Relationships between nitrogen transformation rates and gene abundance in a riparian buffer soil

Effects of marine produced organic matter on the potential estuarine capacity of NOx- removal

Dissolved inorganic nitrogen (DIN) is very high in the Pearl River Estuary (PRE) and nitrate (NO_x^-) removal processes such as denitrification, anaerobic ammonium oxidation (anammox) and dissimilatory nitrate reduction to ammonium (DNRA) are important for determining export of DIN to coastal waters. However, fluxes of NO_x^- removal and influencing factors in the PRE are still unclear. We conducted 4 cruises at 11 sites in the PRE to investigate potential NO_x^- removal rates, their contributions, and corresponding gene abundances, and controlling factors in surface sediments (0-5 cm). The results showed that the potential rates of denitrification, anammox, and DNRA as well as their contributions varied spatially and seasonally. Denitrification (1.98 ± 1.7 μg N g^-1 d^-1) was the major NO_x^- removal processes (68.43 ± 14.61%) while DNRA (0.45 ± 0.28 μg N g^-1 d^-1) contributed 22.61 ± 14.89% in NO_x^- removal. The NO_x^- removal processes and corresponding gene abundances were correlated with the chlorophyll concentrations in both overlying water and sediment, indicating that marine-produced organic matter was the major driver for benthic NO_x^- removal processes. In addition, water column turbidity had important effects on primary production, which affects benthic N processes. Our study provides evidences for that the turbidity-regulated primary production in overlying water is the primary driver for benthic NO_x^- removal processes. The contribution of sediment NO_x^- removal fluxes to water column NO_x^- concentration was low in the upper estuary and increased in the lower estuary where marine produced chlorophyll a was higher. However, daily fluxes of NO_x^- removal were estimated to account for only 0.18-7.22% (mean 1.85 ± 1.62%) of NO_x^- in the whole overlying water column. This suggests that most riverine NO_x^- was exported out into the adjacent coastal waters.

Quantification of denitrifier genes population size and its relationship with environmental factors

The objectives of this study were to use real-time PCR for culture-independent quantification of the copy numbers of 16S rRNA and denitrification functional genes, and also the relationships between gene copy numbers and soil physicochemical properties. In this study, qPCR analysis of the soil samples showed 16S rRNA, nirS, nirK, nosZI and nosZII average densities of 3.0 × 10⁸, 2.25 × 10⁷, 2.9 × 10⁵, 4.0 × 10⁶ and 1.75 × 10⁷ copies per gram of dry soil, respectively. In addition, the abundances of (nirS + nirK), nosZI and nosZII relative to 16S rRNA genes were 1.4-34.1%, 0.06-3.95% and 1.3-39%, respectively, confirming the low proportion of denitrifiers to total bacteria in soil. This showed that the non-denitrifying nosZII-type bacteria may contribute significantly to N₂O consumption in the soil. Furthermore, the shifts in abundance and diversity of the total bacteria and denitrification functional gene copy numbers correlated significantly with the various soil factors. It is the first study in Turkey about the population size of denitrification functional genes in different soil samples. It also aims to draw attention to nitrous oxide-associated global warming.

Diversity and Abundance of the Denitrifying Microbiota in the Sediment of Eastern China Marginal Seas and the Impact of Environmental Factors

Investigating the environmental influence on the community composition and abundance of denitrifiers in marine sediment ecosystem is essential for understanding of the ecosystem-level controls on the biogeochemical process of denitrification. In the present study, nirK-harboring denitrifying communities in different mud deposit zones of eastern China marginal seas (ECMS) were investigated via clone library analysis. The abundance of three functional genes affiliated with denitrification (narG, nirK, nosZ) was assessed by fluorescent quantitative PCR. The nirK-harboring microbiota were dominated by a few operational taxonomic units (OTUs), which were widely distributed in different sites with each site harboring their unique phylotypes. The mean abundance of nirK was significantly higher than that of narG and nosZ genes, and the abundance of narG was higher than that of nosZ. The inconsistent abundance profile of different functional genes along the process of denitrification might indicate that nitrite reduction occurred independently of denitrification in the mud deposit zones of ECMS, and sedimentary denitrification was accomplished by cooperation of different denitrifying species rather than a single species. Such important information would be missed when targeting only a single denitrifying functional gene. Analysis of correlation between abundance ratios and environmental factors revealed that the response of denitrifiers to environmental factors was not invariable in different mud deposit zones. Our results suggested that a comprehensive analysis of different denitrifying functional genes may gain more information about the dynamics of denitrifying microbiota in marine sediments.

