Cultivation of denitrifying bacteria: optimization of isolation conditions and diversity study

Environmentally dependent interactions shape patterns in gene content across natural microbiomes

Sequencing surveys of microbial communities in hosts, oceans and soils have revealed ubiquitous patterns linking community composition to environmental conditions. While metabolic capabilities restrict the environments suitable for growth, the influence of ecological interactions on patterns observed in natural microbiomes remains uncertain. Here we use denitrification as a model system to demonstrate how metagenomic patterns in soil microbiomes can emerge from pH-dependent interactions. In an analysis of a global soil sequencing survey, we find that the abundances of two genotypes trade off with pH; nar gene abundances increase while nap abundances decrease with declining pH. We then show that in acidic conditions strains possessing nar fail to grow in isolation but are enriched in the community due to an ecological interaction with nap genotypes. Our study provides a road map for dissecting how associations between environmental variables and gene abundances arise from environmentally modulated community interactions.

Global patterns in gene content of soil microbiomes emerge from microbial interactions

Microbial metabolism sustains life on Earth. Sequencing surveys of communities in hosts, oceans, and soils have revealed ubiquitous patterns linking the microbes present, the genes they possess, and local environmental conditions. One prominent explanation for these patterns is environmental filtering: local conditions select strains with particular traits. However, filtering assumes ecological interactions do not influence patterns, despite the fact that interactions can and do play an important role in structuring communities. Here, we demonstrate the insufficiency of the environmental filtering hypothesis for explaining global patterns in topsoil microbiomes. Using denitrification as a model system, we find that the abundances of two characteristic genotypes trade-off with pH; nar gene abundances increase while nap abundances decrease with declining pH. Contradicting the filtering hypothesis, we show that strains possessing the Nar genotype are enriched in low pH conditions but fail to grow alone. Instead, the dominance of Nar genotypes at low pH arises from an ecological interaction with Nap genotypes that alleviates nitrite toxicity. Our study provides a roadmap for dissecting how global associations between environmental variables and gene abundances arise from environmentally modulated community interactions.

Start-up of solid-phase denitrification process for treatment of nitrate-rich water in recirculating mariculture system: Carbon source selection and nitrate removal mechanism

Efficient nitrate removal from recirculating mariculture system (RMS) water is of significance since high concentration of nitrate would cause chronic health effects on aquatic organisms and eutrophication. Solid-phase denitrification (SPD) is a safer and more sustainable approach than conventional heterotrophic denitrification by dosing liquid carbon sources. Thus, its application for treating nitrate-rich RMS water was investigated in this study. Poly 3-hydroxybutyrate-co-3-hydroxyvalerate (PHBV) was identified with the best nitrate removal among four kinds of carbon sources. PHBV-filled reactors started with mariculture, municipal and mixing sludges (at the ratio of 1:1) and fed with 200 mg L-1 nitrate-rich RMS water all achieved over 81% nitrate removals with a HRT of 4 days. The dissolved organic carbon concentrations of the reactors were in the range of 3-9 mg L-1. Arcobacter, Halomonas, and Psedomonas were dominant genera responsible for nitrate removal in different reactors. Metagenomic analyses indicate that both denitrification and assimilatory nitrate reduction (ANR) are the main contributors to nitrate removals. Metagenomic results illustrated nirB/D cooperated with nasA may perform ANR pathway, which transformed nitrate to ammonia for biosynthesis. These results indicate that SPD could be a safer alternative for treating nitrate-rich RMS water, and provide new insights into nitrogen metabolism pathways in SPD process.

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.

Salinity effect on an anaerobic methane- and ammonium-oxidising consortium: Shifts in activity, morphology, osmoregulation and syntrophic relationship

Nitrate-dependent anaerobic methane oxidation (AOM) is a microbial process of both ecological significance for global methane mitigation and application potential for wastewater treatment. It is mediated by organisms belonging to the archaeal family 'Candidatus Methanoperedenaceae', which have so far mainly been found in freshwater environments. Their potential distribution in saline environments and their physiological responses to salinity variation were still poorly understood. In this study, the responses of the freshwater 'Candidatus Methanoperedens nitroreducens'-dominated consortium to different salinities were investigated using short- and long-term setups. Short-term exposure to salt stress significantly affected nitrate reduction and methane oxidation activities over the tested concentration range of 15-200‰ NaCl, and 'Ca. M. nitroreducens' showed the higher tolerance to high salinity stress than its partner of anammox bacteria. At high salinity concentration, near marine conditions of 37‰, the target organism 'Ca. M. nitroreducens' showed stabilized nitrate reduction activity of 208.5 µmol day-1 gCDW-1 in long-term bioreactors over 300 days, in comparison to 362.9 and 334.3 µmol day-1 gCDW-1 under low-salinity conditions (1.7‰ NaCl) and control conditions (∼15‰ NaCl). Different partners of 'Ca.  M. nitroreducens' evolved in the consortia with three different salinity conditions, suggesting the different syntrophic mechanisms shaped by changes in salinity. A new syntrophic relationship between 'Ca. M. nitroreducens' and Fimicutes and/or Chloroflexi denitrifying populations was identified under the marine salinity condition. Metaproteomic analysis shows that the salinity changes lead to higher expression of response regulators and selective ion (Na+/H+) channeling proteins that can regulate the osmotic pressure between the cell and its environment. The reverse methanogenesis pathway was, however, not impacted. The finding of this study has important implications for the ecological distribution of the nitrate-dependent AOM process in marine environments and the potential of this biotechnological process for the treatment of high-salinity industrial wastewater.

A review of algorithmic approaches for cell culture media optimization

Cell culture media composition and culture conditions play a crucial role in product yield, quality and cost of production. Culture media optimization is the technique of improving media composition and culture conditions to achieve desired product outcomes. To achieve this, there have been many algorithmic methods proposed and used for culture media optimization in the literature. To help readers evaluate and decide on a method that best suits their specific application, we carried out a systematic review of the different methods from an algorithmic perspective that classifies, explains and compares the available methods. We also examine the trends and new developments in the area. This review provides recommendations to researchers regarding the suitable media optimization algorithm for their applications and we hope to also promote the development of new cell culture media optimization methods that are better suited to existing and upcoming challenges in this biotechnology field, which will be essential for more efficient production of various cell culture products.

Nitrate removal rates, isotopic fractionation, and denitrifying bacteria in a woodchip-based permeable reactive barrier system: a long-term column experiment

This study evaluated the effectiveness of using organic carbon materials (i.e., woodchips) to remove nitrate from groundwater. The results of our flow-through column experiment, which was conducted over 1.6 years, suggested that denitrifying bacteria reduce nitrate by using it as an electron acceptor and woodchips as an electron donor. The nitrate removal rates were sufficiently high (0.39-1.04 mmol L-1 day-1) during the operation of the column. Denitrification process was supported by fractionation of nitrogen and oxygen isotopes (δ15N and δ18O), with the δ15N and δ18O values enriched from 7.4‰ and 22.3‰ to 21.2‰ and 30.4‰, respectively. Enrichment factors ([Formula: see text]) for 15 N and 18O were calculated using the Rayleigh fractionation model, with values of - 13.2‰ for ε15N and - 7.1‰ for ε18O. The fractionation ratio of 15 N to 18O was 1.9:1, confirming denitrification. The most abundant bacterial genera in the soil used for inoculation were Enterobacter (86.7%), Nitrospira (1.8%), and Arthrobacter (1.5%), while those in the column effluent were Macrococcus (37.1%), Escherichia (14.7%), and Shigella (14.6%), indicating that bacterial communities changed in response to geochemical conditions in the column. This study suggests that nitrate in groundwater can be effectively removed using woodchip-based passive treatment systems and that information on isotopic fractionation and denitrifying bacteria can be key tools to understand denitrification.

Monthly dynamics of microbial communities and variation of nitrogen-cycling genes in an industrial-scale expanded granular sludge bed reactor

Introduction

The expanded granular sludge bed (EGSB) is a major form of anaerobic digestion system during wastewater treatment. Yet, the dynamics of microbial and viral communities and members functioning in nitrogen cycling along with monthly changing physicochemical properties have not been well elucidated.

