High Concentrations of the Antibiotic Spiramycin in Wastewater Lead to High Abundance of Ammonia-Oxidizing Archaea in Nitrifying Populations

Phenol-driven ammonium recovery from coal chemical wastewater in a bioelectrochemical system (BES)

Bioelectrochemical systems (BES) have gained considerable attention in the past decade as a potentially sustainable and cost-effective method for coal chemical wastewater (CCW) treatment. However, a scarcity of studies focusing on the recovery NH4+-N in the recycling treatment of CCW via BES technology. In this study, a BES-ammonium recovery system (BES-ARS) was proposed to remove phenol and NH4+-N simultaneously, while NH4+-N was further recovered in a downstream recovery unit. Through systematic evaluation, we identified optimal condition for both phenol and NH4+-N removal. Specifically, an influent phenol-to-ammonium ratio of 2.0 was found to be ideal for maximizing simultaneous removal efficiency. Additionally, an evaluation of the nitrogen distribution showed that 97.9 % of NH4+-N migrated to the cathode chamber, with 82.5 % of NH4+-N being recovered in the absorbent under optimal condition. Furthermore, the solution not only reduces operational costs by up to 68 % compared to conventional treatments, but also conserves energy. This study presents an efficient and environmentally friendly treatment method for treating CCW, while recovering NH4+-N as a valuable resource.

Molecular mechanisms of antibiotic inhibition on microbial dissimilatory iron reduction

Microbe-mediated iron cycling plays a pivotal role in biogeochemical processes. However, the impact of trace-level antibiotics on microbially mediated dissimilatory iron reduction (DIR) remains unexplored. In this study, we investigated the effects of four typical antibiotics on DIR mediated by Shewanella oneidensis MR-1, with a focus on their inhibitory effects on three extracellular electron transfer (EET) pathways: 1) direct EET, 2) soluble redox mediator-dependent EET, and 3) nanowire-mediated EET. Our findings demonstrate a concentration-dependent decline in DIR activity with increasing ceftizoxime concentrations, culminating in complete suppression at 64 μg/L. Polymyxin disrupts the cell membrane, causing structural damage that subsequently impairs the electron transport chain (ETC), leading to a reversible reduction in DIR activity. In contrast, ofloxacin and tetracycline directly down-regulated genes associated with electron production and transfer, thereby suppressing both electron transport system activity and the synthesis of NADH dehydrogenase and c-type cytochromes. This irreversibly disrupts ETC function, blocking S. oneidensis MR-1 from conducting EET and impairing DIR activity. This finding reveals antibiotic-induced alterations in microbial iron metabolism and provides new insights into their potential impact on the environmental iron cycling.

Probe Capture Enrichment Sequencing of amoA Genes Improves the Detection of Diverse Ammonia-Oxidising Archaeal and Bacterial Populations

The ammonia monooxygenase subunit A (amoA) gene has been used to investigate the phylogenetic diversity, spatial distribution and activity of ammonia-oxidising archaeal (AOA) and bacterial (AOB), which contribute significantly to the nitrogen cycle in various ecosystems. Amplicon sequencing of amoA is a widely used method; however, it produces inaccurate results owing to the lack of a 'universal' primer set. Moreover, currently available primer sets suffer from amplification biases, which can lead to severe misinterpretation. Although shotgun metagenomic and metatranscriptomic analyses are alternative approaches without amplification bias, the low abundance of target genes in heterogeneous environmental DNA restricts a comprehensive analysis to a realisable sequencing depth. In this study, we developed a probe set and bioinformatics workflow for amoA enrichment sequencing using a hybridisation capture technique. Using metagenomic mock community samples, our approach effectively enriched amoA genes with low compositional changes, outperforming amplification and meta-omics sequencing analyses. Following the analysis of metatranscriptomic marine samples, we predicted 80 operational taxonomic units (OTUs) assigned to either AOA or AOB, of which 30 OTUs were unidentified using simple metatranscriptomic or amoA gene amplicon sequencing. Mapped read ratios to all the detected OTUs were significantly higher for the capture samples (50.4 ± 27.2%) than for non-capture samples (0.05 ± 0.02%), demonstrating the high enrichment efficiency of the method. The analysis also revealed the spatial diversity of AOA ecotypes with high sensitivity and phylogenetic resolution, which are difficult to examine using conventional approaches.

Impact of adaptation time on lincomycin removal in riverbank filtration: A long-term sand column study

Riverbank filtration (RBF) is an effective pretreatment technology for drinking water, removing organic micropollutants (OMPs) mainly through biodegradation. Despite documented improvements in OMP removal with extended adaptation time, the mechanisms remain poorly understood. This study assessed the removal of 128 OMPs over 82 d in a simulated RBF system, identified those with improved removal, and analyzed their properties. Additionally, microbial community shifts after 400 d of lincomycin exposure were studied to understand the underlying mechanisms. We found that the removal efficiencies of 24 OMPs, including lincomycin and fluconazole, improved by 3-77 % over 82 d while being positively correlated with the presence of tertiary amides and secondary sulfonamides. Lincomycin removal efficiency rose from 20 % to 95 % over 68 days and stayed high. We identified eight potential degradation products of lincomycin, occurring primarily via hydroxylation, N-demethylation, and amide hydrolysis. Additionally, lincomycin notably increased the abundances of specific antibiotic-resistant bacteria (e.g., Thiobacillus, 8.3-fold) and ammonia-oxidizing archaea (e.g., Nitrososphaera, 46.8-fold). The β-lactam resistance gene in Thiobacillus and the amoA gene in Nitrososphaera may enhance lincomycin's removal by promoting its hydrolysis and hydroxylation. Overall, this study provides insights into OMP biodegradation mechanisms and the impact of ng/L levels of lincomycin on microbial communities.

Mixed chlorine/chloramines in disinfected water and drinking water distribution systems (DWDSs): A critical review

Mixed chlorine/chloramines are commonly occurring in real drinking water distribution systems (DWDSs) but often overlooked. This review provides a comprehensive overview of the occurrences, characteristics, analysis methods, and control strategies of mixed chlorine/chloramines in DWDSs. The characteristics of mixed chlorine/chloramine species are summarized for treated water in drinking water treatment plants (DWTPs), secondary disinfection facilities, and DWDSs where different disinfectants could be blended. The key to differentiating and quantifying mixed chlorine/chloramine species is to separate organic chloramines (OCs) from di/tri-chloramines and overcome certain interferences. The complex interactions between water matrixes and chlorine/chloramine species could accelerate pipeline corrosions, enhance emerging disinfection by-products risks, lead to off-flavors in drinking water, and induce bio-instability issues (such as nitrification, microorganism regrowth, and promotion of horizontal gene-transfers). Three promising strategies for alleviating mixed chlorine/chloramine species are recommended, which include (i) removing precursors intensively and reconditioning the treated water, (ii) combining UV irradiation to eliminate undesired chlorine/chloramines species, and (iii) strengthening monitoring, operation, and maintenance management of DWDSs. Finally, the challenges for gaining insights into the mechanisms of mixed chlorine/chloramine species conversion are discussed and promising research directions are proposed.

