Assessing and modeling biocatalysis in field denitrification beds reveals key influencing factors for future constructions

Microbial diversity and gene abundance in denitrifying bioreactors: A comparison of the woodchip surface biofilm versus the interior wood matrix

Excessive amounts of nitrogen (N) and phosphorus (P) can lead to eutrophication in water sources. Woodchip bioreactors have shown success in removing N from agricultural runoff, but less is known regarding P removal. Woodchip bioreactors are subsurface basins filled with woodchips installed downgradient of agricultural land to collect and treat drainage runoff. Microorganisms use the woodchips as a carbon (C) source to transform N in the runoff, with unresolved biological impacts on P. This study aims to explore microbial communities present in the bioreactor and determine whether milling woodchips to probe the microbial communities within them reveals hidden microbial diversities or potential activities. Metagenomic sequencing and bioinformatic analyses were performed on six woodchip samples (i.e., three unmilled and three milled) collected from a 10-year-old woodchip bioreactor treating agricultural tile drainage. All samples had similar DNA purity, yield, quality, and microbial diversity regardless of milling. However, when sequences were aligned against various protein libraries, our results indicated greater relative abundance of denitrification and P transformation proteins on the outside of the woodchips (unmilled), while the interior of woodchips (milled) exhibited more functional gene abundance for carbohydrate breakdown. Thus, it may be important to characterize microbial communities both within woodchips, and on woodchip surfaces, to gain a more holistic understanding of coupled biogeochemical cycles on N, P, and C in woodchip bioreactors. Based on these findings, we advise that future microbial research on woodchips (and potentially other permeable organic materials) examine both the surface biofilm and the interior organic material during initial studies. Once researchers determine where specific proteins or enzymes of interest are most prevalent, subsequent studies may then focus on either one or both aspects, as needed.

Beneficial applications of biofilms

Many microorganisms live in the form of a biofilm. Although they are feared in the medical sector, biofilms that are composed of non-pathogenic organisms can be highly beneficial in many applications, including the production of bulk and fine chemicals. Biofilm systems are natural retentostats in which the biocatalysts can adapt and optimize their metabolism to different conditions over time. The adherent nature of biofilms allows them to be used in continuous systems in which the hydraulic retention time is much shorter than the doubling time of the biocatalysts. Moreover, the resilience of organisms growing in biofilms, together with the potential of uncoupling growth from catalytic activity, offers a wide range of opportunities. The ability to work with continuous systems using a potentially self-advancing whole-cell biocatalyst is attracting interest from a range of disciplines, from applied microbiology to materials science and from bioengineering to process engineering. The field of beneficial biofilms is rapidly evolving, with an increasing number of applications being explored, and the surge in demand for sustainable and biobased solutions and processes is accelerating advances in the field. This Review provides an overview of the research topics, challenges, applications and future directions in beneficial and applied biofilm research.

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.

Nitrate removal and environmental side-effects controlled by hydraulic residence time in woodchip bioreactors treating cold agricultural drainage water

Denitrifying woodchip bioreactors (WBRs) remove nitrate (NO 3 - ) from agricultural drainage water at field-scale, but their efficacy at cold temperatures remains uncertain. This study shows how hydraulic residence time (HRT) controls NO 3 - removal and environmental side-effects of WBRs at low water temperature under pilot-scale conditions with controlled operation of nine WBRs (94 dm3). Hydraulic properties were assessed by a bromide tracer test, and NO 3 - removal, emissions of nitrous oxide (N2O) and methane (CH4), and losses of dissolved organic carbon (DOC) were measured at HRTs of 5-30 h. Inlet NO 3 - concentrations were increasingly reduced at higher HRTs. The relationship between HRT and the efficiency (%) of NO 3 - removal was linear (R a d j 2  = 0.94), while the relationship between HRT and NO 3 - reduction rates (NRR) was logistic (R a d j 2  = 0.88). Gaseous emissions of N2O were equally low at HRTs of 10-30 h, but higher at 5 h (P < 0.05). Methane fluxes were small, but with consistent emissions at HRTs of 20-30 h and uptake at 5-15 h. HRT had limited effect on effluent DOC concentrations, but strong effect on mass losses that were five-fold higher (320 mg L-1) at the HRT of 5 h than at 30 h. In summary, at cold temperatures HRTs of ≤ 20 h resulted in suboptimal NRR, accelerating DOC losses, and increased risk of N2O losses at least below a threshold HRT of 5-10 h. HRTs of 20-30 h gave maximal NRR, smallest losses of DOC and N2O, but an increased risk of CH4 emissions.

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.

