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Journal articles on the topic 'Nitrosopumilus maritimus'

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Published: 2 June 2025

Last updated: 31 July 2025

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1

Schouten, Stefan, Ellen C. Hopmans, Marianne Baas, et al. "Intact Membrane Lipids of “Candidatus Nitrosopumilus maritimus,” a Cultivated Representative of the Cosmopolitan Mesophilic Group I Crenarchaeota." Applied and Environmental Microbiology 74, no. 8 (2008): 2433–40. http://dx.doi.org/10.1128/aem.01709-07.

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ABSTRACT In this study we analyzed the membrane lipid composition of “Candidatus Nitrosopumilus maritimus,” the only cultivated representative of the cosmopolitan group I crenarchaeota and the only mesophilic isolate of the phylum Crenarchaeota. The core lipids of “Ca. Nitrosopumilus maritimus” consisted of glycerol dialkyl glycerol tetraethers (GDGTs) with zero to four cyclopentyl moieties. Crenarchaeol, a unique GDGT containing a cyclohexyl moiety in addition to four cyclopentyl moieties, was the most abundant GDGT. This confirms unambiguously that crenarchaeol is synthesized by species belo

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2

Qin, Wei, Katherine R. Heal, Rasika Ramdasi, et al. "Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota." International Journal of Systematic and Evolutionary Microbiology 67, no. 12 (2017): 5067–79. http://dx.doi.org/10.1099/ijsem.0.002416.

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3

Nelson, Katelyn A., Nicole S. Moin, and Anne E. Bernhard. "Archaeal Diversity and the Prevalence of Crenarchaeota in Salt Marsh Sediments." Applied and Environmental Microbiology 75, no. 12 (2009): 4211–15. http://dx.doi.org/10.1128/aem.00201-09.

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ABSTRACT Crenarchaeal 16S rRNA sequences constituted over 70% of the archaeal clones recovered from three salt marsh sites dominated by different grasses. Group I.1a Crenarchaeota dominated at two sites, while group I.3b Crenarchaeota sequences were most abundant at a third site. Abundances of 16S rRNA genes related to “Candidatus Nitrosopumilus maritimus” differed by site and sampling date.

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4

Ng, Kian-Hong, Vinayaka Srinivas, Ramanujam Srinivasan, and Mohan Balasubramanian. "TheNitrosopumilus maritimusCdvB, but Not FtsZ, Assembles into Polymers." Archaea 2013 (2013): 1–10. http://dx.doi.org/10.1155/2013/104147.

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Euryarchaeota and Crenarchaeota are two major phyla of archaea which use distinct molecular apparatuses for cell division. Euryarchaea make use of the tubulin-related protein FtsZ, while Crenarchaea, which appear to lack functional FtsZ, employ the Cdv (cell division) components to divide. Ammonia oxidizing archaeon (AOA)Nitrosopumilus maritimusbelongs to another archaeal phylum, the Thaumarchaeota, which has both FtsZ and Cdv genes in the genome. Here, we used a heterologous expression system to characterize FtsZ and Cdv proteins fromN. maritimusby investigating the ability of these proteins

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5

Könneke, Martin, Julius Sebastian Lipp, and Kai-Uwe Hinrichs. "Carbon isotope fractionation by the marine ammonia-oxidizing archaeon Nitrosopumilus maritimus." Organic Geochemistry 48 (July 2012): 21–24. http://dx.doi.org/10.1016/j.orggeochem.2012.04.007.

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6

Könneke, Martin, Julius S. Lipp, and Kai-Uwe Hinrichs. "Carbon isotope fractionation by the marine ammonia-oxidizing archaeon Nitrosopumilus maritimus." Organic Geochemistry 48 (May 3, 2012): 21–24. https://doi.org/10.1016/j.orggeochem.2012.04.007.

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Abstract Ammonia-oxidizing archaea (AOA) are abundant and widely distributed microorganisms in aquatic and terrestrial habitats. By catalyzing the first and rate limiting step in nitrification, these chemolithoautotrophs play a significant role in the global nitrogen cycle and contribute to primary production. Here, the carbon isotopic fractionation relative to inorganic carbon source was determined for bulk biomass, biphytanes and polar lipid bound sugars of a marine AOA pure culture. Bulk biomass and biphytanes from <em>Nitrosopumilus maritimus</em> showed identical carbon isotope fractionat

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Pelve, Erik A., Ann-Christin Lindås, Willm Martens-Habbena, José R. de la Torre, David A. Stahl, and Rolf Bernander. "Cdv-based cell division and cell cycle organization in the thaumarchaeon Nitrosopumilus maritimus." Molecular Microbiology 82, no. 3 (2011): 555–66. http://dx.doi.org/10.1111/j.1365-2958.2011.07834.x.

