Sustained organic loading disturbance favors nitrite accumulation in bioreactors with variable resistance, recovery and resilience of nitrification and nitrifiers

Sustained disturbances are relevant for environmental biotechnology as they can lead to alternative stable states in a system that may not be reversible. Here, we tested the effect of a sustained organic loading alteration (food-to-biomass ratio, F:M, and carbon-to-nitrogen ratio, C:N) on activated sludge bioreactors, focusing on the stability of nitrification and nitrifiers. Two sets of replicate 5-L sequencing batch reactors were operated at different, low and high, F:M (0.19–0.36 mg COD/mg TSS/d) and C:N (3.5–6.3 mg COD/mg TKN) conditions for a period of 74 days, following 53 days of sludge acclimation. Recovery and resilience were tested during the last 14 days by operating all reactors at low F:M and C:N (henceforth termed F:M–C:N). Stable nitrite accumulation (77%) was achieved through high F:M–C:N loading with a concurrent reduction in the abundance of Nitrospira. Subsequently, only two of the three reactors experiencing a switch back from high to low F:M–C:N recovered the nitrite oxidation function, with an increase in Nitrobacter as the predominant NOB, without a recovery of Nitrospira. The AOB community was more diverse, resistant and resilient than the NOB community. We showed that functional recovery and resilience can vary across replicate reactors, and that nitrification recovery need not coincide with a return to the initial nitrifying community structure.

Comparison of human and southern sea otter (Enhydra lutris nereis) health risks for infection with protozoa in nearshore waters

Cryptosporidium and Giardia spp. are waterborne, fecally-transmitted pathogens that cause economic loss due to gastroenteritis and beach closures. We applied quantitative microbial risk assessment (QMRA) to determine the health risks for humans and sea otters due to waterborne exposure of Cryptosporidium and Giardia spp. when swimming in three types of surface waters: river, stormwater and wastewater effluent during the wet and dry seasons in the central coast of California. This is the first application of QMRA to estimate both the probability of infection in Southern sea otters and the probability of illness in humans, using microbial source tracking (MST) as a variable. Children swimming close to stormwater discharges had an estimated Cryptosporidium-associated illness probability that exceeded the accepted U.S. EPA criteria (32 illnesses/1000 swimmers or 3.2%). Based on the assumption that sea otters are as susceptible as humans to Cryptosporidium infection, the infection probabilities were close to 2% and 16% when sea otters were swimming at the end of points of rivers and stormwater discharges, respectively. In the case of Giardia, infection probabilities of 11% and 23% were estimated for sea otters swimming at the end of point of wastewater discharges, assuming that sea otters are as susceptible as gerbils and humans, respectively. The results of this QMRA suggest that 1) humans and sea otters are at risk when swimming at outflow sites for rivers, stormwater and treated wastewater effluent; 2) reduced loads of viable protozoan cysts and oocysts in recreational water can lessen the probability of infection of humans and sea otters; and 3) the risk of infection of humans and sea otters can be reduced with the treatment of wastewater to decrease oocyst and cyst viability before effluent is released into the sea.

Induction of gonadal maturation at different temperatures in burbot Lota lota

A rearing experiment was conducted to test whether temperature protocols that differed from a simulation of natural conditions might induce maturation after isothermal grow-out in burbot Lota lota. Lota lota were acclimated to two different temperature regimes: low temperature (LT), close to natural temperature at 4·0° C and elevated, high temperature (HT) at 8·5° C over 40 and 27 days respectively, with all fish then wintered for 47 days. Every second fish was treated with a gonadotropin-releasing hormone analogue. Maturational competence of oocytes was assessed with a germinal vesicle breakdown assay using a novel staining strategy. In both treatments, puberty and maturational progress occurred, characterised by an elevated gonado-somatic index and advanced gonadal stages (histological analysis). Progress of gonadal maturation was reflected by elevated plasma concentrations of testosterone and 11-ketosterone in males and 17β-oestradiol in females. Ovulation was not observed. Sperm could be activated equally across treatments. In general, LT was more effective than HT treatment, indicated by advanced gonadal stages, higher numbers of oocytes undergoing germinal vesicle breakdown in vitro and elevated sex steroid levels. Hormone treatment could improve effectiveness at HT. In conclusion, less drastic temperature regimes as previously reported in combination with hormone treatments seem sufficient to induce maturation in L. lota after isothermal grow-out.

Acute and chronic nitrite toxicity in juvenile pike-perch (Sander lucioperca) and its compensation by chloride

Pike-perch Sander lucioperca is currently considered as one of the most promising candidates for production in freshwater recirculation aquaculture systems (RAS). Here, due to the lack of studies on nitrite (NO(2)(-)) toxicity in pike-perch, a flow-through exposure at 0, 0.44, 0.88, 1.75, 3.5, 7, 14 and 28 mg/L NO(2)(-)-N was carried out to determine the acute and chronic toxicity over a period of 32 days. In juvenile pike-perch, 120 h LC(50) was 6.1mg/L NO(2)(-)-N and at ≥14 mg/L NO(2)(-)-N all fish had died within 24 h. Chronic exposure revealed a significant build up of NO(2)(-) in the plasma as well as in the muscles at ≥0.44 mg/L NO(2)(-)-N peaking in fish exposed to the highest concentration of 3.5 mg/L NO(2)(-)-N after 32 days. Still, due to high individual variation methemoglobin (MetHb) was only significantly increased (p<0.01) at 3.5 mg/L NO(2)(-)-N. No adverse effects on red blood cells (RBC) and hematocrit were observed in any of the treatments. In a second experiment, compensation of NO(2)(-) toxicity at increasing chloride concentrations (40 (freshwater), 65, 90, 140, 240, 440 mg/L Cl(-)) was observed at a constant exposure of 10 mg/L NO(2)(-)-N for 42 days. At ≥240 mg/L Cl(-), NO(2)(-) build-up in blood plasma and muscle was completely inhibited. At lower Cl(-) concentrations (≤140 mg/L), NO(2)(-) was significantly increased in plasma, but only insignificantly elevated in muscle due to high individual variation. MetHb was increased significantly difference only at 40 mg/L Cl(-) (freshwater control) compared to the control. Again, high individual variations were observed. As a conclusion, S. lucioperca is moderately sensitive towards NO(2)(-) and acceptable levels in RAS should hence not exceed 1.75 mg/L NO(2)(-)-N to avoid MetHb formation. However, based on the 120 h LC(50) and a factor of 0.01 according to Sprague (1971), a NO(2)(-) concentration of ≤0.061 mg/L NO(2)(-)-N is considered as "safe." Thereby, no NO(2)(-) should accumulate in the plasma or muscle tissue during chronic exposure. For 10 mg/L NO(2)(-)-N, ≥240 mg/L chloride compensates for NO(2)(-) uptake in plasma and muscle.

