Enrichment and characterization of ammonia-oxidizing archaea from the open ocean: phylogeny, physiology and stable isotope fractionation

Santoro, Alyson E.; Casciotti, Karen L.

doi:10.1038/ismej.2011.58

Cited by 170 publications

(174 citation statements)

References 79 publications

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“…The growth rate of HCA1 was comparable to SCM1 (0.65 d −1 ) and the one described thermophilic AOA, "Candidatus Nitrosocaldus yellowstonii" (0.8 d −1 ) (22,23). The lower growth rate of PS0 was similar to the previously described pelagic AOA enrichments, CN25 and CN75 (0.17 d −1 ) and to the estimated in situ growth rates of AOA in winter polar waters (0.21 d −1 ) (18,28). Because both strains were of similar shape and size to SCM1 ( Fig.…”

Section: Resultssupporting

confidence: 83%

“…Although enrichments of AOA strains belonging to groups I.1a and I.1b from a variety of marine and terrestrial environments have been reported (15)(16)(17)(18)(19)(20)(21)(22), no additional pure cultures of marine representatives have been described since the isolation of Nitrosopumilus maritimus strain SCM1 (henceforth referred to as SCM1) (23). However, many complex biological traits of significance to marine biogeochemistry and marine food webs cannot be unambiguously established using metagenomic, metatranscriptomic studies and enrichment cultures.…”

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confidence: 99%

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Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation

Qin¹,

Amin

Martens‐Habbena³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

310

328

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Ammonia-oxidizing archaea (AOA) are now implicated in exerting significant control over the form and availability of reactive nitrogen species in marine environments. Detailed studies of specific metabolic traits and physicochemical factors controlling their activities and distribution have not been well constrained in part due to the scarcity of isolated AOA strains. Here, we report the isolation of two new coastal marine AOA, strains PS0 and HCA1. Comparison of the new strains to Nitrosopumilus maritimus strain SCM1, the only marine AOA in pure culture thus far, demonstrated distinct adaptations to pH, salinity, organic carbon, temperature, and light. Strain PS0 sustained nearly 80% of ammonia oxidation activity at a pH as low as 5.9, indicating that coastal strains may be less sensitive to the ongoing reduction in ocean pH. Notably, the two novel isolates are obligate mixotrophs that rely on uptake and assimilation of organic carbon compounds, suggesting a direct coupling between chemolithotrophy and organic matter assimilation in marine food webs. All three isolates showed only minor photoinhibition at 15 μE·m −2 ·s −1 and rapid recovery of ammonia oxidation in the dark, consistent with an AOA contribution to the primary nitrite maximum and the plausibility of a diurnal cycle of archaeal ammonia oxidation activity in the euphotic zone. Together, these findings highlight an unexpected adaptive capacity within closely related marine group I Archaea and provide new understanding of the physiological basis of the remarkable ecological success reflected by their generally high abundance in marine environments.marine ammonia-oxidizing archaea | ecophysiology | urea utilization

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Section: Resultssupporting

confidence: 83%

mentioning

confidence: 99%

Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation

Qin¹,

Amin

Martens‐Habbena³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

310

328

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“…enrichment culture indicated that in late exponential phase, 90-95% of the cells are archaeal (26), and scanning electron microscopy shows the culture is dominated by rod-shaped cells with a diameter of 0.17-0.26 μm (mean 0.15 ± 0.02 μm; n = 50 cells) and length of 0.6-1.0 μm (0.78 ± 0.25 μm; SI Appendix, Fig. S1).…”

Section: Resultsmentioning

confidence: 99%

“…The genus name refers to the organism's water column habitat and its ability to oxidize ammonia to nitrite. The species name refers both to the organism's affiliation with a clade of shallow water Thaumarchaeota (26) and its small genome.…”

Section: Resultsmentioning

confidence: 99%

“…Here, we present the closed genome of a marine ammoniaoxidizing Thaumarchaeota assembled from a low-diversity metagenome of an enrichment culture originating from the open ocean and previously described as CN25 (26). We mapped peptides collected from early stationary phase cells to translations of the CN25 genome's predicted ORFs to produce the first global proteome, to our knowledge, from a marine thaumarchaeon.…”

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confidence: 99%

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Genomic and proteomic characterization of “ Candidatus Nitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean

Santoro

Dupont

Richter

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

268

239

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Thaumarchaeota are among the most abundant microbial cells in the ocean, but difficulty in cultivating marine Thaumarchaeota has hindered investigation into the physiological and evolutionary basis of their success. We report here a closed genome assembled from a highly enriched culture of the ammonia-oxidizing pelagic thaumarchaeon CN25, originating from the open ocean. The CN25 genome exhibits strong evidence of genome streamlining, including a 1.23-Mbp genome, a high coding density, and a low number of paralogous genes. Proteomic analysis recovered nearly 70% of the predicted proteins encoded by the genome, demonstrating that a high fraction of the genome is translated. In contrast to other minimal marine microbes that acquire, rather than synthesize, cofactors, CN25 encodes and expresses near-complete biosynthetic pathways for multiple vitamins. Metagenomic fragment recruitment indicated the presence of DNA sequences >90% identical to the CN25 genome throughout the oligotrophic ocean. We propose the provisional name "Candidatus Nitrosopelagicus brevis" str. CN25 for this minimalist marine thaumarchaeon and suggest it as a potential model system for understanding archaeal adaptation to the open ocean.nitrification | marine metagenomics | genome streamlining | archaea

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Significant mixed layer nitrification in a natural iron‐fertilized bloom of the Southern Ocean

Fripiat

Elskens

Trull

et al. 2015

Global Biogeochemical Cycles

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Nitrification, the microbially mediated oxidation of ammonium into nitrate, is generally expected to be low in the Southern Ocean mixed layer. This paradigm assumes that nitrate is mainly provided through vertical mixing and assimilated during the vegetative season, supporting the concept that nitrate uptake is equivalent to the new primary production (i.e., primary production which is potentially available for export). Here we show that nitrification is significant (~40-80% of the seasonal nitrate uptake) in the naturally iron-fertilized bloom over the southeast Kerguelen Plateau. Hence, a large fraction of the nitrate-based primary production is regenerated, instead of being exported. It appears that nitrate assimilation (light dependent) and nitrification (partly light inhibited) are spatially separated between the upper and lower parts, respectively, of the deep surface mixed layers. These deep mixed layers, extending well below the euphotic layer, allow nitrifiers to compete with phytoplankton for the assimilation of ammonium. The high contributions of nitrification to nitrate uptake are in agreement with both low export efficiency (i.e., the percentage of primary production that is exported) and low seasonal nitrate drawdown despite high nitrate assimilation.

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Enrichment and characterization of ammonia-oxidizing archaea from the open ocean: phylogeny, physiology and stable isotope fractionation

Cited by 170 publications

References 79 publications

Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation

Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation

Genomic and proteomic characterization of “ Candidatus Nitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean

Significant mixed layer nitrification in a natural iron‐fertilized bloom of the Southern Ocean

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