Development and evaluation of a TaqMan duplex real-time PCR quantification method for reliable enumeration of Candidatus Microthrix

Assessing spatial distribution, genetic variants, and virulence of pathogen Mycoplasma agassizii in threatened Mojave desert tortoises

Mojave desert tortoises (Gopherus agassizii), a threatened species under the US Endangered Species Act, are long-lived reptiles that experience a chronic respiratory disease. The virulence of primary etiologic agent, Mycoplasma agassizii, remains poorly understood, but it exhibits temporal and geographic variability in causing disease outbreaks in host tortoises. Multiple attempts to culture and characterize the diversity of M. agassizii have had minimal success, even though this opportunistic pathogen chronically persists in nearly every population of Mojave desert tortoises. The current geographic range and the molecular mechanisms of virulence of the type-strain, PS6T, are unknown, and the bacterium is thought to have low-to-moderate virulence. We designed a quantitative polymerase chain reaction (qPCR) targeting three putative virulence genes annotated on the PS6T genome as exo-α-sialidases, enzymes which facilitate growth in many bacterial pathogens. We tested 140 M. agassizii-positive DNA samples collected from 2010 to 2012 across the range of Mojave desert tortoises. We found evidence of multiple-strain infections within hosts. We also found the prevalence of these sialidase-encoding genes to be highest in tortoise populations surrounding southern Nevada, the area from which PS6T was originally isolated. We found a general pattern of loss or reduced presence of sialidase among strains, even within a single host. However, in samples that were positive for any of the putative sialidase genes, one particular gene (528), was positively associated with bacterial loads of M. agassizii and may act as a growth factor for the bacterium. Our results suggest three evolutionary patterns: (1) high levels of variation, possibly due to neutral changes and chronic persistence, (2) a trade-off between moderate virulence and transmission, and (3) selection against virulence in environmental conditions known to be physiologically stressful to the host. Our approach of quantifying genetic variation via qPCR represents a useful model of studying host-pathogen dynamics.

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.

Recent advances in understanding the ecology of the filamentous bacteria responsible for activated sludge bulking

Activated sludge bulking caused by filamentous bacteria is still a problem in wastewater treatment plants around the world. Bulking is a microbiological problem, and so its solution on species-specific basis is likely to be reached only after their ecology, physiology and metabolism is better understood. Culture-independent molecular methods have provided much useful information about this group of organisms, and in this review, the methods employed and the information they provide are critically assessed. Their application to understanding bulking caused by the most frequently seen filament in Japan, 'Ca. Kouleothrix', is used here as an example of how these techniques might be used to develop control strategies. Whole genome sequences are now available for some of filamentous bacteria responsible for bulking, and so it is possible to understand why these filaments might thrive in activated sludge plants, and provide clues as to how eventually they might be controlled specifically.

Abundance of total and metabolically active Candidatus Microthrix and fungal populations in three full-scale wastewater treatment plants

The abundances of total and metabolically active populations of Candidatus Microthrix and Fungi were evaluated by quantitative PCR (qPCR) and retrotranscribed qPCR of ribosomal molecular markers in three different full-scale wastewater treatment plants (WWTPs), in absence of bulking/foaming episodes. Significant differences of the abundance of rDNAs and rRNAs of Candidatus Microthrix and Fungi were observed among the three WWTPs. The average relative abundances of 16S rDNA copies of Candidatus Microthrix to those of Bacteria ranged 3.4-8.9%. Biota-environment analysis (BIO-ENV) demonstrated that the number of copies of both 16S rDNA and rRNA of Candidatus Microthrix increased at longer hydraulic and solids' retention times and with higher nitrate concentrations in the activated sludge. The abundance of Candidatus Microthrix correlated strongly and positively with the removal efficiencies of organic matter and total nitrogen in the tested WWTPs, highlighting the role of these particular microbial group in the performance of these engineered systems.