Understanding the cometabolic degradation of sulfadiazine by an enriched ammonia oxidizing bacteria culture from both extracellular and intracellular perspectives

Antibiotics are widely used drugs in the world and pose serious threats to ecosystems and human health. Although it has been reported that ammonia oxidizing bacteria (AOB) can cometabolize antibiotics, little has been reported on how AOB would respond to the exposure of antibiotics on extracellular and enzymatic levels, as well as the impact of antibiotics on the bioactivity of AOB. Therefore, in this study, a typical antibiotic, sulfadiazine (SDZ), was selected, and a series short-term batch tests using enriched AOB sludge were conducted to investigate the intracellular and extracellular responses of AOB along the cometabolic degradation process of SDZ. The results showed the cometabolic degradation of AOB made the main contribution to SDZ removal. When the enriched AOB sludge was exposed to SDZ, ammonium oxidation rate, ammonia monooxygenase activity, adenosine triphosphate concentration and dehydrogenases activity were negatively affected. The amoA gene abundance increased 1.5 folds within 24 h, which may enhance the uptake and utilization of substrates and maintain stable metabolic activity. In the tests with and without ammonium, the concentration of total EPS increased from 264.9 to 231.1 mg/gVSS to 607.7 and 538.2 mg/gVSS, respectively, under the exposure to SDZ, which was mainly contributed by the increase of proteins in tightly bound extracellular polymeric substances (EPS) and polysacharides in tightly bound EPS and soluble microbial products. The proportion of tryptophan-like protein and humic acid-like organics in EPS also increased. Moreover, SDZ stress stimulated the secretion of three quorum sensing signal molecules, C4-HSL (from 140.3 to 164.9 ng/L), 3OC6-HSL (from 17.8 to 42.4 ng/L) and C8-HSL (from 35.8 to 95.9 ng/L) in the enriched AOB sludge. Among them, C8-HSL may be a key signal molecule that promoted the secretion of EPS. The findings of this study could shed more light on the cometabolic degradation of antibiotics by AOB.

A new strategy for the enrichment of ammonia-oxidizing archaea in wastewater treatment systems: The positive role of quorum-sensing signaling molecules

Ammonia-oxidizing archaea (AOA) play an important role in natural nitrogen cycle, but are difficult to be enriched in wastewater treatment systems. In this experiment, under ambient temperature and high dissolved oxygen, different types of acyl-homoserine lactones (C₆-HSL, C₈-HSL, C₁₀-HSL, C₁₄-HSL and 3-oxo-C₁₄-HSL) were added to five wastewater nitrification systems to achieve AOA enrichment. Results showed that AOA couldn't be detected in the blank group without the addition of signaling molecules, while the AOA could be detected in all the reactors with the addition. The enrichment effect of AOA was not obvious with added 100 or 200 nmol/L signaling molecules, while the enrichment effect was both obvious with added C₈-HSL of 400 nmol/L and C₁₀-HSL of 800 nmol/L. And relative abundance of AOA increased from undetected in the control group to 1.10 % and 0.96 %, respectively. The exogenous signaling molecules may provide new view for AOA enrichment in wastewater treatment systems.

Sustainable nitrogen removal in anammox-mediated systems: Microbial metabolic pathways, operational conditions and mathematical modelling

Anammox-mediated systems have attracted considerable attention as alternative cost-effective technologies for sustainable nitrogen (N) removal from wastewater. This review comprehensively highlights the importance of understanding microbial metabolism in anammox-mediated systems under crucial operation parameters, indicating the potentially wide applications for the sustainable treatment of N-containing wastewater. The partial nitrification-anammox (PN-A), simultaneous PN-A and denitrification (SNAD) processes have demonstrated sustainable N removal from sidestream wastewater. The partial denitrification-anammox (PD-A) and denitrifying anaerobic methane oxidation-anammox (DAMO-A) processes have advanced sustainable N removal efficiency in mainstream wastewater treatment. Moreover, N2O production/emission hotspots are extensively discussed in anammox-based processes and are related to the dominant ammonia-oxidizing bacteria (AOB) and denitrifying heterotrophs. In contrast, N2O is not produced in the metabolism pathways of AnAOB and DAMO-archaea; Moreover, the actual contribution of N2O production by dissimilatory nitrate reduction to ammonium (DNRA) and DAMO-bacteria in their species remains uncertain. Thus, PD-A and DAMO-A processes would achieve reduction in greenhouse gas production, as well as energy consumption for the reliability of N removal efficiencies. In addition to reaction mechanisms, this review covers the mathematical models for simultaneous anammox, partial nitrification and/or denitrification (i.e., PN-A, PD-A, and SNAD). Promising NO3- reduction technologies by endogenous PD, sulfur-driven autotrophic denitrification, and DNRA by anammox are also discussed. In summary, this review provides a better understanding of sustainable N removal in anammox-mediated systems, thereby encouraging future investigation and exploration of the sustainable N bio-treatment from wastewater.

The synergistic mechanism of β-lactam antibiotic removal between ammonia-oxidizing microorganisms and heterotrophs

Nitrifying system is an effective strategy to remove numerous antibiotics, however, the contribution of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and heterotrophs for antibiotic removal are still unclear. In this study, the mechanism of β-lactam antibiotic (cefalexin, CFX) removal was studied in a nitrifying sludge system. Results showed that CFX was synergistically removed by AOB (Nitrosomonas, played a major role) and AOA (Candidatus_Nitrososphaera) through ammonia monooxygenase-mediated co-metabolism, and by heterotrophs (Pseudofulvimonas, Hydrogenophaga, RB41, Thauera, UTCFX1, Plasticicumulans, Phaeodactylibacter) through antibiotic resistance genes (ARGs)-encoded β-lactamases-mediated hydrolysis. Regardless of increased archaeal and heterotrophic CFX removal with the upregulation of amoA in AOA and ARGs, the system exhibited poorer CFX removal performance at 10 mg/L, mainly due to the inhibition of AOB. This study provides new reference for the important roles of heterotrophs and ARGs, opening the possibilities for the application of ARGs in antibiotic biodegradation.

Integrating conventional nitrogen removal with anammox in wastewater treatment systems: Microbial metabolism, sustainability and challenges

The various forms of nitrogen (N), including ammonium (NH₄⁺), nitrite (NO₂^-), and nitrate (NO₃^-), present in wastewaters can create critical biotic stress and can lead to hazardous phenomena that cause imbalances in biological diversity. Thus, biological nitrogen removal (BNR) from wastewaters is considered to be imperatively urgent. Therefore, anammox-based systems, i.e. partial nitrification and anaerobic ammonium oxidation (PN/anammox) and partial denitrification and anammox (PD/anammox) have been universally acknowledged to consider as alternatives, promising and cost-effective technologies for sustainable N removal from wastewaters compared to nitrification-denitrification processes. This review comprehensively presents and discusses the latest advances in BNR technologies, including traditional nitrification-denitrification and anammox-based systems. To a deep understanding of a better-controlled combining anammox with traditional processes, the microbial community diversity and metabolism, as well as, biomass morphological characteristics were clearly reviewed in the anammox-based systems. Explaining simultaneous microbial competition and control of crucial operation parameters in single-stage anammox-based processes in terms of optimization and economic benefits makes this contribution a different vision from available review papers. The most important sustainability indicators, including global warming potential (GWP), carbon footprint (CF) and energy behaviours were explored to evaluate the sustainability of BNR processes in wastewater treatment. Additionally, the challenges and solutions for BNR processes are extensively discussed. In summary, this review helps facilitate a critical understanding of N removal technologies. It is confirmed that sustainability and saving energy would be achieved by anammox-based systems, thereby could be encouraged future outcomes for a sustainable N removal economy.