Methods

Here, by collecting the anaerobic activated sludge samples from a continuously operating industrial-scale EGSB reactor, we conducted 16S rRNA gene amplicon sequencing and metagenome sequencing to reveal the microbial community structure and variation with the ever-changing physicochemical properties along within a year.

Results

We observed a clear monthly variation of microbial community structures, while COD, the ratio of volatile suspended solids (VSS) to total suspended solids (TSS) (VSS/TSS ratio), and temperature were predominant factors in shaping community dissimilarities examined by generalized boosted regression modeling (GBM) analysis. Meanwhile, a significant correlation was found between the changing physicochemical properties and microbial communities (p <0.05). The alpha diversity (Chao1 and Shannon) was significantly higher (p <0.05) in both winter (December, January, and February) and autumn (September, October, and November) with higher organic loading rate (OLR), higher VSS/TSS ratio, and lower temperature, resulting higher biogas production and nutrition removal efficiency. Further, 18 key genes covering nitrate reduction, denitrification, nitrification, and nitrogen fixation pathways were discovered, the total abundance of which was significantly associated with the changing environmental factors (p <0.05). Among these pathways, the dissimilatory nitrate reduction to ammonia (DNRA) and denitrification had the higher abundance contributed by the top highly abundant genes narGH, nrfABCDH, and hcp. The COD, OLR, and temperature were primary factors in affecting DNRA and denitrification by GBM evaluation. Moreover, by metagenome binning, we found the DNRA populations mainly belonged to Proteobacteria, Planctomycetota, and Nitrospirae, while the denitrifying bacteria with complete denitrification performance were all Proteobacteria. Besides, we detected 3,360 non-redundant viral sequences with great novelty, in which Siphoviridae, Podoviridae, and Myoviridae were dominant viral families. Interestingly, viral communities likewise depicted clear monthly variation and had significant associations with the recovered populations (p <0.05).

Discussion

Our work highlights the monthly variation of microbial and viral communities during the continuous operation of EGSB affected by the predominant changing COD, OLR, and temperature, while DNRA and denitrification pathways dominated in this anaerobic system. The results also provide a theoretical basis for the optimization of the engineered system.

Effect of aeration modes on nitrogen removal and N2O emission in the partial nitrification and denitrification process for landfill leachate treatment

The anoxic/multi-aerobic process is widely applied for treating landfill leachate with low carbon to nitrogen ratio. In this study, the effect of two aeration modes in the aerobic phase, i.e. decreasing dissolved oxygen (DO) and increasing DO, on nitrogen removal and N₂O emission in the process were systematically compared. The results demonstrate that the aerobic phase with increasing DO mode has a positive effect on improved total nitrogen removal (78 %) under the COD/N ratio as low as 3.45 and minimized N₂O emission. DO concentration higher than 1.5 mg/L in the aerobic phase reduced nitrogen removal and led to a significant high N₂O emission in the process. Complete nitrite denitrification in the anoxic phase correlated with minimized N₂O emission. Under efficient nitrogen removal stage, N₂O emission factor was 2.4 ± 1.0 % of the total incoming nitrogen. Microbial analysis revealed that increasing DO mode increased the abundance of ammonia oxidizing bacteria and denitrifiers.

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-COD_removed^-1, double that observed for aerobic HRAS. The highest methane yield (322 mL-CH₄ g-VS_sludge^-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.

Denitrification kinetics during aquifer storage and recovery of drainage water from agricultural land

An aquifer storage transfer and recovery (ASTR) system was studied in which tile drainage water (TDW) was injected with relatively high NO₃ (about 14 mg/L) concentrations originating from fertilizers. Here we present the evolution of denitrification kinetics at 6 different depths in the aquifer before, and during ASTR operation. First-order denitrification rate constants increased over time before and during the first days of ASTR operation, likely due to microbial adaptation of the native bacterial community and/or bioaugmentation of the aquifer by denitrifying bacteria present in injected TDW. Push-pull tests were performed in the native aquifer before ASTR operation. Obtained first-order denitrification rate constants were negligible (0.00-0.03 d^-1) at the start, but increased to 0.17-0.83 d^-1 after a lag-phase of about 6 days. During the first days of ASTR operation in autumn 2019, the arrival of injected TDW was studied at 2.5 m distance from the injection well. First-order denitrification rate constants increased again over time (maximum >1 d^-1). Three storage periods without injection were monitored in winter 2019, fall 2020, and spring 2021 during ASTR operation. First-order rate constants ranged between 0.12 and 0.61 d^-1. Denitrification coupled to pyrite oxidation occurred at all depths, but other oxidation processes were indicated as well. NO₃ concentration trends resembled Monod kinetics but were fitted also to a first-order decay rate model to facilitate comparison. Rate constants during the storage periods were substantially lower than during injection, probably due to a reduction in the exchange rate between aquifer solid phases and injected water during the stagnant conditions. Denitrification rate constants deviated maximally a factor 5 over time and depth for all in-situ measurement approaches after the lag-phase. The combination of these in-situ approaches enabled to obtain more detailed insights in the evolution of denitrification kinetics during AS(T)R.

Consumption of N2O by Flavobacterium azooxidireducens sp. nov. Isolated from Decomposing Leaf Litter of Phragmites australis (Cav.)

Microorganisms acting as sinks for the greenhouse gas nitrous oxide (N₂O) are gaining increasing attention in the development of strategies to control N₂O emissions. Non-denitrifying N₂O reducers are of particular interest because they can provide a real sink without contributing to N₂O release. The bacterial strain under investigation (IGB 4-14^T), isolated in a mesocosm experiment to study the litter decomposition of Phragmites australis (Cav.), is such an organism. It carries only a nos gene cluster with the sec-dependent Clade II nosZ and is able to consume significant amounts of N₂O under anoxic conditions. However, consumption activity is considerably affected by the O₂ level. The reduction of N₂O was not associated with cell growth, suggesting that no energy is conserved by anaerobic respiration. Therefore, the N₂O consumption of strain IGB 4-14^T rather serves as an electron sink for metabolism to sustain viability during transient anoxia and/or to detoxify high N₂O concentrations. Phylogenetic analysis of 16S rRNA gene similarity revealed that the strain belongs to the genus Flavobacterium. It shares a high similarity in the nos gene cluster composition and the amino acid similarity of the nosZ gene with various type strains of the genus. However, phylogenomic analysis and comparison of overall genome relatedness indices clearly demonstrated a novel species status of strain IGB 4-14^T, with Flavobacterium lacus being the most closely related species. Various phenotypic differences supported a demarcation from this species. Based on these results, we proposed a novel species Flavobacterium azooxidireducens sp. nov. (type strain IGB 4-14^T = LMG 29709^T = DSM 103580^T).

Biological oxidation methods for the removal of organic and inorganic contaminants from wastewater: A comprehensive review

Enzyme-based bioremediation is a simple, cost-effective, and environmentally friendly method for isolating and removing a wide range of environmental pollutants. This study is a comprehensive review of recent studies on the oxidation of pollutants by biological oxidation methods, performed individually or in combination with other methods. The main bio-oxidants capable of removing all types of pollutants, such as organic and inorganic molecules, from fungi, bacteria, algae, and plants, and different types of enzymes, as well as the removal mechanisms, were investigated. The use of mediators and modification methods to improve the performance of microorganisms and their resistance under harsh real wastewater conditions was discussed, and numerous case studies were presented and compared. The advantages and disadvantages of conventional and novel immobilization methods, and the development of enzyme engineering to adjust the content and properties of the desired enzymes, were also explained. The optimal operating parameters such as temperature and pH, which usually lead to the best performance, were presented. A detailed overview of the different combination processes was also given, including bio-oxidation in coincident or consecutive combination with adsorption, advanced oxidation processes, and membrane separation. One of the most important issues that this study has addressed is the removal of both organic and inorganic contaminants, taking into account the actual wastewaters and the economic aspect.