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8

Walker, C. B., J. R. de la Torre, M. G. Klotz, et al. "Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea." Proceedings of the National Academy of Sciences 107, no. 19 (2010): 8818–23. http://dx.doi.org/10.1073/pnas.0913533107.

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9

Shafiee, Roxana T., Joseph T. Snow, Qiong Zhang, and Rosalind E. M. Rickaby. "Iron requirements and uptake strategies of the globally abundant marine ammonia-oxidising archaeon, Nitrosopumilus maritimus SCM1." ISME Journal 13, no. 9 (2019): 2295–305. http://dx.doi.org/10.1038/s41396-019-0434-8.

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10

Nakagawa, Tatsunori, and David A. Stahl. "Transcriptional Response of the Archaeal Ammonia Oxidizer Nitrosopumilus maritimus to Low and Environmentally Relevant Ammonia Concentrations." Applied and Environmental Microbiology 79, no. 22 (2013): 6911–16. http://dx.doi.org/10.1128/aem.02028-13.

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ABSTRACTThe ability of chemoautotrophic ammonia-oxidizing archaea to compete for ammonia among marine microorganisms at low ambient concentrations has been in part attributed to their extremely high affinity for ammonia, but as yet there is no mechanistic understanding of supporting metabolism. We examined transcription of selected genes for anabolic functions (CO2fixation, ammonia transport, and cell wall synthesis) and a central catabolic function (ammonia oxidation) in the thaumarchaeonNitrosopumilus maritimusSCM1 growing at two ammonia concentrations, as measured by combined ammonia and am

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11

Evans, Thomas W., Martin Könneke, Julius S. Lipp, et al. "Lipid biosynthesis of Nitrosopumilus maritimus dissected by lipid specific radioisotope probing (lipid-RIP) under contrasting ammonium supply." Geochimica et Cosmochimica Acta 242 (December 2018): 51–63. http://dx.doi.org/10.1016/j.gca.2018.09.001.

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12

Ertem, F. B., O. Besler, and H. Demirci. "X-ray crystallography and AlphaFold reveal the structure of acetyl-CoA-carboxylase from Nitrosopumilus maritimus." Acta Crystallographica Section A Foundations and Advances 79, a2 (2023): C1255. http://dx.doi.org/10.1107/s2053273323083663.

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13

Otte, Julia, Achim Mall, Daniel M. Schubert, Martin Könneke, and Ivan A. Berg. "Malonic Semialdehyde Reductase from the Archaeon Nitrosopumilus maritimus Is Involved in the Autotrophic 3-Hydroxypropionate/4-Hydroxybutyrate Cycle." Applied and Environmental Microbiology 81, no. 5 (2014): 1700–1707. http://dx.doi.org/10.1128/aem.03390-14.

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ABSTRACTThe recently described ammonia-oxidizing archaea of the phylumThaumarchaeotaare highly abundant in marine, geothermal, and terrestrial environments. All characterized representatives of this phylum are aerobic chemolithoautotrophic ammonia oxidizers assimilating inorganic carbon via a recently described thaumarchaeal version of the 3-hydroxypropionate/4-hydroxybutyrate cycle. Although some genes coding for the enzymes of this cycle have been identified in the genomes ofThaumarchaeota, many other genes of the cycle are not homologous to the characterized enzymes from other species and c

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14

Hosseinzadeh, Parisa, Shiliang Tian, Nicholas M. Marshall, et al. "A Purple Cupredoxin from Nitrosopumilus maritimus Containing a Mononuclear Type 1 Copper Center with an Open Binding Site." Journal of the American Chemical Society 138, no. 20 (2016): 6324–27. http://dx.doi.org/10.1021/jacs.5b13128.

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15

Amin, Shady A., James W. Moffett, Willm Martens-Habbena, et al. "Copper requirements of the ammonia-oxidizing archaeon Nitrosopumilus maritimus SCM1 and implications for nitrification in the marine environment." Limnology and Oceanography 58, no. 6 (2013): 2037–45. http://dx.doi.org/10.4319/lo.2013.58.6.2037.

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16

Urakawa, Hidetoshi, Willm Martens-Habbena, and David A. Stahl. "High Abundance of Ammonia-Oxidizing Archaea in Coastal Waters, Determined Using a Modified DNA Extraction Method." Applied and Environmental Microbiology 76, no. 7 (2010): 2129–35. http://dx.doi.org/10.1128/aem.02692-09.

