Is a mixture of arbuscular mycorrhizal fungi better for plant growth than single-species inoculants?

Inoculation of arbuscular mycorrhizal fungi (AMF) as plant growth promoters has mostly been conducted using single-species inoculum. In this study, we investigated whether co-inoculation of different native AMF species induced an improvement of plant growth in an ultramafic soil. We analyzed the effects of six species of AMF from a New Caledonian ultramafic soil on plant growth and nutrition, using mono-inoculations and mixtures comprising different numbers of AMF species, in a greenhouse experiment. The endemic Metrosideros laurifolia was used as a host plant. Our results suggest that, when the plant faced multiple abiotic stress factors (nutrient deficiencies and high concentrations of different heavy metals), co-inoculation of AMF belonging to different families was more efficient than mono-inoculation in improving biomass, mineral nutrition, Ca/Mg ratio, and tolerance to heavy metals of plants in ultramafic soil. This performance suggested functional complementarity between distantly related AMF. Our findings will have important implications for restoration ecology and mycorrhizal biotechnology applied to ultramafic soils.

Acute toxicities of pharmaceuticals toward green algae. mode of action, biopharmaceutical drug disposition classification system and quantile regression models.

The acute toxicities of 36 pharmaceuticals towards green algae were estimated from a set of quantile regression models representing the first global quantitative structure-activity relationships. The selection of these pharmaceuticals was based on their predicted environmental concentrations. An agreement between the estimated values and the observed acute toxicity values was found for several families of pharmaceuticals, in particular, for antidepressants. A recent classification (BDDCS) of drugs based on ADME properties (Absorption, Distribution, Metabolism and Excretion) was clearly correlated with the acute ecotoxicities towards algae. Over-estimation of toxicity from our QSAR models was observed for classes 2, 3 and 4 whereas our model results were in agreement for the class 1 pharmaceuticals. Clarithromycin, a class 3 antibiotic characterized by weak metabolism and high solubility, was the most toxic to algae (molecular stability and presence in surface water).

Dynamic extreme values modeling and monitoring by means of sea shores water quality biomarkers and valvometry.

Water quality can be evaluated using biomarkers such as tissular enzymatic activities of endemic species. Measurement of molluscs bivalves activity at high frequency (e.g., valvometry) during a long time period is another way to record the animal behavior and to evaluate perturbations of the water quality in real time. As the pollution affects the activity of oysters, we consider the valves opening and closing velocities to monitor the water quality assessment. We propose to model the huge volume of velocity data collected in the framework of valvometry using a new nonparametric extreme values statistical model. The objective is to estimate the tail probabilities and the extreme quantiles of the distribution of valve closing velocity. The tail of the distribution function of valve closing velocity is modeled by a Pareto distribution with parameter 𝜃 t,τ , beyond a threshold τ according to the time t of the experiment. Our modeling approach reveals the dependence between the specific activity of two enzymatic biomarkers (Glutathione-S-transferase and acetylcholinesterase) and the continuous recording of oyster valve velocity, proving the suitability of this tool for water quality assessment. Thus, valvometry allows in real-time in situ analysis of the bivalves behavior and appears as an effective early warning tool in ecological risk assessment and marine environment monitoring.

Transcriptome profile analysis reveals specific signatures of pollutants in Atlantic eels.

Identifying specific effects of contaminants in a multi-stress field context remain a challenge in ecotoxicology. In this context, "omics" technologies, by allowing the simultaneous measurement of numerous biological endpoints, could help unravel the in situ toxicity of contaminants. In this study, wild Atlantic eels were sampled in 8 sites presenting a broad contamination gradient in France and Canada. The global hepatic transcriptome of animals was determined by RNA-Seq. In parallel, the contamination level of fish to 8 metals and 25 organic pollutants was determined. Factor analysis for multiple testing was used to identify genes that are most likely to be related to a single factor. Among the variables analyzed, arsenic (As), cadmium (Cd), lindane (γ-HCH) and the hepato-somatic index (HSI) were found to be the main factors affecting eel's transcriptome. Genes associated with As exposure were involved in the mechanisms that have been described during As vasculotoxicity in mammals. Genes correlated with Cd were involved in cell cycle and energy metabolism. For γ-HCH, genes were involved in lipolysis and cell growth. Genes associated with HSI were involved in protein, lipid and iron metabolisms. Our study proposes specific gene signatures of pollutants and their impacts in fish exposed to multi-stress conditions.

