R. palustris: The Do-All Aquarium Bacteria

The art of reef aquarium keeping has come a long way in a surprisingly short amount of time. These days, big developments in the trade seem to come one right after the other. Technological advancements in particular have enabled us to successfully maintain and even culture species thought impossible to keep just a decade ago.

As we’ve upped our game, we’ve refined our standards. That is, we are less preoccupied with “chasing parameters” and increasingly focusing on what really matters: The health of our “captive ecosystem.” That is, we don’t just want our systems to look like natural coral reefs, but also to function like them. And by what holistic criteria would one judge the health of an entire ecosystem, whether in the wild or in a glass box? By (1) its own capacity to cycle (and recycle) carbon and nutrients as well as (2) the nutritional/immunological wellbeing of all of its inhabitants, from the fishes and corals down to the countless, diverse microorganisms. 

This approach–the so-called natural reef aquarium method–is hardly new. It has, however, gained a lot of traction and has become much more sophisticated over the decades. No longer are we content just to toss in some unidentified “good” bacteria and shortly thereafter consider the tank “cycled” and complete. Rather, we understand that (just like on natural reefs) there is an unseen but nevertheless essential biological component to the system that is in perpetual flux. 

Specifically, the hobby has seen a surge of interest in microbial food webs. Given the strongly corallicentric direction the marine aquarium industry is heading, recent studies on the aquacultural applications of purple non-sulfur bacteria (PNSB) have been especially exciting.

By the end of this article, you certainly may find yourself wondering how in the hell the marine aquarium industry has failed to widely recognize the value of these microbes; we’re still asking ourselves the same question. East Asian fish and shrimp farmers have relied upon them pretty heavily for over 30 years. They’ve been known right here in the U.S. for some time owing to their usefulness in degrading sewage and industrial wastes. They’ve even been identified as a common coral symbiont. Yet, the most recent notable mention of them in aquarium literature (that we know of) is from a couple cryptic passages in the final volume of the classic trilogy The Reef Aquarium (Delbeek and Sprung, 2005). 

We totally get that you might just want to hear a summary of what PNSB (and PNS ProBio™) can do. But seriously, we’re about to make a LOT of claims. BIG claims. In sum (alright, just a wee spoiler), they (1) remove ammonia and nitrite, (2) remove nitrate and phosphate, (3) contain vitamins as well as essential fatty and amino acids, (4) are rich in carotenoids and (5) act as probiotics. It’s admittedly quite a bit to chew on, so let us take a few steps back and firstly describe what PNSB are and describe their place in the natural environment.

What is this stuff?

Even among prokaryotes, purple bacteria are incredibly ancient organisms. They (or very similar ancestors) first appeared on Earth around 3.2 to 3.5 billion years ago. These lifeforms certainly were obligate anaerobes, as there was no appreciable amount of oxygen in the atmosphere at that time; that would come much later, following the emergence of an oxygenic descendent of the purple bacteria, the cyanobacteria (which makes PNSB ancestral to all plants). 

But hey, an evolutionary history of a few billion years gives a little wiggle room for some adaptation. At least at a cellular level, they are far more advanced than any animal including us humans. They are indeed widely regarded as the most metabolically versatile organisms ever studied. Compared to the purple sulfur bacteria, the purple non-sulfur bacteria are (with a few exceptions) most adaptable. The extant “sulfurs” (mainly Chromatiaceae) are characteristically anaerobic and autotrophic, whereas their “non-sulfur” counterparts (Rhodospirillaceae and some Bradyrhizobiaceae) are mixotrophic and may subsist in either anaerobic or aerobic environments.  

As one might guess from their names, the sulfurs were discovered before the non-sulfurs. This distinction comes from the fact that the former they can use sulfur in the form of sulfide or thiosulfate as an electron donor during photosynthesis. Non-sulfurs, on the other hand, do not rely on sulfur in this manner and in fact can only tolerate it at much lower concentrations. 

