Quantitative responses of potential nitrification and denitrification rates to the size of microbial communities in rice paddy soils

Removal of selected sulfonamides and sulfonamide resistance genes from wastewater in full-scale constructed wetlands

Sulfonamides are high-consumption antibiotics that reach the aquatic environment. The threat related to their presence in wastewater and the environment is not only associated with their antibacterial properties, but also with risk of the spread of drug resistance in bacteria. Therefore, the aim of this work was to evaluate the occurrence of eight commonly used sulfonamides, sulfonamide resistance genes (sul1-3) and integrase genes intI1-3 in five full-scale constructed wetlands (CWs) differing in design (including hybrid systems) and in the source of wastewater (agricultural drainage, domestic sewage/surface runoff, and animal runs runoff in a zoo). The CWs were located in low-urbanized areas in Poland and in Czechia. No sulfonamides were detected in the CW treating agricultural tile drainage water. In the other four systems, four sulfonamide compounds were detected. Sulfamethoxazole exhibited the highest concentration in those four CWs and its highest was 12,603.23 ± 1000.66 ng/L in a CW treating a mixture of domestic sewage and surface runoff. Despite the high removal efficiencies of sulfamethoxazole in the tested CWs (86 %-99 %), it was still detected in the treated wastewater. The sul1 genes occurred in all samples of raw and treated wastewater and their abundance did not change significantly after the treatment process and it was, predominantly, at the level 105 gene copies numbers/mL. Noteworthy, sul2 genes were only found in the influents, and sul3 were not detected. The sulfonamides can be removed in CWs, but their elimination is not complete. However, hybrid CWs treating sewage were superior in decreasing the relative abundance of genes and the concentration of SMX. CWs may play a role in the dissemination of sulfonamide resistance genes of the sul1 type and other determinants of drug resistance, such as the intI1 gene, in the environment, however, the magnitude of this phenomenon is a matter of further research.

Modeling denitrification nitrogen losses in China's rice fields based on multiscale field-experiment constraints

Denitrification plays a critical role in soil nitrogen (N) cycling, affecting N availability in agroecosystems. However, the challenges in direct measurement of denitrification products (NO, N2 O, and N2 ) hinder our understanding of denitrification N losses patterns across the spatial scale. To address this gap, we constructed a data-model fusion method to map the county-scale denitrification N losses from China's rice fields over the past decade. The estimated denitrification N losses as a percentage of N application from 2009 to 2018 were 11.8 ± 4.0% for single rice, 12.4 ± 3.7% for early rice, and 11.6 ± 3.1% for late rice. The model results showed that the spatial heterogeneity of denitrification N losses is primarily driven by edaphic and climatic factors rather than by management practices. In particular, diffusion and production rates emerged as key contributors to the variation of denitrification N losses. These findings humanize a 38.9 ± 4.8 kg N ha-1  N loss by denitrification and challenge the common hypothesis that substrate availability drives the pattern of N losses by denitrification in rice fields.

Nitrogen optimization coupled with alternate wetting and drying practice enhances rhizospheric nitrifier and denitrifier abundance and rice productivity

Optimizing nitrogen (N) fertilization without sacrificing grain yield is a major concern of rice production system because most of the applied N has been depleted from the soil and creating environmental consequences. Hence, limited information is available about nutrient management (NM) performance at a specific site under alternate wetting and drying (AWD) irrigation compared to conventional permanent flooding (PF). We aimed to inquire about the performance of NM practices compared to the farmer's fertilizer practice (FFP) under PF and AWD on rhizospheric nitrifier and denitrifier abundance, rice yield, plant growth, and photosynthetic parameters. Two improved NM practices; nutrient management by pig manure (NMPM); 40% chemical N replaced by pig manure (organic N), and nutrient management by organic slow-release fertilizer (NMSR); 40% chemical N replaced by organic slow-release N were compared. The results showed an increased total grain yield (16.06%) during AWD compared to PF. Compared to conventional FFP, NMPM, and NMSR significantly increased the yields by 53.84 and 29.67%, respectively, during AWD. Meanwhile, PF prompted a yield increase of 45.07 and 28.75% for NMPM and NMSR, respectively, (p < 0.05) compared to FFP. Besides, a significant correlation was observed between grain yield and nitrogen content during AWD (R ² = 0.58, p < 0.01), but no significant correlation was observed during PF. The NMPM contributed to photosynthetic attributes and the relative chlorophyll content under both watering events. Moreover, relatively higher abundances of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were observed during AWD, and the highest value was found after the late panicle stage. Our results suggest that the AWD-NMPM model is the best option to stimulate nitrifier and denitrifier gene abundance and promote rice production.

