Nitrate removal microbiology in woodchip bioreactors: A case-study with full-scale bioreactors treating aquaculture effluents

Mn-oxidizing microalgae and woodchip-denitrifying bioreactor system for recovering manganese and removing nitrogen from electrolytic manganese metal industrial tailwater

Excess manganese (Mn) and NH4+-N emissions from electrolytic manganese metal industrial tailwater may harm the environment. However, previous studies have not combined Mn-oxidizing microalgae to reclaim Mn with woodchip substrates for nitrogen removal from tailwater. Here, a two-stage bioreactor system was constructed to recover Mn by microalgal-mediated bio-oxidation in an algae reactor (AR) and remove nitrogen by denitrification in a woodchip reactor (WR). The results showed that up to 100 % of Mn2+ in the tailwater was removed after a 3-day incubation period. The maximum amount of biogenerated Mn oxide nanoparticles reached 13.34 mg/L with Mn4+ as the main Mn valence. Mn recovery reached 65.69 % through precipitate collection, and the NH4+-N removal efficiency reached 97 % in the AR. Mn oxidation by algae might promote oxidative removal of NH4+-N. NO3--N and total nitrogen removal efficiencies in the WR reached 82-90 % and 65-87 %, respectively, which was attributed to denitrification. The predominance of the denitrification gene narG in the WR may have driven the efficient nitrate removal. Flavobacterium, Acidovora, Massilia, Arcticibacter, and Acinetobacter were the most abundant genera in the WR and represented dominant denitrifying bacteria in the woodchip microbiome, indicating their important contribution to denitrification. Overall, the combined application of Mn-oxidizing algae and woodchip-denitrifying bioreactors may represent an efficient treatment technology for electrolytic manganese wastewater remediation.

Dissolved organic matter characteristics linked to bacterial community succession and nitrogen removal performance in woodchip bioreactors

Woodchip bioreactors are an eco-friendly technology for removing nitrogen (N) pollution. However, there needs to be more clarity regarding the dissolved organic matter (DOM) characteristics and bacterial community succession mechanisms and their association with the N removal performance of bioreactors. The laboratory woodchip bioreactors were continuously operated for 360 days under three influent N level treatments, and the results showed that the average removal rate of TN was 45.80 g N/(m3·day) when the influent N level was 100 mg N/L, which was better than 10 mg N/L and 50 mg N/L. Dynamic succession of bacterial communities in response to influent N levels and DOM characteristics was an important driver of TN removal rates. Medium to high N levels enriched a copiotroph bacterial module (Module 1) detected by network analysis, including Phenylobacterium, Xanthobacteraceae, Burkholderiaceae, Pseudomonas, and Magnetospirillaceae, carrying N-cycle related genes for denitrification and ammonia assimilation by the rapid consumption of DOM. Such a process can increase carbon limitation to stimulate local organic carbon decomposition to enrich oligotrophs with fewer N-cycle potentials (Module 2). Together, this study reveals that the compositional change of DOM and bacterial community succession are closely related to N removal performance, providing an ecological basis for developing techniques for N-rich effluent treatment.

A systematic review on aquaculture wastewater: Pollutants, impacts, and treatment technology

Aquaculture is the major way to solve the global food sacrcity. As the global population increases, the demand for aquaculture increases. Fish feed, drugs and chemicals, and metabolic waste or mortalities of aquatic organisms also increase, eventually resulting in the production of a large amount of aquaculture wastewater. These aquaculture discharges contain a variety of pollutants, such as conventional pollutants, organic compounds, heavy metals, and biological contaminants, inducing occupational hazards and risks, food security, the environment pollution. Proper wastewater treatment technologies are required to remove hazardous pollutants for minimizing their impacts on environmental and human health. Recirculating aquaculture systems, some biological and physicochemical methods have been applied to remove some pollutants from the aquaculture wastewater, but their efficiency in removing pollutants still requires to be further improved for achieving zero-waste discharge and ensuring sustainable aquaculture development. Meanwhile, sound regulation and legislation needs to be established for ensuring the normal operation of aquaculture industries and the standard discharge of wastewater. This review aims to provide comprehensive information of aquaculture wastewater for the researchers and promote the healthy development of aquaculture.

Orthophosphate uptake onto woodchips in denitrifying bioreactors is enhanced by anoxic-(anaerobic-)oxic cycling

Woodchips are widely used as a low-cost and renewable organic carbon source for denitrifying biofilms in passive nutrient removal systems. One limitation of wood-based biofiltration systems is their relatively poor removal of phosphorus (P) from subsurface drainage and stormwaters, necessitating the use of additional filter media when co-treatment of nitrogen (N) and P is required. Here, we show that anoxic-oxic cycling of woodchip media, which enhances nitrate (NO3-) removal by increasing the mobilization of organic carbon from wood, also improves orthophosphate (Pi) uptake onto woodchips. Orthophosphate removal rates in flow-through woodchip columns ranged from 0 to 34.9 μg PO43- L-1 h-1 under continuously-saturated (anoxic) conditions, and increased to 17.5 to 71.9 μg PO43- L-1 h-1 in columns undergoing drying-rewetting (oxic-anoxic) cycles. The highest Pi removal efficiencies were observed in the first 20 h after reactors were re-flooded, and were concurrent with maxima in polyphosphate kinase (ppk) gene expression by the polyphosphate accumulating organisms (PAOs) Accumulibacter spp. and Pseudomonas spp. Batch experiments confirmed that anoxic-anaerobic-oxic pre-incubation conditions led to orthophosphate uptake onto woodchips as high as 74.9 ± 0.8 mg PO43-/kg woodchip, and batch tests with autoclaved woodchips demonstrated that Pi uptake was due to biological processes and not adsorption. NO3- removal in batch tests was also greatest under oxic incubation conditions, attributed to greater carbon availability in hypoxic to anoxic zones in woodchip biofilms. While further research is needed to elucidate the mechanisms controlling enhanced Pi uptake by woodchip biofilms under anoxic-(anaerobic-)oxic cycling, these results suggest a role for enhanced Pi uptake by PAOs in a nature-based system for treatment of nonpoint source nutrients.

