Comparative sensitivity to the fungicide tebuconazole of biofilm and plankton microbial communities in freshwater ecosystems.

Stream and lake ecosystems in agricultural watersheds are exposed to fungicide inputs that can threaten the structure and functioning of aquatic microbial communities. This research analyzes the impact of the triazole fungicide tebuconazole (TBZ) on natural biofilm and plankton microbial communities from sites presenting different degrees of agricultural contamination. Biofilm and plankton communities from less-polluted (LP) and polluted (P) sites were exposed to nominal concentrations of 0 (control), 2 and 20 µg TBZ L(-1) in 3-week microcosm experiments. Descriptors of microbial community structure (bacterial density and chlorophyll-a concentration) and function (bacterial respiration and production and photosynthesis) were analyzed to chart the effects of TBZ and the kinetics of TBZ attenuation in water during the experiments. The results showed TBZ-induced effects on biofilm function (inhibition of substrate-induced respiration and photosynthetic activity), especially in LP-site communities, whereas plankton communities experienced a transitory stimulation of bacterial densities in communities from both LP and P sites. TBZ attenuation was stronger in biofilm (60-75%) than plankton (15-18%) experiments, probably due to greater adsorption on biofilms. The differences between biofilm and plankton responses to TBZ were likely explained by differences in community structure (presence of extracellular polymeric substances (EPS) matrix) and microbial composition. Biofilm communities also exhibited different sensitivity levels according to their in-field pre-exposure to fungicide, with P-site communities demonstrating adaptation capacities to TBZ. This study indicates that TBZ toxicity to non-targeted aquatic microbial communities essentially composed by microalgae and bacteria was moderate, and that its effects varied between stream and lake microbial communities.

Next-generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms.

The recent emergence of barcoding approaches coupled to those of next-generation sequencing (NGS) has raised new perspectives for studying environmental communities. In this framework, we tested the possibility to derive accurate inventories of diatom communities from pyrosequencing outputs with an available DNA reference library. We used three molecular markers targeting the nuclear, chloroplast and mitochondrial genomes (SSU rDNA, rbcL and cox1) and three samples of a mock community composed of 30 known diatom strains belonging to 21 species. In the goal to detect methodological biases, one sample was constituted directly from pooled cultures, whereas the others consisted of pooled PCR products. The NGS reads obtained by pyrosequencing (Roche 454) were compared first to a DNA reference library including the sequences of all the species used to constitute the mock community, and second to a complete DNA reference library with a larger taxonomic coverage. A stringent taxonomic assignation gave inventories that were compared to the real one. We detected biases due to DNA extraction and PCR amplification that resulted in false-negative detection. Conversely, pyrosequencing errors appeared to generate false positives, especially in case of closely allied species. The taxonomic coverage of DNA reference libraries appears to be the most crucial factor, together with marker polymorphism which is essential to identify taxa at the species level. RbcL offers a high resolving power together with a large DNA reference library. Although needing further optimization, pyrosequencing is suitable for identifying diatom assemblages and may find applications in the field of freshwater biomonitoring.

Dramatic changes in a phytoplankton community in response to local and global pressures: a 24-year survey of the river Loire (France).

The impact of climate change and of other anthropogenic pressures on the structure and composition of phytoplankton communities of large European rivers remains poorly documented. Here we report the findings of a study of the changes in the phytoplankton community of the middle segment of the river Loire over the past 24 years. An attempt is made to distinguish between the impact of changes acting at the local scale and that of those acting more globally. A dramatic reduction in phytoplankton abundance was observed, particularly in the mid -1990s; this was concomitant with an increase in the relative proportion of cyanobacteria. At the same time, the phytoplankton community displayed increasing richness and diversity, and little change in its size structure. All these changes seem to be related to local changes, in particular to the reduction in phosphorus concentrations, as well as to changes in climate, throughout modifications in the river discharge and water temperature. Interestingly, herbicide contamination also appeared to be of particular importance in explaining the unexpected increase in the proportion of cyanobacteria in the phytoplankton community after the 1990s. These findings suggest that combinations of numerous anthropogenic pressures acting at different spatial and temporal scales have led to a mix of predictable and unpredictable changes occurring in the phytoplankton community of the river Loire, with probable consequences for the trophic networks in this river.

