Statistical sampling of bacterial strains and its use in bacterial diversity measurement

A new understanding of somatic coliphages belonging to the Microviridae family in urban wastewater

Somatic coliphages (SC) and F-specific RNA coliphages (FRNAPH) have been included in regulations or guidelines by several developed countries as a way of monitoring water safety and the microbiological quality of shellfish harvesting waters. SC are highly diverse in their morphology, size and genome. The Microviridae family contains three genera of phages (Alphatrevirus, Gequatrovirus, and Sinsheimervirus), all having a capsid of similar morphology (icosahedral) and size (25-30 nm in diameter) to that of common pathogenic enteric viruses. Three PCR assays specific for each genus of Microviridae were designed to study these phages in raw and treated wastewater (WW) in order to gain knowledge about the diversity and prevalence of Microviridae among SC, as well as their inactivation and removal during WW treatments. Among the four wastewater treatment plants (WWTPs) monitored here, two WWTPs applied disinfection by UV light as tertiary treatment. First, we noticed that Microviridae represented 10 to 30 % of infectious SC in both raw and treated WW. Microviridae appeared to behave in the same way as all SC during these WW treatments. As expected, the highest inactivation, at least 4 log10, was achieved for infectious Microviridae and SC in both WWTPs using UV disinfection. PCR assays showed that the highest removal of Microviridae reached about 4 log10, but the phage removal can vary greatly between WWTPs using similar treatments. This work forms the basis for a broader evaluation of Microviridae as a viral indicator of water treatment efficiency and WW reuse.

Culture and molecular methods as complementary tools for water quality management

Bacterial communities in a full-scale drinking water treatment plant (DWTP) were characterized using matrix-assisted laser desorption/ionization time of flight mass-spectrometry (MALDI-TOF MS) to identify HPC isolates and the obtained results were compared to 16S rRNA (V4) metabarcoding data acquired in a previous study. Sixty-three samples were collected at nine stages of the potabilization process: river water and groundwater intake, decantation, sand filtration, ozonization, carbon filtration, reverse osmosis, the mixing chamber and post-chlorination drinking water. In total, 1807 bacterial colonies were isolated, 32 % of which were successfully identified to at least the genus level by MALDI-TOF MS using our previously developed Drinking Water Library. Trends in diversity were similar by both approaches, but differences were observed in the detection of taxa, especially at lower hierarchy levels. High bacterial diversity was observed in river and groundwater, where Proteobacteria predominated. The diversity decreased significantly after the chlorination step, where Bacillus sp. (Firmicutes) and an unknown genus of Obscuribacteraceae (Cyanobacteria) were the most prevalent genera according to MALDI-TOF MS and metabarcoding, respectively. The two approaches gave similar results for the decantation, sand filtration and mixing chamber steps, where the most abundant taxon was Flavobacterium. The combined use of these culture-based and culture-independent methods to characterize microbial populations may help to better understand the role of bacteria in water treatment and quality, which will be of value for DWTP management.

Crab shell amendments enhance the abundance and diversity of key microbial groups in sulfate-reducing columns treating acid mine drainage

Substrate amendments composed of crab shell (CS) waste materials have been shown to significantly improve the longevity and performance of acid mine drainage (AMD) treatment systems containing spent mushroom compost (SMC), yet the development of key microbial populations within these systems has not been investigated. To better understand the effects of CS on microbial dynamics in these systems, clone libraries and real-time quantitative PCR (qPCR) were performed on materials from a laboratory-scale AMD treatment system containing SMC and 0 to 100% CS substrate after receiving a continuous flow of AMD for 148 days (428 pore volumes). The proportion of CS in the substrate positively correlated with the diversity of sulfate-reducing bacteria (SRB) and archaeal clones, but negatively correlated with fungal diversity. CS also impacted microbial community structure, as revealed in Unifrac significance and principal coordinate analysis tests. The column containing 100% CS substrate supported 7 different genera of SRB-the most ever observed in an AMD treatment system. Moreover, the copy numbers of functional genes representing fermenters, sulfate reducers, and chitin degraders increased with increasing proportions of CS. These observations agree well with the chemical performance data, further validating that by supporting more abundant key microbial groups, chitinous substrates may provide benefits for improving both the longevity and performance of AMD treatment systems, and may provide similar benefits for the treatment of other environmental contaminants that are amenable to anaerobic bioremediation.Key points• Crab shell improves the longevity and performance of acid mine drainage treatment.• The diversity of sulfate-reducing bacteria is enhanced with crab shell amendments.• Crab shell supports more abundant key microbial groups than spent mushroom compost.

Heterotrophic monitoring at a drinking water treatment plant by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry after different drinking water treatments

The aim of this work was to assess the suitability of matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) for routine heterotrophic monitoring in a drinking water treatment plant. Water samples were collected from raw surface water and after different treatments during two campaigns over a 1-year period. Heterotrophic bacteria were studied and isolates were identified by MALDI-TOF MS. Moreover, the diversity index and the coefficient of population similarity were also calculated using biochemical fingerprinting of the populations studied. MALDI-TOF MS enabled us to characterize and detect changes in the bacterial community composition throughout the water treatment plant. Raw water showed a large and diverse population which was slightly modified after initial treatment steps (sand filtration and ultrafiltration). Reverse osmosis had a significant impact on the microbial diversity, while the final chlorination step produced a shift in the composition of the bacterial community. Although MALDI-TOF MS could not identify all the isolates since the available MALDI-TOF MS database does not cover all the bacterial diversity in water, this technique could be used to monitor bacterial changes in drinking water treatment plants by creating a specific protein profile database for tracking purposes.

