Ecophysiology of the Actinobacteria in activated sludge systems

Temporal metagenomic characterization of microbial community structure and nitrogen modification genes within an activated sludge bioreactor system

IMPORTANCE

Wastewater treatment plays an essential role in minimizing negative impacts on downstream aquatic environments. Microbial communities are known to play a vital role in the wastewater treatment process, particularly in the removal of nitrogen and phosphorus, which can be especially damaging to aquatic ecosystems. There is limited understanding of how these microbial communities may change in response to fluctuating temperatures or how seasonality may impact their ability to participate in the treatment process. The findings of this study indicate that the microbial communities of wastewater are relatively stable both compositionally and functionally across fluctuating temperatures.

Effects of macrophytes on micro - And nanoplastic retention and cycling in constructed wetlands

Macrophytes play the important roles in purifying pollutants of constructed wetlands (CWs), while their effects on CWs exposed to micro/nano plastics are not clear. Therefore, planted and unplanted CWs were established to reveal the impacts of macrophytes (Iris pseudacorus) on the overall performance of CWs under polystyrene micro/nano plastics (PS MPs/NPs) exposure. Results showed that macrophytes effectively enhanced the interception capacities of CWs to PS NPs, and significantly promoted the removal of nitrogen and phosphorus after exposed to PS MPs/NPs. Meanwhile, macrophytes improved the activities of dehydrogenase, urease, and phosphatase. Sequencing analysis showed that macrophytes optimized the composition of microbial communities in CWs and stimulated the growth of functional bacteria involved in nitrogen and phosphorus transformation. Moreover, macrophytes further altered the absolute abundance of nitrogen transformation functional genes (amoA, nxrA, narG and nirS). Functional annotation analysis revealed that macrophytes promoted metabolic functions such as Xenobiotics, Amino acids, Lipids metabolism and Signal transduction, ensuring the metabolic balance and homeostasis of microbes under PS MPs/NPs stress. These results exhibited profound implications for the comprehensive evaluation on the roles of macrophytes in CWs for treating wastewater containing PS MPs/NPs.

Exploring the microbiome, antibiotic resistance genes, mobile genetic element, and potential resistant pathogens in municipal wastewater treatment plants in Brazil

Wastewater treatment plants (WWTPs) have been widely investigated in Europe, Asia and North America regarding the occurrence and fate of antibiotic resistance (AR) elements, such as antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and antibiotic resistant bacteria and pathogens. However, monitoring data about AR elements in municipal WWTPs in Brazil are scarce. This study investigated the abundance of intI1, five ARGs (sul1, tetA, blaTEM, ermB and qnrB) and 16S rRNA in raw and treated wastewater of three WWTPs, using different sewage treatments named CAS (Conventional activated sludge), UASB/BTF (UASB followed by biological trickling filter) and MAS/UV (modified activated sludge with UV disinfection stage). Bacterial diversity and the presence of potentially pathogenic groups were also evaluated, and associations between genetic markers and the bacterial populations were presented. All WWTPs decreased the loads of genetic markers finally discharged to receiving water bodies and showed no evidence of being hotspots for antimicrobial resistance amplification in wastewater, since the abundances of intI1 and ARGs within the bacterial population were not increased in the treated effluents. UASB/BTF showed a similar performance to that of the CAS and MAS/UV, reinforcing the sanitary and environmental advantages of this biological treatment, widely applied for wastewater treatment in warm climate regions. Bacterial diversity and richness increased after treatments, and bacterial communities in wastewater samples differed due to catchment areas and treatment typologies. Potential pathogenic population underwent considerable decrease after the treatments; however, strong significant correlations with intI1 and ARGs revealed potential multidrug-resistant pathogenic bacteria (Aeromonas, Arcobacter, Enterobacter, Escherichia-Shigella, Stenotrophomonas and Streptococcus) in the treated effluents, although in reduced relative abundances. These are contributive results for understanding the fate of ARGs, MGEs and potential pathogenic bacteria after wastewater treatments, which might support actions to mitigate their release into Brazilian aquatic environments in the near future.

Enhanced biological phosphorus removal in aerobic granular sludge reactors by granular activated carbon dosing

This study investigated the effects of granular activated carbon (GAC) addition on the enrichment of polyphosphate accumulating organisms (PAOs), stratification of PAOs in the co-existing GAC-biofilms and granules and biological nutrient removal (BNR) in aerobic granular sludge (AGS) reactors. It was found that BNR increased in the GAC-augmented system. Establishment of enhanced biological phosphorus removal (EBPR) pathway was faster with about 1.7 to 2-fold higher P removal in GAC system than control. EBPR biomass grown in the presence of GAC was segregated into different size fractions for determining BNR and stratification of microbial groups. It was found that EBPR was majorly associated with the large biomass (>0.5 mm) fraction, corroborating with higher abundance of PAOs. Higher P removals of 60 to 70% with characteristic EBPR profiles were observed in 0.5 mm fraction. In contrast, P removals by 0.25 mm fraction were lower at 20 to 35% without EBPR profiles. EBPR biomass (>0.5 mm) fraction was segregated into granules and GAC-biofilms for determining the role of GAC in PAOs enrichment. P release (2.5-3.5 mg L^-1 P) and P uptake (5-7 mg L^-1 P) were higher in the P removal profiles exhibited by GAC-biofilms. In contrast, P release and P uptake were lower with the granules. These differences in P removal profiles resulted in distinct net P removal efficiencies of 70 ± 5% and 50 ± 6% for GAC-biofilms and granules, respectively. These differences in P removals were corroborated by higher abundance of PAOs in the GAC-biofilms than co-existing granules. PAO clade-level enrichment was found to be dependent on substrate wherein acetate feeding enriched PAO clade I, while acetate-propionate feeding caused enrichment of both PAO clade I and II. These results suggest that GAC addition to AGS reactors can aid in enrichment of PAOs, reduce the start-up period for EBPR, and increase P removal efficiencies.

