Microbiology of foaming in activated sludge plants

Bacteriophage-based biocontrol technology to enhance the efficiency of wastewater treatment and reduce targeted bacterial biofilms

Wastewater treatment is an essential process for public health and a sustainable ecosystem. Inadequate wastewater treatment can lead to the release of organic and inorganic pollutants and pathogenic bacteria into the receiving waters which could be further utilized for recreation purposes. The interaction between bacteriophage and bacteria in a wastewater treatment plant plays a major role in maintaining the treatment process. Phage therapy has been proposed as an alternative to conventional treatment methods as bacteriophages can be used on specific targets and leave useful bacteria unharmed. The bacterial species, which are responsible for bulking, foaming, and biofilm formation in a wastewater treatment plant (WWTP) have been identified and their respective phages are isolated to control their growth. Phages with lytic life cycles are preferred to lysogenic. Lytic phages can kill the specific target as they lyse the cell, infect most of the hosts, and have an immediate effect on controlling problems caused by bacteria in a WWTP. The bacteriophages such as T7, SPI1, GTE7, PhaxI, MAG1, MAG2, ϕPh_Se01, ϕPh_Se02, and Bxb1 have been investigated for the removal of bacterial biofilms from wastewater. Novel experimental setups have improved the efficiency of phage therapy in small-scale and pilot-scale experiments. Much more in-depth knowledge of the microbial community and their interaction would help promote the usage of phage therapy in large-scale wastewater treatments. This paper has covered the recent advancements in phage therapy as an effective biocontrol of pathogenic bacteria in the wastewater treatment process and has looked at certain shortcomings that have to be improved.

Minimizing Foaming and Bulking in Activated Sludge with Bacteriophage Treatment: A Review of Mathematical Modeling

The interest in the ability of phages to control bacterial populations has extended from medical applications into the fields of agriculture, aquaculture, and the food industry. In particular, several authors have proposed using bacteriophages as an alternative method to control foaming and bulking in wastewater treatment. This strategy has shown successful results at the laboratory scale. However, this technology is still in development, and there are several challenges to overcome before bacteriophages can be widely used to control foaming and bulking in pilot or larger-scale treatment plants. Several models of the infection mechanisms in individual bacteria–phage pairs have been reported, i.e., for controlled systems with only one bacterium species in the presence of one phage species. However, activated sludge treatment systems largely differ from this situation, which opens a large horizon for future research. Mathematical models will play a key role in this development process, and this review offers an overview of the proposed models: their applications, potential, and challenges. A particular focus is placed on the model properties, such as parameter identifiability and states’ observability, which are essential for process prediction, monitoring, or dynamic optimization.

Biological control of problem bacterial populations causing foaming in activated sludge wastewater treatment plants - phage therapy and beyond

The production of a stable foam on the surfaces of reactors is a global operating problem in activated sludge plants. In many cases these foams are stabilized by hydrophobic members of the Mycolata, a group of Actinobacteria whose outer membranes contains long chain hydroxylated mycolic acids. There is currently no single strategy which works for all foams. One attractive approach is to use lytic bacteriophages specific for the foam stabilizing Mycolata population. Such phages are present in activated sludge mixed liquor, and can be recovered readily from it. However, no phage has been recovered which lyses Gordonia amarae and Gordonia pseudoamarae, probably the most common foaming Mycolata members. Whole genome sequencing revealed that both G. amarae and G. pseudoamarae from plants around the world are particularly well endowed with genes encoding anti-viral defence mechanisms. However, both these populations were lysed rapidly by a parasitic nanobacterium isolated from a plant in Australia. This organism, a member of the Saccharibacteria was also effective against many other Mycolata, thus providing a potential agent for control of foams stabilized by them.

Candidatus Kaistella beijingensis sp. nov., Isolated from a Municipal Wastewater Treatment Plant, Is Involved in Sludge Foaming

Biological foaming (or biofoaming) is a frequently occurring problem in wastewater treatment plants (WWTPs) and is attributed to the overwhelming growth of filamentous bulking and foaming bacteria (BFB). Biological foaming has been intensively investigated, with BFB like Microthrix and Skermania having been identified from WWTPs and implicated in foaming. Nevertheless, studies are still needed to improve our understanding of the microbial diversity of WWTP biofoams and how microbial activities contribute to foaming. In this study, sludge foaming at the Qinghe WWTP of China was monitored, and sludge foams were investigated using culture-dependent and culture-independent microbiological methods. The foam microbiomes exhibited high abundances of Skermania, Mycobacterium, Flavobacteriales, and Kaistella. A previously unknown bacterium, Candidatus Kaistella beijingensis, was cultivated from foams, its genome was sequenced, and it was phenotypically characterized. Ca. K. beijingensis exhibits hydrophobic cell surfaces, produces extracellular polymeric substances (EPS), and metabolizes lipids. Ca. K. beijingensis abundances were proportional to EPS levels in foams. Several proteins encoded by the Ca. K. beijingensis genome were identified from EPS that was extracted from sludge foams. Ca. K. beijingensis populations accounted for 4 to 6% of the total bacterial populations in sludge foam samples within the Qinghe WWTP, although their abundances were higher in spring than in other seasons. Cooccurrence analysis indicated that Ca. K. beijingensis was not a core node among the WWTP community network, but its abundances were negatively correlated with those of the well-studied BFB Skermania piniformis among cross-season Qinghe WWTP communities. IMPORTANCE Biological foaming, also known as scumming, is a sludge separation problem that has become the subject of major concern for long-term stable activated sludge operation in decades. Biological foaming was considered induced by foaming bacteria. However, the occurrence and deterioration of foaming in many WWTPs are still not completely understood. Cultivation and characterization of the enriched bacteria in foaming are critical to understand their genetic, physiological, phylogenetic, and ecological traits, as well as to improve the understanding of their relationships with foaming and performance of WWTPs.

