Nitric Oxide Production from Nitrite Reduction and Hydroxylamine Oxidation by Copper-containing Dissimilatory Nitrite Reductase (NirK) from the Aerobic Ammonia-oxidizing Archaeon, &lt;i&gt;Nitrososphaera viennensis&lt;/i&gt;

Kobayashi, Shun; Hira, Daisuke; Yoshida, Kiyomi; Toyofuku, Masanori; Shida, Yosuke; Ogasawara, Wataru; Yamaguchi, Takashi; Araki, Nobuo; Oshiki, Mamoru

doi:10.1264/jsme2.me18058

Cited by 37 publications

(44 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Two of the genomes (ThauP41 and ThauR71) suggest participation in nitrification; however, the most likely reason that AOA genes were not detected in ThauP25 is that this genome is not complete. The gene nirK was detected in all three genomes, indicating participation in the production of the greenhouse gas nitrous oxide, which was demonstrated by heterologous expression of nirK from Nitrososphaera viennensis [80]. The presence of genes encoding coenzyme F420 are widespread in Thaumarchaeota genomes [9,81].…”

Section: Discussionmentioning

confidence: 99%

Genome-resolved metagenomics analysis provides insights into the ecological role of Thaumarchaeota in the Amazon River and its plume

et al. 2020

View full text Add to dashboard Cite

Background: Thaumarchaeota are abundant in the Amazon River, where they are the only ammonia-oxidizing archaea. Despite the importance of Thaumarchaeota, little is known about their physiology, mainly because few isolates are available for study. Therefore, information about Thaumarchaeota was obtained primarily from genomic studies. The aim of this study was to investigate the ecological roles of Thaumarchaeota in the Amazon River and the Amazon River plume. Results: The archaeal community of the shallow in Amazon River and its plume is dominated by Thaumarchaeota lineages from group 1.1a, which are mainly affiliated to Candidatus Nitrosotenuis uzonensis, members of order Nitrosopumilales, Candidatus Nitrosoarchaeum, and Candidatus Nitrosopelagicus sp. While Thaumarchaeota sequences have decreased their relative abundance in the plume, Candidatus Nitrosopelagicus has increased. One genome was recovered from metagenomic data of the Amazon River (ThauR71 [1.05 Mpb]), and two from metagenomic data of the Amazon River plume (ThauP25 [0.94 Mpb] and ThauP41 [1.26 Mpb]). Phylogenetic analysis placed all three Amazon genome bins in Thaumarchaeota Group 1.1a. The annotation revealed that most genes are assigned to the COG subcategory coenzyme transport and metabolism. All three genomes contain genes involved in the hydroxypropionate/hydroxybutyrate cycle, glycolysis, tricarboxylic acid cycle, oxidative phosphorylation. However, ammonia-monooxygenase genes were detected only in ThauP41 and ThauR71. Glycoside hydrolases and auxiliary activities genes were detected only in ThauP25. Conclusions: Our data indicate that Amazon River is a source of Thaumarchaeota, where these organisms are important for primary production, vitamin production, and nitrification.

show abstract

Section: Discussionmentioning

confidence: 99%

Genome-resolved metagenomics analysis provides insights into the ecological role of Thaumarchaeota in the Amazon River and its plume

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Recently, Kobayashi et al . () demonstrated that a recombinant NirK protein from the soil thaumarchaeote Nitrososphaera viennensis was able to catalyse the production of NO from both NO 2 − reduction and NH 2 OH oxidation. This protein also produced nitrous oxide (N 2 O) from NH 2 OH and NO 2 − (Kobayashi et al ., ).…”

Section: Introductionmentioning

confidence: 99%

“…In another proposed model, two molecules of NO 2 − are generated from NH 2 OH and NO, and NirK is proposed to reduce one of these NO 2 − molecules back into NO, returning it to the NO 2 − -generation module (Kozlowski et al, 2016). Recently, Kobayashi et al (2018) demonstrated that a recombinant NirK protein from the soil thaumarchaeote Nitrososphaera viennensis was able to catalyse the production of NO from both NO 2 − reduction and NH 2 OH oxidation. This protein also produced nitrous oxide (N 2 O) from NH 2 OH and NO 2 − (Kobayashi et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Depth distributions of nitrite reductase (nirK) gene variants reveal spatial dynamics of thaumarchaeal ecotype populations in coastal Monterey Bay

