Analysis of Bacterial Community Structure of Activated Sludge from Wastewater Treatment Plants in Winter

Using machine learning to identify environmental factors that collectively determine microbial community structure of activated sludge

Activated sludge (AS) microbial communities are influenced by various environmental variables. However, a comprehensive analysis of how these variables jointly and nonlinearly shape the AS microbial community remains challenging. In this study, we employed advanced machine learning techniques to elucidate the collective effects of environmental variables on the structure and function of AS microbial communities. Applying Dirichlet multinomial mixtures analysis to 311 global AS samples, we identified four distinct microbial community types (AS-types), each characterized by unique microbial compositions and metabolic profiles. We used 14 classical linear and nonlinear machine learning methods to select a baseline model. The extremely randomized trees demonstrated optimal performance in learning the relationship between environmental factors and AS types (with an accuracy of 71.43%). Feature selection identified critical environmental factors and their importance rankings, including latitude (Lat), longitude (Long), precipitation during sampling (Precip), solids retention time (SRT), effluent total nitrogen (Effluent TN), average temperature during sampling month (Avg Temp), mixed liquor temperature (Mixed Temp), influent biochemical oxygen demand (Influent BOD), and annual precipitation (Annual Precip). Significantly, Lat, Long, Precip, Avg Temp, and Annual Precip, influenced metabolic variations among AS types. These findings emphasize the pivotal role of environmental variables in shaping microbial community structures and enhancing metabolic pathways within activated sludge. Our study encourages the application of machine learning techniques to design artificial activated sludge microbial communities for specific environmental purposes.

A Review of the Dissemination of Antibiotic Resistance through Wastewater Treatment Plants: Current Situation in Sri Lanka and Future Perspectives

The emergence of antibiotic resistance (AR) poses a significant threat to both public health and aquatic ecosystems. Wastewater treatment plants (WWTPs) have been identified as potential hotspots for disseminating AR in the environment. However, only a limited number of studies have been conducted on AR dissemination through WWTPs in Sri Lanka. To address this knowledge gap in AR dissemination through WWTP operations in Sri Lanka, we critically examined the global situation of WWTPs as hotspots for transmitting antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) by evaluating more than a hundred peer-reviewed international publications and available national publications. Our findings discuss the current state of operating WWTPs in the country and highlight the research needed in controlling AR dissemination. The results revealed that the impact of different wastewater types, such as clinical, veterinary, domestic, and industrial, on the dissemination of AR has not been extensively studied in Sri Lanka; furthermore, the effectiveness of various wastewater treatment techniques in removing ARGs requires further investigation to improve the technologies. Furthermore, existing studies have not explored deeply enough the potential public health and ecological risks posed by AR dissemination through WWTPs.

Characterization the microbial diversity and functional genes in the multi-component contaminated groundwater in a petrochemical site

Microorganisms in groundwater at petroleum hydrocarbon (PHC)-contaminated sites are crucial for PHC natural attenuation. Studies mainly focused on the microbial communities and functions in groundwater contaminated by PHC only. However, due to diverse raw and auxiliary materials and the complex production processes, in some petrochemical sites, groundwater suffered multi-component contamination, but the microbial structure remains unclear. To solve the problem, in the study, a petrochemical enterprise site, where the groundwater suffered multi-component pollution by PHC and sulfates, was selected. Using hydrochemistry, 16S rRNA gene, and metagenomic sequencing analyses, the relationships among electron acceptors, microbial diversity, functional genes, and their interactions were investigated. Results showed that different production processes led to different microbial structures. Overall, pollution reduced species richness but increased the abundance of specific species. The multi-component contamination multiplied a considerable number of hydrocarbon-degrading and sulfate-reducing microorganisms, and the introduced sulfates might have promoted the biodegradation of PHC. PRACTITIONER POINTS: The compound pollution of the site changed the microbial community structure. Sulfate can promote the degradation of petroleum hydrocarbons by hydrocarbon-degrading microorganisms. The combined contamination of petroleum hydrocarbons and sulfates will decrease the species richness but increase the abundance of endemic species.

Microbial metabolism of caffeine and potential applications in bioremediation

With increasing global consumption of caffeine-rich products, such as coffee, tea, and energy drinks, there is also an increase in urban and processing waste full of residual caffeine with limited disposal options. This waste caffeine has been found to leach into the surrounding environment where it poses a threat to microorganisms, insects, small animals, and entire ecosystems. Growing interest in harnessing this environmental contaminant has led to the discovery of 79 bacterial strains, eight yeast strains, and 32 fungal strains capable of metabolizing caffeine by N-demethylation and/or C-8 oxidation. Recently observed promiscuity of caffeine-degrading enzymes in vivo has opened up the possibility of engineering bacterial strains capable of producing a wide variety of caffeine derivatives from a renewable resource. These engineered strains can be used to reduce the negative environmental impact of leached caffeine-rich waste through bioremediation efforts supplemented by our increasing understanding of new techniques such as cell immobilization. Here, we compile all of the known caffeine-degrading microbial strains, discuss their metabolism and related enzymology, and investigate their potential application in bioremediation.

Aerobic digestibility of waste aerobic granular sludge (AGS) assessed by respirometry, physical-chemical analyses, modeling and 16S rRNA gene sequencing

Research has evolved on aerobic granular sludge (AGS) process, but still there are very few studies on the treatment of excess AGS sludge, with almost none considering its aerobic digestion. Here therefore, the aerobic digestibility of typical AGS sludge was assessed. Granules were produced from acetate-based synthetic wastewater (WW) and were subjected to aerobic digestion for 64 d. The stabilization process was monitored over time through physical-chemical parameters, oxygen uptake rates (OUR) and 16S rRNA gene sequencing. The microbial analyses revealed that the cultivated granules were dominated by slow-growing bacteria, mainly ordinary heterotrophic organisms with potential for polyhydroxyalkanoates (PHA) aerobic storage (PHA-OHOs), polyphosphate and glycogen accumulating organisms (PAOs and GAOs), fermentative anaerobes and nitrifiers (AOB and NOB). Differential abundance analysis of the bacterial data (before versus after digestion) discriminated between the most vulnerable microbiome genera and those most resistant to aerobic digestion. Furthermore, modeling of the stabilization process determined that the endogenous decay rate constant (bH) for the heterotrophs present in the granules was notably low; bH = 0.05 d-1 (average), four times less than for common activated sludge (AS), which is rated at 0.2 d-1. For first time, the research reveals another important feature of AGS sludge, i.e. the slow-decaying character of its bacteria (along with their known slow-growing character). This results in slower stabilization, need of bigger digesters and reconsideration of the specific OUR limits in biosolids regulations (SOUR limit of 1.5 mg/gTSS.h), for waste AGS compared to conventional waste AS. The study suggests that aerobic digestion of waste AGS (fully-granulated) could differ from that of conventional AS. Future work is needed on aerobic digestibility of real AGS sludges from municipal and industrial WWs, compared to synthetic WWs.

Profiling pathogenic protozoan and their functional pathways in wastewater using 18S rRNA and shotgun metagenomics

Despite extensive research, little is known about the composition of eukaryotic protists in environmental samples. This is due to low parasite concentrations, the complexity of parasite diversity, and a lack of suitable reference databases and standardized protocols. To bridge this knowledge gap, this study used 18S rRNA short amplicon and shotgun metagenomic sequencing approaches to profile protozoan microbial communities as well as their functional pathways in treated and untreated wastewater samples collected from different regions of South Africa. Results demonstrated that protozoan diversity (Shannon index P-value = 0.03) and taxonomic composition (PERMANOVA, P-value = 0.02) was mainly driven by the type of wastewater samples (treated & untreated) and geographic location. However, these WWTPs were also found to contain a core community of protozoan parasites. The untreated wastewater samples revealed a predominant presence of free-living, parasitic, and potentially pathogenic protists typically found in humans and animals, ranging from Alveolata (27 %) phylum (Apicomplexa and Ciliophora) to Excavata (3.88 %) (Discoba and Parasalia) and Amoebozoa (2.84 %) (Entamoeba and Acanthamoeba). Shotgun metagenomics analyses in a subset of the untreated wastewater samples confirmed the presence of public health-importance protozoa, including Cryptosporidium species (3.48 %), Entamoeba hystolitica (6.58 %), Blastocystis hominis (2.91 %), Naegleria gruberi (2.37 %), Toxoplasma gondii (1.98 %), Cyclospora cayetanensis (1.30 %), and Giardia intestinalis (0.31 %). Virulent gene families linked to pathogenic protozoa, such as serine/threonine protein phosphatase and mucin-desulfating sulfatase were identified. Additionally, enriched pathways included thiamine diphosphate biosynthesis III, heme biosynthesis, Methylerythritol 4-Phosphate Pathway, methyl erythritol phosphate (MEP), and pentose phosphate pathways. These findings suggest that protozoan pathogens may possess metabolic and growth potential within WWTPs, posing a severe risk of transmission to humans and animals if inadequately disinfected before release. This study provides a baseline for the future investigation of diverse protozoal communities in wastewater, which are of public health importance.

