Microbial biotechnology and circular economy in wastewater treatment

The role of carbon and nitrogen ratio on sewage sludge microbiota for producing polyhydroxyalkanoates

The products of an advanced sewage sludge fermentation process can be used to generate polyhydroxyalkanoates (PHAs), precursors of bioplastics considered excellent candidates for replacing petroleum-derived plastics. The aerobic feast-anoxic famine cycling strategy has proven to be an efficient method for enriching sewage sludge microbiota with PHA-producing microorganisms. This work evaluated the effect of different carbon to nitrogen ratios (C/N) of 3.5, 2, and 1 g COD/g N for modulating the structure of sewage sludge microbiota to improve PHA production. The study was executed on a pilot plant scale using wasted activated sludge as an organic carbon source derived from an oxic-settling anaerobic plant that collects wastewater from various facilities at the University of Palermo campus. PHA production performance was monitored over three experimental periods characterized by a different C/N ratio. The results showed that lower C/N ratios reduced PHA production with 20, 24, and 26 % w/w of PHAs for COD/N values of 1, 2, and 3.5 g COD/g N, respectively. In parallel, the metataxonomic analysis revealed a higher abundance of PHA-producing microorganisms at the ratio of 3.5 g COD/g N, such as Proteobacteria, specifically Betaproteobacteria. In addition, the analysis showed an increase in fungal abundance and diversity as decrease the ratio C/N decreased. Thus, these findings demonstrate the utility of metataxonomics in elucidating the relationships between operating conditions, bacterial and fungal microbiota structure and the achievement of specific outputs. The insights gained from this study demonstrated a positive correlation between C/N ratios, PHA-producing microorganisms, and PHA yields.

Advancing environmental biotechnology with microbial community modeling rooted in functional 'omics

Emerging biotechnologies that solve pressing environmental and climate emergencies will require harnessing the vast functional diversity of the underlying microbiomes driving such engineered processes. Modeling is a critical aspect of process engineering that informs system design as well as aids diagnostic optimization of performance. 'Conventional' bioprocess models assume homogenous biomass within functional guilds and thus fail to predict emergent properties of diverse microbial physiologies, such as product specificity and community interactions. Yet, recent advances in functional 'omics-based approaches can provide a 'lens' through which we can probe and measure in situ ecophysiologies of environmental microbiomes. Here, we overview microbial community modeling approaches that incorporate functional 'omics data, which we posit can advance our ability to design and control new environmental biotechnologies going forward.

Biotechnological Innovations Unleashing the Potential of Olive Mill Wastewater in Added-Value Bioproducts

Byproducts and wastes from the food processing industry represent an important group of wastes generated annually in large quantities. It is important to note that the amount of this waste will increase with industrialization, and effective solutions must be found urgently. Many wastes that cause environmental pollution are evaluated by their low-tech conversion into products with little economic value, such as animal feed and fertilizer. Therefore, the evaluation of food processing waste using effective recycling techniques has become an interesting subject with increasing population, ongoing biotechnological studies, and advances in technology. The conversion of food waste into biotechnological products via fermentation is a sustainable, environmentally friendly, and economical method in line with the principles of green chemistry. This approach promotes the reuse of food waste by supporting the principles of a circular economy and offers sustainable alternatives to fossil fuels and synthetic chemicals. This contributes to reducing the carbon footprint, preserving soil and water quality, and providing economic sustainability through the production of high-value products. In this study, the properties of olive mill wastewater, an important and valuable waste in the olive oil industry, its environmental aspects, and its use in biotechnological applications that integrate green chemistry are evaluated.

Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants

BACKGROUND

Microorganisms are responsible for nutrient removal and resource recovery in wastewater treatment plants (WWTPs), and their diversity is often studied by 16S rRNA gene amplicon sequencing. However, this approach underestimates the abundance and diversity of Patescibacteria due to the low coverage of commonly used PCR primers for this highly divergent bacterial phylum. Therefore, our current understanding of the global diversity, distribution, and ecological role of Patescibacteria in WWTPs is very incomplete. This is particularly relevant as Patescibacteria are considered to be associated with microbial host cells and can therefore influence the abundance and temporal variability of other microbial groups that are important for WWTP functioning.

