Diversity of bacterial community and detection of nirS- and nirK-encoding denitrifying bacteria in sandy intertidal sediments along Laizhou Bay of Bohai Sea, China

Microbial mechanisms of C/N/S geochemical cycling during low-water-level sediment remediation in urban rivers

Low-water-level regulation has been effectively implemented in the restoration of urban river sediments in Guangzhou City, China. Further investigation is needed to understand the microbial mechanisms involved in pollutant degradation in low-water-level environments. This study examined sediment samples from nine rivers, including low-water-level rivers (LW), tidal waterways (TW), and enclosed rivers (ER). Metagenomic high-throughput sequencing and the Diting pipeline were utilized to investigate the microbial mechanisms involved in sediment C/N/S geochemical cycling during low-water-level regulation. The results reveal that the degree of pollution in LW sediment is lower compared to TW and ER sediment. LW sediment exhibits a higher capacity for pollutant degradation and elimination of black, odorous substances due to its stronger microbial methane oxidation, nitrification, denitrification, anammox, and oxidation of sulfide, sulfite, and thiosulfate. Conversely, TW and ER sediment showcase greater microbial methanogenesis, anaerobic fermentation, and sulfide generation abilities, leading to the persistence of black, odorous substances. Factors such as grit and silt content, nitrate, and ammonia concentrations impacted microbial metabolic pathways. Low-water-level regulation improved the micro-environment for functional microbes, facilitating pollutant removal and preventing black odorous substance accumulation. These findings provide insights into the microbial mechanisms underlying low-water-level regulation technology for sediment restoration in urban rivers.

Diversity, community structure, and abundance of nirS-type denitrifying bacteria on suspended particulate matter in coastal high-altitude aquaculture pond water

Denitrifying bacteria harboring the nitrate reductase S (nirS) gene convert active nitrogen into molecular nitrogen, and alleviate eutrophication in aquaculture water. Suspended particulate matter (SPM) is an important component of aquaculture water and a carrier for denitrification. SPM with different particle sizes were collected from a coastal high-altitude aquaculture pond in Maoming City, China. Diversity, community structure, abundance of nirS-type denitrifying bacteria on SPM and environmental influencing factors were studied using high-throughput sequencing, fluorescence quantitative PCR, and statistical analysis. Pseudomonas, Halomonas, and Wenzhouxiangella were the dominant genera of nirS-type denitrifying bacteria on SPM from the ponds. Network analysis revealed Pseudomonas and Halomonas as the key genera involved in the interaction of nirS-type denitrifying bacteria on SPM in the ponds. qPCR indicated a trend toward greater nirS gene abundance in progressively larger SPM. Dissolved oxygen, pH, temperature, and SPM particle size were the main environmental factors influencing changes in the nirS-type denitrifying bacterial community on SPM in coastal high-altitude aquaculture pond water. These findings increase our understanding of the microbiology of nitrogen cycle processes in aquaculture ecosystem, and will help optimize aquatic tailwater treatment strategies.

Nitrate transformation and source tracking of rivers draining into the Bohai Sea using a multi-tracer approach combined with an optimized Bayesian stable isotope mixing model

Excessive levels of NO3- can result in multiple eco-environmental issues due to potential toxicity, especially in coastal areas. Accurate source tracing is crucial for effective pollutant control and policy development. Bayesian models have been widely employed to trace NO3- sources, while limited studies have utilized optimized Bayesian models for NO3- tracing in the coastal rivers. The Bohai Rim is highly susceptible to ecological disturbances, particularly N pollution, and has emerged as a critical area. Therefore, identification the N fate and understanding their sources contribution is urgent for pollution mitigation efforts. In addition, understanding the influenced key driven factors to source dynamic in the past ten years is also implication to environmental management. In this study, water samples were collected from 36 major river estuaries that drain into the Bohai Sea of North China. The main transformation processes were analyzed and quantified the sources of NO3- using a Bayesian stable isotope mixing model (MixSIAR) with isotopic approach (δ15N-NO3- and δ18O-NO3-). The overall isotopic composition of δ15N-NO3- and δ18O-NO3- in estuary waters ranged from -0.8-19.3‰ (9.3 ± 4.6‰) and from -7.1-10.5‰ (5.0 ± 4.3‰), respectively. The main sources of nitrate in most river estuaries were manure & sewage, and chemical fertilizer, while weak denitrification and mixed processes were observed in Bohai Rim region. A temporal decrease in the nitrogen load entering the Bohai Sea indicates an improvement in water quality in recent years. By incorporating informative priors and utilizing the calculated coefficients, the accuracy of sourcing results was significantly improved. This study highlighted the optimized MixSIAR model enhanced its accuracy for sourcing analysis and providing valuable insights for policy formulation. Future efforts should focus on improving management strategies to reduce nitrogen into the bay.

Benthic microbial biogeographic trends in the North Sea are shaped by an interplay of environmental drivers and bottom trawling effort

Microbial composition and diversity in marine sediments are shaped by environmental, biological, and anthropogenic processes operating at different scales. However, our understanding of benthic microbial biogeography remains limited. Here, we used 16S rDNA amplicon sequencing to characterize benthic microbiota in the North Sea from the top centimeter of 339 sediment samples. We utilized spatially explicit statistical models, to disentangle the effects of the different predictors, including bottom trawling intensity, a prevalent industrial fishing practice which heavily impacts benthic ecosystems. Fitted models demonstrate how the geographic interplay of different environmental and anthropogenic drivers shapes the diversity, structure and potential metabolism of benthic microbial communities. Sediment properties were the primary determinants, with diversity increasing with sediment permeability but also with mud content, highlighting different underlying processes. Additionally, diversity and structure varied with total organic matter content, temperature, bottom shear stress and bottom trawling. Changes in diversity associated with bottom trawling intensity were accompanied by shifts in predicted energy metabolism. Specifically, with increasing trawling intensity, we observed a transition toward more aerobic heterotrophic and less denitrifying predicted metabolism. Our findings provide first insights into benthic microbial biogeographic patterns on a large spatial scale and illustrate how anthropogenic activity such as bottom trawling may influence the distribution and abundances of microbes and potential metabolism at macroecological scales.

