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How PNS Bacteria Promote a Healthier Aquarium

Updated: Mar 6, 2023

In the aquarium hobby, there are Good Tanks and there are Bad Tanks. Good Tanks are stable, do not experience abrupt fluxes in water quality and do not foster pests or disease. Bad Tanks constantly require the addition of chemicals or new filtration in order to maintain water quality. Because of this, they often cultivate unseemly pest algae and opportunistic pathogenic bacteria. Nature tells us that the primary difference between the two is a matter of ​functional microbial diversity​. “Beneficial” microbes directly consume both dissolved and solid wastes, produce valuable nutritious compounds and ward-off destabilizing pests/disease.

Coral reefs are some of the most diverse and productive ecosystems on the planet because of the incalculable microbial diversity they contain. Therefore, functional microbial diversity is one of the most important considerations to establishing a successful reef aquarium.

A Brief Note on Microbes in the Aquarium

No reef aquarium is successfully maintained without establishing a stable and functional microbial community. It is well known that nitrifying bacteria species (​Nitrosomonas,​ ​Nitrobacter​, etc.) are paramount to detoxifying ammonia/nitrite. The value of these nitrifying “biofilter” species is so well-recognized that it has led to a menagerie of commercial probiotics. These products allow the aquarium keeper to ensure that their tank is seeded with specific bacterial strains. Once these bacteria establish a successful population, they sustain themselves by consuming biological wastes--thus generating greater stability for the reef’s other inhabitants.

Microbial seeding through efficacious probiotic products is one of the most important tools available to the 21st Century Reef Aquarist. By promoting the establishment of more and more beneficial bacterial populations, the aquarist is promoting a greater overall functional microbial community. Though there are still relatively few commercial strains of aquarium bacteria available, some new emergents, such as ​Rhodopseudomonas palustris,​ offer considerable benefits to the reef aquarium.

R. palustris​ is a gram-negative, purple non-sulfur bacterium belonging to the family Bradyrhizobiaceae. Using its metabolic superpowers, wild ​R. palustris​ colonies stabilize and enrich marine and freshwater ecosystems worldwide. It has been long studied for its applications in wastewater management and commercial aquaculture. This is because​ R. palustris​ is an aggressive consumer of nitrogenous wastes, but more importantly can consume them in a variety of ways and convert them into nutritious compounds.

Limitations of the Conventional Biofilter

The conventional nitrifying biofilter species, ​Nitrosomonas,​ can only primarily utilize ammonia as an energy source. Using oxygen, ​Nitrosomonas oxidizes ammonia into nitrite, which is then oxidized into nitrate by a separate biofilter species such as ​Nitrobacter​ or ​Nitrospira. Interdependent synergy between ammonia and nitrite oxidizers is the basic function of conventional biofilters. However this traditional complex of nitrifying critters has its strict requirements/limitations:

  • The​ Nitrosomonas​/Nitrobacter ​complex requires large concentrations of O2 to function.

  • The​ Nitrosomonas​/Nitrobacter​ complex requires that both species to grow proportionately (otherwise nitrite accumulates).

  • The ​Nitrosomonas​/Nitrobacter​ complex must be kept in the dark and is highly inefficient in the light.

If any of these conditions are not adequately met, the conventional biofilter will either cease to function or operate below the necessary capacity to support the reef inhabitants. Therefore, there is a pressing need to reinforce a reef’s biological filtration so as to prevent abrupt increases in toxic ammonia/nitrite.

There is another major limitation to the conventional biofilter, namely that it ends with nitrate accumulation which can stress fish/corals and induce blooms of ugly and harmful pest algae. Denitrification is the metabolic process where nitrate is reduced into benign nitrogen gas (which then escapes the aquarium altogether). However this process can only be conducted in the absence of oxygen, which means deep in the rockwork or sand. These areas receive minimal flow and therefore have minimal impact on overall water quality. This reality means that most biofilters will inevitably produce growing concentrations of nitrates, which will have to be removed by mechanical water changes.

An age-old goal of reef aquarium keeping is to increase the functional diversity of biofilters as to foster a greater overall stability and thereby reduce the need for large water changes. Rhodopseudomonas palustris​ compliments, and in many ways, surpasses, the limitations of the conventional biofilter.

R. palustris​’ Swiss-Army Knife Metabolism

To understand the myriad of benefits ​R. palustris​ offers to the reef aquarium system, one must become familiar with its swiss-army knife metabolism.

