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Discussion Starter · #1 · (Edited by Moderator)

Hi, I'm Christopher Taylor, author of the blog Catalogue of Organisms. At that site, I look at the diversity of life on this planet, and I've been asked if I'd like to contribute something for you to read here.

I have to confess, the request initially put me at something of a loss - I haven't any experience of my own in keeping marine aquaria, and only a little with freshwater fish tanks. So I'm not going to talk about fish - not directly, anyway. I'm going to talk about something else that you will all have living in your tanks, in large numbers, and which you've possibly never even noticed - bacteria.

Some of the less fortunate of you may be all too aware of the vital role that bacteria play in your tank. Many people (including, I have to admit, myself), when first setting up a new aquarium, will have tried to put too many fish into the tank too quickly, and then had the absolutely heart-wrenching experience of seeing them die off in quick succession. Not a pleasant experience for you, and I'm sure an even worse one for the fish. If you were more fortunate (or better prepared), you will have learnt all about the necessity for a properly set up nitrogen cycle before you started. Fish produce nitrogen waste products in the form of ammonia, which is highly toxic if allowed to build up.

Bacteria that live on ammonia convert it into nitrite, which is less toxic than ammonia but still pretty unpleasant. Other bacteria then turn the nitrite into nitrate, which is relatively harmless, at least in the short term. In the natural environment, other bacteria then convert the nitrate into completely harmless nitrogen gas, but as these bacteria are generally anaerobic (they live in places without oxygen), they often won't be found in home tanks and most people will have to use more mechanical methods of removing excess nitrates, such as changing the water in the tank. And if you add too many fish to a new tank too quickly, like I did, then toxic ammonia and/or nitrites build up before enough bacteria have grown up to remove them from the water.

So what are these bacteria that are so necessary to your fish? It may surprise you to learn that this isn't as simple a question as it sounds. Not so long ago, researchers thought that they had a pretty good handle on the world's bacterial diversity. Traditionally, bacterial diversity had been studied by culturing them in the laboratory, and by the late 1980s the point had been reached when relatively few undescribed bacteria were turning up in cultures.

In the early 1990s, however, researchers added a new method to bacterial diversity studies - direct genetic analysis of environmental samples. By seeing how many different variants of a particular gene (usually ribosomal DNA) they could extract from a sample, researchers could get an indication of how many different types of bacteria were in that sample. The results were stunning - an incredible diversity of uncultured bacteria were out there. Less than one percent of bacterial species, it turns out, have been described. Traditional culture methods still have their place - new bacterial species still need to be cultured before we can learn many things about them - but we certainly don't know as much as we thought we did.

The bacteria that are usually mentioned in connection to the nitrogen cycle are Nitrosomonas (converting ammonia to nitrite) and Nitrobacter (nitrite to nitrate). Both of these belong to a group called Proteobacteria, which is one of the largest bacterial classes. Nitrosomonas is a member of the subgroup called beta-proteobacteria, while Nitrobacter belongs to the alpha-proteobacteria and is a not-too-distant relative of the Rhizobium bacteria that fix nitrogen in the roots of beans and other legumes. While it seems to be widely assumed that these are the major bacteria involved in nitrogen cycling in aquaria, this is not necessarily the case. A study by Hovanec and DeLong (1996) on bacteria in aquaria found Nitrosomonas to be common in samples from marine aquaria, but nearly absent in freshwater aquaria, while Nitrobacter was undetectable in either. Nitrogen cycling was proceeding as normal in all the aquaria tested, so there was no question that some kind of bacteria was fulfilling the required roles, it just wasn't the bacteria expected.

As it turns out, the bacterium most responsible for converting nitrite to nitrate in aquaria is not Nitrobacter, but Nitrospira (Foesel et al., 2007). Nitrospira was only first described in 1986, and belongs to a small, relatively little-known group of bacteria called Nitrospirae, evolutionarily isolated from nitrogen-cycling Proteobacteria.

The question of which bacterium is most responsible for converting ammonia to nitrite, on the other hand, remains uncertain. One of the most unexpected discoveries of recent years was the potential significance of Crenarchaeota in nitrogen cycling. Crenarchaeota are one of the major subgroups of the Archaea, a distinctive group of prokaryotes (organisms without nuclei in their cells) that many researchers regard as more closely related to eukaryotes such as ourselves than to bacteria such as Nitrosomonas (though, as the ancestors of Archaea and ourselves probably went their separate ways over one billion years ago at least, "more closely" is obviously a relative term).

The first Crenarchaeota to be cultured were from hyperthermophilic environments such as deep-sea sulfur vents. These are organisms that prefer to live their lives at temperatures approaching - sometimes even surpassing - one hundred degrees Celsius. It therefore came as some surprise when environmental DNA samples suggested that Crenarchaeota were not restricted to such environments, but were extremely common at more bearable temperatures. The room-temperature crenarchaeote Candidatus Nitrosopumilus* was successfully characterised in 2005 (Kצnneke et al., 2005), and was found to live on ammonia. And while Foesel et al. (2007) reaffirmed that Nitrosomonas was the most abundant ammonia-oxidising bacterium in marine aquaria, a study by Urakawa et al. (2008) found the exact opposite - that Archaea were more abundant in marine aquaria than Proteobacteria such as Nitrosomonas.

*There are strong restrictions on the naming of new bacteria. The term "Candidatus" before the non-italicised name of a bacterium indicates that that bacterium is well-characterised enough to be recognised, but for some reason (usually that it cannot be maintained in a separate laboratory culture) it can't qualify as a fully "official" species.*

So we still have a lot to learn about aquarium bacteria (or bacteria anywhere, for that matter). It is quite possible that there are even more undescribed species busy maintaining the nutrient balance of your tank, keeping the environment bearable for anything else living in it. The only way to find out is to look.


Foesel, B. U., A. Gieseke, C. Schwermer, P. Stief, L. Koch, E. Cytryn, J. R. de la Torrי, J. van Rijn, D. Minz, H. L. Drake & A. Schramm. 2007. Nitrosomonas Nm143-like ammonia oxidizers and Nitrospira marina-like nitrite oxidizers dominate the nitrifier community in a marine aquaculture biofilm. FEMS Microbiology Ecology 63 (2): 192-204.

Hovanec, T. A., & E. F. DeLong. Comparative analysis of nitrifying bacteria associated with freshwater and marine aquaria. Applied and Environmental Microbiology 62 (8): 2888-2896.

Kצnneke, M., A. E. Bernhard, J. R. de la Torre, C. B. Walker, J. B. Waterbury & D. A. Stahl. 2005. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437: 543-546.

Urakawa, H., Y. Tajima, Y. Numata & S. Tsuneda. 2008. Low temperature decreases the phylogenetic diversity of ammonia-oxidizing Archaea and Bacteria in aquarium biofiltration systems. Applied and Environmental Microbiology 74 (3): 894-900.

Christopher Taylor runs Catalogue of Organisms, a blog with an inordinate fondness for systematics. This is no surprise as Chris is currently studying to get his PhD on the diversity among one particular lifeform--arachnids, making almost full-time use of his university's library facilities. He lives in Australia.

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