Aerobic denitrifying bacterial community with low C/N ratio remove nitrate from micro-polluted water: Metagenomics unravels denitrification pathways

The efficient nitrogen removal from micro-polluted source water is an international challenge to be solved urgently. However, the inner denitrification mechanism of native aerobic denitrifying bacterial communities in response to carbon scarcity remains relatively unclear. Here, the bacterial community XT6, screened from an oligotrophic reservoir, exhibited aerobic denitrifying capacity under low-carbon environments. Up to 76.79-81.64 % of total organic carbon (TOC) and 51.48-67.60 % of NO3--N were removed by XT6 within 48 h at C/N ratios of 2.0-3.0. Additionally, the nitrogen balance experiments further manifested that 26.27-38.13 % of NO3--N was lost in gaseous form. As the C/N ratio decreased, XT6 tended to generate more extracellular polymeric substances (EPS), with the tightly bound EPS showing the largest increase. Pseudomonas and Variovorax were quite abundant in XT6, constituting 59.69 % and 28.65 % of the total sequences, respectively. Furthermore, metagenomics analysis evidenced that XT6 removed TOC and nitrate mainly through the tricarboxylic acid cycle and aerobic denitrification. Overall, the abovementioned results provide a deeper understanding of the nitrogen metabolic pathways of indigenous aerobic denitrifying bacterial communities with low C/N ratios and offer useful guidance for controlling nitrogen pollution in oligotrophic ecosystems.

Microbial succession and denitrifying woodchip bioreactor performance at low water temperatures

Mining activities are increasingly recognized for contributing to nitrogen (N) pollution and possibly also to emissions of the greenhouse gas nitrous oxide (N2O) due to undetonated, N-based explosives. A woodchip denitrifying bioreactor, installed to treat nitrate-rich leachate from waste rock dumps in northern Sweden, was monitored for two years to determine the spatial and temporal distribution of microbial communities, including the genetic potential for different N transformation processes, in pore water and woodchips and how this related to reactor N removal capacity. About 80 and 65 % of the nitrate was removed during the first and second operational year, respectively. There was a succession in the microbial community over time and in space along the reactor length in both pore water and woodchips, which was reflected in reactor performance. Nitrate ammonification likely had minimal impact on N removal efficiency due to the low production of ammonium and low abundance of the key gene nrfA in ammonifiers. Nitrite and N2O were formed in the bioreactor and released in the effluent water, although direct N2O emissions from the surface was low. That these unwanted reactive N species were produced at different times and locations in the reactor indicate that the denitrification pathway was temporally as well as spatially separated along the reactor length. We conclude that the succession of microbial communities in woodchip denitrifying bioreactors treating mining water develops slowly at low temperature, which impacts reactor performance.

Nutrient transport, shear strength and hydraulic characteristics of topsoils amended with mulch, compost and biosolids

Anthropogenic disturbance of soils can disrupt soil structure, diminish fertility, alter soil chemical properties, and cause erosion. Current remediation practices involve amending degraded urban topsoils lacking in organic matter and nutrition with organic amendments (OA) to enhance vegetative growth. However, the impact of OAs on water quality and structural properties at rates that meet common topsoil organic matter specifications need to be studied and understood. This study tested three commonly available OAs: shredded wood mulch, leaf-based compost, and class A Exceptional Quality stabilized sewage sludge (or biosolids) for nutrient (nitrogen and phosphorus) water quality, soil shear strength, and hydraulic properties, through two greenhouse tub studies. Findings showed that nitrogen losses to leachate were greater in the biosolids amended topsoils compared to leaf-compost, mulch amended topsoils, and control treatments. Steady-state mean total nitrogen (N) concentrations from biosolids treatment exceeded typical highway stormwater concentrations by at least 25 times. Soil total N content combined with the carbon:nitrogen ratio were identified to be the governing properties of N leaching in soils. Study soils, irrespective of the type of amendment, reduced the applied (tap) water phosphorus (P) concentration of ∼0.3 mg-P/L throughout the experiment. Contrary to the effects on N leaching, P was successfully retained by the biosolids amendment, due to the presence of greater active iron contents. A breakthrough mechanism for P was observed in leaf compost amended soil, where the effluent concentrations of P continued to increase with each rainfall application, possibly due to an saturation of soil adsorption sites. The addition of OAs also improved the strength and hydraulic properties of soils. The effective interlocking mechanisms between the soil and OA surfaces could provide soil its required strength and stability, particularly on slopes. OAs also improved soil fertility to promote turf growth. Presence of vegetative root zones can further reinforce the soil and control erosion.