Actinobacteria isolated from wastewater treatment plants located in the east-north of Algeria able to degrade pesticides

The pollution of water resources by pesticides poses serious problems for public health and the environment. In this study, Actinobacteria strains were isolated from three wastewater treatment plants (WWTPs) and were screened for their ability to degrade 17 pesticide compounds. Preliminary screening of 13 of the isolates of Actinobacteria allowed the selection of 12 strains with potential for the degradation of nine different pesticides as sole carbon source, including aliette, for which there are no previous reports of biodegradation. Evaluation of the bacterial growth and degradation kinetics of the pesticides 2,4-dichlorophenol (2,4-DCP) and thiamethoxam (tiam) by selected Actinobacteria strains was performed in liquid media. Strains Streptomyces sp. ML and Streptomyces sp. OV were able to degrade 45% of 2,4-DCP (50 mg/l) as the sole carbon source in 30 days and 84% of thiamethoxam (35 mg/l) in the presence of 10 mM of glucose in 18 days. The biodegradation of thiamethoxam by Actinobacteria strains was reported for the first time in this study. These strains are promising for use in bioremediation of ecosystems polluted by this type of pesticides.

Bacterial diversity evolution process based on physicochemical characteristics of sludge treating hydroquinone during acclimation

Hydroquinone is one of the main pollutants in coal-gasification wastewater, which is biologically toxic and difficult to remove. The aerobic biodegradation rate, organic toxicity, and microbial community structure at different acclimation stages of degradation of hydroquinone by activated sludge were investigated. In each acclimation cycle, the removal of hydroquinone reached 100% after 5 days, indicating that high-concentration hydroquinone in the activated sludge could be completely biodegraded. When the microbial flora was inhibited by the influent hydroquinone, the enzyme system experienced stress conditions and led to the secretion of secondary metabolites, extracellular protein of 5-10 kDa mainly contributing to the sludge organic toxicity. Microbial diversity analysis showed that with the increase of the concentration of hydroquinone, β-Proteus bacteria such as Azoarcus and Dechloromonas gradually accumulated, which improved the removal of hydroquinone with aerobic activated sludge in the sequencing batch reactor (SBR) system. As the inhibition degree exceeded the appropriate tolerance range of microorganisms, bacteria would secrete much more secondary metabolites, and the organic toxicity of sludge would reach a relatively high level.

Predation increases multiple components of microbial diversity in activated sludge communities

Protozoan predators form an essential component of activated sludge communities that is tightly linked to wastewater treatment efficiency. Nonetheless, very little is known how protozoan predation is channelled via bacterial communities to affect ecosystem functioning. Therefore, we experimentally manipulated protozoan predation pressure in activated-sludge communities to determine its impacts on microbial diversity, composition and putative functionality. Different components of bacterial diversity such as taxa richness, evenness, genetic diversity and beta diversity all responded strongly and positively to high protozoan predation pressure. These responses were non-linear and levelled off at higher levels of predation pressure, supporting predictions of hump-shaped relationships between predation pressure and prey diversity. In contrast to predation intensity, the impact of predator diversity had both positive (taxa richness) and negative (evenness and phylogenetic distinctiveness) effects on bacterial diversity. Furthermore, predation shaped the structure of bacterial communities. Reduction in top-down control negatively affected the majority of taxa that are generally associated with increased treatment efficiency, compromising particularly the potential for nitrogen removal. Consequently, our findings highlight responses of bacterial diversity and community composition as two distinct mechanisms linking protozoan predation with ecosystem functioning in activated sludge communities.

Identification of key microorganisms in facultative stabilization ponds from dairy industries, using metagenomics

Wastewater stabilization ponds are a natural form of wastewater treatment. Their low operation and maintenance costs have made them popular, especially in developing countries. In these systems, effluents are retained for long periods of time, allowing the microbial communities present in the ponds to degrade the organic matter present, using both aerobic and anaerobic processes. Even though these systems are widespread in low income countries, there are no studies about the microorganisms present in them and how they operate. In this study, we analised the microbial communities of two serial full-scale stabilization ponds systems using whole genome shotgun sequencing. First, a taxonomic profiling of the reads was performed, to estimate the microbial diversity. Then, the reads of each system were assembled and binned, allowing the reconstruction of 110 microbial genomes. A functional analysis of the genomes allowed us to find how the main metabolic pathways are carried out, and we propose several organisms that would be key to this kind of environment, since they play an important role in these metabolic pathways. This study represents the first genome-centred approach to understand the metabolic processes in facultative ponds. A better understanding of these microbial communities and how they stabilize the effluents of dairy industries is necessary to improve them and to minimize the environmental impact of dairy industries wastewater.