Photosynthesis. R. palustris​ can utilize light as an energy source. Doing this requires consumption of carbon, ammonia/nitrate and phosphate. It can (like algae) perform photoautrophy, utilizing inorganic (e.g. CO2) as a carbon source; however, it prefers photoheterotrophy, utilizing organic carbon sources.

Assimilation. Like the aerobic species we mainly target when carbon dosing , ​R. palustris​ can take up ammonia, nitrite, nitrate and phosphate. These nutrients are thereafter exported from the system via protein skimming.

Denitrification. In the absence of oxygen, ​R. palustris​ can reduce nitrate into harmless N2 gas.

Anammox. It appears that R. palustris​ can also conduct a relatively unusual ​comproportionation reaction in which ammonium reacts with nitrite to produce N2 gas and water.

Colonies of​ R. palustris​ will shuffle through these different modes of metabolism as contextualized by the levels of nutrients, light and oxygen around them. This means that ​R. palustris​ need not compete directly with an established biofilter, because it can utilize an enormous range of alternative energy sources. Because it can survive in anaerobic and illuminated conditions, it can occupy an entire range of substrates not available to conventional biofilter species. Yet because it can also utilize ammonia and nitrite, ​R. palustris​ can easily fulfill the ecological niche of an acutely collapsed or disrupted biofilter.

Because ​R. palustris​ is such an effective consumer of nitrogenous wastes, it acts to starve out many troublesome pest algae species which thrive on excess nitrates and phosphates. It is also able to localize itself in areas where these pest algae tend to grow. There is a growing host of work studying​ R. palustris​’ suppression of various bacteria and viruses.

R. palustris’ Nutritional Contribution

Besides its biofiltration capability, the most attractive aspect to ​R. palustris ​is its nutritional content. PNS bacteria in general utilize pigments known as carotenoids in order to capture light for photosynthesis. These carotenoids have a myriad of health benefits to higher organisms which include general anti-inflammatory/antioxidant properties. Carotenoids are anecdotally also known to improve color performance in fish/coral.

PNS​ ​bacteria also contain functional enzymes and proenzymes which benefit the intestinal system of fish and inverts. This has led to growing application of ​R. palustris​ as a feed probiotic for commercial aquaculture species such as carp and shrimp. Certain marine sponge species have demonstrated a symbiotic relationship with living​ R. palustris​ colonies. This opens the prospect for the purposeful use of probiotics to keep previously impossible species alive.

Species most likely to directly consume​ R. palustris include:

  • Corals

  • Sponges

  • Live Feed (rotifers, copepods, brine shrimp, etc.)

  • Sabellid worms

  • Tridacnid clams

  • Porcelain Crabs

  • Other finicky filter-feeders


The photosynthetic purple bacterium ​Rhodopseudomonas palustris​ has both established and unrecognized value to the reef aquarium. ​R. palustris​ can complement and enhance an established biofilter, leading to a more comprehensive elimination of nitrogenous wastes through denitrification. PNS bacteria deprive those nitrogenous wastes to pest algae species and recycles them into nutritious protein and carotenoids. That nutrition is redelivered in a bioavailable form to corals and other delicate invertebrates (clams, sponges etc.).

Hydrospace PNS ProBio live ​Rhodopseudomonas palustris​ cultures represent a New Wave of purposeful probiotic seeding, one that will eventually help make reefkeeping easier, less resource-intensive and perhaps even allow for the husbandry of new species. The deployment of functional microbes reflects a desire by professionals and serious hobbyists to learn from the beautiful complexity of nature, rearranging its elements to create new worlds.

Literature Cited

Alloul, A., Wille, M., Lucenti, P., Bossier, P., Van Stappen, G., & Vlaeminck, S. E. (2021). Purple bacteria as added-value protein ingredient in shrimp feed: Penaeus vannamei growth performance, and tolerance against Vibrio and ammonia stress. ​Aquaculture,​ ​530,​ 735788.

Capone, D. G., Dunham, S. E., Horrigan, S. G., & Duguay, L. E. (1992). Microbial nitrogen transformations in unconsolidated coral reef sediments. ​Marine Ecology Progress Series,​ 75-88.

Getha, K., & VIKINESWARY, S. (1998). Potential Use of the Phototrophic Bacterium, Rhodopseudomonas palustris, as an Aquaculture. ​Asian Fisheries Science,​ ​10,​ 223-232.