Microbial denitrification characteristics of typical decentralized wastewater treatment processes based on 16S rRNA sequencing

Despite the widespread application of decentralized wastewater treatment (WWT) facilities in China, relatively few research has used the multi-media biological filter (MMBF) facilities to investigate the microorganism characteristics. This study utilizes 16S rRNA high-throughput sequencing (HTS) technology to examine the microbial biodiversity of a representative wastewater treatment (WWT) system in an expressway service area. The pathways of nitrogen removal along the treatment route were analyzed in conjunction with water quality monitoring. The distribution and composition of microbial flora in the samples were examined, and the dominant flora were identified using LEfSe analysis. The FAPROTAX methodology was employed to investigate the relative abundance of genes associated with the nitrogen cycle and to discern the presence of functional genes involved in nitrogen metabolism. On average, the method has a high level of efficiency in removing COD, TN, NH3-N, and TP from the effluent. The analysis of the microbial community identified a total of 40 phyla, 111 classes, 143 orders, 263 families, and 419 genera. The phyla that were predominantly observed include Proteobacteria, Acidobacteria, Chloroflexi, Actinobacteria, Nitrospirae, Bacteroidetes. The results show that the system has achieved high performance in nitrogen removal, the abundance of nitrification genes is significantly higher than that of other nitrogen cycle genes such as denitrification, and there are six nitrogen metabolism pathways, primarily nitrification, among which Nitrospirae and Nitrospira are the core differentiated flora that can adapt to low temperature conditions and participate in nitrification, and are the dominant nitrogen removal flora in cold regions. This work aims to comprehensively investigate the diversity and functional properties of the bacterial community in decentralized WWT processes.

Seasonal prevalence of bacteria in the outflow of two full-scale municipal wastewater treatment plants

Despite many modern wastewater treatment solutions, the most common is still the use of activated sludge (AS). Studies indicate that the microbial composition of AS is most often influenced by the raw sewage composition (especially influent ammonia), biological oxygen demand, the level of dissolved oxygen, technological solutions, as well as the temperature of wastewater related to seasonality. The available literature mainly refers to the relationship between AS parameters or the technology used and the composition of microorganisms in AS. However, there is a lack of data on the groups of microorganisms leaching into water bodies whose presence is a signal for possible changes in treatment technology. Moreover, sludge flocs in the outflow contain less extracellular substance (EPS) which interferes microbial identification. The novelty of this article concerns the identification and quantification of microorganisms in the AS and in the outflow by fluorescence in situ hybridization (FISH) method from two full-scale wastewater treatment plants (WWTPs) in terms of 4 key groups of microorganisms involved in the wastewater treatment process in the context of their potential technological usefulness. The results of the study showed that Nitrospirae, Chloroflexi and Ca. Accumulibacter phosphatis in treated wastewater reflect the trend in abundance of these bacteria in activated sludge. Increased abundance of betaproteobacterial ammonia-oxidizing bacteria and Nitrospirae in the outflow were observed in winter. Principal component analysis (PCA) showed that loadings obtained from abundance of bacteria in the outflow made larger contributions to the variance in the PC1 factorial axis, than loadings obtained from abundance of bacteria from activated sludge. PCA confirmed the reasonableness of conducting studies not only in the activated sludge, but also in the outflow to find correlations between technological problems and qualitative and quantitative changes in the outflow microorganisms.

Mechanisms of persistence and impact of ordinary heterotrophic organisms in aerobic granular sludge

The stability of granules, contaminant removal and microbial structure of an aerobic granular sludge (AGS) process were investigated with a focus on ordinary heterotrophic organisms (OHOs). Long-term stable granules and high removals of COD (97 %), NH₄⁺ (98 %), P (85 %) and total N (77 %) were achieved. Sequencing analyses identified 6.6 % of phosphorus-accumulating organisms in the sludge, concordant with the observed bio-P removal capacity. However, OHOs were the most abundant bacteria in the sludge (70-93 %) without resulting in unstable aggregates. Under current dogmas of microbial competition in activated sludge, it seemed contradictory that OHOs could persist in the long term in the AGS where COD was depleted beginning in the anaerobic phase. Microbial analyses showed that OHOs could survive in granules by micropredation, proteolysis, fermentation and EPS consumption. Heterotrophic-nitrification/ aerobic-denitrification was an active pathway in the AGS. These findings contribute to a better understanding of microbial competition in AGS and its stability.

Free ammonia-free nitrous acid based partial nitrification in sequencing batch membrane aerated biofilm reactor

Membrane aerated biofilm reactor (MABR) has attracted a lot of attention as an energy-efficient integrated nitrogen removing technology in recent years. However, it is lacking of understanding to realize stable partial nitrification in MABR because of its unique oxygen transfer mode and biofilm structure. In this study, free ammonia (FA) and free nitrous acid (FNA) based control strategies for partial nitrification with low NH₄⁺-N concentration were proposed in a MABR of sequencing batch mode. The MABR was operated for over 500 days under different influent NH₄⁺-N concentrations. With the influent NH₄⁺-N of around 200 mg-N/L, partial nitrification could be established with relatively low concentration of FA (0.4-2.2 mg-N/L) which suppressed nitrite oxidizing bacteria (NOB) on the biofilm. With lower influent NH₄⁺-N concentration of around 100 mg-N/L, the FA concentration was lower and strengthened suppression strategies based on FNA were needed. With the final pH of operating cycles below 5.0, the FNA produced in the sequencing batch MABR could stabilize partial nitrification by eliminating NOB on the biofilm. Since the activity of ammonia oxidizing bacteria (AOB) was lower without the blow-off of dissolved carbon dioxide in the bubbleless MABR, longer hydraulic retention time was required to reach a low pH for high concentration of FNA to suppress NOB. After exposures to FNA, the relative abundance of Nitrospira was decreased by 94.6%, while the abundance of Nitrosospira increased greatly which became another dominant AOB genus in addition to Nitrosomonas.

A sludge bulking wastewater treatment plant with an oxidation ditch-denitrification filter in a cold region: bacterial community composition and antibiotic resistance genes

Bacterial community structure of activated sludge directly affects the stable operation of WWTPS, and these bacterial communities may carry a variety of antibiotic resistance genes (ARGs), which is a threat to the public health. This study employed 16S rRNA gene sequencing and metagenomic sequencing to investigate the bacterial community composition and the ARGs in a sludge bulking oxidation ditch-denitrification filter WWTP in a cold region. The results showed that Trichococcus (20.34%), Blautia (7.72%), and Faecalibacterium (3.64%) were the main bacterial genera in the influent. The relative abundances of norank_f_Saprospiraceae and Candidatus_Microthrix reached 10.24% and 8.40%, respectively, in bulking sludge, and those of norank_f_Saprospiraceae and Candidatus_Microthrix decreased to 6.56 and 7.10% after the anaerobic tank, indicating that the anaerobic tank had an inhibitory effect on filamentous bacteria. After 20 mJ/cm² UV disinfection, about 540 bacterial genera, such as Romboutsia (7.99%), Rhodoferax (7.98%), and Thermomonas (4.13%), could still be detected in the effluent. The ARGs were 345.11 ppm in the influent and 11.20 ppm in the effluent; 17 subtypes, such as sul1, msrE, aadA5, ErmF, and tet(A), could be detected throughout the entire process. These ARG subtypes were persistent ARGs with a high health risk. Network analysis indicated that the changes in filamentous bacteria norank_f_Saprospiraceae abundance mainly contributed to the abundance shift of MexB, and Acinetobacter mainly increased the abundance of drfA1. These results above will provide theoretical support for the sludge bulking and ARGs controls of WWTPs in cold regions.

Consistency between the metabolic performance of two aerobic granular sludge systems and the functional groups of bacteria detected by amplicon sequencing

Two sequential batch reactors (R1 and R2) of aerobic granular sludge (AGS) were inoculated with activated sludge of different origins. The objective was to investigate the granulation and the consistency between the structure of the microbial communities (16S rRNA amplicon sequencing) in each reactor and their metabolic performance (removal of C, N, and P). Both reactors were fed with acetate-based synthetic wastewater, targeting an anaerobic-aerobic cycle reputed to favor the phosphorus- and glycogen-accumulating organisms (PAO and GAO). Stable granulation was achieved in both reactors, where, instead of PAO, the dominant genera were ordinary heterotrophic organisms (OHO) such as Thauera, Paracoccus, and Flavobacterium known for their high capacity of aerobic storage of polyhydroxyalkanoates (PHA). Generally, there was good consistency between the metabolic behavior of each reactor and the bacterial genera detected. Both reactors showed high removals of C and complete nitrification (Nitrosomonas and Nitrospira detected) but a low level of simultaneous nitrification-denitrification (SND) during the aerated phase. The latter causes that nitrates were recycled to the initial phase, in detriment of PAO selection. Meanwhile, the study showed that selecting slow-growing OHOs (with aerobic storage capacity) favors stable granulation, revealing an alternative AGS technology for C and N removal.

