The shift that sparks nitrification: PML research resolves long-standing mystery within the nitrogen cycle

Nitrification is a two-step microbial process that converts ammonium into nitrate. It plays a major role in ocean chemistry, because nitrate fuels new primary production, and, when it does not work well, nitrification also leads to production of the potent greenhouse gas, nitrous oxide. 

But scientists have long been puzzled. In many ocean regions, ammonium is present, but nitrification is surprisingly variable, sometimes spanning several orders of magnitude. Why?  

The answer, it turns out, lies in how microbes* break down dissolved organic matter in seawater.

*Marine microbes include microalgae, mixoplankton, microzooplankton, bacteria, archaea, viruses, and marine fungi – tiny organisms that drive ocean life and global biogeochemical cycles. 

A new study led by PML’s Professor Kevin Flynn and Dr Luca Polimene of the Joint Research Centre of the European Commission has, for the first time, revealed why nitrification doesn’t always occur even when ammonium is available, finding that the answer is linked to the consumption and transformation of different components of DOM.  

The year-long laboratory experiments, designed and executed by Darren Clark and Susan Kimmance [with authors acknowledging their “herculean” efforts continuing during the depths of the Covid-19 crisis, also aided by Elaine Fileman and Glen Tarran], were supported by computer simulations. Collectively the research shows that the quality of DOM – as it ages from being fresh and labile, to aged and recalcitrant – controls when nitrification can begin. 

While DOM itself is not used by nitrifiers, the way it is broken down has a profound effect on the microbial communities that compete to thrive in seawater – and this turns out to be the hidden switch that controls when nitrification becomes apparent. 

As DOM is processed by microbes – over weeks to months to years – its composition changes dramatically. And at a particular tipping point, when the easier-to-digest forms of DOM have been consumed, ecological space opens up for a specialist group of microbes – the nitrifiers – to thrive. 

The paper’s experiments show this transformation with rare clarity. Over the course of 150–360 days, researchers tracked natural microbial communities process microalgal-derived DOM.  

At the start of the experiments, heterotrophic bacteria (microbes that get their energy by consuming organic carbon, rather than producing their own food) use the abundant labile DOM as fuel, releasing ammonium as a by-product. They also out-compete nitrifiers (slow-growing bacteria and archaea that use ammonium as their energy source, converting this into nitrate and fixing CO₂) for nutrients and space. But as the supply of readily used DOM dwindles, the ecosystem changes, and an entirely new microbial process rises to prominence.  

With competition decreased and in the presence of sufficient ammonium (which accumulated during the processing of the labile DOM), nitrifiers finally gain a foothold. Their slow, steady metabolism becomes advantageous – and nitrification appears to “switched on.” 

No previous study has ever had empirical data demonstrating the full microbial succession linked directly to DOM processing. 

Dr Karen Tait, Microbial Ecologist at PML, and who contributed to analysis of the laboratory experiment, said: 

“Tracking the microbial community over nearly a full year using molecular biological techniques gave us an unusually detailed view of how the prominence of different groups rise and fall as DOM is processed. The downturn in ammonium and rise in nitrate coincided with the late-stage degradation of DOM and the appearance of nitrifying archaea and bacteria.” 

“Watching nitrifiers come to dominate only once the system was carbon-limited was striking – it showed how tightly linked microbial ecology is to larger-scale biogeochemical cycles.” 

The simulation model developed by Professor Kevin Flynn and colleagues’ supports this interpretation. The model simulated the activities of three groups of microbes, aligning with the groups identified using molecular biology: 

• Generalists: fast-growing bacteria that rapidly consume labile DOM 

• Specialists: organisms capable of attacking more complex DOM compounds 

• Nitrifiers: slow-growing chemolithotrophs that depend on ammonium and derive their carbon from fixing CO₂ using the energy gained by oxidising ammonia to nitrate (Yes, not all CO₂-fixation is photosynthetic!) 

The model shows a clear ecological succession: 

• Generalists dominate when fresh and labile DOM is plentiful 

• Specialists take over as the DOM becomes harder to break down 

• Nitrifiers finally rise, growing slowly but steadily once competition for DOM diminishes and the other groups lose their growth advantage 

This microbial “relay race” mirrors the changes recorded in the laboratory bottles. 

Prof Kevin Flynn, Plankton ecophysiology modeller at PML, said: 

“Think of it like a relay race. First, the fast-growing bacteria quickly consume the easily digestible organic matter – the ocean’s equivalent of fast food. But as this runs out, a completely different group of microbes takes over, and this is where things get really interesting.”  

“What we saw in both the experiments and the model is that nitrifiers don’t simply ‘switch on’ because ammonium is present. They appear when the wider microbial community has exhausted the easily exploited DOM. That tipping point changes the competitive landscape, and suddenly nitrification becomes apparent as the winning strategy. It is a beautifully simple mechanism hidden within extraordinarily complex chemistry.” 

“We need empirical studies, and often long-term experiments like those we conducted to understand these key natural processes taking place in our Ocean, that not only shape marine ecosystems but may also influence climate-relevant gases and the long-term storage of carbon.” 

Dr Luca Polimene, of the Joint Research Centre of the European Commission, and Honorary Fellow at PML, spoke of the relevance of the study in a changing climate: 

“Climate change is expected to alter the supply and quality of DOM in the sea. With warmer, more stratified waters, phytoplankton may produce more carbon-rich, recalcitrant DOM. Enhanced production of recalcitrant DOM could favour nitrifiers in the competition with heterotrophic bacteria, in this way altering the balance between CO₂ fixation (through nitrification) and production (through heterotrophic metabolism).  Our work provides a new framework for understanding the interplay between DOM, nitrification, and the impacts of climate change on the marine microbial community.” 

There is another aspect to all of this, however. Ocean acidification decreases the rate of nitrification because it alters the balance of ammonium and ammonia (the latter being the form used in nitrification). How this may affect the formation of rDOM as a form of sequestered carbon, of the greenhouse gas nitrous oxide, and the balance of ammonium and nitrate that supports primary production remains to be explored. 

The full scientific paper, ‘The emergence of nitrification during DOM processing by marine microbial assemblages’, is available via PLOS One here >> 

Paper: Flynn, K.J., et al. (2025).  The emergence of nitrification during DOM processing by marine microbial assemblages. PLOS One.

DOI: https://doi.org/10.1371/journal.pone.0336919