Determination of fecal contamination origin in reclaimed water open-air ponds using biochemical fingerprinting of enterococci and fecal coliforms

Low levels of fecal indicator bacteria (FIB) were recently detected in two reclaimed water open-air ponds used to irrigate a golf course located in Northeastern Spain. The aim of this study was to evaluate the feasibility of a biochemical fingerprinting method to track the origin of fecal contamination in water with low FIB levels, as in the aforementioned ponds. We also aimed to determine whether FIB presence was due to regrowth of the reclaimed water populations or to a contribution of fecal matter whose source was in the golf facility. Three hundred and fifty enterococcal strains and 308 fecal coliform strains were isolated from the ponds and reclamation plant, and they were biochemically phenotyped. In addition, the inactivation of several microbial fecal pollution indicators (fecal coliforms, total bifidobacteria, sorbitol-fermenting bifidobacteria, somatic bacteriophages, and bacteriophages infecting Bacteroides thetaiotaomicron) was studied using a mesocosm in situ in order to obtain information about their decay rate. Although FIB concentration was low, the biochemical fingerprinting provided evidence that the origin of the fecal contamination in the ponds was not related to the reclaimed water. Biochemical fingerprinting thus proved to be a successful approach, since other microbial source-tracking methods perform poorly when dealing with low fecal load matrices. Furthermore, the mesocosm assays indicated that none of the microbial fecal indicators was able to regrow in the ponds. Finally, the study highlights the fact that reclaimed water may be recontaminated in open-air reservoirs, and therefore, its microbial quality should be monitored throughout its use.

Study of azo dye decolorization and determination of cathode microorganism profile in air-cathode microbial fuel cells

Five textile azo dyes, as part of an artificial mixture, were treated in single-chamber air-cathode microbial fuel cells while simultaneously utilizing acetate for electricity production. Remazol Black, Remazol Brilliant Blue, Remazol Turquoise Blue, Reactive Yellow and Reactive Red at concentrations of 40 or 80 mg L(-1) were decolorized to a similar extent, at averages of 78, 95, 53, 93 and 74%, respectively, in 24 hours. During the process of decolorization, electricity generation from acetate oxidation continued. Power densities obtained in the presence of textile dyes ranged from 347 to 521 mW m(-2) at the current density range of 0.071 - 0.086 mA cm(-2). Microbial community analyses of cathode biofilm exhibited dynamic changes in abundant species following dye decolorization. Upon the addition of the first dye, a major change (63%) in microbial diversity was observed; however, subsequent addition of other dyes did not affect the community profile significantly. Actinobacteria, Aquamicrobium, Mesorhizobium, Ochrobactrum, Thauera, Paracoccus, Achromobacter and Chelatacoccus affiliated phylotypes were the major phylotypes detected. Our results demonstrate that microbial fuel cells could be a promising alternative for treatment of textile wastewaters and an active bacterial community can rapidly be established for simultaneous azo dye decolorization and sustainable electricity generation.

Persistence and diversity of faecal coliform and enterococci populations in faecally polluted waters

AIM

To assess the persistence and diversity of faecal bacterial populations (faecal coliforms and enterococci) that have recently been included in microbial source tracking (MST) predictive models.

METHODS AND RESULTS

The analysed bacterial populations included members of the enterococci group (ENT) [Enterococcus faecium (FM), Enterococcus faecalis (FS) and Enterococcus hirae (HIR)] and the faecal coliform group (FC) [diverse Escherichia coli phenotypes (ECP) and cellobiose-negative faecal coliforms (CNFC)]. The inactivation of these distinct groups was monitored over time on-site in river by biochemical fingerprinting, and diversity indices were calculated. Among the different analysed species belonging to the ENT group, HIR persisted longer and was able to replicate in the environment at a higher rate. On the other hand, ECP and NCFC showed a similar persistence throughout the different seasons. The diversity index (Di) for FC increased substantially in the summer after 96 h to a maximum value of 0·96. On the other hand, the Di for ENT diminished over the same period to a value of 0·86, suggesting a different persistence for the different species integrating this group.

CONCLUSIONS

The persistence of ECP, CNFC, FM and FS in the aquatic environment is high, particularly for the members of the FC and in the summer season. On the contrary, HIR is able to replicate in the environment at a high rate even in winter, and therefore, its inclusion in MST predictive models is discouraged.

SIGNIFICANCE AND IMPACT OF THE STUDY

ECP, CNFC, FMFS and HIR have been proposed as additional variables in MST predictive models. However, the different persistence of HIR compared with the other variables should be taken into account for the development of such models.

Long-term cathode performance and the microbial communities that develop in microbial fuel cells fed different fermentation endproducts

To better understand how cathode performance and substrates affected communities that evolved in these reactors over long periods of time, microbial fuel cells were operated for more than 1 year with individual endproducts of lignocellulose fermentation (acetic acid, formic acid, lactic acid, succinic acid, or ethanol). Large variations in reactor performance were primarily due to the specific substrates, with power densities ranging from 835 ± 21 to 62 ± 1mW/m(3). Cathodes performance degraded over time, as shown by an increase in power of up to 26% when the cathode biofilm was removed, and 118% using new cathodes. Communities that developed on the anodes included exoelectrogenic families, such as Rhodobacteraceae, Geobacteraceae, and Peptococcaceae, with the Deltaproteobacteria dominating most reactors. Pelobacter propionicus was the predominant member in reactors fed acetic acid, and it was abundant in several other MFCs. These results provide valuable insights into the effects of long-term MFC operation on reactor performance.