Labeling of Microthrix parvicella in situ: A novel FRET probe based on bisoctyl rhodamine B

Filamentous bacteria, particularly Microthrix parvicella, are mainly responsible for bulking or foaming of activated sludge. Based on the affinity of M. parvicella to the hydrophobic characteristics of long-chain fatty acids, a novel bisoctyl rhodamine B (BORB) and a novel fluorescence resonance energy transfer (FRET) complex probe were prepared herein to study their properties. When the FRET probe was used in in situ activated sludge, M. parvicella was clearly labeled at 20 nmol/L, which was a reduction of 50 times compared to that of the BORB (1 μmol/L) alone and 500 times compared to the carbazole-quinoline probe reported previously. Compared with fluorescence in situ hybridization, M. parvicella could be clearly labeled using BORB and the FRET probe in situ without requiring complicated pretreatments (i.e., shock and broken process, fixed sample, digestion, and lysozyme treatment). This study discusses the facile approach developed for labeling M. parvicella in early warning expansion, thereby inhibiting and controlling sludge bulking in situ.

A novel fluorescent long-chain fatty acid-substituted dye: labeling and biodegrading of Microthrix parvicella

Microthrix parvicella (M. parvicella) is a filamentous bacterium that induces bulking in activated sludge. Here, we used the affinity of long-chain fatty acids (LCFA) for M. parvicella to create a novel fluorescent probe of carbazole modified by LCFA. The structure was characterized by ¹H NMR spectroscopy and mass spectrometry. The spectral properties, photostability, and hydrophobic properties of the probe were also characterized. Fluorescent-labeling results showed that it can label M. parvicella in situ and could be biodegraded via metabolism. The stable docking mode of carbazole probes with different fatty acid chains and lipases was also docked by the density functional tight-binding (DFTB) method.

M. parvicella in situ could be biodegraded by a novel fluorescent probe of carbazole modified by LCFA(FP1).

A probe-based qRT-PCR method to profile immunological gene expression in blood of captive beluga whales (Delphinapterus leucas)

Cytokines are fundamental for a functioning immune system, and thus potentially serve as important indicators of animal health. Quantitation of mRNA using quantitative reverse transcription polymerase chain reaction (qRT-PCR) is an established immunological technique. It is particularly suitable for detecting the expression of proteins against which monoclonal antibodies are not available. In this study, we developed a probe-based quantitative gene expression assay for immunological assessment of captive beluga whales (Delphinapterus leucas) that is one of the most common cetacean species on display in aquariums worldwide. Six immunologically relevant genes (IL-2Rα, -4, -10, -12, TNFα, and IFNγ) were selected for analysis, and two validated housekeeping genes (PGK1 and RPL4) with stable expression were used as reference genes. Sixteen blood samples were obtained from four animals with different health conditions and stored in RNAlater™ solution. These samples were used for RNA extraction followed by qRT-PCR analysis. Analysis of gene transcripts was performed by relative quantitation using the comparative Cq method with the integration of amplification efficiency and two reference genes. The expression levels of each gene in the samples from clinically healthy animals were normally distributed. Transcript outliers for IL-2Rα, IL-4, IL-12, TNFα, and IFNγ were noticed in four samples collected from two clinically unhealthy animals. This assay has the potential to identify immune system deviation from normal state, which is caused by health problems. Furthermore, knowing the immune status of captive cetaceans could help both trainers and veterinarians in implementing preventive approaches prior to disease onset.

On-filter direct amplification of Legionella pneumophila for rapid assessment of its abundance and viability

Guidelines and regulations to control Legionella pneumophila in cooling water systems of large buildings are evolving due to the increasing number of outbreaks. Rapid, on-site, simple, and sensitive quantification methods that are also able to assess viability may be extremely useful in monitoring and control. Culture-based methods for measuring L. pneumophila may take 4-10 days and qPCR-based methods are also slow, requiring at least a day from sample to result, albeit mainly due to the need for sample transport to a centralized laboratory. This study reports a rapid isothermal amplification method for L. pneumophila concentration and detection with live/dead differentiation under field conditions. Using an on-filter direct amplification (i.e., amplification of cells without DNA extraction and purification) approach with propidium monoazide (PMA), and a real time isothermal amplification platform (Gene-Z), L. pneumophila could be detected in 1-2 h at ∼1 cfu/100 ml of tap water. Signature sequences from 16S rRNA and cadA genes were used as genetic markers for L. pneumophila and loop-mediated isothermal amplification (LAMP) primers were designed using Primer Explorer V4. Result were also compared with direct amplification of cells spiked into distilled, tap, and cooling water samples as well as extracted DNA by qPCR. This method may be useful to managers of cooling water systems in large buildings for rapid detection of L. pneumophila. The overall approach of on-site sample concentration, on-filter amplification, and live/dead differentiation may be extended to other organisms where analytical sensitivity and speed are equally important.

