Reconstructing a Thauera genome from a hydrogenotrophic-denitrifying consortium using metagenomic sequence data

Microbial enhanced manganese-autotrophic denitrification in reactor: performance, microbial diversity, potential functions

Autotrophic denitrification technology has gained increasing attention in recent years owing to its effectiveness, economical, and environmentally friendly nature. However, the sluggish reaction rate has emerged as the primary impediment to its widespread application. Herein, a bio-enhanced autotrophic denitrification reactor with modified loofah sponge (LS) immobilized microorganisms was established to achieve efficient denitrification. Under autotrophic conditions, a nitrate removal efficiency of 59.55 % (0.642 mg/L/h) and a manganese removal efficiency of 86.48 % were achieved after bio-enhance, which increased by 20.92 % and 36.34 %. The bioreactor achieved optimal performance with denitrification and manganese removal efficiencies of 99.84 % (1.09 mg/L/h) and 91.88 %. ETSA and 3D-EEM analysis reveled manganese promoting electron transfer and metabolic activity of microorganisms. High-throughput sequencing results revealed as the increase of Mn(II) concentration, Cupriavidus became one of the dominant strains in the reactor. Prediction of metabolic functions results proved the great potential for Mn(II)-autotrophic denitrification of LS bioreactor.

Deciphering the adaptation mechanism of anammox consortia under sulfamethoxazole stress: A model coupling resistance accumulation and interspecies-cooperation

Sulfamethoxazole (SMX) is frequently detected in wastewater where anammox applications are promising. While it has been demonstrated that anammox consortia can adapt to SMX stress, the underlying community adaptation strategy has not yet been fully addressed. Therefore, in this study, we initially ascertained anammox consortia's ability to co-metabolize SMX in batch tests. Then, a 200-day domestication process of anammox consortia under SMX stress was carried out with community variations and transcriptional activities monitored by metagenomic and metatranscriptomic sequencing techniques. Despite the initial drop to 41.88 %, the nitrogen removal efficiency of the anammox consortia rebounded to 84.64 % post-domestication under 5 mg/L SMX. Meanwhile, a 4.85-fold accumulation of antibiotic resistance genes (ARGs) under SMX stress was observed as compared to the control group. Interestingly, the anammox consortia may unlock the SMX-inhibited folate synthesis pathway through a novel interspecies cooperation triangle among Nitrospira (NAA), Desulfobacillus denitrificans (DSS1), and the core anammox population Candidatus Brocadia sinica (AMX1), in which the modified dihydropteroate synthase (encoded by sul1) of NAA reconnected the symbiotic cooperation between AMX1 and DSS1. Overall, this study provides a new model for the adaptation strategies of anammox consortia to SMX stress.

Biological bromate reduction coupled with in situ gas fermentation in H2/CO2-based membrane biofilm reactor

Bromate, a carcinogenic contaminant generated in water disinfection, presents a pressing environmental concern. While biological bromate reduction is an effective remediation approach, its implementation often necessitates the addition of organics, incurring high operational costs. This study demonstrated the efficient biological bromate reduction using H2/CO2 mixture as the feedstock. A membrane biofilm reactor (MBfR) was used for the efficient delivery of gases. Long-term reactor operation showed a high-level bromate removal efficiency of above 95 %, yielding harmless bromide as the final product. Corresponding to the short hydraulic retention time of 0.25 d, a high bromate removal rate of 4 mg Br/L/d was achieved. During the long-term operation, in situ production of volatile fatty acids (VFAs) by gas fermentation was observed, which can be regulated by controlling the gas flow. Three sets of in situ batch tests and two groups of ex situ batch tests jointly unravelled the mechanisms underpinning the efficient bromate removal, showing that the microbial bromate reduction was primarily driven by the VFAs produced from in situ gas fermentation. Microbial community analysis showed an increased abundance of Bacteroidota group from 4.0 % to 18.5 %, which is capable of performing syngas fermentation, and the presence of heterotrophic denitrifiers (e.g., Thauera and Brachymonas), which are known to perform bromate reduction. Together these results for the first time demonstrated the feasibility of using H2/CO2 mixture for bromate removal coupled with in situ VFAs production. The findings can facilitate the development of cost-effective strategies for groundwater and drinking water remediation.