Microbial electrodialysis cell for simultaneous water desalination and hydrogen gas production

A new approach to water desalination is to use exoelectrogenic bacteria to generate electrical power from the biodegradation of organic matter, moving charged ions from a middle chamber between two membranes in a type of microbial fuel cell called a microbial desalination cell. Desalination efficiency using this approach is limited by the voltage produced by the bacteria. Here we examine an alternative strategy based on boosting the voltage produced by the bacteria to achieve hydrogen gas evolution from the cathode using a three-chambered system we refer to as a microbial electrodialysis cell (MEDC). We examined the use of the MEDC process using two different initial NaCl concentrations of 5 g/L and 20 g/L. Conductivity in the desalination chamber was reduced by up to 68 ± 3% in a single fed-batch cycle, with electrical energy efficiencies reaching 231 ± 59%, and maximum hydrogen production rates of 0.16 ± 0.05 m(3) H(2)/m(3) d obtained at an applied voltage of 0.55 V. The advantage of this system compared to a microbial fuel cell approach is that the potentials between the electrodes can be better controlled, and the hydrogen gas that is produced can be used to recover energy to make the desalination process self-sustaining with respect to electrical power requirements.

Differential persistence of F-specific RNA phage subgroups hinders their use as single tracers for faecal source tracking in surface water

The four subgroups of F-specific RNA bacteriophages (I-IV) have been proposed as potential tracers for faecal source tracking. Groups II and III predominate in human sources while groups I and IV are most abundant in animal sources. The four subgroups of naturally occurring F-specific RNA bacteriophages were identified in different samples by plaque hybridization with genotype-specific probes and the persistence of each subgroup was evaluated. The proportions of the F-specific RNA bacteriophage subgroups were measured in wastewaters, after inactivation in surface waters or after wastewater treatment and in mixtures of wastewater of human and animal origin. Our results indicate that phage groups differ in their persistence in the environment and to different disinfecting treatments. The greater survival of subgroups I and II in treated samples hinders the interpretation of results obtained with F-specific RNA bacteriophages. The phages of subgroups III and IV were the least resistant to all treatments. These results should be considered when using genotypes of F-specific RNA as sole tracers for faecal source tracking.

Resistance of faecal coliforms and enterococci populations in sludge and biosolids to different hygienisation treatments

The composition of the most abundant facultative anaerobic bacteria populations [faecal coliforms (FC) and enterococci (ENT)] in sludge can be modified after different treatments. These involve the disposal or reuse of sludge and include: anaerobic digesters, incineration, composting, pasteurization and lime treatments. In this study, three treatment types (mesophilic anaerobic digestion, composting and pasteurization) were compared in terms of their ability to reduce both bacterial populations. The diversity and any changes in composition of main phenotypic groups for both populations were also analyzed. Mesophilic anaerobic digestion (MAD) was carried out at 35 degrees C for 20 days. Digested sludge was then dehydrated by centrifugation at 2,500 rpm. Composting (COM) was performed at 55 degrees C with windrow phases. Pasteurization was assayed at 60 degrees C for 90 min (P60), at 80 degrees C for 60 min (P80). A 1-1.5 log unit reduction was observed for FC, and 1 log unit reduction was noted for ENT by MAD treatment. In composting, this reduction proved higher for FC than for ENT (6 log and 3-4 log units, respectively). Optimal pasteurization was obtained at 80 degrees C for 60 min, resulting in a 5 log unit reduction for FC and a 2 log unit reduction for ENT. High diversity indices (Di) for both bacterial populations were detected both before and after implementation of the different treatments. Analyses of the population's similarity provided that FC were diverse both before and after COM, P60 and P80 treatments. However, no differences were observed on the composition of ENT populations after the different treatments assayed.

Comparison of Vibrio spp. populations found in seawater, in exhibition aquaria, in fish intestine and in fish feed

AIMS

Vibrio populations in the seawater supply and the water of seven exhibition aquaria that simulate various Mediterranean and tropical ecosystems were compared. The similarity of Vibrio populations in the intestine of various fish species, feed and water was examined. Resistance to the antibiotics used in fish health management was analysed for the dominant Vibrio isolates.

METHODS AND RESULTS

Samples were collected for 1 year from seven exhibition tanks reproducing different ecosystems. The diversity and population similarity among vibrios were determined using a miniaturized biochemical phenotyping method. Similar Vibrio populations were found in the water supply and in the water of the Mediterranean ecosystems. However, different Vibrio populations were found in the water of tanks with tropical ecosystems. Vibrio populations in the water seemed to have a greater effect on the composition of intestinal Vibrio populations than those in feed. No resistance to antibiotics was observed, indicating their appropriate use for health management.

CONCLUSIONS

Water characteristics have a greater impact on the composition of Vibrio populations in aquaria and fish intestinal microbiota than bacteria in feed.

SIGNIFICANCE AND IMPACT OF THE STUDY

The microbiological monitoring water could provide valuable information for managing the health of exhibition aquaria.

Assessment of bacterial community structure in a long-term copper-polluted ex-vineyard soil

The influence of long-term copper contamination on the diversity of bacterial communities was investigated in an ex-vineyard soil. Two sites of the same area but exhibiting different 3-fold exchangeable copper (Ex-Cu) concentrations were analysed. Culturable bacterial community structure was assessed using a variety of approaches: determination of culturable bacteria number, analyses of 132 isolates, and denaturing gradient gel lectrophoresis (DGGE) patterns of bacterial biomass grown on agar plates and of soil DNA. There was no significant difference in the number of total heterotrophs at the two sites, whereas the percentage of fast-growing bacteria growing in 1 day, was lower at the site with the higher Ex-Cu content. A high percentage of Cu-tolerant bacteria was found in both sites (63-70%) and it was relatively independent of the Cu content. Shifts in species composition of the culturable bacterial community were detected by analysing isolates from the two soils, Gram-positive bacteria prevailed in the less-polluted soil while Gram-negative bacteria in the more-polluted soil. Each sample site had a community with a different metal resistance pattern. Our study seems to indicate that in this soil ecosystem, copper influenced the culturable bacterial communities, affecting the structural diversity and altering some of the metal resistance of the microorganisms. The Sorensen similarity index calculated on DGGE profiles of 16S rDNA of total and culturable bacterial communities indicated a different species composition at the two sites, although both sites had the same biodiversity degree and different dominance.

