreover, aquarists have for long speculated that GAC can removal desirable substances along with the bad. Protein skimming removes only some of these substances and likely harms/removes many beneficial plankton.

Here again, inoculants containing various “sludge-eating” aerobic heterotrophs are now available as a biocontrol for both particulate and dissolved organics. Some of these products have been extensively used for both marine and freshwater (including pond) applications with good results.

In some cases, simple organic substances (ethanol, acetate, etc.) are actually added to the aquarium water in the hope that the resulting bloom of heterotrophs (primarily bacterioplankton) will consume the balance of excess nutrients (nitrate, phosphate, silicate, etc.). The bloom (which may become evident as a milky haze in the water column) disappears quickly as the bacteria are preyed on by nanoplanktivores or removed by skimming; hence both nutrients and organics are ultimately assimilated by bacterivores or exported from the system via skimmate. This practice, widely known as carbon dosing, is effective for routine removal of moderate accumulations of nutrients; on the other hand, when attempting to reduce very high nutrient concentrations, these blooms (especially if the carbon source is overdosed) can reduce dissolved oxygen to dangerously low levels.

Eastern Secrets

Wastewater management practices (particularly those used in fish and shellfish farms) very often get scaled down for aquarium applications. Purple non-sulfur bacteria inoculants have been used regularly (and quite successfully) in Asian aquaculture operations for decades. It may be a bit surprising that Western counterparts—both in the agricultural and aquarium industries—are only recently catching on to their numerous benefits.

Purple non-sulfur bacteria differ from purple sulfur bacteria in that (1) they do not require (and are indeed less tolerant of) hydrogen sulfide and (2) most can survive in the presence of oxygen.

PNSB are among the most metabolically versatile organisms known. These extremely ancient α-Proteobacteria undergo all four major modes of metabolism:

  1. Photoautotrophy: Obtaining energy from light and carbon from carbon dioxide (like algae)
  2. Chemoheterotrophy: Obtaining both carbon and energy from organic compounds (like fish)
  3. Chemoautotrophy: Obtaining energy from inorganic compounds and carbon from carbon dioxide (like nitrifying bacteria)
  4. Photoheterotrophy : Obtaining energy from light and carbon from organic compounds (like purple and green sulfur bacteria)

PNSB species such as Rhodopseudomonas palustris have been well-studied for their ability to switch between each of these modes of metabolism as environmental changes dictate. They additionally tolerate extremes of temperature. They survive in soils as well as freshwater and marine habitats. Even more, they are capable of fixing nitrogen.

“So what?” you may be asking… Perhaps you just want to know how they’ll ease tank maintenance and help keep your animals healthy. Fair enough. Get ready to be blown away.

Purple Non-Sulfur Bacteria and Nitrogen Cycling

We’ll start with the big one: Nitrogen cycling. PNSB assimilate ammonia. And nitrite. And nitrate. Yes, we typed that right. They perform both nitrification and denitrification. Such has been demonstrated in a simulated aquaculture environment.

In another study, PNSB used in your filtration were shown to completely remove ammonia concentrations of around 5 ppm in as little as five days! This is worth mentioning because ammonia is rather toxic to nitrite-oxidizing bacteria (the ones that convert nitrite to nitrate). What many aquarium hobbyists are unaware of is that the second part of the nitrification process is hindered if initial ammonia concentrations climb high enough to harm nitrite-oxidizers. PNSB help prevent this by suppressing excessively high ammonia levels. What is more, during bioload increases (e.g. animal stocking), PNSB lessen the burden on the biofilter, thereby helping to blunt any resulting ammonia or nitrite spikes that might arise.

The ammonia and nitrite that PNSB metabolize is directly assimilated rather than oxidized to nitrate. Thus, PNSB help to maintain low nitrate concentration through interception of ammonia and nitrite (in addition to their direct uptake of nitrate). Their overall long-term impact on nitrogen cycle efficiency is considerable in that they carry out nitrification (not just denitrification) in anaerobic zones. And, they are fully able to carry out nitrification under bright light—in fact, they love it!

But wait, there’s more… What happens to purple non-sulfur bacteria in nutrient-poor environments such as coral reefs (or properly maintained reef aquaria)? Or in any kind of system after they’ve consumed most of the available nutrients? This is where things really get interesting.

