Unraveling the rate-limiting step in microorganisms' mediation of denitrification and phosphorus absorption/transport processes in a highly regulated river-lake system

River-lake ecosystems are indispensable hubs for water transfers and flow regulation engineering, which have frequent and complex artificial hydrological regulation processes, and the water quality is often unstable. Microorganisms usually affect these systems by driving the nutrient cycling process. Thus, understanding the key biochemical rate-limiting steps under highly regulated conditions was critical for the water quality stability of river-lake ecosystems. This study investigated how the key microorganisms and genes involving nitrogen and phosphorus cycling contributed to the stability of water by combining 16S rRNA and metagenomic sequencing using the Dongping river-lake system as the case study. The results showed that nitrogen and phosphorus concentrations were significantly lower in lake zones than in river inflow and outflow zones (p < 0.05). Pseudomonas, Acinetobacter, and Microbacterium were the key microorganisms associated with nitrate and phosphate removal. These microorganisms contributed to key genes that promote denitrification (nirB/narG/narH/nasA) and phosphorus absorption and transport (pstA/pstB/pstC/pstS). Partial least squares path modeling (PLS-PM) revealed that environmental factors (especially flow velocity and COD concentration) have a significant negative effect on the key microbial abundance (p < 0.001). Our study provides theoretical support for the effective management and protection of water transfer and the regulation function of the river-lake system.

Convergence of biofilm successional trajectories initiated during contrasting seasons

Biofilm communities play a major role in explaining the temporal variation of biogeochemical conditions in freshwater ecosystems, and yet we know little about how these complex microbial communities change over time (aka succession), and from different initial conditions, in comparison to other stream communities. This has resulted in limited knowledge on how biofilm community structure and microbial colonization vary over relevant time scales to become mature biofilms capable of significant alteration of the freshwater environment in which they live. Here, we monitored successional trajectories of biofilm communities from summer and winter in a headwater stream and evaluated their structural state over time by DNA high-throughput sequencing. Significant differences in biofilm composition were observed when microbial colonization started in the summer vs. winter seasons, with higher percentage of algae (Bacillariophyta) and Bacteroidetes in winter-initiated samples but higher abundance of Proteobacteria (e.g., Rhizobiales, Rhodobacterales, Sphingomonadales, and Burkholderiales), Actinobacteria, and Chloroflexi in summer-initiated samples. Interestingly, results showed that despite seasonal effects on early biofilm succession, biofilm community structures converged after 70 days, suggesting the existence of a stable, mature community in the stream that is independent of the environmental conditions during biofilm colonization. Overall, our results show that algae are important in the early development of biofilm communities during winter, while heterotrophic bacteria play a more critical role during summer colonization and development of biofilms.

Research trends and hotspots of aquatic biofilms in freshwater environment during the last three decades: a critical review and bibliometric analysis

Freshwater periphytic biofilms (FPBs), existing widely in various aquatic environments, have attracted extensive attention for many years. In the present study, a bibliometric analysis based on Web of Science Core Collection (WoSCC) was used to understand the research progress, trends, and hot topics of FPBs qualitatively and quantitatively. The results indicated that publications on FPBs have increased from 1991 to 2020 rapidly, and researchers have focused more on the areas of environmental sciences, microbiology, and marine freshwater biology. The most influential countries were mainly the USA, Spain, France, and Germany. Cooperation network analysis reflected that the USA and its affiliated institutions played crucial roles in the research of FPB cooperation, but the collaboration between core author groups still fell short. Based on the analysis of top 20 high-cited FPB documents over the last 30 years, research hotspots mainly included micro-observation and assembly mechanisms of FPBs; interactions of FPBs and pollutants including heavy metals, antibiotic resistance genes, pathogens, organic pollutants, and nanoparticles; and the role of FPBs for biogeochemical cycling, especially nitrogen cycling. Additionally, future research directions were proposed. Overall, this study provides a comprehensive and systematic overview of FPBs, which is useful for research development and researchers who are interested in this area.