Microalgae-based wastewater treatment - Microalgae-bacteria consortia, multi-omics approaches and algal stress response

Sustainable environmental management is one of the important aspects of sustainable development goals. Increasing amounts of wastewaters (WW) from exponential economic growth is a major challenge, and conventional treatment methods entail a huge carbon footprint in terms of energy use and GHG emissions. Microalgae-based WW treatment is a potential candidate for sustainable WW treatment. The nutrients which are otherwise unutilized in the conventional processes are recovered in the beneficial microalgal biomass. This review presents comprehensive information regarding the potential of microalgae as sustainable bioremediation agents. Microalgae-bacterial consortia play a critical role in synergistic nutrient removal, supported by the complex nutritional and metabolite exchange between microalgae and the associated bacteria. Design of effective microalgae-bacteria consortia either by screening or by recent technologies such as synthetic biology approaches are highly required for efficient WW treatment. Furthermore, this review discusses the crucial research gap in microalgal WW treatment - the application of a multi-omics platform for understanding microalgal response towards WW conditions and the design of effective microalgal or microalgae-bacteria consortia based on genetic information. While metagenomics helps in the identification and monitoring of the microbial community throughout the treatment process, transcriptomics, proteomics and metabolomics aid in studying the algal cellular response towards the nutrients and pollutants in WW. It has been established that the integration of microalgal processes into conventional WW treatment systems is feasible. In this direction, future research directions for microalgal WW treatment emphasize the need for identifying the niche in WW treatment, while highlighting the pilot sale plants in existence. Microalgae-based WW treatment could be a potential phase in the waste hierarchy of circular economy and sustainability, considering WWs are a rich secondary source of finite resources such as nitrogen and phosphorus.

Biological Activated Sludge from Wastewater Treatment Plant before and during the COVID-19 Pandemic

The COVID-19 pandemic and the related measures brought a change in daily life that affected the characteristics of the municipal wastewater and further, of the biological activated sludge. The activated sludge process is the most widely used biological wastewater treatment process in developed areas. In this paper, we aim to show the situation of specific investigations concerning the variation of the physicochemical parameters and biological composition of the activated sludge from one conventional wastewater treatment plant from a metropolitan area. The investigations were carried out for three years: 2019, 2020 and 2021. The results showed the most representative taxa of microorganisms: Microtrix, Aspidisca cicada, Vorticella convallaria, Ciliata free of the unknown and Epistylis and Rotifers. Even if other microorganisms were found in the sludge flocs, their small presence did not influence in any way the quality of the activated sludge and of the wastewater treatment process. That is why we conclude that protozoa (especially Flagellates and Ciliates) and rotifers were the most important. Together with the values and variation of the physicochemical parameters, they indicated a good, healthy, and stable activated sludge, along with an efficient purifying treatment process, no matter the loading conditions.

Diversity and Ecophysiology of the Genus OLB8 and Other Abundant Uncultured Saprospiraceae Genera in Global Wastewater Treatment Systems

The Saprospiraceae family within the phylum Bacteroidota is commonly present and highly abundant in wastewater treatment plants (WWTPs) worldwide, but little is known about its role. In this study, we used MiDAS 4 global survey with samples from 30 countries to analyze the abundance and distribution of members of Saprospiraceae. Phylogenomics were used to delineate five new genera from a set of 31 high-quality metagenome-assembled genomes from Danish WWTPs. Newly designed probes for fluorescence in situ hybridization (FISH) revealed rod-shaped morphologies for all genera analyzed, including OLB8, present mostly inside the activated sludge flocs. The genomes revealed potential metabolic capabilities for the degradation of polysaccharides, proteins, and other complex molecules; partial denitrification; and storage of intracellular polymers (glycogen, polyphosphate, and polyhydroxyalkanoates). FISH in combination with Raman microspectroscopy confirmed the presence of intracellular glycogen in Candidatus Brachybacter, Candidatus Parvibacillus calidus (both from the former genus OLB8), and Candidatus Opimibacter, and the presence of polyhydroxyalkanoates in Candidatus Defluviibacterium haderslevense and Candidatus Vicinibacter. These results provide the first overview of the most abundant novel Saprospiraceae genera present in WWTPs across the world and their potential involvement in nutrient removal and the degradation of macromolecules.

Pharmaceutical Pollution in Aquatic Environments: A Concise Review of Environmental Impacts and Bioremediation Systems

The presence of emerging contaminants in the environment, such as pharmaceuticals, is a growing global concern. The excessive use of medication globally, together with the recalcitrance of pharmaceuticals in traditional wastewater treatment systems, has caused these compounds to present a severe environmental problem. In recent years, the increase in their availability, access and use of drugs has caused concentrations in water bodies to rise substantially. Considered as emerging contaminants, pharmaceuticals represent a challenge in the field of environmental remediation; therefore, alternative add-on systems for traditional wastewater treatment plants are continuously being developed to mitigate their impact and reduce their effects on the environment and human health. In this review, we describe the current status and impact of pharmaceutical compounds as emerging contaminants, focusing on their presence in water bodies, and analyzing the development of bioremediation systems, especially mycoremediation, for the removal of these pharmaceutical compounds with a special focus on fungal technologies.

Variations of nitrogen-metabolizing enzyme activity and microbial community under typical loading conditions in full-scale leachate anoxic/aerobic system

Influent loading determines the performance of leachate treatment plant (LTP) facing the dynamic conditions, but enzyme expression in microbial community is unclear. Here, six nitrogen-metabolizing enzymes were detected during nitrification failures (NF), high loading (HL), low loading (LL), and low carbon/nitrogen (LCN) in a 500 m³/d LTP. Nitrogen removal in LL was 15 ± 5% higher than that in HL. The activity of hydroxylamine oxidoreductase decreased by 90% as the influent total nitrogen increased from 2450 mg/L to 3100 mg/L, which might be a critical enzyme causing the nitrification failure. Denitrifying enzyme abated by 1.3% as the carbon/nitrogen dropped by 1% in LCN. With the influent chemical oxygen demand decreased from 22000 mg/L to 12000 mg/L, the relative abundance of norank_f_Saprospiraceae dropped from 33.66% to 11.94%, and finally disappeared, which seems to be an indicator of the high load operation. These findings provide the basis for improving the efficiency of LTPs.

Municipal Wastewaters Carry Important Carbapenemase Genes Independent of Hospital Input and Can Mirror Clinical Resistance Patterns

The spatiotemporal variation of several carbapenemase-encoding genes (CRGs) was investigated in the influent and effluent of municipal WWTPs, with or without hospital sewage input. Correlations among gene abundances, bacterial community composition, and wastewater quality parameters were tested to identify possible predictors of CRGs presence. Also, the possible role of wastewaters in mirroring clinical resistance is discussed. The taxonomic groups and gene abundances showed an even distribution among wastewater types, meaning that hospital sewage does not influence the microbial diversity and the CRG pool. The bacterial community was composed mainly of Proteobacteria, Firmicutes, Actinobacteria, Patescibacteria, and Bacteroidetes. Acinetobacter spp. was the most abundant group and had the majority of operational taxonomic units (OTUs) positively correlated with CRGs. This agrees with recent reports on clinical data. The influent samples were dominated by blaKPC, as opposed to effluent, where blaIMP was dominant. Also, blaIMP was the most frequent CRG family observed to correlate with bacterial taxa, especially with the Mycobacterium genus in effluent samples. Bacterial load, blaNDM, blaKPC, and blaOXA-48 abundances were positively correlated with BOD5, TSS, HEM, Cr, Cu, and Fe concentrations in wastewaters. When influent gene abundance values were converted into population equivalent (PE) data, the highest copies/1 PE were identified for blaKPC and blaOXA-48, agreeing with previous studies regarding clinical isolates. Both hospital and non-hospital-type samples followed a similar temporal trend of CRG incidence, but with differences among gene groups. Colder seasons favored the presence of blaNDM, blaKPC and blaOXA-48, whereas warmer temperatures show increased PE values for blaVIM and blaIMP. IMPORTANCE Wastewater-based epidemiology has recently been recognized as a valuable, cost-effective tool for antimicrobial resistance surveillance. It can help gain insights into the characteristics and distribution of antibiotic resistance elements at a local, national, and even global scale. In this study, we investigated the possible use of municipal wastewaters in the surveillance of clinically relevant carbapenemase-encoding genes (CRGs), seen as critical antibiotic resistance determinants. In this matter, our results highlight positive correlations among CRGs, microbial diversity, and wastewater physical and chemical parameters. Identified predictors can provide valuable data regarding the level of raw and treated wastewater contamination with these important antibiotic resistance genes. Also, wastewater-based gene abundances were used for the first time to observe possible spatiotemporal trends of CRGs incidence in the general population. Therefore, possible hot spots of carbapenem resistance could be easily identified at the community level, surpassing the limitations of health care-associated settings.