As diazotrophs (i.e. nitrogen “fixing” organisms that can assimilate atmospheric nitrogen into organic compounds), PNSB can produce their own source of nutritionally utilizable nitrogen. This they do similarly to the rhizobia (the bacteria that famously have a symbiotic relationship with legume plants) to which they are very closely related. As has been well documented, PNSB form very close relationships with aquatic plants, offering nitrogen-rich fertilizer in return for the plants’ carbon-rich exudates. Recently, fascinating investigations have revealed that a similar relationship occurs between PNSB and zooxanthellate corals. These findings help to explain why coral reef habitats are so productive in such characteristically infertile waters. Some researchers now go so far as to declare PNSB as an integral part of the coral “holobiont.”

Purple Non-Sulfur Bacteria and Carbon Cycling

Their impressive ability to clean water of nitrogenous waste notwithstanding, these microbes have been most extensively used (especially in the US) for their equally impressive ability to consume biowaste. PNSB are “digester” bacteria that consume a rather wide variety of organic substances. For example, they are now commonly relied upon to degrade sludge and even odors from hog farm waste (if you’ve ever been anywhere near hog waste, just let that sink in for a moment).

In aquarium and aquaculture applications, their most valuable contribution is the mineralization of detritus. You might also love them for their taste for plant rubbish. Specifically, they possess enzymes capable of breaking down poorly digestible complex carbohydrates such as cellulose and lignin. This trait makes them indispensable in the refugium or planted plank, where dense vegetation can make physical removal of these wastes difficult.

Their involvement in the removal of dissolved organics is just as important. PNSB in your filtration eliminates a substantial quantity of yellowing compounds from the water. The benefit from this activity is not merely aesthetic; as they digest organics that diffuse into anaerobic zones of the substrate, PNSB competes with sulfate-reducers for food and thereby diminish the production of hydrogen sulfide. Also, by removing organics from anaerobic zones, they shrink the organic load that is ultimately available to obligately heterotrophic aerobes, thereby minimizing the risk of heavy blooms (and the resulting depletion of dissolved oxygen).

PNSB in the Aquarium Microbial Community

Using live purple non-sulfur bacteria in the aquarium is easy with PNS ProBio™. They may be added at any time. When inoculating new systems, they can be introduced alongside “traditional” nitrifiers and will not interfere with their development. They can (and should) be re-added to boost populations any time ammonia or nitrite are detected (e.g. after an accidental overfeeding). For maintenance, they can be used whenever nitrate or detritus begins to accumulate or the water column shows discoloration, especially with little to no filtration.

So long as their bottle is tightly sealed, PNSB remain viable for months at room temperature. This makes it very easy to keep them on hand where they can readily be of service  in your filtration whenever the need arises. And considering all that they do, that could be quite often!

21 thoughts on “Purple Non-Sulfur Bacteria and Natural Aquarium Filtration”

  1. Nathaniel Konkel

    This sounds excellent! Hopefully it works as well as it is proposed to.
    Are there any drawbacks to using the bacteria?

    1. Kenneth Wingerter

      Hi, Nathaniel. Yes, this organism is mindboggling! When considering its metabolic versatility, bear in mind that it had already evolved whilst the Earth’s atmosphere was still nearly devoid of oxygen…

      To answer your question: No, this bacterium is completely non-pathogenic and produces no appreciable amount of harmful metabolites. In fact, it ASSIMILATES ammonia whereas nitrifying bacteria simply CONVERT it into less toxic nitrate. PNSB are most active in anaerobic environments, where they consume dissolved organics without using up oxygen. But we get you–almost seems to good to be true! Fact is, nearly all life on the planet evolved around them. Even today they are found in soils, on aquatic plants, in deep sea sediments, etc… everywhere! And that’s why we believe that PNSB (especially R. palustris) should be in our aquaria.

      Thanks for joining in!

  2. Mind. Blown.
    I’m actually a freshwater aquarist just gathering info on reef systems for a potential new direction, and i stumble across this!! I will definitely be testing these beauties out in a future set up. What a great link in the chain of ‘natural’ systems.
    You mentioned PNSB in freshwater systems as well (at which point i praised the almighty). I assume these would be a different kind of bacteria? A point in the general direction from a freshwater point of view would be massively appreciated …

    1. Kenneth Wingerter

      Hello, Lee.

      Yes, PNS Probio works exactly the same way in freshwater (Rhodopseudomonas palustris is euryhaline, but actually seems to prefer freshwater habitats). It even acts as an aquatic plant symbiont in the same way it does hermatypic corals (that is, as a diazotroph). These bacteria are now extremely popular in intensive freshwater aquaculture operations in East Asia. But they’re finally catching on here as well, particularly in agriculture!

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