Effect of prolonged sludge retention times on the performance of membrane bioreactor and microbial community for leachate treatment under restricted aeration

Leachate treatment is challenging owing to the complex composition of pollutants. This study investigated the treatment performance of a membrane bioreactor (MBR) and the microbial community structure corresponding to the effect of prolonged sludge retention times (SRTs) under restricted aeration. In the present study, a pilot-scale MBR was designed to treat leachate after being pretreated with an anaerobic filter for continuous operation for 240 days. The experimental results showed that removal performance of over 90% was achieved for biochemical oxygen demand, total Kjeldahl nitrogen, ammonia-nitrogen, and suspended solids when the MBR was operated at SRTs of 150-300 days. The results on microbial communities revealed that Proteobacteria, Bacteroidetes, Firmicutes, Planctomycetes, Chloroflexi, and Actinobacteria were the major phyla. Furthermore, ammonia-oxidizing bacteria belonging to Nitrosomonadaceae were considered to play a vital role in the ammonia-nitrogen removal. A high abundance of Rhizobiales was detected on the biofilm of the membrane, which could be the key driver of bio-fouling. The dynamic changes in the microbial community indicate steady performance of MBR and can act as an indicator of membrane bio-fouling. The results of our study highlight that MBR can be viably operated in long SRTs under restricted aeration for leachate treatment with technical, economic, and environmental feasibility for resource recovery.

Recent progress using membrane aerated biofilm reactors for wastewater treatment

The membrane biofilm reactor (MBfR), which is based on the counter diffusion of the electron donors and acceptors into the biofilm, represents a novel technology for wastewater treatment. When process air or oxygen is supplied, the MBfR is known as the membrane aerated biofilm reactor (MABR), which has high oxygen transfer rate and efficiency, promoting microbial growth and activity within the biofilm. Over the past few decades, laboratory-scale studies have helped researchers and practitioners understand the relevance of influencing factors and biological transformations in MABRs. In recent years, pilot- to full-scale installations are increasing along with process modeling. The resulting accumulated knowledge has greatly improved understanding of the counter-diffusional biological process, with new challenges and opportunities arising. Therefore, it is crucial to provide new insights by conducting this review. This paper reviews wastewater treatment advancements using MABR technology, including design and operational considerations, microbial community ecology, and process modeling. Treatment performance of pilot- to full-scale MABRs for process intensification in existing facilities is assessed. This paper also reviews other emerging applications of MABRs, including sulfur recovery, industrial wastewater, and xenobiotics bioremediation, space-based wastewater treatment, and autotrophic nitrogen removal. In conclusion, commercial applications demonstrate that MABR technology is beneficial for pollutants (COD, N, P, xenobiotics) removal, resource recovery (e.g., sulfur), and N₂O mitigation. Further research is needed to increase packing density while retaining efficient external mass transfer, understand the microbial interactions occurring, address existing assumptions to improve process modeling and control, and optimize the operational conditions with site-specific considerations.

Investigation of the Prevalence of Antibiotic Resistance Genes According to the Wastewater Treatment Scale Using Metagenomic Analysis

Although extensive efforts have been made to investigate the dynamics of the occurrence and abundance of antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs), understanding the acquisition of antibiotic resistance based on the WWTP scale and the potential effects on WWTPs is of relatively less interest. In this study, metagenomic analysis was carried out to investigate whether the WWTP scale could be affected by the prevalence and persistence of ARGs and mobile genetic elements (MGEs). As a result, 152 ARG subtypes were identified in small-scale WWTP samples, while 234 ARG subtypes were identified in large-scale WWTP samples. Among the detectable ARGs, multidrug, MLS (macrolide–lincosamide–streptogramin), sulfonamide, and tetracycline resistance genes had the highest abundance, and large and small WWTPs had similar composition characteristics of ARGs. In MGE analysis, plasmids and integrons were 1.5–2.0-fold more abundant in large-scale WWTPs than in small-scale WWTPs. The profile of bacteria at the phylum level showed that Proteobacteria and Actinobacteria were the most dominant bacteria, representing approximately 70% across large- and small-scale WWTPs. Overall, the results of this study elucidate the different abundances and dissemination of ARGs between large- and small-scale WWTPs, which facilitates the development of next-generation engineered wastewater treatment systems.

Rapid aerobic sludge granulation in an integrated oxidation ditch with two-zone clarifiers

Aerobic granular sludge (AGS) was rapidly cultivated in an integrated oxidation ditch with two-zone clarifiers by using a novel external sludge treatment and return mode to treat low concentrations of actual domestic sewage. The selective pressure created by the two-zone clarifiers can retain the well-settling granules and discharge light flocs with poor settleability. The granules stayed in the reactor, which induced bacterial attachment to the granules that acted as nuclei, while the discharged flocs can stimulate microorganisms to secrete large amounts of extracellular polymeric substances (EPS) under the external conditioning of CaCl₂ and natural air drying. Then, this surplus sludge was returned to the reactor to create more small granules that combined with each other through the action of hydraulic shear forces to achieve rapid granulation. The results showed that AGS was formed successfully in the reactor on day 18, and after 51 days of continuous operation, the biomass concentration and settling ability were further improved (the mixed liquor suspended solids (MLSS) and sludge volume index at 5 min (SVI₅) were stable at approximately 3500 mg/L and 40.0 mL/g, respectively). During the whole experimental period, the biological sludge activity was greatly improved, and the EPS and microbial community changed significantly, including an enrichment of microbes with EPS secretion and granule stabilization functions. The study results reveal that the pollutant removal efficiency improved after granulation. Furthermore, this approach required less energy and is eco-friendly for potential full-scale implementation.

