Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies.

Universal oligonucleotide hybridization probes targeting the small-subunit rRNA are commonly used to quantify total microbial representation in environmental samples. Universal probes also serve to normalize results obtained with probes targeting specific phylogenetic groups of microorganisms. In this study, six universal probes were evaluated for stability of probe-target duplexes by using rRNA from nine organisms representing the three domains of Bacteria, Archaea, and Eucarya. Domain-specific variations in dissociation temperatures were observed for all probes. This could lead to a significant bias when these probes are used to quantify microbial populations in environmental samples. We suggest lowering the posthybridization wash stringency for two of the universal probes (S-*-Univ-1390-a-A-18 and S-*-Univ-1392-a-A-15) examined. These two probes were evaluated with traditional and modified hybridization conditions to characterize defined mixtures of rRNAs extracted from pure cultures and rRNA samples obtained from anaerobic digester samples. Probe S-*-Univ-1390-a-A-18 provided excellent estimations of domain-level community composition of these samples and is recommended for future use in microbial ecology studies.     

16S rRNA sequence analysis of bacteria present in foaming activated sludge

The formation of a stable viscous foam on activated sludge aeration basin surfaces is a world wide problem. Foam is usually comprised of filamentous bacteria occurring predominantly in the mixed liquor. The lack of availability of pure cultures of most filaments and the limited amount of characterisation data available for them, means that our current understanding of their taxonomic position is very poor and their relationship to other bacteria are not known. 16S rDNA sequencing was used in an attempt to identify the bacteria in a foaming sample from the Centurion Waste Water Treatment Plant in Gauteng South Africa.     

Group-specific 16S rRNA hybridization probes for determinative and community structure studies of Butyrivibrio fibrisolvens in the rumen.

Oligonucleotide probes covering three phylogenetically defined groups of Butyrivibrio spp. were successfully designed and tested. The specificity of each probe was examined by hybridization to rRNAs from an assortment of B. fibrisolvens isolates as well as additional ruminal and nonruminal bacteria. The sensitivity of the hybridization method was determined by using one of the probes (probe 156). When RNA was extracted from a culture of OB156, the probe was able to detect target cells at densities as low as 10(4) cells/ml. When 10(4) or more target cells/ml were added to cattle rumen samples, detectable hybridization signals were obtained with 1,000 ng of total RNA loaded onto the nylon membrane. In contrast, the sensitivity was reduced to 10(6) target cells/ml at 100 ng of RNA per slot. The probes were used to type 19 novel Butyrivibrio isolates. The phylogenetic placement was confirmed by partial 16S rRNA gene sequencing. The use of the probes in community-based studies indicated that the Butyrivibrio groups examined in this paper did not represent a significant portion of the bacterial 16S rRNA pool in the rumen of the cattle, sheep, and deer examined.     

"Microthrix parvicella", a filamentous bacterium causing bulking and foaming in activated sludge systems: a review of current knowledge

This review summarizes the microbiology and physiology of "Microthrix parvicella" and the methods of its growth control in activated sludge wastewater treatment plants. This filamentous bacterium is of high interest because of its worldwide involvement in severe bulking and foaming at wastewater treatment plants. We present a critical analysis of physiological and kinetic data on "M. parvicella" and discuss its growth and storage abilities in various environments with the aim of understanding the strategies of this organism to successfully compete with other bacteria in activated sludge. Additionally, this review elaborates on research needs for defining reliable control strategies of bulking and foaming based on key features of "M. parvicella".     

Monitoring filamentous bulking in activated sludge systems fed by synthetic or municipal wastewater

The stability with respect to filamentous bulking of two activated sludge fully-aerobic systems, one with a completely mixed tank and one with a channel reactor, fed either by a synthetic wastewater or by a primary-settled municipal wastewater, of variable composition and flow rate, has been investigated. The morphological characteristics of the biomass in terms of floc size and roughness and of filamentous bacteria abundance have been monitored by image analysis. Severe bulking was only observed in the well-mixed tank fed at a constant flow rate by synthetic substrate of constant concentration, when the channel reactor fed in a similar manner was fully stable. Variations of biomass characteristics as well as of settling properties were observed on both systems fed with the real wastewater, but these events were related to the characteristics of the wastewater, as similar changes were observed on the full-scale plant fed with the same substrate. In any case, automated image analysis was an efficient way to monitor in detail the fate of the activated sludge at pilot and full scale.     