Reji

Tolar

Smith

et al. 2019

Environmental Microbiology

View full text Add to dashboard Cite

Summary Ammonia‐oxidizing archaea (AOA) of the phylum Thaumarchaeota are key players in nutrient cycling, yet large gaps remain in our understanding of their ecology and metabolism. Despite multiple lines of evidence pointing to a central role for copper‐containing nitrite reductase (NirK) in AOA metabolism, the thaumarchaeal nirK gene is rarely studied in the environment. In this study, we examine the diversity of nirK in the marine pelagic environment, in light of previously described ecological patterns of pelagic thaumarchaeal populations. Phylogenetic analyses show that nirK better resolves diversification patterns of marine Thaumarchaeota, compared to the conventionally used marker gene amoA. Specifically, we demonstrate that the three major phylogenetic clusters of marine nirK correspond to the three ‘ecotype’ populations of pelagic Thaumarchaeota. In this context, we further examine the relative distributions of the three variant groups in metagenomes and metatranscriptomes representing two depth profiles in coastal Monterey Bay. Our results reveal that nirK effectively tracks the dynamics of thaumarchaeal ecotype populations, particularly finer‐scale diversification patterns within major lineages. We also find evidence for multiple copies of nirK per genome in a fraction of thaumarchaeal cells in the water column, which must be taken into account when using it as a molecular marker.

show abstract

“…We used cluster-specific primers because of their high detectability of diverse nirK and nirS genes. These primers represent the best potential for detecting these genes (Ma et al, 2019), but do not identify genes from archaea (Bonilla-Rosso et al, 2016;Kobayashi et al, 2018) or potentially those from some bacterial or fungal groups (Ma et al, 2019). In addition, the results on taxonomic assignment depend on the fullness of the database.…”

Section: Resultsmentioning

confidence: 99%

Distinct Community Composition of Previously Uncharacterized Denitrifying Bacteria and Fungi across Different Land-Use Types

et al. 2020

View full text Add to dashboard Cite

Recent studies demonstrated that phylogenetically more diverse and abundant bacteria and fungi than previously considered are responsible for denitrification in terrestrial environments. We herein examined the effects of land-use types on the community composition of those denitrifying microbes based on their nitrite reductase gene (nirK and nirS) sequences. These genes can be phylogenetically grouped into several clusters. We used cluster-specific PCR primers to amplify nirK and nirS belonging to each cluster because the most widely used primers only amplify genes belonging to a single cluster. We found that the dominant taxa as well as overall community composition of denitrifying bacteria and fungi, regardless of the cluster they belonged to, differed according to the land-use type. We also identified distinguishing taxa based on individual land-use types, the distribution of which has not previously been characterized, such as denitrifying bacteria or fungi dominant in forest soils, Rhodanobacter having nirK, Penicillium having nirK, and Bradyrhizobium having nirS. These results suggest that land-use management affects the ecological constraints and consequences of denitrification in terrestrial environments through the assembly of distinct communities of denitrifiers.

show abstract

Nitric Oxide Production from Nitrite Reduction and Hydroxylamine Oxidation by Copper-containing Dissimilatory Nitrite Reductase (NirK) from the Aerobic Ammonia-oxidizing Archaeon, <i>Nitrososphaera viennensis</i>

Cited by 37 publications

References 46 publications

Genome-resolved metagenomics analysis provides insights into the ecological role of Thaumarchaeota in the Amazon River and its plume

Genome-resolved metagenomics analysis provides insights into the ecological role of Thaumarchaeota in the Amazon River and its plume

Depth distributions of nitrite reductase (nirK) gene variants reveal spatial dynamics of thaumarchaeal ecotype populations in coastal Monterey Bay

Distinct Community Composition of Previously Uncharacterized Denitrifying Bacteria and Fungi across Different Land-Use Types

Contact Info

Product

Resources

About