Spatiotemporal variations in microcystin concentrations and in the proportions of microcystin-producing cells in several Microcystis aeruginosa populations.

With the aim of explaining the variations in microcystin (MC) concentrations during cyanobacterial blooms, we studied several Microcystis aeruginosa populations blooming in different freshwater ecosystems located in the same geographical area. As assessed by real-time PCR, it appeared that the potentially MC-producing cells (mcyB(+)) were predominant (70 to 100%) in all of these M. aeruginosa populations, with the exception of one population in which non-MC-producing cells always dominated. Apart from the population in the Grangent Reservoir, we found that the proportions of potentially MC-producing and non-MC-producing cells varied little over time, which was consistent with the fact that according to a previous study of the same populations, the intergenic transcribed spacer (ITS) genotype composition did not change (38). In the Grangent Reservoir, the MC-RR variant was the dominant microcystin variant throughout the bloom season, despite changes in the ITS composition and in the proportions of mcyB(+) cells. Finally, the variations in total MC concentrations (0.3 to 15 microg liter(-1)) and in the MC cellular quotas (0.01 to 3.4 pg cell(-1)) were high both between and within sites, and no correlation was found between the MC concentrations and the proportion of mcyB(+) cells. All of these findings demonstrate that very different results can be found for the proportions of potentially MC-producing and non-MC-producing cells and MC concentrations, even in M. aeruginosa populations living in more or less connected ecosystems, demonstrating the importance of the effect of very local environmental conditions on these parameters and also the difficulty of predicting the potential toxicity of Microcystis blooms.

Alternation of anthelmintic treatments: a molecular evaluation for benzimidazole resistance in nematodes.

The evolution of benzimidazoles (BZ) resistance in Teladorsagia circumcincta was investigated in a controlled trial with lambs, submitted to different treatment regimens. Four paddocks were seeded with a T. circumcincta strain constituted by 25% of BZ-resistant nematodes. Ten permanent lambs were allocated to each paddock, from April to November in order to renew the contamination of pasture. Monthly, three tracer lambs were allocated in each paddock. BZ-resistant nematode frequency was determined (PCR diagnosis). The faecal egg count reduction test (permanent lambs) and the number of nematodes in lambs were also determined (permanent and tracer lambs). Four different regimens of treatments were performed: control, levamisole (a non-BZ drug), fenbendazole (a BZ drug), and an alternation of levamisole and fenbendazole every second treatment. The same protocol was repeated on two consecutive grazing seasons, increasing the number of treatments (3 in first year and 5 in second year). The proportions of BZ-resistant nematodes did not change during all the study in both the control and the levamisole paddocks, supporting an equal global fitness of BZ-resistant and susceptible nematodes. Thus, no reversion of BZ resistance is to be expected. In the alternated drug group and in the BZ treated group, BZ-resistant nematodes increased from 25% to 47% and to 78%, respectively. BZ resistance increased proportionally to the selective pressure (number of BZ treatments). The drug alternation is not a good solution to delay importantly the evolution of resistance when more than 25% of nematodes are BZ-resistant. This study is the first evaluation of BZ-resistance evolution (using individual genotyping) in controlled conditions. It showed that when a monogenic anthelmintic resistance is established at 25% in a sexually reproducing nematode population, it seems to be impossible to prevent its increase even when using limited number of BZ treatments.

Molecular approaches for monitoring potentially toxic marine and freshwater phytoplankton species.