Impacts of biostimulation and bioaugmentation on woodchip bioreactor microbiomes

IMPORTANCE

Nitrate pollution is a serious problem in agricultural areas in the U.S. Midwest and other parts of the world. Woodchip bioreactor is a promising technology that uses microbial denitrification to remove nitrate from agricultural subsurface drainage, although the reactor's nitrate removal performance is limited under cold conditions. This study showed that the inoculation of cold-adapted denitrifiers (i.e., bioaugmentation) and the addition of labile carbon (i.e., biostimulation) can influence the microbial populations and enhance the reactor's performance under cold conditions. This finding will help establish a strategy to mitigate nitrate pollution.

Oxic-anoxic cycling promotes coupling between complex carbon metabolism and denitrification in woodchip bioreactors

Denitrifying woodchip bioreactors (WBRs) are increasingly used to manage the release of non-point source nitrogen (N) by stimulating microbial denitrification. Woodchips serve as a renewable organic carbon (C) source, yet the recalcitrance of organic C in lignocellulosic biomass causes many WBRs to be C-limited. Prior studies have observed that oxic-anoxic cycling increased the mobilization of organic C, increased nitrate (NO3 - ) removal rates, and attenuated production of nitrous oxide (N2 O). Here, we use multi-omics approaches and amplicon sequencing of fungal 5.8S-ITS2 and prokaryotic 16S rRNA genes to elucidate the microbial drivers for enhanced NO3 - removal and attenuated N2 O production under redox-dynamic conditions. Transient oxic periods stimulated the expression of fungal ligninolytic enzymes, increasing the bioavailability of woodchip-derived C and stimulating the expression of denitrification genes. Nitrous oxide reductase (nosZ) genes were primarily clade II, and the ratio of clade II/clade I nosZ transcripts during the oxic-anoxic transition was strongly correlated with the N2 O yield. Analysis of metagenome-assembled genomes revealed that many of the denitrifying microorganisms also have a genotypic ability to degrade complex polysaccharides like cellulose and hemicellulose, highlighting the adaptation of the WBR microbiome to the ecophysiological niche of the woodchip matrix.

Denitrifying Woodchip Bioreactors: A Microbial Solution for Nitrate in Agricultural Wastewater-A Review

Nitrate (NO3-) is highly water-soluble and considered to be the main nitrogen pollutants leached from agricultural soils. Its presence in aquatic ecosystems is reported to cause various environmental and public health problems. Bioreactors containing microbes capable of transforming NO3- have been proposed as a means to remediate contaminated waters. Woodchip bioreactors (WBRs) are continuous flow, reactor systems located below or above ground. Below ground systems are comprised of a trench filled with woodchips, or other support matrices. The nitrate present in agricultural drainage wastewater passing through the bioreactor is converted to harmless dinitrogen gas (N2) via the action of several bacteria species. The WBR has been suggested as one of the most cost-effective NO3--removing strategy among several edge-of-field practices, and has been shown to successfully remove NO3- in several field studies. NO3- removal in the WBR primarily occurs via the activity of denitrifying microorganisms via enzymatic reactions sequentially reducing NO3- to N2. While previous woodchip bioreactor studies have focused extensively on its engineering and hydrological aspects, relatively fewer studies have dealt with the microorganisms playing key roles in the technology. This review discusses NO3- pollution cases originating from intensive farming practices and N-cycling microbial metabolisms which is one biological solution to remove NO3- from agricultural wastewater. Moreover, here we review the current knowledge on the physicochemical and operational factors affecting microbial metabolisms resulting in removal of NO3- in WBR, and perspectives to enhance WBR performance in the future.

Daphnia magna as biological harvesters for green microalgae grown on recirculated aquaculture system effluents

The sustainability of recycling aquaculture systems (RAS) is challenged by nutrient discharges, which cause water eutrophication. Efficient treatments for RAS effluents are needed to mitigate its environmental impacts. Microalgae assimilate nutrients and dissolved carbon into microbial biomass with value as feed or food ingredient. However, they are difficult to harvest efficiently. Daphnia magna is an efficient filter feeder that grazes on microalgae at high rates and serves as valuable fish feed. Combining nutrient removal by microalgae and biomass harvesting by D. magna could be a cost-effective solution for wastewater valorization. Nutrient removal from unsterilized aquaculture wastewater was evaluated using the microalgae species Chlorella vulgaris, Scenedesmus dimorphus, and Haematococcus pluvialis. The first two algae were subsequently harvested using D. magna as a grazer, while H. pluvialis failed to grow stably. All phosphorus was removed, while only 50-70 % nitrogen was recovered, indicating phosphorus limitation. Shortening the hydraulic retention time (HRT) or phosphorus dosing resulted in increased nitrogen removal. C. vulgaris cultivation was unstable at 3 days HRT or when supplied with extra phosphorus at 5 days HRT. D. magna grew on produced algae accumulating protein at 20-30 % of dry weight, with an amino acid profile favorable for use as high value fish feed. Thus, this study demonstrates the application of a two steps multitrophic process to assimilate residual nutrients into live feeds suitable for fish.

