Ubiquity and Diversity of Heterotrophic Bacterial nasA Genes in Diverse Marine Environments

Abstract

Nitrate uptake by heterotrophic bacteria plays an important role in marine N cycling. However, few studies have investigated the diversity of environmental nitrate assimilating bacteria (NAB). In this study, the diversity and biogeographical distribution of NAB in several global oceans and particularly in the western Pacific marginal seas were investigated using both cultivation and culture-independent molecular approaches. Phylogenetic analyses based on 16S rRNA and nasA (encoding the large subunit of the assimilatory nitrate reductase) gene sequences indicated that the cultivable NAB in South China Sea belonged to the α-Proteobacteria, γ-Proteobacteria and CFB (Cytophaga-Flavobacteria-Bacteroides) bacterial groups. In all the environmental samples of the present study, α-Proteobacteria, γ-Proteobacteria and Bacteroidetes were found to be the dominant nasA-harboring bacteria. Almost all of the α-Proteobacteria OTUs were classified into three Roseobacter-like groups (I to III). Clone library analysis revealed previously underestimated nasA diversity; e.g. the nasA gene sequences affiliated with β-Proteobacteria, ε-Proteobacteria and Lentisphaerae were observed in the field investigation for the first time, to the best of our knowledge. The geographical and vertical distributions of seawater nasA-harboring bacteria indicated that NAB were highly diverse and ubiquitously distributed in the studied marginal seas and world oceans. Niche adaptation and separation and/or limited dispersal might mediate the NAB composition and community structure in different water bodies. In the shallow-water Kueishantao hydrothermal vent environment, chemolithoautotrophic sulfur-oxidizing bacteria were the primary NAB, indicating a unique nitrate-assimilating community in this extreme environment. In the coastal water of the East China Sea, the relative abundance of Alteromonas and Roseobacter-like nasA gene sequences responded closely to algal blooms, indicating that NAB may be active participants contributing to the bloom dynamics. Our statistical results suggested that salinity, temperature and nitrate may be some of the key environmental factors controlling the composition and dynamics of the marine NAB communities.

Vertical Distribution of Bacterial Communities in the Indian Ocean as Revealed by Analyses of 16S rRNA and nasA Genes

“…The two conserved regions of nasA genes were suitable to primer designation new primers (nasF30, nasR1080). Our results showed gamma-like proteobacterial nasA genes were abundant in the Indian Ocean using the newly designed primers, the results were consistent with the previous studies [15][16][17]. We speculated that Gammaproteobacteria were significantly important in nitrate assimilation.…”

“…The sequence alignments, rarefaction analysis, phylogenetic trees and canonical correspondence analysis (CCA) were using the previous method [17].…”

“…In previous studies, the results showed most of the nasAcontaining bacteria were assigned to Gammaproteobacteria using primer sets nas964 and nasA1735 [15,17]. In order to clarify the fact that the primer bias exists or not in the experiments, a work to improve the primers specific to nasA genes need to be carried out.…”

“…The concentration of nitrate was high in the deep ocean. The spacial distribution of nitrate-assimilating bacteria (NAB) has been investigated using the nasA gene in various oceanic surface waters [15][16][17]. However, these studies were not emphasized on the difference of NAB in the vertical dimension.…”

Microbial community composition and nitrogen availability influence DOC remineralization in the South Pacific Gyre

“…Genes encoding for bacterial assimilatory nitrate reductase (i.e. nasA) are ubiquitous in the marine environment (Jiang et al, 2015) and their abundance has been found to positively correlate with NO 3 − concentrations (Allen et al, 2005). Therefore we hypothesize that both surface-meso microbial communities harbored the capacity for NO 3 − uptake, suggesting that some other environmental factor such as nitrogen limitation or the availability of an energy source, i.e.…”