Bacterial Resistance to β-Lactam Antibiotics in Municipal Wastewater: Insights from a Full-Scale Treatment Plant in Poland

This study investigated enzymatic and genetic determinants of bacterial resistance to β-lactam antibiotics in the biocenosis involved in the process of biological treatment of wastewater by activated sludge. The frequency of bacteria resistant to selected antibiotics and the activity of enzymes responsible for resistance to β-lactam antibiotics were estimated. The phenomenon of selection and spread of a number of genes determining antibiotic resistance was traced using PCR and gene sequencing. An increase in the percentage of bacteria showing resistance to β-lactam antibiotics in the microflora of wastewater during the treatment process was found. The highest number of resistant microorganisms, including multi-resistant strains, was recorded in the aeration chamber. Significant amounts of these bacteria were also present in treated wastewater, where the percentage of penicillin-resistant bacteria exceeded 50%, while those resistant to the new generation β-lactam antibiotics meropenem and imipenem were found at 8.8% and 6.4%, respectively. Antibiotic resistance was repeatedly accompanied by the activity of enzymes such as carbapenemases, metallo-β-lactamases, cephalosporinases and β-lactamases with an extended substrate spectrum. The activity of carbapenemases was shown in up to 97% of the multi-resistant bacteria. Studies using molecular biology techniques showed a high frequency of genes determining resistance to β-lactam antibiotics, especially the blaTEM1 gene. The analysis of the nucleotide sequences of blaTEM1 gene variants present in bacteria at different stages of wastewater treatment showed 50-100% mutual similarity of.

Di(2-ethylhexyl) phthalate and dibutyl phthalate have a negative competitive effect on the nitrification of black soil

Di (2-ethylhexyl) phthalate (DEHP) and dibutyl phthalate (DBP) are the most widely used plasticizers for agricultural mulching films and one of the most common organic pollutants in black soil. However, little is known about the effect of these two contaminants on nitrification in black soil. This study investigated the changes of 20 mg/kg DEHP and DBP on the diversity of nitrification microbial communities, the abundance of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) related genes, and the activities of key enzymes involved in nitrification. During ammonia oxidation, DEHP and DBP had uncompetitive inhibition of urease, reducing the copy number of amoA gene, and microorganisms (Azoarcus, Streptomyces and Caulobacter) would use inorganic nitrogen as a nitrogen source for physiological growth. During nitrite oxidation, the copy number of nxrA gene also reduced, and the relative abundance of chemoautotrophic nitrifying bacteria (Nitrosomonas and Nitrobacter) decreased. Moreover, the path analysis results showed that DEHP and DBP mainly directly or indirectly affect AOB and NOB through three ways. These results help better understand the ecotoxicological effects of DEHP and DBP on AOB and NOB in black soil.

Cometabolic biodegradation of antibiotics by ammonia oxidizing microorganisms during wastewater treatment processes

Studies on antibiotic removal during wastewater treatment processes are crucial since their release into the environment could bring potential threats to human health and ecosystem. Cometabolic biodegradation of antibiotics by ammonia oxidizing microorganisms (AOMs) has received special attentions due to the enhanced removal of antibiotics during nitrification processes. However, the interactions between antibiotics and AOMs are less well-elucidated. In this review, the recent research proceedings on cometabolic biodegradation of antibiotics by AOMs were summarized. Ammonia oxidizing bacteria (AOB), ammonia oxidizing archaea (AOA) and complete ammonia oxidizers (comammox) played significant roles in both nitrification and cometabolic biodegradation of antibiotics. Antibiotics at varying concentrations might pose inhibiting or stimulating effect on AOMs, influencing the microbial activity, community abundance and ammonia monooxygenase subunit A gene expression level. AOMs-induced cometabolic biodegradation products were analyzed as well as the corresponding pathways for each type of antibiotics. The effects of ammonium availability, initial antibiotic concentration, sludge retention time and temperature were assessed on the cometabolic biodegradation efficiencies of antibiotics. This work might provide further insights into the fate and removal of antibiotics during nitrification processes.

LDPE microplastics affect soil microbial communities and nitrogen cycling

Microplastics (MPs) are a contaminant of increasing concern in the environment. However, the impacts of MPs on soil ecosystems and biogeochemical processes like nitrogen cycle have not been well elucidated. In this study, we designed an indoor microcosm experiment to investigate the effects of exposure to low density polyethylene (LDPE) MPs on soil bacterial community and nitrogen cycling function over a 90-day incubation. Next-generation sequencing of the 16S rRNA genes revealed that both 2% and 7% LDPE MPs exposure slightly affected the soil bacterial diversity. Further analysis at the genus level showed differential tolerance to LDPE MPs, the genera Pedomicrobium, Steroidobacter, Pseudonocardia, Nitrospira and Turicibacter were enriched in the soil with 2% (w/w) LDPE MPs amendment, while the genera Pedomicrobium, Mycobacterium and Hyphomicrobium were significantly enriched in the soil with 7% (w/w) LDPE MPs amendment on days 15 and 30. Co-occurrence network analysis further suggested that LDPE MPs changed bacterial network complexity and modularity and Acidobacteria formed intimate associations with each other in responding to LDPE MPs exposure. Additionally, LDPE MPs in soil increased the abundance of nifH, AOBamoA and nirK genes involved in nitrogen cycling in different incubation phases compared to the control. The abundance of AOAamoA genes decreased on day 15 and then increased. Conversely, the abundance of nirS genes increased during the first 15 days and then decreased. These results suggested that both 2% and 7% LDPE MPs impact soil bacterial network structure and alters functional groups involved in soil nitrogen cycling processing.

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.

Selective enrichment of comammox from activated sludge using antibiotics

While the ubiquitous presence of comammox in engineered systems provides the foundation of developing a novel biological nitrogen removal process, factors contributing to the comammox dynamics in engineered systems have not been well resolved. Here, we investigate the long-term effects of ten different antibiotics on microbial community dynamics in activated sludge and the results show that both types and concentrations of antibiotics affect the taxonomic composition of nitrifiers, including comammox, ammonia-oxidizing bacteria, and canonical nitrite-oxidizing bacteria. Specifically, phylogenetically different comammox Nitrospira were selectively enriched by four types of antibiotics (i.e., ampicillin, kanamycin, lincomycin, and trimethoprim). Comparative genomic analysis of the four newly identified comammox clade A Nitrospira revealed that the comammox enriched by antibiotics shared the conserved key metabolic potentials, such as carbon fixation, complete ammonia oxidation, and utilization of hydrogen as alternative electron donors, among the known comammox organisms. Comammox strains enriched in this study also encoded genes involved in formate and cyanate metabolism that were recently reported in comammox clade A organisms from wastewater treatment systems. Our findings highlight that the comammox in activated sludge ecosystems possess high metabolic versatility than previously recognized and could be selectively enriched by some antibiotics.

Enantioselective effects of cyflumetofen on microbial community and related nitrogen cycle gene function in acid-soil

Cyflumetofen (CYF) is a novel chiral acaricide widely used in commercial crops to control mites. The environmental risks exposed by CYF in the soil, especially at the enantiomer level, remain unclear. We found that the (+)-CYF enantiomer was preferentially degraded in acid-soil, resulting in (-)-CYF enrichment. 16S rRNA and qPCR analysis indicated that decreased bacterial abundance by 12.79-61.80% and 2.52-52.48% in (-)-CYF treatment and (+)-CYF treatment, respectively. Diversity was also decreased with (-)-CYF treatment. Interestingly, several beneficial bacteria, for instance, Alphaproteobacteria (class), Sphingomonadaceae (family), and Arthrobacter (specise) were more enriched following (-)-CYF. The abundance of N₂-fixing bacteria showed a sustained reduction with time, and the decrease was 3.24-72.94% with (-)-CYF and 25.37-73.11% with (+)-CYF treatment. Compared with the (+)-CYF treatment could positively promote nitrification, while the treatment (-)-CYF significantly reduced the abundance of amoA gene; namely it significantly negatively affected the nitrification in the nitrogen cycle. Through our further research, we found that Actinobacteria, Alphaproteobacteria, Lysobacter; Sphingomonas, Patescibacteria, Saccharimonadia, and Saccharimonadales showed synergistic effects with the nitrogen cycling-related genes nifH and amoA. These results contribute to a comprehensive environmental risk assessment of CYF in acid-soil at the enantiomer level.