Performance and microbial response to nitrate nitrogen removal from simulated groundwater by electrode biofilm reactor with Ti/CNT/Cu5-Pd5 catalytic cathode

To enhance the removal of nitrate nitrogen (NO3 - -N) in groundwater with a low C/N ratio, electrocatalytic reduction of NO3 - -N has received extensive attention since its electrons can be directly produced in situ while simultaneously providing a clean electronic donor of hydrogen for denitrifying bacteria. In this study, Ti/CNT/CuPd bimetallic catalytic electrodes with different copper-palladium (CuPd) ratios were prepared by electrodeposition onto carbon nanotube (CNT) using titanium (Ti) plates. The results showed that the NO3 - -N conversion rate by Ti/CNT/Cu5-Pd5 electrode was the highest (53.60%) compared with other CuPd electrode ratios because of the combined role of the copper's high NO3 - -N catalytic activity and the palladium's high N2 selectivity. A new type of electrode biofilm reactor (EBR) with Ti/CNT/Cu5-Pd5 cathode, biochar substrate was constructed to explore the removal ability of NO3 - -N in simulated low C/N groundwater. When the influent NO3 - -N concentration was 30 mg/L, under the condition of a 30 mA electronic current and hydraulic retention time (HRT) of 12 h, the removal rate of NO3 - -N could reach as high as 78.1 ± 1.2%, and the N2 conversion rate was 99.7%. The horizontal distribution of microbial communities in EBR showed that the denitrification capacity was significantly improved through the electrochemical catalytic reduction of the Ti/CNT/Cu5-Pd5 cathode and the supply of the hydrogen electron donor to autotrophic denitrogenerating microbes such as Anaerobacillus, Thauera, and Hydrophaga. This study provides a new bimetallic catalytic cathode to enhance the removal of NO3 - -N in groundwater with a low C/N ratio. PRACTITIONER POINTS: The Cu5Pd5/CNTs/Ti electrode is beneficial to the adsorption and reduction of NO3 - -N to N2 . The production of hydrogen electron donors by cathode promoted nitrogen degradation. Activated electrodes together with denitrifying microorganisms contributed to the improved N removal rate.

New insight into the granule formation in the reactor for enhanced biological phosphorus removal

While granulated activated sludge exhibits high productivity, the processes of granule formation are incompletely studied. The processes of granule formation and succession of communities were investigated in a laboratory sequencing batch reactor (SBR) under conditions for enhanced biological phosphorus removal (EBPR) using microbiological and molecular techniques. Active consumption of acetate, primarily by the phosphate-accumulating organisms (PAO), commenced at day 150 of cultivation. This was indicated by the high ratio of molar P-released/acetate uptake (0.73-0.77 P-mol/C-mol), characteristic of PAO. During this period, two types of granule-like aggregates formed spontaneously out of the activated sludge flocs. The aggregates differed in morphology and microbial taxonomic composition. While both aggregate types contained phosphorus-enriched bacterial cells, PAO prevailed in those of morphotype I, and glycogen-accumulating organisms (GAOs) were predominant in the aggregates of morphotype II. After 250 days, the elimination of the morphotype II aggregates from the reactor was observed. The subsequent selection of the community was associated with the development of the morphotype I aggregates, in which the relative abundance of PAO increased significantly, resulting in higher efficiency of phosphorus removal. Metagenomic analysis revealed a predominance of the organisms closely related to Candidatus Accumulibacter IС and IIС and of Ca. Accumulibacter IIB among the PAO. Based on the content of the genes of the key metabolic pathways, the genomes of potential PAO belonging to the genera Amaricoccus, Azonexus, Thauera, Zoogloea, Pinisolibacter, and Siculibacillus were selected. The patterns of physicochemical processes and the microbiome structure associated with granule formation and succession of the microbial communities were revealed.

Biofilm characteristics for providing resilient denitrification in a hydrogen-based membrane biofilm reactor