Nutritional status and gene expression along the somatotropic axis in roach (Rutilus rutilus) infected with the tapeworm Ligula intestinalis

The tapeworm Ligula intestinalis inhibits gametogenesis of its fish host, the roach (Rutilus rutilus). We investigated whether L. intestinalis infection makes significant demands on nutritional resources and consequently manipulates the endocrine somatotropic axis of roach. Two groups of naturally infected and uninfected roach were studied: a field group (natural feeding) and a laboratory group (ad libitum food supply). In females, no significant impact of parasitization on storage substrates (glycogen, lipids, and protein) was detected, whereas in males, either lipid content of the liver (field group) or lipid of the muscle and glycogen of the liver (laboratory group) were slightly decreased. Except for the females of the field group, higher mRNA expression of growth hormone (gh) in the pituitary of infected fish was observed. Furthermore, the expression of hypophyseal somatolactin α and β (slα, slβ) was up-regulated in infected females of the field and laboratory group, respectively. In liver and muscle, mRNA expression of insulin-like growth factors (igf1, igf2) and igf receptor (igfr) remained either unchanged or were up-regulated with infection. Parasitization showed inconsistent effects on gh receptor 1 (ghr1) expression in liver and muscle, whereas ghr2 mRNA was mostly not influenced by infection. In general, the expression profile of genes involved in the somatotropic axis as well as the content of storage substances in infected roach did not resemble that of food-deprived fish either under natural or ad libitum feeding. In conclusion, the present study does not indicate starvation of L. intestinalis infected roach, and it is suggested that the inhibition of reproduction attenuated the nutritional demand of parasitization.

Role of IncP-1β plasmids pWDL7::rfp and pNB8c in chloroaniline catabolism as determined by genomic and functional analyses

Broad-host-range catabolic plasmids play an important role in bacterial degradation of man-made compounds. To gain insight into the role of these plasmids in chloroaniline degradation, we determined the first complete nucleotide sequences of an IncP-1 chloroaniline degradation plasmid, pWDL7::rfp and its close relative pNB8c, as well as the expression pattern, function, and bioaugmentation potential of the putative 3-chloroaniline (3-CA) oxidation genes. Based on phylogenetic analysis of backbone proteins, both plasmids are members of a distinct clade within the IncP-1β subgroup. The plasmids are almost identical, but whereas pWDL7::rfp carries a duplicate inverted catabolic transposon, Tn6063, containing a putative 3-CA oxidation gene cluster, dcaQTA1A2BR, pNB8c contains only a single copy of the transposon. No genes for an aromatic ring cleavage pathway were detected on either plasmid, suggesting that only the upper 3-CA degradation pathway was present. The dcaA1A2B gene products expressed from a high-copy-number vector were shown to convert 3-CA to 4-chlorocatechol in Escherichia coli. Slight differences in the dca promoter region between the plasmids and lack of induction of transcription of the pNB8c dca genes by 3-CA may explain previous findings that pNB8C does not confer 3-CA transformation. Bioaugmentation of activated sludge with pWDL7::rfp accelerated removal of 3-CA, but only in the presence of an additional carbon source. Successful bioaugmentation requires complementation of the upper pathway genes with chlorocatechol cleavage genes in indigenous bacteria. The genome sequences of these plasmids thus help explain the molecular basis of their catabolic activities.

Risks of seawater ozonation in recirculation aquaculture--effects of oxidative stress on animal welfare of juvenile turbot (Psetta maxima, L.)

Ozone is frequently used for water treatment and disinfection in recirculating aquaculture systems. However, due to the fragmentary data on chronic toxicity of ozone produced oxidants (OPO) and its safe concentrations, the daily application of ozone in aquaculture is challenging. To evaluate the chronic effects of sublethal OPO concentrations, juvenile turbot (Psetta maxima, L.) were exposed to OPO concentrations of 0.06, 0.10 and 0.15 mg/l for 21 days. Gills were analysed for histopathological alterations and mRNA expression of heat shock protein 70 (hsp70), hsp90 as well as glutathione-S-transferase (gst) were determined in the gills and the liver after 1d, 7d and 21 d. Histopathologic findings confirmed adverse effects at 0.10-0.15 mg/l, but these (necrosis, lamellar clubbing, hypertrophy, hyperplasia) could only be observed after an extended exposure (mostly 21 d), and were considered as irreversible tissue damage. Hsp70 expression in the gills was only significantly increased at the highest OPO concentration (0.15 mg/l) on 1d and 7d, and returned to basic levels until day 21. Hsp90 mRNA was already increased at 0.10mg/l after 1 and 7 days of exposure, and again was comparable to the control group on day 21. In contrast, elevated gst mRNA expression was only observed on day 7 at 0.10mg and 0.15 mg/l. Although similar trends were observed in the liver for all markers, differences were only significant in exceptional cases due to the high individual variation observed. Thus, mRNA expression in the gills rather than in the liver is recommended as a marker to characterize OPO-induced oxidative stress in turbot. It has to be noted that mRNA expression returned to basic levels on day 21 regardless the actual OPO concentration, suggesting a collapse of adaptive mechanisms as a possible explanation for the observed tissue damage.