RESULTS

Here, we evaluated the in silico coverage of widely used 16S rRNA gene-targeted primer pairs and redesigned a primer pair targeting the V4 region of bacterial and archaeal 16S rRNA genes to expand its coverage for Patescibacteria. We then experimentally evaluated and compared the performance of the original and modified V4-targeted primers on 565 WWTP samples from the MiDAS global sample collection. Using the modified primer pair, the percentage of ASVs classified as Patescibacteria increased from 5.9 to 23.8%, and the number of detected patescibacterial genera increased from 560 to 1576, while the detected diversity of the remaining microbial community remained similar. Due to this significantly improved coverage of Patescibacteria, we identified 23 core genera of Patescibacteria in WWTPs and described the global distribution pattern of these unusual microbes in these systems. Finally, correlation network analysis revealed potential host organisms that might be associated with Patescibacteria in WWTPs. Interestingly, strong indications were found for an association between Patescibacteria of the Saccharimonadia and globally abundant polyphosphate-accumulating organisms of the genus Ca. Phosphoribacter.

CONCLUSIONS

Our study (i) provides an improved 16S rRNA gene V4 region-targeted amplicon primer pair inclusive of Patescibacteria with little impact on the detection of other taxa, (ii) reveals the diversity and distribution patterns of Patescibacteria in WWTPs on a global scale, and (iii) provides new insights into the ecological role and potential hosts of Patescibacteria in WWTPs. Video Abstract.

Envisioning the innovative approaches to achieve circular economy in the water and wastewater sector

Given the challenges of urbanization and rapid resource depletion, policymakers have been compelled to abandon the old sequential paradigm of "take-make-use-dispose" to a circular approach that prioritizes preservation of natural resources. The circular economy represents a sustainable management concept that focuses on reducing, recovering, reusing, and recycling waste. While significant strides have been made in implementing circular economy principles in various industries such as automotive, electronics, and construction, particular attention has been given to the water and wastewater domains due to imbalances in water resources. Here we review the global progress of circular economy adoptability in the water and wastewater domains, considering technical, environmental, economic, and social perspectives. It assesses the current state of circular economy integration in the wastewater domain worldwide and presents approaches to promote and accelerate its adoption. The study critically examines the principles of waste management, known as the 6Rs (reclaim, restore, recycle, reduce, recover, reuse), in order to formulate effective strategies for integrating circular economy practices in the water and wastewater domains. Additionally, the study provides an overview of existing research conducted on different aspects of circular economy. Finally, the study analyzes the challenges and opportunities associated with implementing circular economy principles in the water sector.

Amplicon-guided isolation and cultivation of previously uncultured microbial species from activated sludge

IMPORTANCE

Biological wastewater treatment relies on complex microbial communities that assimilate nutrients and break down pollutants in the wastewater. Knowledge about the physiology and metabolism of bacteria in wastewater treatment plants (WWTPs) may therefore be used to improve the efficacy and economy of wastewater treatment. Our current knowledge is largely based on 16S rRNA gene amplicon profiling, fluorescence in situ hybridization studies, and predictions based on metagenome-assembled genomes. Bacterial isolates are often required to validate genome-based predictions as they allow researchers to analyze a specific species without interference from other bacteria and with simple bulk measurements. Unfortunately, there are currently very few pure cultures representing the microbes commonly found in WWTPs. To address this, we introduce an isolation strategy that takes advantage of state-of-the-art microbial profiling techniques to uncover suitable growth conditions for key WWTP microbes. We furthermore demonstrate that this information can be used to isolate key organisms representing global WWTPs.

Re-flocculation reduces the effectiveness of sewage sludge pretreatment through hydrodynamic disintegration prior to anaerobic digestion

Circular economy model, based on the "make, use, reuse, remake, recycle" approach, is an alternative to progressive depletion of non-renewable fossil fuels. Sewage sludge can be a source of renewable energy obtained through the anaerobic conversion of their organic fraction into biogas. This process is mediated by highly complex microbial communities and its efficiency depends on the availability of substrates to microorganisms. Disintegration of the feedstock in the pre-treatment step may intensify the anaerobic digestion, but re-flocculation of disintegrated sludge (reassembly of the released fractions into larger agglomerates) may result in a reduced availability of the released organic compounds for microbes. Pilot-scale studies on re-flocculation of disintegrated sludge were conducted to select parameters for scaling-up the pre-treatment and intensifying the anaerobic digestion process in two large Polish wastewater treatment plants (WWTPs). Samples of thickened excess sludge from full-scale WWTPs were subjected to hydrodynamic disintegration at three energy density levels of 10 kJ/L, 35 kJ/L and 70 kJ/L. Microscopic analyses of disintegrated sludge samples were carried out twice: i) immediately after the disintegration process at a given energy density level, ii) and after 24-h incubation at 4 °C following the disintegration. Micro-photographs of 30 randomly selected fields of view were taken for each analysed sample. A method of the image analysis was developed as a tool to measure dispersion of sludge flocs to assess the re-flocculation degree. Re-flocculation of the thickened excess sludge occurred within 24 h after hydrodynamic disintegration. This was evidenced by a very high re-flocculation degree, reaching up to 86%, depending on the origin of the sludge and the energy density levels used for the hydrodynamic disintegration.

