Application of metagenomics to biological wastewater treatment

Aerobic granular sludge for swine wastewater treatment: Implications for antibiotic and antibiotic resistance gene elimination

Swine wastewater (SW) contains high levels of traditional pollutants, antibiotics, and antibiotic resistance genes (ARGs), necessitating effective elimination. Two parallel aerobic granular sludge (AGS) reactors, R1 and R2, were constructed and optimized for treating SW from two pig farms, identified as SW1 and SW2. R2 showed higher antibiotic removal efficiency, particularly in the removal of sulfonamides, while fluoroquinolones tended to adsorb onto the sludge. Process optimization by introducing an additional anoxic phase enhanced denitrification and reduced effluent ARG levels, also aiding in the improved removal of fluoroquinolones. The nitrite-oxidizing bacteria (NOB) Nitrospira accumulated after the treatment process, reaching 12.8 % in R1 and 14.1 % in R2, respectively. Mantel's test revealed that pH, NH4+-N, and Mg significantly affected ARGs and microbial community. Sulfadiazine and sulfamethazine were found to significantly impact ARGs and the microbial communities. This study provides innovative insights into the application of AGS for the treatment of real SW.

Biodegradation of poly(butylene adipate terephthalate) and poly(vinyl alcohol) within aquatic pathway

Understanding the environmental fate of biodegradable plastics in aquatic systems is crucial, given the alarming amount of plastic waste and microplastic particles transported through aquatic pathways. In particular, there is a need to analyze the biodegradation of commercialized biodegradable plastics upon release from wastewater treatment plants into natural aquatic systems. This study investigates the biodegradation behaviors of poly(butylene adipate terephthalate) (PBAT) and poly(vinyl alcohol) (PVA) in wastewater, freshwater, and seawater. Biodegradation of PBAT and PVA assessed through biochemical oxygen demand (BOD) experiments and microcosm tests revealed that the type of aquatic system governs the biodegradation behaviors of each plastic, with the highest biodegradation rate achieved in wastewater for both PBAT and PVA (25.6 and 32.2 % in 30 d, respectively). Plastic release pathway from wastewater into other aquatic systems simulated by sequential incubation in different microcosms suggested that PBAT exposed to wastewater and freshwater before reaching seawater was more prone to degradation than when directly exposed to seawater. On the other hand, PVA displayed comparable biodegradation rate regardless of whether it was directly exposed to seawater or had passed through other environments beforehand. Metagenome amplicon sequencing of 16S rRNA genes revealed distinct community shifts dependent on the type of plastics in changing environments along the simulated aquatic pathway. Several bacterial species putatively implicated in the biodegradation of PBAT and PVA are discussed. Our findings underscore the significant influence of pollution routes on the biodegradation of PBAT and PVA, highlighting the potential for wastewater treatment to facilitate rapid degradation compared to direct exposure to pristine aquatic environments.

Microbial valorization of kraft black liquor for production of platform chemicals, biofuels, and value-added products: A critical review

The proper treatment and utilization of kraft black liquor, generated from the pulp and paper industry through the kraft pulping method, is required to reduce environmental impacts prior to the final disposal. It also improves the economic performance through the utilization of waste. Microbial valorization appears to demonstrates the dual benefits of waste management and resource recovery by providing an innovative solution to convert kraft black liquor into resource for reuse. A comprehensive review on the microbial valorization of kraft black liquor, describing the role in valorization and management, is still lacking in the literature, forming the rationale of this article. Thus, the present study reviews and systematically discusses the potential of utilizing microorganisms to valorize kraft black liquor as a sustainable feedstock to develop a numerous portfolio of platform chemicals, bioenergy, and other value-added products. This work contributes to sustainability and resource efficiency within the pulp and paper industry. The recent developments in utilization of synthetic biology tools and molecular techniques, including omics approaches for engineering novel microbial strains, for enhancing kraft black liquor valorization has been presented. This review explores how the better utilization of kraft black liquor in the pulp and paper industry contributes to achieving UN Sustainable Development Goals (SDGs), particularly clean water and sanitation (SDG 6) as well as the affordable and clean energy goal (SDG 7). The current review also addresses challenges related to toxicity, impurities, low productivity, and downstream processing that serve as obstacles to the progress of developing highly efficient bioproducts. The new directions for future research efforts to fill the critical knowledge gaps are proposed. This study concludes that by implementing microbial valorization techniques, the pulp and paper industry can transition from a linear to a circular bioeconomy and eco-friendly manage the kraft black liuor. This approach showed to be effective towards resource recovery, while simultaneously minimizing the environmental burden.