In a hydrogen-based membrane biofilm reactor (H₂-MBfR), the biofilm thickness is considered to be one of the most important factors for denitrification. Thick biofilms in MBfRs are known for low removal fluxes owing to their resistance to substrate transport. In this study, the H₂-MBfR was operated under various loading rates of oxyanions, such as NO₃-N, SO₄-S, and ClO₄^- at an H₂ flux of 1.06 e^- eq/m²-d. The experiment was initiated with NO₃-N, SO₄-S, and ClO₄^- loadings of 0.464, 0.026, and 0.211 e^- eq/m²-d, respectively, at 20 °C. Under the most stressful conditions, the loading rates increased simultaneously to 1.911, 0.869, and 0.108 e^- eq/m²-d, respectively, at 10 °C. We observed improved performance in significantly thicker biofilms (approximately 2.7 cm) compared to previous studies using a denitrifying H₂-MBfR for 120 days. Shock oxyanion loadings led to a decrease in total nitrogen (TN) removal by 20 to 30%, but TN removal returned to 100% within a few days. Similarly, complete denitrification was observed, even at 10 °C. The protective function and microbial diversity of the thick biofilm may allow stable denitrification despite stress-imposing conditions. In the microbial community analysis, heterotrophs were dominant and acetogens accounted for 11% of the biofilm. Metagenomic results showed a high abundance of functional genes involved in organic carbon metabolism and homoacetogenesis. Owing to the presence of organic compounds produced by acetogens and autotrophs, heterotrophic denitrification may occur simultaneously with autotrophic denitrification. As a result, the total removal flux of oxyanions (1.84 e^- eq/m²-d) far exceeded the H₂ flux (1.06 e^- eq/m²-d). Thus, the large accumulation of biofilms could contribute to good resilience and enhanced removal fluxes.

Performance and microbial mechanism of eletrotrophic bio-cathode denitrification under low temperature

Insufficient amount of carbon in wastewater and low temperatures hinder the use of biological nitrogen removal for purification of wastewaters. Nitrogen removal using cold-tolerant electrotrophic cathodic microbes is a novel and unique autotrophic denitrification technique in which electrical current, not chemicals, is used as a source of electrons. In this study, integrated MFC (R_W) and open-circuit MFC (R_O) were cultured and acclimatized in stages at a low temperature (10 °C) to impart cold tolerance to electrotrophic cathodic microbes, investigate the effectiveness of simultaneous nitrification and denitrification (SND) process, and address the possible mechanism of microbial action. The results showed that (i) microbial communities in the R_W system were successfully enriched with the cold-tolerant electrotrophic cathodic microbes after five stages, and (ii) the degree of NH₄⁺-N removal and SND were 75.50% and 81.91%, respectively, but the respective values in the R_O system were only 40.47% and 54.01%. The desirable SND efficiency was obtained in R_W at a DO of ∼0.6 mg/L, a current of ∼20 mA, and pH ∼7.0. In R_W, Thauera, Pesudomonas, and Hydrogenophaga were the main electrotrophic cathodic denitrifying bacteria with cold tolerance capable of degrading ammonia, nitrate, and nitrite through autotrophic denitrification and cathodic-driven bio-electrochemical denitrification. Besides, for R_W, results from high throughput sequencing analysis revealed that the abundance of genes related to energy production and conversion, amino acid transport, and metabolism, signal transduction, environmental adaptation, and enzymatic activity (AMO, HAO, NAR, NIR, NOR, and NOS) were significantly higher than the corresponding parameters of the R_O system. This may explain the reason behind R_W having excellent ammonia and TN removal performance at low temperatures.

Metagenomic Insights into Chicken Gut Antibiotic Resistomes and Microbiomes

The chicken gut microbiota, as a reservoir of antibiotic resistance genes (ARGs), poses a high risk to humans and animals worldwide. Yet a comprehensive exploration of the chicken gut antibiotic resistomes remains incomplete. In this study, we established the largest chicken gut resistance gene catalogue to date through metagenomic analysis of 629 chicken gut samples. We found significantly higher abundance of ARGs in the Chinese chicken gut than that in the Europe. tetX, mcr, and blaNDM, the genes resistant to antibiotics of last resort for human and animal health, were detected in the Chinese chicken gut. The abundance of ARGs was linearly correlated with that of mobile genetic elements (MGEs). The host-tracking analysis identified Escherichia, Enterococcus, Staphylococcus, Klebsiella, and Lactobacillus as the major ARG hosts. Especially, Lactobacillus, an intestinal probiotic, carried multiple drug resistance genes, and was proportional to ISLhe63, highlighting its potential risk in agricultural production processes. We first established a reference gene catalogue of chicken gut antibiotic resistomes. Our study helps to improve the knowledge and understanding of chicken antibiotic resistomes for knowledge-based sustainable chicken meat production. IMPORTANCE The prevalence of antibiotic resistance genes in the chicken gut environment poses a serious threat to human health; however, we lack a comprehensive exploration of antibiotic resistomes and microbiomes in the chicken gut environment. The results of this study demonstrate the diversity and abundance of antibiotic resistance genes and flora in the chicken gut environment and identify a variety of potential hosts carrying antibiotic resistance genes. Further analysis showed that mobile genetic elements were linearly correlated with antibiotic resistance genes abundance, implying that we should pay attention to the role played by mobile genetic elements in antibiotic resistance genes transmission. We established a reference genome of gut antibiotic resistance genes in chickens, which will help to rationalize the use of drugs in poultry farming.

