Numerical modelling of surface aeration and N2O emission in biological water resource recovery.

Biokinetic modelling of N2O production and emission has been extensively studied in the past fifteen years. In contrast, the physical-chemical hydrodynamics of activated sludge reactor design and operation, and their impact on N2O emission, is less well understood. This study addresses knowledge gaps related to the systematic identification and calibration of computational fluid dynamic (CFD) simulation models. Additionally, factors influencing reliable prediction of aeration and N2O emission in surface aerated oxidation ditch-type reactor types are evaluated. The calibrated model accurately predicts liquid sensor measurements obtained in the Lynetten Water Resource Recovery Facility (WRRF), Denmark. Results highlight the equal importance of design and operational boundary conditions, alongside biokinetic parameters, in predicting N2O emission. Insights into the limitations of calibrating gas mass-transfer processes in two-phase CFD models of surface aeration systems are evaluated.

Is it selfish to be filamentous in biofilms? Individual-based modeling links microbial growth strategies with morphology using the new and modular iDynoMiCS 2.0.

Microbial communities are found in all habitable environments and often occur in assemblages with self-organized spatial structures developing over time. This complexity can only be understood, predicted, and managed by combining experiments with mathematical modeling. Individual-based models are particularly suited if individual heterogeneity, local interactions, and adaptive behavior are of interest. Here we present the completely overhauled software platform, the individual-based Dynamics of Microbial Communities Simulator, iDynoMiCS 2.0, which enables researchers to specify a range of different models without having to program. Key new features and improvements are: (1) Substantially enhanced ease of use (graphical user interface, editor for model specification, unit conversions, data analysis and visualization and more). (2) Increased performance and scalability enabling simulations of up to 10 million agents in 3D biofilms. (3) Kinetics can be specified with any arithmetic function. (4) Agent properties can be assembled from orthogonal modules for pick and mix flexibility. (5) Force-based mechanical interaction framework enabling attractive forces and non-spherical agent morphologies as an alternative to the shoving algorithm. The new iDynoMiCS 2.0 has undergone intensive testing, from unit tests to a suite of increasingly complex numerical tests and the standard Benchmark 3 based on nitrifying biofilms. A second test case was based on the "biofilms promote altruism" study previously implemented in BacSim because competition outcomes are highly sensitive to the developing spatial structures due to positive feedback between cooperative individuals. We extended this case study by adding morphology to find that (i) filamentous bacteria outcompete spherical bacteria regardless of growth strategy and (ii) non-cooperating filaments outcompete cooperating filaments because filaments can escape the stronger competition between themselves. In conclusion, the new substantially improved iDynoMiCS 2.0 joins a growing number of platforms for individual-based modeling of microbial communities with specific advantages and disadvantages that we discuss, giving users a wider choice.

Coupling pathway prediction and fluorescence spectroscopy to assess the impact of auxiliary substrates on micropollutant biodegradation.

Some bacteria can degrade organic micropollutants (OMPs) as primary carbon sources. Due to typically low OMP concentrations, these bacteria may benefit from supplemental assimilation of natural substrates present in the pool of dissolved organic matter (DOM). The biodegradability of such auxiliary substrates and the impacts on OMP removal are tightly linked to biotransformation pathways. Here, we aimed to elucidate the biodegradability and effect of different DOM constituents for the carbofuran degrader Novosphingobium sp. KN65.2, using a novel approach that combines pathway prediction, laboratory experiments, and fluorescence spectroscopy. Pathway prediction suggested that ring hydroxylation reactions catalysed by Rieske-type dioxygenases and flavin-dependent monooxygenases determine the transformability of the 11 aromatic compounds used as model DOM constituents. Our approach further identified two groups with distinct transformation mechanisms amongst the four growth-supporting compounds selected for mixed substrate biodegradation experiments with the pesticide carbofuran (Group 1: 4-hydroxybenzoic acid, 4-hydroxybenzaldehyde; Group 2: p-coumaric acid, ferulic acid). Carbofuran biodegradation kinetics were stable in the presence of both Group 1 and Group 2 auxiliary substrates. However, Group 2 substrates would be preferable for bioremediation processes, as they showed constant biodegradation kinetics under different experimental conditions (pre-growing KN65.2 on carbofuran vs. DOM constituent). Furthermore, Group 2 substrates were utilisable by KN65.2 in the presence of a competitor (Pseudomonas fluorescens sp. P17). Our study thus presents a simple and cost-efficient approach that reveals mechanistic insights into OMP-DOM biodegradation.