Rapid Enrichment and Isolation of Polyphosphate-Accumulating Organisms Through 4'6-Diamidino-2-Phenylindole (DAPI) Staining With Fluorescence-Activated Cell Sorting (FACS)

Screening for bacteria with abilities to accumulate valuable intracellular compounds from an environmental community is difficult and requires strategic methods. Combining the experimental procedure for phenotyping living cells in a microbial community with the cell recovery necessary for further cultivation will allow for an efficient initial screening process. In this study, we developed a strategy for the isolation of polyphosphate-accumulating organisms (PAOs) by combining (i) nontoxic fluorescence staining of polyphosphate granules in viable microbial cells and (ii) fluorescence-activated cell sorting (FACS) for the rapid detection and collection of target cells. To implement this screening approach, cells from wastewater sludge samples were stained with 4’6-diamidino-2-phenylindole (DAPI) to target cells with high polyphosphate (polyP) accumulation. We found a staining procedure (10 μg/ml of DAPI for 30 min) that can visualize polyP granules while maintaining viability for the majority of the cells (>60%). The polyP positive cells were recovered by FACS, purified by colony isolation and phylogenetically identified by 16S rRNA gene sequencing. Follow-up analysis confirmed that these isolates accumulate polyP, indicating that DAPI can be implemented in staining living cells and FACS can effectively and rapidly screen and isolate individual cells from a complex microbial community.

Efficient municipal wastewater treatment by oxidation ditch process at low temperature: Bacterial community structure in activated sludge

Temperature is a key element affecting the activity of microorganisms in activated sludge. Low water temperature generally leads to decreasing wastewater treatment efficiency and destroying sludge settleability. In this study, activated sludge samples from a municipal wastewater treatment plant (WWTP) implementing oxidation ditch process was used to investigate the bacterial community characteristics of a system that operates well in a cold region (Xinjiang, China) by high-throughput 16S rRNA gene sequencing. The results showed that the influent temperature was 7-12 °C in winter and 13-17 °C in summer, while the sludge volume index (SVI) of samples was between 51 and 74 mL/g. The average removal efficiencies for chemical oxygen demand (COD), biochemical oxygen demand (BOD₅), suspended solid (SS), ammonia nitrogen (NH₄⁺-N), total nitrogen (TN), and total phosphorus (TP) were 94%, 95%, 95%, 91%, 73% and 89%, respectively. The bacteria were distributed in 32 phyla and 559 genera. The dominant phyla were Proteobacteria (28.85-48.45%), Bacteroidetes (20.00-31.22%), Chloroflexi (3.59-12.23%), Actinobacteria (1.58-15.54%) and Firmicutes (1.38-10.49%). The dominant genera were Saprospiraceae_norank (4.41-12.23%), Comamonadaceae_unclassified (3.82-8.83%), Anaerolineaceae_norank (1.39-9.35%), Dokdonella (1.13-11.26%), Candidatus_Microthrix (0.26-7.50%), Flavobacterium (0.32-8.14%), Ferribacterium (0.36-5.19%) and Nitrospira (0.084-5.37%), which were different from those found in warm-region WWTPs. Contrary to previous studies, the relative abundance of ammonia-oxidizing bacteria (AOB; Nitrosomonas and Nitrosomonadaceae) and nitrite-oxidizing bacteria (NOB; Nitrospira) increased when the temperature decreased. The successful operation of this WWTP suggests that cold-region WWTPs can achieve good pollutants removal efficiency by simultaneously maintaining an ultra-low sludge load and high dissolved oxygen concentration in the oxidation ditch. The findings of this study provide fundamental knowledge required for an efficient and stable operation of WWTPs in cold regions.

Increasing oxygen deficiency changes rare and moderately abundant bacterial communities in coastal soft sediments

Coastal hypoxia is a major environmental problem worldwide. Hypoxia-induced changes in sediment bacterial communities harm marine ecosystems and alter biogeochemical cycles. Nevertheless, the resistance of sediment bacterial communities to hypoxic stress is unknown. We investigated changes in bacterial communities during hypoxic-anoxic disturbance by artificially inducing oxygen deficiency to the seafloor for 0, 3, 7, and 48 days, with subsequent molecular biological analyses. We further investigated relationships between bacterial communities, benthic macrofauna and nutrient effluxes across the sediment-water-interface during hypoxic-anoxic stress, considering differentially abundant operational taxonomic units (OTUs). The composition of the moderately abundant OTUs changed significantly after seven days of oxygen deficiency, while the abundant and rare OTUs first changed after 48 days. High bacterial diversity maintained the resistance of the communities during oxygen deficiency until it dropped after 48 days, likely due to anoxia-induced loss of macrofaunal diversity and bioturbation. Nutrient fluxes, especially ammonium, correlated positively with the moderate and rare OTUs, including potential sulfate reducers. Correlations may reflect bacteria-mediated nutrient effluxes that accelerate eutrophication. The study suggests that even slightly higher bottom-water oxygen concentrations, which could sustain macrofaunal bioturbation, enable bacterial communities to resist large compositional changes and decrease the harmful consequences of hypoxia in marine ecosystems.

Adding an anaerobic step can rapidly inhibit sludge bulking in SBR reactor

Activated sludge from wastewater treatment plants was seeded into a sequencing batch reactor (SBR) in which synthetic wastewater was used as the influent. The sludge was bulked by decreasing the concentration of dissolved oxygen (DO). By adding a 30 min step of anaerobic stirring after the water inflow, the sludge bulking was rapidly inhibited after 10 running cycles, and the sludge volume index (SVI) decreased from 222 to 74 mL·g^-1. The results of high-throughput sequencing showed that the relative abundance of bacteria Thiothrix, bacteria norank_o_Sphingobacteriales and fungi Trichosporon was increased by 6.3, 4.3 and 81.2%, after initial SBR stages, but these bacteria were inhibited by the addition of an anaerobic step, as their relative abundances decreased by 0.7, 0.8 and 14.7%, respectively. The proliferation of Thiothrix, norank_o_Sphingobacteriales and Trichosporon was the primary reason for the observed sludge bulking in the reactor. After the anaerobic step was added, the sludge extracellular polymeric substances (EPS) concentration was increased from 84.4 to 104.0 mg·(gMLSS)^-1 (grams of mixed liquor suspended solids). Thus, the addition of an anaerobic step can inhibit the growth of filamentous bacteria, increasing the sludge EPS concentration and promoting the precipitation of activated sludge.

