Comammox Nitrospira clade B contributes to nitrification in soil

doi:10.1016/j.soilbio.2019.06.004

Soil Biology and Biochemistry

Volume 135, August 2019, Pages 392-395

https://doi.org/10.1016/j.soilbio.2019.06.004 Get rights and content

Highlights

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Demonstration of comammox growth and activity in soil.
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Identified conditions which preferentially select for the growth of comammox.
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Comammox Clade B contributes to nitrification rather than Clade A under low N conditions.

Abstract

Comammox, one nitrifying microorganism carries out the complete oxidation of ammonia to nitrate, have been recently discovered, and are found in a wide range of environments, including soil. However, conditions under which they actually contribute to nitrification in soil have not yet been demonstrated. By ¹³CO₂-based DNA stable isotope probing with real-time quantitative PCR and gene sequence, we reported two uncultured strains, which are closely related to comammox Nitrospira clade B, autotrophically grew in both forest and paddy soils only in the absence of ammonium amendment. Furthermore, all clade B amoA sequences amplified from isotopically enriched genomic DNA in both soils were derived from one or two phylotypes, indicating a low diversity of active comammox strains in soils.

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Main text

Nitrification was long considered a two-step process with ammonia oxidized to nitrite followed by oxidation to nitrate by two functionally-distinct groups: ammonia and nitrite oxidizers (Winogradsky, 1890; Bock and Wagner, 1992; Könneke et al., 2005). However, microorganisms capable of complete oxidation of ammonia to nitrate (comammox) have recently been discovered (van Kessel et al., 2015; Daims et al., 2015; Pinto et al., 2015). Comammox bacteria belong to the genus Nitrospira, organisms

Financial interests

The authors declare no competing financial interests.

Acknowledgments

We thank Dr. Holger Daims from the University of Vienna for his valuable suggestions for this study, data interpretation and manuscript preparation. This work was supported by the National Natural Science Foundation of China (41671232), and the National Key Research and Development Program of China (2016YFD0300901). GN is funded by the AXA Research Fund.