Shifts in the spatiotemporal distribution and sources of nitrous oxide in sediment cores from the Bohai Sea and South Yellow Sea

N₂O is among the most potent greenhouse gases. In this study, we investigated one of the important N₂O production hotspots, the continental margins. We looked at N₂O spatiotemporal distributions in situ as well as the potential contributions of nitrification and denitrification to N₂O production in sediment cores from the Bohai and South Yellow Seas. Real-time PCR and shotgun metagenomics sequencing were used to analyze the microbial communities related to N₂O production. The results showed that N₂O concentrations roughly decreased with depth-a trend that was consistent throughout the year and showed no significant seasonal variations. When all the research stations along the continental margin were considered, the estuary exhibited the lowest average N₂O concentration. Moreover, nitrification was identified as the main process responsible for N₂O production in estuary areas. This study demonstrates that spatial, as opposed to temporal, heterogeneity is the primary factor influencing N₂O concentration differences in sediments.

Variations in nitrogen removal rates and microbial communities over sediment depth in Daya Bay, China

Depth-related variations in the activities, abundances, and community composition of denitrification and anaerobic ammonia oxidation (anammox) bacteria in coastal sediment cores remain poorly understood. In this study, we used ¹⁵N-labelled incubation, quantitative polymerase chain reaction (qPCR), and high-throughput sequencing techniques to reveal the structure and function of denitrifiers and anammox bacteria in sediment cores (almost 100 cm depth) collected in winter and summer from four locations in Daya Bay. The results indicated that the activities and abundances of both denitrifiers and anammox bacteria were detected even in deeper sediments with low concentrations of dissolved inorganic nitrogen (DIN). The potential rates, abundances, and community compositions of denitrifiers and anammox bacteria only varied spatially. In the surface sediment (top 2 cm), denitrifiers had significantly higher activities and abundances than anammox bacteria, but the relative contribution of anammox bacteria to nitrogen loss increased to >60% in the subsurface sediments. Phylogenetic analysis revealed that nirS-type denitrifiers were affiliated to 10 different clusters and Candidatus Scalindua dominated the anammox community in the whole sediments. Furthermore, both denitrification and anammox bacterial communities in the subsurface sediments were distinct from those in the surface sediments. Coupled nitrification and denitrification or anammox may play significant roles in removing fixed N, and the availability of electronic acceptors (e.g. nitrite and nitrate) strongly influenced the N loss activities in the subsurface sediment, emphasising its role as a sink for buried N.

Denitrifier abundance and community composition linked to denitrification potential in river sediments

Denitrification in river sediments plays a very important role in removing nitrogen in aquatic ecosystem. To gain insight into the key factors driving denitrification at large spatial scales, a total of 135 sediment samples were collected from Huaihe River and its branches located in the northern of Anhui province. Bacterial community composition and denitrifying functional genes (nirS, nirK, and nosZ) were measured by high-throughput sequencing and real-time PCR approaches. Potential denitrification rate (PDR) was measured by acetylene inhibition method, which varied from 0.01 to 15.69 μg N g^-1 h^-1. The sequencing results based on 16S rRNA gene found that the main denitrification bacterial taxa included Bacillus, Thiobacillus, Acinetobacter, Halomonas, Denitratisoma, Pseudomonas, Rhodanobacter, and Thauera. Therein, Thiobacillus might play key roles in the denitrification. Total nitrogen and N:P ratio were the only chemical factors related with all denitrification genes. Furthermore, nirS gene abundance could be more susceptible to environmental parameters compared with nirK and nosZ genes. Canonical correspondence analysis indicated that NO₃^-, NO₂^-, NH₄⁺ and IP had the significant impacts on the nirS-encoding bacterial community and spatial distributions. There was a significantly positive correlation between Thiobacillus and nirS gene. We considered that higher numbers of nosZ appeared in nutrient rich sediments. More strikingly, PDR was positively correlated with the abundance of three functional genes. Random forest analysis showed that NH₄⁺ was the most powerful predictor of PDR. These findings can yield practical and important reference for the bioremediation or evaluation of wetland systems.

Nitrogen-cycling gene pool shrunk by species interactions among denser bacterial and archaeal community stimulated by excess organic matter and total nitrogen in a eutrophic bay

Microbial densities, functional genes, and their responses to environment factors have been studied for years, but still a lot remains unknown about their interactions with each other. In this study, the abundances of 7 nitrogen cycling genes in the sediments from Hangzhou Bay were analyzed along with bacterial and archaeal 16S rRNA abundances as the biomarkers of their densities. The amount of organic matter (OM) and total nitrogen (TN) strongly positively correlated with each other and microbial densities, while total phosphate (TP) and ammonia-nitrogen (NH₃-N) did not. Most studied genes were density suppressed, while nirS was density stable, and nosZ and hzo were density irrelevant. This suggests eutrophication could limit inorganic nitrogen cycle pathways and the removal of nitrogen in the sediment and emit more greenhouse gases. This study provides a new insight of microbial community structures, functions and their interactions in the sediments of eutrophic bays.