Isolation and characterization of novel plasmid-dependent phages infecting bacteria carrying diverse conjugative plasmids.

IMPORTANCE: This work was undertaken because plasmid-dependent phages can reduce the prevalence of conjugative plasmids and can be leveraged to prevent the acquisition and dissemination of ARGs by bacteria. The two novel phages described in this study, Lu221 and Hi226, can infect Escherichia coli, Salmonella enterica, Kluyvera sp. and Enterobacter sp. carrying conjugative plasmids. This was verified with plasmids carrying resistance determinants and belonging to the most common plasmid families among Gram-negative pathogens. Therefore, the newly isolated phages could have the potential to help control the spread of ARGs and thus help combat the antimicrobial resistance crisis.

Dynamic calibration of a new secondary settler model using Cand. Microthrix as a predictor of settling velocity.

Climate change is projected to increase the frequency of hydraulic shocks on urban water systems, affecting water resource recovery facilities (WRRFs). In these facilities, the settleability of activated sludge is a critical hydraulic bottleneck. However, to date, the dynamic prediction of hindered settling velocity (v0/rH) has remained unresolved. To address this significant knowledge gap, this study presents an assessment of microbial community predictors of hindered settling velocity. Through a regression analysis of independent laboratory and full-scale experimental data, we identified a close association between the relative abundance of Candidatus Microthrix filamentous bacteria and hindered settling velocity parameter values. While no direct association was observed between filamentous abundance and compression settling parameters, we propose linking the dynamic calibration of the compressive solid stress function to v0/rH. Notably, our results demonstrate, for the first time, the efficacy of dynamic calibration of SST models using the relative abundance of filamentous microbial predictors in a simulation model of the Kloten-Opfikon full-scale WRRF. Furthermore, besides Cand. Microthrix, Thiothrix is found to be a putative predictor for biomolecular SST calibration. These findings shed light on the potential of microbial communities to predict hindered settling velocity in WRRFs and offer valuable insights for improving wastewater treatment processes in the face of climate change challenges.

Narrow host range phages infect essential bacteria for water purification reactions in groundwater-fed rapid sand filters.

Biofiltration is used worldwide to provide safe potable water due to its low energy demand and excellent treatment performance. For instance, in Denmark, over 95% of drinking water is supplied through groundwater-fed rapid sand filters (RSF). Bacteriophages, viruses that infect bacteria, have been shown to shape the taxonomic and functional composition of microbial communities across a range of natural and engineering systems. However, phages in the biofiltration systems are rarely studied, despite the central role microbes play in water purification. To probe this, metagenomic data from surface water, groundwater and mixed source water biofiltration units (n = 26 from China, Europe and USA) for drinking water production were analysed to characterize prokaryotic viruses and to identify their potential microbial hosts. The source water type and geographical location are found to exert influence on the composition of the phageome in biofilters. Although the viral abundance (71,676 ± 17,841 RPKM) in biofilters is only 14.4% and 17.0% lower than those of the nutrient-rich wastewater treatment plants and fresh surface waters, the richness (1,441 ± 1,046) and diversity (Inverse Simpson: 91 ± 61) in biofiltration units are significantly less by a factor of 2-5 and 3-4, respectively. In depth analysis of data from 24 groundwater-fed RSFs in Denmark revealed a core phageome shared by most RSFs, which was consistently linked to dominant microbial hosts involved in key biological reactions for water purification. Finally, the high number of specific links detected between phages and bacterial species and the large proportion of lytic phages (77%) led to the conjecture that phages regulate bacterial populations through predation, preventing the proliferation of dominant species and contributing to the established functional redundancy among the dominant microbial groups. In conclusion, bacteriophages are likely to play a significant role in water treatment within biofilters, particularly through interactions with key bacterial species.