Microbial community origin and fate through a rural wastewater treatment plant

Conventional wastewater treatment relies on a complex microbiota; however, much of this community is still to be characterised. To better understand the origin, dynamics and fate of bacteria within a wastewater treatment plant: untreated primary wastewater, activated sludge, and post-treatment effluent were characterised. From 3,163 Exact Sequence Variants (ESVs), 860 were annotated to species-level. In primary wastewater, 28% of ESVs were putative bacterial species previously associated with humans, 14% with animals and 5% as common to the environment. Differential abundance analysis revealed significant relative reductions in ESVs from potentially humans-associated species from primary wastewater to activated sludge, and significant increases in ESVs from species associated with nutrient cycling. Between primary wastewater and effluent, 51% of ESVs from human-associated species did not significantly differ, and species such as Bacteroides massiliensis and Bacteroides dorei increased. These findings illustrate that activated sludge increased extracellular protease and urease-producing species, ammonia and nitrite oxidizers, denitrifiers and specific phosphorus accumulators. Although many human-associated species declined, some persisted in effluent, including strains of potential health or environmental concern. Species-level microbial assessment may be useful for understanding variation in wastewater treatment efficiency as well as for monitoring the release of microbes into surface water and the wider ecosystem. This article is protected by copyright. All rights reserved.

Ordinary heterotrophic organisms with aerobic storage capacity provide stable aerobic granular sludge for C and N removal

The study investigated the mechanisms and microbial communities underlying the long-term stability and removal performances shown by aerobic granular sludge (AGS) reactor involving polyhydroxyalkanoates (PHA) aerobic-storing bacteria. The characteristics of the sludge, removal performances and bacterial community structure were determined. The prevailing metabolic phenotype was similar in the parent conventional activated sludge (CAS) reactor and its upgraded AGS version, showing high COD and NH₄ uptake, versus low P and N reduction. Polyphosphate and glycogen accumulating organisms, PAO and GAO, were not enriched in the reactors despite initial targeting of anaerobic-aerobic cycle. Instead, PHA-aerobic storing bacteria (Thauera and Paracoccus) were dominant, but revealing a stable AGS system for BOD and N removal. The PAO/GAO failed selection and Thauera overgrowth were analyzed for beneficial use in developing alternative AGS technology for BOD and N removal applications.

MOVIS: A multi-omics software solution for multi-modal time-series clustering, embedding, and visualizing tasks

Thanks to recent advances in sequencing and computational technologies, many researchers with biological and/or medical backgrounds are now producing multiple data sets with an embedded temporal dimension. Multi-modalities enable researchers to explore and investigate different biological and physico-chemical processes with various technologies. Motivated to explore multi-omics data and time-series multi-omics specifically, the exploration process has been hindered by the separation introduced by each omics-type. To effectively explore such temporal data sets, discover anomalies, find patterns, and better understand their intricacies, expertise in computer science and bioinformatics is required. Here we present MOVIS, a modular time-series multi-omics exploration tool with a user-friendly web interface that facilitates the data exploration of such data. It brings into equal participation each time-series omic-type for analysis and visualization. As of the time of writing, two time-series multi-omics data sets have been integrated and successfully reproduced. The resulting visualizations are task-specific, reproducible, and publication-ready. MOVIS is built on open-source software and is easily extendable to accommodate different analytical tasks. An online version of MOVIS is available under https://movis.mathematik.uni-marburg.de/ and on Docker Hub (https://hub.docker.com/r/aanzel/movis).

Analysis of the Bacterial Biocenosis of Activated Sludge Treated with Leachate from Municipal Landfills

The influx of toxic pollutants into wastewater treatment plants can negatively affect the quality of the activated sludge (AS). One source is landfill leachate. The identification of microorganisms present in AS is very important, e.g., while improving wastewater treatment technology. Therefore, the aim of the study was to investigate the effect of raw leachate and after purification of Phragmites australis and Ceratophyllum demersum on the composition of the AS bacterial biocenosis. In addition, AS status was assessed by LIVE/DEAD BacLight ™ fluorescent staining. The obtained results showed that the leachate did not significantly affect the cell membranes of AS bacteria, and even a slight improvement was noted. The research carried out using the next-generation sequencing method shows that the origin of the samples (active and closed storage) and the method of processing do not significantly affect the composition of the AS bacterial biocenosis at higher taxonomic levels. However, at the species level, the appearance of bacteria not previously present in AS was observed, namely: Flavobacterium luticocti, Candidimonas nitroreducens and Nitrobacter hamburgensis. The obtained results suggest that the leachate may be a source of microorganisms positively influencing the condition of AS bacteria.

Diversity of <i>Candidatus</i> Patescibacteria in Activated Sludge Revealed by a Size-‍Fractionation Approach

Uncultivated members of Candidatus Patescibacteria are commonly found in activated sludge treating sewage and are widely distributed in wastewater treatment plants in different regions and countries. However, the phylogenetic diversity of Ca. Patescibacteria is difficult to examine because of their low relative abundance in the environment. Since Ca. Patescibacteria members have small cell sizes, we herein collected small microorganisms from activated sludge using a filtration-based size-fractionation approach (i.e., 0.45–0.22‍ ‍μm and 0.22–0.1‍ ‍μm fractions). Fractionated samples were characterized using 16S rRNA gene amplicon and shotgun metagenomic sequence ana­lyses. The amplicon ana­lysis revealed that the relative abundance of Ca. Patescibacteria increased to 73.5% and 52.5% in the 0.45–0.22‍ ‍μm and 0.22–0.1‍ ‍μm fraction samples, respectively, from 5.8% in the unfractionated sample. The members recovered from the two size-fractionated samples included Ca. Saccharimonadia, Ca. Gracilibacteria, Ca. Paceibacteria, Ca. Microgenomatia, class-level uncultured lineage ABY1, Ca. Berkelbacteria, WS6 (Ca. Dojkabacteria), and WWE3, with Ca. Saccharimonadia being predominant in both fraction samples. The number of operational taxonomic units belonging to Ca. Patescibacteria was approximately 6-fold higher in the size-fractionated samples than in the unfractionated sample. The shotgun metagenomic ana­lysis of the 0.45–0.22‍ ‍μm fractioned sample enabled the reconstruction of 24 high-quality patescibacterial bins. The bins obtained were classified into diverse clades at the family and genus levels, some of which were rarely detected in previous activated sludge studies. Collectively, the present results suggest that the overall diversity of Ca. Patescibacteria inhabiting activated sludge is higher than previously expected.

Biosolid-Amended Soil Enhances Defense Responses in Tomato Based on Metagenomic Profile and Expression of Pathogenesis-Related Genes

Biosolid application is an effective strategy, alternative to synthetic chemicals, for enhancing plant growth and performance and improving soil properties. In previous research, biosolid application has shown promising results with respect to tomato resistance against Fusarium oxysporum f. sp. radicis-lycopersici (Forl). Herein, we aimed at elucidating the effect of biosolid application on the plant-microbiome response mechanisms for tomato resistance against Forl at a molecular level. More specifically, plant-microbiome interactions in the presence of biosolid application and the biocontrol mechanism against Forl in tomato were investigated. We examined whether biosolids application in vitro could act as an inhibitor of growth and sporulation of Forl. The effect of biosolid application on the biocontrol of Forl was investigated based on the enhanced plant resistance, measured as expression of pathogen-response genes, and pathogen suppression in the context of soil microbiome diversity, abundance, and predicted functions. The expression of the pathogen-response genes was variably induced in tomato plants in different time points between 12 and 72 h post inoculation in the biosolid-enriched treatments, in the presence or absence of pathogens, indicating activation of defense responses in the plant. This further suggests that biosolid application resulted in a successful priming of tomato plants inducing resistance mechanisms against Forl. Our results have also demonstrated that biosolid application alters microbial diversity and the predicted soil functioning, along with the relative abundance of specific phyla and classes, as a proxy for disease suppression. Overall, the use of biosolid as a sustainable soil amendment had positive effects not only on plant health and protection, but also on growth of non-pathogenic antagonistic microorganisms against Forl in the tomato rhizosphere and thus, on plant-soil microbiome interactions, toward biocontrol of Forl.