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ABSTRACT Molecular characterizations of environmental microbial populations based on recovery and analysis of DNA generally assume efficient or unbiased extraction of DNA from different sample matrices and microbial groups. Appropriate controls to verify this basic assumption are rarely included. Here three different DNA extractions, performed with two commercial kits (FastDNA and UltraClean) and a standard phenol-chloroform method, and two alternative filtration methods (Sterivex and 25-mm-diameter polycarbonate filters) were evaluated, using the addition of Nitrosopumilus maritimus cells to

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17

Meador, Travis B., Niels Schoffelen, Timothy G. Ferdelman, Osmond Rebello, Alexander Khachikyan, and Martin Könneke. "Carbon recycling efficiency and phosphate turnover by marine nitrifying archaea." Science Advances 6, no. 19 (2020): eaba1799. http://dx.doi.org/10.1126/sciadv.aba1799.

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Thaumarchaeotal nitrifiers are among the most abundant organisms in the ocean, but still unknown is the carbon (C) yield from nitrification and the coupling of these fluxes to phosphorus (P) turnover and release of metabolites from the cell. Using a dual radiotracer approach, we found that Nitrosopumilus maritimus fixed roughly 0.3 mol C, assimilated 2 mmol P, and released ca. 10−2 mol C and 10−5 mol P as dissolved organics (DOC and DOP) per mole ammonia respired. Phosphate turnover may influence assimilation fluxes by nitrifiers in the euphotic zone, which parallel those of the dark ocean. Co

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18

Kaushik, Vineeta, Anchal, and Manisha Goel. "Characterization of Cyclophilin from Thaumarchaeota Nitrosopumilus maritimus: Implications on the Diversity of Chaperone-like Activity in the Archaeal Domain." ACS Omega 7, no. 1 (2021): 70–84. http://dx.doi.org/10.1021/acsomega.1c03216.

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19

Loescher, C. R., A. Kock, M. Koenneke, J. LaRoche, H. W. Bange, and R. A. Schmitz. "Production of oceanic nitrous oxide by ammonia-oxidizing archaea." Biogeosciences Discussions 9, no. 2 (2012): 2095–122. http://dx.doi.org/10.5194/bgd-9-2095-2012.

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Abstract. The recent finding that microbial ammonia oxidation in the ocean is performed by archaea to a greater extent than by bacteria has drastically changed the view on oceanic nitrification. The numerical dominance of archaeal ammonia-oxidizers (AOA) over their bacterial counterparts (AOB) in large parts of the ocean leads to the hypothesis that AOA rather than AOB could be the key organisms for the oceanic production of the strong greenhouse gas nitrous oxide (N2O) which occurs as a by-product of nitrification. Very recently, enrichment cultures of marine ammonia-oxidizing archaea have be

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20

Löscher, C. R., A. Kock, M. Könneke, J. LaRoche, H. W. Bange, and R. A. Schmitz. "Production of oceanic nitrous oxide by ammonia-oxidizing archaea." Biogeosciences 9, no. 7 (2012): 2419–29. http://dx.doi.org/10.5194/bg-9-2419-2012.

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Abstract. The recent finding that microbial ammonia oxidation in the ocean is performed by archaea to a greater extent than by bacteria has drastically changed the view on oceanic nitrification. The numerical dominance of archaeal ammonia-oxidizers (AOA) over their bacterial counterparts (AOB) in large parts of the ocean leads to the hypothesis that AOA rather than AOB could be the key organisms for the oceanic production of the strong greenhouse gas nitrous oxide (N2O) that occurs as a by-product of nitrification. Very recently, enrichment cultures of marine ammonia-oxidizing archaea have bee

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21

Labrenz, Matthias, Eva Sintes, Falko Toetzke, et al. "Relevance of a crenarchaeotal subcluster related to Candidatus Nitrosopumilus maritimus to ammonia oxidation in the suboxic zone of the central Baltic Sea." ISME Journal 4, no. 12 (2010): 1496–508. http://dx.doi.org/10.1038/ismej.2010.78.

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22

Liu, Hao, Peng Zhou, Shunyan Cheung, Yanhong Lu, Hongbin Liu, and Hongmei Jing. "Distribution and Oxidation Rates of Ammonia-Oxidizing Archaea Influenced by the Coastal Upwelling off Eastern Hainan Island." Microorganisms 10, no. 5 (2022): 952. http://dx.doi.org/10.3390/microorganisms10050952.

