The Nitrogen Cycle - The Paradigm Shifts

In an earlier posted article, Archaea The not-so-new-kids-on-the-block, we briefly discussed the emergence of certain species of the Domain Archaea as the prime ammonia oxidizing organisms in both terrestrial and aquatic environments world-wide.
Over the past several years there has been increasing evidence that a similar altering of perceived role dominance is extant in Nitrite oxidation.
Some bacterial and archaeal species defy replication under lab condition and have also defied easy identification by past known means. The bacterium Nitrospira is one such micro-organism. Only recently has a method been developed allowing for somewhat better identification. As a result, what has been discovered has changed the paradigm not only as relates to Nitrite oxidation but also, to a point, Ammonia oxidation.
Enough evidence has been amassed to date to confirm that in many aquatic environments Nitrospira is the dominant Nitrite oxidizing specie instead of Nitrobacter. This is most noticeable in waters that have an elevated Ammonia level. These elevated Ammonia levels inhibit the Nitrite oxidizing process in Nitrobacter but has no effect on the efficiency of Nitrospira. This means in an aquatic habitat where the Nitrogen cycle is not established or balanced Nitrospira will likely be the dominant Nitrite oxidizer with Nitrobacter increasing in numbers only when Ammonia levels have been reduced. This does not mean that Nitrospira’s role becomes diminished. Nitrospira has the almost unique ability to also convert Urea into Ammonia. It forms a quasi-symbiotic relationship with Nitrosomonas and, it is suspected, Archaea, supplying Ammonia in ezchange for Nitrite. So even in an established well-balanced aquatic habitat the Nitrite oxidizing duties are at least shared by Nitrobacter and Nitrospira.
In addition, Nitrospira remain active in anoxic conditions.
No longer are certain processes relegated exclusively to certain micro-organisms, but rather new organisms have emerged as the dominant players that are capable of performing multiple processes in the Nitrogen cycle.
The paradigm continues to shift.

Archaea--Update

In 1977, while Dr. Carl Woese and his colleagues at the University of Illinois were using a then new process of DNA sequencing for studying relationships between bacteria, it was discovered that there were two distinctly different groups. Those “bacteria” that lived at high temperatures (extremophiles) or produced methane formed a group quite different genetically from the usual bacteria. Because of this vast genentic difference in makeup, Dr. Woese proposed that a new domain of life be added…Archaea.

The scientific community was understandable shocked by this proposal and for several years balked at accepting such a major revision in century old thinking. Further research subsequently validated Dr. Woese’s proposal and in 1990 the existing three domains of life (Bacteria, Archaea, Prokaryote) were created.

Initially thought to exist only in extreme environments, those devoid of oxygen and whose temperatures were near or above the boiling point of water, microbiologists soon realized that Archaea are a large and diverse group of organisms that are ubiquitous to all environments-terrestrial and aquatic and significant contributors to the global carbon and nitrogen cycles. It is the role of Archaea in the nitrogen cycle (specifically aquatic) that is of interest and the focus of this document.

Since the acceptance of Archaea as a separate Domain of life, research has been both intensive and massive, delving into all aspects of this life form. Much of this research has been on the role of Archaea in the Nitrogen Cycle with the results of this research simultaneously upending some long held beliefs and yet clarifying other processes.

For Pondkeepers, maintaining the equilibrium of the Nitrogen cycle is of the first order of importance. To be able to do so requires a certain level of knowledge of how the involved biological processes work. Most Pondkeepers know that Ammonia is oxidized by Nitrosomonas bacteria et.al. to Nitrite which is oxidized by Nitrobacter bacteria et.al. to Nitrate which is assimilated by algae and plants or reduced to Nitrogen gas by other bacteria. Archaea do nothing to change this, but supplement the process, providing, shall we say, more efficiency in the initial Ammonia oxidation stage.

AOA (Ammonia Oxidizing Archaea) and AOB (Ammonia Oxidizing Bacteria) both occupy important niches in the Nitrogen cycle. In Oligotrophic (low nutrient) waters, AOA are the predominant organisms and in Eutrophic (high nutrient) waters AOB dominate.

In the world’s oceans, AOA are now known to be the primary oxidizers of Ammonia, replacing AOB which for decades were believed to have performed this function. The same has been found true in many freshwater lakes and even in some soils. So what does this mean to a Pondkeeper?

Although no true research has been undertaken targeting ponds specifically, there have been two (2) papers^1,2 (2011 and 2014) addressing the roles of AOA and AOB in aquaria. Additionally,  a Master’s thesis³ on this subject was also written in 2014. The results of these three (3) documents can logically be applied to garden ponds as both (ponds and aquaria) are closed systems.

What was revealed in all of these research documents was that in established and balanced aquaria, AOA were not only the dominant, but in some cases, the only oxidizer present. This is not to imply that AOB have lost their status as being an integral part of a pond’s Nitrogen cycle, but that their role of importance is limited to establishing the initial balance in a new pond when Ammonia levels are high.

This begs the question: Does this really change anything?

The simple answer is…No. It does, however, because of some unusual characteristics of AOA, offer a different perspective on the Nitrogen cycle process.

For instance, it has been shown that AOA are fully capable of Ammonia oxidation in suboxic (low oxygen) conditions. They have been isolated from the sludge at various Waste Water Treatment Plants which were almost devoid of Oxygen. How Archaea are able to do this is still being researched.

It has also been suggested by some, denied by others, that AOA are still able to function at temperature approaching freezing. If proven true it could make a difference to Pondkeepers in higher Latitudes.

As yet, Archaea have only been found that convert Ammonia. None have been found that oxidize Nitrite. Considering the fact that research into this amazing organism is really in its infancy, future surprising discoveries can certainly not be ruled out.

For certain, with the newly acquired knowledge of AOA and Anamox (a subject for another discussion), a new paradigm is required for the Nitrogen Cycle.

References:

1. Temporal and Spatial Stability of Ammonia-Oxidizing Archaea and Bacteria in   Aquarium Biofilters

     Samik Bagchi1.¤, Siegfried E. Vlaeminck1., Laura A. Sauder2, Mariela Mosquera1,

Josh D. Neufeld2, Nico Boon1

2.  Aquarium nitrification revisited: thaumarchaeota are the dominant ammonia oxidizers in freshwater aquarium biofilters

     Laura A. Sauder, Katja Engel, Jennifer C. Stearns¤, Andre P. Masella, Richard Pawliszyn, Josh D. Neufeld

3. Ecology of Ammonia-oxidizing Archaea and Bacteria in Freshwater Biofilters

     Natasha Alexandria Szabolcs