Deciphering the Assembly Processes of the Key Ecological Assemblages of Microbial Communities in Thirteen Full-Scale Wastewater Treatment Plants

Limited information is currently available on the assembly processes (deterministic vs. stochastic) shaping the compositions of key microbial communities in activated sludge (AS). The relative importance of deterministic and stochastic processes for key bacterial and archaeal assemblages (i.e., core-satellite and habitat generalist-specialist) in AS from 13 wastewater treatment plants in China was investigated using 16S rDNA amplicon sequencing. The results obtained indicated 1,388 and 369 core operational taxonomic units (OTUs), 1,038 and 1,683 satellite OTUs, 255 and 48 habitat generalist OTUs, and 192 and 111 habitat specialist OTUs for Bacteria and Archaea, respectively. The proportions of shared OTUs between core and habitat specialist communities were similar to or higher than those between core and habitat generalist communities, suggesting a stronger inter-linkage between the former two groups. Deterministic processes, indicated by abundance-based β-null models, were responsible for shaping core communities, in which NH₄-N, OrgC/OrgN, Cr, and Ni were the main controlling factors. In contrast, satellite communities were predominantly influenced by stochastic processes. Moreover, we found that deterministic and stochastic processes were mainly responsible for shaping the assembly of habitat specialists and generalists, respectively. However, the influence of deterministic factors on habitat specialists remains unclear. The present study provides novel insights into the assembly mechanisms of AS microbial communities.

Practical approach to the evaluation of industrial wastewater treatment by the application of advanced microbiological techniques

In cork industry, the operation of boiling raw cork generates large volumes of wastewater named Cork Boiling Wastewater (CBW). The main characteristics are the low biodegradability and medium to low acute toxicity, resulting in the necessity of designing advanced biological treatments by possible conventional activated sludge adaptation. In order to evaluate the variation of bacterial population along that process, a study based on optical microscopy, plate count, DNA extraction, qPCR and massive sequencing techniques was performed. Results showed a diminution of the total and volatile solids (TSS and VSS), jointly with a decrease in DNA concentration, general bacteria (16 S) and ammonia-oxidizing bacteria (AOB). After a few hours of testing, diverse microbiological species died while others showed a possible adaptation of the biological system, accompained by a dissolved organic carbon (DOC) reduction. In addition, toxicity tests based on activated sludge showed the development of chronic toxicity through the contact time. Combination of classical and advanced microbiological techniques, such as quantitative real time Polymerase Chain Reaction (qPCR) and metagenomics, was essential to predict the variation of species during the experiment and to conclude if effective biological adaptation could be finally attained for the target complex wastewater.

Diversity of culturable nocardioform actinomycetes from wastewater treatment plants in Spain and their role in the biodegradability of aromatic compounds

Currently, municipal and industrial wastewater treatment plants (WWTPs) are mainly focusing on reduction of biological oxygen demand and on the removal of nutrients. However, there are microorganisms that interfere with the process. In this environment, there is a large diversity of microorganisms that have not been studied in detail and that could provide real and practical solutions to the foaming problems. Among such microorganisms, Gram-positive actinomycete bacteria are of special interest because they are known for producing secondary metabolites as well as chemically diverse compounds and for their capacity to degrade recalcitrant pollutants. Three different media were chosen to isolate actinomycetes from 28 WWTPs in Spain. A total of 189 activated sludge samples were collected; 126 strains were isolated and identified to belong to 1 suborder, i.e. Corynebacterineae, and 7 genera, i.e. Corynebacterium, Dietzia, Gordonia, Mycobacterium, Rhodococcus, Tsukamurella and Williamsia. Furthermore, 71 strains were capable of biodegrading at least 1 aromatic product, and that 27 of them amplified for catA gene. The results of this research help us understand the complexity of the foam-forming microbial populations in Spain and it shows that WWTPs can be a good source of microorganisms that can degrade phenol or naphthalene.

Activated sludge foaming: can phage therapy provide a control strategy?

Foaming in activated sludge systems is a global problem leading to environmental, cosmetic and operational problems. Proliferation of filamentous hydrophobic bacteria (including the Mycolata) are responsible for the stabilisation of foams. Currently no reliable methods exist to control these. Reducing the levels of the filamentous bacteria with bacteriophages below the threshold supporting foaming is an attractive approach to control their impact. We have isolated 88 bacteriophages that target members of the foaming Mycolata. These double stranded DNA phages have been characterised and are currently being assessed for their performance as antifoam agents.