Metagenome-assembled genomes (MAGs) suggest an acetate-driven protective role in gut microbiota disrupted by Clostridioides difficile

Clostridioides difficile may have a negative impact on gut microbiota composition in terms of diversity and abundance, thereby triggering functional changes supported by the differential presence of genes involved in significant metabolic pathways, such as short-chain fatty acids (SCFA). This work has evaluated shotgun metagenomics data regarding 48 samples from four groups classified according to diarrhea acquisition site (community- and healthcare facility-onset) and positive or negative Clostridioides difficile infection (CDI) result. The metagenomic-assembled genomes (MAGs) obtained from each sample were taxonomically assigned for preliminary comparative analysis concerning differences in composition among groups. The predicted genes involved in metabolism, transport, and signaling remained constant in microbiota members; characteristic patterns were observed in MAGs and genes involved in SCFA butyrate and acetate metabolic pathways for each study group. A decrease in genera and species, as well as relative MAG abundance with the presence of the acetate metabolism-related gene, was evident in the HCFO/- group. Increased antibiotic resistance markers (ARM) were observed in MAGs along with the genes involved in acetate metabolism. The results highlight the need to explore the role of acetate in greater depth as a potential protector of the imbalances produced by CDI, as occurs in other inflammatory intestinal diseases.

Targeted whole-genome recovery of single viral species in a complex environmental sample

Characterizing unknown viruses is essential for understanding viral ecology and preparing against viral outbreaks. Recovering complete genome sequences from environmental samples remains computationally challenging using metagenomics, especially for low-abundance species with uneven coverage. We present an experimental method for reliably recovering complete viral genomes from complex environmental samples. Individual genomes are encapsulated into droplets and amplified using multiple displacement amplification. A unique gene detection assay, which employs an RNA-based probe and an exonuclease, selectively identifies droplets containing the target viral genome. Labeled droplets are sorted using a microfluidic sorter, and genomes are extracted for sequencing. We demonstrate this method's efficacy by spiking two known viral genomes, Simian virus 40 (SV40, 5,243 bp) and Human Adenovirus 5 (HAd5, 35,938 bp), into a sewage sample with a final abundance in the droplets of around 0.1% and 0.015%, respectively. We achieve 100% recovery of the complete sequence of the spiked-in SV40 genome with uniform coverage distribution. For the larger HAd5 genome, we cover approximately 99.4% of its sequence. Notably, genome recovery is achieved with as few as one sorted droplet, which enables the recovery of any desired genomes in complex environmental samples, regardless of their abundance. This method enables single-genome whole-genome amplification and targeting characterizations of rare viral species and will facilitate our ability to access the mutational profile in single-virus genomes and contribute to an improved understanding of viral ecology.

Hybrid constructed wetlands and filamentous fungi for treatment of mixed sewage and industrial effluents

Developing countries face multifaceted problems of water pollution and futile measures to combat water pollution. This study was conducted to explore the potential application of sustainable nature-based solutions, hybrid constructed wetlands, and the application of filamentous fungi to treat polluted river water that receives sewage and industrial wastewater. A pilot-scale hybrid constructed wetland design comprising two types of floating plants in distinct tanks along with a floating wetland and a free-water surface wetland connected in series was commissioned and tested. The system successfully removed organic pollution (BOD 94% and COD 90%), nutrients (NH4-N and NO3-N 67% and PO4-P 81%), and heavy metals (Cr 75%, Ni 56%, and Fe 79%) in 40 h and showed a high buffering capacity to cope with the varying pollutant loads. Metagenomics analysis of treated and untreated samples of river water revealed a diversified spatial bacterial community with ~ 25% sequences related to sulfur-metabolizing bacteria, genus Sulfuricurvum. The application of an immobilized strain of A. niger as a mycoremediation technique was also tested. It successfully removed pollutants in the combined sewage and industrial wastewater present in river water: COD (96%), TSS (97%), NH4-N (65%), NO3-N (67%), and PO4-P (78%). This study demonstrated that hybrid constructed wetlands and mycoremediation can be used as sustainable wastewater treatment options in the local context and also in developing countries where most of the conventional wastewater treatment plants do not operate.