Influence of temperature on puberty and maturation of pikeperch, Sander lucioperca

Among external factors, temperature is known to exhibit a prominent role in reproduction of temperate fish species. Here, temperature related induction of puberty in pikeperch Sander lucioperca was investigated. For the first time the key factors of the pikeperch brain-pituitary-gonad axis, targeting the mRNA expression of the luteinising hormone (LH) and the follicle stimulating hormone (FSH), as well as the plasma sex steroids estradiol (E2), testosterone (T), 11-ketotestosteron (11-KT) and 17α,20β-dihydroxy-4-pregnen-3-one (17,20β-P) were addressed in the experiment. Concomitant the maturational stages were described histologically. After 3 months, female pikeperch kept at 12°C revealed significant increases in the GSI and plasma E2 concentration and 90% of the females were mid-vitellogenic. After 5 months, females kept between 9 and 15°C exhibited significant up-regulation of E2 and GSI as well as comparable histological outcome. At 6 and 23°C in nearly all females stagnation of oogenesis was recorded. Congruently, T was increased at 12 and 15°C. Expression analysis revealed a significant up-regulation of LHβ and FSHβ mRNA in females from early-vitellogenesis, and from mid-spermatogenesis in males, correlated to elevated plasma concentrations of steroids (except for E2 in males). In conclusion, moderate temperatures (12-15°C for) for at least 3 months were required to proceed with first maturation in juvenile pikeperch. The most efficient effect was observed at 12°C, while high (23°C) or low (6°C) temperatures prevented gonadal maturation. So temperature was identified as a prime factor in the induction of puberty in pikeperch, as revealed by histological as well as endocrine parameters.

Perchlorate and ethylenethiourea induce different histological and molecular alterations in a non-mammalian vertebrate model of thyroid goitrogenesis

Despite evidence for a conserved role of thyroid-stimulating hormone (TSH) in regulating vertebrate thyroid function, molecular data on thyroid responses to TSH are mainly limited to mammalian species. In this study, we examined histological and molecular changes in the thyroid of Xenopus laevis tadpoles during a 12-day treatment with 20mg/l perchlorate (PER) and 50mg/l ethylenethiourea (ETU). Inhibition of thyroid hormone (TH) synthesis by PER and ETU was evident from developmental retardation, reduced expression of TH-regulated genes and up-regulation of tshb-A mRNA. Thyroid histopathology revealed goiters with strikingly different follicular morphologies following PER and ETU treatment. Using real-time PCR, we analyzed thyroids sampled on day 12 for differential expression of 60 candidate genes. Further temporal analyses were performed for a subset of 14 genes. Relative to the control, PER and ETU treatment modulated the expression of 51 and 49 transcripts, respectively. Particularly genes related to TH synthesis and protein metabolism were similarly affected by PER and ETU. However, several genes were differentially expressed in PER- and ETU-treated tadpoles. Specifically, goiter formation in the PER treatment was associated with low expression of genes related to DNA replication but high expression of negative growth regulators. Results from this work provide for the first time a characterization of gene expression profiles during goitrogenesis in a non-mammalian vertebrate model. Overall, our data suggest that, in addition to TSH over-stimulation, further mechanisms related to the mode of goitrogen action contribute to the regulation of thyroid gene expression.

Molecular quantitative analysis of human viruses in California stormwater

Many human pathogenic viruses are transmitted via the oral-fecal route and water is one possible vector, representing a risk for public health. Sixty-one large-volume water samples from storm drains in California were processed by a two-step hollow fiber ultrafiltration procedure followed by molecular analysis for human enterovirus and adenovirus types. Each sample was spiked with a surrogate, the benign bacteriophage PP7. Both surrogate and human viruses were quantified by newly designed TaqMan PCR assays. Equations were developed that account for the main variables in the procedure: recovery of the ultrafiltration, efficiency of nucleic acid extraction, and effect of inhibitors on the amplification of viral targets. Adenovirus 40/41 was detected in one sample at 230 genomes per liter, and no other adenovirus or enterovirus types were found. Samples that resulted in nondetects are reported together with the corresponding sample-specific limit of detection (S(LOD)), a useful tool when estimating the public health risk associated with the contact or ingestion of water. Virus concentrations did not correlate with traditional viable indicator concentrations or any of the physicochemical parameters measured. In contrast, coliform concentrations were correlated with total suspended solids. To our knowledge, this is the first study where all factors known to influence limits of detection have been investigated and integrated into equations that are widely applicable to the quantification of viruses or other microbial targets by PCR.

Expression of IGF-I and IGF-I receptor in male and female sterlet, Acipenser ruthenus--evidence for an important role in gonad maturation

Recent in vitro studies suggest that insulin-like growth factor I (IGF-I) is involved in cell differentiation and steroidogenesis in the gonad and could therefore function as an important trigger in vivo. In this study, sensitive real-time RT-PCR assays were used to determine IGF-I and the IGF-I receptor (IGF-IR) mRNA expression in maturing male and female sterlet (Acipenser ruthenus) over a period of two years: In the first year, females entering vitellogenesis (maturing female group, MFG) revealed an increase of IGF-I expression in the ovaries in contrast to females that did not enter vitellogenesis (non-maturing female group, NMFG). Congruently, IGF-IR expression was elevated in females at the onset of vitellogenesis (MFG), decreased towards the first winter, and increased to similar levels at late vitellogenesis in the second winter just prior to spawning. In the second year, NMFG reached the onset of vitellogenesis. Here, IGF-I and IGF-IR reached similar levels as previously observed in the first year in MFG. In males, low and constant IGF-I expression was observed in the testis, whereas IGF-IR was expressed at a constant high level comparable to those of females entering vitellogenesis. These findings suggest an involvement of IGF-I as an important paracrine regulator of gonad maturation, particularly in the ovary.