Guérin, J. P., & Rieper-Kirchner, M. (1991). Influence of three bacteria strains on the population dynamics of Tisbe holothuriae (Copepoda, Harpacticoida). ​Helgoländer Meeresuntersuchungen​, ​45​(4), 493-511.

Kim, J. K., & Lee, B. K. (2000). Mass production of Rhodopseudomonas palustris as diet for aquaculture. Aquacultural Engineering​, ​23​(4), 281-293.

Kuo, F. S., Chien, Y. H., & Chen, C. J. (2012). Effects of light sources on growth and carotenoid content of photosynthetic bacteria Rhodopseudomonas palustris. ​Bioresource Technology​, ​113​, 315-318.

Loo, P. L., Vikineswary, S., & Chong, V. C. (2013). Nutritional value and production of three species of purple non-sulphur bacteria grown in palm oil mill effluent and their application in rotifer culture. ​Aquaculture Nutrition,​ 19(​ 6), 895-907.

Peirong, Z., & Wei, L. (2013). Use of fluidized bed biofilter and immobilized Rhodopseudomonas palustris for ammonia removal and fish health maintenance in a recirculation aquaculture system. ​Aquaculture Research,​ ​44(​ 3), 327-334.

Seewaldt, E., Schleifer, K. H., Bock, E., & Stackebrandt, E. (1982). The close phylogenetic relationship of Nitrobacter and Rhodopseudomonas palustris. ​Archives of Microbiology,​ ​131(​ 3), 287-290.

Souza-Santos, L. P., Castel, J., & Santos, P. J. P. (1996). The role of phototrophic sulfur bacteria as food for meiobenthic harpacticoid copepods inhabiting eutrophic coastal lagoons. Coastal Lagoon Eutrophication and Anaerobic Processes (CLEAN.)​ (pp. 79-89). Springer, Dordrecht.

Su, P., Tan, X., Li, C., Zhang, D., Cheng, J. E., Zhang, S., ... & Lu, X. (2017). Photosynthetic bacterium R hodopseudomonas palustris GJ-22 induces systemic resistance against viruses. ​Microbial Biotechnology,​ ​10(​ 3), 612-624.

Su, P., Feng, T., Zhou, X., Zhang, S., Zhang, Y., Cheng, J. E., ... & Liu, Y. (2015). Isolation of Rhp-PSP, a member of YER057c/YjgF/UK114 protein family with antiviral properties, from the photosynthetic bacterium Rhodopseudomonas palustris strain JSC-3b. ​Scientific Reports​, ​5(​ 1), 1-10.

Wang, Y. (2011). Use of probiotics Bacillus coagulans, Rhodopseudomonas palustris and Lactobacillus acidophilus as growth promoters in grass carp (Ctenopharyngodon idella) fingerlings. ​Aquaculture Nutrition,​ ​17(​ 2), e372-e378.

Xue, L., & Zhang, W. (2009). Growth and survival of early juveniles of the marine sponge Hymeniacidon perlevis (Demospongiae) under controlled conditions. Marine Biotechnology, 11(5), 640-649.

Zhang, X. B., Zhu, B. T., Xiong, H., ZHAO, C., & YANG, S. (2015). Simultaneous removal of inorganic nitrogen from aquaculture water by Rhodopseudomonas palustris CQV97. ​Amino Acids & Biotic Resources,​ ​37(​ 4), 38-45.

1,606 views7 comments


Very interesting


Josh V
Josh V
Jul 19, 2021

So this could be a biological control for high nitrates?

Hydrospace LLC
Hydrospace LLC
Jul 20, 2021
Replying to

Actually, PNS bacteria benefit corals in low nutrient systems as well! The reason is that these bacteria are diazotrophs, meaning they can fix nitrogen when ammonia/nitrite/nitrate is scarce. Diazotrophy is basically the opposite of denitrification: Nitrogen gas to ammonia. So, these guys will actually supply ammonia to zooxanthellae (which prefer ammonia to nitrate) as sources of fixed nitrogen become depleted in the environment. No worries, they can't overdo this, because this process is halted in the presence of ammonia (a negative feedback called "ammonia shut-off"). Believe it or not, natural coral reefs generally are nitrogen-limited environments, and it is specifically because of diazotrophic bacteria that they are so productive! For more on this, check out this article from our blog:…


Jorge Cabrera
Jorge Cabrera
Jul 19, 2021

Very informative article. Thank you.


Tina Wahrmund
Tina Wahrmund
Jul 19, 2021

Thanks for the interesting information. I found it very informative.

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