Metagenomic insights into the "window" effect of static magnetic field on nitrous oxide emission from biological nitrogen removal process at low temperature

This study aimed to explore whether the "window" effect of static magnetic field (SMF) on nitrous oxide (N₂O) emission from the biological nitrogen removal process at low temperature existed and reveal its biological mechanism at the gene level. Four sequencing batch reactors (SBRs) with SMFs of 0, 10, 45, and 75 mT were operated continuously for 110 days at 10 °C and the lowest N₂O-Gas cumulative emission (5.50 mg N/day) and N₂O conversion rate (4.28 %) in 45 mT SMF-SBR verified the existence of the "window" effect. In 45 mT SMF-SBR, nearly all enzymatic activities related to N₂O reduction and corresponding functional gene abundances improved significantly. Metagenomic high-throughput sequencing analysis revealed that Alicycliphilus denitricans, Paracoccus denitrificans, Rhodopseudomonas palustris, Pseudomonas stutzeri, and Dechloromonas aromatica, as species related to N₂O reduction, could be separately enriched by applying suitable SMF intensity. Gene functions annotation based on KEGG and CAZy databases indicated that SMF not only accelerated the rate of free ammonia into ammonia-oxidizing bacteria and electrons delivered to the corresponding denitrification reductases, but also enhanced the degradation of complex organic matter into smaller molecules, and thus reducing the production of N₂O via nitrifier denitrification and incomplete denitrification pathways at 10 °C. These findings provided a guideline and presented a blueprint of ecophysiology for the future application of magnetic field to the reduction of N₂O emission in wastewater treatment plants in the cold region.

Envisioning role of ammonia oxidizing bacteria in bioenergy production and its challenges: a review

Ammonia oxidizing bacteria (AOB) play a key role in the biological oxidation of ammonia to nitrite and mark their significance in the biogeochemical nitrogen cycle. There has been significant development in harnessing the ammonia oxidizing potential of AOB in the past few decades. However, very little is known about the potential applications of AOB in the bioenergy sector. As alternate sources of energy represent a thrust area for environmental sustainability, the role of AOB in bioenergy production becomes a significant area of exploration. This review highlights the role of AOB in bioenergy production and emphasizes the understanding of the genetic make-up and key cellular biochemical reactions occurring in AOB, thereby leading to the exploration of its various functional aspects. Recent outcomes in novel ammonia/nitrite oxidation steps occurring in a model AOB - Nitrosomonas europaea propel us to explore several areas of environmental implementation. Here we present the significant role of AOB in microbial fuel cells (MFC) where Nitrosomonas sp. play both anodic and cathodic functions in the generation of bioelectricity. This review also presents the potential role of AOB in curbing fuel demand by producing alternative liquid fuel such as methanol and biodiesel. Herein, the multiple roles of AOB in bioenergy production namely: bioelectricity generation, bio-methanol, and biodiesel production have been presented.

Bacterial Community Structure and Dynamic Changes in Different Functional Areas of a Piggery Wastewater Treatment System

Chemicals of emerging concern (CEC) in pig farm breeding wastewater, such as antibiotics, will soon pose a serious threat to public health. It is therefore essential to consider improving the treatment efficiency of piggery wastewater in terms of microorganisms. In order to optimize the overall piggery wastewater treatment system from the perspective of the bacterial community structure and its response to environmental factors, five samples were randomly taken from each area of a piggery’s wastewater treatment system using a random sampling method. The bacterial communities’ composition and their correlation with wastewater quality were then analyzed using Illumina MiSeq high-throughput sequencing. The results showed that the bacterial community composition of each treatment unit was similar. However, differences in abundance were significant, and the bacterial community structure gradually changed with the process. Proteobacteria showed more adaptability to an anaerobic environment than Firmicutes, and the abundance of Tissierella in anaerobic zones was low. The abundance of Clostridial (39.02%) and Bacteroides (20.6%) in the inlet was significantly higher than it was in the aerobic zone and the anoxic zone (p < 0.05). Rhodocyclaceae is a key functional microbial group in a wastewater treatment system, and it is a dominant microbial group in activated sludge. Redundancy analysis (RDA) showed that chemical oxygen demand (COD) had the greatest impact on bacterial community structure. Total phosphorus (TP), total nitrogen (TN), PH and COD contents were significantly negatively correlated with Sphingobacteriia, Betaproteobacteria and Gammaproteobacteria, and significantly positively correlated with Bacteroidia and Clostridia. These results offer basic data and theoretical support for optimizing livestock wastewater treatment systems using bacterial community structures.

Beta-lactam resistance development during the treatment processes of municipal wastewater treatment plants

This work monitored the effect of a municipal and a village wastewater treatment plant (WWTP) technology on the fate of beta-lactam resistance genes in bacterial populations in different phases of the wastewater treatment process. In case of the municipal WWTP1, the bacteria possessing a high ampicillin resistance (minimal inhibitory concentration (MIC) values of 20 mg/mL) accumulated in the sedimentation tank, which was accompanied with a higher concentration of ampicillin in the wastewater samples (28.09 ng/L) and an increase in the relative abundance of the blaTEM gene in the bacterial population. However, an opposite trend was revealed with the blaNDM-1 gene, making the sedimentation processes of WWTP1 crucial only for the accumulation of the blaTEM gene. Similarly, the comparison with the WWTP2 showed that the accumulation of the ampicillin resistance in bacterial population probably depended on the WWTP technology and wastewater composition. Out of the four tested resistance genes (blaTEM, blaKPC, blaNDM-1, and blaOXA-48), blaTEM and blaNDM-1 genes were the only two detected in this study. According to NGS analysis of bacterial 16 S rRNA gene, Gammaproteobacteria dominated the ampicillin-resistant bacteria of the WWTP sedimentation tanks. Their relative abundance in the bacterial population also increased during the sedimentation processes in WWTP1. It could indicate the role of the bacterial taxon in ampicillin resistance accumulation in this WWTP and show that only 9.29% of the original bacterial population from the nitrification tank is involved in the documented shifts in beta-lactam resistance of the bacterial population.

Metagenomic Exploration of Bacterial Community Structure of Earthworms’ Gut

Living organisms are naturally bestowed with unique and imitable qualities for maintaining ecological balance and earthworms are no exceptions. These so-called keystone species of terrestrial ecosystems are equipped with wonderful machinery, allowing them to nurture soil beautifully. Earthworm gut represents a potential microbial reservoir, having a complex interdependence with the host. The study aimed to profile bacterial community structure of three earthworm species belonging to two different life forms; Perionyx excavatus and Eudrilus eugeniae (epigeic), Polypheretima elongata (endogeic) respectively. Diversity analysis using 16S amplicon sequencing revealed that the dominant phyla were Proteobacteria (34.17-77.88) followed by Actinobacteria (13.43-35.54%), Firmicutes (1.69-15.45%) and Bacteroidetes (0.51-8.12%). The alpha diversity indices explicit similar gut microbiota of Perionyx excavatus and Eudrilus eugeniae and while higher alpha diversity was recorded in comparison to Polypheretima elongata gut. The taxonomic to the phenotypic annotation of 16S rRNA metagenomes revealed that dominance of Gram-negative bacterial community in all earthworm species while, Polypheretima elongata comprises higher percentage (78%) of Gram-negative bacterial community to Perionyx excavatus (32.3%) and Eudrilus eugeniae (38.3%). The oxygen requirement phenotypic analysis showed that all earthworm species were abundant with aerobic followed by anaerobic bacterial groups. Furthermore, functional metabolism phenotypic analysis revealed that a high abundance of ammonia oxidizers (29.3-80.2%), the gut microbiomes showed the relative abundance of sulphate reducer (22.6-78.7%), nitrite reducer (19.8-73.2%), dehalogenators (12.6-25.1%), illustrating in the role of these microbial communities in various degradation and bioremediation processes. The present study signifies the intrinsic gut microbiota of earthworm species for intensified biodegradation.

