Depth-dependent distribution patterns of ammonia- and nitrite-oxidizing microorganisms in the water column of stratified lakes

This study investigates the occurrence and diversity of ammonia- and nitrite-oxidizing prokaryotes in the water columns of four stratified lakes by analyzing 16S rRNA genes in DNA and RNA extracts. The taxonomic composition of nitrifiers differed between two lake types, with considerable depth-related variation within each lake. In large and deep lakes (Zürichsee and Achensee), the oxygenated hypolimnion was dominated by Ca. Nitrosopumilus, accounting for a quarter of the total 16S rRNA genes. Nitrospira rRNA genes were generally an order of magnitude less abundant than those of Ca. Nitrosopumilus. However, analyses of rRNA in the same samples revealed a significantly higher relative abundance of Nitrospira ribosomes, reaching up to one-third of the abundance of Ca. Nitrosopumilus ribosomes. Nitrosospira and Ca. Nitrotoga were the main nitrifiers in the upper hypolimnion of the smaller lakes Piburger See and Hechtsee. The anoxic, deep hypolimnion of these lakes was dominated by the anaerobic ammonium-oxidizing bacterium Ca. Anammoximicrobium. The vertical distribution of Ca. Anammoximicrobium was further resolved using droplet digital PCR, revealing a strong correlation with ammonium concentrations. These findings provide new insights into the niche preferences of nitrifiers and anammox bacteria in lakes, highlighting the importance of depth-dependent environmental gradients in shaping their distribution.