Application of quantile regression to recent genetic and -omic studies.

This paper provides a review of recent applications of quantile regression to the fields of genetic and the emerging -omic studies. It begins with a general background about this statistical approach following the seminal paper of Koenker and Bassett (Econometrica 46:33-50, 1978). Applications are described, as diverse as genetic association studies, penetrance estimation, gene expression, CGH array experiments, RNAseq experiments, methylation data and proteomics. This paper also introduces recent extensions of quantile regression with a particular focus on the Copula-quantile regression, an approach we recently proposed for sib-pair analysis. A real data example from eQTL analysis is then presented and the [Formula: see text] codes, which run the analyses are provided. Finally, we conclude with some statistical software presentation and some general statements about the potential and interests of quantile regression in modern biological experiments.

Water quality assessment by means of HFNI valvometry and high-frequency data modeling.

The high-frequency measurements of valve activity in bivalves (e.g., valvometry) over a long period of time and in various environmental conditions allow a very accurate study of their behaviors as well as a global analysis of possible perturbations due to the environment. Valvometry uses the bivalve's ability to close its shell when exposed to a contaminant or other abnormal environmental conditions as an alarm to indicate possible perturbations in the environment. The modeling of such high-frequency serial valvometry data is statistically challenging, and here, a nonparametric approach based on kernel estimation is proposed. This method has the advantage of summarizing complex data into a simple density profile obtained from each animal at every 24-h period to ultimately make inference about time effect and external conditions on this profile. The statistical properties of the estimator are presented. Through an application to a sample of 16 oysters living in the Bay of Arcachon (France), we demonstrate that this method can be used to first estimate the normal biological rhythms of permanently immersed oysters and second to detect perturbations of these rhythms due to changes in their environment. We anticipate that this approach could have an important contribution to the survey of aquatic systems.

Cadmium-induced genotoxicity in zebrafish at environmentally relevant doses.

Genotoxic effects of cadmium on zebra fish Danio rerio have been assessed by random amplified polymorphic DNA and real time PCR, followed by a comparison of the melting temperature patterns between each amplification reaction. Fish were exposed to two concentrations of cadmium chloride dissolved in the medium (1.9+/-0.6 microg Cdl(-1), C(1); 9.6+/-2.9 microg Cdl(-1), C(2)) for 21 days. A discriminative RAPD probe, OPB11, was first selected producing differential band patterns between control and metal-exposed genomic DNAs. RAPD-PCR showed an increase in the relative hybridization efficiency of OPB11 on the genomic DNAs coming from fish exposed to both Cd concentrations as compared to the control condition. In addition, the RAPD-PCR melting temperature patterns showed that with the OPB11 probe, the frequency of PCR products whose fusion temperature belongs to the [86-87 degrees C] interval decreased with Cd contamination, whereas an increase of frequency for the [78-80 degrees C] and [85-86 degrees C] intervals was correlated with Cd exposure.

Mercury contamination levels in the bioindicator piscivorous fish Hoplias aïmara in French Guiana rivers: mapping for risk assessment.