Proterozoic Acquisition of Archaeal Genes for Extracellular Electron Transfer: A Metabolic Adaptation of Aerobic Ammonia-Oxidizing Bacteria to Oxygen Limitation.

Many aerobic microbes can utilize alternative electron acceptors under oxygen-limited conditions. In some cases, this is mediated by extracellular electron transfer (or EET), wherein electrons are transferred to extracellular oxidants such as iron oxide and manganese oxide minerals. Here, we show that an ammonia-oxidizer previously known to be strictly aerobic, Nitrosomonas communis, may have been able to utilize a poised electrode to maintain metabolic activity in anoxic conditions. The presence and activity of multiheme cytochromes in N. communis further suggest a capacity for EET. Molecular clock analysis shows that the ancestors of ß-proteobacterial ammonia oxidizers appeared after Earth's atmospheric oxygenation when the oxygen levels were >10-4pO2 (present atmospheric level [PAL]), consistent with aerobic origins. Equally important, phylogenetic reconciliations of gene and species trees show that the multiheme c-type EET proteins in Nitrosomonas and Nitrosospira lineages were likely acquired by gene transfer from γ-proteobacteria when the oxygen levels were between 0.1 and 1 pO2 (PAL). These results suggest that ß-proteobacterial EET evolved during the Proterozoic when oxygen limitation was widespread, but oxidized minerals were abundant.

Methanotrophic oxidation of organic micropollutants and nitrogen upcycling in a hybrid membrane biofilm reactor (hMBfR) for simultaneous O2 and CH4 supply.

Pharmaceuticals and other organic micropollutants (OMPs) present in wastewater effluents are of growing concern, as they threaten environmental and human health. Conventional biological treatments lead to limited removal of OMPs. Methanotrophic bacteria can degrade a variety of OMPs. By employing a novel bubble-free hybrid membrane biofilm bioreactor (hMBfR), we grew methanotrophic bacteria at three CH4 loading rates. Biomass productivity and CH4 loading showed a linear correlation, with a maximum productivity of 372 mg-VSS·L-1·d-1, with corresponding biomass concentration of 1117.6 ± 56.4 mg-VSS·L-1. Furthermore, the biodegradation of sulfamethoxazole and 1H-benzotriazole positively correlated with CH4 oxidation rates, with highest biodegradation kinetic constants of 3.58 L·g-1·d-1 and 5.42 L·g-1·d-1, respectively. Additionally, the hMBfR recovered nutrients as microbial proteins, with an average content 39% DW. The biofilm community was dominated by Methylomonas, while the bulk was dominated by aerobic heterotrophic bacteria. The hMBfR removed OMPs, allowing for safer water reuse while valorising CH4 and nutrients.

Plasmid permissiveness of wastewater microbiomes can be predicted from 16S rRNA sequences by machine learning.

MOTIVATION: Wastewater treatment plants (WWTPs) harbor a dense and diverse microbial community. They constantly receive antimicrobial residues and resistant strains, and therefore provide conditions for horizontal gene transfer (HGT) of antimicrobial resistance (AMR) determinants. This facilitates the transmission of clinically important genes between, e.g. enteric and environmental bacteria, and vice versa. Despite the clinical importance, tools for predicting HGT remain underdeveloped. RESULTS: In this study, we examined to which extent water cycle microbial community composition, as inferred by partial 16S rRNA gene sequences, can predict plasmid permissiveness, i.e. the ability of cells to receive a plasmid through conjugation, based on data from standardized filter mating assays using fluorescent bio-reporter plasmids. We leveraged a range of machine learning models for predicting the permissiveness for each taxon in the community, representing the range of hosts a plasmid is able to transfer to, for three broad host-range resistance IncP plasmids (pKJK5, pB10, and RP4). Our results indicate that the predicted permissiveness from the best performing model (random forest) showed a moderate-to-strong average correlation of 0.49 for pB10 [95% confidence interval (CI): 0.44-0.55], 0.43 for pKJK5 (0.95% CI: 0.41-0.49), and 0.53 for RP4 (0.95% CI: 0.48-0.57) with the experimental permissiveness in the unseen test dataset. Predictive phylogenetic signals occurred despite the broad host-range nature of these plasmids. Our results provide a framework that contributes to the assessment of the risk of AMR pollution in wastewater systems. AVAILABILITY AND IMPLEMENTATION: The predictive tool is available as an application at https://github.com/DaneshMoradigaravand/PlasmidPerm.

Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples.

Surveillance of antibiotic resistance genes (ARGs) has been increasingly conducted in environmental sectors to complement the surveys in human and animal sectors under the "One-Health" framework. However, there are substantial challenges in comparing and synthesizing the results of multiple studies that employ different test methods and approaches in bioinformatic analysis. In this article, we consider the commonly used quantification units (ARG copy per cell, ARG copy per genome, ARG density, ARG copy per 16S rRNA gene, RPKM, coverage, PPM, etc.) for profiling ARGs and suggest a universal unit (ARG copy per cell) for reporting such biological measurements of samples and improving the comparability of different surveillance efforts.

Critical evaluation of different mass transfer equations to model N2O emissions from water resource recovery facilities with diffuse aeration.

N2O measurements by liquid sensors in aerated tanks are an input to gas-liquid mass-transfer models for the prediction of N2O off-gas emissions. The prediction of N2O emissions from Water Resource Recovery Facilities (WRRFs) was evaluated by three different mass-transfer models using Benchmark Simulation Model 1 (BSM1) as a reference model. Inappropriate selection of mass-transfer model may result in miscalculation of carbon footprints based on soluble N2O online measurements. The film theory considers a constant mass-transfer expression, while more complex models suggest that emissions are affected by the aeration type, efficiency, and tank design characteristics. The differences among model predictions were 10-16% at dissolved oxygen (DO) concentration of 0.6 g/m3, when biological N2O production was the highest, while the flux of N2O was 20.0-24 kg N2O-N/d. At lower DO, the nitrification rate was low, while at DO higher than 2 g/m3, the N2O production was reduced leading to higher rates of complete nitrification and a flux of 5 kg N2O-N/d. The differences increased to 14-26% in deeper tanks, due to the pressure assumed in the tanks. The predicted emissions are also affected by the aeration efficiency when KLaN2O depends on the airflow instead of the KLaO2. Increasing the nitrogen loading rate under DO concentration of 0.50-0.65 g/m3 increased the differences in predictions by 10-20% in both alpha 0.6 and 1.2. A sensitivity analysis indicated that the selection of different mass-transfer models did not affect the selection of biochemical parameters for N2O model calibration.

Exploring the effects of intermittent aeration on the performance of nitrifying membrane-aerated biofilm reactors.

Membrane-aerated biofilm reactors (MABRs) are an emerging technology for nutrient removal; however, a trade-off remains between their removal rate and oxygen transfer efficiency. This study compares nitrifying flow-through MABRs operated under continuous and intermittent aeration modes at mainstream wastewater ammonia levels. The intermittently-aerated MABRs maintained maximal nitrification rates, including under conditions allowing the oxygen partial pressure on the gas side of the membrane to considerably drop during the no-aeration period. Nitrous oxide emissions of all reactors were comparable and amounted to approximately 20 % of the converted ammonia. Intermittent aeration increased the transformation rate constant of atenolol, yet did not affect the removal of sulfamethoxazole. Seven additional trace organic chemicals were not biodegraded by any of the reactors. The ammonia-oxidizing bacteria in the intermittently-aerated MABRs were dominated by Nitrosospira, previously shown to be abundant at low oxygen concentrations and provide reactor stability under changing conditions. Our findings indicate that intermittently-aerated flow-through MABRs can achieve high nitrification rates and oxygen transfer efficiencies, highlighting the possible implications of air supply discontinuity on nitrous oxide emissions and trace organic chemical biotransformation.

Aerobic biodegradation of quinoline under denitrifying conditions in membrane-aerated biofilm reactor.

