J Soils Sediments (2017) 17:2709–2717 DOI 10.1007/s11368-017-1851-9 FRONTIERS IN SOILS AND SEDIMENTS • REVIEW ARTICLE Comammox—a newly discovered nitrification process in the terrestrial nitrogen cycle Hang-Wei Hu1,2 & Ji-Zheng He1 Received: 11 September 2017 /Accepted: 10 October 2017 /Published online: 18 October 2017 # Springer-Verlag GmbH Germany 2017 Abstract Results and discussion Comammox Nitrospira are environ- Purpose Nitrification, the microbial oxidation of ammonia to mentally widespread and numerically abundant in natural nitrate via nitrite, is a pivotal component of the biogeochemical and engineered habitats. Physiological data, including ammo- nitrogen cycle. Nitrification was conventionally assumed as a nia oxidation kinetics and metabolic versatility, and compara- two-step process in which ammonia oxidation was thought to be tive genomic analysis revealed that comammox organisms catalyzed by ammonia-oxidizing archaea (AOA) and bacteria might functionally outcompete other canonical nitrifiers under (AOB), as well as nitrite oxidation by nitrite-oxidizing bacteria highly oligotrophic conditions. These findings highlight the (NOB). This long-held assumption of labour division between necessity in future studies to re-evaluate the niche differentia- the two functional groups, however, was challenged by the re- tion between ammonia oxidizers and their relative contribu- cent unexpected discovery of complete ammonia oxidizers tion to nitrification in various terrestrial ecosystems by includ- within the Nitrospira genus that are capable of converting am- ing comammox Nitrospira in such comparisons. monia to nitrate in a single organism (comammox). This break- Conclusions The discovery of comammox and their broad through raised fundamental questions on the niche specializa- environmental distribution added a new dimension to our tion and differentiation of comammox organisms with other knowledge of the biochemistry and physiology of nitrification canonical nitrifying prokaryotes in terrestrial ecosystems. and has far-reaching implications for refined strategies to ma- Materials and methods This article provides an overview of nipulate nitrification in terrestrial ecosystems and to maximize the recent insights into the genomic analysis, physiological agricultural productivity and sustainability. characterization and environmental investigation of the comammox organisms, which have dramatically changed Keywords Ammonia oxidation . Comammox . Complete our perspective on the aerobic nitrification process. By using nitrification . Niche separation . Nitrite oxidation . Nitrospira quantitative PCR analysis, we also compared the abundances of comammox Nitrospira clade A and clade B, AOA, AOB and NOB in 300 forest soil samples from China spanning a 1 The discovery of comammox: a paradigm shift wide range of soil pH. − The microbial oxidation of ammonia (NH3) via nitrite (NO2 )to − nitrate (NO3 ), termed nitrification, is a central process of the Responsible editor: Zhihong Xu biogeochemical nitrogen (N) cycle (Fig. 1) (Prosser 2011). The two consecutive nitrification steps, ammonia oxidation (NH3 → * Ji-Zheng He − − → − [email protected] NO2 ) and nitrite oxidation (NO2 NO3 ), were traditionally thought to be catalyzed by two physiologically distinct clades of 1 Faculty of Veterinary and Agricultural Sciences, The University of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria Melbourne, Parkville, VIC 3010, Australia (NOB), respectively, whose close cooperation is essential for the 2 State Key Laboratory of Urban and Regional Ecology, Research complete conversion of ammonia to nitrate (Costa et al. 2006). Center for Eco-Environmental Sciences, Chinese Academy of Since the discovery of ammonia-oxidizing archaea (AOA) as a Sciences, Beijing 100085, China second major type of ammonia oxidizers (Könneke et al. 2005), 2710 J Soils Sediments (2017) 17:2709–2717 Fig. 1 Major processes of the nitrogen cycle. The classical nitrification was assumed as a two-step process performed by two functional groups of organisms: ammonia oxidizers (AOA and AOB) and nitrite- oxidizing bacteria (NOB). Recent studies have shown that comammox Nitrospira can conduct both steps of nitrification, and novel substrates can be used for the generation of ammonium. (Abbreviations: DNRA, dissimilatory reduction to ammonium) nitrification research has received an impetus towards unravelling complete nitrifiers (termed as Bcomammox^—complete am- the niche specialization and ecological significance of AOA that monia oxidizers) might have a competitive advantage over are ubiquitous and abundant in a wide variety of terrestrial eco- canonical ammonia oxidizers and NOB in ammonia- systems (Leininger et al. 2006;Heetal.2007, 2012; Prosser