Genomic evidence for two pathways of formaldehyde oxidation and denitrification capabilities of the species Paracoccus methylovorus sp. nov

Three strains (H4-D09^T, S2-D11 and S9-F39) of a member of the genus Paracoccus attributed to a novel species were isolated from topsoil of temperate grasslands. The genome sequence of the type strain H4-D09^T exhibited a complete set of genes required for denitrification as well as methylotrophy. The genome of H4-D09^T included genes for two alternative pathways of formaldehyde oxidation. Besides the genes for the canonical glutathione (GSH)-dependent formaldehyde oxidation pathway, all genes for the tetrahydrofolate-formaldehyde oxidation pathway were identified. The strain has the potential to utilize methanol and/or methylamine as a single carbon source as evidenced by the presence of methanol dehydrogenase (mxaFI) and methylamine dehydrogenase (mau) genes. Apart from dissimilatory denitrification genes (narA, nirS, norBC and nosZ), genes for assimilatory nitrate (nasA) and nitrite reductases (nirBD) were also identified. The results of phylogenetic analysis based on 16S rRNA genes coupled with riboprinting revealed that all three strains represented the same species of genus Paracoccus. Core genome phylogeny of the type strain H4-D09^T indicated that Paracoccus thiocyanatus and Paracoccus denitrificans are the closest phylogenetic neighbours. The average nucleotide index (ANI) and digital DNA-DNA hybridization (dDDH) with the closest phylogenetic neighbours revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. The major respiratory quinone is Q-10, and the predominant cellular fatty acids are C_18 : 1ω7c, C_19 : 0cyclo ω7c, and C_16 : 0, which correspond to those detected in other members of the genus. The polar lipid profile consists of a diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), aminolipid (AL), glycolipid (GL) and an unidentified lipid (L).On the basis of our results, we concluded that the investigated isolates represent a novel species of the genus Paracoccus, for which the name Paracoccus methylovorus sp. nov. (type strain H4-D09^T=LMG 31941^T= DSM 111585^T) is proposed.

Reinforcement of denitrification in a biofilm electrode reactor with immobilized polypyrrole/anthraquinone-2,6-disulfonate composite cathode

In biofilm electrode reactors (BER), good nitrate removal performance can be achieved through cooperation of heterotrophic and hydrogen autotrophic denitrification under low carbon/nitrogen conditions. In this study, we proposed a more multifunctional composite cathode, which combine immobilized anthraquinone-2,6-disulphonic disodium salt (AQDS) with polypyrrole (PPy) by electrochemical polymerization-doping method. The nitrate removal performance in BER with PPy/AQDS composite cathode was obviously improved, the nitrate removal rate (4.96 mg/L·h) was almost 2.0 times higher than the control BER system, and relatively stabled nitrate removal efficiency (≥90.0%) was also achieved even as the COD/N of 2.50. Compared with the bare graphite felt, PPy/AQDS coating cathode showed much better electrocatalytic activities, which was more advantageous for in situ production of H₂ to support hydrogen autotrophic denitrification process. The PPy-bound AQDS could also act as electron intermediaries, which is beneficial to greatly promote indirect electron process between the denitrifiers and nitrate. Moreover, the PPy/AQDS composite layer formed many particles for improving the specific surface area and bio-attachment site for bacterial attachment, which was conducive for the proliferation of microorganisms and denitrification efficiency. The ratio of biofilm and electrode of PPy/AQDS biocathode was 0.32 ± 0.08, which was 2.46 times than bare electrode (0.13 ± 0.06). Furthermore, enrichment of specific denitrifiers and enhancement of denitrifying enzyme activity was obtained using PPy/AQDS treated electrode, the much higher relative abundance of Thauera of PPy/AQDS biocathode was 1.58 times to the application of bare graphite felt.

Ubiquity and Diversity of Cold Adapted Denitrifying Bacteria Isolated From Diverse Antarctic Ecosystems

Nitrogen cycle has been poorly investigated in Antarctic ecosystems. In particular, how extreme conditions of low temperature, dryness, and high radiation select the microorganisms involved in the cycle is not yet understood. Denitrification is an important step in the nitrogen cycle in which nitrate is reduced stepwise to the gases NO, N2O, and N2. Denitrification is carried out by a wide group of microorganisms spread in the phylogenetic tree. The aim of this work was to isolate and characterize denitrifying bacteria present in different cold environments from Antarctica. Bacterial isolates were obtained from lake, meltwater, sea, glacier ice, ornithogenic soil, and penguin feces samples from King George Island, Fildes peninsula in the Antarctic. Samples were taken during the deicing season in five sampling campaigns. From all the samples we were able to isolate denitrifying strains. A total of 199 bacterial isolates with the capacity to grow in anaerobic mineral media reducing nitrate at 4°C were obtained. The characterization of the isolates by 16S rRNA gene sequence analysis showed a high predominance of the genus Pseudomonas, followed by Janthinobacterium, Flavobacterium, Psychrobacter, and Yersinia. Other minor genera detected were Cryobacterium, Iodobacter, Kaistella, and Carnobacterium. The capacity to denitrify was not previously described for most of the bacteria related to our isolates and in many of them denitrifying genes were not present suggesting the presence of new genes in this extreme environment. Our work demonstrates the ubiquity of denitrification in the Maritime Antarctica and gives important information linking denitrification at cold temperature with taxa in an unequivocal way.

Nitrate Water Contamination from Industrial Activities and Complete Denitrification as a Remediation Option

Freshwater is a scarce resource that continues to be at high risk of pollution from anthropogenic activities, requiring remediation in such cases for its continuous use. The agricultural and mining industries extensively use water and nitrogen (N)-dependent products, mainly in fertilizers and explosives, respectively, with their excess accumulating in different water bodies. Although removal of NO3 from water and soil through the application of chemical, physical, and biological methods has been studied globally, these methods seldom yield N2 gas as a desired byproduct for nitrogen cycling. These methods predominantly cause secondary contamination with deposits of chemical waste such as slurry brine, nitrite (NO2), ammonia (NH3), and nitrous oxide (N2O), which are also harmful and fastidious to remove. This review focuses on complete denitrification facilitated by bacteria as a remedial option aimed at producing nitrogen gas as a terminal byproduct. Synergistic interaction of different nitrogen metabolisms from different bacteria is highlighted, with detailed attention to the optimization of their enzymatic activities. A biotechnological approach to mitigating industrial NO3 contamination using indigenous bacteria from wastewater is proposed, holding the prospect of optimizing to the point of complete denitrification. The approach was reviewed and found to be durable, sustainable, cost effective, and environmentally friendly, as opposed to current chemical and physical water remediation technologies.

Efficacies of Nitrogen Removal and Comparisons of Microbial Communities in Full-Scale (Pre-Anoxic Systems) Municipal Water Resource Recovery Facilities at Low and High COD:TN Ratios

At a low COD:TN ratio (≤5) in influent, maintaining a longer HRT (≥9 h) and longer SRT (≥30 d) are suggested to improve higher N removal efficiency in case of operation at low DO (Dissolved oxygen) level (0.9 ± 0.2 mg-O2/L). However, in case of operation at high DO level (4.0 ± 0.5 mg-O2/L), short HRT (1 h) and typical SRT (17 d) make it possible to achieve nitrogen removal. On the other hand, at a high COD:TN ratio (≥8.4), a typical HRT (9–15 h), SRT (12–19 d), and DO level (1.3–2.6 mg-O2/L) would be applied. Microbial distribution analysis showed an abundance of AOA (Ammonia-oxidizing archaea) under conditions of low DO (≤0.9 mg-O2/L). Nitrosomonas sp. are mostly found in the all investigated water resource recovery facilities (WRRFs). Nitrosospira sp. are only found under operating conditions of longer SRT for WRRFs with a low COD:TN ratio. In comparison between abundances of Nitrobacter sp. and Nitrospira sp., abundances of Nitrobacter sp. are proportional to low DO concentration rather than abundance of Nitrospira sp. A predominance of nosZ-type denitrifiers were found at low DO level. Abundance of denitrifiers by using nirS genes showed an over-abundance of denitrifiers by using nirK genes at low and high COD:TN ratios.