A little bit everywhere

Probably among the most abundant and widely distributed of the PNSB is Rhodopseudomonas palustris. These rod-shaped, flagellated, Gram-negative rhizobia occur everywhere from marshy soils to the surfaces of plants and algae to the guts of sea anemones. It’s entirely possible that there millions of them on your body right now.

Their ubiquitousness in nature comes from their environmental adaptability, which comes from their ability to bounce between all four major metabolic pathways: chemoautotrophy, chemoheterotrophy, photoautotrophy and heteroautotrophy. It survives under widely ranging pH, temperatures and salinity. It is able to adapt to unfavorable light conditions. That all being said, even this extremely high degree of flexibility doesn’t quarantee a seat in any habitat. 

R. palustris, like any other species, must compete for space, food, etc. with other organisms. And let’s just say that the planet has changed a little since it first appeared in the primordial soup. Pliant as it is, it is most at home–and competitive–in anaerobic, moderately illuminated environments with plenty of organic matter around. As such, photoheterotrophy is its favored mode of metabolism.

Reef aquarium microhabitats

R. palustris may invade and successfully colonize numerous types of microhabitats within typical marine aquaria. Given the organism’s odd set of preferences, these hot spots are generally somewhat marginal. For the most part, it swims toward light and away from oxygen (it cannot perform photosynthesis in the presence of oxygen); then, once finding the Goldilocks zone, it moves along this interface in search of food (ideally an organic, rather than inorganic, source of carbon). 

These conditions prevail just under the uppermost layer of a sand bed or just below the surfaces of live rock. Purple bacteria and similar anaerobes very much favor calcium carbonate-based substrates due to their high porosity/permeability which allows just the right amount of solute exchange with the water column. Here, light just barely penetrates. A biofilm of aerobes over the exterior creates a perfect barrier to oxygen. If the purple non-sulfurs are so lucky, a film of purple sulfurs and/or green sulfurs might develop beneath them, thereby protecting them from hydrogen sufide that seeps up from sulfur-reducing bacteria (e.g. Desulfovibrio vulgaris) even deeper below. Tiny pockets in the rock, and interstitial space between sand grains, trap detrital particles, ensuring a good food source.

Left undisturbed, these subsurface films become evident as variously colored (dare we say pretty?) bands develop against the tank panels to resemble a winogradsky column. R. palustris may be appear as rusty orange to bright red to burgundy.

Ceramic biomedia with deep pore structures (such as MarinePure) or filter sponges provide a similar and acceptable microhabitat for R. palustris in particular and for anaerobes in general. These may be placed in any illuminated part of the aquarium system so long as water flows around, but not through, them.

R. palustris is very happy to live within detrital accumulations that commonly develop between/beneath live rock, in dead spots at the bottoms of sumps/refugia, etc. Such a powerful sludge digester that it is used to clear hog wastes, the settled particulates in aquarium systems are but a snack to this species. Its capacity for digesting lignocellulosic compounds is especially impressive; for example, it significantly reduces build-up of cellulose-based rubbish such as that which accumulates beneath the macroalgal bed in a planted refugium. It can also establish itself beneath and devour the sludgy films that envelope porous chemical filter media, thereby improving these products’ performance and increasing service life.

R. palustris is very often found growing in close association with algae and plants of all kinds. In most cases, this is a result of the latters’ secretion of exudates, whether as waste products or as allelopaths, which the bacteria scavenge as a food. In this capacity, R. palustris clears tinted aquarium water by reducing concentrations of dissolved “yellowing compounds.” It moreover protects animals from various inhibitory (especially polyphenolic) substances exuded by plants/algae (e.g. Caulerpa spp.). It is among relatively few organisms that is capable of degrading these aromatic compounds, actually eating them (consuming short-chain organic acids) despite their strong antimicrobial properties.

Perhaps the most unusual (and important) of places that R. palustris can establish itself in a reef aquarium is within the bodies of the animals themselves. Amazingly, this microbe ekes out a living–completely nonpathogenically–within the gut flora of fishes, as a symbiont within corals, etc.