Time-resolved characteristics and production pathways of simulated landfilling N2O emission under different oxygen concentrations

Nitrous oxide (N₂O), an important greenhouse gas, is emitted from landfill reservoirs, especially in the working face, where nitrification and denitrification occur under different O₂ concentrations. In order to explore the effects of O₂ concentration on N₂O emissions and production pathways, the production of N₂O from simulated fresh waste landfilling under 0%, 5%, 10%, and 21% (vol/vol) O₂ concentrations were examined, and ¹⁵N isotopes were used as tracers to determine the contributions of nitrification (NF), heterotrophic denitrification (HD), and nitrification-coupled denitrification (NCD) to N₂O production over a 72-h incubation period. Equal amounts of total nitrogen consumption occurred for all studied O₂ concentration and the simulated waste tended to release more N₂O under 0% and 21% O₂. Heterotrophic denitrification was the main source of N₂O release at the studied oxygen concentrations, contributing 90.51%, 69.04%, 80.75%, and 57.51% of N₂O under O₂ concentrations of 0%, 5%, 10%, and 21%, respectively. Only denitrification was observed in the simulated fresh waste when the oxygen concentration of the bulk atmosphere was 0%. The nitrate reductase (nirS)-encoding denitrifiers in the simulated landfill were also studied and significant differences were observed in the richness and diversity of the denitrifying community at different taxonomic levels. It was determined that optimising the O₂ content is a crucial factor in N₂O production that may allow greenhouse gas emissions and N turnover during landfill aeration to be minimised.

Effects of revetments on soil denitrifying communities in the urban river-riparian interface

The river-riparian interface plays an important role in removal of nitrogen pollution. Many revetments have been built in urban riparian zones, which has affected soil denitrification function of river-riparian interface. However, the impacts of revetments on denitrifying communities of soil in the river-riparian interface are still unclear. In this study, in the case of eliminating the influence of plants, three modes of revetments (No Revetments (NR), Impervious Masonry Revetments (IR), and Permeable Concrete Imitation Pile Revetments (PR)) were employed to determine the influence of revetments on denitrifying communities of soil among three distances from revetments (1.0, 0.6 and 0.3 m). It was shown in comparison with IR and NR, PR promoted the abundance, diversity and relative abundance of major strains in nirS and nirK denitrifying bacteria (P < 0.05), but these effects decreased as distances increased. Compared with the IR (2.95 ± 1.15 × 10⁵ copies g^-1) and NR (4.13 ± 2.14 × 10⁵ copies g^-1), abundances of nirK denitrifying bacteria adjacent to PR (6.19 ± 1.89 × 10⁵ copies g^-1) were significantly higher (P < 0.05). Rubrivivax and Bradyrhizobium were the dominant bacterial genera, accounting for 16.02-23.94% and 29.25%-38.25% of nirS- and nirK- denitrifying bacteria, respectively. SOC and nitrogen availability were the primary factors which influence the gene richness of nirK and nirS, while soil bulk density, sand content and WFPS as the major elements were impacting compositions of nirK and nirS communities. The results will improve the comprehension of theoretical process of denitrification affected by revetment types.

Nutrient removal performance and microbiome of an energy-efficient reciprocation MLE-MBR operated under hypoxic conditions

A critical challenge in the application of membrane bioreactors (MBR) for domestic wastewater treatment is its high energy consumption caused by continuous aeration for biofouling control. To reduce energy consumption and mitigate fouling in membranes, alternative configurations using dynamic shear-enhanced filtration by membrane reciprocation, rotation, and vibration to mechanically impose shear on membrane surfaces have been recently introduced. However, although these methods are effective at lowering energy usage, the nutrient removal efficiencies and microbial community compositions of these systems have not been well studied. In this study, a lab-scale no-aeration reciprocation membrane bioreactor was used to characterize the microbial composition, functional profile and nutrient removal of the reciprocation MBR system operated under hypoxic conditions. Microbial community analysis showed Proteobacteria (35%) and Saccharibacteria (27%) to be the most abundant phyla in the sludge and the biofilm samples, respectively. Nitrogen and phosphorus removal efficiencies were observed at 70% and 50% while the chemical oxygen demand concentration had about a 99% decrease in the effluent. Quantitative PCR of nutrient-removing genes revealed the presence of complete ammonia-oxidizing organisms (comammox) with a mean abundance of 1.88 × 10⁴ gene copies/g sludge, which explains the high ammonia removal despite a low abundance of canonical ammonia-oxidizing bacteria (AOB). Fluorescence in-situ hybridization showed a prevalence of nitrite-oxidizing bacteria (NOB) with clusters that are distant from other nutrient-removing communities, suggesting that their metabolism is not dependent on ammonia oxidizers. The reciprocation MBR configuration may be a suitable, more energy-efficient alternative to conventional air-scouring systems because of its biofouling mitigation and promising nutrient removal performed by the diverse microbial communities in its system.