Genomic structure predicts metabolite dynamics in microbial communities

The metabolic activities of microbial communities play a defining role in the evolution and persistence of life on Earth, driving redox reactions that give rise to global biogeochemical cycles. Community metabolism emerges from a hierarchy of processes, including gene expression, ecological interactions, and environmental factors. In wild communities, gene content is correlated with environmental context, but predicting metabolite dynamics from genomes remains elusive. Here, we show, for the process of denitrification, that metabolite dynamics of a community are predictable from the genes each member of the community possesses. A simple linear regression reveals a sparse and generalizable mapping from gene content to metabolite dynamics for genomically diverse bacteria. A consumer-resource model correctly predicts community metabolite dynamics from single-strain phenotypes. Our results demonstrate that the conserved impacts of metabolic genes can predict community metabolite dynamics, enabling the prediction of metabolite dynamics from metagenomes, designing denitrifying communities, and discovering how genome evolution impacts metabolism.

Metagenomic analysis revealed the sulfur- and iron- oxidation capabilities of heterotrophic denitrifying sludge

Heterotrophic denitrification is widely applied in wastewater treatment processes to remove nitrate. However, the ability of the heterotrophic denitrifying sludge to use inorganic matter as electron donors to perform autotrophic denitrification has rarely been investigated. In this study, we enriched heterotrophic denitrifying sludge and demonstrated its sulfur- and iron- oxidizing abilities and denitrification performance with batch experiments. Based on high-throughput sequencing of 16S rRNA genes, high diversity and abundance of sulfur-oxidizing bacteria (SOB) (e.g., Sulfuritalea, Thiobacillus, and Thiothrix) and iron (II)-oxidizing bacteria (FeOB) (e.g., Azospira and Thiobacillus) were observed. Metagenomic sequencing and genome binning results further suggested that the SOB in the heterotrophic denitrifying sludge were mainly Alphaproteobacteria and Betaproteobacteria instead of Gammaproteobacteria and Epsilonproteobacteria. The similarities of potential iron-oxidizing genes with known sequences were very low (32-51%), indicating potentially novel FeOB species in this system. The findings of this study suggested that the heterotrophic denitrifying sludge harbors diverse mixotrophic denitrifying bacterial species, and based on this finding, we proposed that organic carbon and inorganic electron donors (e.g., sulfur, thiosulfate, and iron) could be jointly used in engineering practices according to the quality and quantity of wastewater to balance the cost and efficiency of the denitrification process.

Gulf of Mexico blue hole harbors high levels of novel microbial lineages

Exploration of oxygen-depleted marine environments has consistently revealed novel microbial taxa and metabolic capabilities that expand our understanding of microbial evolution and ecology. Marine blue holes are shallow karst formations characterized by low oxygen and high organic matter content. They are logistically challenging to sample, and thus our understanding of their biogeochemistry and microbial ecology is limited. We present a metagenomic and geochemical characterization of Amberjack Hole on the Florida continental shelf (Gulf of Mexico). Dissolved oxygen became depleted at the hole's rim (32 m water depth), remained low but detectable in an intermediate hypoxic zone (40-75 m), and then increased to a secondary peak before falling below detection in the bottom layer (80-110 m), concomitant with increases in nutrients, dissolved iron, and a series of sequentially more reduced sulfur species. Microbial communities in the bottom layer contained heretofore undocumented levels of the recently discovered phylum Woesearchaeota (up to 58% of the community), along with lineages in the bacterial Candidate Phyla Radiation (CPR). Thirty-one high-quality metagenome-assembled genomes (MAGs) showed extensive biochemical capabilities for sulfur and nitrogen cycling, as well as for resisting and respiring arsenic. One uncharacterized gene associated with a CPR lineage differentiated hypoxic from anoxic zone communities. Overall, microbial communities and geochemical profiles were stable across two sampling dates in the spring and fall of 2019. The blue hole habitat is a natural marine laboratory that provides opportunities for sampling taxa with under-characterized but potentially important roles in redox-stratified microbial processes.

Microbial community response to ciprofloxacin toxicity in sponge membrane bioreactor

This study aims to offer insights into how ciprofloxacin (CIP) impact bacterial community structures in the Sponge-MBR process when CIP is spiked into hospital wastewater. We found that the CIP toxicity decreased richness critical phylotypes such as phylum class ẟ-, β-, ɣ-proteobacteria, and Flavobacteria that co-respond to suppress denitrification and cake fouling to 37% and 28% respectively. Cluster analysis shows that the different community structures were formed under the influence of CIP toxicity. CIP decreased attached growth biomass by 2.3 times while increasing the concentration of permeate nitrate by 3.8 times, greatly affecting TN removal by up to 26%. Ammonia removal was kept stable by inflating the ammonia removal rate (p < 0.003), with the wealthy Nitrospira genus guaranteeing the nitrification activity. In addition, we observed an increasing richness of Chloroflexi and Planctomycetes, which may play a role in fouling reduction in the Sponge-MBR. Therefore, if the amount of antibiotics in hospital wastewater continues to increase, it is so important to extend biomass retention for denitrification recovery.

Pseudomonas campi sp. nov., a nitrate-reducing bacterium isolated from grassland soil

A novel strain was isolated from grassland soil that has the potential to assimilate ammonium by the reduction of nitrate in the presence of oxygen. Whole genome sequence analysis revealed the presence of an assimilatory cytoplasmic nitrate reductase gene nasA and the assimilatory nitrite reductase genes nirBD which are involved in the sequential reduction of nitrate to nitrite and further to ammonium, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate represents a member of the genus Pseudomonas. The closest phylogenetic neighbours based on 16S rRNA gene sequence analysis are the type strains of Pseudomonas peli (98.17%) and Pseudomonas guineae (98.03%). In contrast, phylogenomic analysis revealed a close relationship to Pseudomonas alcaligenes. Computation of the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) with the closest phylogenetic neighbours of S1-A32-2^T revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. On the basis of these results, it was concluded that the soil isolate represents a novel species of the genus Pseudomonas, for which the name Pseudomonas campi sp. nov. (type strain S1-A32-2^T=LMG 31521^T=DSM 110222^T) is proposed.

Genome-level insights into the operation of an on-site biological wastewater treatment unit reveal the importance of storage time

On-site wastewater treatment systems are gaining popularity in areas where centralized wastewater treatment is not available. In the current case study a domestic activated sludge system was investigated, where treated effluent was stored in a short-term (1 week turn-over time) and a long-term (over 2-3 months) storage tank and was then used for irrigation. This design provided a unique opportunity to assess the chemical and microbial changes of the effluent upon storage. Long-term storage greatly improved both the chemical quality and the degradation efficiency of most organic micropollutants examined, including petroleum hydrocarbons and the pesticide diethyltoluamide. Taxonomic profile of the core microbiome of the effluent was also influenced upon storage. Relative abundance values of the members of Azoarcus and Thauera genera, which are important in degrading polycyclic aromatic hydrocarbons compounds, clearly indicated the biodegrading activity of these microbes across samples. The abundance of xenobiotics degradation functions correlated with the observed organic micropollutant degradation values indicating efficient microbial decomposition of these contaminants. Functions related to infectious diseases also had the highest abundance in the short-term storage tank corresponding well with the relative abundance of indicator organisms and implying to the significance of storage time in the elimination of pathogens. Based on these results, small, on-site wastewater treatment systems could benefit from long-term storage of wastewater effluent.

Microalgal-bacterial granular sludge process outperformed aerobic granular sludge process in municipal wastewater treatment with less carbon dioxide emissions

The aerobic granular sludge (AGS) process and microalgal-bacterial granular sludge (MBGS) process were comparably applied for municipal wastewater treatment in sequencing batch reactors with a height to diameter ratio of eight. For morphological appearances, the yellow aerobic granules were strip-shaped (4.0 mm × 0.62 mm) while the green microalgal-bacterial granules were elliptical-shaped (2.0 mm × 0.75 mm). The dominated rod-shaped bacteria (e.g., Acidobacteria and Bacteroidetes) and the slender configuration might be associated with the strip shape of aerobic granules under weak acid conditions. The nutrients removal performances by MBGS process were generally slightly better than AGS process. In addition, nutrients removal mechanisms were identified to elucidate how organics, ammonia, and phosphorus were removed by AGS process and MBGS process, respectively. Mass balance calculation estimated that MBGS process appeared to achieve much less CO₂ emission (5.8%) compared with AGS process (44.4%). Overall, it proved that MBGS process, with the merits of potentially low energy cost, limited CO₂ emission, and excellent performance, showed more prospects in municipal wastewater treatment than AGS process.