Bacterial community compositions and nitrogen metabolism function in a cattle farm wastewater treatment plant revealed by Illumina high-throughput sequencing

Bacteria play an important role in pollutant transformation in activated sludge-based wastewater treatment plants (WWTPs). Exploring the microbial community structure and diversity is essential to improving the performance of wastewater treatment processes. This study employed Illumina MiSeq high-throughput sequencing to investigate the microbial community composition and diversity in a cattle farm wastewater treatment plant (Cf-WWTP). The results showed that the dominant phyla in the whole process were Proteobacteria, Bacteroidetes, and Firmicutes. The principal coordinate analysis (PCoA) indicated that the different stages had a significant impact on the microbial community structure; Bacteroidetes was the dominant phylum in the anearobic stage and Proteobacteria was the dominant phylum in the anoxic-oxic stage. Redundancy analysis (RDA) revealed that total phosphorus (TP) was the most significant factor that regulated the microbial community composition, followed by chemical oxygen demand (COD), total nitrogen (TN), and pH. Proteobacteria, Patescibacteria, and Chloroflexi were simultaneously negatively correlated with TN, COD, and TP. Nitrogen metabolic pathway and transformation mechanism was elucidated by a complete denitrification function predicted with phylogenetic investigation of communities with reconstruction of unobserved states (PICRUSt), as well as detection of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). These results provide new insights into our understanding of microbial community and metabolic functions of Cf-WWTP.

Supersaturated-oxygen aeration effects on a high-loaded membrane bioreactor (HL-MBR): Biological performance and microbial population dynamics

Conventional diffused aeration systems (such as fine-bubble diffusers) exhibit a poor oxygen transfer in wastewater treatment plants (WWTPs), particularly when operating at sludge concentrations higher than 15 g L^-1. The supersaturated dissolved oxygen (SDOX) system has been proposed as an alternative for supplying dissolved oxygen (DO) at high mixed liquor suspended solids (MLSS) concentrations. The advantages introduced by such technology include the possibility of operating WWTPs at much higher than usual MLSS concentrations, increasing the treatment capacity of WWTPs. Recent studies have demonstrated that the SDOX system has higher oxygen transfer rates (OTRs) and oxygen transfer efficiencies (OTEs) relative to fine-bubble diffusers. However, it is unknown if the high-pressure conditions introduced by SDOX may possibly impact the biological performance of WWTPs. In this study, the effects of SDOX technology on the biological performance of a membrane bioreactor (MBR) were evaluated. The MBR was operated at an MLSS concentration of approximately 15 g L^-1 in four phases as follows: (P1) with bubble diffusers, (P2) with an SDOX unit, (P3) with the bubble diffusers, and (P4) with the SDOX unit. The performance of the MBR was assessed by monitoring the sludge concentration, as well as changes in the particle size distribution (PSD), sludge activity, organic matter removal and nitrification performance, and changes in the microbial community within the MBR. The operational conditions exerted by the SDOX technology did not affect the concentration of active biomass during the study period. The biological performance of the MBR was not affected by the introduction of the SDOX technology. Finally, the microbial community was relatively stable although some variations at the family and genus level were evident during each of the study phases. Therefore, the SDOX system can be proposed as an alternative technology for DO supply in WWTPs increasing the overall treatment capacity.

Insights into the microbial diversity and structure in a full-scale municipal wastewater treatment plant with particular regard to Archaea

Due to limited description of the role and diversity of archaea in WWTPs, the aim of the study was to analyze microbial community structures and diversities with particular regard to Archaea in the samples taken from different stages of the full-scale municipal wastewater treatment plant and effluent receiving water (upstream and downstream discharge point). Our study was focused on showing how the treatment processes influenced the Eubacteria and Archaea composition. Alpha and Beta diversity were used to evaluate the microbial diversity changes in the collected samples. Proteobacteria was the largest fraction ranging from 28% to 67% with 56% relative abundance across all samples. Archaea were present in all stages of WWTP ranged from 1 to 8%. Among the Archaea, two groups of methanogens, acetoclastic (Methanosarcina, Methanosaeta) and hydrogenotrophic methanogens (Methanospirillium, Methanoculleus, Methanobrevibacter) were dominant in the technological stages. The obtained results indicate that the treated wastewater did not significantly affect eubacterial and archaeal composition in receiving water. However, differences in richness, diversity and microbial composition of Eubacteria and Archaea between the wastewater samples taken from the primary and secondary treatment were observed.

Microbial Population Dynamics in Model Sewage Treatment Plants and the Fate and Effect of Gold Nanoparticles

Adequate functioning of a sewage treatment plant (STP) is essential to protect the downstream aquatic environment (ECHA 2017), and information on the degradability of chemicals and their toxicity to activated sludge microorganisms is required. An environmental realistic higher tier test is a STP simulation test as described in OECD 303A (2001) which for nanoparticles can also be used to study their sorption behavior to activated sludge. However, information is limited on the influence of synthetic sewage on the microbial community of the activated sludge. A modified community can result in modifications of the sludge floccules affecting the sorption behavior. The main objective of our study was to show whether a representative microbial diversity remains under standardized test conditions as described in OECD 303A (2001) using synthetic sewage as influent. Furthermore, we investigated whether just considering the functional properties of a STP (elimination of dissolved organic carbon; nitrification), is sufficient for an assessment of gold nanoparticles (AuNPs) or whether the influence on microbial diversity also needs to be considered. AuNPs were used as a case study due to their rising medical applications and therefore increasing probability to reach the sewer and STP. The results can provide significant input for the interpretation of results from the regulatory point of view. To deliver these objectives, the general changes of the microbial population in activated sludge and its influence on the degradation activity (dissolved organic carbon (DOC) and inorganic nitrogen) using freshly collected sludge from the municipal STP in an artificial test system as a model STP in accordance with OECD 303A (2001) were assessed. Additionally, we evaluated the potential impact of AuNPs and its dispersant on the microbial composition and the overall impact on the function of the STP in terms of DOC degradation and nitrogen removal to observe if an assessment based on functional properties is sufficient. The bacteria composition in our study, evaluated at a class level, revealed commonly described environmental bacteria. Proteobacteria (β, α, δ) accounted for more than 50% but also nitrifying bacteria as Nitrospira were present. Our results show that mainly within the first 7 days of an acclimatization phase by addition of synthetic sewage, the bacterial community changed. Even though AuNPs can have antibacterial properties, no adverse effects on the function and structure of the microorganisms in the STP could be detected at concentrations of increased modeled PEC values by a factor of about 10,000. Complementary to other metallic nanomaterials, gold nanomaterials also sorb to a large extent to the activated sludge. If activated sludge is used as fertilizer on agricultural land, gold nanoparticles can be introduced into soils. In this case, the effect on soil (micro)organisms must be investigated more closely, also taking into account the structural diversity.

The driving factors of nematode gut microbiota under long-term fertilization

Animal bodies are colonized by many microorganisms which can provide indispensable services to their hosts. Although nematode gut microbiota has been extensively studied in recent years, the driving factors of gut microbiome of soil nematodes from a long-term fertilization field are unclear. Here, using 16S rRNA gene amplicon sequencing, we explored the nematode gut microbiota under different fertilization patterns (control, inorganic fertilizers and mixed fertilizers) and fertilization durations (5 y, 8 y and 10 y). Our results revealed that nematode gut microbiota was dominated by core bacterial taxa AF502208 (anaerobic bacteria), Enterobacter (plant litter decomposition) and Ancylobacter (organic matter decomposition and nitrogen cycling), significantly distinct from soil microbiome, and the assembly of that was a non-random process, which suggested host conditions contributed to maintaining the gut microbiota. Moreover, fertilization pattern had a greater influence on nematode gut microbiome than fertilization duration. Inorganic fertilization (5.19) significantly reduced the diversity of the nematode gut microbiota (6.68) shown by Shannon index (P < 0.05). Canonical correspondence analysis demonstrates that soil properties such as pH, organic matter, total phosphorus, available phosphorus, ammonium nitrogen, moisture content, nitrate nitrogen and total nitrogen have significant effects on the nematode microbiome. Structured equation models further revealed that fertilization could obviously affect the nematode gut microbiota, and the effects were maintained even when accounting simultaneously for the drivers of soil bacteria and soil properties. This study provides a solid evidence that the shifting of nematode gut microbiota under long-term fertilization was resulted from environmental factors and host conditions, and advance the insights into host-microbiome in the agricultural ecosystems.

Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance

The development of reliable, mixed-culture biotechnological processes hinges on understanding how microbial ecosystems respond to disturbances. Here we reveal extensive phenotypic plasticity and niche complementarity in oleaginous microbial populations from a biological wastewater treatment plant. We perform meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics) on in situ samples over 14 months at weekly intervals. Based on 1,364 de novo metagenome-assembled genomes, we uncover four distinct fundamental niche types. Throughout the time-series, we observe a major, transient shift in community structure, coinciding with substrate availability changes. Functional omics data reveals extensive variation in gene expression and substrate usage amongst community members. Ex situ bioreactor experiments confirm that responses occur within five hours of a pulse disturbance, demonstrating rapid adaptation by specific populations. Our results show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity, and set the foundation for future ecological engineering efforts.