Integrated analysis of established and novel microbial and chemical methods for microbial source tracking

Several microbes and chemicals have been considered as potential tracers to identify fecal sources in the environment. However, to date, no one approach has been shown to accurately identify the origins of fecal pollution in aquatic environments. In this multilaboratory study, different microbial and chemical indicators were analyzed in order to distinguish human fecal sources from nonhuman fecal sources using wastewaters and slurries from diverse geographical areas within Europe. Twenty-six parameters, which were later combined to form derived variables for statistical analyses, were obtained by performing methods that were achievable in all the participant laboratories: enumeration of fecal coliform bacteria, enterococci, clostridia, somatic coliphages, F-specific RNA phages, bacteriophages infecting Bacteroides fragilis RYC2056 and Bacteroides thetaiotaomicron GA17, and total and sorbitol-fermenting bifidobacteria; genotyping of F-specific RNA phages; biochemical phenotyping of fecal coliform bacteria and enterococci using miniaturized tests; specific detection of Bifidobacterium adolescentis and Bifidobacterium dentium; and measurement of four fecal sterols. A number of potentially useful source indicators were detected (bacteriophages infecting B. thetaiotaomicron, certain genotypes of F-specific bacteriophages, sorbitol-fermenting bifidobacteria, 24-ethylcoprostanol, and epycoprostanol), although no one source identifier alone provided 100% correct classification of the fecal source. Subsequently, 38 variables (both single and derived) were defined from the measured microbial and chemical parameters in order to find the best subset of variables to develop predictive models using the lowest possible number of measured parameters. To this end, several statistical or machine learning methods were evaluated and provided two successful predictive models based on just two variables, giving 100% correct classification: the ratio of the densities of somatic coliphages and phages infecting Bacteroides thetaiotaomicron to the density of somatic coliphages and the ratio of the densities of fecal coliform bacteria and phages infecting Bacteroides thetaiotaomicron to the density of fecal coliform bacteria. Other models with high rates of correct classification were developed, but in these cases, higher numbers of variables were required.

Vancomycin- and erythromycin-resistant enterococci in a pig farm and its environment

A high prevalence of vancomycin- and erythromycin-resistant enterococci (VRE and ERE respectively) in a pig farm and its environment was observed. A similar structure and composition of enterococcal populations was detected between urban sewage and those associated with the pig environment. Enterococcus faecium was the most predominant species among VRE isolates from both animal and human origin. The high population similarity index (Sp) obtained comparing VRE and ERE isolates from urban sewage and pig slurry suggests that there are certain strains circulating through the food chain from farms to humans. Erythromycin resistance was present in a wider variety of clones and species of enterococci in both pigs and humans than vancomycin resistance.

Distribution and persistence of fecal bacterial populations in liquid and dewatered sludge from a biological treatment plant

The changes in composition and structure of fecal coliforms (FC) and enterococci (ENT) populations, as well as the elimination of spores of sulphite-reducing bacteria (SRB), were compared between municipal sewage and their derived sludge in a biological treatment plant in order to determine any selective reduction or adsorption to sludge during the treatment process. Additionally, the persistence of antibiotic-resistant enterococcal populations in two kinds of sludge was also considered to evaluate their potential elimination in the treatment process. Microbial indicators, vancomycin-resistant and erythromycin-resistant enterococci were enumerated. The structure and composition of FC and ENT populations were determined by biochemical fingerprinting and clustering analyses. Raw and treated sewage showed a concentration of FC 1 log unit higher than ENT and nearly 2 log units higher than spores of SRB. However, the three studied indicators showed similar concentrations in both types of sludge. Consequently, FC were eliminated in higher proportion than ENT and spores of SRB in sludge. FC and ENT populations showed high diversity and similarity population indexes for all kinds of samples. Antibiotic-resistant enterococci persisted in a similar proportion in respect to total enterococci not only in treated sewage but also in sludge. The persistence of antibiotic-resistant strains in sludge as well as in treated sewage should be considered if they are used for land disposal or for water reutilization, respectively.

Determination of Vibrio scophthalmi and its phenotypic diversity in turbot larvae

The association of Vibrio scophthalmi with turbot larvae was assessed, by molecular methods with a species-specific probe, in the rearing stages of turbot (Scophthalmus maximus) larvae using a routine batch of production at a fish farm. The phenotypic diversity of this bacterial species was also studied to identify predominant phenotypes at successive stages of larval development. Vibrio scophthalmi was detected in all turbot larvae samples except in the sample from day 0 after hatching. The percentage of V. scophthalmi in the intestinal microbiota increased throughout larval development. Vibrio scophthalmi was also detected in live food (brine shrimps) and water from the tanks, but not in the sediment. All turbot larvae, 15-57 day old, showed several V. scophthalmi phenotypes, and a pattern of successive waves of phenotypes was observed during successive larval stages. This indicates that certain strains may colonize the intestine more efficiently and thus maintain their population for longer than other strains. Vibrio scophthalmi populations from turbots of different origin were very similar, suggesting that irrespective of geographical area, turbot populations share similar V. scophthalmi strains. Vibrio scophthalmi strain was not isolated from other cultured fish, only turbot larvae, at the same hatchery receiving water from the same supply.