Methanogenic potential of diclofenac and ibuprofen in sanitary sewage using metabolic cosubstrates

Diclofenac (DCF) and ibuprofen (IBU) are widely used anti-inflammatory drugs and are frequently detected in wastewater from Wastewater Treatment Plants and in aquatic environments. In this study, the methanogenic potential (P) of anaerobic sludge subjected to DCF (7.11 ± 0.02 to 44.41 ± 0.05 mg L^-1) and IBU (6.11 ± 0.01 to 42.61 ± 0.05 mg L^-1), in sanitary sewage, was investigated in batch reactors. Cosubstrates (200 mg L^-1 of organic matter) in the form of ethanol, methanol:ethanol and fumarate were tested separately for the removal of drugs. In the DCF assays, P was 6943 ± 121 μmolCH₄, 9379 ± 259 μmolCH_4, 9897 ± 212 μmolCH₄ and 11,530 ± 368 μmolCH₄ for control, fumarate, methanol:ethanol and ethanol conditions, respectively. In the IBU assays, under the same conditions, P was 6145 ± 101 μmolCH₄, 6947 ± 66 μmolCH₄, 8141 ± 191 μmolCH₄and 10,583 ± 512 μmolCH₄, respectively. Without cosubstrates, drug removal was below 18% for 43.10 ± 0.01 mgDCF L^-1 and 43.12 ± 0.03 mgIBU L^-1, respectively. Higher P and removal of DCF (28.24 ± 1.10%) and IBU (18.72 ± 1.60%) with ethanol was observed for 43.20 ± 0.01 mgDCF L^-1 and 43.42 ± 0.03 mgIBU L^-1, respectively. This aspect was better evidenced with DCF due to its molecular structure, a condition that resulted in a higher diversity of bacterial populations. Through the 16S rRNA sequencing, bacteria genera capable of performing aromatic ring cleavage, β-oxidation and oxidation of ethanol and fatty acids were identified. Higher relative abundance (>0.6%) was observed for Smithella, Sulfuricurvum and Synthophus for the Bacteria Domain and Methanosaeta (>79%) for the Archaea Domain. The use of ethanol favored greater mineralization of organic matter and greater methane production, which can directly assist in the metabolic pathways of microorganisms.

Effect of Denitrifying Bacterial Biomass and Carbon Sources on Nitrate Removal

Denitrification based on immobilized microbial cellulose may offer an economical replacement for conventional treatment for nitrate removal. The environmental and bacterial biomass may influence the rate of biological denitrification processes. This study aimed to investigate the factors that affect denitrification rates, including carbon sources, pH, and bacterial inoculum. Different inoculum biomass of Pseudomonas aeruginosa and various carbon sources of glucose, sucrose, and cellulose with different concentrations were tested to assimilate 100 mg/L of KNO3 as nitrate source. Additionally, five additional inoculations, five different incubation time, and seven different pH levels were studied. The Pseudomonas aeruginosa isolates used different mineral media with three carbon sources, glucose, sucrose, and cellulose, with different concentrations at different rates to denitrify nitrate. The highest denitrification rate was with glucose after 18 hrs and was after 24 hrs when sucrose and cellulose were used, respectively. The bacterial biomass denitrification level was the highest, between 0.8% and 1% of OD600=1. Nitrate removal by Pseudomonas aeruginosa was the highest at pH 7, 8, and 9. This report suggests that when glucose is used as a carbon source, at neutral to alkaline pH, and 1% of denitrifying bacterial biomass, the highest level of biological denitrification process may be achieved.

Characterization of nitrous oxide reduction by Azospira sp. HJ23 isolated from advanced wastewater treatment sludge

A new nitrous oxide (N₂O)-reducing bacterium was isolated from a consortium that was enriched using advanced wastewater treatment sludge as an inoculum and N₂O as the sole nitrogen source. The isolated facultative anaerobe was identified as Azospira sp. HJ23. Azospira sp. HJ23 exhibited optimum N₂O-reducing activity with a C/N ratio of 62 at pH 6 in the temperature range of 37 °C to 40 °C. The optimum carbon source for N₂O reduction was a mixture of glucose and acetate. The maximum rate of N₂O reduction by Azospira sp. HJ23 was 4.8 mmol·g-dry cell^-1·h^-1, and its N₂O-reducing activity was higher than other known N₂O reducers. Azospira sp. HJ23 possessed several functional genes for denitrification. These included narG (NO₃^- reductase), nirK (NO₂^- reductase), norB (NO reductase), and nosZ (N₂O reductase) genes. These results suggest that Azospira sp. HJ23 can be applied in the denitrification process to minimalize N₂O emission.

An appropriate technique for treating rural wastewater by a flow step feed system driven by wind-solar hybrid power

Most rural wastewater treatment facilities require aeration equipment to ensure sufficient dissolved oxygen (DO) during processing. Operation and maintenance are costly, and cannot be met in many areas with poor economic levels. This has led to further deterioration of the rural water environment and aroused much attention. This work reports a plug-flow step feed system utilizing wind and solar hybrid energy for rural wastewater treatment. Under certain climatic conditions, the wind energy and solar energy provided complimentary power generation, and an automatic control system (without batteries) was constructed. The corresponding control logic for multi-energy level operation was developed. Furthermore, the power generation efficiency of the system, the pollutant removal, and its mechanism on the bioreactor were also analyzed. According to the monitoring of meteorological conditions, wind and solar resources at the test site were abundant, and the electricity generated by the power generation was sufficient to meet the operational needs of the equipment. Energy efficiency can reach 80.0%. The characteristics of pollutant removal in each process section were studied on spatial and temporal dimensions. Results showed that the wastewater treatment process reached mean removal efficiencies of chemical oxygen demand (COD_cr), NH₄⁺-N, total nitrogen (TN) and total phosphorus (TP) were 90.2%, 94.3%, 61.4% and 63.1%, respectively. Analyses of microbial community richness and group changes in each anoxic/aerobic reaction chamber in the biofilm reactor showed that the population structure was relatively stable and that there were abundant functional bacteria capable of degrading pollutants in each aerobic and anoxic unit. This system can thus be a more sustainable treatment process than traditional techniques used for rural wastewater treatment, providing a new design approach for low-energy consumption and unattended rural wastewater treatment.

Flocs in disguise? High granule abundance found in continuous-flow activated sludge treatment plants

To date, high performance of full-scale aerobic granular sludge (AGS) technology has been demonstrated on a global scale. Its further integration with existing continuous flow activated sludge (CFAS) treatment plants is the next logical step. All granular sludge reactors operated in sequencing batch reactors (SBR) mode with anaerobic feeding conditions select for growth of phosphorus and glycogen accumulating organisms (PAO and GAO, respectively), which are known to enhance sludge settling characteristics. Therefore, we hypothesized that AGS are commonly present at full-scale CFAS processes with enhanced biological phosphorus removal (EBPR) and low sludge volume index (SVI). This hypothesis was confirmed at 13 EBPR plants, where granules were found present (at plants where SVI was lower than 100 ml/g) with a strong correlation between high granule abundance and low SVI. A wide range of granule abundance was found among the plants, ranging from 0.5% to as high as 80%. Evaluations of the EBPR plant process configurations showed that high granule abundances may be related to selector design features such as high anaerobic food to mass (F/M) ratios, unmixed in-line fermentation, and high influent soluble COD fraction. Granules were also observed at a non-EBPR plant with an aerobic selector receiving high F/M feeds. Quantitative PCR and 16S rRNA gene sequencing analyses revealed higher relative gene abundance of Accumulibacter PAO and Competibacter GAO in the granules over flocs, as well as a correlation between granule abundance and some possible EPS producers such as Flavobacterium and Competibacter. Our results indicated that process configurations that select for slow-growing or EPS-producing heterotrophs play an important role for granule formation in full-scale CFAS systems as previously shown in SBR configurations.