Detailed comparison of bacterial communities during seasonal sludge bulking in a municipal wastewater treatment plant

In this study, pyrosequencing combined with clone library analysis, qPCR, and fluorescent in situ hybridization (FISH) were performed to identify detailed changes of bacterial and filamentous bacterial communities in activated sludge (AS) in 3 types of typical AS samples: sludge bulking (B-AS), excessive bulking (EB-AS), and non-bulking (N-AS). Sludge bulking resulted in a decrease in total bacterial numbers from (6.4 ± 0.18) × 10⁸ gene copies/mL in N-AS to (2.4 ± 0.22) × 10⁸ in EB-AS and a decrease in bacterial diversity from 2757 OTUs in N-AS to 2217 OTUs in EB-AS. With the occurrence of sludge bulking, Actinobacteria and Firmicutes increased sharply, whereas Proteobacteria, which was the predominant phylum in N-AS, decreased markedly. In addition, Nitrospirae, a major lineage of the nitrite-oxidizing bacteria, had quite a low abundance in EB-AS (0.15%), while it was relatively high in N-AS (1.17%). On the other hand, filamentous bacteria accounted for 28.77% and 5.72% of total sequences in EB-AS and N-AS, respectively. More interestingly, 11 types of filamentous bacteria were always present in 3 types of typical AS samples from different stages of sludge bulking, and most of them enriched in EB-AS compared to N-AS. It is noteworthy that, in addition to the frequently reported filamentous bacteria such as Candidatus M. parvicella and Tetrasphaera, novel filamentous species of Trichococcus might exist in this bulking WWTP. Our results reveal that sludge bulking are derived from diverse taxa, which expands previous understanding and provides new insight into the underlying complications of the bulking phenomenon in AS.

Seasonal Changes in Bacterial Communities Cause Foaming in a Wastewater Treatment Plant

Bio-foaming is a major problem in solid separation in activated sludge (AS) wastewater treatment systems. Understanding the changes in bacterial communities during sludge foaming is vital for explaining foam formation. Changes in bacterial communities in the foam, corresponding foaming AS, and non-foaming AS in a seasonal foaming wastewater treatment plant (WWTP) in Northern China were investigated by high-throughput pyrosequencing and molecular quantification-based approaches. We found that bacterial communities of the foam and the corresponding foaming AS were similar but markedly different from those of the non-foaming AS. Actinobacteria was the predominant phylum in the foam and the corresponding foaming AS, whereas Proteobacteria was predominant in the non-foaming AS. Similar to the results of most previous studies, our results showed that Candidatus "Microthrix parvicella" was the predominant filamentous bacteria in the foam and the corresponding foaming AS and was significantly enriched in the foam compared to the corresponding foaming AS. Its abundance decreased gradually with a slow disappearance of sludge foaming, indicating that its overgrowth had a direct relationship with sludge foaming. In addition to Candidatus M. parvicella, Tetrasphaera and Trichococcus might play a role in sludge foaming, because they supported the changes in AS microbial ecology for foam formation. The effluent water quality of the surveyed plant remained stable during the period of sludge foaming, but the microbial consortia responsible for nitrogen and phosphorus transformation and removal markedly changed compared to that in the non-foaming AS. This study adds to the previous understanding of bacterial communities causing foaming in WWTPs.

Innovative biological approaches for monitoring and improving water quality

Water quality is largely influenced by the abundance and diversity of indigenous microbes present within an aquatic environment. Physical, chemical and biological contaminants from anthropogenic activities can accumulate in aquatic systems causing detrimental ecological consequences. Approaches exploiting microbial processes are now being utilized for the detection, and removal or reduction of contaminants. Contaminants can be identified and quantified in situ using microbial whole-cell biosensors, negating the need for water samples to be tested off-site. Similarly, the innate biodegradative processes can be enhanced through manipulation of the composition and/or function of the indigenous microbial communities present within the contaminated environments. Biological contaminants, such as detrimental/pathogenic bacteria, can be specifically targeted and reduced in number using bacteriophages. This mini-review discusses the potential application of whole-cell microbial biosensors for the detection of contaminants, the exploitation of microbial biodegradative processes for environmental restoration and the manipulation of microbial communities using phages.

Study of performances, stability and microbial characterization of a Sequencing Batch Biofilter Granular Reactor working at low recirculation flow

The Sequencing Batch Biofilter Granular Reactor (SBBGR) is a promising wastewater treatment technology characterized by high biomass concentration in the system, good depuration performance and low sludge production. Its main drawback is the high energy consumption required for wastewater recirculation through the reactor bed to ensure both shear stress and oxygen supply. Therefore, the effect of low recirculation flow on the long-term (38 months) performance of a laboratory scale SBBGR was studied. Both the microbial components of the granules, and their main metabolic activities were evaluated (heterotrophic oxidation, nitrification, denitrification, fermentation, sulphate reduction and methanogenesis). The results indicate that despite reduced recirculation, the SBBGR system maintained many of its advantageous characteristics.

Characteristics of mixed microbial culture at different sludge ages: effect on variable kinetics for substrate utilization

The study focused on variable kinetics for substrate utilization, primarily addressing the following issue: Is variable process kinetics observed under different operating conditions and culture history (sludge ages), the result of changes inflicted on the metabolic machinery of the same microbial culture? Or, is this the result of a different microbial population selected under different operating conditions? For this purpose, the study mainly emphasized to assess the microbial population composition sustained at different sludge ages. It explored the relationship between observed process kinetics and microbial population structure using respirometric modeling and high-throughput sequencing of 16S rRNA gene. Experimental results indicated a significant change in the composition of the microbial community fed with the same organic substrate, when the culture history was changed, lower sludge age selecting a different and faster growing microbial community.

Pseudonocardia hispaniensis sp. nov., a novel actinomycete isolated from industrial wastewater activated sludge

A novel actinomycete, designated PA3(T), was isolated from an oil refinery wastewater treatment plant, located in Palos de la Frontera, Huelva, Spain, and characterized taxonomically by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate formed a distinct subclade in the Pseudonocardia tree together with Pseudonocardia asaccharolytica DSM 44247(T). The chemotaxonomic properties of the isolate, for example, the presence of MK-8 (H(4)) as the predominant menaquinone and iso-C(16:0) as the major fatty acid, are consistent with its classification in the genus Pseudonocardia. DNA:DNA pairing experiments between the isolate and the type strain of P. asaccharolytica DSM 44247(T) showed that they belonged to separate genomic species. The two strains were readily distinguished using a combination of phenotypic properties. Consequently, it is proposed that isolate PA3(T) represents a novel species for which the name Pseudonocardia hispaniensis sp. nov. is proposed. The type strain is PA3(T) (= CCM 8391(T) = CECT 8030(T)).