Denitrification efficiency, microbial communities and metabolic mechanisms of corn cob hydrolysate as denitrifying carbon source

In this study, the denitrification efficacy of corn cob hydrolysate (CCH) was compared and analyzed with that of glucose and acetate to determine its feasibility as an additional carbon source, and its metabolic mechanism as a denitrification carbon source was investigated in depth. By constructing a denitrification reactor, it was found that the TN removal rate exceeded 97% and the effluent COD remained below 70 mg/L during the stable operation with CCH as the carbon source, and the denitrification effect was comparable to that of the glucose stage (GS) and the acetate stage (AS). The analysis of the microbial community showed that the dominant phylum was Proteobacteria and Bacteroidota, where the abundance of Bacteroidota in the hydrolysate stage (HS) (24.37%) was significantly higher than that of GS (4.89%) and AS (11.93%). And the analysis at the genus level showed the presence of a large number of genera of organic matter hydrolysis and acid production in HS that were almost absent in other stages, such as Paludibacter (12.83%), Gracilibacteria (4.27%), f__Prolixibacteraceae_Unclassified (2.94%). In addition, the higher fatty acid metabolism and lower sugar metabolism of HS during carbon metabolism were similar to the ratio of AS, suggesting that CCH was mainly fermented to acids and then involved in the tricarboxylic acid (TCA) cycle. During nitrogen metabolism, the high relative abundance of narG, nirS, and nosZ ensured the denitrification process. The results of this study were expected to provide a theoretical basis and data support for promoting denitrification from novel carbon sources.

Field evaluation of four denitrifying woodchip bioreactors for nitrogen removal in eastern South Dakota, United States

Edge-of-field practices such as denitrifying woodchip bioreactors can be used to improve the water quality of agricultural effluents. This study evaluated the effectiveness of four field-scale woodchip bioreactors in removing nitrate‑nitrogen (nitrate-N) from subsurface drainage in eastern South Dakota. Four woodchip bioreactors were installed and monitored between 2014 and 2016 near Arlington, Baltic, Hartford, and Montrose, South Dakota. Results showed that reduction in nitrate-N concentration for the four bioreactors ranged from 7 % to 100 %, corresponding to removal rates of 5 to 27 g N/m³/day for the four bioreactors during the study period. Average Nitrate-N load reduction in the four bioreactors studied ranged from 39 % to 89 % during the study period. Reduction of nitrate-N in the four bioreactors decreased, on average, by 30 % when temperature dropped below 12 °C during the study period. Flow rate and hydraulic retention time (HRT) also influenced nitrate-N removal in the bioreactors as samples collected immediately following rainfall events showed high nitrate-N load removal compared to samples collected later after the rainfall events during the study period.

Occurrence, source tracking and removal of antibiotics in recirculating aquaculture systems (RAS) in southern China

The recirculating aquaculture system (RAS) has attracted much attention in China as a way to rapidly transform and upgrade aquaculture ponds to realize zero-emissions of pollutants in aquaculture tail water. Tail water purification ponds (TWPPs) play an important role in the treatment of aquaculture wastewater. However, until now, there have been few reports on the occurrence of antibiotics in RAS and the removal of antibiotics from the TWPPs of RAS. Therefore, this study focused on the occurrence of antibiotics in a typical ecological RAS. For comparison, the same measurements were simultaneously carried out in nearby open aquaculture ponds and rivers. The pollution level and spatial distribution of antibiotics in the RAS and the removal of antibiotics in the TWPPs were explored. The results showed that (1) eleven and twelve antibiotics were detected in water and sediment samples in the RAS, respectively, but no antibiotics were found in fish muscles and feed. Erythromycin (ERY), lincomycin (LIN), and ciprofloxacin (CFX) were the three main types of antibiotics found in water and sediment samples. (2) The TWPPs of the RAS can effectively remove antibiotics in aquaculture water. The antibiotic concentration in recirculating aquaculture ponds of the RAS was as high as 180 ng/L. After treatments in the TWPPs, the antibiotic concentration of aquaculture water decreased to 81.6 ng/L (3) The antibiotic concentrations in recirculating aquaculture ponds (25.2-180 ng/L) were lower than those in the nearby open aquaculture ponds (126-267.3 ng/L), and the concentration of antibiotics in the sediments of recirculating aquaculture ponds was up to 22.9 ng/g, while that in TWPPs was as high as 56.1 ng/g. In conclusion, the antibiotic residues in the RAS were low after antibiotics were banned in feed in China, and the removal of antibiotics in the TWPPs was more pronounced. Furthermore, cross-contamination was found between the RAS, surrounding open aquaculture ponds and the river, and the water supply of the RAS was likely to be the main contributor of antibiotics in the aquaculture environments. This study can help the government formulate discharge standards for antibiotics in aquaculture and also provide a reference for the transformation and upgrading of aquaculture ponds to achieve a zero-emission aquaculture mode.

Efficient nitrogen removal from onsite wastewater by a novel continuous flow biofilter

