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Using ammonia monooxygenase α-subunit (amoA) gene and 16S rRNA gene, the community structure and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in a nitrogen-removing reactor, which was operated for five phases, were characterized and quantified by cloning, terminal restriction fragment length polymorphism (T-RFLP), and quantitative polymerase chain reaction (qPCR). The results suggested that the dominant AOB in the reactor fell to the genus Nitrosomonas, while the dominant AOA belonged to Crenarchaeotal Group I.1a in phylum Crenarchaeota. Real-time PCR results demonstrated that the levels of AOB amoA varied from 2.9 × 10³ to 2.3 × 10⁵ copies per nanogram DNA, greatly (about 60 times) higher than those of AOA, which ranged from 1.7 × 10² to 3.8 × 10³ copies per nanogram DNA. This indicated the possible leading role of AOB in the nitrification process in this study. T-RFLP results showed that the AOB community structure significantly shifted in different phases while AOA only showed one major peak for all the phases. The analyses also suggested that the AOB community was more sensitive than that of AOA to operational conditions, such as ammonia loading and dissolved oxygen.

Ammonia-oxidizing microorganisms (AOM) contribute to one of the largest nitrogen fluxes in the global nitrogen budget. Four distinct lineages of AOM: ammonia-oxidizing archaea (AOA), beta- and gamma-proteobacterial ammonia-oxidizing bacteria (β-AOB and γ-AOB) and complete ammonia oxidizers (comammox), are thought to compete for ammonia as their primary nitrogen substrate. In addition, many AOM species can utilize urea as an alternative energy and nitrogen source through hydrolysis to ammonia. How the coordination of ammonia and urea metabolism in AOM influences their ecology remains poorly understood. Here we use stable isotope tracing, kinetics and transcriptomics experiments to show that representatives of the AOM lineages employ distinct regulatory strategies for ammonia or urea utilization, thereby minimizing direct substrate competition. The tested AOA and comammox species preferentially used ammonia over urea, while β-AOB favoured urea utilization, repressed ammonia transport in the presence of urea and showed higher affinity for urea than for ammonia. Characterized γ-AOB co-utilized both substrates. These results reveal contrasting niche adaptation and coexistence patterns among the major AOM lineages. Isotope tracing, kinetics and transcriptomics show how members of the four AOM lineages employ different nitrogen use strategies that minimize competition for nitrogen substrates.

Ammonia oxidation carried out by ammonia-oxidizing microorganisms (AOMs) is a central step in the global nitrogen cycle. Aerobic AOMs comprise conventional ammonia-oxidizing bacteria (AOB), novel ammonia-oxidizing archaea (AOA), which could exist in complex and extreme conditions, and complete ammonia oxidizers (comammox), which directly oxidize ammonia to nitrate within a single cell. Anaerobic AOMs mainly comprise anaerobic ammonia-oxidizing bacteria (AnAOB), which can transform NH4+-N and NO2−-N into N2 under anaerobic conditions. In this review, the unique metabolic characteristics, microbial community of AOMs and the influencing factors are discussed. Process applications of nitrification/denitrification, nitritation/denitrification, nitritation/anammox and partial denitrification/anammox in wastewater treatment systems are emphasized. The future development of nitrogen removal processes using AOMs is expected, enrichment of comammox facilitates the complete nitrification performance, inhibiting the activity of comammox and NOB could achieve stable nitritation, and additionally, AnAOB conducting the anammox process in municipal wastewater is a promising development direction.

Nitrification is a key process of the nitrogen (N) cycle in soil with major environmental implications. The recent discovery of ammonia-oxidizing archaea (AOA) questions the traditional assumption of the dominant role of ammonia-oxidizing bacteria (AOB) in nitrification. We investigated AOB and AOA growth and nitrification rate in two different layers of three grassland soils treated with animal urine substrate and a nitrification inhibitor [dicyandiamide (DCD)]. We show that AOB were more abundant in the topsoils than in the subsoils, whereas AOA were more abundant in one of the subsoils. AOB grew substantially when supplied with a high dose of urine substrate, whereas AOA only grew in the Controls without the urine-N substrate. AOB growth and the amoA gene transcription activity were significantly inhibited by DCD. Nitrification rates were much higher in the topsoils than in the subsoils and were significantly related to AOB abundance, but not to AOA abundance. These results suggest that AOB and AOA prefer different soil N conditions to grow: AOB under high ammonia (NH₃) substrate and AOA under low NH₃ substrate conditions.