Comparison of different procedures to stabilize biogas formation after process failure in a thermophilic waste digestion system: influence of aggregate formation on process stability

Following a process failure in a full-scale biogas reactor, different counter measures were undertaken to stabilize the process of biogas formation, including the reduction of the organic loading rate, the addition of sodium hydroxide (NaOH), and the introduction of calcium oxide (CaO). Corresponding to the results of the process recovery in the full-scale digester, laboratory experiments showed that CaO was more capable of stabilizing the process than NaOH. While both additives were able to raise the pH to a neutral milieu (pH>7.0), the formation of aggregates was observed particularly when CaO was used as the additive. Scanning electron microscopy investigations revealed calcium phosphate compounds in the core of the aggregates. Phosphate seemed to be released by phosphorus-accumulating organisms, when volatile fatty acids accumulated. The calcium, which was charged by the CaO addition, formed insoluble salts with long chain fatty acids, and caused the precipitation of calcium phosphate compounds. These aggregates were surrounded by a white layer of carbon rich organic matter, probably consisting of volatile fatty acids. Thus, during the process recovery with CaO, the decrease in the amount of accumulated acids in the liquid phase was likely enabled by (1) the formation of insoluble calcium salts with long chain fatty acids, (2) the adsorption of volatile fatty acids by the precipitates, (3) the acid uptake by phosphorus-accumulating organisms and (4) the degradation of volatile fatty acids in the aggregates. Furthermore, this mechanism enabled a stable process performance after re-activation of biogas production. In contrast, during the counter measure with NaOH aggregate formation was only minor resulting in a rapid process failure subsequent the increase of the organic loading rate.

Identification of functionally relevant populations in enhanced biological phosphorus removal processes based on intracellular polymers profiles and insights into the metabolic diversity and heterogeneity

This study proposed and demonstrated the application of a new Raman microscopy-based method for metabolic state-based identification and quantification of functionally relevant populations, namely polyphosphate accumulating organisms (PAOs) and glycogen accumulating organisms (GAOs), in enhanced biological phosphorus removal (EBPR) system via simultaneous detection of multiple intracellular polymers including polyphosphate (polyP), glycogen, and polyhydroxybutyrate (PHB). The unique Raman spectrum of different combinations of intracellular polymers within a cell at a given stage of the EBPR cycle allowed for its identification as PAO, GAO, or neither. The abundance of total PAOs and GAOs determined by Raman method were consistent with those obtained with polyP staining and fluorescence in situ hybridization (FISH). Different combinations and quantities of intracellular polymer inclusions observed in single cells revealed the distribution of different sub-PAOs groups among the total PAO populations, which exhibit phenotypic and metabolic heterogeneity and diversity. These results also provided evidence for the hypothesis that different PAOs may employ different extents of combination of glycolysis and TCA cycle pathways for anaerobic reducing power and energy generation and it is possible that some PAOs may rely on TCA cycle solely without glycolysis. Sum of cellular level quantification of the internal polymers associated with different population groups showed differentiated and distributed trends of glycogen and PHB level between PAOs and GAOs, which could not be elucidated before with conventional bulk measurements of EBPR mixed cultures.

Genome sequences and characterization of the related Gordonia phages GTE5 and GRU1 and their use as potential biocontrol agents

Activated sludge plants suffer frequently from the operational problem of stable foam formation on aerobic reactor surfaces, which can be difficult to prevent. Many foams are stabilized by mycolic acid-containing Actinobacteria, the mycolata. The in situ biocontrol of foaming using phages is an attractive strategy. We describe two polyvalent phages, GTE5 and GRU1, targeting Gordonia terrae and Gordonia rubrupertincta, respectively, isolated from activated sludge. Phage GRU1 also propagates on Nocardia nova. Both phages belong to the family Siphoviridae and have similar-size icosahedral heads that encapsulate double-stranded DNA genomes (∼65 kb). Their genome sequences are similar to each other but markedly different from those of other sequenced phages. Both are arranged in a modular fashion. These phages can reduce or eliminate foam formation by their host cells under laboratory conditions.

Research advances and challenges in the microbiology of enhanced biological phosphorus removal--a critical review

Enhanced biological phosphorus removal (EBPR) is a well-established technology for removing phosphorus from wastewater. However, the process remains operationally unstable in many systems, primarily because there is a lack of understanding regarding the microbiology of EBPR. This paper presents a review of advances made in the study of EBPR microbiology and focuses on the identification, enrichment, classification, morphology, and metabolic capacity of polyphosphate- and glycogen-accumulating organisms. The paper also highlights knowledge gaps and research challenges in the field of EBPR microbiology. Based on the review, the following recommendations regarding the future direction of EBPR microbial research were developed: (1) shifting from a reductionist approach to a more holistic system-based approach, (2) using a combination of culture-dependent and culture-independent techniques in characterizing microbial composition, (3) integrating ecological principles into system design to enhance stability, and (4) reexamining current theoretical explanations of why and how EBPR occurs.