Soil-based passive biofiltration system is an economically feasible technology for nitrogen removal from onsite wastewater. However, the conventional design requires a large system footprint with limited treatment capacity. In this study, a novel continuous flow biofilter (CFB) with adjustable recirculation and continuous flow pattern was developed for onsite wastewater treatment with a small footprint. Efficient total nitrogen removal (80.1-97.5%) was observed at various hydraulic loadings (0.03-0.12 m³ m^-2 d^-1), nitrogen loadings (1.1-8.6 g N m^-2 d^-1) and recycle ratios (2-3) when treating septic tank effluent (STE), with low effluent TN (0.7-13.6 mg N L^-1). Nitrous oxide was observed in the denitrification effluent indicating incomplete denitrification at elevated dissolved oxygen levels (3.3-5.8 mg L^-1). Nitrogen removal rate (2.9-7.0 g N m^-2 d^-1) and ammonium removal rate (2.4-7.2 g N m^-2 d^-1) were positively correlated with nitrogen loadings increase (1.1-8.6 g N m^-2 d^-1) but were not significantly impacted by the hydraulic loading rate change (0.08-0.12 m³ m^-2 d^-1). The total biomass abundance and nitrifying microorganisms decreased significantly as the nitrification columns depth increased, while homogeneous microbial distribution was observed in the denitrification columns. The abundance of ammonium oxidizing archaea (AOA) increased significantly at increased hydraulic and nitrogen loading rate, while the ammonium oxidizing bacteria (AOB) abundance remained steady. The abundance of functional genes involved in denitrification process (nirS, nirK and nosZ) responded differently when hydraulic and nitrogen loading rate changes. Collectively, this study suggested the CFB could efficiently remove nitrogen from onsite wastewater with fluctuating influent compositions and various hydraulic loadings.

Nitrogen Removal Capacity of Microbial Communities Developing in Compost- and Woodchip-Based Multipurpose Reactive Barriers for Aquifer Recharge With Wastewater

Global water supplies are threatened by climate changes and the expansion of urban areas, which have led to an increasing interest in nature-based solutions for water reuse and reclamation. Reclaimed water is a possible resource for recharging aquifers, and the addition of an organic reactive barrier has been proposed to improve the removal of pollutants. There has been a large focus on organic pollutants, but less is known about multifunctional barriers, that is, how barriers also remove nutrients that threaten groundwater ecosystems. Herein, we investigated how compost- and woodchip-based barriers affect nitrogen (N) removal in a pilot soil aquifer treatment facility designed for removing nutrients and recalcitrant compounds by investigating the composition of microbial communities and their capacity for N transformations. Secondary-treated, ammonium-rich wastewater was infiltrated through the barriers, and the changes in the concentration of ammonium, nitrate, and dissolved organic carbon (DOC) were measured after passage through the barrier during 1 year of operation. The development and composition of the microbial community in the barriers were examined, and potential N-transforming processes in the barriers were quantified by determining the abundance of key functional genes using quantitative PCR. Only one barrier, based on compost, significantly decreased the ammonium concentration in the infiltrated water. However, the reduction of reactive N in the barriers was moderate (between 21 and 37%), and there were no differences between the barrier types. All the barriers were after 1 year dominated by members of Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria, although the community composition differed between the barriers. Bacterial classes belonging to the phylum Chloroflexi showed an increased relative abundance in the compost-based barriers. In contrast to the increased genetic potential for nitrification in the compost-based barriers, the woodchip-based barrier demonstrated higher genetic potentials for denitrification, nitrous oxide reduction, and dissimilatory reduction of nitrate to ammonium. The barriers have previously been shown to display a high capacity to degrade recalcitrant pollutants, but in this study, we show that most barriers performed poorly in terms of N removal and those based on compost also leaked DOC, highlighting the difficulties in designing barriers that satisfactorily meet several purposes.

Anthropogenic nitrate attenuation versus nitrous oxide release from a woodchip bioreactor

Nitrogen loss via overland flow from agricultural land use is a global threat to waterways. On-farm denitrifying woodchip bioreactors can mitigate NO₃^- exports by increasing denitrification capacity. However, denitrification in sub-optimal conditions releases the greenhouse gas nitrous oxide (N₂O), swapping the pollution from aquatic to atmospheric reservoirs. Here, we assess NO₃^--N removal and N₂O emissions from a new edge-of-field surface-flow bioreactor during ten rain events on intensive farming land. Nitrate removal rates (NRR) varied between 5.4 and 76.2 g NO₃^--N m^-3 wetted woodchip d^-1 with a mean of 30.3 ± 7.3 g NO₃^--N m^-3. The nitrate removal efficiency (NRE) was ∼73% in ideal hydrological conditions and ∼18% in non-ideal conditions. The fraction of NO₃^--N converted to N₂O (rN₂O) in the bioreactor was ∼3.3 fold lower than the expected 0.75% IPCC emission factor. We update the global bioreactor estimated Q₁₀ (NRR increase every 10 °C) from a recent meta-analysis with previously unavailable data to >20 °C, yielding a new global Q₁₀ factor of 3.1. Mean N₂O CO₂-eq emissions (431.9 ± 125.4 g CO₂-eq emissions day^-1) indicate that the bioreactor was not significantly swapping aquatic NO₃^- for N₂O pollution. Our estimated NO₃^--N removal from the bioreactor (9.9 kg NO₃^--N ha^-1 yr^-1) costs US$13.14 per kg NO₃^--N removed and represents ∼30% NO₃^--N removal when incorporating all flow and overflow events. Overall, edge-of-field surface-flow bioreactors seem to be a cost-effective solution to reduce NO₃^--N runoff with minor pollution swapping to N₂O.