Quantitative use of fluorescent in situ hybridization to examine relationships between mycolic acid-containing actinomycetes and foaming in activated sludge plants

The formation of viscous foams on aeration basins and secondary clarifiers of activated sludge plants is a common and widespread problem. Foam formation is often attributed to the presence of mycolic acid-containing actinomycetes (mycolata). In order to examine the relationship between the number of mycolata and foam, we developed a group-specific probe targeting the 16S rRNA of the mycolata, a protocol to permeabilize mycolata, and a statistically robust quantification method. Statistical analyses showed that a lipase-based permeabilization method was quantitatively superior to previously described methods (P < 0.05). When mixed liquor and foam samples were examined, most of the mycolata present were rods or cocci, although filamentous mycolata were also observed. A nested analysis of variance showed that virtually all of the measured variance occurred between fields of view and not between samples. On this basis we determined that as few as five fields of view could be used to give a statistically meaningful sample. Quantitative fluorescent in situ hybridization (FISH) was used to examine the relationship between foaming and the concentration of mycolata in a 20-m(3) completely mixed activated sludge plant. Foaming occurred when the number of mycolata exceeded a certain threshold value. Baffling of the plant affected foaming without affecting the number of mycolata. We tentatively estimated that the threshold foaming concentration of mycolata was about 2 x 10(6) cells ml(-1) or 4 x 10(12) cells m(-2). We concluded that quantitative use of FISH is feasible and that quantification is a prerequisite for rational investigation of foaming in activated sludge.     

Actinomycete diversity associated with foaming in activated sludge plants

Large numbers of mycolic acid-containing actinomycetes were isolated from foam and scum samples taken from three activated-sludge sewage-treatment plants using several selective isolation media. Organisms presumptively identified as gordonae formed the dominant population in all of the samples. A representative set of these strains have chemical properties consistent with their classification in the genusGordona. Forty-eight of theGordona strains were compared through 165 unit characters with the type strains of validly described species ofGordona. The resultant data were examined using the Jaccard and simple matching coefficients and clustering achieved using the unweighted pair group method with arithmetic averages algorithm. The numerical classification was only marginally affected by the statistics used or by test error, estimated as 3.92%. The isolates were assigned to five multi-membered and 28 single-membered clusters defined by the simple matching coefficient at the 89% similarity level. With few exceptions, the isolates were sharply separated from theGordona marker strains. Essentially the same classification was obtained when the test strains were examined using a Curie-point pyrolysis mass spectrometric procedure. It can be concluded that the gordonae form a heterogeneous taxonomic group, the members of which can be distinguished from representatives of validly described species ofGordona.     

Relationship of species-specific filament levels to filamentous bulking in activated sludge

To examine the relationship between activated-sludge bulking and levels of specific filamentous bacteria, we developed a statistics-based quantification method for estimating the biomass levels of specific filaments using 16S rRNA-targeted fluorescent in situ hybridization (FISH) probes. The results of quantitative FISH for the filament Sphaerotilus natans were similar to the results of quantitative membrane hybridization in a sample from a full-scale wastewater treatment plant. Laboratory-scale reactors were operated under different flow conditions to develop bulking and nonbulking sludge and were bioaugmented with S. natans cells to stimulate bulking. Instead of S. natans, the filament Eikelboom type 1851 became dominant in the reactors. Levels of type 1851 filaments extending out of the flocs correlated strongly with the sludge volume index, and extended filament lengths of approximately 6 x 10(8) micro m ml(-1) resulted in bulking in laboratory-scale and full-scale activated-sludge samples. Quantitative FISH showed that high levels of filaments occurred inside the flocs in nonbulking sludge, supporting the "substrate diffusion limitation" hypothesis for bulking. The approach will allow the monitoring of incremental improvements in bulking control methods and the delineation of the operational conditions that lead to bulking due to specific filaments.     