The composition and persistence of faecal coliforms and enterococcal populations in sewage treatment plants

AIMS

The changes in structure and composition of faecal coliforms and enterococcal populations in sewage from different treatment plants, and the elimination of vancomycin- and erythromycin-resistant enterococci (VRE and ERE, respectively) in these treatment plants was analysed to determine any selective reduction.

METHODS AND RESULTS

Faecal coliforms, enterococci, VRE, ERE and spores of sulphite-reducing bacteria were enumerated using standard methods. Samples were enriched where necessary in order to isolate antibiotic resistant strains. The structure and composition of these bacterial populations were determined by biochemical fingerprinting and clustering analysis. High diversity and similarity indexes were detected among all the bacterial populations in raw and treated sewage, independently of their origin and the treatment processes employed. Antibiotic resistant strains were detected in all sewage tested and no selective reduction was observed.

CONCLUSIONS

The faecal coliforms and enterococci populations did not differ in the sewage samples studied. The vancomycin and erythromycin resistances of the enterococcal populations were similar in the sewage samples. Resistance to both antibiotics persisted after the treatment process independently of raw sewage flow, faecal origin or size of the human population contributing to sewage. However, sewage of mixed origin (human and animal) presented a lower similarity index for the two bacterial populations compared with that of the other human sewage analysed.

SIGNIFICANCE AND IMPACT OF THE STUDY

Although a significant reduction in bacterial populations was observed, the persistence of VRE and ERE strains in the same proportions in sewage suggests that there is no selective elimination of bacterial populations during the treatment processes. The ability of antibiotic resistance strains to survive sewage treatment systems should be considered in certain water reuse programmes.

The PhenePlate system for studies of the diversity of enterococcal populations from the food chain and the environment

The growing interest in ecological investigations, such as studies of the "flow" of bacteria through the food chain, has resulted in a great need for simple typing techniques for bacteria that can be used when a large number of isolates need to be analysed. The present study describes a simple method for biochemical fingerprinting of enterococci, the PhenePlate RF (PhP-RF) system. The system is based on a 96-well microplate containing eight sets of 11 dehydrated reagents, selected to have a high discriminatory power among enterococcal isolates. The PhP plates are inoculated easily by picking single colonies directly from the primary agar culture and suspending them in the first well of each row in the microplate. The kinetics of each reaction is evaluated by measuring the absorbance value of each well three times during 64 h, whereupon a biochemical fingerprint is calculated as the mean value for each reagent over the three readings. The PhP-RF method was shown to be highly reproducible, even when results were compared between different laboratories. The discriminatory power, measured as Simpson's diversity index (Di), was as high as 0.96 for all enterococci. The PhP-RF method could also be used as a preliminary species identification method, by comparing the biochemical fingerprints of unknown strains to those of a set of reference strains of known species. Most strains of Enterococcus faecalis, Enterococcus faecium and Enterococcus hirae were correctly identified using this method. We conclude that the PhenePlate RF system is useful for rapid typing of enterococcal populations, and it is especially useful as a first screening method for ecological studies, when many isolates per sample need to be analysed.

Evidence for transmission between humans and the environment of a nosocomial strain ofEnterococcus faecium

An ampicillin- and ciprofloxacin-resistant Enterococcus faecium (ARE) strain, named FMSE1, with a characteristic biochemical phenotype, was in a recent study found to dominate among faecal ARE isolates from patients in several Swedish hospitals. In the present study, the prevalence of this strain among 9676 enterococcal isolates from healthy children, hospital sewage, urban sewage, surface water, slaughtered animals (broilers, pigs and cattle) and pig faeces and manure was investigated. Enterococcal isolates having the same biochemical phenotype as the FMSE1 were most common in samples of hospital sewage (50%), surface water (35%), treated sewage (28%) and untreated sewage (17%), but rare in samples from healthy children (0.8%) and animals (2%). PFGE typing of FMSE1-like isolates from hospital sewage indicated that they were closely related to the nosocomial FMSE1 strain. Thus, this study indicated a possible transmission route for nosocomial E. faecium from patients in hospitals to hospital sewage and urban sewage, and further via treatment plants to surface water and possibly back to humans. This proposed route of circulation of drug-resistant enterococci might be further amplified by antibiotic usage in human medicine. In contrast, such transmission from food animals seems to play a negligible role in Sweden.

Comparison of enterococcal populations related to urban and hospital wastewater in various climatic and geographic European regions

AIMS

Scarce knowledge about the distribution of enterococci species in wastewaters limits any statement on their reliability as faecal indicators or the implications of antibiotic resistance transmission by these organisms through the water cycle. Enterococci have been involved in nosocomial infections and the spreading of antibiotic resistance through the food chain. The species distribution of enterococci and the presence of resistant strains to vancomycin and erythromycin were analysed in more than 400 raw and treated urban wastewaters, surface waters receiving these treated wastewaters and hospital wastewaters from three European countries.

METHODS AND RESULTS

A total of 9296 strains were isolated and biochemically phenotyped. The species identification was based on the comparison of biochemical profiles with those of more than 20000 enterococci isolates from an international study. The prevalence of enterococcal isolates resistant to erythromycin (ERE) and vancomycin (VRE) was also analysed. ERE strains were present in a high proportion in all the studied samples. VRE strains were also isolated in all studied countries despite the time elapsed since the use of antimicrobial glycopeptides in animal production was banned in the European Union.