Effects of Riparian Buffer Vegetation and Width: A 12-Year Longitudinal Study

Agricultural contributions of nitrogen are a serious concern for many water resources and have spurred the implementation of riparian buffer zones to reduce groundwater nitrate (NO). The optimum design for buffers is subject to debate, and there are few long-term studies. The objective of this project was to determine the effectiveness over time (12 yr) of buffer types (trees, switchgrass, fescue, native, and a control) and buffer widths (8 and 15 m) by measuring groundwater NO-N and dissolved organic carbon (DOC) trends. At the intermediate groundwater depth (1.5-2.1 m), NO-N reduction effectiveness was 2.5 times greater (46 vs. 16%) for the wider buffer, and, regardless of width, buffer effectiveness increased 0.62% yr. Buffer vegetative type was never statistically significant. In the deep-groundwater depth (2.1-3.5 m), there was no change in NO-N removal over time, although the statistical interaction of width and vegetative type indicated a wide range of removal rates (19-82%). The DOC concentrations were analyzed at the field/buffer and buffer/stream sampling locations. Depending on location position and groundwater sampling depth, DOC concentrations ranged from 1.6 to 2.8 mg L at Year 0 and increased at a rate of 0.13 to 0.18 mg L yr but always remained low (≤5.0 mg L). Greater DOC concentrations in the intermediate-depth groundwater did not increase NO-N removal; redox measurements indicated intermittent reduced soil conditions may have been limiting. This study suggests that riparian buffer width, not vegetation, is more important for NO-N removal in the middle coastal plain of North Carolina for a newly established buffer.

The different potential of sponge bacterial symbionts in N₂ release indicated by the phylogenetic diversity and abundance analyses of denitrification genes, nirK and nosZ

Nitrogen cycle is a critical biogeochemical process of the oceans. The nitrogen fixation by sponge cyanobacteria was early observed. Until recently, sponges were found to be able to release nitrogen gas. However the gene-level evidence for the role of bacterial symbionts from different species sponges in nitrogen gas release is limited. And meanwhile, the quanitative analysis of nitrogen cycle-related genes of sponge microbial symbionts is relatively lacking. The nirK gene encoding nitrite reductase which catalyzes soluble nitrite into gas NO and nosZ gene encoding nitrous oxide reductase which catalyzes N₂O into N₂ are two key functional genes in the complete denitrification pathway. In this study, using nirK and nosZ genes as markers, the potential of bacterial symbionts in six species of sponges in the release of N2 was investigated by phylogenetic analysis and real-time qPCR. As a result, totally, 2 OTUs of nirK and 5 OTUs of nosZ genes were detected by gene library-based saturated sequencing. Difference phylogenetic diversity of nirK and nosZ genes were observed at OTU level in sponges. Meanwhile, real-time qPCR analysis showed that Xestospongia testudinaria had the highest abundance of nosZ gene, while Cinachyrella sp. had the greatest abundance of nirK gene. Phylogenetic analysis showed that the nirK and nosZ genes were probably of Alpha-, Beta-, and Gammaproteobacteria origin. The results from this study suggest that the denitrification potential of bacteria varies among sponges because of the different phylogenetic diversity and relative abundance of nosZ and nirK genes in sponges. Totally, both the qualitative and quantitative analyses of nirK and nosZ genes indicated the different potential of sponge bacterial symbionts in the release of nitrogen gas.