Cocultivation of an ultrasmall environmental parasitic bacterium with lytic ability against bacteria associated with wastewater foams

Many wastewater treatment plants around the world suffer from the operational problem of foaming. This is characterized by a persistent stable foam that forms on the aeration basin, which reduces effluent quality. The foam is often stabilized by a highly hydrophobic group of Actinobacteria known as the Mycolata¹. Gordonia amarae is one of the most frequently reported foaming members¹. With no currently reliable method for treating foams, phage biocontrol has been suggested as an attractive treatment strategy². Phages isolated from related foaming bacteria can destabilize foams at the laboratory scale^3,4; however, no phage has been isolated that lyses G. amarae. Here, we assemble the complete genomes of G. amarae and a previously undescribed species, Gordonia pseudoamarae, to examine mechanisms that encourage stable foam production. We show that both of these species are recalcitrant to phage infection via a number of antiviral mechanisms including restriction, CRISPR-Cas and bacteriophage exclusion. Instead, we isolate and cocultivate an environmental ultrasmall epiparasitic bacterium from the phylum Saccharibacteria that lyses G. amarae and G. pseudoamarae and several other Mycolata commonly associated with wastewater foams. The application of this parasitic bacterium, 'Candidatus Mycosynbacter amalyticus', may represent a promising strategy for the biocontrol of bacteria responsible for stabilizing wastewater foams.

Identification of microorganisms responsible for foam formation in mesophilic anaerobic digesters treating surplus activated sludge

Foaming is a common operational problem in anaerobic digestion (AD) systems, where hydrophobic filamentous microorganisms are usually considered to be the major cause. However, little is known about the identity of foam-stabilising microorganisms in AD systems, and control measures are lacking. This study identified putative foam forming microorganisms in 13 full-scale mesophilic digesters located at 11 wastewater treatment plants in Denmark, using 16S rRNA gene amplicon sequencing with species-level resolution and fluorescence in situ hybridization (FISH) for visualization. A foaming potential aeration test was applied to classify the digester sludges according to their foaming propensity. A high foaming potential for sludges was linked to the abundance of species from the genus Candidatus Microthrix, immigrating with the feed stream (surplus activated sludge), but also to several novel phylotypes potentially growing in the digester. These species were classified to the genera Ca. Brevefilum (Ca. B. fermentans) and Tetrasphaera (midas_s_5), the families ST-12K33 (midas_s_22), and Rikenellaceae (midas_s_141), and the archaeal genus Methanospirillum (midas_s_2576). Application of FISH showed that these potential foam-forming organisms all had a filamentous morphology. Additionally, it was shown that concentrations of ammonium and total nitrogen correlated strongly to the presence of foam-formers. This study provided new insight into the identity of putative foam-forming microorganisms in mesophilic AD systems, allowing for the subsequent surveillance of their abundances and studies of their ecology. Such information will importantly inform the development of control measures for these problematic microorganisms.

Distribution and diversity of filamentous bacteria in wastewater treatment plants exhibiting foaming of Taihu Lake Basin, China

Foaming caused by filamentous bacteria in activated sludge (AS) is a common phenomenon in municipal wastewater treatment plants (WWTPs) in Taihu Lake Basin of South China. In this study, total bacterial and filamentous bacterial communities were comprehensively characterized in AS and foams from eight municipal WWTPs by high-throughput sequencing technology. Results showed that alpha diversities of total bacterial communities in foams were obviously lower than those in AS samples. The bacterial community structures were significantly different between WWTPs rather than sample types (AS vs. foam). For most WWTPs, the Actinobacteria phylum was highly enriched in foams and the most abundant genera in foams were common mycolata. Sixteen filamentous bacteria were identified against the improved bulking and foaming bacteria (BFB) database. Abundance and composition of BFB in different WWTPs and different sample types were significantly different. 'Nostocoida limicola' I Trichococcus and Microthrix were generally dominant in AS samples. The dominant BFB in foams were associated with Microthrix, Skermania, Gordonia, and Mycobacterium. A new Defluviicoccus spp. in cluster III was identified in severe and continuous foams. Moreover, dominant BFB in stable and continuous foams with light level in one typical WWTP were diverse, even, and dynamic. Bacterial co-occurrence network analysis implied that the bacterial community of AS was more sensitive to disturbance than that of foam.

