Nitrifying Organisms Research Articles

Out of sight, but not out of season: Nitrifier distributions and population dynamics in a large oligotrophic lake.

Nitrification is an important control on the form and distribution of nitrogen in freshwater ecosystems. However, the seasonality of nitrogen pools and the diversity of organisms catalyzing this process have not been well documented in oligotrophic lakes. Here, we show that nitrogen pools and nitrifying organisms in Flathead Lake are temporally and vertically dynamic, with nitrifiers displaying specific preferences depending on the season. While the ammonia-oxidizing bacteria (AOB) Nitrosomonadaceae and nitrite-oxidizing bacteria (NOB) Nitrotoga dominate at depth in the summer, the ammonia-oxidizing archaea (AOA) Nitrososphaerota and NOB Nitrospirota become abundant in the winter. Given clear seasonality in ammonium, with higher concentrations during the summer, we hypothesize that the succession between these two nitrifying groups may be due to nitrogen affinity, with AOB more competitive when ammonia concentrations are higher and AOA when they are lower. Nitrifiers in Flathead Lake share more than 99% average nucleotide identity with those reported in other North American lakes but are distinct from those in Europe and Asia, indicating a role for geographic isolation as a factor controlling speciation among nitrifiers. Our study shows there are seasonal shifts in nitrogen pools and nitrifying populations, highlighting the dynamic spatial and temporal nature of nitrogen cycling in freshwater ecosystems.

Metataxonomic Analysis of Microbial Communities in Aquaponic Systems at Two Facilities in the Midwest United States

Aquaponic production relies on microbial activity to convert fish wastes into nutrients for plants. An aquaponic system contains multiple compartments that each have varying environmental pressures that can impact the types of microbes living in the compartment. Furthermore, differences in fish and plant species, system startup and management, and water source can impact microbial communities that colonize an aquaponic system. In this study, we sampled two aquaponic facilities that each operated six replicate aquaponic systems. Metataxonomic analyses were performed on the samples to compare the microbial communities of aquaponic facilities in Minnesota (MN) and Wisconsin (WI), assess the consistency of the microbial communities across multiple systems within a single facility, and evaluate the abundance and types of microbes present within each compartment of a system. Proteobacteria, Bacteroidetes, and Actinobacteria were common in both facilities, but nitrifying organisms were in greater abundance at the WI facility. Microbial communities were largely consistent among systems within a facility, but microbial communities among different compartments of the systems varied. Nitrifying organisms were primarily associated with the biofilter compartment of the MN systems but were found throughout the WI systems, which do not have a dedicated biofiltration compartment. While nitrifying organisms have an important role in an aquaponic system, they comprise less than 10% of the total microbial community of the aquaponic systems we sampled. Other taxa are likely to have equally important roles in the productivity of an aquaponic system, but those taxa and their functions have not been well characterized, and it is unclear how system startup, management, and other factors impact colonization and maintenance of these taxa.

Geochemical factors impacting nitrifying communities in sandy sediments.

Sandy sediment beaches covering 70% of non-ice-covered coastlines are important ecosystems for nutrient cycling along the land-ocean continuum. Subterranean estuaries (STEs), where groundwater and seawater meet, are hotspots for biogeochemical cycling within sandy beaches. The STE microbial community facilitates biogeochemical reactions, determining the fate of nutrients, including nitrogen (N), supplied by groundwater. Nitrification influences the fate of N, oxidising reduced dissolved inorganic nitrogen (DIN), making it available for N removal. We used metabarcoding of 16S rRNA genes and quantitative PCR (qPCR) of ammonia monooxygenase (amoA) genes to characterise spatial and temporal variation in STE microbial community structure and nitrifying organisms. We examined nitrifier diversity, distribution and abundance to determine how geochemical measurements influenced their distribution in STEs. Sediment microbial communities varied with depth (p-value = 0.001) and followed geochemical gradients in dissolved oxygen (DO), salinity, pH, dissolved inorganic carbon and DIN. Genetic potential for nitrification in the STE was evidenced by qPCR quantification of amoA genes. Ammonia oxidiser abundance was best explained by DIN, DO and pH. Our results suggest that geochemical gradients are tightly linked to STE community composition and nitrifier abundance, which are important to determine the fate and transport of groundwater-derived nutrients to coastal waters.