Characteristics of Antibiotic Resistance Genes and Antibiotic-Resistant Bacteria in Full-Scale Drinking Water Treatment System Using Metagenomics and Culturing

The contamination of antibiotic resistance genes (ARGs) may directly threaten human health. This study used a metagenomic approach to investigate the ARG profile in a drinking water treatment system (DWTS) in south China. In total, 317 ARG subtypes were detected; specifically, genes encoding bacitracin, multidrug, and sulfonamide were widely detected in the DWTS. Putative ARG hosts included Acidovorax (6.0%), Polynucleobacter (4.3%), Pseudomonas (3.4%), Escherichia (1.7%), and Klebsiella (1.5%) as the enriched biomarkers in the DWTS, which mainly carried bacitracin, beta-lactam, and aminoglycoside ARGs. From a further analysis of ARG-carrying contigs (ACCs), Stenotrophomonas maltophilia and Pseudomonas aeruginosa were the most common pathogens among the 49 ACC pathogens in the DWTS. The metagenomic binning results demonstrated that 33 high-quality metagenome-assembled genomes (MAGs) were discovered in the DWTS; particularly, the MAG identified as S. maltophilia-like (bin.195) harbored the greatest number of ARG subtypes (n = 8), namely, multidrug (n = 6; smeD, semE, multidrug_transporter, mexE, semB, and smeC), beta-lactam (n = 1; metallo-beta-lactamase), and aminoglycoside [n = 1; aph(3’)-IIb]. The strong positive correlation between MGEs and ARG subtypes revealed a high ARG dissemination risk in the DWTS. Based on the pure-culture method, 93 isolates that belong to 30 genera were recovered from the DWTS. Specifically, multidrug-resistant pathogens and opportunistic pathogens such as P. aeruginosa, Bacillus cereus, and S. maltophilia were detected in the DWTS. These insights into the DWTS’s antibiotic resistome indicated the need for more comprehensive ARG monitoring and management in the DWTS. Furthermore, more effective disinfection methods need to be developed to remove ARGs in DWTSs, and these findings could assist governing bodies in the surveillance of antibiotic resistance in DWTSs.

Evidence for Long-Term Anthropogenic Pollution: The Hadal Trench as a Depository and Indicator for Dissemination of Antibiotic Resistance Genes

Knowledge of the distribution and dissemination of antibiotic resistance genes (ARGs) is essential for understanding anthropogenic impacts on natural ecosystems. The transportation of ARGs via aquatic environments is significant and has received great attention, but whether there has been anthropogenic ARG pollution to the hadal ocean ecosystem has not been well explored. For investigating ecological health concerns, we profiled the ARG occurrence in sediments of the Mariana Trench (MT) (10 890 m), the deepest region of the ocean. Metagenomic-based ARG profiles showed a sudden increase of abundance and diversity in the surface layer of MT sediments reaching 2.73 × 10^-2 copy/cell and 81 subtypes, and a high percentage of ∼63.6% anthropogenic pollution sources was predicted by the Bayesian-modeling classification method. These together suggested that ARG accumulation and anthropogenic impacts have already permeated into the bottom of the deepest corner on the earth. Moreover, six ARG-carrying draft genomes were retrieved using a metagenomic binning strategy, one of which assigned as Streptococcus was identified as a potential bacterial host to contribute to the ARG accumulation in MT, carrying ermF, tetM, tetQ, cfxA2, PBP-2X, and PBP-1A. We propose that the MT ecosystem needs further long-term monitoring for the assessment of human impacts, and our identified three biomarkers (cfxA2, ermF, and mefA) could be used for the rapid monitoring of anthropogenic pollution. Together our findings imply that anthropogenic pollution has penetrated into the deepest region of the ocean and urge for better pollution control to reduce the risk of ARG dissemination to prevent the consistent accumulation and potential threat to the natural environment.

