Enrichment and characterization of ammonia-oxidizing archaea from the open ocean: phylogeny, physiology and stable isotope fractionation
- 12 May 2011
- journal article
- Published by Oxford University Press (OUP) in The ISME Journal
- Vol. 5 (11), 1796-1808
- https://doi.org/10.1038/ismej.2011.58
Abstract
Archaeal genes for ammonia oxidation are widespread in the marine environment, but direct physiological evidence for ammonia oxidation by marine archaea is limited. We report the enrichment and characterization of three strains of pelagic ammonia-oxidizing archaea (AOA) from the North Pacific Ocean that have been maintained in laboratory culture for over 3 years. Phylogenetic analyses indicate the three strains belong to a previously identified clade of water column-associated AOA and possess 16S ribosomal RNA genes and ammonia monooxygenase subunit a (amoA) genes highly similar (98–99% identity) to those recovered in DNA and complementary DNA clone libraries from the open ocean. The strains grow in natural seawater-based liquid medium while stoichiometrically converting ammonia (NH3) to nitrite (NO2−). Ammonia oxidation by the enrichments is only partially inhibited by allylthiourea at concentrations known to completely inhibit cultivated ammonia-oxidizing bacteria. The three strains were used to determine the nitrogen stable isotope effect (15εNH3) during archaeal ammonia oxidation, an important parameter for interpreting stable isotope ratios in the environment. Archaeal 15εNH3 ranged from 13‰ to 41‰, within the range of that previously reported for ammonia-oxidizing bacteria. Despite low amino acid identity between the archaeal and bacterial Amo proteins, their functional diversity as captured by 15εNH3 is similar.Keywords
This publication has 85 references indexed in Scilit:
- Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaeaProceedings of the National Academy of Sciences of the United States of America, 2010
- High Abundance of Ammonia-OxidizingArchaeain Coastal Waters, Determined Using a Modified DNA Extraction MethodApplied and Environmental Microbiology, 2010
- Abundances of crenarchaeal amoA genes and transcripts in the Pacific OceanEnvironmental Microbiology, 2010
- Abundance of Ammonia-Oxidizing Archaea and Bacteria along an Estuarine Salinity Gradient in Relation to Potential Nitrification RatesApplied and Environmental Microbiology, 2010
- Revising the nitrogen cycle in the Peruvian oxygen minimum zoneProceedings of the National Academy of Sciences of the United States of America, 2009
- A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot springProceedings of the National Academy of Sciences of the United States of America, 2008
- SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARBNucleic Acids Research, 2007
- Linking crenarchaeal and bacterial nitrification to anammox in the Black SeaProceedings of the National Academy of Sciences of the United States of America, 2007
- Archaeal nitrification in the oceanProceedings of the National Academy of Sciences of the United States of America, 2006
- Crystal structure of the archaeal ammonium transporter Amt-1 from Archaeoglobus fulgidusProceedings of the National Academy of Sciences of the United States of America, 2005