Foams in Wastewater Treatment Plants: From Causes to Control Methods

The formation of persistent foams can be a critical problem in wastewater treatment plants (WWTPs) as it could lead to a series of operational problems, especially the reduction of the overall system performance. To date, the effects of foaming in the WWTPs are a problem that is currently very common and shared, but which to date is treated mainly only at the management level and still too little studied through a globally shared scientific method: the complexity of the phenomenon and the systems have led to numerous partially contradictory descriptions and hypotheses over the years. The goal must be to suggest future research directions and indicate promising strategies to prevent or control the formation of foams in WWTPs. This study examines and investigates the problem of foams by a methodological approach of research through a review on the state of the art: the factors influencing the formation of foams are described first (such as surfactants and/or extracellular polymeric substances (EPSs)), then the known methods for the evaluation of foaming, both direct and indirect, are presented, with the aim of identifying the correct and best (from the management point of view) control and/or prevention strategies to be applied in the future in WWTPs.

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.

Evaluating the influence of wastewater composition on the growth of Microthrix parvicella by GCxGC/qMS and real-time PCR

This study underlines the significance of long chain fatty acid (LCFA) content in wastewater influents as an influencing factor promoting the growth of Candidatus 'Microthrix parvicella' (M. parvicella), the most common filamentous bacteria causing foam in activated sludge systems worldwide. Quantification of M. parvicella by real-time polymerase chain reaction (real-time PCR) and analysis of LCFAs by means of two-dimensional gas chromatography coupled with mass spectrometry (GCxGC/qMS), involving solid phase micro-extraction (SPME) to enhance sensitivity, were combined for the first time as a monitoring tool. The results indicate a highly significant correlation between the abundance of M. parvicella and the total LCFA loading (r = 0.96) and linolenic acid C18:3 (r = 0.98) in particular. Additionally, comparison of slope values for the direct correlations of all significant LCFAs found in the analyses showed that the influence of LCFAs on M. parvicella growth increases with an increasing degree of unsaturation of carbon chains. These findings suggest that by removing lipid compounds from the incoming waters, substrate availability would be limited for M. parvicella.

Lysis to Kill: Evaluation of the Lytic Abilities, and Genomics of Nine Bacteriophages Infective for Gordonia spp. and Their Potential Use in Activated Sludge Foam Biocontrol

Nine bacteriophages (phages) infective for members of the genus Gordonia were isolated from wastewater and other natural water environments using standard enrichment techniques. The majority were broad host range phages targeting more than one Gordonia species. When their genomes were sequenced, they all emerged as double stranded DNA Siphoviridae phages, ranging from 17,562 to 103,424 bp in size, and containing between 27 and 127 genes, many of which were detailed for the first time. Many of these phage genomes diverged from the expected modular genome architecture of other characterized Siphoviridae phages and contained unusual lysis gene arrangements. Whole genome sequencing also revealed that infection with lytic phages does not appear to prevent spontaneous prophage induction in Gordonia malaquae lysogen strain BEN700. TEM sample preparation techniques were developed to view both attachment and replication stages of phage infection.

Detailed investigation of the microbial community in foaming activated sludge reveals novel foam formers

Foaming of activated sludge (AS) causes adverse impacts on wastewater treatment operation and hygiene. In this study, we investigated the microbial communities of foam, foaming AS and non-foaming AS in a sewage treatment plant via deep-sequencing of the taxonomic marker genes 16S rRNA and mycobacterial rpoB and a metagenomic approach. In addition to Actinobacteria, many genera (e.g., Clostridium XI, Arcobacter, Flavobacterium) were more abundant in the foam than in the AS. On the other hand, deep-sequencing of rpoB did not detect any obligate pathogenic mycobacteria in the foam. We found that unknown factors other than the abundance of Gordonia sp. could determine the foaming process, because abundance of the same species was stable before and after a foaming event over six months. More interestingly, although the dominant Gordonia foam former was the closest with G. amarae, it was identified as an undescribed Gordonia species by referring to the 16S rRNA gene, gyrB and, most convincingly, the reconstructed draft genome from metagenomic reads. Our results, based on metagenomics and deep sequencing, reveal that foams are derived from diverse taxa, which expands previous understanding and provides new insight into the underlying complications of the foaming phenomenon in AS.

Modeling phage induced bacterial disinfection rates and the resulting design implications

The phage induced disinfection rates of Escherichia coli K-12 MG1655 in the presence of coliphage Ec2 were determined under a wide range of phage and bacterial concentrations. These rates were elucidated to determine if phages could be used in water and wastewater treatment systems as a biological based disinfectant. Disinfection rates ranging from 0.13 ± 0.1 to 2.03 ± 0.1 h⁻¹ were observed for E. coli K12. A multiple linear regression model was used to explain the variance in the disinfection rates, and this model demonstrated an interaction effect between the initial phage and bacterial concentrations. Furthermore, the results were modeled with particle aggregation theory, which over predicted the disinfection rates at higher phage and bacterial concentrations, suggesting additional interactions. Finally, the observed and predicted disinfection rates were used to determine additional design parameters. The results suggested that a phage based disinfection process may be suitable for the inactivation of specific pathogens in plug flow reactors, such as the pathogens in hospital wastewater effluents and the bacteria responsible for foaming and sludge bulking in activated sludge processes.