Naphthenic acid anaerobic biodegrading consortia enriched from pristine sediments underlying oil sands tailings ponds

Seepage from oil sands tailings ponds (OSTP), which contain toxic naphthenic acids (NAs), can infiltrate into groundwater. Clay sediment layer beneath is a critical barrier for reducing the infiltration of NAs into the sand sediment layer, where groundwater channels reside. Biodegradation has great potential as a strategy for NAs removal, but little is known about NAs biodegradability and potential functional microbes in these pristine sediments. This study investigated the potential for anaerobic biodegradation of NAs by microbial consortia enriched from clay and sand sediments underlying OSTP, amended with either acid extracted organics or Merichem NAs, under nitrate- and sulfate-reducing conditions. Degradation of NAs only be detected after DOC concentration reached to steady state after 163 days. Microbial community analysis shows that different electron acceptors, sediment types, and NAs sources associated with specific microbial taxa and can explain 14.8, 13.9 % and 5% of variation of microbial community structures, respectively. The DOC and methane were the most important geochemical properties for microbial community variations. This study approved the potential capability of indigenous microbial communities from the pristine sediments in NA degradation, demonstrating the barrier function of pristine clay sediments underlying OSTP in prohibiting organic contaminants from entering into groundwater.

Exploring the linkage between free nitrous acid accumulation and nitrous oxide emissions in a novel static/oxic/anoxic process

In this work, four batch tests were conducted to comprehensively explore the effects of free nitrous acid (FNA) accumulation on nitrous oxide (N₂O) emissions in a novel energy-saving and N₂O-reducing static/oxic/anoxic (SOA) process. With the accumulation of FNA, the N₂O emission factor increased from 1.51% to 4.32%, and the N₂O emission ratio contributed by ammonia-oxidizing bacteria (AOB) increased from 74.0% to 78.6%, accordingly. Mechanism studies show that produced FNA and weakened aerobic metabolism bring synergy to competition between reductases. Aeration conditions and FNA cytotoxicity exert a greater impact on nitrite-oxidizing bacteria than on AOB, thus enhancing the potential for nitrite accumulation. Considering the removal of nitrogen and phosphorus and the reduction of N₂O emissions in the SOA process, it is feasible to keep the average dissolved oxygen above 2.0 mg/L under the premise of nitrite accumulation.

Influence of Hydrogen Electron Donor, Alkaline pH, and High Nitrate Concentrations on Microbial Denitrification: A Review

Bacterial respiration of nitrate is a natural process of nitrate reduction, which has been industrialized to treat anthropic nitrate pollution. This process, also known as “microbial denitrification”, is widely documented from the fundamental and engineering points of view for the enhancement of the removal of nitrate in wastewater. For this purpose, experiments are generally conducted with heterotrophic microbial metabolism, neutral pH and moderate nitrate concentrations (<50 mM). The present review focuses on a different approach as it aims to understand the effects of hydrogenotrophy, alkaline pH and high nitrate concentration on microbial denitrification. Hydrogen has a high energy content but its low solubility, 0.74 mM (1 atm, 30 °C), in aqueous medium limits its bioavailability, putting it at a kinetic disadvantage compared to more soluble organic compounds. For most bacteria, the optimal pH varies between 7.5 and 9.5. Outside this range, denitrification is slowed down and nitrite (NO₂⁻) accumulates. Some alkaliphilic bacteria are able to express denitrifying activity at pH levels close to 12 thanks to specific adaptation and resistance mechanisms detailed in this manuscript, and some bacterial populations support nitrate concentrations in the range of several hundred mM to 1 M. A high concentration of nitrate generally leads to an accumulation of nitrite. Nitrite accumulation can inhibit bacterial activity and may be a cause of cell death.

Microbial reduction of bromate: current status and prospects

Bromate is a disinfection byproduct (DBP) that forms during the ozonation of bromide-containing natural water, which may cause health risks to humans. In this review, we provide an overview of the mechanism of bromate formation, microbial communities and bioreactors that are responsible for bromate reduction. Bromate can be formed through two pathways of bromide oxidation by ozone or by ^·OH, and it can be removed by biological approaches. Members belonging to phyla of Spirochaetes, Proteobacteria, Firmicutes, Actinobacteria, Clostridium, Deinococcus-Thermus and Bacteroidetes have been identified as capable of reducing bromate to bromide. Multiple configurations of biofilm bioreactors have been employed to cultivate microbial communities to perform bromate removal. The rapid development of multiomics has and will continue to accelerate the elucidation of the mechanisms involved in bromate and other DBP conversions, as well as the interaction patterns among different bacterial subdivisions in the bioremoval of DBPs.

