Expanding perspectives of soil nitrification to include ammonia‐oxidizing archaea and comammox bacteria

Lü, Xiaoliang; Taylor, Alfred; Myrold, David D.; Neufeld, Josh D.

doi:10.1002/saj2.20029

Cited by 34 publications

(18 citation statements)

References 202 publications

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“…Since the discovery of comammox Nitrospira in 2015, our understanding of the two-step nitrification process has improved ( Koch et al, 2019 ; Lu et al, 2020 ; Vijayan et al, 2021 ). However, only a few comammox Nitrospira spp.…”

Section: Discussionmentioning

confidence: 99%

Comammox Nitrospira Clade B is the most abundant complete ammonia oxidizer in a dairy pasture soil and inhibited by dicyandiamide and high ammonium concentrations

Hsu

Cameron

et al. 2022

Front. Microbiol.

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The recent discovery of comammox Nitrospira, a complete ammonia oxidizer, capable of completing the nitrification on their own has presented tremendous challenges to our understanding of the nitrification process. There are two divergent clades of comammox Nitrospira, Clade A and B. However, their population abundance, community structure and role in ammonia and nitrite oxidation are poorly understood. We conducted a 94-day microcosm study using a grazed dairy pasture soil amended with urea fertilizers, synthetic cow urine, and the nitrification inhibitor, dicyandiamide (DCD), to investigate the growth and community structure of comammox Nitrospira spp. We discovered that comammox Nitrospira Clade B was two orders of magnitude more abundant than Clade A in this fertile dairy pasture soil and the most abundant subcluster was a distinctive phylogenetic uncultured subcluster Clade B2. We found that comammox Nitrospira Clade B might not play a major role in nitrite oxidation compared to the role of canonical Nitrospira nitrite-oxidizers, however, comammox Nitrospira Clade B is active in nitrification and the growth of comammox Nitrospira Clade B was inhibited by a high ammonium concentration (700 kg synthetic urine-N ha–1) and the nitrification inhibitor DCD. We concluded that comammox Nitrospira Clade B: (1) was the most abundant comammox in the dairy pasture soil; (2) had a low tolerance to ammonium and can be inhibited by DCD; and (3) was not the dominant nitrite-oxidizer in the soil. This is the first study discovering a new subcluster of comammox Nitrospira Clade B2 from an agricultural soil.

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Section: Discussionmentioning

confidence: 99%

Comammox Nitrospira Clade B is the most abundant complete ammonia oxidizer in a dairy pasture soil and inhibited by dicyandiamide and high ammonium concentrations

Hsu

Cameron

et al. 2022

Front. Microbiol.

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“…This study is focused on functionally specialized groups that have a key role in the N cycle such as ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Ammonia oxidizers perform the first and rate-limiting step of nitrification, through the oxidation of ammonia derived from both inorganic fertilization and the mineralization of organic matter (Levičnik-Höfferle et al, 2012;Lu et al, 2020). These nitrifiers exhibit niche and physiological differentiation: while low ammonium supply from mineralization of organic matter favors growth and activity of AOA, AOB prefer high ammonium supply from inorganic fertilizer inputs (Stopnišek et al, 2010;Levičnik-Höfferle et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Ammonia Oxidizing Prokaryotes Respond Differently to Fertilization and Termination Methods in Common Oat’s Rhizosphere

et al. 2021

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Cover crops (CC) have demonstrated beneficial effects on several soil properties yet questions remain regarding their effects on soil microbial communities. Among them, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) have a key role for N cycling in soil and their responses in the rhizosphere of terminated CC deserve further investigation. A greenhouse experiment was established to assess N fertilization (with or without N) and termination methods (glyphosate, mowing, and untreated control) of common oat (Avena sativa L.) as potential drivers of AOA and AOB responses in the rhizosphere. The abundance of amoA genes was determined by quantitative real-time PCR (qPCR), the community structure was assessed with Illumina amplicon sequencing of these genes, while the function was assessed from potential nitrification activity (PNA). While N fertilization had no influence on AOA, the termination method significantly increased amoA gene copies of AOA in mowed plants relative to glyphosate termination or the untreated control (1.76 and 1.49-fold change, respectively), and shifted AOA community structure (PERMANOVA, p<0.05). Ordination methods indicated a separation between AOA communities from control and glyphosate-terminated plants relative to mowed plants for both UniFrac and Aitchison distance. Converserly, N fertilization significantly increased AOB abundance in the rhizosphere of mowed and control plants, yet not in glyphosate-treated plants. Analyses of community structure showed that AOB changed only in response to N fertilization and not to the termination method. In line with these results, significantly higher PNA values were measured in all fertilized samples, regardless of the termination methods. Overall, the results of this study indicated that bacterial and archaeal nitrifiers have contrasting responses to fertlization and plant termination methods. While AOA were responsive to the termination method, AOB were more sensitive to N additions, although, the stimulative effect of N fertilization on amoAAOB abundance was dependent on the termination method.