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Coastal upwelling causes variations in temperature, salinity and inorganic nutrients in the water column, consequently leading to the shift of microbial populations and their metabolic activities. Impacts of the eastern Hainan upwelling (EHU) on the ammonia-oxidizing archaea (AOA) were investigated based on the amoA gene using pyrosequencing and quantitative PCR at both DNA and cDNA levels, together with the determination of the ammonia oxidation (AO) rate measured with 15N-labelled ammonium. By comparing stations with and without upwelling influence, we found that coastal upwelling correlated

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23

Reyes, Carolina, Logan H. Hodgskiss, Melina Kerou, et al. "Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation." ISME Journal 14, no. 11 (2020): 2659–74. http://dx.doi.org/10.1038/s41396-020-0715-2.

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Abstract Ammonia-oxidizing archaea (AOA) are widespread in nature and are involved in nitrification, an essential process in the global nitrogen cycle. The enzymes for ammonia oxidation and electron transport rely heavily on copper (Cu), which can be limited in nature. In this study the model soil archaeon Nitrososphaera viennensis was investigated via transcriptomic analysis to gain insight regarding possible Cu uptake mechanisms and compensation strategies when Cu becomes limiting. Upon Cu limitation, N. viennensis exhibited impaired nitrite production and thus growth, which was paralleled b

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Park, Byoung-Joon, Soo-Je Park, Dae-No Yoon, Stefan Schouten, Jaap S. Sinninghe Damsté, and Sung-Keun Rhee. "Cultivation of Autotrophic Ammonia-Oxidizing Archaea from Marine Sediments in Coculture with Sulfur-Oxidizing Bacteria." Applied and Environmental Microbiology 76, no. 22 (2010): 7575–87. http://dx.doi.org/10.1128/aem.01478-10.

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ABSTRACT The role of ammonia-oxidizing archaea (AOA) in nitrogen cycling in marine sediments remains poorly characterized. In this study, we enriched and characterized AOA from marine sediments. Group I.1a crenarchaea closely related to those identified in marine sediments and “Candidatus Nitrosopumilus maritimus” (99.1 and 94.9% 16S rRNA and amoA gene sequence identities to the latter, respectively) were substantially enriched by coculture with sulfur-oxidizing bacteria (SOB). The selective enrichment of AOA over ammonia-oxidizing bacteria (AOB) is likely due to the reduced oxygen levels caus

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Elling, Felix J., Martin Könneke, Julius S. Lipp, Kevin W. Becker, Emma J. Gagen, and Kai-Uwe Hinrichs. "Effects of growth phase on the membrane lipid composition of the thaumarchaeon Nitrosopumilus maritimus and their implications for archaeal lipid distributions in the marine environment." Geochimica et Cosmochimica Acta 141 (September 2014): 579–97. http://dx.doi.org/10.1016/j.gca.2014.07.005.

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26

Lu, Yanhong, Shunyan Cheung, Ling Chen, et al. "New insight to niche partitioning and ecological function of ammonia oxidizing archaea in subtropical estuarine ecosystem." Biogeosciences 17, no. 23 (2020): 6017–32. http://dx.doi.org/10.5194/bg-17-6017-2020.

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Abstract. Nitrification plays a central role in the estuarine nitrogen cycle. Previous studies in estuary mainly focused on the niche partition between ammonia-oxidizing archaea (AOA) and bacteria (AOB), while the diversity, activity, biogeography, and ecophysiology of different AOA groups remained unclear. Here, we for the first time report on niche partitioning and differentially distributed active populations among diverse AOA (inferred from amoA gene) in a typical subtropical estuary – Pearl River estuary (PRE). In the water column of the PRE, the AOA communities mainly consisted of water

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Hurley, Sarah J., Felix J. Elling, Martin Könneke, et al. "Influence of ammonia oxidation rate on thaumarchaeal lipid composition and the TEX86 temperature proxy." Proceedings of the National Academy of Sciences 113, no. 28 (2016): 7762–67. http://dx.doi.org/10.1073/pnas.1518534113.

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Archaeal membrane lipids known as glycerol dibiphytanyl glycerol tetraethers (GDGTs) are the basis of the TEX86 paleotemperature proxy. Because GDGTs preserved in marine sediments are thought to originate mainly from planktonic, ammonia-oxidizing Thaumarchaeota, the basis of the correlation between TEX86 and sea surface temperature (SST) remains unresolved: How does TEX86 predict surface temperatures, when maximum thaumarchaeal activity occurs below the surface mixed layer and TEX86 does not covary with in situ growth temperatures? Here we used isothermal studies of the model thaumarchaeon Nit

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Moin, Nicole S., Katelyn A. Nelson, Alexander Bush, and Anne E. Bernhard. "Distribution and Diversity of Archaeal and Bacterial Ammonia Oxidizers in Salt Marsh Sediments." Applied and Environmental Microbiology 75, no. 23 (2009): 7461–68. http://dx.doi.org/10.1128/aem.01001-09.

