The diversity and metabolism of culturable nitrate-reducing bacteria from the photic zone of the Western North Pacific Ocean

Abstract

Abstract To better understand bacterial communities and metabolism under nitrogen deficiency, 154 seawater samples were obtained from 0-200 m at 22 stations in the photic zone of the Western North Pacific Ocean and, from them, 634 nitrate-utilizing bacteria were isolated using selective media and culture-dependent methods. Twenty-nine of 94 representative nitrate-utilizing isolates were found to be nitrate reducers, among which Qipengyuania flava, Roseibium aggregatum, Erythrobacter aureus, Vibrio campbellii, and Stappia indica were identified from all tested seawater layers of the photic zone and at almost all stations. The presence of multiple genes for chitin degradation and extracellular peptidases may indicate that almost all nitrate-reducing isolates (28/29) can use chitin and proteinaceous compounds as important sources of carbon and nitrogen. Most strains contained assimilatory nitrate reduction or dissimilatory nitrate reduction to ammonia genes suggesting that nitrate and nitrite could act as electron acceptors to generate ammonia. All of the nitrate-reducing isolates contained genes encoding the assimilatory sulfate reduction pathway, and six of the nitrate-reducing isolates encoded sulfur oxidization genes, indicating that they could oxidize sulfur. Five nitrate-reducing isolates obtained near the chlorophyll a-maximum layer contained a dimethylsulfoniopropionate synthesis gene and three of them contained both dimethylsulfoniopropionate synthesis and cleavage genes. This suggests that nitrate-reducing isolates may participate in dimethylsulfoniopropionate synthesis and catabolism in photic seawater. Collectively, these results reveal nitrate-reducing bacterial diversity and have implications for understanding the role of such strains in the ecology and biogeochemical cycles of nitrogen, carbon, and sulfur in the oligotrophic marine photic zone.