Nocardia foaming control in activated sludge process treating domestic wastewater

In this study, filamentous bacteria (Nocardia amarae) were identified as the major causal microorganism in foaming sludge. The results of growth kinetics study indicated that N. amarae had a relatively strong affinity for non-readily biodegradable fatty acids. N. amarae was able to consume various fatty acids at a constant growth yield from 0.413 to 0.487 g/gCOD. Under common F/M ratio (less than 0.5 g BOD/gMLSS/d) used in activated sludge processes, specific growth rate of N. amarae was found to be more significant than that of non-filamentous bacteria. Based on this feature, a novel technique feast-fast operation (FFO) was developed for the foaming control. The sludge volume index (SVI) rapidly decreased from 300 to 80 mL/g and further stabilized at about 70 mL/g and the system was free from stable foam, while the BOD removal efficiency was maintained above 95%. This control technology effectively suppressed the overgrowth of filaments and improved the settleability of activated sludge without adverse effects on the treatment performance and the process stability.     

Identity and ecophysiology of filamentous bacteria in activated sludge

Excessive growth of filamentous bacteria in activated sludge wastewater treatment plants (WWTPs) can cause serious operational problems. With some filaments there may be the problem of bulking, where inadequate flocculation and settling of the biomass in the secondary clarifier results in a carryover of solids with the final treated liquid effluent. Their proliferation often encourages the development of stable foams on the surface of the reactors, and these foams may impact negatively on plant performance and operation. The availability of culture-independent molecular methods now allows us to identify many of the more common filamentous organisms encountered in WWTPs, which are phylogenetically diverse, affiliating to seven separate bacterial phyla. Furthermore, the extensive data published in the past decade on their in situ behaviour from the application of these culture-independent methods have not been summarized or reviewed critically. Hence, here, we attempt to discuss what we now know about their identity, ecophysiology and ecological niches and its practical value in better managing activated sludge processes. Some of this knowledge is already being applied to control and manage full-scale WWTPs better, and the hope is that this review will contribute towards further developments in this field of environmental microbiology.     

Novel filamentous spore-forming iron bacteria causes bulking in activated sludge

Several Gram-positive iron bacteria were isolated from bulking sludge. They were filamentous and had false branching. They had sheaths with iron deposits and formed spores on modified sucrose casitone yeast extract agar. They did not grow on influsion agar for longer than 1 month but could withstand 80°C for 1 h on the same medium. Adding them to sewage before aeration increased the biochemical oxygen demand of waste water and caused poor settling properties of activated sludges. They were the predominant filamentous micro-organisms in bulking activated sludges. At present, these strains cannot be assigned to recognized taxa of Bacillus spp. or sheathed iron bacteria.     

Bacteriology of activated sludge,in particular the filamentous bacteria

Microscopic examination of bulking activated sludge samples showed the presence of a variety of filamentous microorganisms, some of which have not yet been described in the literature. A method was developed to obtain pure cultures of these threaded bacteria. To date, five clearly different groups of filamentous bacteria may be distinguished by the determination of a few morphological and physiological characteristics of the isolates. A variety of sheathed bacteria are included in Group I. Group II includes non-motile, gram-negative, orange- or yellow-pigmented filamentous bacteria. These microorganisms are thought to be related to some species of the genusFlavobacterium. The gram-negative, threaded bacteria of Group III show a more or less distinct gliding movement and form red colonies on rich agar media. These bacteria may apparently be related to species described in the generaMicroscilla andFlexibacter. The filamentous bacteria of Group IV structurally resemble someCyanophyceae, but do not contain photosynthetic pigments. They are gram-positive and non-motile. A number of unknown, non-motile bacteria which stain gram-positive with a variable number of gram-negative autolyzed cells in the filaments, are assigned to Group V. The properties of the isolated bacteria are described briefly and their occurrence in bulking activated sludge is discussed.     

Ecophysiology of the filamentous Alphaproteobacterium Meganema perideroedes in activated sludge