CONCLUSIONS

Enterococcus faecalis and Ent. faecium were the most abundant species in all the studied wastewaters. All the studied wastewaters demonstrated high diversity and similar population structure and composition. ERE and VRE isolates were detected in most of the wastewaters.

SIGNIFICANCE AND IMPACT OF THE STUDY

Urban and hospital wastewaters are useful targets for the evaluation of the prevalence of ERE and VRE isolates in the environment. It appears that these bacteria could pass through wastewater treatment plants and be transferred to surface waters.

Survival and naphthalene-degrading activity of Rhodococcus sp. strain 1BN in soil microcosms

AIMS

The survival and activity of Rhodococcus sp. strain 1BN, inoculated into naphthalene-contaminated sandy-loam soil microcosms, were studied using classical and molecular methods.

METHODS AND RESULTS

The naphthalene-degrading activity of 1BN in microcosms was examined through viable counts, CO2 production and naphthalene consumption, while its survival after inoculation was monitored by detecting the contemporary presence of alkane and naphthalene degradative genes and by analysing the 16S rDNA specific restriction profile. The inoculation of 1BN did not significantly enhance naphthalene degradation in the naphthalene-contaminated native soil, where 1BN maintained its catabolic activity also when in the presence of indigenous microflora. Instead the rate of naphthalene degradation by the inoculated 1BN was greater in sterile naphthalene-contaminated soil. The level of 1BN was only slightly higher after inoculation regardless of whether indigenous naphthalene-degrading bacteria were present or not and 1BN remained viable even when the substrate was depleted.

CONCLUSIONS

This study documents the colonization and growth of 1BN in a non-sterile, naphthalene-added, sandy-loam soil having an active indigenous naphthalene-degrading population.

SIGNIFICANCE AND IMPACT OF THE STUDY

An active and well-established naphthalene-degrading bacterial population in the native soil did not hamper the survival of the introduced 1BN that, through its activity, enhanced the mineralization rate of naphthalene.

Distribution of genotypes of F-specific RNA bacteriophages in human and non-human sources of faecal pollution in South Africa and Spain

AIMS

To assess whether the distribution of genotypes of F-specific RNA bacteriophages reflects faecal pollution of human and animal origin in water environments.

METHODS AND RESULTS

Stool samples, animal feedlot waste slurries and a wide variety of faecally polluted waters were studied in South Africa and Spain. Genotyping was performed by plaque and spot hybridization with genotype-specific probes. Only genotypes II and III were detected in human stool. Animal faeces contained predominantly, but not exclusively, genotypes I and IV. Raw hospital and municipal sewage contained mostly genotypes II and III, whereas genotypes I and II prevailed in settled sewage, secondary treated sewage and non-point diffuse effluents from developing communities. Abattoir wastewaters contained mostly genotypes I and IV. No differences were observed between the distribution of genotypes in Spain and South Africa.

CONCLUSIONS

Although the association of genotypes II and III with human excreta and I and IV with animal excreta was statistically significant, the results suggest that the association cannot be used for absolute distinction between faecal pollution of human and animal origin.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study contributes greatly to understanding the usefulness of genotypes of F-specific RNA bacteriophages in source tracking of faecal wastes.

The effect of a sewage treatment plant effluent on the faecal coliforms and enterococci populations of the reception river waters

AIMS

A rural sewage treatment plant and the effect of its effluent on the enterococci and faecal coliforms populations of the receiving river waters was evaluated.

METHODS AND RESULTS

The enumeration of bacteria was performed by membrane filtration. Diversity and population similarity were analysed using the PhP-plates system. The treatment plant reduces the number of enterococci and faecal coliforms to values similar to those observed upstream. All water samples showed a high diversity for both bacterial populations. A high similarity in the composition and structure, was detected among all the samples.

CONCLUSIONS

The impact of the disposal of treated sewage on the river did not modify the composition of either bacterial populations in the river water.

SIGNIFICANCE AND IMPACT OF THE STUDY

The biochemical phenotyping of bacterial populations is a reliable tool for ecological and biodiversity studies. The obtained results provide a better understanding of the sewage treatment process and the impact of the treated sewage effluents in the environment.

Diversity of Vibrio spp. populations in several exhibition aquaria with a shared water supply

AIMS

Abiotic factors may influence the settlement of bacterial populations in similar marine environments. Exhibition aquaria are a model for the study of the settlement of bacteria in different environment. Vibrio populations in the seawater reservoir, the Mediterranean tank and the Tropical tank from an exhibition aquarium on the western coast of the Mediterranean were compared and the effect of abiotic factors on the structure of these populations was considered.

METHODS AND RESULTS

High diversity indexes and similar Vibrio populations were found in the water of the reservoir and of the Mediterranean tank, whereas a lower diversity and different main populations were found in the water of the Tropical tank. The antibiotic resistance profiles of the most representative strains, presented a number of differences depending on the origin of the sample.

CONCLUSION

Abiotic conditions, mainly temperature, may determine the structure and composition of Vibrio populations in exhibition aquaria.

SIGNIFICANCE AND IMPACT OF THE STUDY

Bacterial monitoring of water could be useful for health management of aquatic environments.

Study of the potential relationship between the morphology of infectious somatic coliphages and their persistence in the environment

The proportions of different morphological types of infectious somatic coliphages were determined in faecally polluted freshwaters. Myoviridae, followed by Siphoviridae, were the most frequently isolated morphological types in raw sewage, treated sewage and river water collected a few metres downstream from a sewage outfall. However, in river water collected further downstream from the pollution point, in river water after 'in situ' inactivation experiments and in chlorinated raw and treated sewage significant changes in the proportions of the different somatic coliphage morphological types occurred. In all cases, Siphoviridae, especially those with flexible and curled tails, became more abundant to the detriment of Myoviridae.