Effect of Diclofenac Concentration on Activated Sludge Conditions in a Biological Wastewater Treatment Plant

Significant quantities of pharmaceutical substances enter biological wastewater treatment plants, where they interact with activated sludge microorganisms. An example of a pharmaceutical commonly used is the non-steroidal anti-inflammatory drug diclofenac (DCF). The presence of high concentrations of DCF in wastewater can disrupt nutrient removal processes, which are highly sensitive to external environmental factors. This paper discusses the effect of high DCF concentrations (1.04 mg/dm3–12.5 mg/dm3; 0.25 mg/gTS–3.0 mg/gTS) on the efficiency of nitrifying, denitrifying and phosphate-accumulating organisms in the wastewater treatment cycle. The condition of the activated sludge was assessed on the basis of the oxygen and nitrogen uptake rates values and the ability to biologically remove phosphorus compounds from the wastewater. The effect of DCF on the ability of methane-forming bacteria to produce biogas in the anaerobic digester was also investigated. None of the biochemical reactions of activated sludge were inhibited at applied DCF concentrations. A 33% reduction in biogas production was observed at a DCF dose of 0.0391 mg/gTS. Slight deviations from the typical course of biochemical transformation of ammonium compounds were recorded at a DCF concentration of 3 mg/gTS of sludge. However, in the concentration range studied, no negative effect of DCF, on the operation of the activated sludge, was found.

Light, ammonium, pH, and phytoplankton competition as environmental factors controlling nitrification

AbstractThe biogeochemical cycling of nitrogen (N) plays a critical role in supporting marine ecosystems and controlling primary production. Nitrification, the oxidation of ammonia (NH3) by microorganisms, is an important process in the marine N cycle, supplying nitrate (), the primary source of N that fuels new phytoplankton growth, and the primary substrate for the microbial process of denitrification. Understanding nitrification in the Chukchi Sea, the shallow sea overlying the continental shelf north of Alaska and the Bering Strait, is particularly important as phytoplankton growth there has been shown to be limited by N. However, the controls on nitrification in the water column and potential effects of climate change remain unknown. This study seeks to characterize the controls on nitrification in the Chukchi Sea. We found light to be a strong control on nitrification rates. Nitrification was undetectable at light levels above 23 μmol photons m−2 s−1. Subsequently, sea ice concentration was related to nitrification, with rates being higher at stations with high ice cover where light transmission to the water column was reduced. High ammonium () concentrations also enhanced nitrification, suggesting that nitrifying organisms were substrate‐limited, likely due to competition for from phytoplankton. Unlike previous experimental studies, we found that nitrification rates were higher under low pH conditions. As the effects of ocean acidification and warming disproportionately impact the Arctic, nitrification rates will undoubtedly be affected. Our results will help guide future studies on potential implications of climate change on the biogeochemistry of N in the Chukchi Sea.

The effects of low oxidation-reduction potential on the performance of full-scale hybrid membrane-aerated biofilm reactors

Membrane-Aerated Biofilm Reactors (MABRs) are becoming a popular process intensification alternative within wastewater treatment plants (WWTP). Indeed, the nitrogen removal capacity of aerobic/anoxic/anaerobic reactors can be substantially enhanced with reduced energy consumption and footprint requirements. However, little is known about how oxidation–reduction potential (ORP) may impact their overall process performance. This study aims to report some of these effects by showing the results of almost three years of monitoring of two hybrid MABRs (R1, R2) adjacent to an existing Biodenipho™ facility. In Period 1 (P1), R1 and R2 were fed with anaerobic mixed liquor from the selector for the biological phosphorus removal zone. In Period 2 (P2), external aeration was introduced to increase ORP values (R1, R2), and membranes were replaced (R1) or cleaned (R2). Results show an increase in nitrification rates: from 0.27 and 0.33 g N m−2 d−1 in R1/R2 during P1 to 1.0 and 0.80 g N m−2 d−1 in R1/R2 during P2. 16 s rRNA amplicon sequencing analysis revealed that the relative abundance of nitrifying organisms increased from 0.2 to 6.7 % in R1 and 0.8 to 5.3 % in R2 in P2 (in detriment of microbes with fermenting capabilities). Energy dispersive X-ray spectroscopy confirmed the presence of coating substances under the lowest ORP (P1), which could be pyrite and its precursors like mackinawite. Overall, it is hypothesized that low ORP conditions (P1) had a detrimental effect on nitrification performance, as it promoted the reduction of different iron and sulfur compounds, which in turn a) precipitate in the biofilm as FeS increasing mass transfer limitations and competing with biomass for space; b) re-oxidize increasing the internal oxygen demand; c) inhibit nitrifiers growth.

Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds.

The ammonia-oxidizing bacterium Nitrosomonas europaea has been widely recognized as an important player in the nitrogen cycle as well as one of the most abundant members in microbial communities for the treatment of industrial or sewage wastewater. Its natural metabolic versatility and extraordinary ability to degrade environmental pollutants (e.g., aromatic hydrocarbons such as benzene and toluene) enable it to thrive under various harsh environmental conditions. Constraint-based metabolic models constructed from genome sequences enable quantitative insight into the central and specialized metabolism within a target organism. These genome-scale models have been utilized to understand, optimize, and design new strategies for improved bioprocesses. Reduced modeling approaches have been used to elucidate Nitrosomonas europaea metabolism at a pathway level. However, genome-scale knowledge about the simultaneous oxidation of ammonia and pollutant metabolism of N. europaea remains limited. Here, we describe the reconstruction, manual curation, and validation of the genome-scale metabolic model for N. europaea, iGC535. This reconstruction is the most accurate metabolic model for a nitrifying organism to date, reaching an average prediction accuracy of over 90% under several growth conditions. The manually curated model can predict phenotypes under chemolithotrophic and chemolithoorganotrophic conditions while oxidating methane and wastewater pollutants. Calculated flux distributions under different trophic conditions show that several key pathways are affected by the type of carbon source available, including central carbon metabolism and energy production.

Systematic calibration of N2O emissions from a full-scale WWTP including a tracer test and a global sensitivity approach

Nitrous oxide (N2O) is a greenhouse gas (GHG) emitted during biological nitrogen removal from wastewater treatment plants (WWTPs). Some modelling tools have been proposed to predict N2O emissions during the design and operation of WWTPs. In this study, the novel ASM2d-N2O model, which accounts for the production of N2O in nutrient removal WWTPs, was used to study the associated emissions from a full-scale WWTP with two independent lines. Firstly, the hydraulics of the WWTP was characterized by a residence time distribution test, showing the flow was equally divided into the two treatment lines (49.3 vs. 50.7%), that each reactor worked as an ideal continuous stirred tank reactor and the secondary settler model flux was similar to a plug-flow reactor. The ASM2d-N2O model was then calibrated using experimental data obtained under dynamic conditions. A global sensitivity analysis was used to select, among 59 model parameters, five candidates that resulted to be related to nitrifying organisms. Different parameter subsets up to four parameters were evaluated, being the subset [µNOB, qAOB_AMO, KO2_NOB, KNO2_NOB] the best, achieving 53.3% reduction of the calibration cost function. The model fit obtained provided a reasonably description of nutrients and N2O emission trends, considering the inherent operational variability suffered in full-scale WWTPs. Finally, a simulation-based study showed that, for the given WWTP and operational conditions, an unbalanced distribution of flow-rate between the two treatment lines did not result in a significant increase on N2O emissions. The results obtained show that this model can be a suitable tool for predicting N2O emissions in full-scale WWTPs, and can therefore be used to find operational conditions that help to minimise these emissions.