Effect of Electrostatic Field Strength on Bioelectrochemical Nitrogen Removal from Nitrogen-Rich Wastewater

The effect of electrostatic fields on the bioelectrochemical removal of ammonium and nitrite from nitrogen-rich wastewater was investigated at strengths ranging from 0.2 to 0.67 V/cm in bioelectrochemical anaerobic batch reactors. The electrostatic field enriched the bulk solution with electroactive bacteria, including ammonium oxidizing exoelectrogens (AOE) and denitritating electrotrophs (DNE). The electroactive bacteria removed ammonium and nitrite simultaneously with alkalinity consumption through biological direct interspecies electron transfer (DIET) in the bulk solution. However, the total nitrogen (ammonium and nitrite) removal rate increased from 106.1 to 166.3 mg N/g volatile suspended solids (VSS).d as the electrostatic field strength increased from 0.2 to 0.67 V/cm. In the cyclic voltammogram, the redox peaks corresponding to the activities of AOE and DNE increased as the strength of the electrostatic field increased. Based on the microbial taxonomic profiling, the dominant genera involved in the bioelectrochemical nitrogen removal were identified as Pseudomonas, Petrimonas, DQ677001_g, Thiopseudomonas, Lentimicrobium, and Porphyromonadaceae_uc. This suggests that the electrostatic field of 0.67 V/cm significantly improves the bioelectrochemical nitrogen removal by enriching the bulk solution with AOE and DNE and promoting the biological DIET between them.

Effect of modified basic oxygen furnace slag on the controlled release of nitrate nitrogen and the functional microbial community in soil

The specific surface area and active adsorption sites of basic oxygen furnace (BOF) slag increase after BOF modification. The addition of modified BOF slag to the soil may enable the control of nitrate nitrogen (NO₃-N) leaching and also affect the functional microflora in the soil. In this study, soil column leaching experiments were conducted to explore the effects of adding modified slag to the soil on the controlled release of NO₃-N and the main functional microbial communities involved in nitrification and denitrification processes. The experimental design included seven column groups: a soil control group (CT); soil groups with 2.5%, 5%, and 10% raw slag (S1, S2, S3); and soil groups with 2.5%, 5%, and 10% modified slag (MS1, MS2, MS3) that were subjected to three cycles of leaching, each of which were comprised of five leaching treatments. After the three cycles of leaching, significantly less NO₃-N had leached from the modified slag group compared to the CT and the raw slag groups (P < 0.05). Although both slag treatments increased soil pH and decreased the oxidation reduction potential of the soil leaching solution, the addition of modified slag had less effect on soil pH than the addition of raw slag. During column leaching, the group with modified slag had a higher gene abundance of functional microflora compared with the group with raw slag. Similarly, the modified slag group had a higher diversity and richness of denitrifying bacteria, ammonia-oxidizing archaea, and ammonia-oxidizing bacteria than the raw slag group. In conclusion, the addition of modified slag to soil effectively decreased the NO₃-N leaching and had relatively little effect on the functional microbial community in the soil.

The influence of upflow velocity and hydraulic retention time changes on taxonomic and functional characterization in Fluidized Bed Reactor treating commercial laundry wastewater in co-digestion with domestic sewage

A large-scale (19.8L) Fluidized Bed Reactor (FBR) operated for 592 days was used to assess the removal performance of linear alkylbenzene sulfonate (LAS). Adjustments in hydraulic retention time (HRT) (18 and 30 h), ethanol (50, 100, 200 mg L^-1) and linear alkylbenzene sulfonate (LAS) concentration (6.3-24.7 mg L^-1) with taxonomic and functional characterization of biomass using Whole Genome Shotgun Metagenomic (WGSM) represented a major step forward for optimizing biological treatments of LAS. In addition, the variation of the upflow velocity (0.5, 0.7 and 0.9 cm s^-1) was investigated, which is a parameter that had not yet been correlated with the possibilities of LAS removal in FBR. Lower Vup (0.5 cm s^-1) allied to higher ethanol concentration (200 mg L^-1) resulted in lower LAS removal (29%) with predominance of methanogenic archaea and genes related to methanogenesis, while higher Vup (0.9 cm s^-1) led to aerobic organisms and oxidative phosphorylation genes. An intermediate Vup (0.7 cm s^-1) and higher HRT (30 h) favored sulfate reducing bacteria and genes related to sulfur metabolism, which resulted in the highest LAS (83%) and COD (77%) removal efficiency.

Consumption of N2O and other N-cycle intermediates by Gemmatimonas aurantiaca strain T-27

Bacteria affiliated with the phylum Gemmatimonadetes are found in high abundance in many terrestrial and aquatic environments, yet little is known about their metabolic capabilities. Difficulty in their cultivation has prompted interest in identifying better growth conditions for metabolic studies, especially related to their ability to reduce N₂O, a potent greenhouse gas. T-27 Gemmatimonas aurantiaca is one of few cultivated strains of Gemmatimonadetes available for physiological studies. Our objective was to test this organism's ability to use nitrite, nitrate, and N₂O, and mineral forms of assimilable NH₄ ⁺ at concentrations not typically used in tests for compound utilization. Cultures incubated under anaerobic conditions with nitrate, nitrite or N₂O failed to grow or show depletion of these substrates. Nitrate and nitrite (1 mM) were not used even when cells were grown aerobically with the O₂ allowed to deplete first. N₂O reduction only commenced in the presence of O₂ and continued to be depleted when refed to the culture under anaerobic, microaerobic and aerobic atmospheres. Carbon mineralization was coupled to the electron-accepting processes, with higher reducing equivalents needed for N₂O utilization under aerobic atmospheres. N₂O was reduced to N₂ in the presence of 20% O₂, however the rate of this reaction is reduced in the presence of high O₂ concentration. This study demonstrated that G. aurantiaca T-27 possesses unique characteristics for assimilative and dissimilative N processes with new implications for cultivation strategies to better assess the metabolic abilities of Gemmatimonadetes.

Effects of interchange ratio on sludge reduction and microbial community structures in an anaerobic/anoxic/oxic process with combined anaerobic side-stream reactor

Oxic-settling-anaerobic (OSA) process is effective in minimizing sludge production, by inserting an anaerobic side-stream reactor (ASSR) in the recycling bypass. Interchange ratio (IR), the quantity ratio of sludge entering the ASSR to the sludge in the main stream reactors, is one of the most important parameters for OSA process. In the present study, a laboratory-scale anaerobic/anoxic/oxic (A²/O) process combined with an ASSR (A²/O-ASSR) was operated for 366 days in parallel with a conventional A²/O process to investigate the effects of IR on sludge reduction. IR was assigned values of 5%, 8%, 10%, and 15%, and the A²/O-ASSR process achieved 14.0%, 16.0%, 24.1%, and 13.7% of sludge reduction, respectively. At the optimum IR of 10%, high through-put sequencing analysis showed that the microbes responsible for pollutant removal and ubiquitous in wastewater treatment remained predominant in the two systems, and slow-growing microbes related to hydrolysis, nitrogen and phosphorus removal increased in the A²/O-ASSR process, which probably played a key role in sludge reduction. 40.6-58.6% of sludge reduction was caused by sludge decay in the ASSR. The tiny amount of extracellular polymeric substance released in the A²/O-ASSR process was subthreshold to cause remarkable sludge reduction.

A novel micro-ferrous dosing strategy for enhancing biological phosphorus removal from municipal wastewater

Ferrous salts have been widely used to enhance phosphorus removal in full-scale wastewater treatment plants, with an average dosage of 0.24-0.35 mM. However, such high dosage inevitably caused serious concerns on operation, potential biological toxicity and excessive sludge production. Thus, this study investigated the effect of micro-dosing of ferrous salt at the level of 0.02 mM on enhanced biological phosphorus removal (EBPR) in sequencing batch reactors. Results showed that micro-dosing of ferrous salt enhanced the overall performance, with average COD, TN and TP removal of more than 4.2%, 2.0% and 5.8%, respectively. In addition, the sequencing analysis further revealed that micro-ferrous dosing could significantly improve the diversity and richness of the microbial community (p < 0.05), whereas the regular dosing of ferrous salts (0.25 mM) negatively impacted on the EBPR performance. It was found that the abundances of phosphorus accumulating organisms (PAOs) in R2 (micro-dosing) were nearly 1.5-fold and 2-fold higher than those in R1 (control) and R3 (regular dosing). The contributions of biological and chemical pathways towards the observed phosphorus removal were also determined according to the phosphorus releasing rate. For micro-dosage and regular dosage of ferrous salts, phosphorus removal mainly relied on biological phosphorus removal and chemical phosphorus removal, respectively. It appears from this this study that the micro-ferrous dosing strategy is practically feasible and economically viable for enhanced phosphorus removal from municipal wastewater.