Comparison of the effects of salinity on microbial community structures and functions in sequencing batch reactors with and without carriers

This study investigated and compared the microbial communities between a sequencing batch reactor (SBR) without carriers and a hybrid SBR with addition of carriers for the treatment of saline wastewater. The two systems were operated over 292 days with alternating aerobic/anoxic mode (temperature: 28℃, salinity: 0.0-3.0%). High removal efficiency of chemical oxygen demand (COD) and total inorganic nitrogen (TIN) was achieved in both the SBR (above 86.7 and 95.4% respectively) and hybrid SBR (above 84.4 and 94.0%) at 0.0-2.5% salinity. Further increasing salinity to 3.0% decreased TIN removal efficiency to 78.4% in the hybrid SBR. Steep decline of biodiversity and relative abundance of ammonia-oxidizing bacteria (AOB) contributed to the worse performance. More genera related to sulfide-oxidizing and sulfate-reducing bacteria were detected in the hybrid SBR than the SBR at 3.0% salinity. The abundance of halotolerant bacteria increased with the salinity increase for both reactors, summing up to 25.5% in the suspended sludge (S-sludge) from the SBR, 28.9 and 22.9% in the S-sludge and biofilm taken from the hybrid SBR, respectively. Nitrification and denitrification via nitrate was the main nitrogen removal pathway in the SBR and hybrid SBR at 0.0 and 0.5% salinity, while partial nitrification and denitrification via nitrite became the key process for nitrogen removal in the two reactors when the salinity was increased to 1.0-3.0%. Higher abundance of anaerobic ammonium-oxidizing (ANAMMOX) and sulfide-oxidizing autotrophic denitrification (SOAD) bacteria were found in the hybrid SBR at 3.0% salinity.

The roles of environmental variation and spatial distance in explaining diversity and biogeography of soil denitrifying communities in remote Tibetan wetlands

The relative importance of local environments and dispersal limitation in shaping denitrifier community structure remains elusive. Here, we collected soils from 36 riverine, lacustrine and palustrine wetland sites on the remote Tibetan Plateau and characterized the soil denitrifier communities using high-throughput amplicon sequencing of the nirS and nirK genes. Results showed that the richness of nirS-type denitrifiers in riverine wetlands was significantly higher than that in lacustrine wetlands but not significantly different from that in palustrine wetlands. There was no clear distinction in nir community composition among the three kinds of wetlands. Irrespective of wetland type, the soil denitrification rate was positively related to the abundance, but not the α-diversity, of denitrifying communities. Soil moisture, carbon availability and soil temperature were the main determinants of diversity [operational taxonomic unit (OTU) number] and abundance of thenirS-type denitrifier community, while water total organic carbon, soil NO3- and soil moisture were important in controlling nirK-type denitrifier diversity and abundance. The nirS community composition was influenced by water electrical conductivity, soil temperature and water depth, while the nirK community composition was affected by soil electrical conductivity. Spatial distance explained more variation in the nirS community composition than in the nirK community composition. Our findings highlight the importance of both environmental filtering and spatial distance in explaining diversity and biogeography of soil nir communities in remote and relatively undisturbed wetlands.

Community dynamics and activity of nirS-harboring denitrifiers in sediments of the Indus River Estuary

Denitrification is an important pathway for reactive nitrogen removal from aquatic ecosystems. In this study, the biodiversity, abundance, and activity of cytochrome cd₁-type nitrate reductase gene (nirS)-harboring denitrifiers in the sediments of the Indus River Estuary were examined by molecular and isotope-tracing techniques. Results showed that the nirS-harboring denitrifier communities showed significant geographical variations along the estuarine salinity gradient. Real-time quantitative PCR showed that the abundance of nirS-harboring denitrifiers ranged from 5.3 × 10⁶ to 2.5 × 10⁸ copies g^-1, without significant spatiotemporal variation. The potential rates of denitrification varied from 0.01 to 6.27 μmol N kg^-1 h^-1 and correlated significantly to TOC and Fe(II) (P < 0.05). On the basis of ¹⁵N isotope-tracing experiments, the denitrification process contributed 18.4-99.4% to the total nitrogen loss in the sediments of the Indus River Estuary. This study provides novel insights into the microbial mechanism of nitrogen removal process in estuarine ecosystems.

Impact of tidally induced residual circulations on chemical oxygen demand (COD) distribution in Laizhou Bay, China

To understand the impact of hydrodynamics on pollutant transport in Laizhou Bay, China, we conducted numerical simulations using Mike 21. The model was calibrated with good agreements to field monitoring data at various monitoring stations. The simulation results show a clockwise and an anti-clockwise tidally-induced residual circulation in the western and eastern bay, respectively. Historical COD monitoring data also indicate two rings of high COD concentration in the same regions of the bay. This suggests that the hydrodynamics of tidal and residual currents is the main cause of the ring-shaped high COD concentration field in the bay. Pollutant inputs from inland rivers are also important for the COD distribution, making the near-shore side of the COD ring higher than the offshore side. Regions with higher retention time in the bay are usually associated with higher COD concentrations. This study is useful in understanding the mechanism of pollutant spatial distribution and subsequent pollution control in a sea bay.

Denitrification characterization of dissolved oxygen microprofiles in lake surface sediment through analyzing abundance, expression, community composition and enzymatic activities of denitrifier functional genes

The responses of denitrifiers and denitrification ability to dissolved oxygen (DO) concent in different layers of surface lake sediments are still poorly understood. Here, the optimal denitrification condition was constructed based on response surface methodology (RSM) to analyze the denitrification characteristics of surface sediments. The aerobic zone (AEZ), hypoxic zone (HYZ), up-anoxic zone (ANZ-1) and sub-anoxic zone (ANZ-2) were partitioned based on the oxygen contents, and sediments were collected using a customized-designed sub-millimeter scale sampling device. Integrated real-time quantitative PCR, Illumina Miseq-based sequencing and denitrifying enzyme activities analysis revealed that denitrification characteristics varied among different DO layers. Among the four layers, the DNA abundance and RNA expression levels of norB, nirS and nosZ were the highest at the aerobic layer, hypoxic layer and up-axoic layer, respectively. The hypoxia and up-anaerobic layer were the active nitrogen removal layers, since these two layers displayed the highest DNA abundance, RNA expression level and enzyme activities of denitrification functional genes. The abundance of major denitrifying bacteria showed significant differences among layers, with Azoarcus, Pseudogulbenkiania and Rhizobium identified as the main nirS, nirK and nosZ-based denitrifiers. Pearson’s correlation revealed that the response of denitrifiers to environmental factors differed greatly among DO layers. Furthermore, napA showed higher DNA abundance and RNA expression level in the aerobic and hypoxic layers than anaerobic layers, indicating that aerobic denitrifiers might play important roles at these layers.