Microalgal multiomics-based approaches in bioremediation of hazardous contaminants

The enhanced industrial growth and higher living standards owing to the incessant population growth have caused heightened production of various chemicals in different manufacturing sectors globally, resulting in pollution of aquatic systems and soil with hazardous chemical contaminants. The bioremediation of such hazardous pollutants through microalgal processes is a viable and sustainable approach. Accomplishing microalgal-based bioremediation of polluted wastewater requires a comprehensive understanding of microalgal metabolic and physiological dynamics. Microalgae-bacterial consortia have emerged as a sustainable agent for synergistic bioremediation and metabolite production. Effective bioremediation involves proper consortium functioning and dynamics. The present review highlights the mechanistic processes employed through microalgae in reducing contaminants present in wastewater. It discusses the multi-omics approaches and their advantages in understanding the biological processes, monitoring, and dynamics among the partners in consortium through metagenomics. Transcriptomics, proteomics, and metabolomics enable an understanding of microalgal cell response toward the contaminants in the wastewater. Finally, the challenges and future research endeavors are summarised to provide an outlook on microalgae-based bioremediation.

Treatment of high-strength saline bilge wastewater by four pilot-scale aerobic moving bed biofilm reactors and comparison of the microbial communities

Four Pilot-scale Moving Bed Biofilm Reactors (MBBRs) were operated for the treatment of real, saline, bilge wastewater. The MBBRs were connected in pairs to create two system configurations with different filling ratios (20%, 40%) and were operated in parallel. The inflow organic loading rate (OLR) varied from 3.6 ± 0.2 to 7.8 ± 0.6 g COD L-1 d-1, salinity was >15 ppt and three hydraulic residence times (HRTs) were tested 48, 30 and 24 h. In both systems, the first-stage bioreactors (R1 and R3) eliminated the higher part of the organic load (57%-65%). The second-stage bioreactors (R2 and R4) removed an additional fraction (18%-31%) of the organic load received by the effluent of R1 and R3, respectively. The microbial communities of the influent wastewater, suspended, and attached biomass were determined using 16S rRNA gene amplicon sequencing analysis. The evolution of the microbial communities was investigated and compared over the different operational phases. The microbial communities of the biofilm presented higher diversity and greater stability in composition over time, while the suspended biomass exhibited intense and rapid changes in the dominance of genera. Proteobacteria, Bacteroidetes and Firmicutes were highly present in the biofilm. The genera Celeribacter, Novispirillum, Roseovarius (class: Alphaproteobacteria) and Formosa (class: Flavobacteriia) were highly present during all operational phases. Principal Component Analysis (PCA) was used to identify similarities between samples, exhibiting high relation of samples according to the series of the bioreactor (1st, 2nd).

Metagenomics reveals the microbial community and functional metabolism variation in the partial nitritation-anammox process: From collapse to recovery

Mainstream partial nitritation-anammox (PNA) process easily suffers from performance instability and even reactor collapse in application. Thus, it is of great significance to unveil the characteristic of performance recovery, understand the intrinsic mechanism and then propose operational strategy. In this study, we combined long-term reactor operation, batch tests, and metagenomics to reveal the succession of microbial community and functional metabolism variation from system collapse to recovery. Proper aeration control (0.10-0.25 mg O2/L) was critical for performance recovery. It was also found that Candidatus Brocadia became the dominant flora and its abundance increased from 3.5% to 11.0%. Significant enhancements in carbon metabolism and phospholipid biosynthesis were observed during system recovery, and the genes abundance related to signal transduction was dramatically increased. The up-regulation of sdh and suc genes showed the processes of succinate dehydrogenation and succinyl-CoA synthesis might stimulate the production of amino acids and the synthesis of proteins, thereby possibly improving the activity and abundance of AnAOB, which was conducive to the performance recovery. Moreover, the increase in abundance of hzs and hdh genes suggested the enhancement of the anammox process. Changes in the abundance of key genes involved in nitrogen metabolism indicated that nitrogen removal pathway was more diverse after system recovery. The achievement of performance recovery was driven by anammox, nitrification and denitrification coupled with dissimilatory nitrate reduction to ammonium. These results provide deeper insights into the recovery mechanism of PNA system and also provide a potential regulation strategy for the stable operation of the mainstream PNA process.