Promoted microbial denitrification and carbon dioxide fixation via photogenerated electrons stored in novel core/shell memory photocatalysts in darkness

Excess nitrogen in water and greenhouse gases, especially atmospheric carbon dioxide (CO₂) from the rapid development of modern society have become an acute threat to the environment. Herein, novel core/shell structured g-C₃N₄@WO₃ memory photocatalyst was fabricated by coating g-C₃N₄ on the surface of WO₃ nanoparticles and applied in the simultaneous coupling of memory photocatalysts and microbial communities (SCMPMC) for the synergistic removal of microbial nitrate and CO₂ fixation in darkness. The results showed that ∼98.6% of nitrate was removed and ∼17.7% of CO₂ was fixed in darkness by microorganisms in the presence of g-C₃N₄@WO₃ memory photocatalyst within 48 h. Besides, the investigation of the mechanism evidenced that g-C₃N₄@WO₃ memory photocatalyst can promote electron transfer in the SCMPMC system. Moreover, key enzyme activities (i.e., NAR, NIR, CAT, and ETSA) were accelerated, indicating that the activities of enzymes within microorganisms could be remarkably enhanced by the continuous release of stored electrons by the g-C₃N₄@WO₃ memory photocatalyst in the dark. Furthermore, microbial community analysis revealed that the g-C₃N₄@WO₃ memory photocatalyst increased the relative abundance of denitrifiers (i.e., Acidobacterota, Actinobacteria, Chloroflexi, and Proteobacteria) and CO₂-assimilating microorganisms (i.e., Pseudomonas), in the treated communities compared with the original community in river sediment, demonstrating the positive effects of g-C₃N₄@WO₃ memory photocatalyst on river sediment microbial communities. The results in this study could shed new light on the establishment of promising synergistic microbial nitrate removal and CO₂ fixation methods and mechanisms in darkness.

Shallow groundwater fluctuation: An ignored soil N loss pathway from cropland

Nitrogen (N) pollution originating from agricultural land is among the major threats to shallow groundwater (SG). Soil N losses due to the SG table fluctuation are neglected, although a large number of studies have been conducted to evaluate N losses through leaching and runoff. Herein, the characteristics of N losses driven by SG table fluctuation were investigated using the microcosm experiment and surveyed data from the croplands around Erhai Lake. According to the results achieved, the total N (TN) loss mainly occurred during the initial 12 days when the soil was flooded, then presented N immobilized by soil and finally, basically balanced between influent and effluent after 50 days. The results demonstrated that 1.7% of the original soil TN storage (0-100 cm) was lost. The alternation of drying and flooding could greatly increase TN loss up to 1086 kg hm^-2, which was 2.72 times as much as that of continuous flooding flow. The amount of soil N losses to groundwater was closely related to the soil profile biochemical characteristics (water content, soil microbial immobilization, mineralization, nitrification, and denitrification processes). Soil N loss from crop fields driven by SG table fluctuation is 26 and 6 times of the runoff and leaching losses, respectively, while the soil N loss from the vegetable fields is 33 and 4 times of the runoff and leaching losses. The total amount of N losses from the croplands around the Erhai Lake caused by flooding of shallow groundwater (SG) in 2016 was estimated at 3506 Mg. The estimations showed that N losses would decrease by 16% if vegetables are replaced with staple food crops. These results imply that the adjustment of the planting structure was the key measure to reduce soil N storage and mitigate groundwater contamination.

A review on nirS-type and nirK-type denitrifiers via a scientometric approach coupled with case studies

The denitrification process plays an important role in improving water quality and is a source/sink of nitrous oxide to the atmosphere. The second important rate-limiting step of the denitrification process is catalyzed by two enzymes with different structures and unrelated evolutionary relationships, namely, the Cu-type nitrite reductase encoded by the nirK gene and the cytochrome cd1-type nitrite reductase encoded by the nirS gene. Although some relevant reviews have been published on denitrifiers, most of these reviews do not include statistical analysis, and do not compare the nirS and nirK communities in-depth. However, a systematic study of the nirS-type and nirK-type denitrifying communities and their response to environmental factors in different ecosystems is needed. In this review, a scientometric approach combined with case studies was used to study the nirS-type and nirK-type denitrifiers. The scientometric approach demonstrated that Pseudomonas, Paracoccus, and Thauera are the most frequently mentioned nirS-type denitrifiers, while Pseudomonas and Bradyrhizobium are the top two most frequently mentioned nirK-type denitrifiers. Among various environmental factors, the concentrations of nitrite, nitrate and carbon sources were widely reported factors that can influence the abundance and structure of nirS-type and nirK-type denitrifying communities. Case studies indicated that Bradyrhizobium was the major genus detected by high-throughput sequencing in both nirS and nirK-type denitrifiers in soil systems. nirS-type denitrifiers are more sensitive to the soil type, soil moisture, pH, and rhizosphere effect than nirK. To clarify the relationships between denitrifying communities and environmental factors, the DNA stable isotope probe combined with metagenomic sequencing is needed for new denitrifier detections.