Aerobic denitrification is being investigated as a novel biological nitrogen removal process, yet the knowledge on aerobic denitrification is limited to pure culture isolations and its occurrence in bioreactors remains unclear. This study investigated the feasibility and capacity of applying aerobic denitrification in membrane aerated biofilm reactor (MABR) for biological treatment of quinoline-laden wastewater. Stable and efficient removals of quinoline (91.5 ± 5.2%) and nitrate (NO3-) (86.5 ± 9.3%) were obtained under different operational conditions. Enhanced formation and function of extracellular polymeric substances (EPS) were observed at increasing quinoline loadings. MABR biofilm was highly enriched with aerobic quinoline-degrading bacteria, with a predominance of Rhodococcus (26.9 ± 3.7%) and secondary abundance of Pseudomonas (1.7 ± 1.2%) and Comamonas (0.94 ± 0.9%). Metagenomic analysis indicated that Rhodococcus contributed significantly to both aromatic degradation (24.5 ± 21.3%) and NO3- reduction (4.5 ± 3.9%), indicating its key role in aerobic denitrifying quinoline biodegradation. At increasing quinoline loadings, abundances of aerobic quinoline degradation gene oxoO and denitrifying genes of napA, nirS and nirK increased; there was a significant positive correlation of oxoO with nirS and nirK (p < 0.05). Aerobic quinoline degradation was likely initiated by hydroxylation, encoded by oxoO, followed by stepwise oxidations through 5,6-dihydroxy-1H-2-oxoquinoline or 8-hydroxycoumarin pathway. The results advance our understanding of quinoline degradation during biological nitrogen removal, and highlight the potential implementation of aerobic denitrification driven quinoline biodegradation in MABR for simultaneous removal of nitrogen and recalcitrant organic carbon from coking, coal gasification and pharmaceutical wastewaters.

Biofilm thickness controls the relative importance of stochastic and deterministic processes in microbial community assembly in moving bed biofilm reactors.

Deterministic and stochastic processes are believed to play a combined role in microbial community assembly, though little is known about the factors determining their relative importance. We investigated the effect of biofilm thickness on community assembly in nitrifying moving bed biofilm reactors using biofilm carriers where maximum biofilm thickness is controlled. We examined the contribution of stochastic and deterministic processes to biofilm assembly in a steady state system using neutral community modelling and community diversity analysis with a null-modelling approach. Our results indicate that the formation of biofilms results in habitat filtration, causing selection for phylogenetically closely related community members, resulting in a substantial enrichment of Nitrospira spp. in the biofilm communities. Stochastic assembly processes were more prevalent in biofilms of 200 µm and thicker, while stronger selection in thinner (50 µm) biofilms could be driven by hydrodynamic and shear forces at the biofilm surface. Thicker biofilms exhibited greater phylogenetic beta-diversity, which may be driven by a variable selection regime caused by variation in environmental conditions between replicate carrier communities, or by drift combined with low migration rates resulting in stochastic historical contingency during community establishment. Our results indicate that assembly processes vary with biofilm thickness, contributing to our understanding of biofilm ecology and potentially paving the way towards strategies for microbial community management in biofilm systems.

Electrochemical disinfection may increase the spread of antibiotic resistance genes by promoting conjugal plasmid transfer.

Current in the milliampere range can be used for electrochemical inactivation of bacteria. Yet, bacteria-including antibiotic resistant bacteria (ARB) may be subjected to sublethal conditions due to imperfect mixing or energy savings measures during electrochemical disinfection. It is not known whether such sublethal current intensities have the potential to stimulate plasmid transfer from ARB. In this study, conjugal transfer of plasmid pKJK5 was investigated between Pseudomonas putida strains under conditions reflecting electrochemical disinfection. Although the abundance of culturable and membrane-intact donor and recipient cells decreased with applied current (0-60 mA), both transconjugant density and transconjugant frequency increased. Both active chlorine and superoxide radicals were generated electrolytically, and ROS generation was induced. In addition, we detected significant over expression of a core oxidative stress defense gene (ahpCF) with current. Expression of selected conjugation related genes (traE, traI, trbJ, and trbL) also significantly correlated with current intensity. ROS accumulation, SOS response and subsequent derepression of conjugation are therefore the plausible consequence of sublethal current exposure. These findings suggest that sublethal intensities of current can enhance conjugal plasmid transfer, and that it is essential that conditions of electrochemical disinfection (applied voltage, current density, time and mixing) are carefully controlled to avoid conjugal ARG transmission.

