Ammonia-oxidizing archaea and complete ammonia-oxidizing Nitrospira in water treatment systems

Abstract

Nitrification, the oxidation of ammonia to nitrate via nitrite, is important for many engineered water treatment systems. The sequential steps of this respiratory process are carried out by distinct microbial guilds, including ammonia-oxidizing bacteria (AOB) and archaea (AOA), nitrite-oxidizing bacteria (NOB), and newly discovered members of the genus Nitrospira that conduct complete ammonia oxidation (comammox). Even though all of these nitrifiers have been identified within water treatment systems, their relative contributions to nitrogen cycling are poorly understood. Although AOA contribute to nitrification in many wastewater treatment plants, they are generally outnumbered by AOB. In contrast, AOA and comammox Nitrospira typically dominate relatively low ammonia environments such as drinking water treatment, tertiary wastewater treatment systems, and aquaculture/aquarium filtration. Studies that focus on the abundance of ammonia oxidizers may misconstrue the actual role that distinct nitrifying guilds play in a system. Understanding which ammonia oxidizers are active is useful for further optimization of engineered systems that rely on nitrifiers for ammonia removal. This review highlights known distributions of AOA and comammox Nitrospira in engineered water treatment systems and suggests future research directions that will help assess their contributions to nitrification and identify factors that influence their distributions and activity.

Keywords: Ammonia oxidation; Ammonia-oxidizing archaea; Comammox; Nitrification; Nitrospira; Water treatment; amoA.

Graphical abstract

Fig. 1

The nitrogen cycle, with an emphasis on nitrification-mediating microorganisms. Ammonia (NH₃/NH₄⁺) and nitrite (NO₂⁻) oxidation are the first and second step of nitrification, respectively. Complete ammonia oxidation (comammox) involves both steps of nitrification within a single organism. Oxidation reactions are shown with green arrows, reduction reactions are shown with blue arrows, and non-redox reactions are shown with gray arrows. DNRA is dissimilatory nitrite reduction to ammonia, anammox is anaerobic ammonia oxidation. R-NH₂ indicates organic molecules containing nitrogen as amine groups (i.e., biomass), NO is nitric oxide, NO₃⁻ is nitrate, N₂O is nitrous oxide, and N₂ is dinitrogen. This figure is adapted from Stein and Klotz (2016).

Fig. 2

Phylogenetic relationships of AOA, AOB, and comammox Nitrospira based on AmoA amino acid sequences. Environments of origin for each sequence are grouped into major categories and shown to the right of each sequence entry. Comammox Nitrospira sequences originate from metagenomic and cultivation studies, with cultivated species shown in red. The sequence alignment is inferred using the Le Gascuel evolutionary model (Le and Gascuel, 2008), and the maximum likelihood method was used to construct the tree, using a discrete Gamma distribution to model evolutionary rate differences among sites (4 categories (+G, parameter = 2.9096)). The AmoA sequences of AOA were used to root the tree.