Establishment of microbial model communities capable of removing trace organic chemicals for biotransformation mechanisms research

BACKGROUND

Removal of trace organic chemicals (TOrCs) in aquatic environments has been intensively studied. Some members of natural microbial communities play a vital role in transforming chemical contaminants, however, complex microbial interactions impede us from gaining adequate understanding of TOrC biotransformation mechanisms. To simplify, in this study, we propose a strategy of establishing reduced-richness model communities capable of removing diverse TOrCs via pre-adaptation and dilution-to-extinction.

RESULTS

Microbial communities were adapted from tap water, soil, sand, sediment deep and sediment surface to changing concentrations of 27 TOrCs mixture. After adaptation, the communities were further diluted to reduce diversity into 96 deep well plates for high-throughput cultivation. After characterizing microbial structure and TOrC removal performance, thirty taxonomically non-redundant model communities with different removal abilities were obtained. The pre-adaptation process was found to reduce the microbial richness but to increase the evenness and phylogenetic diversity of resulting model communities. Moreover, phylogenetic diversity showed a positive effect on the number of TOrCs that can be transformed simultaneously. Pre-adaptation also improved the overall TOrC removal rates, which was found to be positively correlated with the growth rates of model communities.

CONCLUSIONS

This is the first study that investigated a wide range of TOrC biotransformation based on different model communities derived from varying natural microbial systems. This study provides a standardized workflow of establishing model communities for different metabolic purposes with changeable inoculum and substrates. The obtained model communities can be further used to find the driving agents of TOrC biotransformation at the enzyme/gene level.

Wastewater microbial diversity versus molecular analysis at a glance: a mini-review

Microorganisms play a vital role in biological wastewater treatment by converting organic and toxic materials into harmless substances. Understanding microbial communities' structure, taxonomy, phylogeny, and metabolic activities is essential to improve these processes. Molecular microbial ecology employs molecular techniques to study community profiles and phylogenetic information since culture-dependent approaches have limitations in providing a comprehensive understanding of microbial diversity in a system. Genomic advancements such as DNA hybridization, microarray analysis, sequencing, and reverse sample genome probing have enabled the detailed characterization of microbial communities in wastewater treatment facilities. This mini-review summarizes the current state of knowledge on the diversity of microorganisms in wastewater treatment plants, emphasizing critical microbial processes such as nitrogen and phosphorus removal.

Advances in Algomics technology: Application in wastewater treatment and biofuel production

Advanced sustainable bioremediation is gaining importance with rising global pollution. This review examines microalgae's potential for sustainable bioremediation and process enhancement using multi-omics approaches. Recently, microalgae-bacterial consortia have emerged for synergistic nutrient removal, allowing complex metabolite exchanges. Advanced bioremediation requires effective consortium design or pure culture based on the treatment stage and specific roles. The strain potential must be screened using modern omics approaches aligning wastewater composition. The review highlights crucial research gaps in microalgal bioremediation. It discusses multi-omics advantages for understanding microalgal fitness concerning wastewater composition and facilitating the design of microalgal consortia based on bioremediation skills. Metagenomics enables strain identification, thereby monitoring microbial dynamics during the treatment process. Transcriptomics and metabolomics encourage the algal cell response toward nutrients and pollutants in wastewater. Multi-omics role is also summarized for product enhancement to make algal treatment sustainable and fit for sustainable development goals and growing circular bioeconomy scenario.

Simultaneous phosphorus recovery from wastewater and sludge by a novel denitrifying phosphorus removal system

A novel process was proposed for simultaneous denitrification and phosphorus (P) recovery. The increased nitrate concentration facilitated the activity of denitrifying P removal (DPR) in P enrichment, which stimulated P uptake and storage, making P more readily accessible for release into the recirculated stream. The total P content in the biofilm (TP_biofilm) rose to 54.6 ± 3.5 mg/g SS as the nitrate concentration increased from 15.0 to 25.0 mg/L, while the P concentration of the enriched stream reached 172.5 ± 3.5 mg/L. Moreover, the abundance of denitrifying polyphosphate accumulating organisms (DPAOs) increased from 5.6% to 28.0%, and the increased nitrate concentration facilitated the process of carbon, nitrogen, and P metabolism due to the rise in the genes involved in critical functions of metabolism. Acid/alkaline fermentation analysis indicated that the EPS release was the primary P-release pathway. Additionally, pure struvite crystals were obtained from the enriched stream and fermentation supernatant.