Genomic profiling of Nitrospira species reveals ecological success of comammox Nitrospira.

BACKGROUND: The discovery of microorganisms capable of complete ammonia oxidation to nitrate (comammox) has prompted a paradigm shift in our understanding of nitrification, an essential process in N cycling, hitherto considered to require both ammonia oxidizing and nitrite oxidizing microorganisms. This intriguing metabolism is unique to the genus Nitrospira, a diverse taxon previously known to only contain canonical nitrite oxidizers. Comammox Nitrospira have been detected in diverse environments; however, a global view of the distribution, abundance, and diversity of Nitrospira species is still incomplete. RESULTS: In this study, we retrieved 55 metagenome-assembled Nitrospira genomes (MAGs) from newly obtained and publicly available metagenomes. Combined with publicly available MAGs, this constitutes the largest Nitrospira genome database to date with 205 MAGs, representing 132 putative species, most without cultivated representatives. Mapping of metagenomic sequencing reads from various environments against this database enabled an analysis of the distribution and habitat preferences of Nitrospira species. Comammox Nitrospira's ecological success is evident as they outnumber and present higher species-level richness than canonical Nitrospira in all environments examined, except for marine and wastewaters samples. The type of environment governs Nitrospira species distribution, without large-scale biogeographical signal. We found that closely related Nitrospira species tend to occupy the same habitats, and that this phylogenetic signal in habitat preference is stronger for canonical Nitrospira species. Comammox Nitrospira eco-evolutionary history is more complex, with subclades achieving rapid niche divergence via horizontal transfer of genes, including the gene encoding hydroxylamine oxidoreductase, a key enzyme in nitrification. CONCLUSIONS: Our study expands the genomic inventory of the Nitrospira genus, exposes the ecological success of complete ammonia oxidizers within a wide range of habitats, identifies the habitat preferences of (sub)lineages of canonical and comammox Nitrospira species, and proposes that horizontal transfer of genes involved in nitrification is linked to niche separation within a sublineage of comammox Nitrospira. Video Abstract.

Quantification and fate of plasmid-specific bacteriophages in wastewater: Beyond the F-coliphages.

Plasmid-specific bacteriophages specifically infect bacteria carrying conjugal plasmids. While wastewater has been used as isolation source for such phages, to date, only the distribution and ecology of RNA phages specific to the F plasmid have been described, because they serve as a water quality indicator. Yet, several other plasmid classes have higher clinical and ecological relevance, and the distribution, fate, and ecology of the phages that target them remain uncharacterized. We aimed to (i) provide an experimental platform to quantify the abundance of plasmid-specific phages applicable to several different conjugal plasmid classes, (ii) describe the distribution of such phages in wastewater systems, and (iii) relate their abundance to plasmid abundance and to municipal wastewater treatment processes. We introduced four model conjugal plasmids, belonging to incompatibility groups IncP-1, IncN, IncHI1, or IncF into an avirulent Salmonella enterica strain, for which somatic phages are at low abundance in wastewater. These strains were used in double layer agar assays with waters from contrasting sources. Plasmid-specific phages were common in wastewater but rare in river water. Hospital wastewater contained significantly more IncP-1-, but fewer IncF- and IncN- specific phages than domestic wastewater. This pattern did not match that of plasmid abundance estimated by Inc group targeting high-throughput quantitative PCR. The comparison between influent and effluent of wastewater treatment plants revealed a reduction in phage concentration by ca. 2 log, without significant contribution of primary settling. Overall, the ubiquity of these phages hints at their importance for plasmid ecology, and can provide opportunities in water quality monitoring and in ecological management of mobile resistance genes.