New insights into antibiotic resistome in drinking water and management perspectives: A metagenomic based study of small-sized microbes

The proliferation of antibiotic resistance genes (ARGs) in drinking water and their potential horizontal transfer to pathogenic microbes may cause failure of antibiotics. However, antimicrobial resistome monitoring in drinking water is not currently routine. The bacterial hosts of ARGs, especially small-sized microbes in drinking water, may not be effectively removed by membrane filtration disinfection and thus pose threats to human health. In the present study, using metagenomic based approach, we investigated antibiotic resistome of small-sized microbes (0.2-0.45 μm) in 20 household drinking water samples from 12 cities in Mainland China, Hong Kong and Singapore. A total of 265 ARG subtypes belonging to 17 ARG types were detected at abundances ranging from 4.0 × 10^-2 to 1.0 × 10⁰ copies/cell. Multidrug, bacitracin and aminoglycoside resistance genes are dominant, and 43 ARG subtypes were specifically carried by small-size microbes. Metagenomic assembly strategy revealed fragments of three opportunistic pathogen, i.e. Pseudomonas alcaligenes, Pseudomonas aeruginosa and Mycobacterium gordonae, carried mexW, aph(3')-I and aac(2')-I, respectively. Drinking water samples were classified into three groups based on the presence of ARG, pathogen and ARG-carrying pathogen. These new insights into the antibiotic resistome of small microbes in drinking water over a broad scale indicate the need for more comprehensive ARGs monitoring and surveillance of drinking water supplies. These findings, together with the perspectives and strategies proposed in this study, could support initiatives to improve drinking water safety.

Elucidating functional microorganisms and metabolic mechanisms in a novel engineered ecosystem integrating C, N, P and S biotransformation by metagenomics

Denitrifying sulfur conversion-associated enhanced biological phosphorous removal (DS-EBPR) system is not only a novel wastewater treatment process, but also an ideal model for microbial ecology in a community context. However, it exists the knowledge gap on the roles and interactions of functional microorganisms in the DS-EBPR system for carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) bioconversions. We use genome-resolved metagenomics to build up an ecological model of microbial communities in a lab-scale DS-EBPR system with stable operation for more than 400 days. Our results yield 11 near-complete draft genomes that represent a substantial portion of the microbial community (39.4%). Sulfate-reducing bacteria (SRB) and sulfide-oxidizing bacteria (SOB) promote complex metabolic processes and interactions for C, N, P and S conversions. Bins 1-4 and 10 are considered as new potential polyphosphate-accumulating organisms (PAOs), in which Bins 1-4 can be considered as S-related PAOs (S-PAOs) with no previously cultivated or reported members. Our findings give an insight into a new ecological system with C, N, P and S simultaneous bioconversions and improve the understanding of interactions among SRB, SOB, denitrifiers and PAOs within a community context.

Stability of aerobic granular sludge under condition of low influent C/N ratio: Correlation of sludge property and functional microorganism

Aerobic granular sludge process treating domestic wastewater with low C/N ratio is necessary to be studied for rapid urbanization in China and other countries. In this study, two parallel reactors with different influent C/N ratio (15 in R1, 5 in R2) were established. Compared to the disintegrated granule in R1 with high influent C/N ratio, granules with large size (650 μm) and compact structure (integrity coefficient <0.1) were stable in R2 along with influent C/N ratio decreased to 5. High-through sequencing illustrated the functional microbes like Thauera and Paracoccus enriched under low influent C/N ratio, and principal component analysis further showed these microbes were positive correlation with tryptophan and protein-like substances in extracellular polymeric substances (EPS) and granular strength. It was indicated that under low influent C/N ratio, several resistant microbes like Thauera (19.5%) enriched and then secreted tryptophan and protein-like substances, and stable granules with multi-functional microbes could be formed finally.

Inhibition by free nitrous acid (FNA) and the electron competition of nitrite in nitrous oxide (N2O) reduction during hydrogenotrophic denitrification

Hydrogenotrophic denitrification is a promising technology for nitrate removal from organic-deficient wastewater or groundwater, and the attention of nitrous oxide (N₂O) emission during this process is required. Both nitrite and free nitrous acid (FNA or HNO₂) were reported to exert significant effects on N₂O reduction in heterotrophic denitrification, whereas, little knowledge has been obtained in hydrogenotrophic denitrification. In this study, we conducted a series of batch tests to comprehensively investigate the effects of nitrite, pH and FNA on N₂O production and reduction in a hydrogenotrophic denitrification process. The results showed that N₂O reduction rate decreased under both conditions of low pH and presence of nitrite, which would exert synergetic inhibition on N₂O reduction. The potential mechanisms that give rise to the results included electron competition and FNA inhibition. Electron competition between nitrite and N₂O reductases occurred when both nitrite and N₂O were added, which might contribute to the decrease in the N₂O reduction rate. The electron supply, which was obtained from the uptake of molecular hydrogen, declined with increasing FNA concentration according to a logarithmic model (R² = 0.9240). Additionally, the electron consumption rate of N₂O reductase to nitrite reductase ratio was initially stable and then decreased with increasing FNA concentration. The inhibition of N₂O reduction by FNA was determined to be reversible. The study suggested that both of the electron supply and N₂O reduction in hydrogenotrophic denitrification could be inhibited by FNA.

Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey

BACKGROUND

Excesses of antibiotic resistance genes (ARGs), which are regarded as emerging environmental pollutants, have been observed in various environments. The incidence of ARGs in drinking water causes potential risks to human health and receives more attention from the public. However, ARGs harbored in drinking water remain largely unexplored. In this study, we aimed at establishing an antibiotic resistome catalogue in drinking water samples from a wide range of regions and to explore the potential hosts of ARGs.

RESULTS

A catalogue of antibiotic resistome in drinking water was established, and the host-tracking of ARGs was conducted through a large-scale survey using metagenomic approach. The drinking water samples were collected at the point of use in 25 cities in mainland China, Hong Kong, Macau, Taiwan, South Africa, Singapore and the USA. In total, 181 ARG subtypes belonging to 16 ARG types were detected with an abundance range of 2.8 × 10^-2 to 4.2 × 10^-1 copies of ARG per cell. The highest abundance was found in northern China (Henan Province). Bacitracin, multidrug, aminoglycoside, sulfonamide, and beta-lactam resistance genes were dominant in drinking water. Of the drinking water samples tested, 84% had a higher ARG abundance than typical environmental ecosystems of sediment and soil. Metagenomic assembly-based host-tracking analysis identified Acidovorax, Acinetobacter, Aeromonas, Methylobacterium, Methyloversatilis, Mycobacterium, Polaromonas, and Pseudomonas as the hosts of ARGs. Moreover, potential horizontal transfer of ARGs in drinking water systems was proposed by network and Procrustes analyses.

CONCLUSIONS

The antibiotic resistome catalogue compiled using a large-scale survey provides a useful reference for future studies on the global surveillance and risk management of ARGs in drinking water. .

Spatiotemporal heterogeneity of core functional bacteria and their synergetic and competitive interactions in denitrifying sulfur conversion-assisted enhanced biological phosphorus removal

Denitrifying sulfur conversion-assisted enhanced biological phosphorus removal (DS-EBPR) has recently been developed for simultaneously removing nitrogen and phosphorus from saline sewage with minimal sludge production. This novel process could potentially enable sustainable wastewater treatment. Yet, the core functional bacteria and their roles are unknown. Here, we used high-throughput 16S rRNA gene sequencing coupled with principal coordinates analysis and ANOVA with Tukey's test to unravel the spatiotemporal heterogeneity of functional bacteria and their synergetic and competitive interactions. We did not find any obvious spatial heterogeneity within the bacterial population in different size-fractionated sludge samples, but the main functional bacteria varied significantly with operation time. Thauera was enriched (9.26~13.63%) as become the core functional genus in the DS-EBPR reactors and links denitrifying phosphorus removal to sulfide oxidation. The other two functional genera were sulfate-reducing Desulfobacter (4.31~12.85%) and nitrate-reducing and sulfide-oxidizing Thiobacillus (4.79~9.92%). These bacteria cooperated in the DS-EBPR process: Desulfobacter reduced sulfate to sulfide for utilization by Thiobacillus, while Thauera and Thiobacillus competed for nitrate and sulfide as well as Thauera and Desulfobacter competed for acetate. This study is the first to unravel the interactions among core functional bacteria in DS-EBPR, thus improving our understanding of how this removal process works.

Effect of carbon source type on intracellular stored polymers during endogenous denitritation (ED) treating landfill leachate