Full-scale bioreactor pretreatment of highly toxic wastewater from styrene and propylene oxide production

The wastewater originating from simultaneous production of styrene and propylene oxide (SPO) is classified as highly polluted with chemical oxygen demand level in the range 5965 to 9137mgL(-1)-as well as highly toxic. The dilution factor providing for a 10 percent toxic effect of wastewater samples in a test with Paramecium caudatum was 8.0-9.5. Biological approach for pretreatment and detoxification of the wastewater under full-scale bioreactor conditions was investigated. The number of suspended microorganisms and the clean up efficiency were increased up to 5.5-6.58×10(8)CFUmL(-1) and 88 percent, respectively during the bioreactor's operation. Isolates in the Citrobacter, Burkholderia, Pseudomonas, and Paracoccus genera were dominant in the mature suspended, as well as the immobilized microbial community of the bioreactor. The most dominant representatives were tested for their ability to biodegrade the major components of the SPO wastewater and evidence of their role in the treatment process was demonstrated. The investigated pretreatment process allowed the wastewater to be detoxified for conventional treatment with activated sludge and was closely related to the maturation of the bioreactor's microbial community.

Isolation and characterization of bacteriophages infecting nocardioforms in wastewater treatment plant

Activated sludge plants (ASP) are associated with the stable foaming problem worldwide. Apart from the physical and chemical treatment methods, biological treatment method has been least explored and may prove to be a novel and ecofriendly approach to tackle the problem of stable foam formation. In ASP Nocardia species are commonly found and are one of the major causes for forming sticky and stable foam. This study describes the isolation and characterization of three Nocardia bacteriophages NOC1, NOC2, and NOC3 for the control of Nocardia species. The bacteriophages isolated in this study have shown promising results in controlling foam producing bacterial growth under laboratory conditions, suggesting that it may prove useful in the field as an alternative biocontrol agent to reduce the foaming problem. To the best of our knowledge to date no work has been published from India related to biological approach for the control of foaming.

Use of an aerobic selector to overcome filamentous bulking in an activated sludge wastewater treatment plant

An urban wastewater treatment plant (WWTP) with two different parallel lines of treatment and located in the north of Portugal was studied during four months, following recurrent episodes of filamentous bulking caused by Sphaerotilus natans and eventual occurrences of Nocardioforms and Type 1863. An aerobic selector was introduced in both lines in the beginning of the studied period, suppressed in one of the lines during six weeks, and then put into operation again until the end of the study. A total of 14 filamentous bacteria morphotypes were identified. The results showed that the presence of an aerobic biological selector in continuous operation prevented the overgrowth of the filamentous Type 1863, of Nocardioforms and, in particular, of S. natans. Simultaneously, it allowed lowering the oxygen levels in the aeration tanks without negative consequences in the overall performance of the WWTP, namely bulking occurrence. Dissolved oxygen (DO) in the aeration tank varied initially between 2 and 3 mg/L, but the introduction of the selector enabled to lower it to 1-1.5 mg/L in the aeration tank and around 0.5 mg/L in the selector. A significant energy save was allowed, even considering the aeration of the selector. The results are more relevant if one considers the fact that the main cause of the bulking problems in this WWTP was the overgrowth of S. natans, a filamentous bacterium known to be stimulated by low DO levels.

Taxonomic precision of different hypervariable regions of 16S rRNA gene and annotation methods for functional bacterial groups in biological wastewater treatment

High throughput sequencing of 16S rRNA gene leads us into a deeper understanding on bacterial diversity for complex environmental samples, but introduces blurring due to the relatively low taxonomic capability of short read. For wastewater treatment plant, only those functional bacterial genera categorized as nutrient remediators, bulk/foaming species, and potential pathogens are significant to biological wastewater treatment and environmental impacts. Precise taxonomic assignment of these bacteria at least at genus level is important for microbial ecological research and routine wastewater treatment monitoring. Therefore, the focus of this study was to evaluate the taxonomic precisions of different ribosomal RNA (rRNA) gene hypervariable regions generated from a mix activated sludge sample. In addition, three commonly used classification methods including RDP Classifier, BLAST-based best-hit annotation, and the lowest common ancestor annotation by MEGAN were evaluated by comparing their consistency. Under an unsupervised way, analysis of consistency among different classification methods suggests there are no hypervariable regions with good taxonomic coverage for all genera. Taxonomic assignment based on certain regions of the 16S rRNA genes, e.g. the V1&V2 regions – provide fairly consistent taxonomic assignment for a relatively wide range of genera. Hence, it is recommended to use these regions for studying functional groups in activated sludge. Moreover, the inconsistency among methods also demonstrated that a specific method might not be suitable for identification of some bacterial genera using certain 16S rRNA gene regions. As a general rule, drawing conclusions based only on one sequencing region and one classification method should be avoided due to the potential false negative results.

Profiling bulking and foaming bacteria in activated sludge by high throughput sequencing

Bulking and foaming bacteria (BFB) are notorious in wastewater treatment although they are always presented in the normal activated sludge and playing certain roles other than being harmful. Previous studies using microscopy or conventional molecular methods could hardly get the full profile of the BFB in the normal activated sludge. In this study, high throughput sequencing was adopted to investigate the BFB community, which was sub-dominant in activated sludge from 14 global wastewater treatment plants. The full-length 16S rRNA gene sequences of BFB groups were collected from previous studies to build a database for local BLAST and subsequent taxonomic assignment. The total BFB percentage in each sample ranged from 1.86% to 8.99% according to the 16S rRNA gene V4 pyrotags detected at the BLAST similarity cutoff of 97%. The most abundant and frequent BFB groups are 'Nostocoida limicola' I and II, Mycobacterium fortuitum, Type 1863, and 'Microthrix parvicella'. The BFB among the activated sludge samples were both biogeographically and technological distributed to some extent. An extending application was performed to evaluate and design oligonucleotides probes based on the rich information of high similar sequences. Our study also gave an exemplified case of investigation on the specific sub-dominant functional groups in complex bacterial communities revealed by high throughput sequencing.