Diversity, persistence, and virulence of Aeromonas strains isolated from drinking water distribution systems in Sweden

The Aeromonas populations in 13 Swedish drinking water distribution systems, representing different treatments, were investigated. From each system, water samples were collected four times during the period from May to September 1994 from raw water and water after treatment and at two to five sites within the distribution system. In total, 220 water samples were collected. From samples containing presumptive Aeromonas, up to 32 colonies were analyzed by the PhenePlate Aeromonas (PhP-AE) system, which is a highly discriminating biochemical fingerprinting method. Selected isolates from different phenotypes (PhP types) were further identified by the API 20 NE system and by gas-liquid chromatography analysis of fatty acid methyl esters (FAMEs). Selected isolates were also assayed for their potential to produce hemolysin and cytotoxin and for their ability to adhere to human intestinal cells. In total, 117 water samples (53%) contained presumptive Aeromonas which numbered up to 10(6) CFU/100 ml in raw water and up to 750 CFU/100 ml in tap water. Among the 2,117 isolates that were subjected to typing by the PhP-AE system, more than 300 distinct PhP types were found, of which the majority occurred only sporadically. Raw (surface) water samples usually contained many different PhP types, showing high diversity indices (Di) (median Di = 0.95). The Aeromonas populations in samples collected from within the distribution systems were less diverse (median Di = 0.58) and were often dominated by one major PhP type that was found on several sampling occasions. Seventeen such major PhP types could be found and were represented in 1,037 isolates (49%). Identification by API 20 NE and FAME analysis revealed that most of the major PhP types were Aeromonas hydrophila or belonged to unidentified Aeromonas species. Hemolysin and cytotoxin production was observed in most major PhP types (representing 87 and 54% of the assayed isolates, respectively), and adherence was found in 89% of the isolates that produced cytotoxin. Thus, the data presented here show that although raw water may contain very diverse Aeromonas populations, the populations seemed to be remarkably stable within the studied water distribution systems, and that some potentially pathogenic Aeromonas strains could persist for several months in drinking water.

Problems in measuring bacterial diversity and a possible solution

The indices of species diversity used by plant and animal ecologists are not appropriate for bacterial diversity because of the inherent difficulty of defining a bacterial species. Arbitrary cutoff points to define a species or biotype lead to severe statistical problems. We suggest in this paper that a mean dissimilarity-based index without any attempt to define a species provides a statistically sound measurement of bacterial diversity.

Seasonal incidence of and antibiotic resistance among Aeromonas species isolated from domestic wastewater before and after treatment in stabilization ponds

The efficiency of stabilization pond treatment of domestic wastewater in removing culturable cells of motile Aeromonas and its influence on the incidence of resistance to seven antibiotics were investigated in this study. Removal efficiency was higher (P < 0.001) in the warm months (98.8%) than in the cold months (97%). Among the 264 isolates, 163 were Aeromonas caviae, 24 were A. hydrophila, and 54 were A. sobria. Twenty-three isolates could not be identified to the species level. In the influent, A. caviae dominated in both cold and warm months. In the water samples originating from the influent, A. sobria was present at higher percentages in the warm period. All the isolates were resistant to amoxicillin and most of them (73%) exhibited resistance to cephalothin. Of the three species tested, A. sobria was more susceptible to antibiotics than either A. caviae or A. hydrophila. The most striking difference among the species was seen in resistance to cephalothin. There were 91 % of A. caviae strains and 96% of A. hydrophila isolates that were resistant to cephalothin. However, only 9% of A. sobria strains exhibited resistance to this drug. The high incidence of resistance in raw sewage was connected with a high proportion of A. caviae, whereas in the water samples collected from the effluent during the warm months, a high proportion of A. sobria decreased the total amount of multiple-resistant bacteria. Results demonstrated the need for identification to the species level.

Gut microflora of two saltmarsh detritivore thalassinid prawns,Upogebia africana andCallianassa kraussi

The presence and digestive capabilities of bacteria associated with the digestive systems and habitats of two saltmarsh-burrowing detritivore thalassinid prawns (Upogebia africana andCallianassa kraussi) was examined.U. africana is a filter-feeding prawn inhabiting muddy deposits, whereasC. kraussi, a deposit feeder, inhabits coarser more sandy deposits. Scanning electron microscopy was used to examine the gut lining and associated microflora and the nature of the ingested food of both prawns. The gut contents of both prawns included plant fragments, fragmented diatoms, partially degraded protozoa, and bacteria attached to organic matter. In bothU. africana andC. kraussi the midgut walls and gut contents were extensively coated by filamentous bacteria which were absent in the hindgut. The hindgut epithelium ofU. africana was coated by mats of rodshaped bacteria, not reported in marine invertebrates previously. The digestive glands of both species contained bacteria in the lumen. Isolation of gut and habitat bacteria suggests that bothU. africana andC. kraussi maintain a gut microflora distinct from the habitat microflora. Bacteria isolated from the guts of both species of prawn differed from those isolated from their respective habitats with regards to both the genera isolated and their digestive capabilities. The dominant genera isolated from the guts of bothU. africana andC. kraussi wereVibrio andPseudomonas, with an unidentified fermenter andPseudomonas, respectively dominating in the digestive glands. Bacteria of the genusAcinetobacter dominated the isolates from the habitats of both species of prawn. Resident gut bacteria isolated from the guts of both species of prawn exhibited lipase, protease, chitinase, and lysozyme, but not cellulase activity, and may contribute to nitrogen aquisition by the prawns. Isolates from the prawns' habitat exhibited alginase, gelatinase, and lipase activity, a few (3%) fromU. africana habitat having cellulases. In this study a distinction between resident gut bacteria and transient gut bacteria was made. Results suggest that some habitat bacteria remain viable in the guts ofU. africana, but not inC. kraussi.