Weaponising microbes for peace

There is much human disadvantage and unmet need in the world, including deficits in basic resources and services considered to be human rights, such as drinking water, sanitation and hygiene, healthy nutrition, access to basic healthcare, and a clean environment. Furthermore, there are substantive asymmetries in the distribution of key resources among peoples. These deficits and asymmetries can lead to local and regional crises among peoples competing for limited resources, which, in turn, can become sources of discontent and conflict. Such conflicts have the potential to escalate into regional wars and even lead to global instability. Ergo: in addition to moral and ethical imperatives to level up, to ensure that all peoples have basic resources and services essential for healthy living and to reduce inequalities, all nations have a self-interest to pursue with determination all available avenues to promote peace through reducing sources of conflicts in the world. Microorganisms and pertinent microbial technologies have unique and exceptional abilities to provide, or contribute to the provision of, basic resources and services that are lacking in many parts of the world, and thereby address key deficits that might constitute sources of conflict. However, the deployment of such technologies to this end is seriously underexploited. Here, we highlight some of the key available and emerging technologies that demand greater consideration and exploitation in endeavours to eliminate unnecessary deprivations, enable healthy lives of all and remove preventable grounds for competition over limited resources that can escalate into conflicts in the world. We exhort central actors: microbiologists, funding agencies and philanthropic organisations, politicians worldwide and international governmental and non-governmental organisations, to engage - in full partnership - with all relevant stakeholders, to 'weaponise' microbes and microbial technologies to fight resource deficits and asymmetries, in particular among the most vulnerable populations, and thereby create humanitarian conditions more conducive to harmony and peace.

Hydrodynamic disintegration of thickened excess sludge and maize silage to intensify methane production: Energy effect and impact on microbial communities

The aim of this project was to study the combination of two methods to increase methane production: feedstock pretreatment by hydrodynamic disintegration and co-digestion of maize silage (MS) with thickened excess sludge (TES). Disintegration of TES alone resulted in a 15% increase in specific methane production from 0.192 Nml/gVS (TES + MS) to 0.220 Nml/gVS (pretreated TES + MS). The energy balance revealed additional energy (0.14 Wh) would cover only the energy expenditure for the mechanical pretreatment and would not allow for net energy profit. Identification of the methanogenic consortia by 16S rRNA gene amplicon sequencing revealed that Chloroflexi, Bacteroidota, Firmicutes, Proteobacteria and Actinobacteriota were five most abundant bacteria phyla, with Methanothrix and Methanolinea as the dominant methanogens. Principal component analysis did not show any effect of feedstock pretreatment on methanogenic consortia. Instead, the composition of inoculum was the decisive factor in shaping the microbial community structure.

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

Introduction

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

Methods

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

Results

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

Discussion

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

Metagenomic binning with assembly graph embeddings

MOTIVATION

Despite recent advancements in sequencing technologies and assembly methods, obtaining high-quality microbial genomes from metagenomic samples is still not a trivial task. Current metagenomic binners do not take full advantage of assembly graphs and are not optimized for long-read assemblies. Deep graph learning algorithms have been proposed in other fields to deal with complex graph data structures. The graph structure generated during the assembly process could be integrated with contig features to obtain better bins with deep learning.

RESULTS

We propose GraphMB, which uses graph neural networks to incorporate the assembly graph into the binning process. We test GraphMB on long-read datasets of different complexities, and compare the performance with other binners in terms of the number of High Quality (HQ) genome bins obtained. With our approach, we were able to obtain unique bins on all real datasets, and obtain more bins on most datasets. In particular, we obtained on average 17.5% more HQ bins when compared with state-of-the-art binners and 13.7% when aggregating the results of our binner with the others. These results indicate that a deep learning model can integrate contig-specific and graph-structure information to improve metagenomic binning.