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The discovery of comammox Nitrospira has altered our perception of the nitrogen biogeochemical cycle. However, their functional importance compared to canonical ammonia oxidisers (i.e., ammonia-oxidising bacteria (AOB) and archaea (AOA)) in agricultural soils remains elusive, especially in acidic soils. Here, we assessed the functional importance of these functional guilds in nitrification and nitrous oxide (N₂O) emissions in three acidic agricultural soils by using a range of nitrification inhibitors (acetylene, 3,4-dimethylpyrazole phosphate (DMPP) and different concentrations of 1-octyne) and monitored their community assemblage and population dynamics. The sensitivity of comammox Nitrospira clade A to 1-octyne varied across soils, highlighting that the inappropriate use of 1-octyne can lead to misestimation of comammox activity. AOA were key NH₃ oxidisers in the three soils, while AOB also contributed significantly to nitrification in one soil. In contrast, comammox Nitrospira always played a minor role in ammonia oxidation and N₂O emissions, likely due to their low abundances, restricted cellular kinetic properties and N₂O production mechanisms. Together, this study demonstrates that comammox Nitrospira play a less important role in ammonia oxidation and N₂O production in acidic agricultural soils than AOA and AOB, thereby providing important novel insights into the mitigation of nitrogen fertiliser loss and N₂O emissions.
AOB Nitrosospira cluster 3a.2 (D11) dominates N<inf>2</inf>O emissions in fertilised agricultural soils
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Ammonia-oxidation process directly contribute to soil nitrous oxide (N₂O) emissions in agricultural soils. However, taxonomy of the key nitrifiers (within ammonia oxidising bacteria (AOB), archaea (AOA) and complete ammonia oxidisers (comammox Nitrospira)) responsible for substantial N₂O emissions in agricultural soils is unknown, as is their regulation by soil biotic and abiotic factors. In this study, cumulative N₂O emissions, nitrification rates, abundance and community structure of nitrifiers were investigated in 16 agricultural soils from major crop production regions of China using microcosm experiments with amended nitrogen (N) supplemented or not with a nitrification inhibitor (nitrapyrin). Key nitrifier groups involved in N₂O emissions were identified by comparative analyses of the different treatments, combining sequencing and random forest analyses. Soil cumulative N₂O emissions significantly increased with soil pH in all agricultural soils. However, they decreased with soil organic carbon (SOC) in alkaline soils. Nitrapyrin significantly inhibited soil cumulative N₂O emissions and AOB growth, with a significant inhibition of the AOB Nitrosospira cluster 3a.2 (D11) abundance. One Nitrosospira multiformis-like OTU phylotype (OTU34), which was classified within the AOB Nitrosospira cluster 3a.2 (D11), had the greatest importance on cumulative N₂O emissions and its growth significantly depended on soil pH and SOC contents, with higher growth at high pH and low SOC conditions. Collectively, our results demonstrate that alkaline soils with low SOC contents have high N₂O emissions, which were mainly driven by AOB Nitrosospira cluster 3a.2 (D11). Nitrapyrin can efficiently reduce nitrification-related N₂O emissions by inhibiting the activity of AOB Nitrosospira cluster 3a.2 (D11). This study advances our understanding of key nitrifiers responsible for high N₂O emissions in agricultural soils and their controlling factors, and provides vital knowledge for N₂O emission mitigation in agricultural ecosystems.
Visualizing small-scale subsurface NH<inf>3</inf> and pH dynamics surrounding nitrogen fertilizer granules and impacts on nitrification activity
2024, Soil Biology and Biochemistry
In agricultural soils, nitrogen (N) fertilizer is typically applied as ammonium salts or urea, and undergoes microbially mediated oxidation. However, insights regarding substrate concentrations nitrifiers are exposed to in the zones immediately surrounding N fertilizer granules remain unexamined, as well as how this affects the activity or inhibition of nitrifier groups adapted to different ranges of ammonia (NH₃) concentrations. To examine millimeter scale changes in soil chemistry after sub-surface fertilizer granule application with high spatiotemporal resolution, we applied a newly developed NH₃ and pH planar optical sensor (optode) system. With this system, we visualized in situ subsurface NH₃ production, diffusion, and associated pH shifts in an agricultural soil following the application (from 5 min up to 65.5 h) of ammonium chloride (NH₄Cl) or urea granules in a laboratory study. Ammonia from both NH₄Cl and urea granules diffused up to 1.5 and 2 cm and reached maximum concentrations of >49 and >130 ppm_v, respectively. Spatially informed destructive subsampling (0.5–2 cm from granules) revealed that nitrate accumulation was greatest closest (0.5–1 cm) to the ammonium chloride granules, while nitrite was not detected. In contrast, urea application resulted in both nitrite and nitrate accumulation, with the highest concentrations detected furthest (1.5–2 cm) from urea granules. Urea hydrolysis also caused a significant localized pH increase, while ammonium chloride caused a circular elevated pH zone migrating outwards leaving a decreased pH at the center. Transcription of the ammonia-oxidizing bacterial amoA gene was highest in areas furthest (1.5–2 cm) from the urea granules, while there were no significant differences in amoA transcription with increasing distance from the NH₄Cl granules. Ammonia-oxidizing archaea and comammox amoA transcripts were not detected. This study is the first to directly visualize small-scale subsurface changes in NH₃ concentration and pH after fertilizer granule application and relate these to nitrification activity.
Comammox Nitrospira dominates the nitrification in artificial coniferous forest soils of the Qilian Mountains
2024, Science of the Total Environment