The role of the IGF-I system for vitellogenesis in maturing female sterlet, Acipenser ruthenus Linnaeus, 1758

Transition from previtellogeneic to vitellogenic oocyte growth is a critical phase for folliculogenesis in sturgeon and may often be postponed for several years. Recent findings on the involvement of insulin-like growth factor I (IGF-I) in cell differentiation processes of oocyte follicle and ovarian steroidogenesis of teleosts in vitro led to the hypothesis that paracrine IGF-I could function as a potential trigger in vivo. For the first time, IGF-I and its corresponding receptor (IGF-IR) were identified in a non-teleostean fish. Real-time PCR assays for IGF-I and IGF-IR mRNA were established, normalising mRNA expression of the target genes to beta-microglobulin (beta2m). We clearly show that expression of IGF-I in the gonad is a substantial source for IGF-I-mediated effects in follicles compared to liver, brain, muscle and adipose tissue. Among these tissues, IGF-IR mRNA was highest in the gonad. With regard to different cohorts of coexisting follicles, highest expression of IGF-I and IGF-IR were met in developing follicles, indicating that IGF-I functions as an intraovarian modulator of follicle faith. Comparing previtellogenic follicles in females that matured within two years with non-maturing females f the same age, revealed an increases of 2.3-fold for IGF-I and 2.8-fold for IGF-IR mRNA expression in maturing females. These findings implicate an important role of paracrine IGF-I in early vitellogenesis and identify it as candidate vitellogenesis inducing factor (VIF), determining the faith of the follicle.

Detection of Salmonella spp. in water using magnetic capture hybridization combined with PCR or real-time PCR

The removal of target DNA by magnetic capture hybridization (MCH) from constituents inhibitory to amplification by polymerase chain reaction (PCR) was evaluated using Salmonella as the test pathogen. Hybrids were subjected to both conventional and quantitative real-time PCR (qPCR). When PCR inhibitors commonly found in water were added to the reaction, MCH-PCR increased the detection sensitivity on the order of 8 to 2,000-fold compared with the system using only PCR. To determine the selectivity of MCH for target DNA (Salmonella), different amounts of non-target DNA (Escherichia coli) were added to the qPCR reaction. The highest non-target DNA concentration interfered with the amplification by qPCR alone, while MCH-qPCR was unaffected. Average recovery of Salmonella DNA by MCH-qPCR was 31% using optimized buffers, washing solutions and enzymatic digestion. A recovery function was proposed in order to calculate the real cell number based on the measured value. Preliminary testing confirmed the suitability of this method for analysis of natural waters.

Architecture of a nascent Sphingomonas sp. biofilm under varied hydrodynamic conditions

The architecture of a Sphingomonas biofilm was studied during early phases of its formation, using strain L138, a gfp-tagged derivative of Sphingomonas sp. strain LB126, as a model organism and flow cells and confocal laser scanning microscopy as experimental tools. Spatial and temporal distribution of cells and exopolymer secretions (EPS) within the biofilm, development of microcolonies under flow conditions representing varied Reynolds numbers, and changes in diffusion length with reference to EPS production were studied by sequential sacrificing of biofilms grown in multichannel flow cells and by time-lapse confocal imaging. The area of biofilm in terms of microscopic images required to ensure representative sampling varied by an order of magnitude when area of cell coverage (2 x 10(5) microm(2)) or microcolony size (1 x 10(6) microm(2)) was the biofilm parameter under investigation. Hence, it is necessary to establish the inherent variability of any biofilm metric one is attempting to quantify. Sphingomonas sp. strain L138 biofilm architecture consisted of microcolonies and extensive water channels. Biomass and EPS distribution were maximal at 8 to 9 mum above the substratum, with a high void fraction near the substratum. Time-lapse confocal imaging and digital image analysis showed that growth of the microcolonies was not uniform: adjacently located colonies registered significant growth or no growth at all. Microcolonies in the biofilm had the ability to move across the attachment surface as a unit, irrespective of fluid flow direction, indicating that movement of microcolonies is an inherent property of the biofilm. Width of water channels decreased as EPS production increased, resulting in increased diffusion distances in the biofilm. Changing hydrodynamic conditions (Reynolds numbers of 0.07, 52, and 87) had no discernible influence on the characteristics of microcolonies (size, shape, or orientation with respect to flow) during the first 24 h of biofilm development. Inherent factors appear to have overriding influence, vis-a-vis environmental factors, on early stages of microcolony development under these laminar flow conditions.