Recent advances in the biological treatment of wastewater rich in emerging pollutants produced by pharmaceutical industrial discharges

Pharmaceuticals and personal care products present potential risks to human health and the environment. In particular, wastewater treatment plants often detect emerging pollutants that disrupt biological treatment. The activated sludge process is a traditional biological method with a lower capital cost and limited operating requirements than more advanced treatment methods. In addition, the membrane bioreactor combines a membrane module and a bioreactor, widely used as an advanced method for treating pharmaceutical wastewater with good pollution performance. Indeed, the fouling of the membrane remains a major problem in this process. In addition, anaerobic membrane bioreactors can treat complex pharmaceutical waste while recovering energy and producing nutrient-rich wastewater for irrigation. Wastewater characterizations have shown that wastewater's high organic matter content facilitates the selection of low-cost, low-nutrient, low-surface-area, and effective anaerobic methods for drug degradation and reduces pollution. However, to improve the biological treatment, researchers have turned to hybrid processes in which all physical, chemical, and biological treatment methods are integrated to remove various emerging contaminants effectively. Hybrid systems can generate bioenergy, which helps reduce the operating costs of the pharmaceutical waste treatment system. To find the most effective treatment technique for our research, this work lists the different biological treatment techniques cited in the literature, such as activated sludge, membrane bioreactor, anaerobic treatment, and hybrid treatment, combining physicochemical and biological techniques.

Co-treatment of landfill leachate with urban wastewater by chemical, physical and biological processes: Fenton oxidation preserves autochthonous bacterial community in the activated sludge process

The impact of Fenton oxidation (FO) and Air stripping (AS) pre-treatments on the bacterial community of a biological activated sludge (B-AS) process for the co-treatment of mature landfill leachate (MLL) and urban wastewater (UWW) was assessed. In this work high-throughput sequencing was used to identify changes in the composition of the bacterial communities when exposed to different landfill leachate's pre-treatments. The combination of FO and AS to increase biodegradability (BOD₅/COD) and reduce ammonia concentration (NH₃) respectively, allowed to successfully operate the B-AS and effectively treat MLL. In particular, BOD₅/COD resulted to be the key factor for bacterial community shifting. The microbiological community of the B-AS, mainly composed by the phylum Bacteroidota (Saprospiraceae, PHOS-HE51, Chitinophagaceae) after FO pre-treatment, shifted to Pseudomonadota (Caulobacteraceae and Hyphomicrobiaceae) when FO was not used. At the same time a drastic reduction in BOD₅ removal was observed (90%-58%). On the other hand, high NH₃ concentration affected the abundance of the family Saprospiraceae, known to play a key role in the degradation of complex organic compounds in B-AS. The results obtained suggest that a suitable combination of pre-treatments can reduce the negative effect of MLL on the B-AS process, reducing the pressure on autochthonous bacteria and therefore the acclimatization time of the biological process.

Enhanced Bio-P removal: Past, present, and future - A comprehensive review

Excess amounts of phosphorus (P) and nitrogen (N) from anthropogenic activities such as population growth, municipal and industrial wastewater discharges, agriculture fertilization and storm water runoffs, have affected surface water chemistry, resulting in episodes of eutrophication. Enhanced biological phosphorus removal (EBPR) based treatment processes are an economical and environmentally friendly solution to address the present environmental impacts caused by excess P present in municipal discharges. EBPR practices have been researched and operated for more than five decades worldwide, with promising results in decreasing orthophosphate to acceptable levels. The advent of molecular tools targeting bacterial genomic deoxyribonucleic acid (DNA) has also helped us reveal the identity of potential polyphosphate-accumulating organisms (PAO) and denitrifying PAO (DPAO) responsible for the success of EBPR. Integration of process engineering and environmental microbiology has provided much-needed confidence to the wastewater community for the successful implementation of EBPR practices around the globe. Despite these successes, the process of EBPR continues to evolve in terms of its microbiology and application in light of other biological processes such as anaerobic ammonia oxidation and on-site carbon capture. This review provides an overview of the history of EBPR, discusses different operational parameters critical for the successful operation of EBPR systems, reviews current knowledge of EBPR microbiology, the influence of PAO/DPAO on the disintegration of microbial communities, stoichiometry, EBPR clades, current practices, and upcoming potential innovations.