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ABSTRACT Diversity and abundance of ammonia-oxidizing Betaproteobacteria (β-AOB) and archaea (AOA) were investigated in a New England salt marsh at sites dominated by short or tall Spartina alterniflora (SAS and SAT sites, respectively) or Spartina patens (SP site). AOA amoA gene richness was higher than β-AOB amoA richness at SAT and SP, but AOA and β-AOB richness were similar at SAS. β-AOB amoA clone libraries were composed exclusively of Nitrosospira-like amoA genes. AOA amoA genes at SAT and SP were equally distributed between the water column/sediment and soil/sediment clades, while AOA a

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29

Stieglmeier, Michaela, Andreas Klingl, Ricardo J. E. Alves, et al. "Nitrososphaera viennensis gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon from soil and a member of the archaeal phylum Thaumarchaeota." International Journal of Systematic and Evolutionary Microbiology 64, Pt_8 (2014): 2738–52. http://dx.doi.org/10.1099/ijs.0.063172-0.

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A mesophilic, neutrophilic and aerobic, ammonia-oxidizing archaeon, strain EN76T, was isolated from garden soil in Vienna (Austria). Cells were irregular cocci with a diameter of 0.6–0.9 µm and possessed archaella and archaeal pili as cell appendages. Electron microscopy also indicated clearly discernible areas of high and low electron density, as well as tubule-like structures. Strain EN76T had an S-layer with p3 symmetry, so far only reported for members of the Sulfolobales . Crenarchaeol was the major core lipid. The organism gained energy by oxidizing ammonia to nitrite aerobically, thereb

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Woebken, Dagmar, Bernhard M. Fuchs, Marcel M. M. Kuypers, and Rudolf Amann. "Potential Interactions of Particle-Associated Anammox Bacteria with Bacterial and Archaeal Partners in the Namibian Upwelling System." Applied and Environmental Microbiology 73, no. 14 (2007): 4648–57. http://dx.doi.org/10.1128/aem.02774-06.

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ABSTRACT Recent studies have shown that the anaerobic oxidation of ammonium by anammox bacteria plays an important role in catalyzing the loss of nitrogen from marine oxygen minimum zones (OMZ). However, in situ oxygen concentrations of up to 25 μM and ammonium concentrations close to or below the detection limit in the layer of anammox activity are hard to reconcile with the current knowledge of the physiology of anammox bacteria. We therefore investigated samples from the Namibian OMZ by comparative 16S rRNA gene analysis and fluorescence in situ hybridization. Our results showed that “Candi

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Liu, Xiao-Lei, Julius S. Lipp, Jeffrey H. Simpson, Yu-Shih Lin, Roger E. Summons, and Kai-Uwe Hinrichs. "Mono- and dihydroxyl glycerol dibiphytanyl glycerol tetraethers in marine sediments: Identification of both core and intact polar lipid forms." Geochimica et Cosmochimica Acta 89 (April 28, 2012): 102–15. https://doi.org/10.1016/j.gca.2012.04.053.

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Abstract Hydroxylated glycerol dialkyl glycerol tetraethers (hydroxy-GDGTs) were detected in marine sediments of diverse depositional regimes and ages. Mass spectrometric evidence, complemented by information gleaned from two-dimensional (2D) <sup>1</sup>H–<sup>13</sup>C nuclear magnetic resonance (NMR) spectroscopy on minute quantities of target analyte isolated from marine sediment, allowed us to identify one major compound as a monohydroxy-GDGT with acyclic biphytanyl moieties (OH-GDGT-0). NMR spectroscopic and mass spectrometric data indicate the presence of a tertiary hydroxyl group

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Wan, Yu, Xiaohong Ruan, Jie Wang, and Xiaojun Shi. "Spatial and Seasonal Variations in the Abundance of Nitrogen-Transforming Genes and the Microbial Community Structure in Freshwater Lakes with Different Trophic Statuses." International Journal of Environmental Research and Public Health 16, no. 13 (2019): 2298. http://dx.doi.org/10.3390/ijerph16132298.

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Identifying nitrogen-transforming genes and the microbial community in the lacustrine sedimentary environment is critical for revealing nitrogen cycle processes in eutrophic lakes. In this study, we examined the diversity and abundance of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), denitrifying bacteria (DNB), and anammox bacteria (AAOB) in different trophic status regions of Lake Taihu using the amoA, Arch-amoA, nirS, and hzo genes as functional markers. Quantitative Polymerase Chain Reaction (qPCR) results indicated that the abundance of the nirS gene was the highest,

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Kraft, Beate, and Donald E. Canfield†. "Microbe Profile: Nitrosopumilus maritimus." Microbiology 168, no. 7 (2022). http://dx.doi.org/10.1099/mic.0.001207.