In French Guiana, native populations present high level of mercury contamination, which has been linked to the consumption of contaminated fishes. The goal of this study is to undertake a cartography of mercury contamination levels in fishes from the six main Guiana rivers. The selected species for this study is the ubiquitous piscivorous fish Hoplias aimara. A total number of 575 fishes from 134 discrete fishing sites are regrouped into 51 river sectors. Results from this study permits to rank the six main Guiana rivers by their mean level of contamination: Oyapock (0.548 mg kg-1), Comté (0.624 mg kg-1), Maroni (0.671 mg kg-1), Approuague (0.684 mg kg-1), Mana (0.675 mg kg-1), and Sinnamary (1.025 mg kg-1). The contamination is however not spatially homogenous along each river, and a map of the different levels of mercury contamination in fishes is provided. Sectors of low mean Hg contamination are observed both upstream (0.471 mg kg-1) and downstream (0.424 mg kg-1), corresponding to areas without any influence of gold mining activities and areas under the influence of estuarine dilution, respectively. Anoxia and gold mining activities are found to be the two main factors responsible for the high mercury concentration in fish muscles. While mean levels of mercury contaminations are higher in anoxia areas (1.029 mg kg-1), contaminations induced by gold mining activities (0.717 mg kg-1) present the most harmful consequences to human populations. No significant differences in Hg concentrations are observed between 2005 and 2014 for neither a pristine nor a gold mining area, while Hg concentration differences are observed between former (0.550 mg kg-1) and current gold mining sites (0.717 mg kg-1).

Cadmium uptake by the European eel: trophic transfer in field and experimental investigations.

Due to its status of threatened species and being heavily contaminated by metals, the European eel (Anguilla anguilla) was selected to investigate cadmium contamination levels of fish settled along a historically cadmium-contaminated hydrosystem, the Garonne-Gironde continuum (France), according to its various location sites and fish length. Results have shown an important site effect on cadmium concentrations in liver but not in gills, highlighting the possible predominance of the trophic exposure route. Subsequently, uncontaminated eels were experimentally exposed to cadmium by water uptake and/or trophic route(s). Eels were fed with different preys: white shrimps collected in an unpolluted area in the Gironde estuary, and cadmium-enriched shrimps. Data obtained tend to show that the use of cadmium-enriched food during experimental investigations triggers an underestimation of the metal trophic transfer rate. These two complementary approaches provide some elements to suggest that the trophic route plays an important role in cadmium contamination of wild eels.

The 'storm of the century' (December 1999) and the accidental escape of Siberian sturgeons (Acipenser baerii) into the gironde estuary (southwest France). An original approach for metal contamination.

GOAL, SCOPE AND BACKGROUND: The Gironde estuary is considered as a reference ecosystem with a large fish assemblage (75 species) and the presence of eleven diadromous species. However, geochemical studies and biomonitoring using oysters have shown high metal pollution levels. During the December 1999 hurricane, more than 5,000 young Siberian sturgeons (Acipenser baerii) accidentally escaped from a fish farm into the estuary, where this species had not been present until then. METHODS: In 2002/2003, thirteen sturgeons were collected from the estuary and twelve were obtained from the fish farm, from the same initial batch. Analysis of five metals (cadmium, zinc, copper, lead, mercury) measured in the gills, muscle, liver and kidneys, revealed significantly higher levels of cadmium, lead and mercury in the sturgeon collected from the estuary compared with those from the fish farm. RESULTS AND DISCUSSION: Metal analysis of the stomach contents of fish collected from the estuary and artificial food used in the fish farm indicated that dietary exposure might account for the differences observed. Nevertheless, metal concentrations in sturgeons that had spent about three years in the Gironde estuary may be considered low when compared with other species (mullets, eels) or with data in the literature regarding concentrations able to induce structural and functional perturbations in fish. As the introduced Siberian sturgeons live in the same place and feed on the same prey as the juveniles of the endangered A. sturio, our results indicate in the short-term that this strictly protected species does not appear to be much affected by the polymetallic pollution in the Gironde estuary. Marked differences in the concentrations of three metals (Cd, Pb, Hg) were established in four organs (gills, liver, skeletal muscle, kidneys) of Siberian sturgeons between specimens that had accidentally escaped into the Gironde estuary (France) during the December 1999 hurricane and were collected in March/June 2003 and specimens from the same initial batch at the fish farm. RECOMMENDATIONS AND PERSPECTIVES: Based on these results, a programme will be set up, with sampling campaigns carried out in the estuary every two years, with systematic monitoring of age in order to check the origin of individuals, in conjunction with sampling of sturgeon from the fish farm. This programme will complement other studies on several biological species representative of the main trophic levels in the estuary, especially the plankton component, benthic macroinvertebrates and oysters.

Inorganic mercury detection by valve closure response in the freshwater clam Corbicula fluminea: integration of time and water metal concentration changes.