Complete ammonia oxidizers (Comammox, CMX) are a newly discovered and important component of the nitrogen cycle. While CMX Nitrospira has been detected in various ecosystems, few studies so far have focused on the relative contribution and co-occurrence network of ammonia oxidizing archaea (AOA), bacteria (AOB), and CMX Nitrospira in artificial forest ecosystems (tree plantations). We evaluated the dynamics of composition, co-occurrence patterns and contribution of soil microbial nitrifiers to nitrification in soil of various tree species with different ages in the Qilian Mountains employing the space for time substitution approach, quantitative PCR and high-throughput sequencing technology. Generally, plantation development significantly reduced soil potential nitrification rates. Inhibition experiments and modular analysis showed that AOA played leading roles in nitrification of abandoned farmland and 17-year-old Hippophae rhamnoides, whereas CMX Nitrospira dominated in 36-year-old Picea crassifolia, 36-year-old Picea crassifolia and Larix gmelinii mixed plantation, and 50-year-old Picea crassifolia. The dominant AOA and CMX Nitrospira lineages in all samples were Group I.1b and Clade B, respectively. The assembly of nitrifier community was governed by stochastic processes, in which dispersal limitation made a significant contribution. The nitrifiers coexist in a mutualistic manner, albeit with possible functional redundancy, while the modular analysis revealed the aggregation pattern of the four modules in different artificial forests' soil. The Mantel test showed that modular formation is mainly affected by NH₄⁺ and SOM. These results broaden our current understanding of the relation between CMX Nitrospira and canonical ammonia oxidizers in terrestrial ecosystems, and provide empirical evidence for not only niche differentiation, but also the relative contribution and co-occurrence patterns of nitrifying communities in an artificial forest ecosystem.
Comammox dominate soil nitrification under different N fertilization regimes in semi-arid areas of Northeast China
2024, Applied Soil Ecology
The newly identified complete ammonia oxidation (Comammox), which is capable of oxidizing ammonia directly to nitrate, has complemented the knowledge of nitrification in the global nitrogen (N) cycle. Knowledge of the community compositions and contributions to nitrification of autotrophic ammonia-oxidizing archaea (AOA) and bacteria (AOB) and Comammox remain void. In this study, the abundance, community compositions, and contributions to nitrification of AOA, AOB, and Comammox were observed in five N gradients (0, 90, 150, 210, and 270 kg ha⁻¹) in a semi-arid area of Northeast China. The results indicated that, compared with low N application rates, higher N application rates significantly improved the soil ammonia monooxygenase (AMO) and the hydroxylamine oxidase (HAO) activities while total nitrogen (TN) was noted to be the main factor driving AMO and HAO activities. Soil potential nitrification rate (PNR) significantly increased with the increase in N application rate, and soil PNR was positively correlated with TN, nitrate nitrogen (NO₃⁻-N), soil organic matter (SOM), and ammonium nitrogen (NH₄⁺-N). The structural equation model (SEM) showed that TN was the main factor driving the community composition of Comammox; SOM had a greatest effect on the community composition of AOA while NH₄⁺-N had a greatest effect on the community composition of AOB. The soil PNR had a direct effect on the yield. Overall, the findings of this study highlighted that N application was more conducive to the reproduction of soil nitrifying microorganisms while Comammox was the dominant contributor to nitrification under N fertilization regimes in the semi-arid area of Northeast China.
Abundance, diversity and physiological preferences of comammox Nitrospira in urban groundwater
2023, Science of the Total Environment
Complete ammonia oxidizer (comammox Nitrospira), catalyze complete nitrification process in a single organism, are frequently detected in groundwater ecosystem. However, the ecological niches and environmental driving factors of comammox Nitrospira in urban groundwater are largely unknown. Here we investigated the communities of ammonia oxidizers in urban groundwater located in Shanghai city, China. Quantitative analysis demonstrated the dominance of comammox Nitrospira over classical ammonia oxidizers (ammonia-oxidizing archaea and bacteria, AOA and AOB). Phylogenetic analysis showed clades B and A2 comprise the majority of comammox Nitrospira groups. Temperature was one of the most vital factors affecting comammox Nitrospira community. Furthermore, clade A comammox Nitrospira can be enriched by urea substrate, which was in line with the ability of utilizing urea by the pure clade A comammox culture Nitrospira inopinata. In addition, we observed that relatively low temperature (<20 °C) and high copper levels (>0.04 mg L⁻¹) can stimulate the growth of comammox Nitrospira. Overall, this study revealed the presence, diversity and physiological preferences of comammox Nitrospira in urban groundwater nitrification, shedding insights on the ecological roles of comammox Nitrospira in subsurface environment.

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Short CommunicationComammox Nitrospira clade B contributes to nitrification in soil

Highlights

Abstract

Section snippets

Main text

Financial interests

Acknowledgments

Trends in Microbiology

Soil Biology and Biochemistry

Soil Biology and Biochemistry

Oxidation of inorganic nitrogen compounds as an energy source

The Prokaryotes

Complete nitrification by Nitrospira bacteria

Nature

The consequences of niche and physiological differentiation of archaeal and bacterial ammonia oxidisers for nitrous oxide emissions

The ISME Journal

Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle

Nature

Isolation of an autotrophic ammonia-oxidizing marine archaeon

Nature

Short Communication
Comammox Nitrospira clade B contributes to nitrification in soil