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.

Prevention of Gordonia and Nocardia stabilized foam formation by using bacteriophage GTE7

Most activated sludge treatment plants suffer from the presence of foams on the surfaces of their aeration reactors. These are often stabilized by hydrophobic mycolic acid-synthesizing actinobacterial species. A polyvalent Siphoviridae phage, GTE7, which lysed several Gordonia and Nocardia species, is described here. Its genome has a modular structure similar to that described for Rhodococcus phage ReqiDocB7. In laboratory-scale experiments, we showed that GTE7 prevents stabilization of foams by these Gordonia and Nocardia species.

Phylogenetic diversity and metabolic potential of activated sludge microbial communities in full-scale wastewater treatment plants

The activated sludge process is an essential process for treating domestic and industrial wastewaters in most wastewater treatment plants (WWTPs). This process consists of a mixture of general and special microorganisms in a form of a complex enrichment population. Thus, the exploration of activated sludge microbial communities is crucial to improve the performance of activated sludge process. In this study, we investigated the phylogenetic diversity and metabolic potential of activated sludge microbial communities in full-scale WWTPs. Four 16S rRNA gene clone libraries were constructed from activated sludge samples. In all samples, Proteobacteria was the most abundant phylogenetic group, followed by Bacteroidetes and Firmicutes. The dominance of Proteobacteria was further demonstrated by denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP). Some specific genera, e.g., Nitrosomonas, Thauera, and Dechloromonas, which significantly correlate with the functions and performance of wastewater treatment, were abundant in all samples. A large number of unclassified sequences were found in the library, suggesting that a wide variety of novel species may inhabit complex activated sludge communities. The structures of the bacterial community did not differ significantly among samples. All samples utilized the vast majority of 31 carbon sources of an EcoPlate (Biolog), suggesting that activated sludge microbial communities possess high metabolic potential and equivalent functions required for wastewater treatment.

Characterization of the genome of the polyvalent lytic bacteriophage GTE2, which has potential for biocontrol of Gordonia-, Rhodococcus-, and Nocardia-stabilized foams in activated sludge plants

Hydrophobic Actinobacteria are commonly associated with the stabilization of foams in activated sludge systems. One possible attractive approach to control these foam-stabilizing organisms is the use of specific bacteriophages. We describe the genome characterization of a novel polyvalent DNA phage, GTE2, isolated from activated sludge. This phage is lytic for Gordonia terrae, Rhodococcus globerulus, Rhodococcus erythropolis, Rhodococcus erythropolis, Nocardia otitidiscaviarum, and Nocardia brasiliensis. Phage GTE2 belongs to the family Siphoviridae, possessing a characteristic icosahedral head encapsulating a double-stranded DNA linear genome (45,530 bp) having 10-bp 3'-protruding cohesive ends. The genome sequence is 98% unique at the DNA level and contains 57 putative genes. The genome can be divided into two components, where the first is modular and encodes phage structural proteins and lysis genes. The second is not modular, and the genes harbored there are involved in DNA replication, repair, and metabolism. Some have no known function. GTE2 shows promising results in controlling stable foam production by its host bacteria under laboratory conditions, suggesting that it may prove useful in the field as a biocontrol agent.

Removal of phenols, thiocyanate and ammonium from coal gasification wastewater using moving bed biofilm reactor

A laboratory-scale moving bed biofilm reactor (MBBR) with a volume of 4 L was used to study the biodegradation of coal gasification wastewater. Maximum removal efficiencies of 81%, 89%, 94% and 93% were obtained for COD, phenols, SCN(-) and NH(4)(+)-N, respectively. NO(2)(-)-N accumulation induced increase of effluent COD concentration when the hydraulic residence time (HRT) decreased. Phenols removal was not affected when the HRT decreased from 48 to 32 h. Effluent SCN(-) and NH(4)(+)-N concentration increased with the decrease of the HRT, and decreased gradually when the HRT returned to 48 h. Batch experiments were carried out to study performance of the suspended and attached growth biomass in the MBBR.

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.

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.

The role of dispersed nocardioform filaments in activated sludge foaming

Activated sludge foaming caused by filamentous microorganisms is a major wastewater treatment plant operating problem. This paper presents the results of an investigation of the role of dispersed nocardioforms in activated sludge foaming. Dispersed nocardioforms had a greater propensity for foaming than floc-bound nocardioforms. The mode of effluent withdrawal from an aeration basin plays a major role in determining the relative proportion of dispersed and floc-bound nocardioforms in the activated sludge. Reactors with "trapping" features (sub-surface mixed liquor withdrawal) had significantly higher dispersed nocardioform populations than reactors with "non-trapping" features (surface mixed liquor withdrawal). High dispersed nocardioform filament concentrations were correlated with a high propensity for foaming. Cationic polymer and polyaluminum chloride reduced foaming by flocculating dispersed nocardioforms, thereby converting them to floc-bound nocardioforms. Low non-ionic surfactant concentrations changed the relative proportions of dispersed and floc-bound nocardioforms by deflocculating floc-bound filaments and converting them to the dispersed growth form. This could act as a trigger for initiating the rapid-onset nocardioform foaming events observed at activated sludge plants.

