Habitat partitioning of denitrifying bacterial communities carrying <i>nirS</i> or <i>nirK</i> genes in the stratified water column of Lake Kinneret, Israel

The community composition of denitrifying bacteria was studied in the stratified water column of Lake Kinneret. The nitrite reductase genes <i>nirS</i> and <i>nirK</i> were amplified by PCR from water samples taken at 1, 14, 19 and 22 m depth, which represent the epi-, meta- and hypolimnion of the lake. The PCR products were analyzed with terminal restriction fragment length polymorphism (T-RFLP) and clone libraries. The highest diversity of <i>nirS</i> denitrifying communities was observed at 1 m depth. According to the T-RFLP profiles and clone libraries of <i>nirS</i> products, 2 groups of denitrifiers were common to and dominant in all depths. Deduced protein sequences from one of these groups displayed low identity (77%) with other <i>nirS</i> sequences reported in GenBank. Denitrifying bacterial communities with <i>nirK</i> were most diverse at 22 m and showed highest similarity to those at 19 m depth. Sequences unrelated to <i>nirK</i> dominated the clone libraries from 1 m depth, suggesting that denitrifying bacteria with copper-containing nitrite reductase were less frequent at this depth. The results suggest that microorganisms with <i>nirK</i> and those with <i>nirS</i> respond differently to the environmental conditions in the stratified water column of Lake Kinneret.