Herold et al. present an integrated meta-omics framework to investigate how mixed microbial communities, such as oleaginous bacterial populations in biological wastewater treatment plants, respond with distinct adaptation strategies to disturbances. They show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity.

Is Anoxic Operation Effective to Control Nitrate Build-Up and Sludge Loss for the Combined Partial Nitritation and Anammox (CPNA) Process?

There were three main issues of long start-up period, nitrate build-up and sludge loss during the operation of combined partial-nitritation anammox (CPNA). To fully start up the CPNA reactor, the fast achievement of partial-nitritation (PN) was the first step. Firstly, the PN process was successfully achieved within 22 days by 2 mg·L−1 hydroxylamine (NH2OH) addition and online intermittent aeration control at 0.2~0.3 mg·L−1 dissolved oxygen (DO). Then, a novel strategy of adding anoxic stirring phase between feeding and aeration period during CPNA operation was applied. It was shown effective to control nitrate build-up since the mole ratio of NO3−-N production and NH4+-N removed (MNRR) was mostly below 15%. Also, the procedure adjustment was proven useful to alleviate sludge loss by sustaining filamentous bacteria that could act as biomass framework and reduce nitrate substrate. The filamentous denitrifying bacteria could cause sludge bulking. The total nitrogen removal rate (TNRR) varied from 0.20 to 0.45 kg·m−3·d−1 during CPNA operation. In Stage III, after adding anoxic stirring phase, the abundance of nitrogen transformation functional microorganism’s nitrite oxidizing bacteria (NOB) was below 1.6%, which was one order of magnitude lower than Anammox and ammonia oxidizing bacteria (AOB).

Better understanding of the activated sludge process combining fluorescence-based methods and flow cytometry: A case study

This study aims to demonstrate the validity of fluorescence-based methods, together with flow cytometry, as a complementary tool to conventional physicochemical analyses carried out in wastewater treatment plants (WWTPs), for the control of the currently largely unknown activated sludge process. Staining with SYTO 9, propidium iodide and 5-(and 6)-carboxy-2',7'-difluorodihydrofluorescein diacetate (carboxy-H₂DFFDA) was used for cell viability and oxidative stress monitoring of the bacterial population forming the activated sludge of a WWTP. Throughout the period of research, several unstable periods were detected, where the non-viable bacteria exceeded the 75% of the total bacterial population in the activated sludge, but only in one case the cells with oxidative stress grew to 9%, exceeding the typical values of 2%-5% of this plant. These periods coincided in two cases with high values of total suspended solids (SST) and chemical oxygen demand (COD) in the effluent, and with an excess of ammonia in other case. A correlation between flow cytometric and physicochemical data was found, which enabled to clarify the possible origin of each case of instability in the biological system. This experience supports the application of bacterial fluorescence staining, together with flow cytometric analysis, as a simple, rapid and reliable tool for the control and better understanding of the bacteria dynamics in a biological wastewater treatment process.

Comparison of Bacterial Community Structure and Diversity in Traditional Gold Mining Waste Disposal Site and Rice Field by Using a Metabarcoding Approach

Traditional small-scale gold mining mostly use mercury to extract the gold from ores. However, mercury contamination in the environment can affect the composition and structure of the bacterial community. The purpose of this study was to determine the effect of mercury contamination on the bacterial community in the traditional gold mining waste disposal site and in the rice field. Mercury analysis was carried out using the CVAFS method. Analysis of bacterial communities and structure was carried out based on the results of metabarcoding of the V3-V4 16S rRNA regions obtained from paired-end Illumina MiSeq reads. The results showed that the sample from the mining waste disposal site had a mercury level of 230 mg/kg, while the sample from the rice field had 3.98 mg/kg. The results showed that there were differences in microbial composition and community structure in both locations. With the total reads of 57,031, the most dominant phylum was Firmicutes in the mining disposal site sample. Meanwhile, with the total reads of 33,080, the sample from rice field was dominated by Planctomycetes. The abundant classes of bacteria in the mining waste disposal site, from the highest were Bacilli, Gammaproteobacteria and Planctomycetia, while the sample from the rice field was dominated by the Planctomycetia and Acidobacteria subdivision 6. The families that dominated the sample in disposal site were Bacillaceae and Aeromonadaceae, while the sample from the rice field was dominated by Gemmataceae. The abundant genera in both locations were Bacillus and Gemmata. This study concluded that the high level of mercury in the soil reduced the richness and diversity of bacterial phyla and lower taxa. There was also a shift in the dominance of phyla and lower taxa in both locations. This study provides an understanding of the microbial community structure in the area that is highly contaminated with mercury to open insight into the potential of these bacteria for mercury bioremediation.

Thermomonas aquatica sp. nov., isolated from an industrial wastewater treatment plant

A white-coloured, Gram-stain-negative, aerobic, rod-shaped bacterium (designated strain SY21^T) was isolated from waste-activated sludge. Optimal growth occurred at 28 °C and pH 7.0. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain SY21^T exhibited 16S rRNA gene sequence similarities of 95.5-98.0 % to Thermomonas species and clustered with the type species of the genus Thermomonas. In strain SY21^T, the predominant respiratory quinone was ubiquinone Q-8, and the cellular fatty acids consisted mainly of iso-C_15 : 0, C_16 : 0, iso-C_11 : 0 3-OH, summed feature 3 and summed feature 9. The major polar lipids were phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. The genomic DNA G+C content was determined to be 67.9 mol% and the DNA-DNA relatedness between strain SY21^T and the closest phylogenetically related strain, Thermomonas carbonis KCTC 42013^T, was 35.0±0.1 %. Based on the distinct phenotypic, chemotaxonomic and phylogenetic properties, strain SY21^T represents a novel species of the genus Thermomonas, for which the name Thermomonas aquatica sp. nov. is proposed. The type strain is SY21^T (=KCTC 62191^T=NBRC 113114^T).

Profiling Bacterial Diversity and Potential Pathogens in Wastewater Treatment Plants Using High-Throughput Sequencing Analysis

Next-generation sequencing provides new insights into the diversity and structure of bacterial communities, as well as the fate of pathogens in wastewater treatment systems. In this study, the bacterial community structure and the presence of pathogenic bacteria in three wastewater treatment plants across Gauteng province in South Africa were studied. The physicochemical results indicated that the quality of wastewater varies considerably from one plant to the others. Proteobacteria, Actinobacteria, Firmicutes, and Chloroflexi were the dominant phyla across the three wastewater treatment plants, while Alphaproteobacteria, Actinobacteria, Bacilli, and Clostridia were the dominant classes. The dominant bacterial functions were highly associated with carbohydrate, energy, and amino acid metabolism. In addition, potential pathogenic bacterial members identified from the influent/effluent samples included Roseomonas, Bacillus, Pseudomonas, Clostridium, Mycobacterium, Methylobacterium, and Aeromonas. The results of linear discriminant analysis (LDA) effect size analysis also confirmed that these bacterial pathogens were significantly abundant in the wastewater treatment systems. Further, the results of this study highlighted that the presence of bacterial pathogens in treated effluent pose a potential contamination risk, transmitted through soil, agriculture, water, or sediments. There is thus a need for continuous monitoring of potential pathogens in wastewater treatment plants (WWTPs) in order to minimize public health risk.

Molecular Biology-Based Analysis of the Interactive Effect of Nickel and Xanthates on Soil Bacterial Community Diversity and Structure

Metals and mineral flotation collector’s toxicity to the soil living system greatly compromise the sustainability of mining and ore processing. Their effects on the soil microbial community, the most active soil component, remain less understood and addressed particularly with regards to xanthates and their combination with metals. This study analyzed the interactive effects of Ni and xanthates, potassium ethyl xanthate and sodium isopropyl xanthate, on the soil bacterial community through an efficient molecular biology-based technique, the Miseq (Illumina). Both soil microbial community diversity and structure were more affected by xanthates than by Ni. The five most dominant phyla, representing 96.31% of the whole bacterial community, comprised Proteobacteria (54.16%), Firmicutes (17.51%), Actinobacteria (15.59%), Acidobacteria (4.87%), and Chloroflexi (4.16%). Different soil treatments exhibited greater difference in the species abundance/dominance than in the species numbers. Proteobacteria was the most dominant in the presence of xanthates, individually or in mixtures with nickel, while Firmicutes exhibited its highest proportion in the Ni/xanthate-treated samples. The most abundant and proportionally different bacterial species between different treatments were presented. The most abundant bacterial strains identified should be explored more for their potential application in biomining and for the prediction and biologically-based treatment and remediation of Ni and xanthate-contaminated systems.