Seasonal effects of river flow on microbial community coalescence and diversity in a riverine network

Terrestrial microbial communities may take advantage of running waters and runoff to enter rivers and mix with aquatic microorganisms. However, the environmental factors governing the interchange of the microbial community within a watercourse and its surrounding environment and the composition of the resulting community are often underestimated. The present study investigated the effect of flow rate on the mixing of water, soil, sediment and biofilm at four sites along the Lancang River and one branch of the river in winter and summer and, in turn, the resultant changes in the microbial community within each habitat. 16S rRNA gene-based Illumina high-throughput sequencing illustrated that bacterial communities were apparently distinct among biofilm, water, soil and sediment. Biofilms had the lowest richness, Shannon diversity and evenness indices compared with other habitats, and those three indices in all habitats increased significantly from winter to summer. SourceTracker analysis showed a significant coalescence between the bacterial communities of sediment, water and biofilm samples at lower flow rates. Additionally, the proportion of Betaproteobacteria in sediment and biofilms increased with a decrease in flow rate, suggesting the flow rate had a strong impact on microbial community composition and exchange among aquatic habitats. These results were further confirmed by a Mantel test and linear regression analysis. Microbial communities in all samples exhibited a significant but very weak distance-decay relationship (r = 0.093, P = 0.024). Turbidity played a much more important role on water bacterial community structure in summer (i.e. rainy season) (BIOENV, r = 0.92). Together, these results suggest that dispersal is an important factor affecting bacterial community structure in this system.

Effects of microplastic biofilms on nutrient cycling in simulated freshwater systems

Microplastic surfaces could be colonized by microorganisms and form biofilms in aquatic ecosystem, which can participate in the nitrogen (N) and phosphorus (P) cycles. In this work, polypropylene squares were deployed in a pond for 30 days for microplastic biofilms colonization and then were transported to indoor microcosms at an environmental relevant level to study their effects on N and P cycling. Results showed that microplastic biofilms could accelerate ammonia and nitrite oxidation as well as denitrification. Presence of microplastic biofilms accumulated P temporarily and increased alkaline phosphatase activities (APA) in the system. Later in the experiment, disintegration of matured biofilms released N and P into the water. Mass balance calculation suggested possible N input caused by biological nitrogen fixation. Our results demonstrated that microplastics associated biofilms have the ability to alter the N and P cycling processes in aquatic system. However, additional works are required to further quantify the extent of such impact.

Interactions between dicyandiamide and periphytic biofilms in paddy soils and subsequent effects on nitrogen cycling

Dicyandiamide (DCD) is commonly used as nitrification inhibitors which has the potential to reduce nitrogen loss from paddy soils. In paddy systems, periphytic biofilms are commonly presented at the soil/water interface and show significant effects on nutrient cycling. However, the interaction between DCD and periphytic biofilms in paddy and subsequent effects on nitrogen cycling is unclear. In this work, microcosm experiments were carried out to study the interaction between the periphytic biofilms and DCD and the potential influence on nitrogen cycling from in paddy. Results showed that DCD affected the development of periphytic biofilms, while the presence of periphytic biofilms accelerated DCD degradation. Results also showed DCD application reduced nitrification potential mainly by inhibiting ammonia-oxidizing bacteria (AOB). Higher DCD dosage increased NH₃ volatilization loss. However, presence of periphytic biofilm reduced the NH₃ volatilization loss but increased denitrification. Our work contributes to a better understanding on the nitrogen cycling processes in paddy, and provides useful information for the improvement of nitrogen utilization efficiency and the control of non-point source pollution.

Responses of Periphyton Microbial Growth, Activity, and Pollutant Removal Efficiency to Cu Exposure

Periphyton is an effective matrix for the removal of pollutants in wastewater and has been considered a promising method of bioremediation. However, it still needs to be verified whether periphyton can maintain microbial activity and pollutant removal efficiency when dealing with the influence with complex components, and the underlying mechanisms of periphyton need to be revealed further. Herein, this study investigated the microbial growth, activity and functional responses of periphyton after removal of Cu from wastewater. Results showed that the cultivated periphyton was dominated by filamentous algae, and high Cu removal efficiencies by periphyton were obtained after 108 h treatments. Although 2 mg/L Cu²⁺ changed the microalgal growth (decreasing the contents of total chlorophyll-a (Chla), the carbon source utilization and microbial metabolic activity in periphyton were not significantly affected and even increased by 2 mg/L Cu²⁺. Moreover, chemical oxygen demand (COD) removal rates were sustained after 0.5 and 2 mg/L Cu²⁺ treatments. Our work showed that periphyton had strong tolerance and resistance on Cu stress and is environmentally friendly in dealing with wastewater containing heavy metals, as the microbial functions in pollutant removal could be maintained.