Molecular Biomarkers and Influential Factors of Denitrification in a Full-Scale Biological Nitrogen Removal Plant

Three denitrifying bacteria, Paracoccus spp., Thauera spp., Pseudomonas-like spp., and two functional genes, nitrate reductase (narG and napA), were studied as potential biomarkers for total nitrogen removal. These bacterial genera and the functional genes showed significant negative correlations with total nitrogen in the effluent (TN_eff). Thauera spp. had the highest correlation (r = −0.793, p < 0.001) with TN_eff, and narG-like and napA genes also showed significant correlations (r = −0.663 and −0.643, respectively), suggesting functional genes have equal validity to 16S rRNA genes in monitoring denitrification performance. The most explanatory variables were a combination of constituents, with temperature emerging as the most important in Pearson’s correlation and redundancy analysis. Thauera spp. had the highest correlation with temperature (r = 0.739) followed closely by Paracoccus spp. (r = 0.705). Denitrification was also significantly affected by pH (r = 0.369), solids retention time (r = −0.377), total nitrogen_in (r = 0.635), and organic matter in the influent (biochemical oxygen demand and chemical oxygen demand; r = 0.320 and 0.522, respectively). Our data verified that major denitrifiers’ 16S rRNA genes and nitrate reductase genes were better biomarkers than the biomass concentration, and any of the biomarkers could track denitrification in real time.

Nutrient removal and microbial community structure variation in the two-sludge system treating low carbon/nitrogen domestic wastewater

A two-sludge system with separated phosphorus removal unit and nitrification unit was used to treat the actual municipal sewage deficient in organic carbon sources, with the carbon/nitrogen (C/N) ratio of 4.39. The system was first operated as anaerobic/oxic-nitrification (A/O-N) mode for 60 days (phase I), and then transformed into anaerobic/anoxic/oxic-nitrification (A/A/O-N) mode for the next following 80 days (phase II). Noteworthy, oxygen and nitrate acted as electronic acceptors for phosphorus removal in chronological order. Results indicated that deep phosphorus removal and complete nitrification were achieved at both phase I and phase II, and the system exhibited a higher microbial diversity. Microbial community abundance on genus level analysis indicated that Dechloromonas and Accumulibacter were respectively accumulated with 11.6 and 2.42% abundance (A/A/O sludge); and 9.31 and 1.29% Nitrospira and Nitrosomonas occupied the biofilm, and they performed denitrifying phosphorus removal (DNPR) and nitrification, respectively.

Nitrite and nitrate as electron acceptors for bioelectrochemical ammonium oxidation under electrostatic field

Bioelectrochemical ammonium oxidation with nitrite and nitrate as electron acceptors was investigated in bulk solution exposed to electrostatic field. In a bioelectrochemical reactor, electroactive nitrogen removal bacteria including ammonium oxidizing exoelectrogens (AOE) and denitrifying electrotrophs (DNE) were enriched by electrostatic field of 0.2 V/cm in a bulk solution containing nitrite, nitrate, and ammonium. Ammonium was oxidized simultaneously with decreases in nitrite and nitrate as electron acceptors due to direct interspecies electron transfer between AOE and DNE. The specific ammonium oxidation rate was 48 mg NH₄-N/g VSS.d when nitrate fraction was 1/3 in the electron acceptor composed of nitrite and nitrate. The specific ammonium oxidation rate gradually decreased with increasing nitrate fraction. However, it was still 24 mg NH₄-N/g VSS.d when nitrate was the only electron acceptor. This indicates that nitrate can be used as an electron acceptor for bioelectrochemical ammonium oxidation, although it is a less effective than nitrite. This finding provides an advantage that strict nitritation which selectively produces nitrite from ammonium can be avoided when treating ammonia-rich wastewater in a bioelectrochemical reactor.

Microbial community structure associated with submarine groundwater discharge in northern Java (Indonesia)

Submarine groundwater discharge (SGD) can be an important pathway for chemical or biological pollutants from land to the ocean around the world. However, studies on the microbial communities associated with SGD in Southeast Asia, which has been hypothesized as SGD hotspot, remain scarce. In this study, we examined the microbial community composition with 16S rRNA gene sequencing along the hydrological continuum of an SGD site in a tropical urban area of Indonesia. Of the observed parameters in this study, salinity and temperature were the most determinant variables explaining patterns in microbial community composition. The bacterial taxon Burkholderiaceae was predominantly found in low salinity samples, including those from terrestrial groundwater and brackish pore water, while cyanobacteria of the genus Synechococcus sp. CC9902 were indicative of saline SGD and seawater samples. The composition of microbial taxa in each sample pointed to the influence of shallow terrestrial groundwater in the beach pore water, while seawater recirculation dominated the SGD sampling points situated further offshore. We identified taxa containing fecal indicators and potential pathogens at the SGD compartments; however, while a likely explanation, we could not conclude with certainty that SGD was a conduit for these bacteria. Overall, the results from this study show that microbial community analysis can highlight hydrological processes and water quality at the SGD site; thus, they could be useful for environmental policymakers to formulate water management strategies in coastal areas.

Enrichment, Isolation, and Characterization of High-Affinity N2O-Reducing Bacteria in a Gas-Permeable Membrane Reactor

The recent discovery of nitrous oxide (N₂O)-reducing bacteria suggests a potential biological sink for the potent greenhouse gas N₂O. For an application toward N₂O mitigation, characterization of more isolates will be required. Here, we describe the successful enrichment and isolation of high-affinity N₂O-reducing bacteria using a N₂O-fed reactor (N₂OFR). Two N₂OFRs, where N₂O was continuously and directly supplied as the sole electron acceptor to a biofilm grown on a gas-permeable membrane, were operated with acetate or a mixture of peptone-based organic substrates as an electron donor. In parallel, a NO₃^- -fed reactor (NO₃FR), filled with a nonwoven sheet substratum, was operated using the same inoculum. We hypothesized that supplying N₂O vs NO₃^- would enhance the dominance of distinct N₂O-reducing bacteria. Clade II type nosZ bacteria became rapidly enriched over clade I type nosZ bacteria in the N₂OFRs, whereas the opposite held in the NO₃FR. High-throughput sequencing of 16S rRNA gene amplicons revealed the dominance of Rhodocyclaceae in the N₂OFRs. Strains of the Azospira and Dechloromonas genera, canonical denitrifiers harboring clade II type nosZ, were isolated with high frequency from the N₂OFRs (132 out of 152 isolates). The isolates from the N₂OFR demonstrated higher N₂O uptake rates (V_max: 4.23 × 10^-3-1.80 × 10^-2 pmol/h/cell) and lower N₂O half-saturation coefficients (K_m,N2O: 1.55-2.10 μM) than a clade I type nosZ isolate from the NO₃FR. Furthermore, the clade II type nosZ isolates had higher specific growth rates on N₂O than nitrite as an electron acceptor. Hence, continuously and exclusively supplying N₂O in an N₂OFR allows the enrichment and isolation of high-affinity N₂O-reducing strains, which may be used as N₂O sinks in bioaugmentation efforts.