Low temperature Moving Bed Bioreactor denitrification as mitigation measure to reduce agricultural nitrate losses

The negative impact of agriculture on the quality of local water streams is widely recognized. Fertilizer residues not taken up by the crops leach into the drainage water and enter the surface water, resulting in eutrophication. Despite various initiatives to prevent this leaching by optimizing fertilizer schemes, the desired effect was not achieved, and the focus has shifted to denitrifying end-of-pipe techniques. Because the available area for installing such treatment systems is often limited, the development of intensified systems is a trend that has emerged recently. In this scope, the main goal of this study was therefore to investigate the suitability of a denitrifying Moving Bed Bioreactor (MBBR) as a low footprint technology, which can compete with conventional technologies. Two parallel lab-scale pilot MBBRs, one at low temperature and one at ambient temperature, were operated for 850 days to investigate the effectiveness and robustness under changing process parameters (hydraulic retention time (HRT), temperature, shutdown). Eventually, the system was scaled up to a full-scale installation and monitored during a full drainage season in the field. The pilot-scale MBBRs achieved removal efficiencies above 90% under optimal conditions (high C/N ratio and minimal HRT of 8 h), even while operating at low temperatures. The robustness of the system was also demonstrated by the immediate start-up after a shutdown period of 220 days. Overall, the full-scale MBBR treated 2910.1 m³ drainage water and removed approximately 59 kg NO₃-N. Unfortunately, the average removal efficiency, i.e., 70%, was lower than the lab-scale system, but by intensifying the mixing in the MBBR, improved results were obtained. Nitrite accumulation was furthermore also prevented.

Comparison of microbial communities in replicated woodchip bioreactors

Denitrification in woodchip bioreactors is a microbial process, but the effects of variations in bioreactors operation on microbial community structure are not well understood. Here, our goals were to understand hydraulic retention time (HRT) as a factor that influences woodchip bioreactor microbial community variation and structure in replicated field bioreactors and to evaluate relationships between microbial community membership and marker genes for denitrification. We used a combination of quantitative polymerase chain reaction of nirS, nirK, nosZI, and nosZII and 16S rRNA amplicon sequencing to characterize the microbial communities of nine pilot-scale woodchip bioreactors located at Iowa State University. Our results showed dynamic microbial communities but with persistent taxa between two sampling years and three HRTs. Similarities between functional gene copy numbers across sampling year and HRT indicate that the potential for denitrification is conserved despite differences in the microbial communities. These results are evidence that there are specific and persistent taxa within replicated bioreactors. Woodchip bioreactor microbial community membership is recommended to be the focus of future studies to better understand the relationship between microbial community functions and bioreactor management.

Microbially facilitated nitrogen cycling in tropical corals

Tropical scleractinian corals support a diverse assemblage of microbial symbionts. This 'microbiome' possesses the requisite functional diversity to conduct a range of nitrogen (N) transformations including denitrification, nitrification, nitrogen fixation and dissimilatory nitrate reduction to ammonium (DNRA). Very little direct evidence has been presented to date verifying that these processes are active within tropical corals. Here we use a combination of stable isotope techniques, nutrient uptake calculations and captured metagenomics to quantify rates of nitrogen cycling processes in a selection of tropical scleractinian corals. Denitrification activity was detected in all species, albeit with very low rates, signifying limited importance in holobiont N removal. Relatively greater nitrogen fixation activity confirms that corals are net N importers to reef systems. Low net nitrification activity suggests limited N regeneration capacity; however substantial gross nitrification activity may be concealed through nitrate consumption. Based on nrfA gene abundance and measured inorganic N fluxes, we calculated significant DNRA activity in the studied corals, which has important implications for coral reef N cycling and warrants more targeted investigation. Through the quantification and characterisation of all relevant N-cycling processes, this study provides clarity on the subject of tropical coral-associated biogeochemical N-cycling.

Denitrifying bioreactor microbiome: Understanding pollution swapping and potential for improved performance

Denitrifying woodchip bioreactors are a best management practice to reduce nitrate-nitrogen (NO₃ -N) loading to surface waters from agricultural subsurface drainage. Their effectiveness has been proven in many studies, although variable results with respect to performance indicators have been observed. This paper serves the purpose of synthesizing the current state of the science in terms of the microbial community, its impact on the consistency of bioreactor performance, and its role in the production of potential harmful by-products including greenhouse gases, sulfate reduction, and methylmercury. Microbial processes other than denitrification have been observed in these bioreactor systems, including dissimilatory nitrate reduction to ammonia (DNRA) and anaerobic ammonium oxidation (anammox). Specific gene targets for denitrification, DNRA, anammox, and the production of harmful by-products are identified from bioreactor studies and other environmentally relevant systems for application in bioreactor studies. Lastly, cellulose depletion has been observed over time via increasing ligno-cellulose indices, therefore, the microbial metabolism of cellulose is an important function for bioreactor performance and management. Future work should draw from the knowledge of soil and wetland ecology to inform the study of bioreactor microbiomes.