Nitrate addition promotes the nitrogen cycling processes under the co-contaminated tetrabromobisphenol A and copper condition in river sediment

Tetrabromobisphenol A (TBBPA) and copper (Cu) are the main pollutants at e-waste recycling sites and the effects of their biotoxicity on microorganisms have drawn extensive attention. Nitrate-based bioremediation has been applied to organic pollutant-contaminated sediments since nitrate is a favorable electron acceptor for microbes. However, the effects of TBBPA and Cu on nitrogen (N)-cycling microorganisms and bioremediation in co-contaminated sediments remain unclear. Thus, our study examined the effects of TBBPA and Cu with/without nitrate addition on the TBBPA biodegradation efficiencies, microbial activities, and N functional genes. It was found the biodegradation efficiencies of TBBPA were improved by the nitrate addition from 34.7% to 59.3% and from 22.6% to 42.8% in the TBBPA and TBBPA-Cu contaminated groups, respectively. The inhibitions of the catalase activity increased with the nitrate addition because of the anaerobic respiration of the microorganisms. In addition, the potential denitrification rate exhibited an increasing trend from 6.46 to 8.23 mg-N kg^-1 dry sediment day^-1 during the period of 15-90 days after adding nitrate to the co-contaminated group, whereas the potential nitrification rate exhibited an opposite trend and decreased from 4.47 to 3.19 mg-N kg^-1 dry sediment day^-1. The denitrification gene abundances of the N-cycling genes were 10⁷-10⁸ orders of magnitude higher and significantly increased in the nitrate addition groups. The amoA gene abundances were lower than the denitrification gene abundances and were 10⁵-10⁶ orders of magnitude in the same groups. Moreover, the interaction types of the pollutants on the gene abundances were changed from synergistic to antagonistic as nitrate addition. Our study emphasized the gap of knowledge on nitrate addition affecting N-cycling microbes in the combined pollutants exposure sediments, and will be helpful for further bioremediation in different contaminated scenarios.

Importance of denitrification driven by the relative abundances of microbial communities in coastal wetlands

Excessive nitrogen (N) loadings from human activities have led to increased eutrophication and associated water quality impacts in China's coastal wetlands. Denitrification accounts for significant reduction of inorganic N to nitrous oxide (N₂O) or dinitrogen gas (N₂), and thereby curtails harmful effects of N pollution in coastal and marine ecosystems. However, the molecular drivers and limiting steps of denitrification in coastal wetlands are not well understood. Here, we quantified the abundances of functional genes involved in N cycling and determined denitrification rates using ¹⁵N paring technique in the coastal wetland sediments of Bohai Economic Rim in eastern China. Denitrification accounting for 80.7 ± 12.6% of N removal was the dominant pathway for N removal in the coastal wetlands. In comparison, anaerobic ammonium oxidation (ANAMMOX) removed up to 36.9 ± 7.3% of inorganic N. Structural equation modeling analysis indicated that the effects of ammonium on denitrification potential were mainly mediated by the relative abundances of nosZ/nirS, nirS/(narG + napA) and amoA/nirK. Denitrification was limited by the relative strength of two steps, namely N₂O reduction to N₂ and nitrite (NO₂^-) reduction to nitric oxide (NO). Our results suggest that the relative abundances of functional genes which are more stable than sediment chemical compounds in the context of environmental changes are indictive of denitrification potential in coastal wetlands.

Seasonal distribution of nitrifiers and denitrifiers in urban river sediments affected by agricultural activities

Nitrifiers and denitrifiers play a critical role in nitrogen removal in urban river sediments that are also affected by agricultural activities. However, the seasonal variations and vertical profile of these organisms in these river sediments are not well understood. In this study, the seasonal and depth (0 to 30 cm) distributions of the abundance and activity of nitrifiers and denitrifiers in sediments of the Pearl River in Guangzhou city were quantifying via qPCR and RT-qPCR according to various nitrifying and denitrifying functional genes, and their diversities were analyzed via high-throughput sequencing on an Illumina MiSeq platform. Results show that the distribution of nitrifiers and denitrifiers in these urban sediments were more abundant and active during the summer than winter; had distinct vertical distributions in the bacterial numbers and activity, with higher activity of the nirS gene (yearly averaged RNA:DNA 2.5% at 18 to 22 cm, vs. a yearly-depth average of 0.65%) but with lower overall numbers (yearly averaged 2.1 × 10⁶ copies g^-1 at 18 to 22 cm, vs. a yearly-depth average of 12.5 × 10⁶ copies g^-1); and their amoA and nosZ gene diversities in the sediments exhibited a correlation with the communities in nearby agricultural soils.