AVAILABILITY AND IMPLEMENTATION

GraphMB is available from https://github.com/MicrobialDarkMatter/GraphMB.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Circular Economy Framework for Energy Recovery in Phytoremediation of Domestic Wastewater

Circular economy (CE) strategy is crucial in developing towards sustainable growth. It was created to promote resource utilization and the elimination of waste production. This article aimed to study the possibilities of using the CE framework in wastewater bioremediation and energy recovery using hydroponic tanks. The integration of phytoremediation with bioenergy, construction and lifespan of hydroponic tanks in phytoremediation of wastewater, selection of aquatic plants and the expected challenges in the implementation of CE in phytoremediation of wastewater were discussed. The plant-based biomass harvested and the relative growth rate (RGR) of the selected plants from the phytoremediation process was evaluated. The findings obtained indicated that the selected plants tripled in weight after 14 days cultivation period at different retention times. E. crassipes recorded the highest growth with 2.5 ± 0.03 g g−1 d−1, followed by S. molesta with 1.33 ± 0.05 g g−1 d−1 and then P. stratiotes recorded 0.92 ± 0.27 g g−1 d−1 at the end of the cultivation period. Therefore, the selected plants have been identified as having the potential to be used in phytoremediation as well as a source of energy production. The outcome of our review suggested the adoption of a lifecycle assessment as the CE framework for the phytoremediation of wastewater.

MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants

Microbial communities are responsible for biological wastewater treatment, but our knowledge of their diversity and function is still poor. Here, we sequence more than 5 million high-quality, full-length 16S rRNA gene sequences from 740 wastewater treatment plants (WWTPs) across the world and use the sequences to construct the ‘MiDAS 4’ database. MiDAS 4 is an amplicon sequence variant resolved, full-length 16S rRNA gene reference database with a comprehensive taxonomy from domain to species level for all sequences. We use an independent dataset (269 WWTPs) to show that MiDAS 4, compared to commonly used universal reference databases, provides a better coverage for WWTP bacteria and an improved rate of genus and species level classification. Taking advantage of MiDAS 4, we carry out an amplicon-based, global-scale microbial community profiling of activated sludge plants using two common sets of primers targeting regions of the 16S rRNA gene, revealing how environmental conditions and biogeography shape the activated sludge microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 966 genera and 1530 species that represent approximately 80% and 50% of the accumulated read abundance, respectively. Finally, we show that for well-studied functional guilds, such as nitrifiers or polyphosphate-accumulating organisms, the same genera are prevalent worldwide, with only a few abundant species in each genus.

Microbial communities are responsible for biological wastewater treatment. Here, Dueholm et al. generate more than 5 million high-quality, full-length 16S rRNA gene sequences from wastewater treatment plants across the world to construct a database with a comprehensive taxonomy, providing insights into diversity and function of these microbial communities.

Decentralized high-strength wastewater treatment using a compact aerobic baffled bioreactor

Decentralized wastewater treatment is a potential solution to the economic and sustainability issues associated with current wastewater infrastructure requirements for rural and expanding urban settings. However, wastewater produced from small-scale operations (domestic, industrial, agricultural, defense, etc.) are often found to have higher pollution concentrations than municipal wastewater and is referred to as "blackwater" in the study. A baffled bioreactor (BBR) was employed to carry out blackwater treatment. The results of this study showed the removal of organic content and inorganic nitrogen was high in all of the feed amounts tested and increased corresponding to an increase in feed amount. Microbial diversity results supported that the feed amount was the most important factor in treatment performance. The microbial community was more diverse at higher feed amounts than lower feed amounts. A non-metric multidimensional scaling (NMDS) analysis revealed that higher feed amounts enriched Verrucomicrobiaceae, unclassified Sphingomonadales, unclassified Burkholderiales in the microbial community, and facilitated the removal of total solids, total nitrogen, and NO₃^-. The energy and exergy analyses showed the consumption of 5.02 Wh/L wastewater energy with a universal exergy efficiency of 61% at the feed amount of 3750 LPD. An economic analysis further delineated the treatment cost profiles of the decentralized unit under four different energy case scenarios of electricity from the grid, propane gas engine for remote rural communities, diesel engine (I) using standard U.S. market diesel fuel costs for remote rural communities and scientific research bases, and diesel engine (II) using the fully burdened cost of diesel fuel for military contingency bases and other extreme environmental scenarios.