A critical review on the effects of antibiotics on anammox process in wastewater

Anaerobic ammonium oxidation (anammox) has recently become of significant interest due to its capability for cost-effective nitrogen elimination from wastewater. However, anaerobic ammonia-oxidizing bacteria (AnAOB) are sensitive to environmental changes and toxic substances. In particular, the presence of antibiotics in wastewater, which is considered unfavorable to the anammox process, has become a growing concern. Therefore, it is necessary to evaluate the effects of these inhibitors to acquire information on the applicability of the anammox process. Hence, this review summarizes our knowledge of the effects of commonly detected antibiotics in water matrices, including fluoroquinolone, macrolide, β-lactam, chloramphenicol, tetracycline, sulfonamide, glycopeptide, and aminoglycoside, on the anammox process. According to the literature, the presence of antibiotics in wastewater could partially or completely inhibit anammox reactions, in which antibiotics targeting protein synthesis or DNA replication (excluding aminoglycoside) were the most effective against the AnAOB strains.

Influences of hexafluoropropylene oxide (HFPO) homologues on soil microbial communities

Hexafluoropropylene oxide (HFPO) homologues, as emerging perfluoroalkyl substances (PFASs) to replace legacy PFASs, have wide applications in the organofluorine industry and have been detected in the global environment. However, it is still unclear what effect HFPO homologues will exert on microbial abundance, community structure and function. The objective of this study was to assess potential impacts of HFPO homologue acids on archaea, bacteria, and ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the soil environment. Grassland soil microcosms were supplemented with low (0.1 mg/kg) or high (10 mg/kg) dosages of dimer, trimer and tetramer acids of HFPO (HFPO-DA, HFPO-TA, and HFPO-TeA), respectively. The amendment of HFPO homologues acids initially decreased the abundance of archaea and bacteria but increased them in the later period. The addition of HFPO homologues acids raised AOA abundance but restrained AOB growth during the whole incubation. AOA and AOB community structures showed considerable variations. Potential nitrifying rate (PNR) showed an increase in the initial period followed by a decline in the later period. HFPO-DA had a lasting and suppressive effect on AOB and PNR even at a nearly environmental level. Overall, HFPO homologues with different carbon chain lengths had different impacts on soil microbial community and ammonia oxidation.

Microbial community functional structure in an aerobic biofilm reactor: Impact of streptomycin and recovery

Antibiotics can affect microbial community structure and promote antibiotic resistance. However, the course of microbial community recovery in wastewater treatment systems after antibiotic disturbance remains unclear. Herein, multiple molecular biology tools, including 16S amplicon sequencing, GeoChip 5.0, quantitative polymerase chain reaction (qPCR), and metagenomic sequencing, were used to investigate the year-long (352 d) recovery of the microbial community functional structure in an aerobic biofilm reactor. Nitrification was completely inhibited under 50 mg/L of streptomycin spiking (STM_50) due to the significant reduction of ammonia-oxidizing bacteria, but recovered to original pre-disturbance levels after streptomycin removal, indicating the high resilience of ammonia-oxidizing bacteria. Bacterial community richness and diversity decreased significantly under STM_50 (p < 0.05), but recovered to levels similar to those observed before disturbance after 352 d. In contrast, bacterial composition did not recover to the original structure. The carbon degradation and nitrogen cycling functional community significantly changed after recovery compared to that observed pre-disturbance (p < 0.05), thus indicating functional redundancy. Additionally, levels of aminoglycoside and total antibiotic resistance genes under STM_50 (relative abundance, 0.33 and 0.80, respectively) and after one year of recovery (0.12 and 0.29, respectively) were higher than the levels detected pre-disturbance (0.04 and 0.24, respectively). This study provides an overall depiction of the recovery of the microbial community functional structure after antibiotic exposure. Our findings give notice that recovery caused by antibiotic disturbance in the water environment should be taken more seriously, and that engineering control strategies should be implemented to prevent the antibiotic pollution of wastewater.

Minimum influent concentrations of oxytetracycline, streptomycin and spiramycin in selecting antibiotic resistance in biofilm type wastewater treatment systems

It has been demonstrated that antibiotic resistance could be induced and selected under high antibiotic concentrations in biological wastewater treatment systems. However, little is available regarding the minimum concentrations of antibiotics for selecting antibiotic resistance during wastewater treatment. Herein, the minimum influent concentrations of oxytetracycline, streptomycin, and spiramycin in selecting antibiotic resistance in biofilm type wastewater treatment systems were investigated by spiking respective antibiotic into wastewater with an antibiotic dose increasing from 0 to 0.1, 1, 5, 25, 50 mg/L stepwise over a period of 606 days. Significant increase (p < .01) in the total abundance of antibiotic resistance genes was observed for both streptomycin and oxytetracycline at a dose of 0.1 mg/L according to metagenomic sequencing, while the concentration levels leading to significant increases (p < .05) in resistant bacteria ratio were higher: 5 mg/L for streptomycin and 25 mg/L for oxytetracycline. Although resistome abundance increased with the increase of spiramycin dose, neither the corresponding Macrolide-Lincosamide-Streptogramin (MLS) resistance genes nor the resistant bacteria ratio showed perceptible increase. Partial canonical correspondence analysis showed that both bacterial community shift and mobile genetic elements alteration contributed to the enrichment of resistomes under the presence of streptomycin and oxytetracycline. Regarding spiramycin which is mainly targeting on Gram-positive bacteria, the dominance of the intrinsically resisting Gram-negative bacteria in the biofilm microbiota might be responsible for the vague change of MLS resistant determinants under the spiramycin stress. The results demonstrated that it is possible to prevent the development of antibiotic resistance during wastewater treatment by controlling the influent streptomycin and oxytetracyline concentrations below 0.1 mg/L. This work proposed an actionable approach for the management of antibiotic production wastewater.

Emerging perfluoroalkyl substance impacts soil microbial community and ammonia oxidation

Legacy perfluoroalkyl and poly-fluoroalkyl substances (PFASs) are gradually phased out because of their persistence, bioaccumulation, toxicity, long-distance transport and ubiquity in the environment. Alternatively, emerging PFASs are manufactured and released into the environment. It is accepted that PFASs can impact microbiota, although it is still unclear whether emerging PFASs are toxic towards soil microbiota. However, it could be assumed that OBS could impact soil microorganisms because it had similar chemical properties (toxicity and persistence) as legacy PFASs. The present study aimed to explore the influences of an emerging PFAS, namely sodium p-perfluorous nonenoxybenzene sulfonate (OBS), on archaeal, bacterial, and ammonia-oxidizing archaea (AOA) and bacteria (AOB) communities and ammonia oxidation. Grassland soil was amended with OBS at different dosages (0, 1, 10 and 100 mg/kg). After OBS amendment, tolerant microorganisms (e.g., archaea and AOA) were promoted, while susceptive microorganisms (e.g., bacteria and AOB) were inhibited. OBS amendment greatly changed microbial structure. Potential nitrifying activity was inhibited by OBS in a dose-dependent manner during the whole incubation. Furthermore, AOB might play a more important role in ammonia oxidation than AOA. Overall, OBS influenced ammonia oxidation by regulating the activity, abundance and structure of ammonia-oxidizing microorganisms, and could also exert influences on total bacterial and archaeal populations.