Taking care of business

To return briefly to our original point, the marine aquarium hobby has been around for a sort of long time now. For sure, aquarists have come a long way; some aspire to go much further. It’s great that we’ve pretty much mastered the husbandry of beautiful, naturally plenteous stonies like Acropora; that being said, we still don’t even know where to begin with some beautiful, naturally plenteous softies such as Dendronephthya.

But we’re getting there. As we continue to progress as aquarists, we’ll need better and better tools. And that certainly won’t always mean devising novel gadgetry; we can (as in many past instances) refine this art simply by taking a closer look at what Nature does.  

As regards natural tools, Rhodopseudomonas palustris is like a freaking Swiss Army knife. We shall here conclude by elaborating upon the five major contributions R. palustris can make in reef aquarium systems.

  1.  Nitrification

Nutrient-rich (i.e. polluted) coral reefs are not coral reefs for very long due to one factor–algal growth. Corals (especially reef-building corals) derive their fixed nitrogen not from the seawater but rather from an internal source–but we’ll get to that in a just a bit.

Once upon a time, we didn’t think too deeply about aquarium microbiology beyond getting our systems “cycled” (i.e. populated with large colonies of obligately aerobic nitrifying bacteria), even if we were left with lots of nitrate; no ammonia/nitrite=no problem. Then, low-nutrient (e.g. low nitrate) systems became another way to go. Now, low-nutrient systems are the way to go. This isn’t as much a new trend as it is a new capability; thanks to improved technology/husbandry practices, oligotrophic (very nutrient-poor) conditions are possible to maintain in aquaria. 

While it is within their ability to carry out true nitrification, R. palustris is most valuable in the aquarium microbial community for its ability to remove ammonia and nitrite from anoxic regions of the system. This particular withdrawl of nutrients is a photoassimilative process, meaning that they take up nitrogenous compounds into their bodies rather than converting them into nitrate (i.e. algae fertilizer). R. palustris assimilates both ammonia and ammonium. It is even positively chemotaxic to nitrite (e.g. swims toward it). Though it is a heterotroph, it will not compete with nitrifyers in your “biofilter” as it so strongly prefers anaerobic environments. Indeed, its presence seems to impact the whole microbial community in a manner that promotes stability and improves general water quality. 

  1. Nitrate/phosphate removal 

A good many aquarists struggle to keep nitrate and phosphate levels in check. That is why so many would benefit from the use of R. palustris. This species safely removes nitrate in both aerobic and anaerobic conditions. Yes, same for phosphate. In so doing, it competes effectively with nuisance algae and prolongs the life of certain kinds of chemical filter media. It is faster-acting and easier to culture than true denitrifying bacteria (e.g. Thiobacillus).

  1. Nutrition

Here’s an area where R. palustris really excels. One study found it to be quite rich in protein–72-74%! On top of that, it’s full of the essential fatty acids stearic and oleic acid. It also contains a lot of amino acids such as aspartate. All this wholesomeness is readily digestible since the organism (being a bacterium and not an alga) has no tough, cellulose-based cell wall.

It gets even better. Marine ecologists have always wondered how corals (especially stony corals) could be so productive in such oligotrophic waters. They only learned why fairly recently: Nitrogen-fixing bacteria.

The most astounding thing about R. palustris is that it is a pretty damn good diazotroph (i.e. nitrogen fixer). Just like the rhizobial bacteria that live within the root nodules of leguminous plants (and to which it is closely related), it can create ammonia from nitrogen gas. 

Wait… it makes ammonia? Isn’t that bad? Not in the least! It’s not just “not bad” but pretty awesome. This is because (1) the process is energetically expensive and carried out only under acute nitrogen starvation and (2) it does not occur within the water column but rather the inside of corals where nutrients are immediately taken up and utilized by the hungry zooxanthellae. As in natural, nutrient-poor reef environments, this arrangement allows for the high productivity of endosymbiotic algae (i.e. zooxanthellae) while contributing nothing to the growth of benthic (e.g. film and turf) algae.