Roadmapping the Transition to Water Resource Recovery Facilities: The Two Demonstration Case Studies of Corleone and Marineo (Italy)

The current exploitation of freshwater, as well as the significant increase in sewage sludge production from wastewater treatment plants (WWTPs), represent nowadays a critical issue for the implementation of sustainable development consistent with the circular economy concept. There is an urgent need to rethink the concept of WWTPs from the conventional approach consisting in pollutant removal plants to water resource recovery facilities (WRRFs). The aim of this paper is to provide an overview of the demonstration case studies at the Marineo and Corleone WRRFs in Sicily (IT), with the final aim showing the effectiveness of the resources recovery systems, as well as the importance of plant optimization to reduce greenhouse gas (GHG) emissions from WRRFs. This study is part of the H2020 European Project “Achieving wider uptake of water-smart solutions—Wider-Uptake”, which final aim is to demonstrate the water-smart solution feasibility in the wastewater sector. The main project goal is to overcome the existing barriers that hamper the transition to circularity through the implementation of a governance analysis tool. The preliminary actions in the two demonstration cases are first presented, while, subsequently, the water-smart solutions to be implemented are thoroughly described, highlighting their roles in the transition process. The achieved preliminary results underlined the significant potential of WRRF application, a great chance to demonstrate the feasibility of innovative solutions in the wastewater sector to overcome the existing social, administrative and technical barriers.

Resource recovery from industrial effluents through the cultivation of microalgae: A review

Industrial effluents such as pharmaceutical residues, pesticides, dyes, and metal processes holds abundant value-added products (VAPs), where its recovery has become essential. The purpose of such recovery is for sustainable treatment, which is an approach that considers the economic, social, and environmental aspects. Microalgae with its potential in the recovery process from effluents, can reduce energy usage of waste management strategies and regenerate nutrients such as carbon, phosphorus, and nitrogen. Microalgae cultures offer the use of inorganic materials by microalgae for their growth and the help of bacteria to produce biomass, thus, resulting in the absence of secondary emissions due to its ability to eliminate volatile organic compounds. Moreover, recovered bioactive compounds are transformed into bioethanol, bio-fertilizers, biopolymer, health supplements and animal feed. Therefore, it is significant to focus on an economical and efficient utilization of microalgae in recovering nutrients that can be further used in various commercial applications.

High Diversity and Functional Potential of Undescribed "Acidobacteriota" in Danish Wastewater Treatment Plants

Microbial communities in water resource recovery facilities encompass a large diversity of poorly characterized lineages that could have undescribed process-critical functions. Recently, it was shown that taxa belonging to "Acidobacteriota" are abundant in Danish full-scale activated sludge wastewater treatment plants (WWTP), and here we investigated their diversity, distribution, and functional potential. "Acidobacteriota" taxa were identified using a comprehensive full-length 16S rRNA gene reference dataset and amplicon sequencing surveys across 37 WWTPs. Members of this phylum were diverse, belonging to 14 families, eight of which are completely uncharacterized and lack type strains. Several lineages were abundant, with relative abundances of up to 5% of the microbial community. Genome annotation and metabolic reconstruction of 50 high-quality "Acidobacteriota" metagenome-assembled genomes (MAGs) from 19 WWTPs showed high metabolic diversity and potential involvement in nitrogen and phosphorus removal and iron reduction. Fluorescence in situ hybridization (FISH) using newly-designed probes revealed cells with diverse morphologies, predominantly located inside activated sludge flocs. FISH in combination with Raman microspectroscopy revealed ecophysiological traits in probe-defined cells from the families Holophagaceae, Thermoanaerobaculaceae, and Vicinamibacteraceae, and families with the placeholder name of midas_f_502, midas_f_973, and midas_f_1548. Members of these lineages had the potential to be polyphosphate-accumulating organisms (PAOs) as intracellular storage was observed for the key compounds polyphosphate and glycogen.

