Abstract
Ammonia oxidizing archaea (AOA) are microbes that are widely distributed in the ocean that convert ammonia to nitrite for energy acquisition in the presence of oxygen. Recent study has unraveled highly diverse sublineages within the previously defined AOA ecotypes (i.e., water column A (WCA) and water column B (WCB)), although the eco-physiology and environmental determinants of WCB subclades remain largely unclear. In this study, we examined the AOA communities along the water columns (40–3000 m depth) in the Costa Rica Dome (CRD) upwelling region in the eastern tropical North Pacific Ocean. Highly diverse AOA communities that were significantly different from those in oxygenated water layers were observed in the core layer of the oxygen minimum zone (OMZ), where the dissolved oxygen (DO) concentration was < 2μM. Moreover, a number of AOA phylotypes were found to be enriched in the OMZ core. Most of them were negatively correlated with DO and were also detected in other OMZs in the Arabian Sea and Gulf of California, which suggests low oxygen adaptation. This study provided the first insight into the differential niche partitioning and environmental determinants of various subclades within the ecotype WCB. Our results indicated that the ecotype WCB did indeed consist of various sublineages with different eco-physiologies, which should be further explored.
Highlights
Nitrification is a microbe-mediated sequential oxidation of ammonia to nitrate that interconnects the biological nitrogen fixation and nitrogen loss processes in the nitrogen cycle
By quantifying ammonia mono-oxygenase gene fragments with quantitative polymerase chain reaction, previous studies conducted in various marine environments showed that ammonia oxidizing Thaumachaeota (AOA) were several orders of magnitude more abundant than ammonia oxidizing bacteria (AOB) in oceanic waters [5,11,12]
After square root transformation, four environmental variables were used in redundancy analysis (RDA) to unravel the environmental determinants of water column B (WCB) subclades (Figure S3: include all AOA subclades in RDA), and depth and salinity were not included in RDA due to high linear dependencies on oxygen and temperature
Summary
Nitrification is a microbe-mediated sequential oxidation of ammonia to nitrate that interconnects the biological nitrogen fixation and nitrogen loss processes in the nitrogen cycle. Later studies discovered that ammonia oxidizing Thaumachaeota (AOA) were the major ammonia oxidizers in the ocean, and they are distributed ubiquitously in marine water columns, estuaries, sediments [5,6,7] as well as marine oxygen minimum zones (OMZs) [5,8,9,10]. A recent global synthesis of AOA phylogeny pointed out that AOA clades, which contributed over 55% amoA phylotypes to the global database, lack cultivated representatives [21] This has greatly hindered our understanding of the roles and life strategies of the abundant AOA in the global biogeochemical cycle. Considering the high diversity of marine AOA and the strong relationship between ammonia oxidation activity and oxygen level leads to speculation that the unique environment in the OMZ may select low-oxygen tolerating AOA groups and result in a unique AOA community.
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