Harmful phytoplankton species are a growing problem in freshwater and marine ecosystems, because of their ability to synthesize toxins that threaten both animal and human health. The monitoring of these microorganisms has so far been based on conventional methods, mainly involving the microscopic counting and identification of cells, and using analytical and bioanalytical methods to identify and quantify the toxins. However, the increasing number of microbial sequences in the GeneBank database and the development of new tools in the last 15 years nowadays enables the use of molecular methods for detection and quantification of harmful phytoplankton species and their toxins. These methods provide species-level identification of the microorganisms of interest, and their early detection in the environment by PCR techniques. Moreover, real time PCR can be used to quantify the cells of interest, and in some cases to evaluate the proportion of toxin-producing and non-toxin-producing genotypes in a population. Recently, microarray technologies have also been used to achieve simultaneous detection and semi-quantification of harmful species in environmental samples. These methods look very promising, but so far their use remains limited to research. The need for validation for routine use and the cost of these methods still hamper their use in monitoring programs.

Variations in the microcystin production of Planktothrix rubescens (cyanobacteria) assessed from a four-year survey of Lac du Bourget (France) and from laboratory experiments.

Between 1999 and 2002, a routine survey of water quality in the Lac du Bourget was performed to study the dynamics and microcystin (MC) production of Planktothrix rubescens. Using liquid chromatography coupled to diode array detection and mass spectrometry, we found that two main variants ([D-Asp3] and [D-Asp3, Dhb7] microcystin-RR) were produced. The proportion of these two variants was not influenced by the depth or season of sampling. Expressed in microcystin-LR equivalents, high microcystin concentrations were recorded from August to December each year, reaching values of up to 6.7 microg L-1. A significant correlation was found between the microcystin cell content and the cell densities of P. rubescens. Cellular quotas of microcystins ranged from 0.1 to 0.3 pg cell-1. Simultaneously, laboratory experiments were performed on a strain of P. rubescens isolated from the lake to assess the potential impact of various P-PO4 (3-) concentrations on intra- and extracellular microcystin production. Unlike natural populations, this strain only produced [D-Asp3] MC-RR. The intracellular microcystin content was similarly correlated to the cell density, but the cellular quota was slightly higher (0.3-0.7 pg cell-1) than in the natural population. Again, as in the natural population, a linear relationship was found between growth rate and microcystin production rate. These findings support the hypothesis that environmental factors, such as phosphate concentrations, have no direct impact on microcystin production by P. rubescens, but act indirectly by affecting growth rate.

Genetic diversity in Microcystis populations of a French storage reservoir assessed by sequencing of the 16S-23S rRNA intergenic spacer.

We compared the genetic diversity of the 16S-23S spacer of the rRNA gene (ITS1) in benthic and pelagic colonies of the Microcystis genus isolated from two different sampling stations with different depths and at two different sampling times (winter and summer) in the French storage reservoir of Grangent. In all, 66 ITS1 sequences were found in the different clone libraries. The nucleotide diversity of all the sampled isolates were in the same range (average number = 0.022) regardless of their origin, showing that several clones are involved in the summer bloom event and contribute to the high biomass production. Phylogenetic study and analysis of molecular variance (AMOVA) revealed no obvious genetic differentiation between the benthic and pelagic isolates. This finding confirms that the Microcystis genus in this lake is characterized by having both a benthic phase in winter and spring allowing this organism to survive in unfavorable environmental conditions, and a pelagic phase in summer and autumn when environmental conditions allow them to grow in the water column. Finally, comparing these sequences with those available in the GenBank database showed that some highly conserved genotypes are found throughout the world.

Comparison of eukaryotic phytobenthic community composition in a polluted river by partial 18S rRNA gene cloning and sequencing.