Characterizing the growing microorganisms at species level in 46 anaerobic digesters at Danish wastewater treatment plants: A six-year survey on microbial community structure and key drivers

Anaerobic digestion (AD) is a key technology at many wastewater treatment plants (WWTPs) for converting primary and surplus activated sludge to methane-rich biogas. However, the limited number of surveys and the lack of comprehensive datasets have hindered a deeper understanding of the characteristics and associations between key variables and the microbial community composition. Here, we present a six-year survey of 46 anaerobic digesters, located at 22 WWTPs in Denmark, which is the first and largest known study of the microbial ecology of AD at WWTPs at a regional scale. For three types of AD (mesophilic, mesophilic with thermal hydrolysis pretreatment, and thermophilic), we present the typical value range of 12 key parameters including operational variables and performance parameters. High-resolution bacterial and archaeal community analyses were carried out at species level using amplicon sequencing of >1,000 samples and the new ecosystem-specific MiDAS 3 reference database. We detected 42 phyla, 1,600 genera, and 3,584 species in the bacterial community, where 70% of the genera and 93% of the species represented environmental taxa that were only classified based on MiDAS 3 de novo placeholder taxonomy. More than 40% of the bacterial species were found not to grow in the mesophilic and thermophilic digesters and were only present due to immigration with the feed sludge. Ammonium concentration was the main driver shaping the bacterial community while temperature and pH were main drivers for the archaea in the three types of ADs. Sub-setting for the growing microbes improved significantly the correlation analyses and revealed the main drivers for the presence of specific species. Within mesophilic digesters, feed sludge composition and other key parameters (organic loading rate, biogas yield, and ammonium concentration) correlated with specific growing species. This survey provides a comprehensive insight into community structure at species level, providing a foundation for future studies of the ecological significance/characteristics and function of the many novel or poorly described taxa.

Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing

Microorganisms play crucial roles in water recycling, pollution removal and resource recovery in the wastewater industry. The structure of these microbial communities is increasingly understood based on 16S rRNA amplicon sequencing data. However, such data cannot be linked to functional potential in the absence of high-quality metagenome-assembled genomes (MAGs) for nearly all species. Here, we use long-read and short-read sequencing to recover 1083 high-quality MAGs, including 57 closed circular genomes, from 23 Danish full-scale wastewater treatment plants. The MAGs account for ~30% of the community based on relative abundance, and meet the stringent MIMAG high-quality draft requirements including full-length rRNA genes. We use the information provided by these MAGs in combination with >13 years of 16S rRNA amplicon sequencing data, as well as Raman microspectroscopy and fluorescence in situ hybridisation, to uncover abundant undescribed lineages belonging to important functional groups.

Enhancing a Transition to a Circular Economy in the Water Sector: The EU Project WIDER UPTAKE

Wastewater treatment plants (WWTPs) require an urgent transition from a linear to a circular economy operation/design concept with a consequent resource recovery and more sustainable waste management. Natural resources have to be preserved, and wastes have to become an opportunity for recovering resources and materials (water reuse, energy, sludge reuse). However, the transition toward a circular economy is a complex and long process due to the existence of technical, economic, social and regulatory barriers. These existing barriers are critical challenges for a modern and sustainable WWTP concept. The recovery of resources must be considered a strategic target from the earliest process-design phase. In this context, the European Union’s Horizon 2020 project “Achieving wider uptake of water-smart solutions—WIDER UPTAKE” aims to overcome the existing barriers (technological, regulatory, organizational, social and economic) toward the transition from a linear to a circular economy model for WWTPs. This study is aimed at increasing the awareness of the existing barriers to a circular economy and summarizes the key contributions of the WIDER UPTAKE project in terms of water reuse, sludge reuse and nutrient recovery.

Microbial invasions in sludge anaerobic digesters

Among processes that control microbial community assembly, microbial invasion has received little attention until recently, especially in the field of anaerobic digestion. However, knowledge of the principles regulating the taxonomic and functional stability of microbial communities is key to truly develop better predictive models and effective management strategies for the anaerobic digestion process. To date, available studies focus on microbial invasions in digesters feed with activated sludge from municipal wastewater treatment plants. Herein, this review summarizes the importance of invasions for anaerobic digestion management, the ecological theories about microbial invasions, the traits of activated sludge microorganisms entering the digesters, and the resident communities of anaerobic reactors that are relevant for invasions and the current knowledge about the success and impacts of invasions, and discusses the research needs on this topic. The initial data indicate that the impact of invasions is low and only a small percentage of the mostly aerobic microorganisms present in the activated sludge feed are able to become stablished in the anaerobic digesters. However, there are still numerous unknowns about microbial invasions in anaerobic digestion including the influence of anaerobic feedstocks or process perturbances that new approaches on microbial ecology could unveil. KEY POINTS: • Microbial invasions are key processes to develop better strategies for digesters management. • Knowledge on pathogen invasions can improve anaerobic digestion microbial safety. • To date, the number of successful invasions on anaerobic digesters from activated sludge organisms is low. • Feed organisms detected in digesters are mostly inactive residual populations. • Need to expand the range of invaders and operational scenarios studied.