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Nitrosopumilus maritimus is a marine ammonia-oxidizing archaeon with a high affinity for ammonia. It fixes carbon via a modified hydroxypropionate/hydroxybutyrate cycle and shows weak utilization of cyanate as a supplementary energy and nitrogen source. When oxygen is depleted, N. maritimus produces its own oxygen, which may explain its regular occurrence in anoxic waters. Several enzymes of the ammonia oxidation and oxygen production pathways remain to be identified.

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Johnson, Jerome, Bradley B. Tolar, Bilge Tosun, et al. "Crystal structure of the 4-hydroxybutyryl-CoA synthetase (ADP-forming) from nitrosopumilus maritimus." Communications Biology 7, no. 1 (2024). http://dx.doi.org/10.1038/s42003-024-06432-x.

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AbstractThe 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle from ammonia-oxidizing Thaumarchaeota is currently considered the most energy-efficient aerobic carbon fixation pathway. The Nitrosopumilus maritimus 4-hydroxybutyryl-CoA synthetase (ADP-forming; Nmar_0206) represents one of several enzymes from this cycle that exhibit increased efficiency over crenarchaeal counterparts. This enzyme reduces energy requirements on the cell, reflecting thaumarchaeal success in adapting to low-nutrient environments. Here we show the structure of Nmar_0206 from Nitrosopumilus maritimus SCM1, which r

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35

Law, Kai P., Wei He, Jianchang Tao, and Chuanlun Zhang. "Characterization of the Exometabolome of Nitrosopumilus maritimus SCM1 by Liquid Chromatography–Ion Mobility Mass Spectrometry." Frontiers in Microbiology 12 (July 1, 2021). http://dx.doi.org/10.3389/fmicb.2021.658781.

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Marine Thaumarchaeota (formerly known as the marine group I archaea) have received much research interest in recent years since these chemolithoautotrophic organisms are abundant in the subsurface ocean and oxidize ammonium to nitrite, which makes them a major contributor to the marine carbon and nitrogen cycles. However, few studies have investigated the chemical composition of their exometabolome and their contributions to the pool of dissolved organic matter (DOM) in seawater. This study exploits the recent advances in ion mobility mass spectrometry (IM-MS) and integrates this instrumental

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Hoppstock, Lukas, Franziska Trusch, Christoph Lederer, Pieter van West, Martin Koenneke, and Peter Bayer. "NmPin from the marine thaumarchaeote Nitrosopumilus maritimus is an active membrane associated prolyl isomerase." BMC Biology 14, no. 1 (2016). http://dx.doi.org/10.1186/s12915-016-0274-1.

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37

Voland, Robert W., Hongsen Wang, Héctor D. Abruña, and Kyle M. Lancaster. "Nitrous oxide production via enzymatic nitroxyl from the nitrifying archaeon Nitrosopumilus maritimus." Proceedings of the National Academy of Sciences 122, no. 3 (2025). https://doi.org/10.1073/pnas.2416971122.

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Ammonia oxidizing archaea (AOA) are among the most abundant microorganisms on earth and are known to be a major source of nitrous oxide (N 2 O) emissions, although biochemical origins of this N 2 O remain unknown. Enzymological details of AOA nitrogen metabolism are broadly unavailable. We report the recombinant expression, purification, and characterization of a multicopper oxidase, Nmar_1354, from the AOA Nitrosopumilus maritimus . We show that Nmar_1354 selectively produces nitroxyl (HNO) by coupling the oxidation of the obligate nitrification intermediate hydroxylamine (NH 2 OH) to dioxyge

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Destan, Ebru, Busra Yuksel, Bradley B. Tolar, et al. "Structural insights into bifunctional thaumarchaeal crotonyl-CoA hydratase and 3-hydroxypropionyl-CoA dehydratase from Nitrosopumilus maritimus." Scientific Reports 11, no. 1 (2021). http://dx.doi.org/10.1038/s41598-021-02180-8.