We compared the species composition in phytobenthic communities at different sampling sites in a small French river presenting polluted and unpolluted areas. For each sampling point, the total DNA was extracted and used to construct an 18S rRNA gene clone library after PCR amplification of a ca 400 bp fragment. Phytobenthic community composition was estimated by random sequencing of several clones per library. Most of the sequences corresponded to the Bacillariophyceae and Chlorophyceae groups. By combining phylogenetic and correspondence analyses, we showed that our molecular approach is able to estimate and compare the species composition at different sampling sites in order to assess the environmental impact of xenobiotics on phytobenthic communities. Changes in species composition of these communities were found, but no evident decrease in the diversity. We discuss the significance of these changes with regard to the existing level of pollution and their impact on the functionality of the ecosystem. Our findings suggest that it is now possible to use faster molecular methods (DGGE, ARISA.) to test large numbers of samples in the context of ecotoxicological studies, and thus to assess the impact of pollution in an aquatic ecosystem.

Environmental context of Cylindrospermopsis raciborskii (Cyanobacteria) blooms in a shallow pond in France.

Cylindrospermopsis raciborskii, a potentially toxic blooming cyanobacterium (blue-green alga), responsible for public health problems in Australia, was identified in France in 1994 in a shallow pond south of Paris. A program monitoring the occurrence of C. raciborskii in this pond was conducted from July 1998 to October 1999. The phytoplankton assemblages were studied, and limnological parameters (water temperature, dissolved oxygen, pH, conductivity, and dissolved inorganic nutrients) were measured. By multivariate analysis (principal component analysis), we showed that sufficiently high temperatures to allow the germination of akinetes, relatively low nutrient concentrations (soluble reactive phosphorus with a mean concentration of 1 microM and nitrate between 0 and 5 microM, except in February 1999 (21 microM)) and a characteristic high and constant sulfate concentration (8981+/-471 microM) seemed to be the main factors involved in the proliferation of C. raciborskii in the "Francs-Pêcheurs" (FP) pond. In the light of these findings and of bibliographic data, C. raciborskii would seem to be characterized by good adaptability, but also by low competitiveness with other phytoplanktonic species in the temperate study area.

Diversity of benzimidazole-resistance alleles in populations of small ruminant parasites.

The resistance of gastro-intestinal nematodes of small ruminants (sheep and goat) to benzimidazole anthelmintic drugs seems to be linked primarily to a single mutation in the isotype 1 beta-tubulin gene. This study was carried out to investigate the origin and diversity of benzimidazole-resistance alleles in trichostrongylid nematodes. We sequenced a 550 bp fragment of the isotype 1 beta-tubulin gene from several benzimidazole-resistant Teladorsagia circumcincta populations isolated from dairy goat farms in the central and south-western France. We also sequenced the same beta-tubulin fragment from Trichostrongylus colubriformis and Haemonchus contortus populations in south-western France. We found eight benzimidazole-resistance alleles in all T. circumcincta populations studied, six in H. contortus populations, and only one in T. colubriformis populations. In most cases, only one benzimidazole-resistance allele was present in T. circumcincta and H. contortus populations, but two alleles were found in a fewer number of them. Some T. circumcincta populations shared the same benzimidazole-resistance allele whereas some others had a specific benzimidazole-resistance allele. Similar findings were obtained for H. contortus. As no parasites are introduced once the flock of dairy goat farms has been constituted, these data indicate for the three studied species that rare pre-existing benzimidazole-resistance alleles already present before the isolation of populations had been selected. On the other hand, the fact that some benzimidazole-resistance alleles were specific to one population of T. circumcincta or H. contortus, seems to be in agreement with the hypothesis of the selection of spontaneous mutations. Thus, the origin of benzimidazole-resistance alleles in trichostrongylid nematodes seems to involve primarily the selection of rare alleles and possibly of spontaneous mutations.

Molecular approaches to studying benzimidazole resistance in trichostrongylid nematode parasites of small ruminants.

Molecular techniques are of growing importance in the study of anthelmintic resistance in trichostrongylid worm populations. A knowledge of the genetic determinants of benzimidazole (BZ) resistance has made it possible to construct a molecular tool for genotyping individual worms, in respect of mutation of the beta-tubulin gene responsible for BZ resistance. This tool offers new possibilities in the diagnosis of BZ resistance, and also in the study of anthelmintic use and other breeding management factors that can affect the selection of BZ-resistant alleles in worm populations. New molecular methods have also made it possible to study the origin and diversity of BZ-resistant alleles in trichostrongylid populations. The results demonstrate the value of a multidisciplinary approach to the study of anthelmintic resistance, combining molecular, ecological and epidemiological techniques.