Upgrading municipal lagoons in temperate and cold climates: Total nitrogen removal and phosphorus assimilation at ultra‐low temperatures

AbstractIn this study, a municipal lagoon with high wintertime effluent total ammonia nitrogen (TAN) concentrations was upgraded with a pilot‐scale nitrifying‐nitrifying‐denitrifying (NIT‐NIT‐DENIT) moving bed biofilm reactor (MBBR) treatment train to characterize its effluent over wintertime operation, investigate the feasibility of upgrading lagoons to achieve substantial biological total nitrogen removal across ultra‐low temperatures (0.6–3.0) and to investigate nitrification inhibition pathways in facultative lagoon systems at ultra‐low temperatures. Throughout the study, it was observed that the system substantially reduced total nitrogen (TN) and total phosphorus (TP) effluent concentrations by an average of 69.8 ± 24.5% and 74.7 ± 20.1%, respectively. Furthermore, it was observed that sulfide toxicity may play an important role in the inhibition of nitrifying organisms in lagoons. Finally, the MBBR treatment technology has emerged as a suitable and sustainable upgrade technology for existing lagoon and waste stabilization pond facilities operating in temperate, northern and cold climate countries.

Depth Profile of Nitrifying Archaeal and Bacterial Communities in the Remote Oligotrophic Waters of the North Pacific

Nitrification is a vital ecosystem function in the open ocean that regenerates inorganic nitrogen and promotes primary production. Recent studies have shown that the ecology and physiology of nitrifying organisms is more complex than previously postulated. The distribution of these organisms in the remote oligotrophic ocean and their interactions with the physicochemical environment are relatively understudied. In this work, we aimed to evaluate the depth profile of nitrifying archaea and bacteria in the Eastern North Pacific Subtropical Front, an area with limited biological surveys but with intense trophic transferences and physicochemical gradients. Furthermore, we investigated the dominant physicochemical and biological relationships within and between ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB) as well as with the overall prokaryotic community. We used a 16S rRNA gene sequencing approach to identify and characterize the nitrifying groups within the first 500 m of the water column and to analyze their abiotic and biotic interactions. The water column was characterized mainly by two contrasting environments, warm O2-rich surface waters with low dissolved inorganic nitrogen (DIN) and a cold O2-deficient mesopelagic layer with high concentrations of nitrate (NO3–). Thaumarcheotal AOA and bacterial NOB were highly abundant below the deep chlorophyll maximum (DCM) and in the mesopelagic. In the mesopelagic, AOA and NOB represented up to 25 and 3% of the total prokaryotic community, respectively. Interestingly, the AOA community in the mesopelagic was dominated by unclassified genera that may constitute a novel group of AOA highly adapted to the conditions observed at those depths. Several of these unclassified amplicon sequence variants (ASVs) were positively correlated with NO3– concentrations and negatively correlated with temperature and O2, whereas known thaumarcheotal genera exhibited the opposite behavior. Additionally, we found a large network of positive interactions within and between putative nitrifying ASVs and other prokaryotic groups, including 13230 significant correlations and 23 sub-communities of AOA, AOB, NOB, irrespective of their taxonomic classification. This study provides new insights into our understanding of the roles that AOA may play in recycling inorganic nitrogen in the oligotrophic ocean, with potential consequences to primary production in these remote ecosystems.

Larger Anammox Granules not only Harbor Higher Species Diversity but also Support More Functional Diversity.

Granule-based partial nitritation and anammox (PN/A) represents one of the most energy-efficient biotechniques for ammonium removal from wastewater. The PN/A granules appear in a continuum of sizes, yet little is known about the extent to which microbial communities and microbial metabolisms are partitioned between size-fractionated granules. Here, we divided granules harvested from a pilot-scale PN/A reactor into five discrete size fractions (<0.2, 0.2-0.5, 0.5-0.8, 0.8-1.0, and >1.0 mm). The composition and functional attribute of five pools of the size-fractionated granules were characterized by 16S ribosomal RNA (rRNA) gene amplicon and metagenomic and metatranscriptomic sequencing to provide a comprehensive insight into the key microbial group in a PN/A system. Larger granules were shown to not only harbor higher microbial diversity but also support more diverse functions than smaller granules. De novo coassembly and binning of metagenomic reads yielded 22 draft genomes of dominant microorganisms, which allowed us to infer an ecological model of the microbial ecosystem in anammox-based granules. This genome-based ecological model indicates that nitrifying organisms in smaller granules feed nitrite to anammox bacteria in larger granules. The results improve our understanding of the PN/A system, especially for the metabolic interactions between small and large granules.