Compatibility of the green fluorescent protein and a general nucleic acid stain for quantitative description of a Pseudomonas putida biofilm

Better understanding of biofilm development is essential for making optimal use of beneficial biofilms as well as for devising effective control strategies for detrimental biofilms. Analysis of biofilm structure and quantification of biofilm parameters using optical (including confocal) microscopy and digital image analysis techniques are becoming routine in many laboratories. The purpose of this study was to evaluate a dual labeling technique based on fluorescence signals from the green fluorescent protein (GFP) and those resulting from staining with the general nucleic acid stain SYTO 60 for the quantitative description of a model biofilm. For this purpose, a Pseudomonas putida KT2442 derivative was genetically tagged with the green fluorescent protein gene. Biofilm formation by this strain was investigated using flow cells and confocal laser scanning microscopy (CLSM). Percentage surface coverage as well as microcolony size quantified using GFP and SYTO 60 signals showed significant correlation (R=0.99). The results indicated that intrinsic labelling of this model biofilm using constitutively expressed proteins such as GFP can be used for real-time biofilm observation and generation of reliable quantitative data, comparable to those obtained using conventional methods such as nucleic acid staining. Non-destructive time series observation of GFP-expressing biofilms in flow-cells can thus be confidently used for four-dimensional (x, y, z, t) analysis and quantification of biofilm development. The results also point to the possibility of using GFP and SYTO 60 to study dual species biofilms, as quantitative data generated using both fluorophore signals are comparable.

Microbial communities and their interactions in biofilm systems: an overview

Several important advances have been made in the study of biofilm microbial populations relating to their spatial structure (or architecture), their community structure, and their dependence on physicochemical parameters. With the knowledge that hydrodynamic forces influence biofilm architecture came the realization that metabolic processes may be enhanced if certain spatial structures can be forced. An example is the extent of plasmid-mediated horizontal gene transfer in biofilms. Recent in situ work in defined model systems has shown that the biofilm architecture plays a role for genetic transfer by bacterial conjugation in determining how far the donor cells can penetrate the biofilm. Open channels and pores allow for more efficient donor transport and hence more frequent cell collisions leading to rapid spread of the genes by horizontal gene transfer. Such insight into the physical environment of biofilms can be utilized for bioenhancement of catabolic processes by introduction of mobile genetic elements into an existing microbial community. If the donor organisms themselves persist, bioaugmentation can lead to successful establishment of newly introduced species and may be a more successful strategy than biostimulation (the addition of nutrients or specific carbon sources to stimulate the authochthonous population) as shown for an enrichment culture of nitrifying bacteria added to rotating disk biofilm reactors using fluorescent in situ hybridization (FISH) and microelectrode measurements of NH4+, NO2-, NO3-, and O2. However, few studies have been carried out on full-scale systems. Bioaugmentation and bioenhancement are most successful if a constant selective pressure can be maintained favoring the promulgation of the added enrichment culture. Overall, knowledge gain about microbial community interactions in biofilms continues to be driven by the availability of methods for the rapid analysis of microbial communities and their activities. Molecular tools can be grouped into those suitable for ex situ and in situ community analysis. Non-spatial community analysis, in the sense of assessing changes in microbial populations as a function of time or environmental conditions, relies on general fingerprinting methods, like DGGE and T-RFLP, performed on nucleic acids extracted from biofilm. These approaches have been most useful when combined with gene amplification, cloning and sequencing to assemble a phylogenetic inventory of microbial species. It is expected that the use of oligonucleotide microarrays will greatly facilitate the analysis of microbial communities and their activities in biofilms. Structure-activity relationships can be explored using incorporation of 13C-labeled substrates into microbial DNA and RNA to identify metabolically active community members. Finally, based on the DNA sequences in a biofilm, FISH probes can be designed to verify the abundance and spatial location of microbial community members. This in turn allows for in situ structure/function analysis when FISH is combined with microsensors, microautoradiography, and confocal laser scanning microscopy with advanced image analysis.

Bioaugmentation of a sequencing batch biofilm reactor by horizontal gene transfer

Bioaugmentation by introduction of catabolic genes residing on mobile genetic elements into the microbial community of a soil or wastewater environment might be an alternative to bioaugmentation by addition of bacterial cells with chromosomally encoded catabolic genes. This study investigates the possibility to enhance degradation of the xenobiotic model compound 2,4-dichlorophenoxyacetic acid in a sequencing batch biofilm reactor (SBBR) by using the conjugative plasmid pJP4 carrying genes for 2,4-D degradation. After introduction of a plasmid donor strain to a lab-scale SBBR operated without 2,4-D, the number of plasmid-carrying cells first dropped, and then increased after switching to 2,4-D as the sole carbon source. The donor cells were unable to grow in the applied synthetic wastewater with 2,4-D as the sole carbon source. Transconjugants could be detected both by culture-dependent and culture-independent methods in the 2,4-D degrading biofilm. In contrast to 90% 2,4-D degradation in the bioaugmented reactor within 40 h, a control reactor which had not received the plasmid still contained 60% of the initial 2,4-D concentration after 90 h. This experiment clearly demonstrates the introduction of 2,4-D degradative genes into a microbial biofilm and indicates that horizontal gene transfer is a promising tool for bioaugmentation of reactors treating wastewater.

Three-dimensional distribution of GFP-labeled Pseudomonas putida during biofilm formation on solid PAHs assessed by confocal laser scanning microscopy

Confocal laser scanning microscopy was used to monitor the colonization pattern of the gfp-labeled derivative strain of Pseudomonas putida ATCC 17514 on fluorene and phenanthrene crystals. The in situ experiments showed that P. putida tends to grow directly on phenanthrene, forming a biofilm on accessible crystalline surfaces. On the other hand, no significant biofilm formation was observed in the presence of fluorene. The results obtained showed that substrate properties affected bacterial strategy regarding uptake.

Using quantitative real-time PCR to determine the hygienic status of cattle manure

We developed a suitable system of DNA extraction and real-time quantitative polymerase chain reaction (qPCR) for the specific and sensitive quantification of pathogens and other relevant (indicator) organisms in recalcitrant material such as cattle manure. PCR inhibition by coextraction of humic compounds was minimized in this system, resulting in detection sensitivity of one target DNA copy per reaction well. Data from qPCR analysis for Escherichia coli agreed with cultivation based results, but orders of magnitude more fecal enterococci, Enterobacteriaceae and Campylobacter jejuni, were determined by qPCR than by cultivation. These bacteria may have been in a potentially hazardous active but non-cultivable state. The qPCR system is much less time consuming than conventional cultivation, highly specific, can detect non-cultivable organisms, provides high measurement throughput, and is cost attractive. It should be considered as an alternative in various application areas for (prescribed routine) cultivation based assays, e.g. for biosafety and hygiene monitoring.