Microbiological characterization of a fuel-oil contaminated site including numerical identification of heterotrophic water and soil bacteria

Seven soil samples and seven groundwater samples from a site contaminated with fuel-oil were investigated using several chemical and microbiological techniques. In soil samples, 500 to 7,500 mg/kg of total hydrocarbons were found. These samples contained no n-alkanes but iso- and branched chain alkanes. No polychlorinated biphenyls could be detected. Microbiological investigations included estimations of total cell counts, viable cell counts on different media, and numbers of methylotrophic, denitrifying, sulphate reducing, anaerobic (with the exception of methanogenic organisms), and hydrocarbon degrading bacteria. Viable and hydrocarbon degrading bacteria were found in all samples. A total of 1,366 pure cultures was characterized morphologically and physiologically and identified by numerical identification using a data base of more than 4,000 reference strains. Groundwater samples were dominated by gram-negative bacteria of the generaPseudomonas, Comamonas, Alcaligenes, andAcinetobacter, which were also found in soil samples. In addition, more grampositive bacteria belonging to the generaArthrobacter, Nocardia, andBacillus could be isolated from soil samples.

Aeromonas species in stabilization ponds in the arid region of Marrakesh, Morocco, and relation to fecal-pollution and climatic factors

During the period 12 July 1985 to 23 December 1987, water samples were collected in two-week intervals for estimates ofAeromonas species in a waste treatment system located in the arid region of Marrakech, Morocco. Fecal coliforms, temperature, and chemical oxygen demand were measured simultaneously withAeromonas species densities. Statistical methods were utilized to analyze the significance of average differences and temporal patterns ofAeromonas species numbers.Removal ofAeromonas in the whole system did not exceed 1.14 log.Aeromonas densities showed significantly higher resistance to the treatment process when compared with fecal coliforms; however, abundance of the two groups presented a similar seasonal change. The highest numbers occurred during the cold months, while the lowest appeared in the warm months. Statistical time-series analyses of the densities data showed the seasonal and cyclic distribution ofAeromonas in this treatment plant.These temporal changes were simultaneously observed in all the stations investigated and were negatively correlated with water temperature values.Aeromonas populations were dominated byA. caviae andA. hydrophila in the inlet samples. These two species were rapidly eliminated in the treatment plant. The temporal distribution ofA. caviae was similar to the change in densities ofAeromonas and fecal coliforms. The seasonal fluctuations of abundance ofAeromonas were probably related to this species, which dominated in the winter samples but dropped during the summer. Meanwhile,A. sobria dominated all the final effluent samples. This greater survival ofA. sobria and its known pathogenicity may limit the re-use of treated water for irrigation of fodder plants.

Biochemical fingerprinting of water coliform bacteria, a new method for measuring phenotypic diversity and for comparing different bacterial populations

A simple, automated microplate system for biochemical characterization of water isolates can be used to obtain fingerprints of the bacterial flora from various water samples. Mathematical models for calculating the diversities and similarities between bacterial populations are described for such fingerprints. The diversity may give information on whether an indigenous or allochthonous flora is present, and the similarities between bacterial populations, as calculated by using a population similarity coefficient (Sp), may indicate contaminations between different water samples. The system was demonstrated on coliform bacterial populations from various water samples, with or without suspected intercontamination. For unrelated water samples, the Sps were close to 0, whereas repeated samples of the same source showed Sps of 0.64 to 0.74. The Sp values from several water samples were also clustered to form a dendrogram, thus indicating the relative similarities between the bacterial populations to confirm suspected common sources of pollution.

Physiological Diversity and Distributions of Heterotrophic Bacteria in Deep Cretaceous Sediments of the Atlantic Coastal Plain

A series of 23 intact core segments was obtained from two distinct deep subsurface geological formations, the Middendorf and the Cape Fear formations, underlying the southeastern coastal plain of South Carolina. The Middendorf formation in this region consists of permeable, saturated, sandy sediments; the Cape Fear formation consists mainly of less permeable sediments. The core segments were separated by vertical distances ranging from several centimeters to 48 m. Aerobic chemoheterotrophic bacteria were enumerated on a dilute medium, and populations ranged from 3.1 to 6.4 log CFU g of sediment -1 in the Middendorf cores and from below detection to 4.3 log CFU g -1 in the Cape Fear cores. A total of 198 morphologically distinct colony types were isolated, purified, and subjected to 108 different physiological measurements. The isolates from the two formations were distinct (i.e., they produced substantially different response patterns to the various physiological measurements), as were those in different core samples from the same formation. Cluster analysis revealed 21 different biotypes based on similarities of 75% or higher in response patterns to 21 physiological assays. One biotype contained 57 (29%) of the subsurface isolates, 10 biotypes contained 5 or more isolates, and the remainder had 4 or fewer. The organic compounds that were most commonly metabolized by the subsurface bacteria included Tween 40 (85%) and β-hydroxybutyric acid (60%). Organic acids, in general, were also commonly metabolized by the subsurface bacteria. Isolates from the Cape Fear core segments were capable of metabolizing a higher percentage of the substrates than were bacteria isolated from the Middendorf formation. Although the heterogeneous distributions of bacteria in deep subsurface sediments may make it difficult to use aquifer microcosms to predict in situ biotransformation rates, the diversity of the physiological properties of these organisms offers promise for in situ remediation of contaminants.