Influence of light and temperature on the development and denitrification potential of periphytic biofilms

Periphytic biofilms are microbial aggregates commonly present in submerged aquatic environments and play a significant role in nutrient cycling. In recent years, utilization of natural periphytic biofilms in wastewater treatment and water restoration attracts growing research interests. Light and temperature are two important environmental factors known to affect the development of periphytic biofilms and can be manipulated for the regulation of the biofilm properties. In this work, effects of light and temperature on the development and function (denitrification potential) of periphytic biofilms were investigated using a microcosm experiment. Results showed that thicker periphytic biofilms with higher Chlorophyll a, extracellular polymeric substances (EPS), and total phosphorus contents were developed under higher temperature. Whereas, biomass accumulation was more rapid for periphytic biofilms under higher irradiance. The denitrification potential rate was negatively associated with irradiance, which can be linked to the influence of irradiance on biofilm structure and microbial composition. A relatively lower irradiance is recommended when using periphytic biofilms in nitrogen removal from wastewater.

Abiotic autumnal organic matter deposition and grazing disturbance effects on epilithic biofilm succession

Stream epilithic biofilm community assembly is influenced in part by environmental factors. Autumn leaf deposition is an annual resource subsidy to streams, but the physical effects of leaves settling on epilithic biofilms has not been investigated.We hypothesized that bacterial and microeukaryotic community assembly would follow a successional sequence that was mediated by abiotic effects that were simulating leaf deposition (reduced light and flow) and by biotic (snail grazing)disturbance. This hypothesis was tested using an in situ experimental manipulation. Ambient biofilms had greater algal biomass and distinct ARISA community profiles compared to biofilms developed under manipulated conditions. There were no significant differences in biofilm characteristics associated with grazing, suggesting that results were driven by reduced light/flow rather than invertebrate disturbance; however, grazing appeared to increase bacterial taxon richness.Interestingly at day 38, all treatments grouped together in ordination space and had similar algal/total biomass ratios. We suggest that algal priming promoted a shift in ambient biofilms but that this effect is dependent upon successional timing of algal establishment. These data demonstrate that abiotic effects were more influential than local grazing disturbance and imply that leaf litter deposition may have bottom-up effects on the stream ecosystem through altered epilithic biofilms.

In situ bioremediation of surface waters by periphytons

Environmentally benign and sustainable biomeasures have become attractive options for the in situ remediation of polluted surface waters. In this paper, we review the current state of reported experiments utilizing naturally occurring periphyton. These are microbial communities consisting of heterotrophic and photoautotrophic microorganisms that are reportedly capable of remediating surface waters which suffer from pollution due to a variety of contaminants. In our review, we focus on four aspects of bioremediation: multiple contaminant removal, the processes involved in contaminant removal, successful cell immobilization technologies and finally, the consideration of safety in aquaculture. It has been noted that recent developments in immobilization technologies offer a fresh approach facilitating the application of periphyton. The use of periphyton biofilm overcomes several disadvantages of single species microbial aggregates. The inclusion of periphyton, as a stable micro-ecosystem, is a promising in situ strategy to restore decimated surface water ecosystems.

Development of associations between microalgae and denitrifying bacteria in streams of contrasting anthropogenic influence

We compared the development of microalgal and bacterial-denitrifier communities within biofilms over 28 days in a restored-prairie stream (RP) and a stream receiving treated wastewater effluent (DER). Inorganic nutrient concentrations were an order of magnitude greater in DER, and stream waters differed in the quality of dissolved organics (characterized via pyrolysis-GC/MS). Biofilm biomass and the densities of algae and bacteria increased over time in both systems; however, algal and denitrifier community composition and the patterns of development differed between systems. Specifically, algal and denitrifier taxonomic composition stabilized more quickly in DER than RP, whereas the rates of algal and denitrifier succession were more closely coupled in RP than DER. We hypothesize that, under unenriched conditions, successional changes in algal assemblages influence bacterial denitrifiers due to their dependence on algal exudates, while under enriched conditions, this relationship is decoupled. Between-system differences in organic signatures supported this, as RP biofilms contained more labile, aliphatic compounds than DER. In addition, potential denitrification rates (DNP) were negatively correlated with the percentage of aromatic compounds within the biofilm organic signatures, suggesting a significant relationship between algal exudate composition and denitrification. These results are significant because anthropogenic factors that affect biofilm community composition may alter their capacity to perform critical ecosystem services.