Effects of ferroferric oxide on propionate methanogenesis in sequencing batch reactors: Microbial community structure and metagenomic analysis

This study investigated the effects of ferroferric oxide (Fe₃O₄) on propionate methanogenesis in anaerobic sequencing batch reactor (ASBR). Compared to ASBR_C (without Fe₃O₄ addition), the addition of 10 g/L Fe₃O₄ (ASBR_Fe) decreased the maximum methane production rate by 69.6 % when propionate was used as the sole substrate. The addition of Fe₃O₄ reduced the contents of humic substances, riboflavin and nicotinamide adenine dinucleotide in extracellular polymeric substances. Therefore, Fe₃O₄ inhibited interspecies electron transfer of microorganisms through electronic mediators. Microbial community analysis revealed that Fe₃O₄ addition increased the relative abundance of acetate oxidizing bacterium (Mesotoga), but decreased the abundance of hydrogenotrophic methanogen (Methanobacterium). Further metagenomics analysis indicated that Fe₃O₄ increased the abundance of acetate oxidation genes and decreased that of hydrogenotrophic methanogenesis, quorum sensing and V/A-type ATPase genes. Thus, Fe₃O₄ reduced propionate methanogenesis during anaerobic digestion. The overall results indicate that Fe₃O₄ addition inhibits methanogenesis for treatment of propionate-contaminated wastewater in ASBR.

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.

Caecal microbial communities, functional diversity, and metabolic pathways in Ross 308 broiler chickens fed with diets containing different levels of Marama (Tylosema esculentum) bean meal

The caecum of a chicken harbors complex microbial communities that play vital roles in feed digestion, nutrient absorption, and bird health. Understanding the caecal microbial communities could help improve feed utilization efficiency and chicken product quality and, ultimately, deliver sustainable poultry production systems. Thus, this study assessed the caecal microbial communities and their functional diversity and metabolic pathways in broilers reared on diets containing different levels of marama (Tylosema esculentum) bean meal (MBM). A total of 350, day-old male Ross 308 broiler chicks were randomly allocated to five dietary treatments formulated as follows: a soybean-based standard broiler diet (Con_BC); Con_BC in which soybean products were substituted with 7 (M7_BC), 14 (M14_BC), 21 (M21_BC), and 28% (M28_BC) MBM. The dietary treatments were distributed to 35 replicate pens (10 birds each). After 42 days of feeding, the birds were slaughtered and thereafter caecal samples were collected from each replicate pen. Subsequently, the samples were pooled per treatment group for metagenomics sequence analysis. The results revealed that the bacteria domain (99.11%), with Bacteroides, Firmicutes and Proteobacteria being the most prominent phyla (48.28, 47.52, and 4.86%, respectively). Out of 846 genera obtained, the most abundant genera were Bacteroides, Clostridium, Alistipes, Faecalibacterium, Ruminococcus, Eubacterium, and Parabacterioides. At the genus level, the alpha-diversity showed significant (p < 0.05) difference across all treatment groups. Based on the SEED subsystem, 28 functional categories that include carbohydrates (14.65%), clustering-based subsystems (13.01%), protein metabolism (10.12%) were obtained. The KO analysis revealed 183 endogenous pathways, with 100 functional pathways associated with the metabolism category. Moreover, 15 pathways associated with carbohydrates were observed. The glycolysis/gluconeogenesis, galactose metabolism, pyruvate metabolism (15.32, 12.63, and 11.93%) were the most abundant pathways. Moreover, glycoside hydrolases (GH1, GH5, and GH13) were the most prominent carbohydrates-active enzymes. Therefore, results presented in this study suggest that dietary MB meal can improve microbial communities and their functional and metabolic pathways, which may help increase poultry production.

Are Wetlands as an Integrated Bioremediation System Applicable for the Treatment of Wastewater from Underground Coal Gasification Processes?

Underground coal gasification (UCG) can be considered as one of the clean coal technologies. During the process, the gas of industrial value is produced, which can be used to produce heat and electricity, liquid fuels or can replace natural gas in chemistry. However, UCG does carry some environmental risks, mainly related to potential negative impacts on surface and groundwater. Wastewater and sludge from UCG contain significant amounts of aliphatic and aromatic hydrocarbons, phenols, ammonia, cyanides and hazardous metals such as arsenic. This complicated matrix containing high concentrations of hazardous pollutants is similar to wastewater from the coke industry and, similarly to them, requires complex mechanical, chemical and biological treatment. The focus of the review is to explain how the wetlands systems, described as one of bioremediation methods, work and whether these systems are suitable for removing organic and inorganic contaminants from heavily contaminated industrial wastewater, of which underground coal gasification wastewater is a particularly challenging example. Wetlands appear to be suitable systems for the treatment of UCG wastewater and can provide the benefits of nature-based solutions. This review explains the principles of constructed wetlands (CWs) and provides examples of industrial wastewater treated by various wetland systems along with their operating principles. In addition, the physicochemical characteristics of the wastewater from different coal gasifications under various conditions, obtained from UCG’s own experiments, are presented.

