Rethinking the N cycle

New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation

This paper is relevant to our next lectures and is hyper-linked to on the lecture slides. The paper has a lot of details but here I have taken the main points.

Nitrogen is fundamental to the structures and biochemical processes that define life. Our understanding of how this element is cycled on Earth has changed drastically in just the last few years. First by the discovery of anaerobic ammonium oxidation in natural systems, and more recently by the discovery of aerobic ammonia oxidation within the domain Archaea.

In the conventional view of nitrification (NH3-NO2_-NO3_), the metabolic labour is divided between two distinct groups of organisms, ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). Denitrification (NO3_-NO2_-NO-N2O-N2) is primarily heterotrophic, facultative, occurs under low oxygen conditions and is widespread among over 50 different genera. In this mini review, the authors focus on recent developments related to the microbial ecology of anaerobic and archaeal ammonia oxidation.

Heterotrophic denitrification was considered the only sink for fixed nitrogen under anoxic conditions in natural systems. But then anaerobic ammonium oxidation (anammox) to N2 gas was obtained from anoxic (denitrifying) bioreactors of wastewater treatment plants by ‘anammox’ bacteria that have unique features. These features include; the use of hydrazine (N2H4, i.e., rocket fuel) as a free catabolic intermediate, the biosynthesis of ladderane lipids and the presence of an anammoxosome (intracytoplasmic compartment).

Anammox has been found to be ubiquitous and will likely to be found in virtually any N-containing ecosystem with a pronounced suboxic zone or chemocline. The process has been found to be going on in a number of environments using a combination of 15N-based tracer studies, analysis of ladderane lipid biomarkers, fluorescent in situ hybridization and phylogenetic and quantitative PCR analysis of 16S rRNA sequences. More sophisticated tracer methods and/or gene marker studies are needed to assess the importance of this process in the environment and research is underway. However studies so far indicate that anammox is probably responsible for 30–50% of all marine N loss.

The review also summarizes studies that have found ‘new players in the N cycle’. They are among the mesophilic Crenarchaeota which are mesophilic archaea that are now recognized to be an ubiquitous component of marine plankton. The genes and associated enzymes of ammonia oxidation are being found in many archaea clades. The review concludes that ammonia oxidizing archaea are much more abundant than ammonia oxidizing bacteria.

The review has a whole section discussing these new paradigms. It says that the processes can only be characterized by employing multiple, complimentary approaches, to address a growing number of questions. One such question is; if N loss in oxygen minimum zones is principally driven by the autotrophic process of anammox rather than heterotrophic denitrification, what happens to organic carbon, if it is not remineralized via denitrification? There are many other questions posed that ask us to rethink the N cycle.

It is clear that the microbial ecology of anammox bacteria and AOA will be an area of active research for years to come, and will be essential to our understanding of the global N and carbon cycles going forward.