Climate change effects on denitrification performance of woodchip bioreactors treating agricultural tile drainage

Denitrifying woodchip bioreactors (WBRs) are a nature-based technology that are increasingly used to control nonpoint source nitrate (NO3-) pollution in agricultural catchments. The treatment effectiveness of WBRs depends on temperature and hydraulic retention time (HRT), both of which are affected by climate change. Warmer temperatures will increase microbial denitrification rates, but the extent to which the resulting benefits to treatment performance may be offset by intensified precipitation and shorter HRTs is not clear. Here, we use three years of monitoring data from a WBR in Central New York State to train an integrated hydrologic-biokinetic model describing links among temperature, precipitation, bioreactor discharge, denitrification kinetics, and NO3- removal efficiencies. Effects of climate warming are assessed by first training a stochastic weather generator with eleven years of weather data from our field site, and then adjusting the distribution of precipitation intensities according to the Clausius-Clapeyron relationship between water vapor and temperature. Modeling results indicate, in our system, faster denitrification rates will outweigh the influence of intensified precipitation and discharge under warming, leading to net improvements in NO3- load reductions. Median cumulative NO3- load reductions at our study site from May - October are projected to increase from 21.7% (interquartile range 17.4%-26.1%) under baseline hydro-climate to 41.0% (interquartile range 32.6-47.1%) with a + 4 °C change in mean air temperature. This improved performance under climate warming is driven by strong nonlinear dependence of NO3- removal rates on temperature. Temperature sensitivity may increase with woodchip age and lead to stronger temperature-response in systems like this one with a highly aged woodchip matrix. While the impacts of hydro-climatic change on WBR performance will depend on site-specific properties, this hydrologic-biokinetic modeling approach provides a framework for assessing climate impacts on the effectiveness of WBRs and other denitrifying nature-based systems.

Effect of low salinity on nitrogen removal from municipal wastewater via a double-anammox process coupled with nitritation and denitratation: Performance and microbial structure

Saline wastewater present in municipal pipe networks poses challenges to biological nitrogen removal due to its inhibition on microorganisms. This study focuses on the effects of low salinity (0.0%, 0.4%, 0.7% and 1.0%) on a system featuring a combination of nitritation/anammox in oxic stage and denitratation/anammox in anoxic stage (double-anammox) in a step-feed SBR for municipal wastewater over a period of 130 days. The results showed that a maximum nitrogen removal efficiency of 81.2% was achieved at a salinity of 1.0% with anammox contribution of 76.5%. Analysis of anammox contribution and sludge activities discovered that low salinity promoted both nitritation and denitratation, further enhancing the coupling with anammox. Further, microbial analysis confirmed that Ca. Brocadia was enriched on biofilms from 0.21% to 0.51% and Nitrosomonas was enriched in flocs from 0.50% to 1.04%. Overall, the double-anammox process appears to be a promising method for the treatment of saline wastewater.

Achieving synergetic treatment of sludge supernatant, waste activated sludge and secondary effluent for wastewater treatment plants (WWTPs) sustainable development

A novel process that combines partial nitrification, fermentation and Anammox-partial denitrification (NFAD) was proposed to co-treat ammonia rich sludge supernatant (NH₄⁺-N = 1194.1 mg/L), external WAS (MLSS = 22092.6 mg/L) and WWTP secondary effluent (NO₃^--N = 58.6 mg/L). Three separated reactors were used for partial nitrification (PN-SBR), integrated fermentation and denitrification (IFD-SBR) and combined Anammox-partial denitrification (AD-UASB), respectively. The process resulted in excellent nitrogen removal efficiency (NRE) of 98.7%, external sludge reduction efficiency (SRE) of 44.6% and external sludge reduction rate of 4.1 kg/m³ after 200 days of continuous operation. IFD-SBR and AD-UASB contributed towards 89.4% and 9.2% nitrogen removal, respectively. In AD-UASB, cooperation between Anammox bacteria (4.1% Candidatus Brocadia) and partial denitrifying bacteria (3.2% Thauera) resulted in significant stability of Anammox pathway, which contributed up to 84.1% nitrogen removal in the combined Anammox-partial denitrification process. NFAD saved up to 100% organic resource demand and 25% of aeration consumption compared with the traditional nitrification-denitrification process.

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.

Temperature Sensitivity and Composition of Nitrate-Reducing Microbiomes from a Full-Scale Woodchip Bioreactor Treating Agricultural Drainage Water

Denitrifying woodchip bioreactors (WBR), which aim to reduce nitrate (NO3-) pollution from agricultural drainage water, are less efficient when cold temperatures slow down the microbial transformation processes. Conducting bioaugmentation could potentially increase the NO3- removal efficiency during these specific periods. First, it is necessary to investigate denitrifying microbial populations in these facilities and understand their temperature responses. We hypothesized that seasonal changes and subsequent adaptations of microbial populations would allow for enrichment of cold-adapted denitrifying bacterial populations with potential use for bioaugmentation. Woodchip material was sampled from an operating WBR during spring, fall, and winter and used for enrichments of denitrifiers that were characterized by studies of metagenomics and temperature dependence of NO3- depletion. The successful enrichment of psychrotolerant denitrifiers was supported by the differences in temperature response, with the apparent domination of the phylum Proteobacteria and the genus Pseudomonas. The enrichments were found to have different microbiomes' composition and they mainly differed with native woodchip microbiomes by a lower abundance of the genus Flavobacterium. Overall, the performance and composition of the enriched denitrifying population from the WBR microbiome indicated a potential for efficient NO3- removal at cold temperatures that could be stimulated by the addition of selected cold-adapted denitrifying bacteria.