Chendi Yu

Tidal pumping facilitates dissimilatory nitrate reduction in intertidal marshes

Intertidal marshes are alternately exposed and submerged due to periodic ebb and flood tides. The tidal cycle is important in controlling the biogeochemical processes of these ecosystems. Intertidal sediments are important hotspots of dissimilatory nitrate reduction and interacting nitrogen cycling microorganisms, but the effect of tides on dissimilatory nitrate reduction, including denitrification, anaerobic ammonium oxidation and dissimilatory nitrate reduction to ammonium, remains unexplored in these habitats. Here, we use isotope-tracing and molecular approaches simultaneously to show that both nitrate-reduction activities and associated functional bacterial abundances are enhanced at the sediment-tidal water interface and at the tide-induced groundwater fluctuating layer. This pattern suggests that tidal pumping may sustain dissimilatory nitrate reduction in intertidal zones. The tidal effect is supported further by nutrient profiles, fluctuations in nitrogen components over flood-ebb tidal cycles, and tidal simulation experiments. This study demonstrates the importance of tides in regulating the dynamics of dissimilatory nitrate-reducing pathways and thus provides new insights into the biogeochemical cycles of nitrogen and other elements in intertidal marshes.

Effects of silver nanoparticles on nitrification and associated nitrous oxide production in aquatic environments

Silver nanoparticles inhibit nitrification but enhance nitrous oxide production by nitrifying organisms. Silver nanoparticles (AgNPs) are the most common materials in nanotechnology-based consumer products globally. Because of the wide application of AgNPs, their potential environmental impact is currently a highly topical focus of concern. Nitrification is one of the processes in the nitrogen cycle most susceptible to AgNPs but the specific effects of AgNPs on nitrification in aquatic environments are not well understood. We report the influence of AgNPs on nitrification and associated nitrous oxide (N2O) production in estuarine sediments. AgNPs inhibited nitrification rates, which decreased exponentially with increasing AgNP concentrations. The response of nitrifier N2O production to AgNPs exhibited low-dose stimulation (<534, 1476, and 2473 μg liter−1 for 10-, 30-, and 100-nm AgNPs, respectively) and high-dose inhibition (hormesis effect). Compared with controls, N2O production could be enhanced by >100% at low doses of AgNPs. This result was confirmed by metatranscriptome studies showing up-regulation of nitric oxide reductase (norQ) gene expression in the low-dose treatment. Isotopomer analysis revealed that hydroxylamine oxidation was the main N2O production pathway, and its contribution to N2O emission was enhanced when exposed to low-dose AgNPs. This study highlights the molecular underpinnings of the effects of AgNPs on nitrification activity and demonstrates that the release of AgNPs into the environment should be controlled because they interfere with nitrifying communities and stimulate N2O emission.

Effects of multiple antibiotics exposure on denitrification process in the Yangtze Estuary sediments

Denitrification is a dominant reactive nitrogen removal pathway in most estuarine and coastal ecosystems, and plays a significant role in regulating N2O release. Although multiple antibiotics residues are widely detected in aquatic environment, combined effects of antibiotics on denitrification remain indistinct. In this work, 5 classes of antibiotics (sulfonamides, chloramphenicols, tetracyclines, macrolides, and fluoroquinolones) were selected to conduct orthogonal experiments in order to explore their combined effects on denitrification. 15N-based denitrification and N2O release rates were determined in the orthogonal experiments, while denitrifying functional genes were examined to illustrate the microbial mechanism of the combined antibiotics effect. Denitrification rates were inhibited by antibiotics treatments, and synergistic inhibition effect was observed for multiple antibiotics exposure. Different classes of antibiotics had different influence on N2O release rates, but multiple antibiotics exposure mostly led to stimulatory effect. Abundances of denitrifying functional genes were inhibited by multiple antibiotics exposure due to the antimicrobial properties, and different inhibition on denitrifiers may be the major mechanism for the variations of N2O release rates. Combined effects of antibiotics on denitrification may lead to nitrate retention and N2O release in estuarine and coastal ecosystems, and consequently cause cascading environmental problems, such as greenhouse effects and hyper-eutrophication.

Evidence for complete nitrification in enrichment culture of tidal sediments and diversity analysis of clade a comammox Nitrospira in natural environments

Complete ammonia oxidizers (comammox), as novel microbial communities, are predicted to play an important role in the nitrogen cycle. Here we reported the presence of complete nitrification in tidal sediments and examined the diversity and abundance of comammox in natural ecosystems. Metagenome and metatranscriptome of the enrichment culture from tidal sediments harbored the genes of comammox. Near-complete comammox AmoA/B/C- and Hao-like sequences showed close relationships to the known comammox (with sequence identity from 79 to 99%) rather than classical betaproteobacterial ammonia-oxidizing bacteria (β-AOB) (57 to 66%) and ammonia-oxidizing archaea (AOA) (24 to 38%). To analyze the diversity of comammox in natural environments, a new primer set targeting clade A comammox Nitrospira (COM-A) amoA genes was designed based on sequences obtained in this study and sequences from published database. In silico evaluation of the primers showed the high coverage of 89 and 100% in the COM-A amoA database. Application of the primers in six different ecosystems proved their strong availability. Community composition of COM-A suggested a relatively higher diversity than β-AOB in similar environments. Quantification results showed that COM-A amoA genes accounted for about 0.4–5.6% in total amoA genes. These results provide novel insight into our perception of the enigmatic comammox and have significant implications for profound understanding of complex nitrification process.

DNRA in intertidal sediments of the Yangtze Estuary

Dissimilatory nitrate reduction to ammonium (DNRA) plays an important role in regulating the fate of reactive nitrogen in estuarine and coastal ecosystems. In this work, intertidal sediments of the Yangtze Estuary were collected in January and August of 2015, respectively. Potential rates of DNRA and associated functional gene were investigated with nitrogen isotope-tracing and molecular techniques. The measured DNRA rates ranged from 0.14 to 5.57 μmol 15N kg-1 h-1 in the intertidal sediments. DNRA rates were tightly related to abundance of nrfA gene (p <0.001), demonstrating that fermentation reaction may be the dominant pathway of DNRA in the study area. Redundancy analysis (RDA) showed a relationship between DNRA and organic matter and NO2-, suggesting that these substrates stimulated the metabolism of DNRA microorganisms. On the other hand, the correlation between abundances of nrfA gene and Fe2+ and sulfide in the RDA analysis implied that oxidation of both Fe2+ and sulfide can enhance fermentative DNRA by providing extra free energy. DNRA converted approximately 2.29 × 105 t of nitrate to ammonia annually in the sampling area of the Yangtze Estuary, and most of the converted ammonium was retained in the estuarine ecosystem. DNRA may further contribute to eutrophication in the Yangtze Estuary, and also in the other hypereutrophic estuaries.