Short sludge age denitrification as alternative process for energy and nutrient recovery.

High rate activated sludge (HRAS) systems redirect organics into highly biodegradable sludge and nutrients into microbial proteins. This study evaluates anoxic HRAS for nitrogen and carbon recovery. The reactor treated synthetic wastewater at solids retention times (SRTs) of 5, 3 and 1 days. Denitrification rates varied between 0.15 and 0.19 g-NO3-N g-TSS-1 d-1 (total suspended solids per day) and all conditions showed favourable settling. The highest sludge yield, obtained at SRT 1 d, was 0.75 g-TSS g-CODremoved-1, double that observed for aerobic HRAS. The highest methane yield (322 mL-CH4 g-VSsludge-1) was obtained from sludge wasted at 3 d SRT. Both 1 d and 3 d SRTs showed favourable energy recovery, with 14 % of the organics recovered as methane. All conditions yielded sludge with protein content ranging between 24 and 27 % of dry weight and similar amino acid profile, comparable to traditional proteins. Thus, denitrifying HRAS recovers resources as its aerobic counterpart, allowing for nitrogen removal via denitrification, more stable compared to mainstream partial nitritation anammox typically combined with aerobic HRAS.

Assessing the substrate specificity of a micropollutant degrading strain: generalist or specialist?

Natural dissolved organic matter (DOM) can serve as an additional substrate for organic micropollutant (OMP) degrading bacteria, thus influencing OMP biodegradation in aquatic systems. DOM biodegradation depends on the OMP degrader's ability to grow on different DOM constituents, and on its capability to compete for DOM constituents against the rest of the resident aquatic microbial community. This study aimed to investigate the growth of a model OMP degrader strain, Novosphingobium sp. KN65.2 (assumed specialist), isolated for its ability to mineralize carbofuran, on thirteen DOM constituents; compare its metabolic capabilities to those of a common freshwater strain (Pseudomonas fluorescens sp. P17) (generalist); and to evaluate competition for specific compounds. Growth experiments were carried out in pure- and mixed culture batch experiments. The DOM constituents tested included aromatic amino acids and a range of phenolic acids (lignin derivatives). The OMP degrader could biodegrade approximately half of the tested compounds. It showed a high specialization for substrates containing a hydroxyl-group in the para-position of the primary aromatic ring substituent. However, its broad substrate range enabled the strain to grow on the same number of auxiliary substrates as the generalist. Moreover, the OMP degrader was able to successfully compete against the generalist for the biodegradation of one (4-hydroxybenzaldehyde) out of three substrates (4-hydroxybenzoic acid, 4-hydroxybenzaldehyde, L-tyrosine), which were biodegraded by both strains. The study results provide insight on the substrate specificity of a model OMP degrader, which can inform development of modeling frameworks investigating the influence of DOM on OMP biodegradation.

Efficient management of the nitritation-anammox microbiome through intermittent aeration: absence of the NOB guild and expansion and diversity of the NOx reducing guild suggests a highly reticulated nitrogen cycle.

Obtaining efficient autotrophic ammonia removal (aka partial nitritation-anammox, or PNA) requires a balanced microbiome with abundant aerobic and anaerobic ammonia oxidizing bacteria and scarce nitrite oxidizing bacteria. Here, we analyzed the microbiome of an efficient PNA process that was obtained by sequential feeding and periodic aeration. The genomes of the dominant community members were inferred from metagenomes obtained over a 6 month period. Three Brocadia spp. genomes and three Nitrosomonas spp. genomes dominated the autotrophic community; no NOB genomes were retrieved. Two of the Brocadia spp. genomes lacked the genomic potential for nitrite reduction. A diverse set of heterotrophic genomes was retrieved, each with genomic potential for only a fraction of the denitrification pathway. A mutual dependency in amino acid and vitamin synthesis was noted between autotrophic and heterotrophic community members. Our analysis suggests a highly-reticulated nitrogen cycle in the examined PNA microbiome with nitric oxide exchange between the heterotrophs and the anammox guild.