An integral part of the so-called coral holobiont, these bacteria consume organic wastes secreted by its host while supplying a continuous source of fixed nitrogen to the zooxanthellae. R. palustris is one of several diazotrophs commonly observed living in the mucus, tissues and skeleton of corals.

  1. Carotenoid supplementation

For those filter-feeders that sift it from the water column (corals, sponges, clams, etc.), and the detritivores that consume it along with the detritus (copepods, amphipods, isopods, etc.), and also for those fish that eat pods (mandains, seahorses, gobies, etc.), R. palustris confers additional benefits in the form of carotenoid pigments

Pigments such as astaxanthin are literally worth their weight in gold, and one of the big reasons for this is that they are fantastic colorants. Consumed in a manner that leaves intact their bioavailablity, they can really brighten an animal up (especially reds and oranges). But that’s hardly all. The pigments in R. palustris have been found to be powerful antioxidants with impressive free radical scavenging capability. Some of these pigments are also formidable antimicrobials, capable of killing both gram-positive and gram-negative enemy microbes.

  1. Probiotic protection

This microbe isn’t joking around when it comes to protecting its turf. In addition to its carotenoids, it synthesizes actual, potent antibiotics. This includes streptomycin, to which even antibiotic-resistant strains of Vibrio are sensitive. This has huge implications for aquarium keeping and aquaculture, as Vibrio is believed to be responsible for numerous deadly afflictions such as rapid tissue necrosis (RTN) in corals, acute hepatopancreatic necrosis disease (AHPND) in shrimp, flesh erosion disease in seahorses, and so on. Because it is known to remain viable in the animal gut, it can be added to fish or coral feed for direct probiotic support.

Using R. palustris in the reef tank

With the availability of PNS ProBio™, a carotenoid-rich live Rhodopseudomonas palustris culture, there has never been a better time to take your reef system in a new, more natural direction. This quality product is used to cycle, establish and mature new systems; it can alternately be used to purify and revitalize old systems. It is just as effective in freshwater as it is in marine aquaria!

Here’s a rundown of the major benefits of this ancient super-microbe: 

  • Proven to support rapid and complete nitrogen cycling from ammonia through nitrate.
  • Proven to aggressively take up phosphate.
  • Proven to provide excellent and highly digestible nutrition for diverse aquatic species, being rich in protein, amino acids, fatty acids and B vitamins.
  • Proven to promote coral growth as a symbiotic diazotroph.
  • Loaded with carotenoid pigments that are proven to provide color, antioxidant activity and disease prevention.
  • Armed with antibiotics with proven effectiveness against highly virulent pathogens such as Vibrio.

Of course, there are no purple non-sulfur bacteria that can raise a poorly maintained aquarium from the grave. It competes with, but cannot immediately eradicate, unwanted algae. It helps to prevent disease but is not a medication. It might not be capable of keeping nitrate and phosphate concentrations near zero if the tank is chronically overstocked and overfed. And, neither this nor anything will ever eliminate the need to perform regular water changes. 

PNS ProBio


However, especially with regular use, you will see a healthier, cleaner, more stable captive ecosystem–just as hard scientific evidence has demonstrated possible time and again. PNSB aren’t just found on coral reefs, they’re in the corals themselves! If you want your reef tank to function more like the real thing–well, now you know what to do. With Rhodopseudomonas palustris as part of your aquarium’s microbial community, you’ve got a few billion years of evolution at your back.

327 thoughts on “R. palustris: The Do-All Aquarium Bacteria”

  1. Very interested in this product…is it similar in action to Vibrant? Is there a reason the two could not be used in tandem?

    1. Kenneth Wingerter

      Different people seem to get very different results with Vibrant, and the manufacturer doesn’t state what species of microbes it contains, so we unfortunately cannot answer those excellent questions with any certainty! We might leave you with this, however… We’ve seen very directly (controlled experiments in jars) where R. palustris outcompetes/eliminates microalgae, yet it does not appear to harm macroalgae or impede its growth. We suspect that the very different interactions of this bacterium with microalgae and macroalgae has to do with its activity as a diazotroph (see article!).