Aim Ammonia‐oxidizing archaea (AOA) and bacteria (AOB) are the primary agents for nitrification, converting ammonia (NH4+) into nitrate (NO3−) and modulating plant nitrogen (N) utilization and terrestrial N retention. However, there is still lack of a unifying framework describing the patterns of global AOA and AOB distribution. In particular, biotic interactions are rarely integrated into any of the conceptual models. Location World‐wide. Time period 2005–2016. Major taxa studied Ammonia‐oxidizing archaea and ammonia‐oxidizing bacteria. Methods A meta‐analysis and synthesis were conducted to obtain a general picture of global AOA and AOB distribution and identify the primary driving factors. A microcosm experiment was then conducted to assess effects of relative carbon to nitrogen availability for heterotrophic microbes on AOA and AOB in two distinct soils. A mesocosm experiment was further carried out to characterize the effects of plant roots and their arbuscular mycorrhizal fungi (AMF) on AOA and AOB abundances using hyphae‐ or root‐ingrowth techniques. Results Our meta‐analysis showed that soil carbon to nitrogen (C/N) ratios explained the most variance in AOA and AOB abundances, although soil pH had a significant effect. Experimental results demonstrated that high cellulose and mineral N inputs increased total microbial biomass and microbial activities, but inhibited AOA and AOB, suggesting microbial inhibition of AOA and AOB. Also, AMF and roots suppressed AOA and AOB, respectively. Main conclusions Our study provides convincing evidence illustrating that relative carbon to nitrogen availability can predominantly affect the abundances of AOA and AOB. Our experimental results further validate that biotic competition among plants, heterotrophic microbes and ammonia oxidizers for substrate N is the predominant control upon AOA and AOB abundances. Together, these findings provide new insights into the role of abiotic and biotic factors in modulating terrestrial AOA and AOB abundances and their potential applications for management of nitrification in an increasing reactive N world.

Nitrification is a central component of the global nitrogen cycle. Ammonia oxidation, the first step of nitrification, is performed in terrestrial ecosystems by both ammonia‐oxidizing bacteria (AOB) and ammonia‐oxidizing archaea (AOA). Published studies indicate that soil pH may be a critical factor controlling the relative abundances of AOA and AOB communities. In order to determine the relative contributions of AOA and AOB to ammonia oxidation in two agricultural acidic Scottish soils (pH 4.5 and 6), the influence of acetylene (a nitrification inhibitor) was investigated during incubation of soil microcosms at 20 °C for 1 month. High rates of nitrification were observed in both soils in the absence of acetylene. Quantification of respective amoA genes (a key functional gene for ammonia oxidizers) demonstrated significant growth of AOA, but not AOB. A significant positive relationship was found between nitrification rate and AOA, but not AOB growth. AOA growth was inhibited in the acetylene‐containing microcosms. Moreover, AOA transcriptional activity decreased significantly in the acetylene‐containing microcosms compared with the control, whereas no difference was observed for the AOB transcriptional activity. Consequently, growth and activity of only archaeal but not bacterial ammonia oxidizer communities strongly suggest that AOA, but not AOB, control nitrification in these two acidic soils.

Recently, partial nitrification has been adopted widely as a first step of both nitrite shunt and deammonification processes towards efficient and economical nitrogen removal from wastewater. Effective partial nitrification relies on stimulating the first step of nitrification while inhibiting the second step and by consequence accumulating ammonia-oxidizing bacteria (AOB). Successful AOB accumulation depends upon the knowledge of their microbial characteristics and kinetics parameters as well as the main parameters that can selectively inhibits NOBs’ growth or allow AOBs to outcompete them. Several bioreactors configurations either in suspended or attached growth have been used towards achieving partial nitrification using different inhibition conditions. This review aims to illustrate an up to date version of the metabolism and factors affecting AOB growth and summarize the current bioreactors configurations in all lab-scale and full-scale applications for AOB. Moreover, successful partial nitrification attempts in the literature in suspended and attached growth systems have been complied. Additionally, the possibility of improving the current applications of AOB and the integration into the operation of existing WWTPs in order to transform into water resources recovery facility has been presented.