Submarine groundwater discharge and chemical behavior of tracers in Laizhou Bay, China

Naturally occurring radon (²²²Rn) and radium isotopes are widely used to trace water mixing and submarine groundwater discharge (SGD) in the coastal zones. However, their activities in groundwater are variable both spatially and temporally. Here, time series sampling of ²²²Rn and radium was conducted to investigate their behavior in intertidal groundwater of Laizhou Bay, China. The result shows that groundwater redox conditions have an important impact on the behavior of tracers. The activities of tracers will decrease under oxidizing conditions and increase under reducing conditions. Radon and radium mass balance models were used to evaluate the flushing time and SGD based on spatial surveys in Laizhou Bay. The flushing time is estimated to be 32.9-55.3 d with coupled models, which agrees well with the result of tidal prism model. The trace-derived SGD in the whole bay ranges from 6.1 × 10⁸ to 9.0 × 10⁸ m³/d and the re-circulated seawater (RSGD) ranges from 5.5 × 10⁸ to 8.5 × 10⁸ m³/d. The average SGD and RSGD fluxes are 22.8 and 21.1 times greater than the Yellow River discharge in April 2014, respectively. The study provides a better understanding of the dynamics of coastal groundwater and behavior of tracers in a well-studied bay system.

In Situ Water Quality Improvement Mechanism (Nitrogen Removal) by Water-Lifting Aerators in a Drinking Water Reservoir

A field scale experiment was performed to explore the nitrogen removal performance of the water and surface sediment in a deep canyon-shaped drinking water reservoir by operating WLAs (water-lifting aerators). Nitrogen removal performance was achieved by increasing the densities and N-removal genes (nirK and nirS) of indigenous aerobic denitrifiers. After the operation of WLAs, the total nitrogen removal rate reached 29.1 ± 0.8% in the enhanced area. Ammonia and nitrate concentrations were reduced by 72.5 ± 2.5% and 40.5 ± 2.1%, respectively. No nitrite accumulation was observed. Biolog results showed improvement of carbon metabolism and carbon source utilization of microbes in the enhanced area. Miseq high-throughput sequencing indicated that the denitrifying bacteria percentage was also higher in the enhanced area than that in the control area. Microbial communities had changed between the enhanced and control areas. Thus, nitrogen removal through enhanced indigenous aerobic denitrifiers by the operation of WLAs was feasible and successful at the field scale.

Microbial diversity and community structure in agricultural soils suffering from 4 years of Pb contamination

Heavy metal pollution has become a widespread environmental problem due to rapid economic development. The phylogenetic diversity and structure of microbial communities in lead (Pb)-contaminated Lou soils were investigated using Illumina MiSeq sequencing of 16S rRNA genes. The presence of Pb2+ in soil showed weak impact on the diversity of soil bacteria community, but it influenced the abundance of some genera of bacteria, as well as soil physicochemical properties. We found significant differences in the relative abundances of heavy-metal-resistant bacteria such as Bacillus, Streptococcus, and Arthrobacter at the genus level. Available Pb and total Pb negatively correlated with soil organic matter but positively affected available phosphorus. The abundance of main bacteria phyla was highly correlated with total Pb. The relative abundance of Gemmatimonadetes, Nitrospirae, and Planctomycetes was negatively correlated with total Pb. Collectively, Pb influences both the microbial community composition and physicochemical properties of soil.

Overall bacterial community composition and abundance of nitrifiers and denitrifiers in a typical macrotidal estuary

Coupled nitrogen cycling processes can alleviate the negative effects of eutrophication caused by excessive nitrogen load in estuarine ecosystems. The abundance and diversity of nitrifiers and denitrifiers across different environmental gradients were examined in the sediment of Hangzhou Bay. Quantitative PCR and Pearson's correlation analyses suggested that the bacterial ammonia-oxidizers (AOB) were the dominant phylotypes capable of ammonia oxidation, while the nirS-encoding denitrifiers predominated in the denitrification process. Simultaneously, nitrite and pH were found to be the two major factors influencing amoA and nir gene abundances, and the distribution of bacterial communities. Moreover, the ratio of nirS/AOB amoA gene abundance showed negative correlation with nitrite concentration. Fluorescence in situ hybridization further demonstrated that AOB and acetate-denitrifying cells were closely connected and formed obvious aggregates in the sediment. Together, all these results provided us a preliminary insight for coupled nitrification-denitrification processes in the sediment of Hangzhou Bay.

Response of ammonia oxidizing archaea and bacteria to decabromodiphenyl ether and copper contamination in river sediments

Ammonia oxidation plays a fundamental role in river nitrogen cycling ecosystems, which is normally governed by both ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB). Co-contamination of typical emerging pollutant Polybrominated diphenyl ethers (PBDEs) and heavy metal on AOA and AOB communities in river sediments remains unknown. In this study, multiple analytical tools, including high-throughput pyrosequencing and real-time quantitative PCR (qPCR), were used to reveal the ammonia monooxygenase (AMO) activity, subunit alpha (amoA) gene abundance, and community structures of AOA and AOB in river sediments. It was found that the inhibition of AMO activities was increased with the increase of decabromodiphenyl ether (BDE 209, 1-100 mg kg^-1) and copper (Cu, 50-500 mg kg^-1) concentrations. Moreover, the synergic effects of BDE 209 and Cu resulted in a higher AMO activity reduction than the individual pollutant BDE 209. The AOA amoA copy number declined by 75.9% and 83.2% and AOB amoA gene abundance declined 82.8% and 90.0% at 20 and 100 mg kg^-1 BDE 209 with a 100 mg kg^-1 Cu co-contamination, respectively. The pyrosequencing results showed that both AOB and AOA community structures were altered, with a higher change of AOB than that of AOA. The results demonstrated that the AOB microbial community may be better adapted to BDE 209 and Cu pollution, while AOA might possess a greater capacity for stress resistance. Our study provides a better understanding of the ecotoxicological effects of heavy metal and micropollutant combined exposure on AOA and AOB in river sediments.

