title: Determining the distribution of marine and coastal ammonia-oxidizing archaea and bacteria using a quantitative approach.
abstract: The oxidation of ammonia to nitrite is the first and often rate-limiting step in nitrification and plays an important role in both nitrogen and carbon cycling. This process is carried out by two distinct groups of microorganisms: ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). This chapter describes methods for measuring the abundance of AOA and AOB using ammonia monooxygenase subunit A (amoA) genes, with a particular emphasis on marine and coastal systems. We also describe quantitative measures designed to target two specific clades of marine AOA: the "shallow" (group A) and "deep" (group B) water column AOA.
authors.affiliation: Department of Environmental Earth System Science, Stanford University, Stanford, California, USA.
authors.forename: Annika C
authors.initials: AC
authors.lastname: Mosier
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Francis
mesh_terms: D000641:Ammonia / Q000378:metabolism*; D001105:Archaea / Q000145:classification* / Q000235:genetics; D020562:Betaproteobacteria / Q000145:classification* / Q000235:genetics; D019641:DNA, Archaeal / Q000235:genetics / Q000302:isolation & purification; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D009566:Nitrates / Q000378:metabolism; D058465:Nitrification; D009573:Nitrites / Q000378:metabolism; D010084:Oxidation-Reduction; D010088:Oxidoreductases / Q000378:metabolism; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012623:Seawater / Q000382:microbiology*; D017421:Sequence Analysis
chemical_list: D019641:DNA, Archaeal; D004269:DNA, Bacterial; D009566:Nitrates; D009573:Nitrites; D000641:Ammonia; D010088:Oxidoreductases; C045582:ammonia monooxygenase