Review of Circular Economy in urban water sector: Challenges and opportunities in India

Increasing urbanization and rapid depletion of resources have forced authorities to shift from traditional linear system of take-make-use-dispose to circular system of resource conservation. Circular Economy (CE) is a sustainable development approach that works on the waste management strategy of reduce, reuse, recycle, and recover. Considerable work has been performed on CE in various sectors such as in electronic sector, construction sector, automotive sector, etc. However, CE in the water sector is gaining rapid attention, because of imbalance in water resources and the prevailing linear approach. The aim of this study is to review the world-wide growth of CE concept in the water sector from an economic, environmental, social, and technical perspective. 98 publications were selected by systematic literature review and categorized in economic, environmental, social, and technical criteria including a combination of multiple criteria. In this study, the world-wide status of CE implementation in the water sector is assessed and strategies to encourage and enhance CE implementation are proposed. The six BS8001:2017 principles and 6Rs (reduce, reuse, recycle, reclaim, recover, restore) of waste management are critically analyzed for deriving recommendations and successful implementation of CE in water sector. Finally, challenges and opportunities to implement CE in the water sector in India are discussed.

MiDAS 3: An ecosystem-specific reference database, taxonomy and knowledge platform for activated sludge and anaerobic digesters reveals species-level microbiome composition of activated sludge

The function of the microbiomes in wastewater treatment systems and anaerobic digesters is dictated by the physiological activity of their members and complex interactions between them. Since functional traits are often conserved at low taxonomic ranks (genus, species, strain), high resolution taxonomic classification is crucial to understand the role of microbes in any ecosystem. Here we present MiDAS 3, a comprehensive 16S rRNA gene reference database based on full-length 16S rRNA gene amplicon sequence variants (FL-ASVs) derived from activated sludge and anaerobic digester systems in Denmark. The new database proposes unique provisional names for all unclassified microorganisms down to species level, providing a new and much-needed tool for microbiome research. The MiDAS 3 database was used to analyze the microbiome in 20 Danish wastewater treatment plants with nutrient removal, sampled over 13 years. The 50 most abundant species belonged to 42 genera, including 14 genera with provisional 'midas' name. Of those, 20 have no known function in the system, which highlights the need for more efforts towards elucidating the role of important members of wastewater treatment ecosystems. The new MiDAS 3 database also forms the backbone of the MiDAS Field Guide - an online resource linking the identity of microorganisms in wastewater treatment systems to available data related to their functional importance. The new field guide contains a complete list of genera (>1800) and species (>4200) found in activated sludge and anaerobic digesters in Denmark, but is also relevant to wastewater systems across the world. The identity of the microbes is linked to functional information, where available, and the website provides the possibility to BLAST new sequences against the MiDAS 3 database. The MiDAS Field Guide is a collaborative platform acting as an online knowledge repository, facilitating understanding of wastewater treatment ecosystem function.

Visualizing the invisible: class excursions to ignite children's enthusiasm for microbes