Comparative Metagenomics Reveals Enhanced Nutrient Cycling Potential after 2 Years of Biochar Amendment in a Tropical Oxisol

The complex structural and functional responses of agricultural soil microbial communities to the addition of carbonaceous compounds such as biochar remain poorly understood. This severely limits the predictive ability for both the potential enhancement of soil fertility and greenhouse gas mitigation. In this study, we utilized shotgun metagenomics in order to decipher changes in the microbial community in soil microcosms after 14 days of incubation at 23°C, which contained soils from biochar-amended and control plots cultivated with Napier grass. Our analyses revealed that biochar-amended soil microbiomes exhibited significant shifts in both community composition and predicted metabolism. Key metabolic pathways related to carbon turnover, such as the utilization of plant-derived carbohydrates as well as denitrification, were enriched under biochar amendment. These community shifts were in part associated with increased soil carbon, such as labile and aromatic carbon compounds, which was likely stimulated by the increased available nutrients associated with biochar amendment. These findings indicate that the soil microbiome response to the combination of biochar addition and to incubation conditions confers enhanced nutrient cycling and a small decrease in CO₂ emissions and potentially mitigates nitrous oxide emissions.IMPORTANCE The incorporation of biochar into soil is a promising management strategy for sustainable agriculture owing to its potential to sequester carbon and improve soil fertility. Expanding the addition of biochar to large-scale agriculture hinges on its lasting beneficial effects on the microbial community. However, there exists a significant knowledge gap regarding the specific role that biochar plays in altering the key biological soil processes that influence plant growth and carbon storage in soil. Previous studies that examined the soil microbiome under biochar amendment principally characterized only how the composition alters in response to biochar amendment. In the present study, we shed light on the functional alterations of the microbial community response 2 years after biochar amendment. Our results show that biochar increased the abundance of genes involved in denitrification and carbon turnover and that biochar-amended soil microcosms had a reduction in cumulative CO₂ production.

Effects of Oenanthe javanica on Nitrogen Removal in Free-Water Surface Constructed Wetlands under Low-Temperature Conditions

To investigate the role and microorganism-related mechanisms of macrophytes and assess the feasibility of Oenanthe javanica (Blume) DC. in promoting nitrogen removal in free-water surface constructed wetlands (FWS-CWS) under low temperatures (<10 °C), pilot-scale FWS-CWS, planted with O. javanica, were set up and run for batch wastewater treatment in eastern China during winter. The presence of macrophytes observably improved the removal rates of ammonia nitrogen (65%-71%) and total nitrogen (41%-48%) (p < 0.05), with a sharp increase in chemical oxygen demand concentrations (about 3-4 times). Compared to the unplanted systems, the planted systems not only exhibited higher richness and diversity of microorganisms, but also significantly higher abundances of bacteria, ammonia monooxygenase gene (amoA), nitrous oxide reductase gene (nosZ), dissimilatory cd1-containing nitrite reductase gene (nirS), and dissimilatory copper-containing nitrite reductase gene (nirK) in the substrate. Meanwhile, the analysis of the microbial community composition further revealed significant differences. The results indicate that enhanced abundances of microorganisms, and the key functional genes involved with nitrogen metabolism in the planted systems played critical roles in nitrogen removal from wastewater in FWS-CWS. Furthermore, abundant carbon release from the wetland macrophytes could potentially aid nitrogen removal in FWS-CWS during winter.

Benefits of a Bacillus probiotic to larval fish survival and transport stress resistance

The need for sustainable bacterial management approaches in aquaculture is crucial for advancement of the industry. Probiotics are a promising strategy as evidenced by benefits demonstrated in intensive larviculture of various marine fish species. In this study we investigate the effects of a mixed Bacillus species (B. licheniformis and B. amyloliquefaciens) probiotic on rearing of larval common snook (Centropomus undecimalis). Experimental treatments included (1) probiotics supplemented to the water and live feed, (2) probiotics supplemented to the water only, and (3) no probiotic controls. Data from two separate trials indicated up to 2.5 times higher survival with probiotic addition, as well as 20% higher survival 7 days following a transport event. These benefits were not explained by faster growth, measured water quality parameters, or innate immune enzyme activities. Microbiota analysis indicated the importance of system stabilization prior to larval stocking to improve rearing success and probiotic performance. ied Potential probiotic benefits include accelerated gastrointestinal tract development, enhanced immunity, inhibition of opportunistic bacteria, and improvements to water quality parameters. Results suggest this probiotic should be tested in other marine fish species in order to reduce larval rearing bottlenecks.

Alcohol ethoxylate degradation of activated sludge is enhanced by bioaugmentation with Pseudomonas sp. LZ-B

An effective bioaugmentation strategy was developed for the removal of alcohol ethoxylates (AEs) from municipal wastewater. An AE-degrading strain, Pseudomonas sp. LZ-B, was isolated from an activated sludge. Strain LZ-B was able to degrade 96.8% of 200 mg/L C₁₂E₄ (Brij 30) within 24 h and showed significant biomass increase and removal of total oxygen concentration (TOC). The optimal degradation temperature and pH value were 37 °C and 6.0, respectively. The strain demonstrated greater potential to degrade five different molecular weight AEs within 5 days. HPLC-MS/MS analysis demonstrated that the major metabolites obtained were polyethylene glycol (PEG) and carboxylated AE chains. Activated sludge has a low ability to remove AEs. After inoculation of strain LZ-B into the activated sludge reactor, Strain LZ-B successfully colonized the activated sludge, and AE removal efficiency increased to more than 95% when the hydraulic retention time (HRT) was 10 h. After strain LZ-B cleaved the AE chains, the sludge microbial communities easily removed PEG fragments to facilitate complete biodegradation of AEs. This is the first report describing bioaugmentation to increase AE degradation in an activated sludge system.

Alicycliphilus: current knowledge and potential for bioremediation of xenobiotics

Alicycliphilus is a promising candidate for participating in the development of novel xenobiotics bioremediation processes. Members of the Alicycliphilus genus are environmental bacteria mostly found in polluted sites such as landfills and contaminated watercourses, and in sewage sludges from wastewater treatment plants. They exhibit a versatile metabolism and the ability to use oxygen, nitrate and chlorate as terminal electron acceptors, which allow them to biodegrade xenobiotics under oxic or anoxic conditions. Pure cultures of Alicycliphilus strains are able to biodegrade some pollutants such as industrial solvents (acetone, cyclohexanol and N-methylpyrrolidone), aromatic hydrocarbons (benzene, toluene and anthracene), as well as polyurethane varnishes and foams, and they can even transform Cr(VI) to Cr(III). In addition, Alicycliphilus has also been identified in bacterial communities involved in wastewater treatment plants for denitrification, and the degradation of emerging pollutants such as triclosan, nonylphenol, N-heterocyclic aromatic compounds (indole and quinoline), and antibiotics (tetracycline and oxytetracycline). This work summarizes the current knowledge on the Alicycliphilus genus, describing its different metabolic characteristics, focusing on its xenobiotic biodegradation abilities and examining the distinct pathways and molecular bases that sustain them. We also discuss the progress made in genetic manipulation and 'omics' analyses, as well as Alicycliphilus participation in novel bioremediation strategies.

Enhanced biodiesel industry wastewater treatment via a hybrid MBBR combined with advanced oxidation processes: analysis of active microbiota and toxicity removal

In the present study, a multistage route is proposed for the treatment of biodiesel industry wastewater (BWW) containing around 1000 mg L^-1 of total organic carbon (TOC), 3500 mg L^-1 of chemical oxygen demand (COD), and 1325 mg L^-1 of oil and grease. Initially, BWW aerobic biodegradability was assessed via Zhan-Wellens biodegradability test to confirm the appropriate treatment route. Then, a hybrid moving bed bioreactor (MBBR) system was chosen as the first treatment stage. The hybrid MBBR achieved 69 and 68% removal of COD and TOC removals, respectively, and provided great conditions for biomass growth. The bacterial community present in the hybrid MBBR was investigated by PCR-DGGE and potential biodegraders were identified such as: members of Desulfuromonadales, Nocardioidaceae and Pseudomonadaceae. Since biodegradation in the hybrid MBBR alone was unable to meet quality requirements, advanced oxidation processes, such as Fenton and photo-Fenton, were optimized for application as additional treatment stages. Physicochemical properties and acute toxicity of BWW were analyzed after the multistage routes: hybrid MBBR + Fenton, hybrid MBBR + photo-Fenton and hybrid MBBR + UV-C_254nm/H₂O₂. Hybrid MBBR + Fenton or photo-Fenton showed overall COD removal efficiencies greater than 95% and removed acute toxicity, thus being appropriate integrated routes for the treatment of real BWW. Graphical abstract ᅟ.