Algae support populations of heterotrophic, nitrifying, and phosphate-accumulating bacteria in the treatment of poultry litter anaerobic digestate

The objective of this study was to investigate the impact that algae have on bacterial treatment of poultry litter slurry anaerobic digestate. We hypothesized that algae could provide benefits to heterotrophic and nitrifying organisms, due in part to provision of dissolved oxygen. No other studies, to our knowledge, have shown that algae provide benefits to nitrifying bacteria in the treatment of anaerobic digestates. Batch cultures of the native digestate community were grown alone or with the addition of activated sludge microorganisms and/or the green algae, Chlorella sorokiniana. Water quality measurements, 16S rRNA sequencing, and quantitative PCR were utilized to elucidate the impacts of algae on bacterial populations involved in organics removal and nutrient cycling. The presence of activated sludge promoted algal growth by 29%, nitrogen uptake by 53%, and phosphate removal by 21%. In turn, the presence of algae promoted a 57% increase in organics removal by heterotrophic bacteria. Algae also promoted full oxidation of ammonium to nitrate by nitrifying bacteria whereas incomplete nitrification was observed in the absence of algae. This result was likely driven by algal support of the commamox bacteria, Nitrospira, which otherwise died off in the anaerobic digestate. We also show here, for the first time, that C. sorokiniana sustained the relative abundance of the phosphate-accumulating bacteria, Candidatus Accumulibacter, whereas this organism declined in relative abundance by 94% when algae were absent (p < 0.001). These results suggest that C. sorokiniana supports particular heterotrophs, nitrifiers, and phosphate-accumulating bacteria, thereby improving treatment of poultry litter anaerobic digestate.

Microbial Nitrogen Metabolism in Chloraminated Drinking Water Reservoirs.

Ammonia availability due to chloramination can promote the growth of nitrifying organisms, which can deplete chloramine residuals and result in operational problems for drinking water utilities. In this study, we used a metagenomic approach to determine the identity and functional potential of microorganisms involved in nitrogen biotransformation within chloraminated drinking water reservoirs. Spatial changes in the nitrogen species included an increase in nitrate concentrations accompanied by a decrease in ammonium concentrations with increasing distance from the site of chloramination. This nitrifying activity was likely driven by canonical ammonia-oxidizing bacteria (i.e., Nitrosomonas) and nitrite-oxidizing bacteria (i.e., Nitrospira) as well as by complete-ammonia-oxidizing (i.e., comammox) Nitrospira-like bacteria. Functional annotation was used to evaluate genes associated with nitrogen metabolism, and the community gene catalogue contained mostly genes involved in nitrification, nitrate and nitrite reduction, and nitric oxide reduction. Furthermore, we assembled 47 high-quality metagenome-assembled genomes (MAGs) representing a highly diverse assemblage of bacteria. Of these, five MAGs showed high coverage across all samples, which included two Nitrosomonas, Nitrospira, Sphingomonas, and Rhizobiales-like MAGs. Systematic genome-level analyses of these MAGs in relation to nitrogen metabolism suggest that under ammonia-limited conditions, nitrate may be also reduced back to ammonia for assimilation. Alternatively, nitrate may be reduced to nitric oxide and may potentially play a role in regulating biofilm formation. Overall, this study provides insight into the microbial communities and their nitrogen metabolism and, together with the water chemistry data, improves our understanding of nitrogen biotransformation in chloraminated drinking water distribution systems.IMPORTANCE Chloramines are often used as a secondary disinfectant when free chlorine residuals are difficult to maintain. However, chloramination is often associated with the undesirable effect of nitrification, which results in operational problems for many drinking water utilities. The introduction of ammonia during chloramination provides a potential source of nitrogen either through the addition of excess ammonia or through chloramine decay. This promotes the growth of nitrifying microorganisms and provides a nitrogen source (i.e., nitrate) for the growth for other organisms. While the roles of canonical ammonia-oxidizing and nitrite-oxidizing bacteria in chloraminated drinking water systems have been extensively investigated, those studies have largely adopted a targeted gene-centered approach. Further, little is known about the potential long-term cooccurrence of complete-ammonia-oxidizing (i.e., comammox) bacteria and the potential metabolic synergies of nitrifying organisms with their heterotrophic counterparts that are capable of denitrification and nitrogen assimilation. This study leveraged data obtained for genome-resolved metagenomics over a time series to show that while nitrifying bacteria are dominant and likely to play a major role in nitrification, their cooccurrence with heterotrophic organisms suggests that nitric oxide production and nitrate reduction to ammonia may also occur in chloraminated drinking water systems.

