Isotopic Signature of N
            <sub>2</sub>
            O Produced by Marine Ammonia-Oxidizing Archaea

Santoro, Alyson E.; Buchwald, Carolyn; McIlvin, Matthew R.; Casciotti, Karen L.

doi:10.1126/science.1208239

Cited by 381 publications

(421 citation statements)

References 44 publications

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“…Traditionally, heterotrophic denitrification and autotrophic nitrification are viewed as the main sources for N 2 O production in soils (Barnard et al 2005;Wrage et al 2001). In fact, processes such as heterotrophic nitrification by fungi (Eylar and Schmidt 1959), anaerobic oxidation of NH 4 + (Santoro et al 2011), and codenitrification by fungi and actinomycetes (Laughlin and Stevens 2002; have been identified to produce N 2 O. However, in humid environments, heterotrophic denitrification is widely accepted as the dominant source of N 2 O production, followed by autotrophic nitrification (Davidson et al 1986).…”

Section: Denitrification and N 2 O Emissionmentioning

confidence: 99%

Effects of nitrogen deposition and fertilization on N transformations in forest soils: a review

et al. 2015

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Purpose Understanding how process-specific nitrogen (N) transformations in natural forest soils are modified by N deposition and fertilization is critically important to gain mechanistic insights on the links between global N deposition and N enrichment and loss in forest soils. Materials and methods Here we identify the general characteristics and the main mechanisms of N deposition-and fertilization-induced modifications in multiple N transformations, including N immobilization, N mineralization, nitrification (autotrophic nitrification and heterotrophic nitrification), and denitrification, in forest soils by literature survey. Results and discussion Overall, N status, soil C/N ratios, C availability, and soil pH are key factors separately and/or interactively affecting the effects of N deposition and fertilization on forest soil N transformations. In the N-limited stage, N deposition and fertilization can act as a stimulator of N mineralization by removing microbial N limitation and reducing the C/N ratios of the substrate being decomposed. In the Nunlimited stage, N added to forest ecosystems can retard N mineralization, which may primarily be a result of decreased microbial activity due to soil acidification and low C availability. The changes in N mineralization may drive a corresponding change in N immobilization, autotrophic nitrification, and denitrification. Despite the fact that ammonia-oxidizing archaea (AOA) has a higher affinity than ammonia-oxidizers (AOB) for low-concentration ammonia (NH 3 ), low NH 3 availability may still limit the rate of ammonia oxidation (autotrophic nitrification) in acidic forest soils even in the case of high NH 4 + input. Heterotrophic nitrification, however, may be favored if soil C/N ratios and pH decrease with N deposition and fertilization. The responses of denitrification and N 2 O emission to N deposition and fertilization in forests may be nonlinear, with a trend of stimulation in the short term but a decline over time, partly because soil pH has a contrast effect on denitrification capacity and N 2 O emission. Conclusions There are various effects of N deposition and fertilization on forest soil N transformations; thus, their responses to N deposition are still not well characterized and understood. N deposition-and fertilization-induced modifications in soil N transformations have important implications for N enrichment, N loss, and soil acidification in forest ecosystems. In the future, more research is required to investigate on dissimilatory nitrate reduction to ammonium (DNRA) process and link microbial community characteristics and functions of microbial extracellular enzymes with these rate processes in forest soils to narrow the uncertainty in evaluating and predicting ecosystem responses to global N deposition.

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Section: Denitrification and N 2 O Emissionmentioning

confidence: 99%

Effects of nitrogen deposition and fertilization on N transformations in forest soils: a review

et al. 2015

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“…Ammonia-oxidizing Thaumarchaea are thought to be a major source of N 2 O in marine systems, based on its natural abundance isotopic composition (Santoro et al, 2010;Santoro et al, 2011). Nitrite reductase is potentially involved in N 2 O production and we find thaumarchaeal nirK to be highly expressed in the marine water column (Figure 6b).…”

Section: Expression Of Thaumarchaeal Nirk and Amoa In Monterey Baymentioning

confidence: 83%

“…In AOB, NirK is involved in production of the potent greenhouse gas nitrous oxide (N 2 O) through 'nitrifier denitrification' (Dundee and Hopkins, 2001;Shaw et al, 2006). AOA also produce N 2 O, part of which appears to be formed through a reductive pathway (for example, nitrite reduction; Santoro et al, 2011). Nitrite reduction mediated by nitrifiers contributes significantly to N 2 O release to the atmosphere from both terrestrial (Webster and Hopkins, 1996;Kool et al, 2011) and marine (Dore et al, 1998;Santoro et al, 2011) ecosystems.…”