Bioremediation by earthworms on soil microbial diversity and partial nitrification processes in oxytetracycline-contaminated soil

A large proportion (60-90%) of ingested tetracyclines are released to slurry, soils, surface waters and ground water, which has raised extensive concerns and may pose a risk to the soil ecosystem. A 56-day experiment was conducted to study the bioremediation by earthworms on soil microbial diversity and partial nitrification processes in oxytetracycline (OTC)-contaminated soil. The results showed that high OTC concentration significantly decreased the activity of soil bacteria, ammonia-oxidizing bacteria (AOB) and archaea (AOA). Earthworms were found to accelerate the degradation efficiency and rate of OTC, and its main metabolites were 4-epi-oxytetracycline (EOTC) and 2-acetyl-2-decarboxamido-oxytetracycline (ADOTC). Earthworms had an important role in the bioremediation of soil microbial diversity by degrading OTC and its metabolite (EOTC), especially in the high OTC condition. Additionally, the results indicated that the effects of earthworms on the degradation of OTC could remediate the abundances of 16S rRNA and AOB amoA genes and the NO₃^- content in both low and high OTC-contaminated soils. The structural equation model suggested that earthworms could remediate the microbial diversity, the abundances of 16s rRNA and AOB amoA genes by accelerating the degradation of OTC, which contributed to the bioremediation by earthworms on soil microbial diversity and partial nitrification processes in oxytetracycline-contaminated soil.

Occurrence of 40 pharmaceutically active compounds in hospital and urban wastewaters and their contribution to Mahdia coastal seawater contamination

In the present study, the occurrence of 40 pharmaceuticals belonging to several therapeutic groups was investigated for the first time in hospital effluent, wastewater treatment plant influent and effluent, and seawater in Mahdia, Tunisia. Forty-six samples were collected within a 6-month sampling period. Pharmaceuticals were analyzed using solid-phase extraction followed by ultra-performance liquid chromatography-triple quadrupole mass spectrometry. Thirty-three out of the forty target compounds were detected over a wide concentration of ranges, from nanograms per liter to micrograms per liter, depending on the type of sample. Maximum values were detected for caffeine at 902 μgL^-1 in hospital wastewater. This compound, as well as salicylic acid, sulfadiazine, and sulfamethizole, were detected in all samples. The average concentration of total pharmaceuticals in hospital wastewater (340 μgL^-1) was higher than those detected in influent and effluent wastewater and seawater (275.11 and 0.2 μgL^-1, respectively). Risk quotients (RQs) were also estimated to provide a preliminary environmental risk assessment and results revealed that sulfadiazine, sulfamethoxazole, and fluoxetine could pose medium/high risk to the tested aquatic organisms for maximum measured concentrations in wastewater (including hospital and WWTP samples). Although the measured environmental concentrations (MECs) detected in seawater samples might not pose a toxic effect to the aquatic organisms (except for salicylic acid, sulfamethoxazole and fluoxetine), further researches are needed due to the continuous release of wastewater in the environment and the limited efficiency of wastewater treatment processes.

Fates of antibiotic resistance genes in a distributed swine wastewater treatment plant

This study explores the prevalence, emission, and reduction of five ARGs (sulI, tetA, mphB, qnrD, and mcr-1) and integron (intI) through a distributed swine wastewater purification facility and the effluent-receiving environment. Typical metal resistance genes (MRGs), pathogenic bacterial indicators, the bacterial community, and wastewater properties were also explored to determine their effects on the fates of ARGs. Results indicated that the purification process could hardly effectively remove ARGs' prevalence. 3.1 × 10⁴ -7.1 × 10⁸  copies/L were present after purification, and 4%-57% of them persisted in the subsequent creek and adjacent soil. 16S rRNA sequencing suggested that the discharge of wastewater significantly changed the bacterial community in receiving creek and soil. Molecular ecological networks analysis detected the wide co-occurrence among ARGs, MRGs, and PBGs, which could further facilitate the propagation of antibiotic resistance. ARG incidence and specific bacterial genera were closely correlated, suggesting an extensive hosting relationship. Redundancy analyses showed wastewater organics and nutrients showed positive correlation to most ARGs' abundance, but negatively correlated to their relative abundance. PRACTITIONER POINTS: Fate of five ARGs and intI was studied in a swine wastewater treatment system. The treatment process could not effectively reduce ARGs' abundance. ARGs and pathogens in wastewater were transferred to the receiving creek and soil. The network analysis found wide co-occurrence among ARGs, metal resistance genes, and pathogens. Wastewater nutrients positively correlated to ARG's abundance but negatively correlated to their relative abundance.

Abundance and community composition of comammox bacteria in different ecosystems by a universal primer set

Complete ammonia oxidizing bacteria (CAOB) have been recognized as a new member of ammonia-oxidizing microorganisms (AOMs) due to its single-step nitrification capability. However, the abundance and diversity of CAOB in environmental ecosystems were still far from known owing to the lack of specific molecular marker. Herein, a universal primer set specifically targeting both clades of CAOB amoA gene with high specificity and coverage was successfully designed. Intriguingly, real-time quantitative PCR tests revealed that CAOB were ubiquitous and unexpectedly abundant in agricultural soils, river sediments, intertidal zones, drinking water and wastewater treatment systems. Phylogenetic analysis indicated that clade A existed in all the five types of ecosystems, while clade B were only detected in soil and sediment samples. Four sub-clusters were further classified within clade A, in which N. nitrosa cluster dominated CAOB amoA in activated sludge samples while the new recognized soil cluster was the primary constitute in soils. Moreover, the niche specialization between different CAOB species and the environmental conditions were supposed to be the primary driven force to shape the diversity and community of CAOB. This study provided a strong evidence in support of the ubiquities and high abundances of CAOB in various environmental ecosystems and highlighted the significance of including CAOB as the new member of AOMs to re-evaluate the biogeochemical nitrogen cycle.

Enhanced hydrolyzed polyacrylamide removal from water by an aerobic biofilm reactor-ozone reactor-aerobic biofilm reactor hybrid treatment system: Performance, key enzymes and functional microorganisms

Degradation of hydrolyzed polyacrylamide-containing (HPAM-containing) wastewater was investigated in a lab-scale aerobic-ozonic-aerobic hybrid treatment system. When the HPAM concentration was 500 mg L^-1 and the ozone dose was 25 g O₃/g TOC, the HPAM removal rate reached 90.79%. Experimental results obtained from gel permeation chromatography (GPC) and rheometer indicated that the refractory HPAM was decomposed into small-molecule compounds. High performance liquid chromatography (HPLC) analysis showed that there was no acrylamide (AM) in the effluent of the system. Microbial communities in two aerobic biofilm reactors (ABRs) were analyzed by Illumina MiSeq Sequencing, which indicated that norank_f_Cytophagaceae, Meiothermus, Bacillus, etc. were keystone functional bacterial genera and Methanobacterium, norank_p_Bathyarchaeota, norank_c_Marine_Group_Ⅰ, etc. were dominant functional archaeal groups. To our knowledge, this is the first study to treat HPAM-containing wastewater using an aerobic-ozonic-aerobic hybrid process. Good removal efficiencies and presence of functional microorganisms demonstrated that the hybrid treatment system was practical for treating HPAM-containing wastewater.