Controls and Adaptive Management of Nitrification in Agricultural Soils.

Agriculture is responsible for over half of the input of reactive nitrogen (N) to terrestrial systems; however improving N availability remains the primary management technique to increase crop yields in most regions. In the majority of agricultural soils, ammonium is rapidly converted to nitrate by nitrification, which increases the mobility of N through the soil matrix, strongly influencing N retention in the system. Decreasing nitrification through management is desirable to decrease N losses and increase N fertilizer use efficiency. We review the controlling factors on the rate and extent of nitrification in agricultural soils from temperate regions including substrate supply, environmental conditions, abundance and diversity of nitrifiers and plant and microbial interactions with nitrifiers. Approaches to the management of nitrification include those that control ammonium substrate availability and those that inhibit nitrifiers directly. Strategies for controlling ammonium substrate availability include timing of fertilization to coincide with rapid plant update, formulation of fertilizers for slow release or with inhibitors, keeping plant growing continuously to assimilate N, and intensify internal N cycling (immobilization). Another effective strategy is to inhibit nitrifiers directly with either synthetic or biological nitrification inhibitors. Commercial nitrification inhibitors are effective but their use is complicated by a changing climate and by organic management requirements. The interactions of the nitrifying organisms with plants or microbes producing biological nitrification inhibitors is a promising approach but just beginning to be critically examined. Climate smart agriculture will need to carefully consider optimized seasonal timing for these strategies to remain effective management tools.

Ozonation of the dye Reactive Red 239 and biodegradation of ozonation products in a moving-bed biofilm reactor: Revealing reaction products and degradation pathways

The ozonation of the azo dye Reactive Red 239 (RR 239) was investigated in a bench-scale reactor. Decolorization and organic matter removal were monitored in batch assays. The toxicity of the dye and its ozonation products to the test-organism Aliivibrio fischeri was also assessed. Identification of ozonation products was performed using analytical techniques (GC-MSD and high resolution mass spectrometry). Ozonated and non-ozonated dye solutions were supplemented with organic matter (glucose) and nutrients sources and subjected to biological treatment in a moving-bed biofilm reactor (MBBR). Five experimental runs were conducted, varying the influent characteristics and monitoring organic matter removal and nitrification performance. Identification of residual compounds in the effluent was also performed. Color was very rapidly removed by ozonation, but the degree of mineralization achieved was rather low. Moreover, toxicity was completely removed after 4 min of ozone reaction. Based on the ozonation products, a two-way mechanism was proposed for the degradation of RR 239 by ozone. Further biological treatment in the MBBR revealed that the removal of organic matter (evaluated as COD) was not affected by the ozonation products. However, nitrification efficiency dropped significantly when the dye or the ozonated dye was fed to the bioreactor. Furthermore, inhibition of nitrite oxidizers resulted in partial nitrification and consequent accumulation of nitrite, which consisted of the main oxidized nitrogen specie in the reactor effluent. The identification of compounds resulting from the ozonation and biological treatment steps suggests that the partial inhibition of nitrifying organisms was possibly caused by triazine- and benzofuran-related organic compounds. Nevertheless, their adverse effect on nitrification was found to be reversible and practically ceased once these compounds were removed from the influent. Overall, the results revealed that the combination of ozonation and MBBR for the treatment of azo dye containing-wastewaters is promising but the ozone-based process should be optimized in order to enable the degradation of compounds inhibiting nitrification.