Glycogen accumulating organisms (GAOs) capable of storing organic compounds as polyhydroxyalkanoate (PHA) have been used for endogenous denitritation (ED), but the effect of carbon sources type on nitrogen removal performance of GAOs treating landfill leachate is unclear. In this study, a successful ED system treating landfill leachate (COD/NH4(+)-N (C/N): 4) without external carbon source addition was applied. The mature leachate with C/N of 1 was used as the feeding base solution, with acetate, propionate, and glucose examined as the carbon sources, and their effects on yields and compositions of PHA produced by GAOs were determined and associated with nitrogen removal performance. In the case of sole carbon source, acetate was much easier to be stored than propionate and glucose, which led to a higher nitrogen removal efficiency. Glucose had the lowest amount of PHA storage and led to the lowest performance. In the case of composite carbon sources (two scenarios: acetate + propionate; acetate + propionate + glucose), GAOs stored sufficient PHA and exhibited similar nitrogen removal efficiencies. Moreover, type of carbon source influenced the compositions of PHA. The polyhydroxybutyrate (PHB) fraction in PHA was far more than polyhydroxyvalerate (PHV) in all tests. PHV was synthesized only when acetate existed in carbon source. The microbial diversity analysis revealed that Proteobacteria was the most abundant phylum. Among the 108 genera detected in this ED system, the genera responsible for denitritation were Thauera, Paracoccus, Ottowia and Comamonadaceae_unclassified, accounting for 46.21% of total bacteria. Especially, Paracoccus and Comamonadaceae_unclassified transformed the carbon source into PHA for denitritation, and carried out endogenous denitritation.

Microbiological mechanism of the improved nitrogen and phosphorus removal by embedding microbial fuel cell in Anaerobic-Anoxic-Oxic wastewater treatment process

Anaerobic-Anoxic-Oxic (AA/O) wastewater treatment process is a widely used wastewater treatment process for simultaneous nitrogen and phosphorus removal. Microbial fuel cell (MFC) can generate electricity and treat the organic wastewater simultaneously. Our previous research showed that embedding MFC in AA/O wastewater treatment process could enhance the pollutants removal efficiency. However, the mechanism was not clear. In this study, a lab-scale corridor-style AA/O reactor with MFC embedded was operated and both the total nitrogen and total phosphorus removal efficiencies were enhanced. DGGE and Illumina Miseq results demonstrated that both the microbial community structures on the surface of the cathode and in the suspensions of cathode chamber have been changed. The percentage of Thauera and Emticicia, identified as denitrifying bacteria, increased significantly in the suspension liquid when the MFC was embedded in the AA/O reactor. Moreover, the genus Rheinheimera were significantly enriched on the cathode surface, which might contribute to both the nitrogen removal enhancement and electricity generation.

Metagenomic Assembly Reveals Hosts of Antibiotic Resistance Genes and the Shared Resistome in Pig, Chicken, and Human Feces

The risk associated with antibiotic resistance disseminating from animal and human feces is an urgent public issue. In the present study, we sought to establish a pipeline for annotating antibiotic resistance genes (ARGs) based on metagenomic assembly to investigate ARGs and their co-occurrence with associated genetic elements. Genetic elements found on the assembled genomic fragments include mobile genetic elements (MGEs) and metal resistance genes (MRGs). We then explored the hosts of these resistance genes and the shared resistome of pig, chicken and human fecal samples. High levels of tetracycline, multidrug, erythromycin, and aminoglycoside resistance genes were discovered in these fecal samples. In particular, significantly high level of ARGs (7762 ×/Gb) was detected in adult chicken feces, indicating higher ARG contamination level than other fecal samples. Many ARGs arrangements (e.g., macA-macB and tetA-tetR) were discovered shared by chicken, pig and human feces. In addition, MGEs such as the aadA5-dfrA17-carrying class 1 integron were identified on an assembled scaffold of chicken feces, and are carried by human pathogens. Differential coverage binning analysis revealed significant ARG enrichment in adult chicken feces. A draft genome, annotated as multidrug resistant Escherichia coli, was retrieved from chicken feces metagenomes and was determined to carry diverse ARGs (multidrug, acriflavine, and macrolide). The present study demonstrates the determination of ARG hosts and the shared resistome from metagenomic data sets and successfully establishes the relationship between ARGs, hosts, and environments. This ARG annotation pipeline based on metagenomic assembly will help to bridge the knowledge gaps regarding ARG-associated genes and ARG hosts with metagenomic data sets. Moreover, this pipeline will facilitate the evaluation of environmental risks in the genetic context of ARGs.

Capturing prokaryotic dark matter genomes

Prokaryotes are the most diverse and abundant cellular life forms on Earth. Most of them, identified by indirect molecular approaches, belong to microbial dark matter. The advent of metagenomic and single-cell genomic approaches has highlighted the metabolic capabilities of numerous members of this dark matter through genome reconstruction. Thus, linking functions back to the species has revolutionized our understanding of how ecosystem function is sustained by the microbial world. This review will present discoveries acquired through the illumination of prokaryotic dark matter genomes by these innovative approaches.