Effect of benzimidazole under-dosing on the resistant allele frequency in Teladorsagia circumcincta (Nematoda).

This experiment was designed to determine the effects of under-dosing on the frequency of benzimidazole resistant allele in the nematode Teladorsagia circumcincta. Fenbendazole (FBZ) was tested at 1/32, 1/16, 1/8 and 1/4 of the recommended dose for sheep (5 mg/kg body weight). The fraction of the susceptible homozygote (SS), susceptible heterozygote (RS) and resistant homozygote (RR) genotypes were compared among FBZ dose groups to evaluate differences between SS and RS genotype selective advantage. Almost all SS genotype worms were eliminated by 1/4 of the FBZ recommended dose, whereas a significant fraction of the RS genotype worms survived treatment. The selective advantage was 4.5 times higher for the RS genotype. This selective advantage was determined at 1/4 of the manufacturer's recommended dose of FBZ. This value should be taken as an indictor of the selective advantage of RS over the SS genotype when lambs are under-dosed. A computer simulation was used to study the putative spread of anthelmintic resistance over a range of RS selective advantages (2, 4.5 and 10-fold), with two average sizes of individual host worm population (20 or 2000 worms/host) and two initial R allele frequencies (0.1%, or 1%). In all situations, the lowest selective advantage of the RS genotype over the SS genotype was sufficient to promote the spread of resistance in susceptible populations. When the RS genotype had no selective advantage over the SS genotype, genetic drift almost always led to the loss of the R allele, except in the largest populations (average size = 2000 worms).

Mitochondrial DNA variation in benzimidazole-resistant and -susceptible populations of the small ruminant parasite Teladorsagia circumcincta.

The genetic diversity of the mtDNA ND4 gene in 11 Teladorsagia circumcincta populations from France and Morocco was assessed by sequencing. Some of these nematode populations were resistant to benzimidazole (BZ) anthelmintics, while others were susceptible. The nucleotide diversity in all populations studied was very high, probably due to a high mutation rate in nematodes, but there was no significant difference between them. This suggests that no strong, recurrent bottlenecks occur during the acquisition of BZ resistance by a worm population. The conservation of genetic variations during the acquisition of BZ resistance is probably due to the fact that anthelmintic treatments do not kill all the susceptible adult worms and to the presence of numerous free-living larvae that are not submitted to this anthelmintic pressure. There was no genetic subdivision between worm populations on a small geographical scale (less than 200 km), but significant F(ST)s were found on a larger geographical scale. This kind of subdivision cannot be explained by different genetic flows between populations because all these populations were isolated from each other. This subdivision is probably due to the breeding management practices and the large size of these worm populations, which limit genetic drift.

A molecular tool for species identification and benzimidazole resistance diagnosis in larval communities of small ruminant parasites.

This report describes a molecular method for determining in a first step the generic composition of a nematode community and in a second step, the resistance of each species to benzimidazole (BZ). We first established a polymerase chain reaction (PCR) linked to a restriction fragment length polymorphism strategy using the isotype 1 beta-tubulin gene. This method overcame the limitations of morphological identification of larval stages of trichostrongylid nematode species. Geographically distant isolates from the three main gastrointestinal species in temperate zones, Teladorsagia circumcincta, Haemonchus contortus, and Trichostrongylus colubriformis, were distinguished using this method. We then used an allele-specific PCR (AS-PCR) to detect mutations of residue 200 of the beta-tubulin, which is implicated in BZ resistance. The sequences of several samples confirmed the BZ-resistance genotype determined by AS-PCR. The ability to process large numbers of samples simultaneously makes this PCR-based strategy particularly suitable for epidemiological studies. It may also be useful for monitoring the emergence of resistant alleles in nematode communities.

