Ubiquity and Dominance of Comammox Over AOB and AOA and their Links To ARGs in Antarctic Lake Sediments

Complete ammonia oxidizers (comammox), oxidizing ammonia to nitrate directly, have been found to exist widely in multiple environments, but their distribution patterns are still under-explored in Antarctic environments. For the first time, the sediments were collected from West Antarctic lakes to investigate distribution patterns and community structure for comammox, ammonia oxidizing archaea (AOA) and bacteria (AOB), and nitrite-oxidizing bacteria (NOB), as well as the associations between ammonia oxidizers and antibiotic resistance genes (ARGs). Comammox clade B and AOB were dominant ammonia oxidizers, with the abundances of (1.62 ± 0.10) × 10² - (5.21 ± 0.74) × 10⁶ and (0.17 ± 0.05) × 10⁵ - (4.79 ± 0.65) × 10⁵ copies g^{- 1} sediment, respectively. Comammox clade B, instead of clade A, occurred in all sediments, exhibiting higher abundances than AOB and AOA in most of the sediments. The abundances for comammox clade B demonstrated significant positive correlation (p < 0.01) with NH₄⁺-N levels, but negative correlation (p < 0.05) with C: N ratios. The coexistence of ammonia oxidizers in lake sediments was jointly structured by niche differentiation and environmental variables, and pH, modulated by penguin guano input, was found to be the most crucial factor in shaping their community structure. Co-occurrence network analyses revealed strong synergistic interactions between comammox and AOB, AOA, NOB, which played a critical role in nitrification processes. Our results further confirmed that comammox could act as important hosts for ARGs, hence stimulated their transmission and proliferation in the sediments. This study presented novel insights into the distribution patterns for ammonia oxidizers, their niche differentiation and the associations with ARGs in natural lake sediments of West Antarctica.