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AbstractThe ammonia-oxidizing thaumarchaeal 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle is one of the most energy-efficient CO2 fixation cycles discovered thus far. The protein encoded by Nmar_1308 (from Nitrosopumilus maritimus SCM1) is a promiscuous enzyme that catalyzes two essential reactions within the thaumarchaeal 3HP/4HB cycle, functioning as both a crotonyl-CoA hydratase (CCAH) and 3-hydroxypropionyl-CoA dehydratase (3HPD). In performing both hydratase and dehydratase activities, Nmar_1308 reduces the total number of enzymes necessary for CO2 fixation in Thaumarchaeota, redu

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Liu, Li, Daniel M. Schubert, Martin Könneke, and Ivan A. Berg. "(S)-3-Hydroxybutyryl-CoA Dehydrogenase From the Autotrophic 3-Hydroxypropionate/4-Hydroxybutyrate Cycle in Nitrosopumilus maritimus." Frontiers in Microbiology 12 (July 5, 2021). http://dx.doi.org/10.3389/fmicb.2021.712030.

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Ammonia-oxidizing archaea of the phylum Thaumarchaeota are among the most abundant organisms that exert primary control of oceanic and soil nitrification and are responsible for a large part of dark ocean primary production. They assimilate inorganic carbon via an energetically efficient version of the 3-hydroxypropionate/4-hydroxybutyrate cycle. In this cycle, acetyl-CoA is carboxylated to succinyl-CoA, which is then converted to two acetyl-CoA molecules with 4-hydroxybutyrate as the key intermediate. This conversion includes the (S)-3-hydroxybutyryl-CoA dehydrogenase reaction. Here, we heter

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Law, Kai P., Wei He, Jianchang Tao, and Chuanlun Zhang. "A Novel Approach to Characterize the Lipidome of Marine Archaeon Nitrosopumilus maritimus by Ion Mobility Mass Spectrometry." Frontiers in Microbiology 12 (December 2, 2021). http://dx.doi.org/10.3389/fmicb.2021.735878.

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Archaea are differentiated from the other two domains of life by their biomolecular characteristics. One such characteristic is the unique structure and composition of their lipids. Characterization of the whole set of lipids in a biological system (the lipidome) remains technologically challenging. This is because the lipidome is innately complex, and not all lipid species are extractable, separable, or ionizable by a single analytical method. Furthermore, lipids are structurally and chemically diverse. Many lipids are isobaric or isomeric and often indistinguishable by the measurement of mas

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Shafiee, Roxana T., Joseph T. Snow, Svenja Hester, Qiong Zhang, and Rosalind E. M. Rickaby. "Proteomic response of the marine ammonia‐oxidising archaeon Nitrosopumilus maritimus to iron limitation reveals strategies to compensate for nutrient scarcity." Environmental Microbiology, May 6, 2021. http://dx.doi.org/10.1111/1462-2920.15491.

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Zhou, Yangkai, An Yan, Jiawen Yang, et al. "Ultrastructural insights into cellular organization, energy storage and ribosomal dynamics of an ammonia-oxidizing archaeon from oligotrophic oceans." Frontiers in Microbiology 15 (April 26, 2024). http://dx.doi.org/10.3389/fmicb.2024.1367658.

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IntroductionNitrososphaeria, formerly known as Thaumarchaeota, constitute a diverse and widespread group of ammonia-oxidizing archaea (AOA) inhabiting ubiquitously in marine and terrestrial environments, playing a pivotal role in global nitrogen cycling. Despite their importance in Earth’s ecosystems, the cellular organization of AOA remains largely unexplored, leading to a significant unanswered question of how the machinery of these organisms underpins metabolic functions.MethodsIn this study, we combined spherical-chromatic-aberration-corrected cryo-electron tomography (cryo-ET), scanning t

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Klein, Timothy, Logan H. Hodgskiss, Max Dreer, et al. "Distinct Patterns of Antibiotic Sensitivities in Ammonia‐Oxidising Archaea." Environmental Microbiology 27, no. 3 (2025). https://doi.org/10.1111/1462-2920.70063.

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ABSTRACTAmmonia‐oxidising archaea (AOA) are important microorganisms contributing towards the nitrogen flux in the environment. Unlike archaea from other major phyla, genetic tools are yet to be developed for the AOA, and identification of antibiotic resistance markers for selecting mutants is required for a genetic system. The aim of this study was to test the effects of selected antibiotics (hygromycin B, neomycin, apramycin, puromycin, novobiocin) on pure cultures of three well studied AOA strains, ‘Candidatus Nitrosocosmicus franklandianus C13’, Nitrososphaera viennensis EN76 and Nitrosopu

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Shafiee, Roxana T., Poppy J. Diver, Joseph T. Snow, Qiong Zhang, and Rosalind E. M. Rickaby. "Marine ammonia-oxidising archaea and bacteria occupy distinct iron and copper niches." ISME Communications 1, no. 1 (2021). http://dx.doi.org/10.1038/s43705-021-00001-7.