Section: Introductionmentioning

confidence: 99%

Diversity, abundance and expression of nitrite reductase (nirK)-like genes in marine thaumarchaea

2012

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Ammonia-oxidizing archaea (AOA) are widespread and abundant in aquatic and terrestrial habitats and appear to have a significant impact on the global nitrogen cycle. Like the ammonia-oxidizing bacteria, AOA encode a gene homologous to copper-containing nitrite reductases (nirK), which has been studied very little to date. In this study, the diversity, abundance and expression of thaumarchaeal nirK genes from coastal and marine environments were investigated using two mutually excluding primer pairs, which amplify the nirK variants designated as AnirKa and AnirKb. Only the AnirKa variant could be detected in sediment samples from San Francisco Bay and these sequences grouped with the nirK from Candidatus Nitrosopumilus maritimus and Candidatus Nitrosoarchaeum limnia. The two nirK variants had contrasting distributions in the water column in Monterey Bay and the California Current. AnirKa was more abundant in the epi- to mesopelagic Monterey Bay water column, whereas AnirKb was more abundant in the meso- to bathypelagic California Current water. The abundance and community composition of AnirKb, but not AnirKa, followed that of thaumarchaeal amoA, suggesting that either AnirKa is not exclusively associated with AOA or that commonly used amoA primers may be missing a significant fraction of AOA diversity in the epipelagic. Interestingly, thaumarchaeal nirK was expressed 10–100-fold more than amoA in Monterey Bay. Overall, this study provides valuable new insights into the distribution, diversity, abundance and expression of this alternative molecular marker for AOA in the ocean.

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“…However, a recent study suggests that AOA reduce nitrite through a pathway known as 'nitrifier-denitrification', resulting in globally significant production of nitrous oxide (N 2 O), an important greenhouse gas (Santoro et al, 2011). Although culture-based studies of MGI physiology have not demonstrated nitrite reduction, genes with homology to nitrite reductase (nirK) and several cupredoxin domaincontaining multicopper oxidases thought to be involved in nitrite reduction were identified in the N. maritimus genome (Walker et al, 2010).…”

Section: Species-resolved Transcriptomics Of Ammonia Oxidation Genesmentioning

confidence: 99%

Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume

2012

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Ammonia-oxidizing Archaea (AOA) are among the most abundant microorganisms in the oceans and have crucial roles in biogeochemical cycling of nitrogen and carbon. To better understand AOA inhabiting the deep sea, we obtained community genomic and transcriptomic data from ammonium-rich hydrothermal plumes in the Guaymas Basin (GB) and from surrounding deep waters of the Gulf of California. Among the most abundant and active lineages in the sequence data were marine group I (MGI) Archaea related to the cultured autotrophic ammonia-oxidizer, Nitrosopumilus maritimus. Assembly of MGI genomic fragments yielded 2.9 Mb of sequence containing seven 16S rRNA genes (95.4–98.4% similar to N. maritimus), including two near-complete genomes and several lower-abundance variants. Equal copy numbers of MGI 16S rRNA genes and ammonia monooxygenase genes and transcription of ammonia oxidation genes indicates that all of these genotypes actively oxidize ammonia. De novo genomic assembly revealed the functional potential of MGI populations and enhanced interpretation of metatranscriptomic data. Physiological distinction from N. maritimus is evident in the transcription of novel genes, including genes for urea utilization, suggesting an alternative source of ammonia. We were also able to determine which genotypes are most active in the plume. Transcripts involved in nitrification were more prominent in the plume and were among the most abundant transcripts in the community. These unique data sets reveal populations of deep-sea AOA thriving in the ammonium-rich GB that are related to surface types, but with key genomic and physiological differences.

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Isotopic Signature of N ₂ O Produced by Marine Ammonia-Oxidizing Archaea

Cited by 381 publications

References 44 publications

Effects of nitrogen deposition and fertilization on N transformations in forest soils: a review

Effects of nitrogen deposition and fertilization on N transformations in forest soils: a review

Diversity, abundance and expression of nitrite reductase (nirK)-like genes in marine thaumarchaea

Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume

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Isotopic Signature of N 2 O Produced by Marine Ammonia-Oxidizing Archaea

Cited by 381 publications

References 44 publications

Effects of nitrogen deposition and fertilization on N transformations in forest soils: a review

Effects of nitrogen deposition and fertilization on N transformations in forest soils: a review

Diversity, abundance and expression of nitrite reductase (nirK)-like genes in marine thaumarchaea

Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume

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Isotopic Signature of N ₂ O Produced by Marine Ammonia-Oxidizing Archaea