Microbial communities in full-scale woodchip bioreactors treating aquaculture effluents

Woodchip bioreactors are being successfully applied to remove nitrate from commercial land-based recirculating aquaculture system (RAS) effluents. In order to understand and optimize the overall function of these bioreactors, knowledge on the microbial communities, especially on the microbes with potential for production or mitigation of harmful substances (e.g. hydrogen sulfide; H₂S) is needed. In this study, we quantified and characterized bacterial and fungal communities, including potential H₂S producers and consumers, using qPCR and high throughput sequencing of 16S rRNA gene. We took water samples from bioreactors and their inlet and outlet, and sampled biofilms growing on woodchips and on the outlet of the three full-scale woodchip bioreactors treating effluents of three individual RAS. We found that bioreactors hosted a high biomass of both bacteria and fungi. Although the composition of microbial communities of the inlet varied between the bioreactors, the conditions in the bioreactors selected for the same core microbial taxa. The H₂S producing sulfate reducing bacteria (SRB) were mainly found in the nitrate-limited outlets of the bioreactors, the main groups being deltaproteobacterial Desulfobulbus and Desulfovibrio. The abundance of H₂S consuming sulfate oxidizing bacteria (SOB) was 5-10 times higher than that of SRB, and SOB communities were dominated by Arcobacter and other genera from phylum Epsilonbacteraeota, which are also capable of autotrophic denitrification. Indeed, the relative abundance of potential autotrophic denitrifiers of all denitrifier sequences was even 54% in outlet water samples and 56% in the outlet biofilm samples. Altogether, our results show that the highly abundant bacterial and fungal communities in woodchip bioreactors are shaped through the conditions prevailing within the bioreactor, indicating that the bioreactors with similar design and operational settings should provide similar function even when conditions in the preceding RAS would differ. Furthermore, autotrophic denitrifiers can have a significant role in woodchip biofilters, consuming potentially produced H₂S and removing nitrate, lengthening the operational age and thus further improving the overall environmental benefit of these bioreactors.

Thawing Yedoma permafrost is a neglected nitrous oxide source

In contrast to the well-recognized permafrost carbon (C) feedback to climate change, the fate of permafrost nitrogen (N) after thaw is poorly understood. According to mounting evidence, part of the N liberated from permafrost may be released to the atmosphere as the strong greenhouse gas (GHG) nitrous oxide (N₂O). Here, we report post-thaw N₂O release from late Pleistocene permafrost deposits called Yedoma, which store a substantial part of permafrost C and N and are highly vulnerable to thaw. While freshly thawed, unvegetated Yedoma in disturbed areas emit little N₂O, emissions increase within few years after stabilization, drying and revegetation with grasses to high rates (548 (133–6286) μg N m⁻² day⁻¹; median with (range)), exceeding by 1–2 orders of magnitude the typical rates from permafrost-affected soils. Using targeted metagenomics of key N cycling genes, we link the increase in in situ N₂O emissions with structural changes of the microbial community responsible for N cycling. Our results highlight the importance of extra N availability from thawing Yedoma permafrost, causing a positive climate feedback from the Arctic in the form of N₂O emissions.

During permafrost thaw, nitrogen can be released as the greenhouse gas nitrous oxide, but the magnitude of this flux is unknown. Nitrous oxide emissions from ice-rich permafrost deposits are reported here, showing that emissions increase after thawing and stabilization and could represent an unappreciated positive climate feedback in the Arctic.

Microbiome Structure and Function in Woodchip Bioreactors for Nitrate Removal in Agricultural Drainage Water

Woodchip bioreactors are increasingly used to remove nitrate (NO₃^–) from agricultural drainage water in order to protect aquatic ecosystems from excess nitrogen. Nitrate removal in woodchip bioreactors is based on microbial processes, but the microbiomes and their role in bioreactor efficiency are generally poorly characterized. Using metagenomic analyses, we characterized the microbiomes from 3 full-scale bioreactors in Denmark, which had been operating for 4–7 years. The microbiomes were dominated by Proteobacteria and especially the genus Pseudomonas, which is consistent with heterotrophic denitrification as the main pathway of NO₃^– reduction. This was supported by functional gene analyses, showing the presence of the full suite of denitrification genes from NO₃^– reductases to nitrous oxide reductases. Genes encoding for dissimilatory NO₃^– reduction to ammonium were found only in minor proportions. In addition to NO₃^– reducers, the bioreactors harbored distinct functional groups, such as lignocellulose degrading fungi and bacteria, dissimilatory sulfate reducers and methanogens. Further, all bioreactors harbored genera of heterotrophic iron reducers and anaerobic iron oxidizers (Acidovorax) indicating a potential for iron-mediated denitrification. Ecological indices of species diversity showed high similarity between the bioreactors and between the different positions along the flow path, indicating that the woodchip resource niche was important in shaping the microbiome. This trait may be favorable for the development of common microbiological strategies to increase the NO₃^– removal from agricultural drainage water.

New insight to the role of microbes in the methane exchange in trees: evidence from metagenomic sequencing

Methane (CH₄ ) exchange in tree stems and canopies and the processes involved are among the least understood components of the global CH₄ cycle. Recent studies have focused on quantifying tree stems as sources of CH₄ and understanding abiotic CH₄ emissions in plant canopies, with the role of microbial in situ CH₄ formation receiving less attention. Moreover, despite initial reports revealing CH₄ consumption, studies have not adequately evaluated the potential of microbial CH₄ oxidation within trees. In this paper, we discuss the current level of understanding on these processes. Further, we demonstrate the potential of novel metagenomic tools in revealing the involvement of microbes in the CH₄ exchange of plants, and particularly in boreal trees. We detected CH₄ -producing methanogens and novel monooxygenases, potentially involved in CH₄ consumption, in coniferous plants. In addition, our field flux measurements from Norway spruce (Picea abies) canopies demonstrate both net CH₄ emissions and uptake, giving further evidence that both production and consumption are relevant to the net CH₄ exchange. Our findings, together with the emerging diversity of novel CH₄ -producing microbial groups, strongly suggest microbial analyses should be integrated in the studies aiming to reveal the processes and drivers behind plant CH₄ exchange.