Use of the pAL5000 replicon in PAH-degrading mycobacteria: application for strain labelling and promoter probing

Three environmental Mycobacterium strains (LB501T, LB307T and VM552) able to degrade anthracene, phenanthrene or pyrene, respectively, were successfully electroporated with pAL5000-based plasmids containing the green fluorescent protein (gfp) gene of Aequoria victoria under the control of the hsp60 promoter of Mycobacterium bovis following a slightly modified standard procedure. Transformants showed irregular gfp expression profiles. Four plasmid derivatives were constructed that contained gene promoters isolated from, and adapted to, gene expression in polycyclic aromatic hydrocarbon (PAH)-degrading mycobacteria. One derivative directed strong and homogeneous expression of GFP, allowing dual analysis of both GFP- and PAH-derived fluorescence as assessed by confocal laser scanning microscopy. The results reported here demonstrate the suitability of the pAL5000 replicon for the development of recombinant DNA-based studies in PAH-degrading Mycobacterium spp.

Community structure of micro- and macroflocs in pin-point sludge and the influence of sludge age and potassium addition on microfloc formation

Settling problems caused by pin-point sludge constitute a serious problem in biological wastewater treatment, particularly in many industrial plants. Until now, most studies focused on the relationship between pin-point sludge formation and either shearing forces or the impact of toxicants. This study deals with the community structure in both the micro- and macrofloc fraction which was analyzed by fluorescent in situ hybridization (FISH) and BIOLOG substrate utilization patterns. It was shown that each fraction consisted of different microbial communities with unique metabolic profiles suggesting that pin-point sludge formation is not due to dispersal of intact flocs but to microcolonies growing separately. Alternatively, macroflocs may have an architecture leading to segregation of microbial communities after floc dispersal. Further it could be shown that the formation of microflocs was influenced by sludge age. The best sludge sedimentation was obtained for a sludge age of 5 and 10 days. Additional analysis of extracellular polymeric substances (EPS) suggested that the lower protein to carbohydrate ratio of 10-day-old sludge led to better flocculation compared to 20-day-old sludge containing similar total amounts of EPS. From a practical point of view, addition of potassium (0.1 g/l) effected a noticeable improvement of sludge settleability.

Objective threshold selection procedure (OTS) for segmentation of scanning laser confocal microscope images

The determination of volumes and interface areas from confocal laser scanning microscopy (CLSM) images requires the identification of component objects by segmentation. An automated method for the determination of segmentation thresholds for CLSM imaging of biofilms was developed. The procedure, named objective threshold selection (OTS), is a three-dimensional development of the approach introduced by the popular robust automatic threshold selection (RATS) method. OTS is based on the statistical properties of local gray-values and gradients in the image. By characterizing the dependence between a volumetric feature and the intensity threshold used for image segmentation, the former can be determined with an arbitrary confidence level, with no need for user intervention. The identification of an objective segmentation procedure renders the possibility for the full automation of volume and interfacial area measurement. Images from two distinct biofilm systems, acquired using different experimental techniques and instrumental setups were segmented by OTS to determine biofilm volume and interfacial area. The reliability of measurements for each case was analyzed to identify optimal procedure for image acquisition. The automated OTS method was shown to reproduce values obtained manually by an experienced operator.

A new method for extraction of extracellular polymeric substances from biofilms and activated sludge suitable for direct quantification of sorbed metals

A method for extraction of extracellular polymeric substances (EPSs) with a dicyclohexyl-18-crown-6 ether was developed to determine levels of organic and inorganic contaminants sorbed to EPS. The crown ether selectively binds alkaline and alkaline earth metals but not heavy metals. The effectiveness of the extraction procedure was higher than that of 2 other methods tested and comparable with that of a method based on a cation exchange resin. On average it was possible to extract 20% of the TOC, 12% of the total protein content, and 4% of the total carbohydrate content of sludge or biofilm biomass. Metal sorption studies in activated sludge showed no influence of exposure time on the fractionation of metals within the biomass. Metals sorbed mostly to cellular material. In biofilms 12.2% of the cadmium and 9.1% of the zinc added was found in the EPS. In activated sludge EPS contained only 2.9% zinc. The distribution of metals within the biomass was dose dependent. The percentage of metals found in EPS decreased with increasing metal concentration. This indicates a higher affinity of metals for cellular binding sites. Time course experiments in a rotating biofilm annular reactor, which consisted of an external cylinder with removable slides and an internal solid drum, revealed a gradual change in zinc concentration associated with EPS, although the total zinc concentration in the biomass remained constant. Concurrently, the amount of extractable EPS decreased. This was a consequence of a microbial population shift, with bacterial counts decreasing and algal and fungal biomass increasing. Using confocal laser scanning microscopy and the fluorescent metal complexing agent Newport Green for in situ detection of zinc it was shown that metals were bound to algae and fungi in the latter part of the experiment. The biofilm became more and more heterogeneous coinciding with a decrease in EPS. To summarize, the observed sorption behavior of metals cannot be explained with the conventional paradigm of EPS as hydrophilic gel. Obviously, different binding mechanisms must be invoked to explain the role of EPS in the sorption and removal of toxic substances in activated sludge and biofilm systems. It is important to consider the microbial population to understand differences in sorption in different matrices.

