Nitrogen-cycling functional genes in brackish and freshwater sediments in Yodo River in Japan

Abstract

A DNA microarray analysis targeting nitrogen-cycling functional genes was applied to monitor sediment microbes in the Juso Lagoon (brackish area) and the Shirokita Wando (freshwater area) along the Yodo River in Japan in 2014-2015. The microarray contained 905 oligonucleotide probes for the nif, amo, hao/hzo, nap, nar, nirK, nirS, nrf, cnor, qnor, and nos genes. Diverse genes were detected in the sediment samples. Especially in the summer brackish area, about 70 probes were detected, 26-31, 11-12, and 31-32 of which targeted genes on nitrogen-fixation, nitrification, and denitrification, respectively. Canonical correspondence analysis showed that the nitrogen-cycling functional gene profiles of the sediment microbes were characterized by nitrification activity, denitrification activity, conductivity, pH, temperature, and vegetation of their habitats.