Biodegradation of propionitrile by Klebsiella oxytoca immobilized in alginate and cellulose triacetate gel

A microbial process for the degradation of propionitrile by Klebsiella oxytoca was studied. The microorganism, K. oxytoca, was isolated from the discharged wastewater of metal plating factory in southern Taiwan and adapted for propionitrile biodegradation. The free and immobilized cells of K. oxytoca were then examined for their capabilities on degrading propionitrile under various conditions. Alginate (AL) and cellulose triacetate (CT) techniques were applied for the preparation of immobilized cells. The efficiency and produced metabolic intermediates and end-products of propionitrile degradation were monitored in bath and continuous bioreactor experiments. Results reveal that up to 100 and 150 mM of propionitrile could be removed completely by the free and immobilized cell systems, respectively. Furthermore, both immobilized cell systems show higher removal efficiencies in wider ranges of temperature (20-40 degrees C) and pH (6-8) compared with the free cell system. Results also indicate that immobilized cell system could support a higher cell density to enhance the removal efficiency of propionitrile. Immobilized cells were reused in five consecutive degradation experiments, and up to 99% of propionitrile degradation was observed in each batch test. This suggests that the activity of immobilized cells can be maintained and reused throughout different propionitrile degradation processes. A two-step pathway was observed for the biodegradation of propionitrile. Propionamide was first produced followed by propionic acid and ammonia. Results suggest that nitrile hydratase and amidase were involved in the degradation pathways of K. oxytoca. In the continuous bioreactor, both immobilized cells were capable of removing 150 mM of propionitriles completely within 16h, and the maximum propionitriles removal rates using AL and CT immobilized beads were 5.04 and 4.98 mM h(-1), respectively. Comparing the removal rates obtained from batch experiments with immobilized cells (AL and CT were 1.57 and 2.18 mM h(-1) at 150 mM of propionitrile, respectively), the continuous-flow bioreactor show higher potential for practical application.

Widespread abundance of functional bacterial amyloid in mycolata and other gram-positive bacteria

Until recently, extracellular functional bacterial amyloid (FuBA) has been detected and characterized in only a few bacterial species, including Escherichia coli, Salmonella, and the gram-positive organism Streptomyces coelicolor. Here we probed gram-positive bacteria with conformationally specific antibodies and revealed the existence of FuBA in 12 of 14 examined mycolata species, as well as six other distantly related species examined belonging to the phyla Actinobacteria and Firmicutes. Most of the bacteria produced extracellular fimbriae, sometimes copious amounts of them, and in two cases large extracellular fibrils were also produced. In three cases, FuBA was revealed only after extensive removal of extracellular material by saponification, indicating that there is integrated attachment within the cellular envelope. Spores of species in the genera Streptomyces, Bacillus, and Nocardia were all coated with amyloids. FuBA was purified from Gordonia amarae (from the cell envelope) and Geodermatophilus obscurus, and they had the morphology, tinctorial properties, and beta-rich structure typical of amyloid. The presence of approximately 9-nm-wide amyloids in the cell envelope of G. amarae was visualized by transmission electron microscopy analysis. We conclude that amyloid is widespread among gram-positive bacteria and may in many species constitute a hitherto overlooked integral part of the spore and the cellular envelope.

A universal threshold concept for hydrophobic mycolata in activated sludge foaming

Recent studies using quantitative fluorescence in situ hybridization (FISH) have supported the principle that there are mycolata concentration thresholds, above which foaming is likely to occur. In this study, we surveyed 14 wastewater treatment plants (WWTPs) in the UK, using quantitative FISH, to establish that the principle of a mycolata threshold (2 x 10(6) mycolata cells ml(-1) mixed liquor suspended solids) is an empirical though widely held value. In addition, we designed, optimized and applied probes for members of the less hydrophobic mycolata genera Corynebacterium and Dietzia, to show that these organisms dominated the mycolata populations in two non-foaming WWTPs where the mycolata concentrations were above the threshold value. We propose that the mycolata threshold value is only applicable to hydrophobic members of the mycolata.

Enhanced biological phosphorus removal and recovery

Activated sludge systems designed for enhanced nutrient removal are based on the principle of altering anaerobic and aerobic conditions for growth of microorganisms with a high capacity of phosphorus accumulation. Most often, filamentous bacteria constitute a component of the activated sludge microflora. The filamentous microorganisms are responsible for foam formation and activated sludge bulking. The results obtained confirm unanimously that the filamentous bacteria have the ability of phosphorus uptake and accumulation as polyphosphates. Hydrodynamic disintegration of the foam microorganisms results in the transfer of phosphorus and metal cations and ammonium-nitrogen into the liquid phase. It was demonstrated that the disintegration of foam permits the removal of a portion of the nutrients in the form of struvite.

Uptake of phosphorus by filamentous bacteria and the role of cation on polyphosphates composition

Many microorganisms have the ability to store phosphorus as polyphosphates in volutin granules. The aim of the research was to characterise the phosphorus sequestered by filamentous microorganisms present in the foam. Also the importance of required cations like potassium and magnesium in the process of phosphorus uptake by filamentous microorganisms was examined. Electron microscopy and energy dispersive X - ray analysis were used to define the composition of polyphosphate granules in filamentous bacteria.