Biological nitrification inhibitors (BNIs) present an environmentally friendly approach to reduce nitrogen losses and enhance nitrogen use efficiency, with plant-derived triterpenoids emerging as promising candidates. We evaluated 18 triterpenoids as BNIs using in vitro assays with soil ammonia-oxidizing bacteria (AOB) ( Nitrosospira multiformis , Nitrosomonas ureae ) and archaea (AOA) ( Nitrososphaera viennensis , Nitrosotalea sinensis ) at high and low concentrations. A Graph Neural Network framework was applied to predict nitrification inhibition (NI) and identify structural features, including key functional groups, linked to inhibitory patterns. Triterpenoids were more active on AOA, demonstrating higher efficacy than sakuranetin (a known BNI), but did not inhibit AOB. Six triterpenoids showed inhibitory activity on AOA (29–100%), with 3-O-acetyl-11-keto-beta boswellic acid and 11-keto-beta boswellic acid as the most potent inhibitors (ammonia oxidation inhibition > 94%), followed by echinocystic acid (> 87%), ursolic acid (> 74%), asiatic acid (> 65%), and echinocystic acid-3-O-glucoside (29–94%). In silico analyses predicted accurately the activity of model inhibitors such as DMPP, MHPP, and ethoxyquin on AOB and AOA, respectively, and the limited activity of triterpenoids on AOB, but did not predict their strong inhibitory effects on AOA, underscoring the need for expanded datasets for model refinement. The selective activity of some triterpenoids on AOA is hypothesized to involve interference with 3-hydroxy-3-methylglutaryl-CoA reductase, a key enzyme in archaeal membrane biosynthesis, although this requires experimental validation. Still, strain-specific responses suggest the involvement of additional mechanisms. This study provides the first experimental evidence for the potential of plant-derived triterpenoids as BNIs, supporting their relevance for sustainable agriculture. Graphical Abstract Key points • Triterpenoids strongly inhibited AOA but had no effect on AOB nitrification activity. • Six ursane/oleanane-type triterpenoids showed strong AOA inhibition beyond known BNIs. • Inhibition patterns suggest triterpenoid structure relates to AOA selectivity.

An aerobic 15N microcosmic experiment was conducted to compare the inhibitory effects of the biological nitrification inhibitor (BNI), methyl 3-(4-hydroxyphenyl) propionate (MHPP) at rates of 500 and 1000 mg kg−1 with the synthetic nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) at 1% of applied NH4+, on the gross nitrification rate (n_gross) and on the abundance and community composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) of two contrasting soils (pH: 5.10 vs. 8.15, clay content 17.8 vs. 30.8). DMPP inhibited 56.6% of n_gross in the acidic soil and 50.3% in the calcareous soil, whereas MHPP inhibited 18.3–55.5% of n_gross in the acidic soil and 14.1–20.2% in the calcareous soil. MHPP used at the high rate showed the same inhibition on n_gross as DMPP in the acidic soil but not in the calcareous soil. DMPP and MHPP likely regulated n_gross by causing niche differentiation between AOA and AOB. Moreover, the community composition of AOB was more sensitive to nitrification inhibitor application than that of AOA, particularly in the acidic soil. However, the response of AOB community composition was less sensitive to the application of MHPP than to that of DMPP. MHPP mainly targeted Nitrosospira clusters 3a.2, 3b.2, and 9 of the AOB in the acidic soil.

Nitrification is a vital process in the biological removal of inorganic nitrogen compounds. In order to ensure the stability and effectiveness of this process, buffer solutions should be added to the system to maintain neutral to slightly alkaline conditions. With a focus on the newly discovered comammox Nitrospira , this research investigates the transition of the nitrifying community within a biofilm reactor under different acidic levels (initiated at pH 6 and gradually decreased to pH 5). During the 305-day continuous operation experiment, it was observed that responsible ammonia oxidizers transitioned from ammonia-oxidizing bacteria (AOB) during the initial stages (setup stage and early stage of pH 6) to comammox Nitrospira under pH 5.5 and pH 5. Further analysis using next-generation sequencing targeting both the 16S rRNA region and amoA region revealed a shift in the dominant cluster of both Nitrospirae and comammox Nitrospira under varying pH conditions. Our study identified a distinct cluster of comammox Nitrospira that is phylogenetically closed to sequences found in acidic environments, but exhibits dissimilarity from known comammox Nitrospira isolates and the majority of environmental sequences. This cluster was found to be prevalent in the acidic biofilm reactor studied and thrived particularly well at pH 5. These findings underscore the potential significance of this distinct, uncultivated group of comammox Nitrospira in performing ammonia oxidation under acidic conditions. Key points • Ammonia was effectively removed under pH 5.5 and 5 in the biofilm reactor • The dominant ammonia oxidizer was comammox Nitrospira when pH was 5.5 and 5 • A potential acidophilic cluster of comammox Nitrospira was identified in this acidic biofilm reactor