and depleted biofilms, microbial aggregates, soils and sediments, Nicol 2012;Huetal.2014). Although the relative contribution of where comammox do not have to share the energy derived AOA and AOB to nitrification is still in debate, increasing evi- from nitrification with a partner organism (Costa et al. 2006; dence supports their niche separation on the basis of the physio- Kuypers 2015;Nunes-Alves2016). logical, cellular and genomic differences between AOA and This hypothesis was recently proved to be true by the suc- AOB—the high efficiency of metabolism and high substrate af- cessful enrichment of the bacterial organisms capable of com- finity suits an oligotrophic lifestyle of AOA in acidic soils and N- plete nitrification from a deep oil well (Daims et al. 2015)and limited environments (He et al. 2007, 2012; Lehtovirta-Morley an aquaculture system (van Kessel et al. 2015) through grow- et al. 2011; Zhang et al. 2012;Huetal.2015b). In addition to their ing biofilm samples supplied continuously with low concen- functional importance in nitrification, AOA can also substantially trations of ammonium. In contrast to known ammonia oxi- contribute to formation of nitrous oxide (N2O) (Stieglmeier et al. dizers and NOB, the assembled complete genomes of 2014;Hinketal.2016)—a potent greenhouse gas and a major comammox Nitrospira harbour the full set of genes encoding ozone-depleting substance (Hu et al. 2015a, 2017). By contrast, ammonia monooxygenase (AMO) and hydroxylamine dehy- NOB, including members of Nitrospira, Nitrobacter and drogenase (HAO) for ammonia oxidation, and genes encoding Nitrococcus genera, have received less attention though they have nitrite oxidoreductase (NXR) for nitrite oxidation (Daims been repeatedly reported that abundance of Nitrospira exceeded et al. 2015; van Kessel et al. 2015;Camejoetal.2017), indic- those of AOA and AOB in various ecosystems (Foesel et al. ative of their genetic potential for complete nitrification. The 2008; Gruber-Dorninger et al. 2015). comammox organisms enriched from both studies were re- The catalysis of the two nitrification steps by two distinct stricted to the widely distributed lineage II of the genus groups of organisms—ammonia oxidizers and NOB—has Nitrospira,suggestingthatcomammoxNitrospira might be been a central hypothesis in nitrification research for over a common nitrifiers in terrestrial and aquatic ecosystems century (Costa et al. 2006). The close coupling of ammonia (Daims et al. 2015 , 2016). The presence of comammox might oxidation and nitrite oxidation was used to explain the fre- help to explain some previous observations, for example (i) quently observed co-occurrence of ammonia oxidizers with the usually low nitrite concentrations in the environment if NOB in nitrifying consortia (Arp and Bottomley 2006). This comammox Nitrospira do not release nitrite as an intermediate functional separation, however, has puzzled scientists for a during complete nitrification and (ii) the high abundances of long time because complete oxidation of ammonia to nitrate Nitrospira bacteria, often exceeding AOA and AOB, if some in one organism was theoretically assumed to be energetically of these Nitrospira are actually belonging to comammox advantageous compared with separated nitrification steps (Wang et al. 2015; Daims et al. 2016). (Costa et al. 2006). Therefore, a single organism with lower These findings have fundamentally changed our perspec- growth rates but higher growth yields than canonical ammonia tive on the microbial regulation of the aerobic nitrification oxidizers was postulated to be present in nature to perform process and point to comammox Nitrospira as a novel and both nitrification steps (Costa et al. 2006). These hypothetical important nitrifying component with a potentially J Soils Sediments (2017) 17:2709–2717 2711 underappreciated role in the biogeochemical N cycle target the comammox amoA clade A and clade B was devel- (Kuypers 2015; Nunes-Alves 2016;Santoro2016). oped and validated in a recent study (Pjevac et al. 2017). By Considering the potential ecological importance of using the newly designed primer, a considerable diversity of comammox and our limited knowledge on this novel group comammox organisms harbouring unique amoA gene was of ammonia oxidizers, the biochemical and physiological detected in engineered systems, rice paddy soils, forest soils, characterizations of the enriched comammox organisms, the rice rhizosphere and brackish lake sediment (Pjevac et al. environmental investigation of comammox and the explora- 2017). Comammox amoA clade A comprised 14 ~ 34% of tion of their relative contribution to nitrification in various the total amoA gene abundance in the activated sludge from ecosystems will be a new focus of