Effects of antibiotic residuals in dewatered sludge on the behavior of ammonia oxidizers during vermicomposting maturation process

Antibiotics existed in dewatered sludge may affect the organic decomposition and nitrification efficiency of vermicomposting process, and thus lowering the agricultural value of sludge vermicompost. However, few studies have focused on the effects of antibiotics during vermicomposting process of sludge, notably for the maturated phage. Hence, this study aimed to investigate the effects of antibiotics on the nitrification rate and the features of ammonia oxidizing archaea (AOA) and bacteria (AOB) during vermicomposting maturated phage of sludge. The treatments including the additions of tetracycline and ofloxacin with high and low concentrations were compared with the control without adding antibiotics. The results showed the antibiotics enhanced the nitrification rate of 15.8%-42% in vermicomposting maturated phage compared with the counterpart, with a better stimulating effect in the low concentration of tetracycline. The population of amoA genes increased in antibiotic treatments with low concentrations but decreased in these with high concentrations. In addition, high through-put sequencing results revealed that the tetracycline had a stronger influence on the α and β diversities of AOA and AOB, relative to the ofloxacin. In contrast to the AOB, the AOA played a more important role in ammonia oxidization, in the presence of antibiotics. This study suggests that the antibiotics of dewatered sludge can strongly affect the ammonia oxidization process through modifying the numbers and community structures of AOA and AOB during vermicomposting and these effects are associated with the types and concentrations of antibiotics.

Clomazone influence soil microbial community and soil nitrogen cycling

We designed an indoor mesocosm experiment to investigate the long-term effects of exposure to clomazone, a widely used herbicide, on soil microbial communities and their nitrogen (N) cycling functions. Clomazone was applied to two typical soils from China at three concentrations: 0.8 (the recommended dosage), 8 and 80 mg kg^-1 soil dry weight, and the mix was incubated for 90 days. Samples were removed periodically for assay with several techniques. The half-lives of clomazone in this experiment were 11-126 d. Results were significant only for the highest clomazone concentration. Next-generation sequencing of the 16S and 18S rDNA genes revealed that bacterial diversity significantly decreased whereas fungal abundance increased after day 60 but with no detectable effect on the microbial community. Hierarchical cluster and principal coordinates analysis revealed that the bacterial community structure was negatively impacted. Linear discriminant analysis of effect size identified Sphingomonas and Arthrobacter as the predominant bacterial species. Finally, we measured soil NH₄⁺ and NO₃^- concentrations and used real-time PCR to analyze the abundance of the N-cycling genes, nifH and amoA. In the first 30 days, the NO₃^--N content and the number of ammonia-oxidizing bacteria increased. N₂-fixing bacteria were inhibited after 60 days, but the NH₄⁺-N concentration remained unchanged and was likely provided by ammoniation.

Newly designed primer pair revealed dominant and diverse comammox amoA gene in full-scale wastewater treatment plants

The discovery of complete ammonia oxidizing bacteria (CAOB) capable of performing the two-step nitrification process on their own has fundamentally upended our traditional perception. However, their environmental distribution and ecological significance in driving ammonia oxidation are still urgently awaited to be assessed. In this study, the diversity and abundance of CAOB amoA gene in wastewater treatment plants (WWTPs) were presented taking advantage of a newly designed primer pair specifically targeting CAOB amoA gene. Phylogenetic results demonstrated the novel amoA gene formed a clearly distinct cluster from the canonical amoA and pmoA genes. Among the five well-supported sub-clusters, Nitrospira nitrosa cluster accounted for 94.34% of all the currently retrieved sequences from WWTPs. More importantly, qPCR results demonstrated a remarkably high abundance of CAOB amoA gene, which were up to 182.7-fold more abundant than AOB amoA gene. This study provided new dimension and fundamental basis for future researches towards biogeochemical nitrogen cycle.

Incorporation of 13C-HCO3- by ammonia-oxidizing archaea and bacteria during ammonia oxidation of sludge from a municipal wastewater treatment plant

Ammonia-oxidizing archaea (AOA) have recently been proposed as potential players for ammonia removal in wastewater treatment plants (WWTPs). However, there is little evidence directly showing the contribution of AOA to ammonia oxidation in these engineered systems. In this study, DNA-stable isotope probing (DNA-SIP) with labeled ¹³C-HCO₃^- was introduced to sludge from a municipal WWTP. Quantitative PCR demonstrated that AOA amoA genes outnumbered AOB amoA genes in this WWTP sludge. AOA amoA gene sequence analysis revealed that AOA present in this WWTP were specific to one subcluster within the group 1.1b Thaumarchaeota. When ammonia was supplied to DNA-SIP incubation, the DNA-SIP profiles demonstrated the incorporation of the ¹³C into AOA and AOB. However, the ¹³C was not found to be assimilated into both microorganisms in the incubation without ammonia. Specific primers were designed to target amoA genes of AOA belonging to the subcluster found in this WWTP. Applying the primers to DNA-SIP experiment revealed that AOA of this subcluter most likely utilized inorganic carbon during ammonia oxidation under the studied conditions.

Effect of sulfadiazine and trimethoprim on activated sludge performance and microbial community dynamics in laboratory-scale membrane bioreactors and sequencing batch reactors at 8°C

The effect of antibiotics sulfadiazine and trimethoprim on activated sludge operated at 8°C was investigated. Performance and microbial communities of sequencing batch reactors (SBRs) and Membrane Bioreactors (MBRs) were compared before and after the exposure of antibiotics to the synthetic wastewater. The results revealed irreversible negative effect of these antibiotics in environmentally relevant concentrations on nitrifying microbial community of SBR activated sludge. In opposite, MBR sludge demonstrated fast adaptation and more stable performance during the antibiotics exposure. Dynamics of microbial community was greatly affected by presence of antibiotics. Bacteria from classes Betaproteobacteria and Bacteroidetes demonstrated the potential to develop antibiotic resistance in both wastewater treatment systems while Actinobacteria disappeared from all of the reactors after 60 days of antibiotics exposure. Altogether, results showed that operational parameters such as sludge retention time (SRT) and reactor configuration had great effect on microbial community composition of activated sludge and its vulnerability to antibiotics. Operation at long SRT allowed archaea, including ammonium oxidizing species (AOA) such as Nitrososphaera viennensis to grow in MBRs. AOA could have an important role in stable nitrification performance of MBR-activated sludge as a result of tolerance of archaea to antibiotics. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2708, 2019.

Antibiotic resistance genes and intI1 prevalence in a swine wastewater treatment plant and correlation with metal resistance, bacterial community and wastewater parameters

The livestock wastewater treatment plant represents an important reservoir of antibiotic resistance determinants in the environment. The study explored the prevalence of five antibiotic resistance genes (ARGs, including sulI, tetA, qnrD, mphB and mcr-1) and class 1 integron (intI1) in a typical livestock wastewater treatment plant, and analyzed their integrated association with two metal resistance genes (copA and czcA), two pathogens genes (Staphylococcus and Campylobacter), bacterial community and wastewater properties. Results indicated that all investigated genes were detected in the plant. The treatment plant could not completely remove ARGs abundances, with up to 2.2 × 10⁴~3.7 × 10⁸ copies/L of them remaining in the effluent. Mcr-1 was further enriched by 27-fold in the subsequent pond. The correlation analysis showed that mphB significantly correlateed with tetA and intI. Mcr-1 strongly correlated with copA. MphB and intI significantly correlated with czcA. The correlations implied a potential co-selection risk of bacterial resistant to antibiotics and metals. Redundancy analyses indicated that qnrD and mcr-1 strongly correlated with 13 and 14 bacterial genera, respectively. Most ARGs positively correlated to wastewater nutrients, indicating that an efficient reduction of wastewater nutrients would contribute to the antibiotic resistance control. The study will provide useful implications on fates and reductions of ARGs in livestock facilities and receiving environments.

