Nitrosopumilus adriaticus sp. nov. and Nitrosopumilus piranensis sp. nov., two ammonia-oxidizing archaea from the Adriatic Sea and members of the class Nitrososphaeria

Bayer, Barbara; Vojvoda, Jana; Reinthaler, Thomas; Reyes, Carolina; Pinto, Maria; Herndl, Gerhard J.

doi:10.1099/ijsem.0.003360

Cited by 67 publications

(75 citation statements)

References 86 publications

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“…1 and Table S2 ). While the topology of this species tree was broadly congruent with those of the single-gene trees based on 16S rRNA and amoA genes, forming four basal order-level lineages within the phylum Thaumarchaeota [ 26 , 27 , 36 , 37 ], the higher resolution of the phylogenomic analysis clearly differentiated closely related Nitrosopumilus strains (Fig. 1 ).…”

Section: Resultsmentioning

confidence: 60%

Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea

et al. 2020

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Ammonia-oxidizing archaea (AOA) are among the most abundant and ubiquitous microorganisms in the ocean, exerting primary control on nitrification and nitrogen oxides emission. Although united by a common physiology of chemoautotrophic growth on ammonia, a corresponding high genomic and habitat variability suggests tremendous adaptive capacity. Here, we compared 44 diverse AOA genomes, 37 from species cultivated from samples collected across diverse geographic locations and seven assembled from metagenomic sequences from the mesopelagic to hadopelagic zones of the deep ocean. Comparative analysis identified seven major marine AOA genotypic groups having gene content correlated with their distinctive biogeographies. Phosphorus and ammonia availabilities as well as hydrostatic pressure were identified as selective forces driving marine AOA genotypic and gene content variability in different oceanic regions. Notably, AOA methylphosphonate biosynthetic genes span diverse oceanic provinces, reinforcing their importance for methane production in the ocean. Together, our combined comparative physiological, genomic, and metagenomic analyses provide a comprehensive view of the biogeography of globally abundant AOA and their adaptive radiation into a vast range of marine and terrestrial habitats.

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Section: Resultsmentioning

confidence: 60%

Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea

et al. 2020

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“…For autotrophic ammonia‐oxidizers, it is much more costly to produce these extracellular compounds. The carbon yield from nitrification of N. adriaticus has previously been reported to be ~0.1 (fmol C fixed cell −1 d −1 / fmol N oxidized cell −1 d −1 ) (Bayer et al ., a). If we assume an extraction efficiency between 2% and 50%, the fraction of DOC exuded by Nitrosopumilus spp.…”

Section: Resultsmentioning

confidence: 99%

Ammonia‐oxidizing archaea release a suite of organic compounds potentially fueling prokaryotic heterotrophy in the ocean

Bayer

Hansman

Bittner

et al. 2019

Environmental Microbiology

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Summary Ammonia‐oxidizing archaea (AOA) constitute a considerable fraction of microbial biomass in the global ocean, comprising 20%–40% of the ocean's prokaryotic plankton. However, it remains enigmatic to what extent these chemolithoautotrophic archaea release dissolved organic carbon (DOC). A combination of targeted and untargeted metabolomics was used to characterize the exometabolomes of three model AOA strains of the Nitrosopumilus genus. Our results indicate that marine AOA exude a suite of organic compounds with potentially varying reactivities, dominated by nitrogen‐containing compounds. A significant fraction of the released dissolved organic matter (DOM) consists of labile compounds, which typically limit prokaryotic heterotrophic activity in open ocean waters, including amino acids, thymidine and B vitamins. Amino acid release rates corresponded with ammonia oxidation activity and the three Nitrosopumilus strains predominantly released hydrophobic amino acids, potentially as a result of passive diffusion. Despite the low contribution of DOC released by AOA (~0.08%–1.05%) to the heterotrophic prokaryotic carbon demand, the release of physiologically relevant metabolites could be crucial for microbes that are auxotrophic for some of these compounds, including members of the globally abundant and ubiquitous SAR11 clade.

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“…The calculated depth-integrated ammonium oxidation by this method (1.5 mmol m −2 d −1 ) is remarkably similar to the rate (1.6 mmol m −2 d −1 ) obtained by Dore and Karl (1996) for ALOHA using inhibitor-sensitive dark 14 C uptake assays. We then used the stoichiometry of ammonia oxidation (i.e., ratio of CO 2 fixed per NH + 4 oxidized of 0.1) to calculate the potential contribution of ammonia oxidation (nitrification) to the dark DIC fixation (Belser, 1984;Bayer et al, 2019). The remaining dark fixation was assumed to originate from other chemoautotrophic processes and anaplerotic metabolism.…”

Section: Contribution Of Dark Inorganic Carbon Fixation To Overall Ocmentioning

confidence: 99%

Ideas and perspectives: Is dark carbon fixation relevant for oceanic primary production estimates?

Baltar

Herndl

2019

Biogeosciences

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Abstract. About half of the global primary production (PP) is generated in the euphotic layer of the ocean. The 14C method developed by Steemann Nielsen (Nielsen, 1952) more than half a century ago has been the most frequently used method to determine PP in all aquatic systems. This method includes dark incubations to exclude the non-phototrophic dissolved inorganic carbon (DIC) fixation. The presence of significant dark DIC fixation rates has been habitually used to suggest the inaccuracy of the 14C method to determine autotrophic phytoplankton primary production. However, we suggest that the dark DIC fixation rates should be incorporated into global oceanic carbon production estimates since the total production of organic matter does not originate only from photosynthesis but also from other processes such as chemoautotrophic and anaplerotic processes. Here we analyzed data collected over almost 30 years from the longest available oceanic time series and calculated that the inclusion of dark DIC fixation would increase oceanic PP estimates by 5 %–22 % when total dark DIC fixation is included or by 2.5 %–11 % when only considering the nighttime DIC fixation. We conclude that dark DIC fixation should be included into global oceanic primary production estimates as it represents newly synthesized organic carbon (ca. 1.2–11 Pg C yr−1) available for the marine food web.

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Nitrosopumilus adriaticus sp. nov. and Nitrosopumilus piranensis sp. nov., two ammonia-oxidizing archaea from the Adriatic Sea and members of the class Nitrososphaeria

Cited by 67 publications

References 86 publications

Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea

Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea

Ammonia‐oxidizing archaea release a suite of organic compounds potentially fueling prokaryotic heterotrophy in the ocean

Ideas and perspectives: Is dark carbon fixation relevant for oceanic primary production estimates?

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