A comprehensive study of the ecophysiology of the filamentous Meganema perideroedes affiliated to the Alphaproteobacteria, possessing a "Nostocoida limicola Type II" filamentous morphology was conducted. This morphotype often causes serious bulking problems in activated sludge wastewater treatment plants, and hardly anything is known about its physiology. The study was carried out by applying a suite of in situ methods in an industrial activated sludge treatment plant with excessive growth of this species. The experiments revealed a very versatile organism able to take up a large variety of organic substrates under aerobic conditions. It had a remarkably high storage capacity forming polyhydroxyalkanoates from most substrates tested. When nitrate was present as e-acceptor, the number of substrates to be consumed by M. perideroedes was more restricted compared to aerobic conditions. With nitrite as e-acceptor, only acetate and glucose among the substrates tested could be assimilated and used for storage and possibly growth. This indicated that M. perideroedes might be able to denitrify under certain conditions, which is unusual for filamentous bacteria in activated sludge. No substrate uptake or storage was seen under anaerobic conditions. M. perideroedes was relatively hydrophobic, compared to other filamentous bacteria and microcolonies present in the sludge, indicating the presence of a hydrophobic sheath. Several excreted surface-associated exoenzymes were detected in the sludge, but M. perideroedes never showed any activity, except once after a breakdown in the production facility. This confirmed that M. perideroedes mainly grows on soluble substrates. Based on the studies of the ecophysiology of M. perideroedes, potential control strategies are suggested.     

A novel method of enumerating Nocardia amarae in foaming activated sludge

Various experimental investigations were carried out in order to develop a novel method of enumerating Nocardia amarae in foaming activated sludge using n-octadecane as a carbon source (OD medium). Colonies of N. amarae isolate appeared about 3 d earlier on OD medium than on MS medium. N. amarae counts on OD medium with 20 mg/l of nalidixic acid, using both synthetic and practical activated sludges, were always higher than those on MS medium. It is concluded that OD medium with nalidixic acid was more effective for the count of N. amarae in activated sludge than MS medium.     

Upgrading activated sludge systems and reduction in excess sludge

Most of 200 Activated Sludge Plant in Iran are overloaded and as a result, their efficiency is low. In this work, a pilot plant is manufactured and put into operation in one of the wastewater treatment plants in the west of Tehran. Instead of conventional activated sludge, a membrane bioreactor and an upflow anaerobic sludge blanket reactor used as a pretreatment unit in this pilot. For the sake of data accuracy and precision, an enriched municipal wastewater was opted as an influent to the pilot. Based on the attained result, the optimum retention time in this system was 4h, and the overall COD removal efficiency was 98%. As a whole, the application of this retrofit would increase the plant's capacity by a factor of 5 and reducing the excess sludge by a factor of 10. The sludge volume index in the anaerobic reactor was about 12 after granulation occurred.     

Isolation and characterization of filamentous bacteria present in bulking activated sludge

Summary Several types of filamentous microorganisms were observed and identified in samples of poorly settling (bulking) activated sludge. The major types encountered and the frequency (percentage) of appearance in the total of all treatment plants sampled were: Eikelboom type 0041 (60), type 1701 (45), Haliscomenobacter hydrossis (35), type 021N (30), Thiothrix spp. (20), and Sphaerotilus natans (20). Isolation techniques and culture media were developed and used to recover 42 axenic strains of filamentous bacteria from sludge samples collected. The isolates were identified as strains of Thiothrix, Beggiatoa, S. natans, and Eikelboom types 021N, 1701, 0041, and 0803. Nutritional and differential characterization of the bacteria was important to the differentiation of groups which could not be easily distinguished on the basis of morphology. Although certain treatment plant operating parameters (organic loading) seemed associated with the presence of specific filamentous organism types, possible interaction among factors precluded definite establishment of a cause and effect relationship for most of the treatment plant characteristics and organisms observed.     

Effects of synthetic polymer on the filamentous bacteria in activated sludge

Filamentous bulking is one of the solid-liquid separation problems always seen in activated sludge process. The addition of synthetic polymer is always one of the popular ways for the treatment plant operator to immediately solve the poor sludge settling problem. Therefore, it may be interesting to understand the effects of synthetic polymer on the filamentous bacteria in activated sludge. In this study, synthetic polymer was applied to a lab-scale wastewater treatment system with the filamentous bulking problem. The population structure of filamentous bacteria and sludge characteristics were investigated under different conditions. When synthetic polymer was added into the system, it was found that poor sludge settleability caused by filamentous bulking was temporarily solved and filamentous branches growing outside the flocs were damaged or inhibited. However, filamentous growth was still observed inside the flocs. After the addition of polymer was halted, filamentous branches extended out of the flocs immediately. Very serious filamentous bulking occurred and sludge settleability became much worse than that occurring before the addition of polymer. And, it took several weeks for the system to return to normal operation.