Ammonia-Oxidizing Archaea (AOA) Play with Ammonia-Oxidizing Bacteria (AOB) in Nitrogen Removal from Wastewater

An increase in the number of publications in recent years indicates that besides ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) may play an important role in nitrogen removal from wastewater, gaining wide attention in the wastewater engineering field. This paper reviews the current knowledge on AOA and AOB involved in wastewater treatment systems and summarises the environmental factors affecting AOA and AOB. Current findings reveal that AOA have stronger environmental adaptability compared with AOB under extreme environmental conditions (such as low temperature and low oxygen level). However, there is still little information on the cooperation and competition relationship between AOA and AOB, and other microbes related to nitrogen removal, which needs further exploration. Furthermore, future studies are proposed to develop novel nitrogen removal processes dominated by AOA by parameter optimization.

Effects of trifluralin on the soil microbial community and functional groups involved in nitrogen cycling

Large amounts of trifluralin are applied each year for weed control; however, its effects on soil microbial communities and functions are unknown. Two agricultural soils, one silty loam and one silty clay were spiked with TFL (0, 0.84, 8.4, and 84 mg kg^-1) and studied the effects using a laboratory microcosm approach. The half-lives were 44.19-61.83 d in all cases. Bacterial abundance increased 1.12-5.56 times by TFL, but the diversity decreased. From the next-generation sequencing results, TFL altered the bacterial community structure, which initially diverged from the control community structure, then recovered, and then diverged again. Linear discriminant analysis effect size indicated that Sphingomonas and Xanthomonadaceae were the predominant species on day 7 and 15 in TFL treatments. N₂-fixing bacteria were initially increased, then decreased, and then recovered, and it was positively correlated with NH₄⁺-N content. Compared with the control, ammonia-oxidizing bacteria were decreased by 25.51-92.63%, ammonia-oxidizing archaea were decreased by 17.12-85.21% (except day 7), and the NO₃^--N concentration was also inhibited. In contrast to bacteria, fungal abundance was inhibited without any observable effects on fungal diversity or community structure. These results suggest that TFL impacts soil bacterial community and alters functional microorganisms involved in soil N processing.

Contribution of ammonia-oxidizing archaea and ammonia-oxidizing bacteria to ammonia oxidation in two nitrifying reactors

In this study, two laboratory nitrifying reactors (NRI and NRII), which were seeded by sludge from different sources and operated under different operating conditions, were found to possess distinct dominant ammonia-oxidizing microorganisms. Ammonia-oxidizing archaeal (AOA) amoA genes outnumbered ammonia-oxidizing bacterial (AOB) amoA genes in reactor NRI, while only AOB amoA genes were detectable in reactor NRII. The AOA amoA gene sequences retrieved from NRI were characterized within the Nitrososphaera sister cluster of the group 1.1b Thaumarchaeota. Two inhibitors for ammonia oxidation, allylthiourea (ATU) and 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO), were applied individually and as a mixture to observe the ammonia-oxidizing activity of both microorganisms in the reactors' sludge. The results indicated that AOA and AOB jointly oxidized ammonia in NRI, while AOB played the main role in ammonia oxidation in NRII. DNA-stable isotope probing with labeled ¹³C-HCO₃^- was performed on NRI sludge. Incorporation of ¹³C into AOA and AOB implied that both microorganisms may perform autotrophy during ammonia oxidation. Taken together, the results from this study provide direct evidence demonstrating the contribution of AOA and AOB to ammonia oxidation in the nitrifying reactors.

Cultivation and Genomic Analysis of "Candidatus Nitrosocaldus islandicus," an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland

Ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota are the only known aerobic ammonia oxidizers in geothermal environments. Although molecular data indicate the presence of phylogenetically diverse AOA from the Nitrosocaldus clade, group 1.1b and group 1.1a Thaumarchaeota in terrestrial high-temperature habitats, only one enrichment culture of an AOA thriving above 50°C has been reported and functionally analyzed. In this study, we physiologically and genomically characterized a newly discovered thaumarchaeon from the deep-branching Nitrosocaldaceae family of which we have obtained a high (∼85%) enrichment from biofilm of an Icelandic hot spring (73°C). This AOA, which we provisionally refer to as "Candidatus Nitrosocaldus islandicus," is an obligately thermophilic, aerobic chemolithoautotrophic ammonia oxidizer, which stoichiometrically converts ammonia to nitrite at temperatures between 50 and 70°C. "Ca. N. islandicus" encodes the expected repertoire of enzymes proposed to be required for archaeal ammonia oxidation, but unexpectedly lacks a nirK gene and also possesses no identifiable other enzyme for nitric oxide (NO) generation. Nevertheless, ammonia oxidation by this AOA appears to be NO-dependent as "Ca. N. islandicus" is, like all other tested AOA, inhibited by the addition of an NO scavenger. Furthermore, comparative genomics revealed that "Ca. N. islandicus" has the potential for aromatic amino acid fermentation as its genome encodes an indolepyruvate oxidoreductase (iorAB) as well as a type 3b hydrogenase, which are not present in any other sequenced AOA. A further surprising genomic feature of this thermophilic ammonia oxidizer is the absence of DNA polymerase D genes - one of the predominant replicative DNA polymerases in all other ammonia-oxidizing Thaumarchaeota. Collectively, our findings suggest that metabolic versatility and DNA replication might differ substantially between obligately thermophilic and other AOA.

Divergent Responses of Forest Soil Microbial Communities under Elevated CO2 in Different Depths of Upper Soil Layers

Numerous studies have shown that the continuous increase of atmosphere CO2 concentrations may have profound effects on the forest ecosystem and its functions. However, little is known about the response of belowground soil microbial communities under elevated atmospheric CO2 (eCO2) at different soil depth profiles in forest ecosystems. Here, we examined soil microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) after a 10-year eCO2 exposure using a high-throughput functional gene microarray (GeoChip). The results showed that eCO2 significantly shifted the compositions, including phylogenetic and functional gene structures, of soil microbial communities at both soil depths. Key functional genes, including those involved in carbon degradation and fixation, methane metabolism, denitrification, ammonification, and nitrogen fixation, were stimulated under eCO2 at both soil depths, although the stimulation effect of eCO2 on these functional markers was greater at the soil depth of 0 to 5 cm than of 5 to 15 cm. Moreover, a canonical correspondence analysis suggested that NO3-N, total nitrogen (TN), total carbon (TC), and leaf litter were significantly correlated with the composition of the whole microbial community. This study revealed a positive feedback of eCO2 in forest soil microbial communities, which may provide new insight for a further understanding of forest ecosystem responses to global CO2 increases.IMPORTANCE The concentration of atmospheric carbon dioxide (CO2) has continuously been increasing since the industrial revolution. Understanding the response of soil microbial communities to elevated atmospheric CO2 (eCO2) is important for predicting the contribution of the forest ecosystem to global atmospheric change. This study analyzed the effect of eCO2 on microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) in a forest ecosystem. Our findings suggest that the compositional and functional structures of microbial communities shifted under eCO2 at both soil depths. More functional genes involved in carbon, nitrogen, and phosphorus cycling were stimulated under eCO2 at the soil depth of 0 to 5 cm than at the depth of 5 to 15 cm.

Characteristics of microbial community functional structure of a biological coking wastewater treatment system

Nitrogenous heterocyclic compounds are key pollutants in coking wastewater; however, the functional potential of microbial communities for biodegradation of such contaminants during biological treatment is still elusive. Herein, a high throughput functional gene array (GeoChip 5.0) in combination with Illumina HiSeq2500 sequencing was used to compare and characterize the microbial community functional structure in a long run (500days) bench scale bioreactor treating coking wastewater, with a control system treating synthetic wastewater. Despite the inhibitory toxic pollutants, GeoChip 5.0 detected almost all key functional gene (average 61,940 genes) categories in the coking wastewater sludge. With higher abundance, aromatic ring cleavage dioxygenase genes including multi ring1,2diox; one ring2,3diox; catechol represented significant functional potential for degradation of aromatic pollutants which was further confirmed by Illumina HiSeq2500 analysis results. Response ratio analysis revealed that three nitrogenous compound degrading genes- nbzA (nitro-aromatics), tdnB (aniline), and scnABC (thiocyanate) were unique for coking wastewater treatment, which might be strong cause to increase ammonia level during the aerobic process. Additionally, HiSeq2500 elucidated carbozole and isoquinoline degradation genes in the system. These findings expanded our understanding on functional potential of microbial communities to remove organic nitrogenous pollutants; hence it will be useful in optimization strategies for biological treatment of coking wastewater.