Populations related to Alkanindiges, a novel genus containing obligate alkane degraders, are implicated in biological foaming in activated sludge systems

Activated sludge mixed liquor and biological foam samples were collected from five full-scale municipal wastewater treatment plants in Illinois, all of which were exhibiting biological foaming at the time of sampling. Oligonucleotide probe hybridization consistently measured higher levels of Gammaproteobacteria rRNA in the foam as compared with the mixed liquor for all treatment plants analysed. Cloning and sequencing of 16S rRNA gene amplicons led to the identification of populations which were abundant in each of the treatment plants. These populations were related to the Alkanindiges/Acinetobacter cluster within the Gammaproteobacteria. Further analysis of the 16S rRNA sequences indicated that they clustered in three phylogenetic groups outside the main Alkanindiges/Acinetobacter cluster, suggesting that these groups may represent new taxa. Terminal-restriction fragment length polymorphism analysis showed that these populations were enriched in the foam compared with the underlying mixed liquor similar to the enrichment of the Gammaproteobacteria measured by oligonucleotide probe membrane hybridization. The observed enrichment in foam samples is suggestive of a role for these populations in foam formation or stabilization, and their presence in all treatment plants analysed in this study may be indicative of their widespread abundance in foaming plants.

Cause and pre-alarm control of bulking and foaming by Microthrix parvicella--a case study in triple oxidation ditch at a wastewater treatment plant

The cause and control of foaming and bulking in triple oxidation ditch at a wastewater treatment plant (WWTP) were investigated. The results showed that the foaming and bulking was mainly caused by the excessive propagation of Microthrix parvicella, and mostly occurred in the cold winter and spring. Batch and continuous flow experiments indicated that biological techniques such as reducing sludge retention time (SRT) and increasing F/M ratio, chemical methods such as addition of chlorine (NaOCl), quaternary ammonium salt (QAS), or cationic polyacrylamide flocculants (PAM), polyaluminum salt (PAC) could decrease Sludge Volume Index (SVI) and control foaming and bulking at different levels. In practical application, the shorter SRT was effective to control foaming and bulking in initial stage, although it took longer time. Addition of 10gClkgMLSSd(-1) could gradually change the activated sludge with serious foaming and bulking to normal state within a week. Pre-alert control strategies should be established for the control of filamentous foaming and bulking.

Ecophysiology of mycolic acid-containing Actinobacteria (Mycolata) in activated sludge foams

Increasing incidences of activated sludge foaming have been reported in the last decade in Danish plants treating both municipal and industrial wastewaters. In most cases, foaming is caused by the presence of Actinobacteria; branched mycolic acid-containing filaments (the Mycolata) and the unbranched Candidatus'Microthix parvicella'. Surveys from wastewater treatment plants revealed that the Mycolata were the dominant filamentous bacteria in the foam. Gordonia amarae-like organisms and those with the morphology of Skermania piniformis were frequently observed, and they often coexisted. Their identity was confirmed by FISH, using a new permeabilization procedure. It was not possible to identify all abundant Mycolata using existing FISH probes, which suggests the presence of currently undetectable and potentially undescribed populations. Furthermore, some Mycolata failed to give any FISH signal, although substrate uptake experiments with microautoradiography revealed that they were physiologically active. Ecophysiological studies were performed on the Mycolata identified by their morphology or FISH in both foams and mixed liquors. Large differences were seen among the Mycolata in levels of substrate assimilation and substrate uptake abilities in the presence of different electron acceptors. These differences were ascribed mainly to the presence of currently undescribed Mycolata species and/or differences in foam age.

New group-specific 16S rDNA primers for monitoring foaming mycolata during saline waste-water treatment

Newly designed group-specific PCR primers for denaturing gradient gel electrophoresis (DGGE) were used to investigate foaming mycolata from a bioreactor treating an industrial saline waste-water. Genetic profiles on DGGE gels were different with NaCl at 1.65 and 8.24 g l(-1), demonstrating that mycolata community was affected by salinity. A semi-nested PCR strategy resulted in more bands in community genetic profiles than direct amplification. DNA sequencing of bands confirmed the efficacy of the novel primers with sequences recovered being most similar to foam producing mycolata. The new group-specific primers/DGGE approach is a new step toward a more complete understanding of functionally important groups of bacteria involved in biological treatment of waste-water.

Millisia brevis gen. nov., sp. nov., an actinomycete isolated from activated sludge foam

The taxonomic position of two mycolic-acid-producing actinomycetes, isolates J81Tand J82, which were recovered from activated sludge foam, was clarified. Comparative 16S rRNA gene sequence studies indicated that the organisms formed a distinct lineage within theCorynebacterineae16S rRNA gene tree. The taxonomic integrity of this group was underpinned by a wealth of phenotypic data, notably characteristic rudimentary right-angled branching. In addition, isolate J81Tcontained the following:meso-diaminopimelic acid, arabinose and galactose;N-glycolated muramic acid residues; a dihydrogenated menaquinone with eight isoprene units as the predominant isoprenologue; a fatty acid profile rich in oleic and palmitoleic acids and with relatively small proportions of myristic, stearic and tuberculostearic acids; mycolic acids with 44–52 carbons; and diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides as major polar lipids. Strain J81Twas found to have a chemotaxonomic profile that serves to distinguish it from representatives of all of the other taxa classified as belonging to the suborderCorynebacterineae. In the light of these data, it is proposed that the two isolates be classified in a novel monospecific genus. The name proposed for this taxon isMillisia brevisgen. nov., sp. nov.; strain J81T(=DSM 44463T=NRRL B-24424T) is the type strain ofMillisia brevis.