  2. A lot to read and a lot to learn. But as they say, knowledge is power…or in this case a way to help stabilize your reef and encourage growth and longevity to your corals and other livestock. So definitely adding this to my shopping list from now on.

  3. Kudos to Algae Barn for being upfront and educational. Just added this to my shopping cart. Probably an ingredient in a few of the “trade secret” additives that are being marketed.

  4. I’ve always with diversifying life in my tanks when I start them up. I ask other local reefers for a small capful of sand from their systems. Seemed to always have the best cycles that way.

  5. This is super fascinating and could be a real advance in the reefing game. Im certainly going to order a bottle on my next Algae Barn order!!.
    Is there any worry when starting to use this product?? Especially in established reef tanks?

    1. Kenneth Wingerter

      No worries at all! We’ve administered 4x overdoses (experimentally) with no ill effect. This microbe is totally nonpathogenic and occurs on reefs (even inside corals) naturally. While it can really jump-start a new system, it works well in established systems, particularly for safely degrading deep accumulations of detritus.

  6. I dose bacteria every other day, my tank has never looked better and my nutrients are always in check and stable, this is what we should be looking more into rather then spending thousands of dollars on equipment.

  7. Holy crap!!! Excellent article, best one so far!! I have already book marked this product and WILL be buying for sure!! WOW.

    1. Kenneth Wingerter

      You should! We suggest adding it to seahorse food, whether live foods such as brine shrimp (via gut loading) or frozen foods (after thawing); it remains viable in the fish’s stomach/intestines as a probiotic, and produces antibiotics such as streptomycin and kanamycin (which are effective at controlling Vibrio-related illnesses such as seahorse flesh erosion disease and snout rot).

  8. Is there an amount of different types of bacteria that would be too many too add to a tank? Or more is better? I’ve been told not to add more than one on a single day, how far apart would recommend I add them?

    1. Kenneth Wingerter

      Hi, Chris.

      R. palustris can be added at any time (with or without other bacteria), whether seeding dry rock in a new system or removing detritus in an established system. In fact, because they prefer anaerobic areas, they won’t (unlike many aerobic heterotrophs) interfere with aerobic nitrifying bacteria (Nitrosomonas, Nitrobacter, etc.) during or following the cycling period (this is something we understood intuitively, but also confirmed with a highly regarded expert in bacterial nitrification). If anything, these “pioneer” bacteria actually promote the growth and diversity of other beneficial microbes (one reason they’re so often used in agriculture)! In short, these bacteria are a win-win.

  9. Great detail and information on everything you need to know about what actually should be in your tank and for all your fish!! Happy 2020 everyone!!

    1. Kenneth Wingerter

      Intuitively, we’ve always believed that it cannot be overdosed, because it is completely nontoxic and nonpathogenic. Even so, we tested this product extensively for two years on both freshwater and marine systems and were never able to overdose, even when we attempted to do so. For example, we repeatedly applied 4x overdoses on zoanthids as well as LPS, SPS and soft corals, and they only seemed to love it.

  10. This article has convinced me to get some super porous media and a bottle of PNS pro bio for my reef. Thanks for the great read!

    1. Kenneth Wingerter

      Hi Jonathan,

      We believe you’re totally onto something there. This bacteria does so much that we haven’t gotten around to it yet, but we definitely intend to elaborate a bit on possible special applications. And one of those suggested uses for sure will be soaking it in a sponge or ceramic medium like MarinePure and then simply dropping it in the sump or refugium–instant anaerobic bacterial nitrate control!

  11. This article has some fantastic info that is applicable to my system directly. I love learning new things to improve the habitat for my reef animals.

  12. I never realized how many things factor into building an ecosystem until I started up my saltwater tank. It’s like learning creation all over again from actual beings all the way down to the tiniest bacteria! It’s crazy how far we’ve advanced in our aquaculture research and how far we’ll go to create our own little ocean right in the comfort of our home(:

  13. Andika Sitanaya

    how about with Rhodobacter capsulatus ?
    i cant found your products in my country, i found local brand contain this bacteria but it contain also with Rhodobacter capsulatus

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