Response of ammonia oxidizing archaea and bacteria to decabromodiphenyl ether and copper contamination in river sediments

Ammonia oxidation plays a fundamental role in river nitrogen cycling ecosystems, which is normally governed by both ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB). Co-contamination of typical emerging pollutant Polybrominated diphenyl ethers (PBDEs) and heavy metal on AOA and AOB communities in river sediments remains unknown. In this study, multiple analytical tools, including high-throughput pyrosequencing and real-time quantitative PCR (qPCR), were used to reveal the ammonia monooxygenase (AMO) activity, subunit alpha (amoA) gene abundance, and community structures of AOA and AOB in river sediments. It was found that the inhibition of AMO activities was increased with the increase of decabromodiphenyl ether (BDE 209, 1-100 mg kg^-1) and copper (Cu, 50-500 mg kg^-1) concentrations. Moreover, the synergic effects of BDE 209 and Cu resulted in a higher AMO activity reduction than the individual pollutant BDE 209. The AOA amoA copy number declined by 75.9% and 83.2% and AOB amoA gene abundance declined 82.8% and 90.0% at 20 and 100 mg kg^-1 BDE 209 with a 100 mg kg^-1 Cu co-contamination, respectively. The pyrosequencing results showed that both AOB and AOA community structures were altered, with a higher change of AOB than that of AOA. The results demonstrated that the AOB microbial community may be better adapted to BDE 209 and Cu pollution, while AOA might possess a greater capacity for stress resistance. Our study provides a better understanding of the ecotoxicological effects of heavy metal and micropollutant combined exposure on AOA and AOB in river sediments.

Microbial community analysis of simultaneous ammonium removal and Fe3+ reduction at different influent ammonium concentrations

This study investigates the impacts of influent ammonium concentrations on the microbial community in immobilized heterotrophic ammonium removal system. Klebsiella sp. FC61, the immobilized species, has the ability to perform simultaneous ammonium removal and Fe³⁺ reduction. It was found that average ammonium removal rate decreased from 0.308 to 0.157 mg/L/h, as the influent NH₄⁺-N was reduced from 20 to 10 mg/L. Meanwhile, at a total Fe³⁺ concentration of 20 mg/L, the average Fe³⁺ reduction removal efficiency and rate decreased from 44.61% and 0.18 mg/L/h, to 27.10% and 0.11 mg/L/h, respectively. High-throughput sequencing was used to observe microbial communities in bioreactor Samples B1, B2, and B3, after exposure to different influent NH₄⁺-N conditions. Results show that higher influent NH₄⁺-N concentrations increased microbial richness and diversity and that Klebsiella sp. FC61 play a functional role in the simultaneous removal of NH₄⁺-N and Fe³⁺ reduction in bioreactor systems.

Change in microbial community in landfill refuse contaminated with antibiotics facilitates denitrification more than the increase in ARG over long-term

In this study, the addition of sulfamethazine (SMT) to landfill refuse decreased nitrogen intermediates (e.g. N₂O and NO) and dinitrogen (N₂) gas fluxes to <0.5 μg-N/kg-refuse·h^-1, while the N₂O and N₂ flux were at ~1.5 and 5.0 μg-N/kg-refuse·h^-1 respectively in samples to which oxytetracycline (OTC) had been added. The ARG (antibiotic resistance gene) levels in the refuse increased tenfold after long-term exposure to antibiotics, followed by a fourfold increase in the N₂ flux, but SMT-amended samples with the largest resistome facilitated the denitrification (the nitrogen accumulated as NO gas at ~6 μg-N/kg-refuse·h^-1) to a lesser extent than OTC-amended samples. Further, deep sequencing results show that long-term OTC exposure partially substituted Hyphomicrobium, Fulvivirga, and Caldilinea (>5%) for the dominant bacterial hosts (Rhodothermus, ~20%) harboring nosZ and norB genes that significantly correlated with nitrogen emission pattern, while sulfamethazine amendment completely reduced the relative abundance of the "original inhabitants" functioning to produce NO_x gas reduction. The main ARG carriers (Pseudomonas) that were substantially enriched in the SMT group had lower levels of denitrifying functional genes, which could imply that denitrification is influenced more by bacterial dynamics than by abundance of ARGs under antibiotic pressures.

Effect of antibiotics on bacterial populations: a multi-hierachical selection process

Antibiotics have been widely used for a number of decades for human therapy and farming production. Since a high percentage of antibiotics are discharged from the human or animal body without degradation, this means that different habitats, from the human body to river water or soils, are polluted with antibiotics. In this situation, it is expected that the variable concentration of this type of microbial inhibitor present in different ecosystems may affect the structure and the productivity of the microbiota colonizing such habitats. This effect can occur at different levels, including changes in the overall structure of the population, selection of resistant organisms, or alterations in bacterial physiology. In this review, I discuss the available information on how the presence of antibiotics may alter the microbiota and the consequences of such alterations for human health and for the activity of microbiota from different habitats.

Improvement of the soil nitrogen content and maize growth by earthworms and arbuscular mycorrhizal fungi in soils polluted by oxytetracycline

Interactions between earthworms (Eisenia fetida) and arbuscular mycorrhizal fungi (Rhizophagus intraradices, AM fungi) have been suggested to improve the maize nitrogen (N) content and biomass and were studied in soils polluted by oxytetracycline (OTC). Maize was planted and amended with AMF and/or earthworms (E) in the soil with low (1mgkg(-1) soil DM) or high (100mgkg(-1) soil DM) amounts of OTC pollution in comparison to soil without OTC. The root colonization, shoot and root biomass, shoot and root N contents, soil nitrogen forms, ammonia-oxidizing bacteria (AOB) and archaea (AOA) were measured at harvest. The results indicated that OTC decreased maize shoot and root biomass (p<0.05) by mediating the soil urease activity and AOB and AOA abundance, which resulted in a lower N availability for maize roots and shoots. There was a significant interaction between earthworms and AM fungi on the urease activity in soil polluted by OTC (p<0.05). Adding earthworms or AM fungi could increase the maize biomass and N content (p<0.05) in OTC polluted soil by increasing the urease activity and relieving the stress from OTC on the soil N cycle. AM fungi and earthworms interactively increased maize shoot and root biomass (p<0.05) in the OTC polluted soils through their regulation of the urease activity and the abundance of ammonia oxidizers, resulting in different soil NH4(+)-N and NO3(-)-N contents, which may contribute to the N content of maize shoots and roots. Earthworms and AM fungi could be used as an efficient method to relieve the OTC stress in agro-ecosystems.

Microbiote shift in sequencing batch reactors in response to antimicrobial ZnO nanoparticles

Zinc oxide nanoparticles (ZnO NPs) have been monitored in wastewater treatment plants as their potential adverse effects on functional microorganisms have been causing increasing concern.

A novel hollow capsule-like recyclable functional ZnO/C/Fe3O4 endowed with three-dimensional oriented recognition ability for selectively photodegrading danofloxacin mesylate

The functional ZnO/C/Fe₃O₄ exhibits high photocatalytic activity and possesses good selectivity.