Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean
Christopher A. Francis,Kathryn J. Roberts,J. Michael Beman,Alyson E. Santoro,Brian B. Oakley +4 more
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TLDR
Using PCR primers designed to specifically target archaeal amoA, AOA is found to be pervasive in areas of the ocean that are critical for the global nitrogen cycle, including the base of the euphotic zone, suboxic water columns, and estuarine and coastal sediments.Abstract:
Nitrification, the microbial oxidation of ammonia to nitrite and nitrate, occurs in a wide variety of environments and plays a central role in the global nitrogen cycle. Catalyzed by the enzyme ammonia monooxygenase, the ability to oxidize ammonia was previously thought to be restricted to a few groups within the β- and γ-Proteobacteria. However, recent metagenomic studies have revealed the existence of unique ammonia monooxygenase α-subunit (amoA) genes derived from uncultivated, nonextremophilic Crenarchaeota. Here, we report molecular evidence for the widespread presence of ammonia-oxidizing archaea (AOA) in marine water columns and sediments. Using PCR primers designed to specifically target archaeal amoA, we find AOA to be pervasive in areas of the ocean that are critical for the global nitrogen cycle, including the base of the euphotic zone, suboxic water columns, and estuarine and coastal sediments. Diverse and distinct AOA communities are associated with each of these habitats, with little overlap between water columns and sediments. Within marine sediments, most AOA sequences are unique to individual sampling locations, whereas a small number of sequences are evidently cosmopolitan in distribution. Considering the abundance of nonextremophilic archaea in the ocean, our results suggest that AOA may play a significant, but previously unrecognized, role in the global nitrogen cycle.read more
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pH-dependent distribution of soil ammonia oxidizers across a large geographical scale as revealed by high-throughput pyrosequencing
TL;DR: The results suggest that the distribution of ammonia oxidizers across large-scale biogeographical settings can be largely predicted along the soil pH gradient, thus providing important indications for the ecological characteristics of AOA and AOB in different soils.
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Nitrification in terrestrial hot springs of Iceland and Kamchatka
Laila J. Reigstad,Andreas Richter,Holger Daims,Tim Urich,Tim Urich,Lorenz Schwark,Christa Schleper,Christa Schleper +7 more
TL;DR: Evidence is provided for an active role of archaea in nitrification of hot springs in a wide range of pH values and at a high temperature, and addition of ammonium to the hot spring samples before incubation yielded a more than twofold higher potential nitrification rate, indicating that the process was limited by ammonia supply.
Journal ArticleDOI
Ammonium and nitrite oxidation at nanomolar oxygen concentrations in oxygen minimum zone waters
Laura A. Bristow,Tage Dalsgaard,Laura Tiano,Daniel B. Mills,Anthony D. Bertagnolli,Jody J. Wright,Steven J. Hallam,Osvaldo Ulloa,Donald E. Canfield,Niels Peter Revsbech,Bo Thamdrup +10 more
TL;DR: It is demonstrated that two key aerobic processes, ammonium oxidation and nitrite oxidation, persist even at low oxygen levels of 5–30 nM (∼0.01% air saturation); assessment of the oxygen (O2) sensitivity of these processes down to the O2 concentrations present in the OMZ core is essential for understanding and modeling nitrogen loss in OMZs.
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Microbial oceanography: paradigms, processes and promise.
TL;DR: There is a unique opportunity, using recent advances in molecular ecology, metagenomics, remote sensing of microorganisms and ecological modelling, to achieve a comprehensive understanding of marine micro organisms and their susceptibility to environmental variability and climate change.
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Life without light: microbial diversity and evidence of sulfur- and ammonium-based chemolithotrophy in Movile Cave.
Yin Chen,Liqin Wu,Rich Boden,Alexandra Hillebrand,Deepak Kumaresan,Hélène Moussard,Mihai Baciu,Yahai Lu,J. Colin Murrell +8 more
TL;DR: DNA-based stable-isotope probing analyses showed that Thiobacillus spp.
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