Microbiology of 'Candidatus Accumulibacter' in activated sludge

‘Candidatus Accumulibacter’ is a biotechnologically important bacterial group that can accumulate large amounts of intracellular polyphosphate, contributing to biological phosphorus removal in wastewater treatment. Since its first molecular identification more than a decade ago, this bacterial group has drawn significant research attention due to its high abundance in many biological phosphorus removal systems. In the past 6 years, our understanding of Accumulibacter microbiology and ecophysiology has advanced rapidly, largely owing to genomic information obtained through shotgun metagenomic sequencing efforts. In this review, we focus on the metabolism, physiology, fine‐scale population structure and ecological distribution of Accumulibacter, aiming to integrate the information learned so far and to present a more complete picture of the microbiology of this important bacterial group.

An examination of the mechanisms for stable foam formation in activated sludge systems

Screening pure cultures of 65 mycolic acid producing bacteria (Mycolata) isolated mainly from activated sludge with a laboratory based foaming test revealed that not all foamed under the conditions used. However, for most, the data were generally consistent with the flotation theory as an explanation for foaming. Thus a stable foam required three components, air bubbles, surfactants and hydrophobic cells. With non-hydrophobic cells, an unstable foam was generated, and in the absence of surfactants, cells formed a greasy surface scum. Addition of surfactant converted a scumming population into one forming a stable foam. The ability to generate a foam depended on a threshold cell number, which varied between individual isolates and reduced markedly in the presence of surfactant. Consequently, the concept of a universal threshold applicable to all foaming Mycolata is not supported by these data. The role of surfactants in foaming is poorly understood, but evidence is presented for the first time that surfactin synthesised by Bacillus subtilis may be important.

Effect of aspartate and glutamate on the fate of enhanced biological phosphorus removal process and microbial community structure

This study investigated the fate of enhanced biological phosphorus removal (EBPR) and changes in microbial speciation in a sequencing batch reactor (SBR) fed with aspartate and glutamate. It involved SBR operation for 288 days, batch tests for observation of metabolic functions together with microscopic and phylogenetic analyses. Polyphosphate accumulating organisms (PAOs) were observed in abundance with complete removal of phosphorus. Fluorescence in situ hybridization (FISH) combined with 4',6-dia-midino-2-phenylindole (DAPI) staining confirmed the accumulation of polyphosphate by Rhodocyclus-related and Actinobacterial PAOs. Aspartate seemed to favor the competitive growth of Rhodocyclus-related PAOs since EBPR population used the common biochemical pathways followed by Rhodocyclus-related PAOs in the aspartate fed batch tests. In the glutamate fed batch reactors, however, Actinobacterial PAOs appeared to be competitively selected which explains the lower levels of PHA generation. Even though operational conditions did not change, effective EBPR could not be maintained during the latter part of the study.

Genome sequence and characterization of the Tsukamurella bacteriophage TPA2

The formation of stable foam in activated sludge plants is a global problem for which control is difficult. These foams are often stabilized by hydrophobic mycolic acid-synthesizing Actinobacteria, among which are Tsukamurella spp. This paper describes the isolation from activated sludge of the novel double-stranded DNA phage TPA2. This polyvalent Siphoviridae family phage is lytic for most Tsukamurella species. Whole-genome sequencing reveals that the TPA2 genome is circularly permuted (61,440 bp) and that 70% of its sequence is novel. We have identified 78 putative open reading frames, 95 pairs of inverted repeats, and 6 palindromes. The TPA2 genome has a modular gene structure that shares some similarity to those of Mycobacterium phages. A number of the genes display a mosaic architecture, suggesting that the TPA2 genome has evolved at least in part from genetic recombination events. The genome sequence reveals many novel genes that should inform any future discussion on Tsukamurella phage evolution.

An analysis of the bacterial community in a membrane bioreactor fed with photo-Fenton pre-treated toxic water

A photo-Fenton-membrane bioreactor (MBR) coupled system is an innovative tool for the treatment of wastewater containing high quantities of contaminants. In this paper, wastewater with 200 mg l(-1) of dissolved organic carbon (DOC) of a selected mixture of five commercial pesticides: Vydate®, Metomur®, Couraze®, Ditimur-40®, and Scala® was treated by combining photo-Fenton and MBR. The effect of photo-treated pollutants on MBR operation was investigated by studying the population changes that occurred with time in the activated sludge of the biological system. Pre-treatment with photo-Fenton was carried out (only up to 34% of mineralization of DOC) and, after MBR treatment, 98% of biodegradation efficiency was obtained. During the biological treatment, little changes in the activated sludge population were detected by DGGE analysis, maintaining acceptable biodegradation efficiency, which points out the robustness of the MBR treatment versus changes in feed composition.

A guide to successful bioprospecting: informed by actinobacterial systematics

New structurally diverse natural products are discovered when novel screening procedures are introduced or when high quality biological materials from new sources are examined in existing screens, hence it is important to foster these two aspects of novelty in drug discovery programmes. Amongst prokaryotes, actinomycetes, notably streptomycetes, remain a rich source of new natural products though it has become increasingly difficult to find such metabolites from common actinomycetes as screening 'old friends' leads to the costly rediscovery of known compounds. The bioprospecting strategy which is the subject of this review is based upon the premise that new secondary metabolites can be found by screening relatively small numbers of dereplicated, novel actinomycetes isolated from marine sediments. The success of the strategy is exemplified by the discovery of a range of novel bioactive compounds, notably atrop-abyssomicin C and proximicins A, B and C from Verrucosispora strains isolated from sediment samples taken from the Sea of Japan and the Raune Fjord, respectively, and the dermacozines derived from Dermacoccus strains isolated from the Challenger Deep of the Mariana Trench in the Pacific Ocean. The importance of current advances in prokaryotic systematics in work of this nature is stressed and a plea made that resources be sought to train, support and employ the next generation of actinobacterial systematists.