Design Mechanism and Property of the Novel Fluorescent Probes for the Identification of Microthrix Parvicella In Situ

In this study, two novel fluorescent probes, probe A and probe B were designed, synthesized and characterized, based on Microthrix parvicella (M. parvicella) preferring to utilize long-chain fatty acid (LCFA), for the labeling of M. parvicella in activated sludge. The molecular structure of probe A and probe B include long-chain alkane and LCFA, respectively. The results indicated that probe A and probe B had a large stokes shift of 118 nm and 120 nm and high quantum yield of 0.1043 and 0.1058, respectively, which were significantly helpful for the fluorescent labeling. As probe A was more stable than probe B in activated sludge, and the fluorescence intensity keep stable during 24 h, probe A was more suitable for labeling M. parvicella in situ. In addition, through the Image Pro Plus 6 (IPP 6) analysis, a quantitative relationship was established between sludge volume index (SVI) and integral optical density (IOD) of the labeled M. parvicella in activated sludge samples. The relationship between IOD and SVI conforms to Logistic curve (R² = 0.94).

Quantifying in situ growth rate of a filamentous bacterial species in activated sludge using rRNA:rDNA ratio

If the in situ growth rate of filamentous bacteria in activated sludge can be quantified, researchers can more accurately assess the effect of operating conditions on the growth of filaments and improve the mathematical modeling of filamentous bulking. We developed a method to quantify the in situ specific growth rate of Sphaerotilus natans (a model filament) in activated sludge using the species-specific 16S rRNA:rDNA ratio. Primers targeting the 16S rRNA of S. natans were designed, and real-time PCR and RT-PCR were used to quantify DNA and RNA levels of S. natans, respectively. A positive linear relationship was found between the rRNA:rDNA ratio (from 440 to 4500) and the specific growth rate of S. natans (from 0.036 to 0.172 h^-1) using chemostat experiments. The in situ growth rates of S. natans in activated sludge samples from three water reclamation facilities were quantified, illustrating how the approach can be applied in a complex environment such as activated sludge.

Influence of different anoxic time exposures on active biomass, protozoa and filamentous bacteria in activated sludge

Medium-sized wastewater treatment plants are considered too small to implement anaerobic digestion technologies and too large for extensive treatments. A promising option as a sewage sludge reduction method is the inclusion of anoxic time exposures. In the present study, three different anoxic time exposures of 12, 6 and 4 hours have been studied to reduce sewage sludge production. The best anoxic time exposure was observed under anoxic/oxic cycles of 6 hours, which reduced 29.63% of the biomass production compared with the oxic control conditions. The sludge under different anoxic time exposures, even with a lower active biomass concentration than the oxic control conditions, showed a much higher metabolic activity than the oxic control conditions. Microbiological results suggested that both protozoa density and abundance of filamentous bacteria decrease under anoxic time exposures compared to oxic control conditions. The anoxic time exposures 6/6 showed the highest reduction in both protozoa density, 37.5%, and abundance of filamentous bacteria, 41.1%, in comparison to the oxic control conditions. The groups of crawling ciliates, carnivorous ciliates and filamentous bacteria were highly influenced by the anoxic time exposures. Protozoa density and abundance of filamentous bacteria have been shown as promising bioindicators of biomass production reduction.

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.

