High diversity of ammonia-oxidizing archaea in permanent and seasonal oxygen-deficient waters of the eastern South Pacific.

The community structure of putative aerobic ammonia-oxidizing archaea (AOA) was explored in two oxygen-deficient ecosystems of the eastern South Pacific: the oxygen minimum zone off Peru and northern Chile (11°S–20°S), where permanent suboxic and low-ammonium conditions are found at intermediate depths, and the continental shelf off central Chile (36°S), where seasonal oxygen deficient and relatively high-ammonium conditions develop in the water column, particularly during the upwelling season. The AOA community composition based on the ammonia monooxygenase subunit A (amoA) genes changed according to the oxygen concentration in the water column and the ecosystem studied, showing a higher diversity in the seasonal low-oxygen waters. The majority of the archaeal amoA genotypes was affiliated to the uncultured clusters A (64%) and B (35%), with Cluster A AOA being mainly associated with higher oxygen and ammonium concentrations and Cluster B AOA with permanent oxygen- and ammonium-poor waters. Q-PCR assays revealed that AOA are anabundant community (up to 10 5 amoA copies ml–1), while bacterial amoA genes from b proteobacteria were undetected. Our results thus suggest that a diverse uncultured AOA community, for which, therefore, we do not have any physiological information, to date, is an important component of the nitrifying community in oxygen-deficient marine ecosystems, and particularly in rich coastal upwelling zones.