Abundances of crenarchaeal amoA genes and transcripts in the Pacific Ocean

Environ Microbiol. 2010 Mar;12(3):679-88. doi: 10.1111/j.1462-2920.2009.02108.x. Epub 2009 Nov 25.


Planktonic Crenarchaea are thought to play a key role in chemolithotrophic ammonia oxidation, a critical step of the marine nitrogen (N) cycle. In this study, we examined the spatial distributions of ammonia-oxidizing Crenarchaea across a large (approximately 5200 km) region of the central Pacific Ocean. Examination of crenarchaeal 16S rRNA, ammonia monooxygenase subunit A (amoA) genes, and amoA transcript abundances provided insight into their spatial distributions and activities. Crenarchaeal gene abundances increased three to four orders of magnitude with depth between the upper ocean waters and dimly lit waters of the mesopelagic zone. The resulting median value of the crenarchaeal amoA: 16S rRNA gene ratio was 1.3, suggesting the majority of Crenarchaea in the epi- and mesopelagic regions of the Pacific Ocean have the metabolic machinery for ammonia oxidation. Crenarchaeal amoA transcript abundances typically increased one to two orders of magnitude in the transitional zone separating the epipelagic waters from the mesopelagic (100-200 m), before decreasing into the interior of the mesopelagic zone. The resulting gene copy normalized transcript abundances revealed elevated amoA expression in the upper ocean waters (0-100 m) where crenarchaeal abundances were low, with transcripts decreasing into the mesopelagic zone as crenarchaeal gene abundances increased. These results suggest ammonia-oxidizing Crenarchaea are active contributors to the N cycle throughout the epi- and mesopelagic waters of the Pacific Ocean.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Ammonia / metabolism
  • Crenarchaeota / enzymology*
  • Crenarchaeota / genetics*
  • Oxidoreductases / genetics*
  • Oxidoreductases / metabolism
  • Pacific Ocean
  • RNA, Ribosomal, 16S / genetics
  • Seawater / microbiology*
  • Water Microbiology*


  • RNA, Ribosomal, 16S
  • Ammonia
  • Oxidoreductases
  • ammonia monooxygenase