Environmentally relevant microorganisms

The development of molecular microbial ecology in the 1990s has allowed scientists to realize that microbial populations in the natural environment are much more diverse than microorganisms so far isolated in the laboratory. This finding has exerted a significant impact on environmental biotechnology, since knowledge in this field has been largely dependent on studies with pollutant-degrading bacteria isolated by conventional culture methods. Researchers have thus started to use molecular ecological methods to analyze microbial populations relevant to pollutant degradation in the environment (called environmentally relevant microorganisms, ERMs), although further effort is needed to gain practical benefits from these studies. This review highlights the utility and limitations of molecular ecological methods for understanding and advancing environmental biotechnology processes. The importance of the combined use of molecular ecological and physiological methods for identifying ERMs is stressed.

Improved permeabilization protocols for fluorescence in situ hybridization (FISH) of mycolic-acid-containing bacteria found in foams

Formation of thick, stable foams and scums on activated sludge wastewater treatment plants is a worldwide problem, and to better understand what causes this foam and to cure it, there is a need to identify and quantify the bacteria present there. Fluorescence in situ hybridisation (FISH) overcomes the difficulties experienced with microscopic methods of identification for the mycolic-acid-containing actinomycetes (the mycolata), which are present in foams, where many share the morphotype of right-angled branching filaments. However, the presence of hydrophobic mycolic acids in their cell wall makes this group of bacteria particularly difficult to permeabilise, which greatly reduces the usefulness of FISH. While several permeabilisation treatments have been described, none appear to adequately permeabilise all genera of the mycolata. In this study several protocols for permeabilisation were assessed with both pure cultures of selected genera of the mycolata and foam samples. Combining mild acid hydrolysis with enzyme treatments (either mutanolysin/lysozyme or lipase/proteinase K) was found to be the most effective method, although other evidence presented here suggests that negative FISH results can not always be explained in terms of cell permeability to the probes.

Development of a DNA microarray chip for the identification of sludge bacteria using an unsequenced random genomic DNA hybridization method

A tool, based upon the DNA microarray chip, for the identification of specific bacteria from activated sludge, using the hybridization of genomic DNA with random probes, is described. This chip was developed using the genomic DNAs from Gordonia amarae, the natural filamentous actinomycete that causes sludge foaming and bulking, as well as a nonfilamentous floc forming bacterium (Zoogloea ramigera) and the skin pathogen Mycobacterium peregrinum without any sequence information. The sets of target probes on amine-coated glass were made from a genomic library, constructed with PCR products derived from randomly fragmented genomic DNAs extracted from pure cultures of the three strains. Initial hybridization results, when pure cultures were employed, showed the specificity of the probes as well as the resolution of the system, demonstrating the capabilities of this system to identify specific bacterial strains. The microarray was also tested for its ability to distinguish specific bacteria from among mixed bacterial communities, such as in sludge, soil, or spiked genomic DNA samples. The results showed that the probes are specific, with only mild cross-hybridization occurring in a small number of cases. Furthermore, the chip clearly discriminated the presence of all three strains when they were present alone or together within mixed samples. Moreover, using the spot intensity and DNA hybridization kinetics, the starting genomic DNA concentrations could be estimated relatively well, which would make it possible to predict the number of specific bacteria present within the test samples. Therefore, the random genomic hybridization approach, i.e., without any sequence information available for the probes, is a practical protocol for the identification of and screening for specific bacteria within any complex bacterial community from the environmental samples, such as in activated sludge, although the possibility of cross-hybridization may still exist.

A survey of filamentous organisms at the Deer Island treatment plant

The Deer Island Treatment Plant (DITP) treating both domestic and industrial wastewater, has a peak flow capacity of up to 1270 million gallons per day (MGD) (3342 m3 min(-1). The DITP contains a Pilot Plant, which consists of two identical pure oxygen activated sludge treatment trains, each with a maximum capacity of 1 MGD (2.63 m3 min(-1)) to simulate the maximum flow of the full size facility. This study documents the community of filamentous organisms living in the activatedsludge under various operational conditions in the Pilot Plant. Sixteen types of filamentous organisms were identified. The major filamentous organisms present in the Pilot Plant were Type 1701, Type 0041, Sphaerotilus natans, Microthrix parvicella, and Nocardia sp. Nocardia sp. was quite dominant in the early stages of the experimental period during high ambient temperatures (summer), indicating that temperature is one determining factor in the distribution of Nocardia sp. Thiothrix sp. was very sensitive to the dissolved oxygen (DO) level, with low DO values favoring the growth of the organisms. Microbiological observations made during the start-up and stable operation of the full-scale secondary treatment plant (maximum capacity 780 MGD) are also reported. No dominant filamentous species existed during the start-up period. Type 0803 and Type 1701, indicators of low oxygen level for the applied food to microorganism ratio, confirmed the low DO conditions of activated sludge tanks.