Genome Sequence of an Ammonia-Oxidizing Soil Archaeon, “Candidatus Nitrosoarchaeum koreensis” MY1

Kim, Byung Kwon; Jung, Man Young; Dong, Yu; Park, Soo Je; Oh, Tae Kwang; Rhee, Sang Dal; Kim, Jihyun F.

doi:10.1128/jb.05717-11

Cited by 105 publications

(84 citation statements)

References 24 publications

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“…For example, RSA3 and SCM1 are the only members of their genus harboring a putative high-affinity phosphate-specific transport (Pst) system (pstSCABU; Nmar_0479/ 0481-0484; Figure 3b), which might be correlated with the extremely low concentration of dissolved inorganic phosphate in the Atlantis-BSI (o1 mM; Bougouffa et al, 2013); the other species are predicted to have the low-affinity phosphate inorganic transporter. The Pst system occurs also in non-marine thaumarchaea (Kim et al, 2011;Blainey et al, 2011;Spang et al, 2012; Figure 3b), suggesting that phosphorus limitation is not necessarily confined to marine Thaumarchaeota.…”

Section: Functional Plasticity In the Genus Nitrosopumilusmentioning

confidence: 99%

Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea

et al. 2014

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The bottom of the Red Sea harbors over 25 deep hypersaline anoxic basins that are geochemically distinct and characterized by vertical gradients of extreme physicochemical conditions. Because of strong changes in density, particulate and microbial debris get entrapped in the brine-seawater interface (BSI), resulting in increased dissolved organic carbon, reduced dissolved oxygen toward the brines and enhanced microbial activities in the BSI. These features coupled with the deep-sea prevalence of ammonia-oxidizing archaea (AOA) in the global ocean make the BSI a suitable environment for studying the osmotic adaptations and ecology of these important players in the marine nitrogen cycle. Using phylogenomic-based approaches, we show that the local archaeal community of five different BSI habitats (with up to 18.2% salinity) is composed mostly of a single, highly abundant Nitrosopumilus-like phylotype that is phylogenetically distinct from the bathypelagic thaumarchaea; ammonia-oxidizing bacteria were absent. The composite genome of this novel Nitrosopumilus-like subpopulation (RSA3) co-assembled from multiple single-cell amplified genomes (SAGs) from one such BSI habitat further revealed that it shares B54% of its predicted genomic inventory with sequenced Nitrosopumilus species. RSA3 also carries several, albeit variable gene sets that further illuminate the phylogenetic diversity and metabolic plasticity of this genus. Specifically, it encodes for a putative proline-glutamate 'switch' with a potential role in osmotolerance and indirect impact on carbon and energy flows. Metagenomic fragment recruitment analyses against the composite RSA3 genome, Nitrosopumilus maritimus, and SAGs of mesopelagic thaumarchaea also reiterate the divergence of the BSI genotypes from other AOA.

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Section: Functional Plasticity In the Genus Nitrosopumilusmentioning

confidence: 99%

Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea

et al. 2014

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“…In ammoniaoxidizing bacteria, this second step is performed by hydroxylamine dehydrogenase (EC 1.7.2.6); however, no homologues of hydroxylamine dehydrogenaseencoding genes have been identified in genome sequences obtained from any pure or enrichment culture of Thaumarchaea (Walker et al, 2010;Kim et al, 2011;Tourna et al, 2011;Spang et al, 2012). In addition to NH 2 OH, there is also evidence that nitric oxide (NO) plays an important role in the Thaumarchaeotal but not in the bacterial ammonia oxidation pathway (Shen et al, 2013;Martens-Habbena et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Pathways and key intermediates required for obligate aerobic ammonia-dependent chemolithotrophy in bacteria and Thaumarchaeota

et al. 2016

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Chemolithotrophic ammonia-oxidizing bacteria and Thaumarchaeota are central players in the global nitrogen cycle. Obligate ammonia chemolithotrophy has been characterized for bacteria; however, large gaps remain in the Thaumarchaeotal pathway. Using batch growth experiments and instantaneous microrespirometry measurements of resting biomass, we show that the terrestrial Thaumarchaeon Nitrososphaera viennensis EN76 T exhibits tight control over production and consumption of nitric oxide (NO) during ammonia catabolism, unlike the ammonia-oxidizing bacterium Nitrosospira multiformis ATCC 25196 T . In particular, pulses of hydroxylamine into a microelectrode chamber as the sole substrate for N. viennensis resulted in iterative production and consumption of NO followed by conversion of hydroxylamine to nitrite. In support of these observations, oxidation of ammonia in growing cultures of N. viennensis, but not of N. multiformis, was inhibited by the NO-scavenger PTIO. When based on the marginal nitrous oxide (N 2 O) levels detected in cell-free media controls, the higher levels produced by N. multiformis were explained by enzyme activity, whereas N 2 O in N. viennensis cultures was attributed to abiotic reactions of released N-oxide intermediates with media components. Our results are conceptualized in a pathway for ammonia-dependent chemolithotrophy in Thaumarchaea, which identifies NO as an essential intermediate in the pathway and implements known biochemistry to be executed by a proposed but still elusive copper enzyme. Taken together, this work identifies differences in ammonia-dependent chemolithotrophy between bacteria and the Thaumarchaeota, advances a central catabolic role of NO only in the Thaumarchaeotal pathway and reveals stark differences in how the two microbial cohorts contribute to N 2 O emissions.

