Newly described microbe drives ammonia removal in cleaning of drinking water

Tuesday 12 Nov 19


Barth F. Smets
DTU Environment
+45 45 25 22 30


Hans-Jørgen Albrechtsen
DTU Environment
+45 45 25 15 86

Recent Publication

Gülay, A. S. J. Fowler, K. Tatari, B. Thamdrup, H.-J. Albrechtsen, W. A. Al-Soud, S. J. Sørensen, B. F. Smets. 2019. DNA and RNA-SIP reveal Nitrospira spp. as key drivers of nitrification in groundwater-fed biofilters. mBIO On line doi: 10.1101/703868

Previous Relevant Publications

Tatari, K., B. F. Smets, H.J. Albrechtsen. 2013. A novel bench-scale column assay to investigate site-specific nitrification biokinetics in biological rapid sand filters. Water Res.  47: 6380-6387 doi: 10.1016/j.watres.2013.08.005

Palomo, A., A. Gülay, S. J. Fowler, S. Rasmussen, T. Sicheritz-Ponten, B. F. Smets. 2016. Metagenomic analysis of rapid gravity filter microbial communities suggest novel physiology of  Nitrospira spp. ISME Journal.10: 2569-2581 doi:10.1038/ismej.2016.63

Tatari,K, S. Musovic, A. Gülay, A. Dechesne, H.-J. Albrechtsen, B. F. Smets. 2017 Density and distribution of nitrifying guilds in rapid sand filters for drinking water production: dominance of Nitrospira spp. Water. Res. 127: 239-248 doi: 10.1016/j.watres.2017.10.023

Fowler, S. J., A. Palomo, A. Dechesne, P.D. Mines, B. F. Smets. 2018 Comammox Nitrospira are abundant ammonia oxidizers in diverse groundwater-fed rapid sand filter communities. Environ. Microbiol. 20, 1002–1015. doi: 10.1111/1462-2920.14033

A team of researchers from DTU, SDU, and KU has provided conclusive evidence that the recently described enigmatic microbe, called comammox Nitrospira, drives nitrification in rapid sand filters that are used to prepare drinking water from groundwater.

Since the dawn of microbiology, it was thought that nitrification – the processes of ammonia to nitrate oxidation – a central part of the biogeochemical nitrogen cycle was performed in two steps by two distinct and complementary groups of micro-organisms, called ammonia oxidizing bacteria and nitrite oxidizing bacteria, respectively.

Near the end of 2015, four research groups nearly simultaneously published the observation of a hitherto unknown metabolism called ‘complete ammonia oxida-tion’ or ‘comammox’. Indeed, a microorganism was discovered – of the genus Nitrospira – with the ability to oxidize ammonia ‘in one step’ to nitrate. The research team at DTU had obtained evidence of the existence of such bacterium by reassembling a microbial genome from the extracted DNA of the microbial community present in a rapid sand filter, the typical process by which groundwater is polished to generate potable water.

Occurrence in the environment
While the early pure cultures studies had shown that comammox Nitrospira can perform ammonia to nitrate oxidation, so far no rigorous proof for the occurrence or significance of this metabolism in the environment had been provided.

Providing definitive proof of ‘which microbe does what’ in the environment is no trivial task, because it is difficult to make the right measurements and microbes occur typically in very complex communities comprising of 1000s of different types, and a myriad of processes and interactions take place.

So here the researchers did the next best thing: they brought a sample of the rapid sand filter material – intact with the total microbial community - to the laboratory. They had developed a method to keep the environmental conditions in the laboratory nearly identical to the conditions in the field. Under those conditions, the microbes revealed themselves. They identified which microbes of the total microbial community were active under various feeding conditions – using a technique called Stable Isotope Probing. In Stable Isotope Probing, activity is verified based on the active synthesis of new nucleic acid, which can be extracted and physically separated from old nucleic acid because the incorporation of the stable isotope makes it slightly heavier. This separated new nucleic acid is then subject to sequence analysis from which researchers determine the active microbes.

“With this analysis, we were able to show that with ammonia as the primary energy source, Nitrospira types were the most active – and were at least 10-fold more active than any of the typical ammonia oxidizing bacteria! In addition, Nitrospira types made up as much as 20 to 50 % of the total microbial community,” says Prof. Barth F. Smets from DTU Environmental Engineering, senior author and coordinator of the research, recently published in the journal mBIO.

“Clearly then, we have provided conclusive evidence that comammox Nitrospira is able to display its metabolism under environmental conditions – and drives nitrification in the examined rapid sand filter environments”

A lot remains to be learned
This finding strongly support that this novel microbe not only exists but can be essential for nitrification in technical water purification processes. Prof. Smets and his research group have noted the dominance of this unique microbe in every rapid sand filter they have examined in Denmark – but they still do not know what conditions are essential for its success. For example, it does not dominate in all water purification systems around the world – and even in the Danish systems other nitrifying microbes are often present.

“The ability to ensure full nitrification is a true asset when preparing drinking water, as incomplete nitrification results in the accumulation of nitrite, a compound with severe human toxicity,” says Prof. H.J. Albrechtsen, co-author of the study. Identifying the environmental conditions that favor the presence of comammox Nitrospira is, therefore, a priority from both a basic and applied perspective.

Prof. Smets believes they have only scratched the surface of comammox Nitrospira and a lot remains to be learned. The research was originally funded by the Danish Strategic Research Council and the Villum Foundation. His group is now actively searching for continued support to develop a better understanding of both the ecology and evolutionary biology of comammox Nitrospira, and has the ambition to develop more efficient and robust nitrification processes based on comammox Nitrospira.

News and filters

Get updated on news that match your filter.
13 DECEMBER 2019