A review on the immobilization of pepsin: A Lys-poor enzyme that is unstable at alkaline pH values

Pepsin is a protease used in many different applications, and in many instances, it is utilized in an immobilized form to prevent contamination of the reaction product. This enzyme has two peculiarities that make its immobilization complex. The first one is related to the poor presence of primary amino groups on its surface (just one Lys and the terminal amino group). The second one is its poor stability at alkaline pH values. Both features make the immobilization of this enzyme to be considered a complicated goal, as most of the immobilization protocols utilize primary amino groups for immobilization. This review presents some of the attempts to get immobilized pepsin biocatalyst and their applications. The high density of anionic groups (Asp and Glu) make the anion exchange of the enzyme simpler, but this makes many of the strategies utilized to immobilize the enzyme (e.g., amino-glutaraldehyde supports) more related to a mixed ion exchange/hydrophobic adsorption than to real covalent immobilization. Finally, we propose some possibilities that can permit not only the covalent immobilization of this enzyme, but also their stabilization via multipoint covalent attachment.

Alteration in microbial community and antibiotic resistance genes mediated by microplastics during wastewater ultraviolet disinfection

Microplastics (MPs) could be as a vector to colonize microorganisms and antibiotic resistance gene (ARGs) in surface water. However, little information is known regarding their changes by the presence of MPs in wastewater treatment. Here, the effects of different concentrations and sizes of polystyrene microplastics (PSMPs) on the distribution and removal of microbial communities and ARGs under ultraviolet disinfection of urban sewage have been systematically studied. Results showed that the presence of MPs altered abundance and functions of microorganisms in wastewater, despite different effects on different types of microorganisms. The most abundant ARGs in original disinfection tank sewage was rpoB2 (6.34%). A certain concentration range of MPs can improve the ability of specific types of ARGs in the UV disinfection process. Compared to the system without PSMPs, the content of Deinococcus-Thermus and Bacteroidetes phylum increased, while Actinobacteria and Proteobacteria phylum decreased in the presence of MPs. The microbial functions, especially the genetic information processing and metabolism were altered by the presence of PSMPs. In addition, PSMPs altered the content of ARGs, where the contents of OXA-182 and ErmH were increased, while adeF and ANT3-Iic were decreased. PSMPs also decreased the free ARB content in wastewater by providing colonization sites. The UV disinfection efficiency of microorganisms and ARGs was also intervened by PSMPs since they provided colonization sites and increased the water turbidity. The findings indicated that PSMPs altered the distribution and removal of microbial community and ARGs in ultraviolet disinfection of wastewater, highlighting the combined risks.

Progress in the interaction of dissolved organic matter and microbes (1991-2020): a bibliometric review

Dissolved organic matter (DOM) and microbes are key in the planetary carbon cycle, and research on them can lead to a better understanding of the global carbon cycle and an improved ability to cope with environmental challenges. Several papers have reviewed one or several aspects of the interaction of DOM and microbes, but no overall review has been performed. Here, we bibliometrically analyzed all publications from the Web of Science on DOM and microbes (1991-2020). The results showed that studies on DOM and microbes grew exponentially during this period; the USA contributed the most to the total publications, and China has had the fastest increasing rate since 2010. Moreover, we used the Latent Dirichlet Allocation model to identify topics and determine their (cold or hot) trends by analyzing the abstracts of 9851 publications related to DOM and microbes. A total of 96 topics were extracted, and these topics that are related to the source, composition, and removal path of DOM and the temporal-spatial patterns of DOM and microbes consistently rose from 1991 to 2020. Most studies have used accurate and rapid methods combined with microbiological genetic approaches to study the interaction of DOM and microbes in terrestrial and aquatic ecosystems. The results also showed that the impacts of climate change and land use on the interaction of DOM and microbes, and topics related to human health have received considerable attention. In the future, the interaction mechanism of DOM and microbes and its response to environmental change should be further elucidated.