Influence of algal community structure on denitrification rates in periphyton cultivated on artificial substrata

We conducted a field survey of periphyton cultivated on benthic mesh installations in freshwater aquatic systems, including two constructed wetlands and a pond, and also studied periphyton grown on a benthic mesh in laboratory mesocosms. The objectives of this study were to (1) determine if periphyton cultivated on benthic mesh denitrifies at higher rates than the underlying sediments and (2) determine if denitrification rates within periphyton vary with characteristics such as algal and bacterial community structure and biomass. We measured denitrification potential rates of field and laboratory periphyton by the acetylene inhibition method. We characterized algal community composition by algal identification and bacterial community composition by terminal restriction fragment length polymorphisms. Periphyton collected on benthic mesh from our field sites denitrified at significantly higher rates than the underlying sediments, regardless of sampling site or season. Results from both our field survey and laboratory studies indicated a significant, positive correlation between diatom presence and denitrification rate. In our laboratory studies, we found that periphyton with the highest diatom abundance showed the highest denitrification rates as well as a distinct bacterial community composition. These results suggest a synergistic relationship between diatoms and denitrifying bacteria that warrants further study.

Investigating freshwater periphyton community response to uranium with phospholipid fatty acid and denaturing gradient gel electrophoresis analyses

Periphyton communities can be used as monitors of ecosystem health and as indicators of contamination in lotic systems. Measures of biomass, community structure, and genetic diversity were used to investigate impacts of uranium (U) exposure on periphyton. Laboratory exposures of periphyton in river water amended with 238U were performed for 5 days, followed by 2 days of U depuration in unamended river water. Productivity as measured by biomass was not affected by concentrations up to 100 microg238U L(-1). Phospholipid fatty acid (PLFA) profiles and denaturing gradient gel electrophoresis (DGGE) banding patterns revealed no changes in community or genetic structure related to U exposure. We suggest that the periphyton community as a whole was not significantly impacted by exposures of 238U up to a concentration of 100 microgL(-1). These findings have significance for the assessment and prediction of U impacts on aquatic ecosystems.

Enhancement and inhibition of denitrification by fluid-flow and dissolved oxygen flux to stream sediments

Microscale measurements of nitrate (NO3-) and dissolved oxygen (DO) concentrations in sediments were made in a laboratory channel under turbulent fluid-flow conditions to examine the effects of DO flux on denitrification rates. DO concentrations and flux within sediments increased with increasing velocity in the surface water. Under low fluid-flow conditions (shear stress velocity, u* < 0.23 cm s(-1)), increasing velocity increased NO3- loss from the bulk flow. For high fluid-flow conditions (u* > 0.39 cm s(-1)), increasing velocity inhibited NO3-loss. Sediment cores were collected and sliced to measure the depth distribution of denitrifying biomass in sediments. Quantities of nirK and nirS genes were higher within the surface layer and decreased with depth in the sediments. Microscale concentration profiles of DO and NO3- revealed that denitrification occurs within a thin region just below the oxic-anoxic interface in sediments. The interplay of mass transfer and DO flux generated threshold conditions for NO3- loss by denitrification. These results suggest that for a given sediment and environmental conditions (chemical, physical, microbiological), there exists an optimal range in velocities for enhancing denitrification in aquatic systems.

Influence of flow conditions and system geometry on nitrate use by benthic biofilms: implications for nutrient mitigation

The effects of substratum geometry and overlying velocity on nitrate use by periphyton were assessed. Periphyton was cultivated at an average current velocity of 0.5 cm s(-1) in laboratory mesocosms (120 cm long, 60 cm wide) on polyethylene nets of three different geometries, "1-lay er", "3-layer", and "bedform" structures, overlaying a thin bed of sand. Bulk nitrate use was then measured as the reduction of nitrate concentration in the overlying water under average velocities of 0.005, 0.05, and 0.5 cm s(-1). Periphyton structural characteristics were quantified as algal/bacterial biomass, algal species composition, and bacterial densities. Accrual of microbial biomass increased monotonically with increasing benthic net surface area, with upper sections of structures supporting the highest biomass. Maximum rates of nitrate removal were measured in the bedform geometry at intermediate velocity (173 mg NO3-N m(-2) d(-1)), and the lowest was measured with 1-layer geometry at the fastest velocity (11 mg NO3-N m(-2) d(-1)). Oxygen microprofiles within biofilms demonstrated that hydrodynamic conditions and benthic structure both play a key role in the regulation of microbial processing of nitrate delivered from the water column by promotion of denitrification in downstream sections of bedform substrata. Interactions between hydrodynamic conditions and substratum geometry are expected to regulate microbial activity in all surficial natural and engineered environments and must be parameterized to forecast long-term average biochemical transformation rates in rivers and other dynamic aquatic systems.