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“…N 2 O can also be produced during ammonium (NH + 4 ) oxidation, a chemolithoautotrophic process by which NH + 4 is oxidized aerobically either by bacteria or archaea. However, the pathways of N 2 O production appear to differ between ammonium oxidizers from these two domains (Blainey et al, 2011;Kim et al, 2011;Spang et al, 2012;Kozlowski et al, 2016). While N 2 O is a minor product in ammonium oxidation (up to 10 % relative to NO − 2 production; Goreau et al, 1980), the yield of N 2 O produced by nitrifiers relative to NO − 2 increases ∼ 20 times as O 2 saturation in the atmosphere diminishes to 1 % (Kester et al, 1977).…”

Section: Introductionmentioning

confidence: 99%

Vertical segregation among pathways mediating nitrogen loss (N<sub>2</sub> and N<sub>2</sub>O production) across the oxygen gradient in a coastal upwelling ecosystem

2017

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Abstract. The upwelling system off central Chile (36.5 • S) is seasonally subjected to oxygen (O 2 )-deficient waters, with a strong vertical gradient in O 2 (from oxic to anoxic conditions) that spans a few metres (30-50 m interval) over the shelf. This condition inhibits and/or stimulates processes involved in nitrogen (N) removal (e.g. anammox, denitrification, and nitrification). During austral spring (September 2013) and summer (January 2014), the main pathways involved in N loss and its speciation, in the form of N 2 and/or N 2 O, were studied using 15 N-tracer incubations, inhibitor assays, and the natural abundance of nitrate isotopes along with hydrographic information. Incubations were developed using water retrieved from the oxycline (25 m depth) and bottom waters (85 m depth) over the continental shelf off Concepción, Chile. Results of 15 N-labelled incubations revealed higher N removal activity during the austral summer, with denitrification as the dominant N 2 -producing pathway, which occurred together with anammox at all times. Interestingly, in both spring and summer maximum potential N removal rates were observed in the oxycline, where a greater availability of oxygen was observed (maximum O 2 fluctuation between 270 and 40 µmol L −1 ) relative to the hypoxic bottom waters (< 20 µmol O 2 L −1 ). Different pathways were responsible for N 2 O produced in the oxycline and bottom waters, with ammonium oxidation and dissimilatory nitrite reduction, respectively, as the main source processes. Ammonium produced by dissimilatory nitrite reduction to ammonium (DNiRA) could sustain both anammox and nitrification rates, including the ammonium utilized for N 2 O production. The temporal and vertical variability of δ 15 N-NO − 3 confirms that multiple N-cycling processes are modulating the isotopic nitrate composition over the shelf off central Chile during spring and summer. N removal processes in this coastal system appear to be related to the availability and distribution of oxygen and particles, which are a source of organic matter and the fuel for the production of other electron donors (i.e. ammonium) and acceptors (i.e. nitrate and nitrite) after its remineralization. These results highlight the links between several pathways involved in N loss. They also establish that different mechanisms supported by alternative N substratesPublished by Copernicus Publications on behalf of the European Geosciences Union. 4796A. Galán et al.: Vertical segregation among pathways mediating nitrogen loss are responsible for substantial accumulation of N 2 O, which are frequently observed as hotspots in the oxycline and bottom waters. Considering the extreme variation in oxygen observed in several coastal upwelling systems, these findings could help to understand the ecological and biogeochemical implications due to global warming where intensification and/or expansion of the oceanic OMZs is projected.

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Genome Sequence of an Ammonia-Oxidizing Soil Archaeon, “Candidatus Nitrosoarchaeum koreensis” MY1

Cited by 105 publications

References 24 publications

Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea

Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea

Pathways and key intermediates required for obligate aerobic ammonia-dependent chemolithotrophy in bacteria and Thaumarchaeota

Vertical segregation among pathways mediating nitrogen loss (N<sub>2</sub> and N<sub>2</sub>O production) across the oxygen gradient in a coastal upwelling ecosystem

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Genome Sequence of an Ammonia-Oxidizing Soil Archaeon, “Candidatus Nitrosoarchaeum koreensis” MY1

Cited by 105 publications

References 24 publications

Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea

Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea

Pathways and key intermediates required for obligate aerobic ammonia-dependent chemolithotrophy in bacteria and Thaumarchaeota

Vertical segregation among pathways mediating nitrogen loss (N&lt;sub&gt;2&lt;/sub&gt; and N&lt;sub&gt;2&lt;/sub&gt;O production) across the oxygen gradient in a coastal upwelling ecosystem

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Vertical segregation among pathways mediating nitrogen loss (N<sub>2</sub> and N<sub>2</sub>O production) across the oxygen gradient in a coastal upwelling ecosystem