Chemical mixtures and fluorescence in situ hybridization analysis of natural microbial community in the Tiber river

The Water Framework Directive (WFD) regulates freshwater and coastal water quality assessment in Europe. Chemical and ecological water quality status is based on measurements of chemical pollutants in water and biota together with other indicators such as temperature, nutrients, species compositions (phytoplankton, microalgae, benthos and fish) and hydromorphological conditions. However, in the current strategy a link between the chemical and the ecological status is missing. In the present WFD, no microbiological indicators are foreseen for integrating the different anthropogenic pressures, including mixtures of chemicals, nutrients and temperature changes, to provide a holistic view of the freshwater ecosystem water quality. The main aim of this work was to evaluate if natural microbial populations can be valuable indicators of multiple stressors (e.g. chemical pollutants, temperature, nutrients etc.) to guide preventive and remediation actions by water authorities. A preliminary survey was conducted to identify four sites reflecting a contamination gradient from the source to the mouth of a river suitable to the objectives of the European Marie Curie project, MicroCoKit. The River Tiber (Italy) was selected as a pilot case study to investigate the correlation between bacteria taxa and the chemical status of the river. The main physicochemical parameters, inorganic elements, organic pollutants and natural microbial community composition were assessed at four selected sites corresponding to pristine, agricultural, industrial and urban areas for three consecutive years. The overall chemical results indicated a correspondence between different groups of contaminants and the main contamination sources at the selected sampling points. Phylogenetic analysis of the microbial community analyzed by Fluorescence In Situ Hybridization method (FISH) revealed differences among the four sampling sites which could reflect an adaptive bacterial response to the different anthropogenic pressures.

Identification of eukaryotic microorganisms with 18S rRNA next-generation sequencing in wastewater treatment plants, with a more targeted NGS approach required for Cryptosporidium detection

While some microbial eukaryotes can improve effluent quality in wastewater treatment plants (WWTPs), eukaryotic waterborne pathogens are a threat to public health. This study aimed to identify Eukarya, particularly faecal pathogens including Cryptosporidium, in different treatment stages (influent, intermediate and effluent) from four WWTPs in Western Australia (WA). Three WWTPs that utilise stabilisation ponds and one WWTP that uses activated sludge (oxidation ditch) treatment technologies were sampled. Eukaryotic 18S rRNA (18S) was targeted in the wastewater samples (n = 26) for next-generation sequencing (NGS), and a mammalian-blocking primer was used to reduce the amplification of mammalian DNA. Overall, bioinformatics analyses revealed 49 eukaryotic phyla in WWTP samples, and three of these phyla contained human intestinal parasites, which were primarily detected in the influent. These human intestinal parasites either had a low percent sequence composition or were not detected in the intermediate and effluent stages and included the amoebozoans Endolimax sp., Entamoeba sp. and Iodamoeba sp., the human pinworm Enterobius vermicularis (Nematoda), and Blastocystis sp. subtypes (Sarcomastigophora). Six Blastocystis subtypes and four Entamoeba species were identified by eukaryotic 18S NGS, however, Cryptosporidium sp. and Giardia sp. were not detected. Real-time polymerase chain reaction (PCR) also failed to detect Giardia, but Cryptosporidium-specific NGS detected Cryptosporidium in all WWTPs, and a total of nine species were identified, including five zoonotic pathogens. Although eukaryotic 18S NGS was able to identify some faecal pathogens, this study has demonstrated that more specific NGS approaches for pathogen detection are more sensitive and should be applied to future wastewater pathogen assessments.

Evaluation of 16S next-generation sequencing of hypervariable region 4 in wastewater samples: An unsuitable approach for bacterial enteric pathogen identification

Recycled wastewater can carry human-infectious microbial pathogens and therefore wastewater treatment strategies must effectively eliminate pathogens before recycled wastewater is used to supplement drinking and agricultural water supplies. This study characterised the bacterial composition of four wastewater treatment plants (WWTPs) (three waste stabilisation ponds and one oxidation ditch WWTP using activated sludge treatment) in Western Australia. The hypervariable region 4 (V4) of the bacterial 16S rRNA (16S) gene was sequenced using next-generation sequencing (NGS) on the Illumina MiSeq platform. Sequences were pre-processed in USEARCH v10.0 and denoised into zero-radius taxonomic units (ZOTUs) with UNOISE3. Taxonomy was assigned to the ZOTUs using QIIME 2 and the Greengenes database and cross-checked with the NCBI nr/nt database. Bacterial composition of all WWTPs and treatment stages (influent, intermediate and effluent) were dominated by Proteobacteria (29.0-87.4%), particularly Betaproteobacteria (9.0-53.5%) and Gammaproteobacteria (8.6-34.6%). Nitrifying bacteria (Nitrospira spp.) were found only in the intermediate and effluent of the oxidation ditch WWTP, and denitrifying and floc-forming bacteria were detected in all WWTPs, particularly from the families Comamonadaceae and Rhodocyclales. Twelve pathogens were assigned taxonomy by the Greengenes database, but comparison of sequences from genera and families known to contain pathogens to the NCBI nr/nt database showed that only three pathogens (Arcobacter venerupis, Laribacter hongkongensis and Neisseria canis) could be identified in the dataset at the V4 region. Importantly, Enterobacteriaceae genera could not be differentiated. Family level taxa assigned by Greengenes database agreed with NCBI nr/nt in most cases, however, BLAST analyses revealed erroneous taxa in Greengenes database. This study highlights the importance of validating taxonomy of NGS sequences with databases such as NCBI nr/nt, and recommends including the V3 region of 16S in future short amplicon NGS studies that aim to identify bacterial enteric pathogens, as this will improve taxonomic resolution of most, but not all, Enterobacteriaceae species.

Anadromous Arctic Char Microbiomes: Bioprospecting in the High Arctic

Northern populations of Arctic char (Salvelinus alpinus) can be anadromous, migrating annually from the ocean to freshwater lakes and rivers in order to escape sub-zero temperatures. Such seasonal behavior demands that these fish and their associated microbiomes adapt to changes in salinity, temperature, and other environmental challenges. We characterized the microbial community composition of anadromous S. alpinus, netted by Inuit fishermen at freshwater and seawater fishing sites in the high Arctic, both under ice and in open water. Bacterial profiles were generated by DNA extraction and high-throughput sequencing of PCR-amplified 16S ribosomal RNA genes. Results showed that microbial communities on the skin and intestine of Arctic char were statistically different when sampled from freshwater or saline water sites. This association was tested using hierarchical Ward's linkage clustering, showing eight distinct clusters in each of the skin and intestinal microbiomes, with the clusters reflecting sampling location between fresh and saline environments, confirming a salinity-linked turnover. This analysis also provided evidence for a core composition of skin and intestinal bacteria, with the phyla Proteobacteria, Firmicutes, and Cyanobacteria presenting as major phyla within the skin-associated microbiomes. The intestine-associated microbiome was characterized by unidentified genera from families Fusobacteriaceae, Comamonadaceae, Pseudomonadaceae, and Vibrionaceae. The salinity-linked turnover was further tested through ordinations that showed samples grouping based on environment for both skin- and intestine-associated microbiomes. This finding implies that core microbiomes between fresh and saline conditions could be used to assist in regulating optimal fish health in aquaculture practices. Furthermore, identified taxa from known psychrophiles and with nitrogen cycling properties suggest that there is additional potential for biotechnological applications for fish farm and waste management practices.

Disentangling the Drivers of Diversity and Distribution of Fungal Community Composition in Wastewater Treatment Plants Across Spatial Scales

Activated sludge microbial community composition is a key bio-indicator of the sustainability of wastewater treatment systems. Therefore, a thorough understanding of the activated sludge microbial community dynamics is critical for environmental engineers to effectively manage the wastewater treatment plants (WWTPs). However, fungal communities associated with activated sludge have been poorly elucidated. Here, the activated sludge fungal community in 18 geographically distributed WWTPs was determined by using Illumina sequencing. The results showed that differences in activated sludge fungal community composition were observed among all WWTPs and also between oxidation ditch and anaerobic-anoxic-aerobic (A/A/O) systems. Ascomycota was the largest phyla, followed by Basidiomycota in all samples. Sporidiobolales and Pezizales were the most abundant order in oxidation ditch and A/A/O systems, respectively. The network analysis indicated cooperative and co-occurrence interactions between fungal taxa in order to accomplish the wastewater treatment process. Hygrocybe sp., Sporobolomyces sp., Rhodotorula sp., Stemphylium sp., Parascedosporium sp., and Cylindrocarpon sp., were found to have statistically significant interactions. Redundancy analysis revealed that temperature, total phosphorus, pH, and ammonia nitrogen were significantly affected the fungal community. This study sheds light on providing the ecological characteristics of activated sludge fungal communities and useful guidance for improving wastewater treatment performance efficiency.