Spatial variation of microbial communities in sediments along the environmental gradients from Xiaoqing River to Laizhou Bay

The Laizhou Bay is famous for aquaculture, but has been subject to eutrophication and contamination for years. High concentrations of nutrients from the Xiaoqing River are considered as the main cause for significant eutrophication in the west of Laizhou Bay. Here we present results of the research on sedimentary microbial assemblages along this spatial gradient between riverine and marine environments by high-throughput sequencing. The predominant phyla/classes of bacteria and fungi clustered the samples into two distinct provinces, while discriminant taxa of each province were strongly associated with spatial factors and inorganic nitrogen. Spatial variation of bacterial communities was mainly related with the distribution of phosphates, suggesting a phosphate-limitation pattern for the bacterial communities. Alpha- and beta-diversity of fungal communities exhibited a significant correlation with water depth. We consider the distinct distributional gradients of bacterial and fungal communities partly explain the different roles in the biogeochemical processes of coastal sediment.

Distinct distribution patterns of proteobacterial nirK- and nirS-type denitrifiers in the Yellow River estuary, China

Denitrification is considered to be the critical process in removing reactive nitrogen in estuarine ecosystems. In the present study, the abundance, diversity, and community structure of nirK- and nirS-type denitrifiers were compared in sediments from the Yellow River estuary. Quantitative polymerase chain reaction showed that the 2 types of denitrifiers exhibited different distribution patterns among the samples, indicating their distinct habitat preference. Phylogenetic analysis revealed that most of the sequences from clusters I, III, IV, and V for nirK-type denitrifiers were dominant and were distributed at sites where dissolved oxygen (DO) was lower, and the sequences in the other clusters were dominant at sites with higher DO. However, there was no spatially heterogeneous distribution for the nirS-type denitrifier community. Canonical correlation analysis and correlation analysis demonstrated that the community structure of nirK was more responsive to environmental factors than was that of nirS. Inversely, the abundance and α-diversity targeting nirS gene could be more easily influenced by environmental parameters. These findings can extend our current knowledge about the distribution patterns of denitrifying bacteria and provide a basic theoretical reference for the dynamics of denitrifying communities in estuarine ecosystem of China.

Diversity of Cultivable Protease-Producing Bacteria in Laizhou Bay Sediments, Bohai Sea, China

Protease-producing bacteria are widespread in ocean sediments and play important roles in degrading sedimentary nitrogenous organic materials. However, the diversity of the bacteria and the proteases involved in such processes remain largely unknown especially for communities in enclosed sea bays. Here, we investigated the diversity of the extracellular protease-producing bacteria and their protease types in Laizhou Bay. A total of 121 bacterial isolates were obtained from sediment samples in 7 sites and their protease types were characterized. The abundance of cultivable protease-producing bacteria was about 10⁴ CFU g^-1 of sediment. Phylogenetic analysis based on 16S rRNA gene sequences suggest that the isolates belonged to 17 genera from 4 phyla including Firmicutes, Actinobacteria, Proteobacteria and Bacteroidetes, and mainly dominated by the genera Pseudoalteromonas (40.5%), Bacillus (36.3%), and Photobacterium (5.8%). The diversity and community structure varied among different sampling sites but no significant correlation was observed with soil sediment's characteristics. Enzyme activity and inhibition tests further revealed that all isolates secreted proteases that were inhibited by serine and/or metalloprotease inhibitors, and a smaller proportion was inhibited by inhibitors of cysteine and/or aspartic proteases. Furthermore, all isolates effectively degraded casein and/or gelatin with only a few that could hydrolyze elastin, suggesting that the bacteria were producing different kinds of serine proteases or metalloproteases. This study provided novel insights on the community structure of cultivable protease-producing bacteria near the Yellow River estuary of an enclosed sea bay.

Rapid Identification and Quantification of Aureococcus anophagefferens by qPCR Method (Taqman) in the Qinhuangdao Coastal Area: A Region for Recurrent Brown Tide Breakout in China

Since 2009, Aureococcus anophagefferens has caused brown tide to occur recurrently in Qinhuangdao coastal area, China. Because the algal cells of A. anophagefferens are so tiny (~3 µm) that it is very hard to identify exactly under a microscope for natural water samples, it is very urgent to develop a method for efficient and continuous monitoring. Here specific primers and Taqman probe are designed to develop a real-time quantitative PCR (qPCR) method for identification and quantification continually. The algal community and cell abundance of A. anophagefferens in the study area (E 119°20'-119°50' and N 39°30'-39°50') from April to October in 2013 are detected by pyrosequencing, and are used to validate the specification and precision of qPCR method for natural samples. Both pyrosequencing and qPCR shows that the targeted cells are present only in May, June and July, and the cell abundance are July > June > May. Although there are various algal species including dinoflagellata, diatom, Cryptomonadales, Chrysophyceae and Chlorophyta living in the natural seawater simultaneously, no disturbance happens to qPCR method. This qPCR method could detect as few as 10 targeted cells, indicating it is able to detect the algal cells at pre-bloom levels. Therefore, qPCR with Taqman probe provides a powerful and sensitive method to monitor the brown tide continually in Qinhuangdao coastal area, China. The results provide a necessary technology support for forecasting the brown tide initiation, in China.