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AbstractAmmonia oxidation by archaea and bacteria (AOA and AOB), is the first step of nitrification in the oceans. As AOA have an ammonium affinity 200-fold higher than AOB isolates, the chemical niche allowing AOB to persist in the oligotrophic ocean remains unclear. Here we show that marine isolates, Nitrosopumilus maritimus strain SCM1 (AOA) and Nitrosococcus oceani strain C-107 (AOB) have contrasting physiologies in response to the trace metals iron (Fe) and copper (Cu), holding potential implications for their niche separation in the oceans. A greater affinity for unchelated Fe may allow

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Joseph, Valsamma, Geethu Chellappan, S. Aparajitha, et al. "Molecular characterization of bacteria and archaea in a bioaugmented zero-water exchange shrimp pond." SN Applied Sciences 3, no. 4 (2021). http://dx.doi.org/10.1007/s42452-021-04392-z.

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AbstractIn the zero-water exchange shrimp culture pond maintained with the application of indigenous bioaugmentor, low levels of total ammonia–nitrogen were reported, indicating the relevance of indigenous microbial communities. Sediments (0–5 cm layer) were sampled from the pond (85th day) and the bacterial and archaeal communities; specifically, the ammonia oxidizers (ammonia-oxidizing bacteria, ammonia-oxidizing archaea, and anaerobic ammonia-oxidizing bacteria) in the sediment metagenome of the pond were analysed using the 16S rRNA and functional genes. Bacterial and archaeal 16S rRNA gene

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Hernández-Magaña, Elisa, and Beate Kraft. "Nitrous oxide production and consumption by marine ammonia-oxidizing archaea under oxygen depletion." Frontiers in Microbiology 15 (September 4, 2024). http://dx.doi.org/10.3389/fmicb.2024.1410251.

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Ammonia-oxidizing archaea (AOA) are key players in the nitrogen cycle and among the most abundant microorganisms in the ocean, thriving even in oxygen-depleted ecosystems. AOA produce the greenhouse gas nitrous oxide (N2O) as a byproduct of ammonia oxidation. Additionally, the recent discovery of a nitric oxide dismutation pathway in the AOA isolate Nitrosopumilus maritimus points toward other N2O production and consumption pathways in AOA. AOA that perform NO dismutation when exposed to oxygen depletion, produce oxygen and dinitrogen as final products. Based on the transient accumulation of N

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Kinateder, Thomas, Carina Mayer, Julian Nazet, and Reinhard Sterner. "Improving enzyme functional annotation by integrating in vitro and in silico approaches: The example of histidinol phosphate phosphatases." Protein Science 33, no. 2 (2024). http://dx.doi.org/10.1002/pro.4899.

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AbstractAdvances in sequencing technologies have led to a rapid growth of public protein sequence databases, whereby the fraction of proteins with experimentally verified function continuously decreases. This problem is currently addressed by automated functional annotations with computational tools, which however lack the accuracy of experimental approaches and are susceptible to error propagation. Here, we present an approach that combines the efficiency of functional annotation by in silico methods with the rigor of enzyme characterization in vitro. First, a thorough experimental analysis o

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Baker, Brett J., Emily Hyde, and Pedro Leão. "Nature should be the model for microbial sciences." Journal of Bacteriology, August 19, 2024. http://dx.doi.org/10.1128/jb.00228-24.

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ABSTRACT Until recently, microbiologists have relied on cultures to understand the microbial world. As a result, model organisms have been the focus of research into understanding Bacteria and Archaea at a molecular level. Diversity surveys and metagenomic sequencing have revealed that these model species are often present in low abundance in the environment; instead, there are microbial taxa that are cosmopolitan in nature. Due to the numerical dominance of these microorganisms and the size of their habitats, these lineages comprise mind-boggling population sizes upward of 10 28 cells on the

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Wan, Xianhui S., Lei Hou, Shuh-Ji Kao, et al. "Pathways of N ₂ O production by marine ammonia-oxidizing archaea determined from dual-isotope labeling." Proceedings of the National Academy of Sciences 120, no. 11 (2023). http://dx.doi.org/10.1073/pnas.2220697120.

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The ocean is a net source of the greenhouse gas and ozone-depleting substance, nitrous oxide (N 2 O), to the atmosphere. Most of that N 2 O is produced as a trace side product during ammonia oxidation, primarily by ammonia-oxidizing archaea (AOA), which numerically dominate the ammonia-oxidizing community in most marine environments. The pathways to N 2 O production and their kinetics, however, are not completely understood. Here, we use 15 N and 18 O isotopes to determine the kinetics of N 2 O production and trace the source of nitrogen (N) and oxygen (O) atoms in N 2 O produced by a model ma

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