Time-resolved study of biofilm architecture and transport processes using experimental and simulation techniques: the role of EPS

Cellular material and extracellular polymeric substances are the basic structural elements in biofilm systems. The structure and role of EPS for biofilm development and metabolic processes have not been precisely determined and, therefore, have not yet been included as a necessary element in modelling and simulation studies. This is due to the difficulty of experimentally detecting the extracellular polymeric substances in situ and differentiating them from cellular material on the one hand, and to the subsequent uncertainty about appropriate models--e.g. rigid hindrances, porous microstructure or visco-elastic structure--on the other hand. In this work, we report on the use of confocal laser scanning microscopy to monitor the development of a monoculture biofilm of Sphingomonas sp. grown in a flow cell. The bacterial strain was genetically labelled resulting in strong constitutive expression of the green fluorescent protein. The development of extracellular polymeric substances was followed by binding of the lectin concavalin A to cell exopolysaccharides. The growth of the resulting strain was digitally recorded by automated confocal laser scanning microscopy. In addition, local velocity profiles of fluorescent carboxylate-modified microspheres were observed on pathlines throughout the biofilm. The CLSM image stacks were used as direct input for the explicit modelling and three-dimensional numerical simulation of flow fields and solute transport processes based on the conservation laws of continuum mechanics. At present, a strongly simplifying EPS-model is applied for numerical simulations. The EPSs are preliminarily assumed to behave like a rigid and dense hindrance with diffusive-reactive solute transport.

Evaluation of fluorescently labeled lectins for noninvasive localization of extracellular polymeric substances in Sphingomonas biofilms

Three strains of Sphingomonas were grown as biofilms and tested for binding of five fluorescently labeled lectins (Con A-type IV-TRITC or -Cy5, Pha-E-TRITC, PNA-TRITC, UEA 1-TRITC, and WGA-Texas red). Only ConA and WGA were significantly bound by the biofilms. Binding of the five lectins to artificial biofilms made of the commercially available Sphingomonas extracellular polysaccharides was similar to binding to living biofilms. Staining of the living and artificial biofilms by ConA might be explained as binding of the lectin to the terminal mannosyl and terminal glucosyl residues in the polysaccharides secreted by Sphingomonas as well as to the terminal mannosyl residue in glycosphingolipids. Staining of the biofilms by WGA could only be explained as binding to the Sphingomonas glycosphingolipid membrane, binding to the cell wall, or nonspecific binding. Glycoconjugation of ConA and WGA with the target sugars glucose and N-acetylglucosamine, respectively, was used as a method for evaluation of the specificity of the lectins towards Sphingomonas biofilms and Sphingomonas polysaccharides. Our results show that the binding of lectins to biofilms does not necessarily prove the presence of specific target sugars in the extracellular polymeric substances (EPS) in biofilms. The lectins may bind to non-EPS targets or adhere nonspecifically to components of the biofilm matrix.

Regulation of the cnr cobalt and nickel resistance determinant of Ralstonia eutropha (Alcaligenes eutrophus) CH34

The linked resistance to nickel and cobalt of Ralstonia eutropha-like strain CH34 (Alcaligenes eutrophus CH34) is encoded by the cnr operon, which is localized on the megaplasmid pMOL28. The regulatory genes cnrYXH have been cloned, overexpressed, and purified in Escherichia coli. CnrY fractionated as a 10.7-kDa protein in in vitro translation assays. CnrX, a periplasmic protein of 16.5 kDa, was overproduced and purified as a histidine-tagged fusion protein in E. coli. His-CnrX was found to possess a secondary structure content rich in alpha-helical and beta-sheet structures. CnrH, a sigma factor of the extracytoplasmic function family, was purified as an N-terminally histidine-tagged fusion. In gel shift mobility assays, His-CnrH, in the presence of E. coli core RNA polymerase enzyme, could retard at least two different promoter DNA targets, cnrYp and cnrHp, localized within the cnrYXH locus. These promoters and their transcription start sites were confirmed by primer extension. Purified His-CnrX did not inhibit the DNA-binding activity of His-CnrH and is therefore unlikely to be an anti-sigma factor, as previously hypothesized (EMBL M91650 description entry). To study the transcriptional response of the regulatory locus to metals and to probe promoter regions, transcriptional fusions were constructed between fragments of cnrYXH and the luxCDABE, luciferase reporter genes. Nickel and cobalt specifically induced the cnrYXH-luxCDABE fusion at optimal concentrations of 0.3 mM Ni(2+) and 2.0 mM Co(2+) in a noncomplexing medium for metals. The two promoter regions P(Y) (upstream cnrY) and P(H) (upstream cnrH) were probed and characterized using this vector and were found to control the nickel-inducible regulatory response of the cnr operon. The cnrHp promoter was responsible for full transcription of the cnrCBA structural resistance genes, while the cnrYp promoter was necessary to obtain metal-inducible transcription from the cnrHp promoter. The zinc resistance phenotype (ZinB) of a spontaneous cnr mutant strain, AE963, was investigated and could be attributed to an insertion of IS1087, a member of the IS2 family of insertion elements, within the cnrY gene.

High rates of conjugation in bacterial biofilms as determined by quantitative in situ analysis

Quantitative in situ determination of conjugative gene transfer in defined bacterial biofilms using automated confocal laser scanning microscopy followed by three-dimensional analysis of cellular biovolumes revealed conjugation rates 1,000-fold higher than those determined by classical plating techniques. Conjugation events were not affected by nutrient concentration alone but were influenced by time and biofilm structure.

Detection of Salmonella spp. and Listeria monocytogenes in suspended organic waste by nucleic acid extraction and PCR

A nucleic acid-based method for the detection of the bacterial pathogens Salmonella spp. and Listeria monocytogenes in biological waste was developed. The detection limits were less than 10 cells per ml of biological waste. The method does not include a phenol extraction step and can be easily performed in 1 to 2 days.