Aquaculture industry: Supply and demand, best practices, effluent and its current issues and treatment technology

The aquaculture industry has become increasingly important and is rapidly growing in terms of providing a protein food source for human consumption. With the increase in the global population, demand for aquaculture is high and is estimated to reach 62% of the total global production by 2030. In 2018, it was reported that the demand for aquaculture was 46% of the total production, and with the current positive trends, it may be possible to increase tremendously in the coming years. China is still one of the main players in global aquaculture production. Due to high demand, aquaculture production generates large volumes of effluent, posing a great danger to the environment. Aquaculture effluent comprises solid waste and dissolved constituents, including nutrients and contaminants of emerging concern, thereby bringing detrimental impacts such as eutrophication, chemical toxicity, and food insecurity. Waste can be removed through culture systems, constructed wetlands, biofloc, and other treatment technologies. Some methods have the potential to be applied as zero-waste discharge treatment. Thus, this article analyses the supply and demand for aquaculture products, the best practices adopted in the aquaculture industry, effluent characteristics, current issues, and effluent treatment technology.

Metagenomic analyses of microbial structure and metabolic pathway in solid-phase denitrification systems for advanced nitrogen removal of wastewater treatment plant effluent: A pilot-scale study

The pilot-scale solid-phase denitrification systems supporting with poly(3-hydroxybutyrateco-3-hydroxyvalerate) (PHBV) and PHBV-sawdust were constructed for advanced nitrogen removal from wastewater treatment plants (WWTPs) effluent, and the impacts of biomass blended carbon source on microbial community structure, functions and metabolic pathways were analyzed by metagenomic sequencing. PHBV-sawdust system achieved the optimal denitrification performance with higher NO₃^--N removal efficiency (96.58%), less DOC release (9.00 ± 4.16 mg L ^- 1) and NH₄⁺-N accumulation (0.37 ± 0.32 mg L ^- 1) than PHBV system. Metagenomic analyses verified the significant differences in the structure of microbial community between systems and the presence of four anaerobic anammox bacteria. Compared with PHBV, the utilization of PHBV-sawdust declined the relative abundance of genes encoding enzymes for NH₄⁺-N generation and increased the relative abundance of genes encoding enzymes involved in anammox, which contributed to the reduction of NH₄⁺-N in effluent. What's more, the encoding gene for electrons generation in glycolysis metabolism obtained higher relative abundance in PHBV-sawdust system. A variety of lignocellulase encoding genes were significantly enriched in PHBV-sawdust system, which guaranteed the stable carbon supply and continuous operation of system. The results of this study are expected to provide theoretical basis and data support for the promotion of solid-phase denitrification.

Carbon availability shifts the nitrogen removal pathway and microbial community in biofilm airlift reactor

This study investigated the response of nitrogen removal performance and microbial community to different carbon composites in biofilm airlift reactors for wastewater treatment. Three reactors were filled with poly (butylene succinate) and bamboo powder composite at the blending ratio of 9:1, 1:1 and 1:9. Increasing the component of bamboo powder in the carrier reduced the carbon availability and had an adverse effect on nitrate removal efficiency. However, bamboo powder improved the ammonia removal rate which mainly through autotrophic nitrification. Three reactors exhibited distinct microbial compositions in both bacterial and fungal diversity. High inclusion of bamboo power decreased the relative abundance of denitrifiers Denitromonas and increased the relative abundance of nitrifiers, including Nitromonas, Nitrospina and Nitrospira. Moreover, correlation network revealed a competitive interaction between the taxa responsible for ammonia removal and nitrate removal processes. Those results indicated the feasibility of steering nitrogen removal pathway through carrier formulation in wastewater treatment.

Substrate type determines microbial activity and community composition in bioreactors for nitrate removal by denitrification at low temperature

High levels of nitrogen originating from blasting operations, for example at mining sites or quarries, risk contaminating water bodies through leaching from waste rock dumps. Woodchip bioreactors can be a simple and cost-effective way of reducing nitrate concentrations in the leachate. In this study we investigated how bottle sedge, barley straw, and pine woodchips used as electron donors for denitrification influenced microbial community composition and nitrate removal in lab-scale bioreactors during 270 days. The reactors were operated to ensure that nitrate was never limiting and to achieve similar nitrate removal (%). Distinct bacterial communities developed due to the different substrates, as determined by sequencing of the 16S rRNA gene. Sedge and straw reactors shared more taxa with each other than with woodchips and throughout the experimental period, sedge and straw were more diverse than woodchips. Cellulose degrading bacteria like Fibrobacteres and Verrucomicrobia were detected in the substrates after 100-150 days of operation. Nitrate removal rates were highest in the sedge and straw reactors. After initial fluctuations, these reactors removed 5.1-6.3 g N m^-3 water day^-1, which was 3.3-4.4 times more than in the woodchip reactors. This corresponded to 48%, 42%, and 44% nitrate removal for the sedge, straw, and woodchip reactors respectively. The functional communities were characterized by quantitative PCR and denitrification was the major nitrate removing process based on genetic potential and water chemistry, although sedge and straw developed a capacity for ammonification. Gene ratios suggested that denitrification was initially incomplete and terminating with nitrous oxide. An increase in abundances of nitrous oxide reducing capacity in all substrate types towards the end increased the potential for less emissions of the greenhouse gas nitrous oxide.