Importance of the mutation of amino acid 200 of the isotype 1 beta-tubulin gene in the benzimidazole resistance of the small-ruminant parasite Teladorsagia circumcincta.

In this work we demonstrated that the acquisition of benzimidazole (BZ) resistance in the small-ruminant parasite Teladorsagia circumcincta is linked to the selection of individuals that are characterized by a tyrosine (Tyr) at amino acid 200 of their isotype 1 beta-tubulin gene. This mutation appears to be recessive, since only homozygous mutant (Tyr/Tyr) individuals survived after BZ treatment of two resistant populations in which the three genotypes (rr, rs, ss) were initially present. In comparison with natural BZ-susceptible populations, a decrease in the restriction polymorphism (RFLP) of the isotype 1 beta-tubulin gene was observed in natural resistant populations. It seems that this decrease in beta-tubulin polymorphism results from the selection of homozygous mutant individuals.

PCR diagnosis of benzimidazole-susceptibility or -resistance in natural populations of the small ruminant parasite, Teladorsagia circumcincta.

We have developed a new molecular tool for the diagnosis of the benzimidazole (BZ)-susceptibility or resistance in Teladorsagia circumcincta a nematode parasite of small ruminants. This tool is based on the use of the PCR and allows the genotyping of resistant (rr) or susceptible (rS and SS) adult worms or larvae. By using four primers in the same reaction mixture, worms can be genotyped in regard to the mutation on the residue 200 (phenylalanine to tyrosine) of the beta-tubulin which is implicated in BZ resistance. A very high proportion of homozygous SS (Phe/Phe) individuals characterized the BZ susceptible populations, whereas a variable proportion of homozygous rr (Tyr/Tyr) individuals characterized the BZ resistant populations. A positive correlation was observed between the LD50 estimated by egg hatch assay, and the proportion of mutant homozygous individuals rr (Tyr/Tyr). Our PCR method allows the rapid genotyping of numerous worms and permits the detection of the first resistant individuals in a worm population.

Microsatellite markers for typing Aspergillus fumigatus isolates.

The use of microsatellites as highly polymorphic DNA markers for the typing of isolates of Aspergillus fumigatus was investigated. Four CA repeats were selected by screening an A. fumigatus DNA library with a (CA)10 oligonucleotide. Primers flanking these CA repeats were designed to amplify each locus. One primer of each pair was labeled with a fluorophore, and the PCR products were analyzed with an automatic sequencer and the GeneScan software. For each primer set and for a given isolate, one band was detected and was assigned to an allele because A. fumigatus is haploid. With 50 clinical isolates, 50 environmental isolates, and 2 reference strains we obtained 12, 11, 10, and 23 different alleles for the four CA microsatellites, respectively (discriminatory power, 0.994). The results were identical by whatever DNA extraction technique was used. Interestingly, no clustering between environmental and clinical isolates was observed, suggesting that every isolate is potentially pathogenic. Microsatellite markers appear suitable for use in large epidemiological studies of invasive aspergillosis.

Fitness of benzimidazole-resistant and -susceptible worms of Teladorsagia circumcincta, a nematode parasite of small ruminants.

We compared, some fitness-related traits of benzimidazole resistant (rr) and susceptible (rS, SS) worms of Teladorsagia circumcincta, a gastrointestinal parasite of the small ruminants, under laboratory conditions. PCR was used to determine the genotypes (rr, SS, rS) and the fitness of each was compared within the same strain. There was no significant difference in egg production, development rate from egg to infective larvae stage, establishment of these larvae in the host or the survival of adult worms and infective larvae for the 3 genotypes. The same results were obtained for the establishment rate of larvae in the host and the production of infective larvae under conditions of strong competition between resistant and susceptible worms. The fact that there were no differences in fitness suggests that the installation of benzimidazole resistance in a worm population is irreversible. This agrees with field observations.