In situ microscopy as a tool for the monitoring of filamentous bacteria: a case study in an industrial activated sludge system dominated by M. parvicella

The present study demonstrates the application of in situ microscopy for monitoring the growth of filamentous bacteria which can induce disturbances in an industrial activated sludge process. An in situ microscope (ISM) is immersed directly into samples of activated sludge with Microthrix parvicella as dominating species. Without needing further preparatory steps, the automatic evaluation of the ISM-images generates two signals: the number of individual filaments per image (ISM-filament counting) and the total extended filament length (TEFL) per image (ISM-online TEFL). In this first version of the image-processing algorithm, closely spaced crossing filament-segments or filaments within bulk material are not detected. The signals show highly linear correlation both with the standard filament index and the TEFL. Correlations were further substantiated by comparison with real-time polymerase chain reaction (real-time PCR) measurements of M. parvicella and of the diluted sludge volume index. In this case study, in situ microscopy proved to be a suitable tool for straightforward online-monitoring of filamentous bacteria in activated sludge systems. With future adaptation of the system to different filament morphologies, including cross-linking filaments, bundles, and attached growth, the system will be applicable to other wastewater treatment plants.

A Novel Separation Method of Microthrix parvicella Filaments from Activated Sludge by a Hydrophobic Plate

The aim of this paper is to develop a novel method to separate Microthrix parvicella (M. parvicella) filaments from activated sludge easily and quickly, as there are a few difficulties in the isolation of M. parvicella filaments, such as complicated isolation process, time consuming, etc. In this work, a series of hydrophobic plate with and without microchannels have been prepared for the separation of M. parvicella filaments. The results showed that the presence of microchannels and hydrophobic property of the hydrophobic plates affected the separation efficiency of M. parvicella significantly. The scanning electron microscope and Keyence Digital Microscope analysis results showed that the diameter of microchannels was similar to the width of M. parvicella filament, which was beneficial for the fastening of M. parvicella filaments on the plate. The hydrophobic property of the prepared plates was tested by contact angle of water droplets, and the results displayed that the polydimethylsiloxane (PDMS) plate possessed the highest contact angle compared with that of other plates, like polymethylmethacrylate, polystyrene plate, and PDMS plate with no hydrophobic microchannels. Thus, it was concluded that the high separation efficiency of PDMS plates to M. parvicella filaments was due to its best hydrophobic property.

Development and validation of a harmonized TaqMan-based triplex real-time RT-PCR protocol for the quantitative detection of normalized gene expression profiles of seven porcine cytokines

Dysregulation of cytokine responses plays a major role in the pathogenesis of severe and life-threatening infectious diseases like septicemia or viral hemorrhagic fevers. In pigs, diseases like African and classical swine fever are known to show exaggerated cytokine releases. To study these responses and their impact on disease severity and outcome in detail, reliable, highly specific and sensitive methods are needed. For cytokine research on the molecular level, real-time RT-PCRs have been proven to be suitable. Yet, the currently available and most commonly used SYBR Green I assays or heterogeneous gel-based RT-PCRs for swine show a significant lack of specificity and sensitivity. The latter is however absolutely essential for an accurate quantification of rare cytokine transcripts as well as for detection of small changes in gene expressions. For this reason, a harmonized TaqMan-based triplex real-time RT-PCR protocol for the quantitative detection of normalized gene expression profiles of seven porcine cytokines was designed and validated within the presented study. Cytokines were chosen to represent different immunological pathways and targets known to be involved in the pathogenesis of the above mentioned porcine diseases, namely interleukin (IL)-1β, IL-2, IL-4, IL-6, IL-8, tumor necrosis factor (TNF)-α and interferon (IFN)-α. Beta-Actin and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) served as reference genes for normalization. For absolute quantification a synthetic standard plasmid was constructed comprising all target cytokines and reference genes within a single molecule allowing the generation of positive control RNA. The standard as well as positive RNAs from samples, and additionally more than 400 clinical samples, which were collected from animal trials, were included in the validation process to assess analytical sensitivity and applicability under routine conditions. The resulting assay allows the reliable assessment of gene expression profiles and provides a broad applicability to any kind of immunological research in swine.