The objective of the present study was to monitor water-quality assessment by a biological method. Optimum dissolved inorganic mercury sensitivity in the freshwater bivalve Corbicula fluminea was estimated using a combined approach to determine their potentials and limits in detecting contaminants. Detection by bivalves is based on shell closure, a protective strategy when exposed to a water contaminant. To take the rate of spontaneous closures into account, stress associated with fixation by one valve in common valvometers was integrated, and the spontaneous rhythm was associated with daily activity. The response in conditions where the probability of spontaneous closing is the lowest was thus taken into account. To develop dose-response curves, impedance valvometry, in which lightweight impedance electrodes are applied to study free-ranging animals in low-stress conditions, also was used combined with a new analytical approach. The logistic regression dose-response curves take into account variations in both response time and metal concentration in water to significantly improve the methods aiming at determining the optimal sensitivity threshold response. This approach demonstrates that in C. fluminea, inorganic mercury concentrations under the range of 2.0 to 5.1 microg/L (95% confidence interval) cannot be detected within 5 h of addition.

Mercurial exposure of residents of Santarém and Oriximiná cities (Pará, Brazil) through fish consumption.

A survey of the mercurial exposure of residents of Santarém and Oriximiná showed a differential mercurial impregnation between men and women. At the level of both cities, the mean hair mercury concentrations were 1.5 ± 0.5 (90th and 95th percentiles: 2.8 and 4.3) and 2.52 ± 0.09 µg g Hg/g (90th and 95th percentiles: 4.7 and 8.1) for women and men, respectively. The mercurial contamination appeared significantly closely linked to the daily amount of consumed fish. Carnivore species pescada branca (Plagioscion squamosissimus) and apapá (Pellona castelnaeana) and non-carnivore species pacú (Mylossoma duriventre) and aracú (Schizodon fasciatus) were consumed by 22, 19, 55 and 25% of people, respectively, and the mean mercury concentrations within fish flesh were 1.44 ± 0.11, 1.66 ± 0.19, 0.48 ± 0.09 and 0.49 ± 0.06 µg/g dry weight, respectively. Men aged above 35 were significantly more contaminated than those below. The mean hair concentrations of men were 5.20 ± 1.25 and 1.50 ± 0.22 µg/g, for those aged above 35 and below, respectively. The probability for women of childbearing age from both cities to present a hair mercury concentration above 1 µg Hg/g (corresponding to the US Environmental Protection Agency reference dose) was equal to 0.30 (95% confidence interval of 0.24-0.36). The probability of hair mercury concentration to be above the lowest observable adverse effect level (LOAEL) (0.3 µg Hg/g) was equal to 0.79 (95% confidence interval: 0.73-0.86).

The key role of metallothioneins in the bivalve Corbicula fluminea during the depuration phase, after in situ exposure to Cd and Zn.

An experimental study of the role of metallothioneins (MTs) in Cd and Zn depuration processes in the freshwater bivalve Corbicula fluminea was conducted after in situ exposure on the river Lot (France). Specimens of adult C. fluminea were first transplanted from a lacustrine reference site to a polymetallic polluted station (Bouillac, (B)) for a 42-days' exposure period from September to November 1996. They were then depurated after transfer to the laboratory, and were sub-sampled periodically until May 1997. During the first phase, MT concentrations measured with the Mercury-Saturation Assay were induced for a factor of 3.5 compared with time 0, whereas metal uptake showed accumulation factors of 17 and 4 for Cd and Zn, respectively. During the depuration phase, Cd and Zn concentrations decreased by 18 and 70%, respectively, giving estimated biological half-lives of 500 and 40 days. During the same period, MT concentrations decreased by 37% after transfer under unpolluted conditions, especially between 0 and 3 days, suggesting that MTs play a predominant role in Cd depuration. The quantity of Cd sequestered by the MT fraction, after size-exclusion liquid chromatography, represents on average 40% of the total Cd bioaccumulated in the soft body of the molluscs, compared with only 4-9% for total accumulated Zn. This essential metal was principally bound to low molecular weight proteins, which represented 20% of total Zn. Furthermore, it was observed that MTs had a key role in Cd remanence in the bivalves, and it was also reported that other proteins or small peptides were involved in the depuration of Zn.