We have recently argued that, because microbes have pervasive - often vital - influences on our lives, and that therefore their roles must be taken into account in many of the decisions we face, society must become microbiology-literate, through the introduction of relevant microbiology topics in school curricula (Timmis et al. 2019. Environ Microbiol 21: 1513-1528). The current coronavirus pandemic is a stark example of why microbiology literacy is such a crucial enabler of informed policy decisions, particularly those involving preparedness of public-health systems for disease outbreaks and pandemics. However, a significant barrier to attaining widespread appreciation of microbial contributions to our well-being and that of the planet is the fact that microbes are seldom visible: most people are only peripherally aware of them, except when they fall ill with an infection. And it is disease, rather than all of the positive activities mediated by microbes, that colours public perception of 'germs' and endows them with their poor image. It is imperative to render microbes visible, to give them life and form for children (and adults), and to counter prevalent misconceptions, through exposure to imagination-capturing images of microbes and examples of their beneficial outputs, accompanied by a balanced narrative. This will engender automatic mental associations between everyday information inputs, as well as visual, olfactory and tactile experiences, on the one hand, and the responsible microbes/microbial communities, on the other hand. Such associations, in turn, will promote awareness of microbes and of the many positive and vital consequences of their actions, and facilitate and encourage incorporation of such consequences into relevant decision-making processes. While teaching microbiology topics in primary and secondary school is key to this objective, a strategic programme to expose children directly and personally to natural and managed microbial processes, and the results of their actions, through carefully planned class excursions to local venues, can be instrumental in bringing microbes to life for children and, collaterally, their families. In order to encourage the embedding of microbiology-centric class excursions in current curricula, we suggest and illustrate here some possibilities relating to the topics of food (a favourite pre-occupation of most children), agriculture (together with horticulture and aquaculture), health and medicine, the environment and biotechnology. And, although not all of the microbially relevant infrastructure will be within reach of schools, there is usually access to a market, local food store, wastewater treatment plant, farm, surface water body, etc., all of which can provide opportunities to explore microbiology in action. If children sometimes consider the present to be mundane, even boring, they are usually excited with both the past and the future so, where possible, visits to local museums (the past) and research institutions advancing knowledge frontiers (the future) are strongly recommended, as is a tapping into the natural enthusiasm of local researchers to leverage the educational value of excursions and virtual excursions. Children are also fascinated by the unknown, so, paradoxically, the invisibility of microbes makes them especially fascinating objects for visualization and exploration. In outlining some of the options for microbiology excursions, providing suggestions for discussion topics and considering their educational value, we strive to extend the vistas of current class excursions and to: (i) inspire teachers and school managers to incorporate more microbiology excursions into curricula; (ii) encourage microbiologists to support school excursions and generally get involved in bringing microbes to life for children; (iii) urge leaders of organizations (biopharma, food industries, universities, etc.) to give school outreach activities a more prominent place in their mission portfolios, and (iv) convey to policymakers the benefits of providing schools with funds, materials and flexibility for educational endeavours beyond the classroom.

Oxidative dehalogenation and denitration by a flavin-dependent monooxygenase is controlled by substrate deprotonation

Enzymes that are capable of detoxifying halogenated phenols (HPs) and nitrophenols (NPs) are valuable for bioremediation and waste biorefining. HadA monooxygenase was found to perform dual functions of oxidative dehalogenation (hydroxylation plus halide elimination) and denitration (hydroxylation plus nitro elimination). Rate constants associated with individual steps of HadA reactions with phenol, halogenated phenols and nitrophenols were measured using combined transient kinetic approaches of stopped-flow absorbance/fluorescence and rapid-quench flow techniques. Density functional theory was used to calculate the thermodynamic and electronic parameters associated with hydroxylation and group elimination steps. These parameters were correlated with the rate constants of hydroxylation, group elimination, and overall product formation to identify factors controlling individual steps. The results indicated that the hydroxylation rate constant is higher when the pK a of the phenolic group is lower, i.e. it is more easily deprotonated, but not higher when the energy gap between the E LUMO of the C4a-hydroperoxy-FAD intermediate and the E HOMO of the phenolate substrate is lower. These data suggest that the substrate deprotonation has a higher energy barrier than the -OH transfer, and thus controls the hydroxylation step. For the group elimination, the process is controlled by the ability of the C-X bond to break. For the overall product formation (hydroxylation and group elimination combined), this analysis showed that the rate constant of product formation is dependent on the pK a value of the substrate, indicating that the overall reaction is controlled by substrate deprotonation. This step also likely has the highest energy barrier and thus controls the overall process of oxidative dehalogenation and denitration by HadA. This report is the first to identify a key mechanistic factor controlling the enzymatic processes of oxidative dehalogenation and denitration.

Microbial biotechnology and circular economy in wastewater treatment

Microbial biotechnology is essential for the development of circular economy in wastewater treatment by integrating energy production and resource recovery into the production of clean water. A comprehensive knowledge about identity, physiology, ecology, and population dynamics of process‐critical microorganisms will improve process stability, reduce CO2 footprints, optimize recovery and bioenergy production, and help finding new approaches and solutions. Examples of research needs and perspectives are provided, demonstrating the great importance of microbial biotechnology.