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“…Nitrification is a two-step process: first is the oxidation of ammonia during which the NH 4 + ion is converted into NO 2 – , and second is the oxidation of nitrite during which the NO 2 – ion is converted to NO 3 – . Ammonia oxidation can be processed by ammonia-oxidizing bacteria (AOB) (such as Nitrosomonas and Nitrosospira species of Betaproteobacteria , and Nitrosococcus species of Gammaproteobacteria ) and ammonia-oxidizing archaea (AOA) ( Hayatsu et al, 2017 ; Nacke et al, 2017 ; Lu et al, 2020 ; Lukumbuzya et al, 2020 ). Recent advances have found that AOA communities are more abundant than AOB, whereas AOB may have more functions during nitrification in the upland rice system ( Banning et al, 2015 ; He et al, 2018 ; Liang et al, 2020 ).…”

Section: Pathways Of N Cycle In Rice-based Systemsmentioning

confidence: 99%

Recent trends in nitrogen cycle and eco-efficient nitrogen management strategies in aerobic rice system

Farooq

Wang

Uzair³

et al. 2022

Front. Plant Sci.

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Rice (Oryza sativa L.) is considered as a staple food for more than half of the global population, and sustaining productivity under a scarcity of resources is challenging to meet the future food demands of the inflating global population. The aerobic rice system can be considered as a transformational replacement for traditional rice, but the widespread adaptation of this innovative approach has been challenged due to higher losses of nitrogen (N) and reduced N-use efficiency (NUE). For normal growth and developmental processes in crop plants, N is required in higher amounts. N is a mineral nutrient and an important constituent of amino acids, nucleic acids, and many photosynthetic metabolites, and hence is essential for normal plant growth and metabolism. Excessive application of N fertilizers improves aerobic rice growth and yield, but compromises economic and environmental sustainability. Irregular and uncontrolled use of N fertilizers have elevated several environmental issues linked to higher N losses in the form of nitrous oxide (N2O), ammonia (NH3), and nitrate (NO3–), thereby threatening environmental sustainability due to higher warming potential, ozone depletion capacities, and abilities to eutrophicate the water resources. Hence, enhancing NUE in aerobic rice has become an urgent need for the development of a sustainable production system. This article was designed to investigate the major challenge of low NUE and evaluate recent advances in pathways of the N cycle under the aerobic rice system, and thereby suggest the agronomic management approaches to improve NUE. The major objective of this review is about optimizing the application of N inputs while sustaining rice productivity and ensuring environmental safety. This review elaborates that different soil conditions significantly shift the N dynamics via changes in major pathways of the N cycle and comprehensively reviews the facts why N losses are high under the aerobic rice system, which factors hinder in attaining high NUE, and how it can become an eco-efficient production system through agronomic managements. Moreover, it explores the interactive mechanisms of how proper management of N cycle pathways can be accomplished via optimized N fertilizer amendments. Meanwhile, this study suggests several agricultural and agronomic approaches, such as site-specific N management, integrated nutrient management (INM), and incorporation of N fertilizers with enhanced use efficiency that may interactively improve the NUE and thereby plant N uptake in the aerobic rice system. Additionally, resource conservation practices, such as plant residue management, green manuring, improved genetic breeding, and precision farming, are essential to enhance NUE. Deep insights into the recent advances in the pathways of the N cycle under the aerobic rice system necessarily suggest the incorporation of the suggested agronomic adjustments to reduce N losses and enhance NUE while sustaining rice productivity and environmental safety. Future research on N dynamics is encouraged under the aerobic rice system focusing on the interactive evaluation of shifts among activities and diversity in microbial communities, NUE, and plant demands while applying N management measures, which is necessary for its widespread adaptation in face of the projected climate change and scarcity of resources.

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Expanding perspectives of soil nitrification to include ammonia‐oxidizing archaea and comammox bacteria

Cited by 34 publications

References 202 publications

Comammox Nitrospira Clade B is the most abundant complete ammonia oxidizer in a dairy pasture soil and inhibited by dicyandiamide and high ammonium concentrations

Comammox Nitrospira Clade B is the most abundant complete ammonia oxidizer in a dairy pasture soil and inhibited by dicyandiamide and high ammonium concentrations

Ammonia Oxidizing Prokaryotes Respond Differently to Fertilization and Termination Methods in Common Oat’s Rhizosphere

Recent trends in nitrogen cycle and eco-efficient nitrogen management strategies in aerobic rice system

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