Automated confocal laser scanning microscopy and semiautomated image processing for analysis of biofilms

The purpose of this study was to develop and apply a quantitative optical method suitable for routine measurements of biofilm structures under in situ conditions. A computer program was designed to perform automated investigations of biofilms by using image acquisition and image analysis techniques. To obtain a representative profile of a growing biofilm, a nondestructive procedure was created to study and quantify undisturbed microbial populations within the physical environment of a glass flow cell. Key components of the computer-controlled processing described in this paper are the on-line collection of confocal two-dimensional (2D) cross-sectional images from a preset 3D domain of interest followed by the off-line analysis of these 2D images. With the quantitative extraction of information contained in each image, a three-dimensional reconstruction of the principal biological events can be achieved. The program is convenient to handle and was generated to determine biovolumes and thus facilitate the examination of dynamic processes within biofilms. In the present study, Pseudomonas fluorescens or a green fluorescent protein-expressing Escherichia coli strain, EC12, was inoculated into glass flow cells and the respective monoculture biofilms were analyzed in three dimensions. In this paper we describe a method for the routine measurements of biofilms by using automated image acquisition and semiautomated image analysis.

Two-component regulatory system involved in transcriptional control of heavy-metal homoeostasis in Alcaligenes eutrophus

The czc determinant, which mediates resistance to Co2+, Zn2+ and Cd2+ in Alcaligenes eutrophus CH34 by cation efflux, is regulated by a two-component regulatory system composed of the sensor histidine kinase CzcS and the response activator CzcR (in addition to other components previously described). Regulatory genes are arranged in an upstream regulatory region (URR) and a downstream regulatory region (DRR). Transcription of czcCBA and of the URR was regulated by heavy-metal cations. DNA sequencing of the region downstream of czcD revealed the presence of the czcR and czcS genes which together with czcD form the DRR. Regulation of the DRR was studied with a czcD::lacZ translational fusion and a czcS::lux transcriptional fusion. Expression of both genes is also regulated by heavy metals. The genes of the URR yielded three mRNAs of approx. 1200, 500 and 200 nucleotides, respectively. The genes czcCBA for the cation/proton antiporter CzcCBA were transcribed by one operon as a transcript of 6200 nucleotides.

Plasmids for heavy metal resistance in Alcaligenes eutrophus CH34: mechanisms and applications

Alcaligenes eutrophus CH34 is the main representative of a group of strongly related strains (mostly facultative chemolithotrophs) that are well adapted to environments containing high levels of heavy metals. It harbors the megaplasmids pMOL28 and pMOL30 which carry resistance determinants to Co2+, Ni2+, CrO(4)2-, Hg2+, Tl+, Cd2+, Cu2+ and Zn2+. Among the best characterized determinants are the cnr operon (resistance to Co, Ni) on pMOL28 and the czc operon on pMOL30 (resistance to Co, Cd and Zn). Although the two systems reveal a significant degree of amino acid similarity in the structural genes, the regulation of the operons is different. The resistance mechanism in both cases is based on efflux. The efflux mechanism leads to a pH increase outside of the cytoplasmic membrane. Metals are sequestered from the external medium through the bioprecipitation of metal carbonates formed in the saturated zone around the cell. This latter phenomenon can be exploited in bioreactors designed to remove metals from effluents. The bacteria are immobilized on composite membranes in a continuous tubular membrane reactor (CTMR). The effluent continuously circulates through the intertubular space, while the external surface of the tubes is in contact with the growth medium. Metal crystals are eventually removed by the effluent stream and collected on a glass bead column. The system has been applied to effluents containing Cd, Zn, Co, Ni and Cu. By introducing catabolic plasmids involved in the aerobic degradation of PCBs and 2,4-D into metal-resistant A. eutrophus strains, the application range was widened to include effluents polluted with both organic and inorganic substances. Biosensors have been developed which are based on the fusion of genes induced by metals to a reporter system, the lux operon of Vibrio fischeri. Bacterial luciferases produce light through the oxidation of fatty aldehydes. The gene fusions are useful both for the study of regulatory genes and for the determination of heavy metal concentrations in the environment.

Tributyltin-resistant bacteria from estuarine and freshwater sediments

Resistance to tributyltin (TBT) was examined in populations from TBT-polluted sediments and nonpolluted sediments from an estuary and from fresh water as well as in pure cultures isolated from those sediments. The 50% effective concentrations (EC50s) for populations were higher at a TBT-polluted freshwater site than at a site without TBT, suggesting that TBT selected for a TBT-resistant population. In contrast, EC50s were significantly lower for populations from a TBT-contaminated estuarine site than for those from a site without TBT, suggesting that other factors in addition to TBT determine whether populations become resistant. EC50s for populations from TBT-contaminated freshwater sediments were nearly 30 times higher than those for populations from TBT-contaminated estuarine sediments. We defined a TBT-resistant bacterium as one which grows on trypticase soy agar containing 8.4 microM TBT, a concentration which prevented the growth of 90% of the culturable bacteria from these sediments. The toxicity of TBT in laboratory media was influenced markedly by the composition of the medium and whether it was liquid or solid. Ten TBT-resistant isolates from estuarine sediments and 19 from freshwater sediments were identified to the genus level. Two isolates, each a Bacillus sp., may be the first gram-positive bacteria isolated from fresh water in the presence of a high concentration of TBT. There was a high incidence of resistance to heavy metals: metal resistance indices were 0.76 for estuarine isolates and 0.68 for freshwater isolates.(ABSTRACT TRUNCATED AT 250 WORDS)