Diversity and relative abundance of ammonia- and nitrite-oxidizing microorganisms in the offshore Namibian hypoxic zone.

Nitrification, the microbial oxidation of ammonia (NH3) to nitrite (NO2–) and NO2– to nitrate (NO3–), plays a vital role in ocean nitrogen cycling. Characterizing the distribution of nitrifying organisms over environmental gradients can help predict how nitrogen availability may change with shifting ocean conditions, for example, due to loss of dissolved oxygen (O2). We characterized the distribution of nitrifiers at 5 depths spanning the oxic to hypoxic zone of the offshore Benguela upwelling system above the continental slope off Namibia. Based on 16S rRNA gene amplicon sequencing, the proportional abundance of nitrifiers (ammonia and nitrite oxidizers) increased with depth, driven by an increase in ammonia-oxidizing archaea (AOA; Thaumarchaeota) to up to 33% of the community at hypoxic depths where O2 concentrations fell to ~25 μM. The AOA community transitioned from being dominated by a few members at oxic depths to a more even representation of taxa in the hypoxic zone. In comparison, the community of NO2–-oxidizing bacteria (NOB), composed primarily of Nitrospinae, was far less abundant and exhibited higher evenness at all depths. The AOA:NOB ratio declined with depth from 41:1 in the oxic zone to 27:1 under hypoxia, suggesting potential variation in the balance between NO2– production and consumption via nitrification. Indeed, in contrast to prior observations from more O2-depleted sites closer to shore, NO2– did not accumulate at hypoxic depths near this offshore site, potentially due in part to a tightened coupling between AOA and NOB.

Does the feeding strategy enhance the aerobic granular sludge stability treating saline effluents?

The development and stability of aerobic granular sludge (AGS) was studied in two Sequencing Batch Reactors (SBRs) treating fish canning wastewater. R1 cycle comprised a fully aerobic reaction phase, while R2 cycle included a plug-flow anaerobic feeding/reaction followed by an aerobic reaction phase. The performance of the AGS reactors was compared treating the same effluents with variable salt concentrations (4.97–13.45 g NaCl/L) and organic loading rates (OLR, 1.80–6.65 kg CODs/(m3·d)). Granulation process was faster in R2 (day 34) than in R1 (day 90), however the granular biomass formed in the fully aerobic configuration was more stable to the variable feeding composition. Thus, in R1 solid retention times (SRT), up to 15.2 days, longer than in R2, up to 5.8 days, were achieved. These long SRTs values helped the retention of nitrifying organisms and provoked the increase of the nitrogen removal efficiency to 80% in R1 while it was approximately of 40% in R2. However, the presence of an anaerobic feeding/reaction phase increased the organic matter removal efficiency in R2 (80–90%) which was higher than in R1 with a fully aerobic phase (75–85%). Furthermore, in R2 glycogen-accumulating organisms (GAOs) dominated inside the granules instead of phosphorous-accumulating organisms (PAOs), suggesting that GAOs resist better the stressful conditions of a variable and high-saline influent. In terms of AGS properties an anaerobic feeding/reaction phase is not beneficial, however it enables the production of a better quality effluent.

Structural and Functional Interrogation of Selected Biological Nitrogen Removal Systems in the United States, Denmark, and Singapore Using Shotgun Metagenomics.