Polystyrene nanoplastics change the functional traits of biofilm communities in freshwater environment revealed by GeoChip 5.0

There is an increasing concern regarding the potential effects of nanoplastics (NPs) on freshwater ecosystems. Considering the functional values of biofilms in freshwater, knowledge on whether and to what extent NPs can influence the ecosystem processes of biofilms were still limited. Herein, the freshwater biofilms cultured in lab were exposed to 100 nm polystyrene NPs (PS-NPs) of different dosages (1 and 10 mg/L) for 14 days. Confocal laser scanning microscope observation indicated that biofilms were dominated by filamentous, and spiral algae species and the intensity of extracellular polymeric substances increased under PS-NPs exposure. GeoChip 5.0 analysis revealed that PS-NPs exposure triggered a significant increase in functional genes α diversity (p < 0.05) and altered biofilms' functional structure. Furthermore, the abundance of genes involved in the total carbon and nitrogen cycling were increased under PS-NPs exposure. The abundance of nitrogen fixation genes experienced the most pronounced increase (24.4%) under 1 mg/L PS-NPs treatment, consistent with the increase of ammonium in overlying water. Whereas antibiotic resistance genes and those related to photosynthetic pigments production were suppressed. These results provided direct evidence for PS-NPs' effects on the biofilm functions in terms of biogeochemical cycling, improving our understanding of the potentials of NPs on freshwater ecosystems.

Resistance and Resilience of Soil Nitrogen Cycling to Drought and Heat Stress in Rehabilitated Urban Soils

In the context of climate change and biodiversity loss, rehabilitation of degraded urban soils is a means of limiting artificialization of terrestrial ecosystems and preventing further degradation of soils. Ecological rehabilitation approaches are available to reinitiate soil functions and enhance plant development. However, little is known about the long-term stability of rehabilitated soils in terms of soil functions when further natural or anthropogenic perturbations occur. Based on rehabilitated urban soils, the present study sought to evaluate the resistance and resilience of soil functions linked to carbon cycling and phosphate dynamics in addition to nitrogen cycling and related microbial communities after a heat and drought stress. A laboratory experiment was conducted in microcosms under controlled temperature conditions, with four contrasted soils collected from a rehabilitated urban brownfield; an initial, non-rehabilitated soil (IS), a technosol with a high organic matter level (HO), and two technosols with less organic matter (LO1 and LO2), together with their respective controls (no stress). Changes in potential denitrification (PDR), nitrification (PNR) rates, and their interactive relationships with soil microbial activities and soil physicochemical properties were determined following a combined heat (40°C) and drought stress period of 21 days. Measurements were carried out immediately after the stress (resistance), and then also 5, 30, and 92 days after soil rewetting at 60% water holding capacity (resilience). Microbial activities involved in soil functions such as carbon cycling and phosphate dynamics proved to be of low resistance in all soils except for IS; however, they were resilient and recovered rapidly after rewetting. On the other hand, the microbial activities and gene abundances that were measured in relation to nitrogen cycling processes showed that for denitrification, activities were more rapidly resilient than gene abundances whereas for nitrification the activities and gene abundances were resilient in the same way. Results suggest that, unless the soils contain high amounts of organic matter, microbial communities in imported soils can be more vulnerable to environmental pressures such as drought and heat than communities already present. This should be considered when rehabilitating degraded soils.

Long-term effects of decabromodiphenyl ether on denitrification in eutrophic lake sediments: Different sensitivity of six-type denitrifying bacteria

The widespread use of polybrominated diphenyl ethers inevitably results in their increased release into natural waters and subsequent deposition in sediments. However, their long-term effects on the bacteria participating in each step of denitrification in eutrophic lake sediments are still unknown. Here, we conducted a one-year microcosm experiment to determine the long-term effects of decabromodiphenyl ether (BDE-209), at low (2 mg kg^-1 dry weight) and high (20 mg kg^-1 dry weight) contamination levels, on six-type denitrifying bacteria and their activities in sediments collected from Taihu Lake, a typical eutrophic lake in China. At the end of the experiment, sediment denitrifying reductase activities were inhibited by BDE-209 at both levels, with the greatest inhibition seen for nitric oxide reductase activity. The higher nitrate concentration in the contaminated sediments was attributed to the inhibition of nitrate reductase activities. The abundances of six-type denitrifying genes (narG, napA, nirK, nirS, norB, and nosZ) significantly decreased under high BDE-209 treatment, and narG and napA genes were more sensitive to the toxicity of BDE-209. The results from pyrosequencing showed that BDE-209, at either treatment concentration, decreased the six-type denitrifying bacterial diversities and altered their community composition. This shift of six-type denitrifying bacterial communities might also be driven by the debrominated products concentrations of BDE-209 and variations in sediment inorganic nitrogen concentrations. In particular, some genera from phylum Proteobacteria such as Pseudomonas, Cupriavidus, and Azoarcus were decreased significantly because of BDE-209 and its debrominated products.