Altitude-scale variation in nitrogen-removal bacterial communities from municipal wastewater treatment plants distributed along a 3600-m altitudinal gradient in China

Microbial ecological information on the nitrogen removal processes in wastewater treatment plants (WWTPs) has been of considerable importance as a means for diagnosing the poor performance of nitrogen removal. In this study, the altitude-scale variations in the quantitative relationships and community structures of betaproteobacteria ammonia-oxidizing bacteria (βAOB) and nitrite-reducing bacteria containing the copper-containing nitrite reductase gene (nirK-NRB) and the cytochrome cd1-containing nitrite reductase gene (nirS-NRB) were investigated in 18 municipal WWTPs distributed along a 3660-masl altitude gradient in China. An altitude threshold associated with the proportions of NRB to total bacteria, NRB to βAOB and nirK-NRB to nirS-NRB was detected at approximately 1500m above sea level (masl). Compared with the stable proportions below 1500masl, the proportions exhibited a pronounced decreasing trend with increased altitude above 1500masl. Spearman correlation analysis indicated that the trend was significantly driven by altitude as well as multiple wastewater and operational variables. The community structure dissimilarity of βAOB, nirK-NRB and nirS-NRB showed significant and positive correlations with altitudinal distance between WWTPs. Redundancy analyses indicated that the variation in community structures above 1500masl were predominantly associated with wastewater, followed by operation and altitude. In summary, although the variations of nitrogen-removal bacterial community in WWTPs were driven dominantly by wastewater and operational variables, altitude was also an important variable influencing the quantitative relationships and community structures of nitrogen-removal bacteria in WWTPs particularly above 1500masl.

Bacterial community compositions in sediment polluted by perfluoroalkyl acids (PFAAs) using Illumina high-throughput sequencing

The characterization of bacterial community compositions and the change in perfluoroalkyl acids (PFAAs) along a natural river distribution system were explored in the present study. Illumina high-throughput sequencing was used to explore bacterial community diversity and structure in sediment polluted by PFAAs from the Xiaoqing River, the area with concentrated fluorochemical facilities in China. The concentration of PFAAs was in the range of 8.44-465.60 ng/g dry weight (dw) in sediment. Perfluorooctanoic acid (PFOA) was the dominant PFAA in all samples, which accounted for 94.2 % of total PFAAs. High-level PFOA could lead to an obvious increase in relative abundance of Proteobacteria, ε-Proteobacteria, Thiobacillus, and Sulfurimonas and the decrease in relative abundance of other bacteria. Redundancy analysis revealed that PFOA played an important role in the formation of bacterial community, and PFOA at higher concentration could reduce the diversity of bacterial community. When the concentration of PFOA was below 100 ng/g dw in sediment, no significant effect on microbial community structure was observed. Thiobacillus and Sulfurimonas were positively correlated with the concentration of PFOA, suggesting that both genera were resistant to PFOA contamination.

Macroscale distribution of virioplankton and heterotrophic bacteria in the Bohai Sea

In light of limited research into the relationship between the macroscale distribution and dynamic changes of microplankton in the shallow Bohai Sea, here we used flow cytometry to analyse samples collected from the Bohai Sea channel in winter and summer. Results showed that the average of both viral abundance (VA) and bacterial abundance (BA) were lower in winter (3.61 × 10(7) and 1.84 × 10(6) cells/mL, respectively) than in summer (7.47 × 10(7) and 5.05 × 10(6) cells/mL, respectively). At all 16 stations, VA was one order of magnitude greater than BA, with a positive relationship between one another. In the horizontal distribution, variations in VA and BA followed a similar trend, and both were obviously higher near-shore than offshore. In the vertical distribution, variations in both VA and BA did not show a clear relationship with water depth. VA and BA in summer were 2.1 and 2.7 times those in winter, respectively. Spearman correlation analysis showed that both VA and BA were correlated with the concentration of PO4-P in winter (positive) and NO3-N in summer (negative). Additionally, BA showed a negative correlation with salinity. It is clear that the macroscale distribution of these two kinds of microbes in the Bohai Sea is related to seasonal variation and nutrient availability.

Sediment properties and trace metal pollution assessment in surface sediments of the Laizhou Bay, China

Spatial distribution, ecological risk, pollutant source, and transportation of trace metals in surface sediments, as well as the sediment properties, were analyzed in this study to assess the pollution status of trace metal in the Laizhou Bay, China. Results of provenance analyses indicate that surface sediments were primarily from weathering products carried by the surrounding short rivers and partially from loess matters carried by the Yellow River. Variations of trace metal concentrations were mostly controlled by the accumulation of weathering products, organic matters, and the hydrodynamics. Geoaccumulation index suggests that no Cr pollution occurred in the study area, and Cu, Pb, and Zn pollutions appeared only at a few stations. Comparatively, Cd and As pollutions were at noticeably weak to moderate level at many stations. The combination of six trace metals in this study had a 21% probability of being toxic in our study area based on sediment quality guidelines. Enrichment factors (EFs) and statistical analyses indicate that Cu, Pb, and Zn were primarily derived from the natural process of weathering. By contrast, Cd, As, and Cr (especially Cd and As) were provided by the anthropogenic activities to a large extent. Due to the dilution of coarse-grained sediments, there was even no contamination at some of stations that were obviously influenced by humans. Based on the current study of transportation process of fine-grained sediments in combination with the spatial distribution of EFs, it is found that the migration of anthropogenic trace metals was mainly controlled by the tide in the Laizhou Bay. The study suggests that an effective strategies and remedial measures should be designed and undertaken to prevent further anthropogenic Cd and As pollutions in this area in the future.