Conventional biological nitrogen removal (BNR), comprised of nitrification and denitrification, is traditionally employed in wastewater treatment plants (WWTPs) to prevent eutrophication in receiving water bodies. More recently, the combination of selective ammonia to nitrite oxidation (nitritation) and autotrophic anaerobic ammonia oxidation (anammox), collectively termed deammonification, has also emerged as a possible energy- and cost-effective BNR alternative. Herein, we analyzed microbial diversity and functional potential within 13 BNR processes in the United States, Denmark, and Singapore operated with varying reactor configuration, design, and operational parameters. Using next-generation sequencing and metagenomics, gene-coding regions were aligned against a custom protein database expanded to include all published aerobic ammonia oxidizing bacteria (AOB), nitrite oxidizing bacteria (NOB), anaerobic ammonia oxidizing bacteria (AMX), and complete ammonia oxidizing bacteria (CMX). Overall contributions of these N-cycle bacteria to the total functional potential of each reactor was determined, as well as that of several organisms associated with denitrification and/or structural integrity of microbial aggregates (biofilm or granules). The potential for these engineered processes to foster a broad spectrum of microbial catabolic, anabolic, and carbon assimilation transformations was elucidated. Seeded sidestream DEMON® deammonification systems and single-stage nitritation-anammox moving bed biofilm reactors (MBBRs) and a mainstream Cleargreen reactor designed to enrich in AOB and AMX showed lower enrichment in AMX functionality than an enriched two-stage nitritation-anammox MBBR system treating mainstream wastewater. Conventional BNR systems in Singapore and the United States had distinct metagenomes, especially relating to AOB. A hydrocyclone process designed to recycle biomass granules for mainstream BNR contained almost identical structural and functional characteristics in the overflow, underflow, and inflow of mixed liquor (ALT) rather than the expected selective enrichment of specific nitrifying or AMX organisms. Inoculum used to seed a sidestream deammonification process unexpectedly contained <10% of total coding regions assigned to AMX. These results suggest the operating conditions of engineered bioprocesses shape the resident microbial structure and function far more than the bioprocess configuration itself. We also highlight the advantage of a systems- and metagenomics-based interrogation of both the microbial structure and potential function therein over targeting of individual populations or specific genes.

Bioaugmentation with Nitrifying Granules in Low-SRT Flocculent Activated Sludge at Low Temperature.

Nitrifying granules were grown in a sidestream reactor fed municipal anaerobic digestion centrate and added in an initial slug dose and subsequent smaller daily doses to a non-nitrifying mainstream activated sludge system at 12 °C and 2.5-day aerobic solids retention time (SRT) to increase its nitrification capacity. Effluent NH3-N concentrations less than 1 mg/L were achieved with bioaugmentation, and nitrification was immediately lost when granules were removed after 30 days of bioaugmentation. Molecular microbial analyses indicated that nitrifying organisms remained attached to granules in the mainstream system with little loss to the flocculent sludge. Maximum specific nitrification activity of the bioaugmented granules decreased in mainstream treatment but the nitrification capacity remained due to new granule growth in the mainstream. This study demonstrated that bioaugmentation with sidestream nitrifying granules can intensify nitrification capacity in low-SRT, low-temperature flocculent activated sludge systems to achieve low effluent NH3-N concentrations and nitrogen removal.

Nitrification in intertidal sponge Cinachyrella cavernosa

The nitrification process in different sections of the sponges remains unresolved, despite several studies on the nitrogen cycling pathways in the tissues of temperate and Arctic sponges. In this study, the abundance, diversity and activity of the associated nitrifying organisms in intracellular, intercellular, extracellular and cortex of a tropical intertidal sponge, Cinachyrella cavernosa, were investigated using most probable number, next-generation sequencing and incubation method, respectively. The nitrification rate and the abundance of nitrifying bacteria showed significant difference among different sections. The nitrification rate in C. cavernosa was 2–12× higher than the reported values in other sponge species from temperate and Arctic regions. Nitrification rate in sponge cortex was 2× higher than in intercellular and extracellular sections. Ammonium and nitrite oxidisers ranged from 103 to 104 CFU g−1 in the sponge with a high number of ammonium and nitrite oxidisers in the cortex. Nitrifiers belonging to Nitrosomonas, Nitrospira, Nitrospina, Nitrobacter and Nitrosopumilus were present in different sections of the sponge, with nitrifying archaea dominating the intracellular section and nitrifying bacteria dominating other sections. This study reports for the first time the nitrification inside the sponge cells. The study also suggests that the intertidal sponge, C. cavernosa, harbours metabolically active nitrifiers in different sections of the sponge body with different rates of nitrification. Thus, nitrifiers play an important role in ammonia detoxification within the sponge and also contribute to the nitrogen budget of the coastal ecosystem.