Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea

@article{Walker2010NitrosopumilusMG,
  title={Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea},
  author={Christopher B. Walker and Jose R. de la Torre and Martin G. Klotz and Hidetishi Urakawa and Nicolas Pinel and Daniel J. Arp and C{\'e}line Brochier-Armanet and Patrick S. G. Chain and Patricia P. Chan and A. Gollabgir and James Hemp and Michael H{\"u}gler and Elizabeth A. Karr and Martin K{\"o}nneke and Maria W. Shin and Thomas J. Lawton and Todd M. Lowe and Willm Martens-Habbena and Luis Alberto Sayavedra-Soto and D Lang and Stefan M. Sievert and Amy C. Rosenzweig and Gerard Manning and David A. Stahl},
  journal={Proceedings of the National Academy of Sciences},
  year={2010},
  volume={107},
  pages={8818 - 8823}
}
Ammonia-oxidizing archaea are ubiquitous in marine and terrestrial environments and now thought to be significant contributors to carbon and nitrogen cycling. The isolation of Candidatus “Nitrosopumilus maritimus” strain SCM1 provided the opportunity for linking its chemolithotrophic physiology with a genomic inventory of the globally distributed archaea. Here we report the 1,645,259-bp closed genome of strain SCM1, revealing highly copper-dependent systems for ammonia oxidation and electron… 
Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil
TLDR
The cultivation and isolation of an AOA from soil is described, showing it grows on ammonia or urea as an energy source and is capable of using higher ammonia concentrations than the marine isolate, Nitrosopumilus maritimus.
Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers
TLDR
It is shown that AOA of marine and terrestrial environments share unique and well-conserved pathways of carbon and nitrogen metabolism, and hypotheses about missing steps in these pathways are raised, and specific metabolic innovations associated with the Nitrososphaerales mediating growth and survival in the soil milieu are identified.
Nitrogen metabolism and kinetics of ammonia-oxidizing archaea.
TLDR
The isolation of Nitrosopumilus maritimus strain SCM1 provided the first direct evidence that Group I archaea indeed gain energy from ammonia oxidation and a respirometry setup particularly suited for activity measurements in dilute microbial cultures with extremely low oxygen uptake rates was developed.
Chemoautotrophic growth of ammonia-oxidizing Thaumarchaeota enriched from a pelagic redox gradient in the Baltic Sea
TLDR
Growth by an AOA belonging to the genus Nitrosoarchaeum can be sustained largely by chemoautotrophy, as revealed by enriching AOA from a brackish, oxygen-depleted water-column in the Landsort Deep, central Baltic Sea.
Physiological and genomic analysis of “Candidatus Nitrosocosmicus agrestis”, an ammonia tolerant ammonia-oxidizing archaeon from vegetable soil
TLDR
The physiological and genomic characteristics of an ammonia tolerant soil AOA strain Candidatus Nitrosocosmicus agrestis are presented and some mechanisms of this AOA adapting to a variety of environments and tolerating to high ammonia are proposed.
Cultivation of Autotrophic Ammonia-Oxidizing Archaea from Marine Sediments in Coculture with Sulfur-Oxidizing Bacteria
TLDR
The experiments suggest that AOA may be important nitrifiers in low-oxygen environments, such as oxygen-minimum zones and marine sediments, and that archaeal cells became the dominant prokaryotes after biweekly transfers for 20 months.
The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations.
TLDR
The complete genome sequence of Candidatus Nitrososphaera gargensis is obtained from an enrichment culture, representing a different evolutionary lineage of AOA frequently found in high numbers in many terrestrial environments and it is shown that thaumarchaeota produce cofactor F420 as well as polyhydroxyalkanoates.
Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation
  • W. Qin, S. Amin, +7 authors D. Stahl
  • Biology, Medicine
    Proceedings of the National Academy of Sciences
  • 2014
TLDR
It is shown that some coastal marine AOA can remain active with increasing acidification of the oceans and provide new understanding of the physiological basis of the remarkable ecological success reflected by their generally high abundance in marine environments.
Proteomic response of the marine ammonia-oxidising archaeon, Nitrosopumilus maritimus to iron limitation reveals strategies to compensate for nutrient scarcity.
TLDR
It is hypothesised that an elevated uptake of exogenous phosphonates under Fe limitation may either supplement N. maritimus' endogenous methylphosphonate biosynthesis pathway or enhance the production of phosphonate-containing exopolysaccharides known to efficiently bind environmental Fe.
Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation
Significance CO2 fixation is the most important biosynthesis process on Earth, enabling autotrophic organisms to synthesize their entire biomass from inorganic carbon at the expense of energy
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