Copper detection in the Asiatic clam Corbicula fluminea: optimum valve closure response.

When exposed to a contaminant, bivalves close their shell as a protective strategy. The aim of the present study was to estimate the maximum expected dissolved copper sensitivity in the freshwater bivalve Corbicula fluminea using a new approach to determine their potential and limit to detect contaminants. To take into account the rate of spontaneous closures, we integrated stress problems associated with fixation by a valve in usual valvometers and the spontaneous rhythm associated with nycthemeral activity, to optimize the response in conditions where the probability of spontaneous closing was lowest. Moreover, we used an original system with impedance valvometry, using lightweight impedance electrodes, to study free-ranging animals in low stress conditions combined with an analytical approach describing dose-response curves by logistic regression, with valve closure reaction as a function of response time and concentration of contaminant. In C. fluminea, we estimated that copper concentrations >4 microg/l (95% confidence interval (CI(95%)), 2.3-8.8 microg/l) must be detected within 5 h after Cu addition. Lower values could not be distinguished from background noise. The threshold values were 2.5 times higher than the values reported in the literature.

Copper detection in the Asiatic clam Corbicula fluminea: optimum valve closure response.

When exposed to a contaminant, bivalves close their shell as a protective strategy. The aim of the present study was to estimate the maximum expected dissolved copper sensitivity in the freshwater bivalve Corbicula fluminea using a new approach to determine their potential and limit to detect contaminants. To take into account the rate of spontaneous closures, we integrated stress problems associated with fixation by a valve in usual valvometers and the spontaneous rhythm associated with nycthemeral activity, to optimize the response in conditions where the probability of spontaneous closing was lowest. Moreover, we used an original system with impedance valvometry, using lightweight impedance electrodes, to study free-ranging animals in low stress conditions combined with an analytical approach describing dose-response curves by logistic regression, with valve closure reaction as a function of response time and concentration of contaminant. In C. fluminea, we estimated that copper concentrations > 4 microg/l (95% confidence interval (CI95%), 2.3-8.8 microg/l) must be detected within 5 h after Cu addition. Lower values could not be distinguished from background noise. The threshold values were 2.5 times lower than the values reported in the literature.

Estimation of potential and limits of bivalve closure response to detect contaminants: application to cadmium.

Bivalve closure responses to detect contaminants have often been studied in ecotoxicology as an aquatic pollution biosensor. We present a new laboratory procedure to estimate its potential and limits for various contaminants and animal susceptible to stress. The study was performed in the Asiatic clam Corbicula fluminea and applied to cadmium. To take into account the rate of spontaneous closures, we integrated stress problems associated with fixation by a valve in common apparatus and the spontaneous rhythm associated with circadian activity to focus on conditions with the lowest probability of spontaneous closing. Moreover, we developed an original system by impedance valvometry, using light-weight impedance electrodes, to study free-ranging animals in low-stress conditions and a new analytical approach to describe valve closure behavior as a function of response time and concentration of contaminant. In C. fluminea, we show that cadmium concentrations above 50 microg/L can be detected within less than 1 h, concentrations down to 16 microg/L require 5 h of integration time, and values lower than 16 microg/L cannot be distinguished from background noise. Our procedure improved by a factor of six the cadmium sensitivity threshold reported in the literature. Problems of field applications are discussed.

Quantile regression model for a diverse set of chemicals: application to acute toxicity for green algae.

The potential of quantile regression (QR) and quantile support vector machine regression (QSVMR) was analyzed for the definitions of quantitative structure-activity relationship (QSAR) models associated with a diverse set of chemicals toward a particular endpoint. This study focused on a specific sensitive endpoint (acute toxicity to algae) for which even a narcosis QSAR model is not actually clear. An initial dataset including more than 401 ecotoxicological data for one species of algae (Selenastrum capricornutum) was defined. This set corresponds to a large sample of chemicals ranging from classical organic chemicals to pesticides. From this original data set, the selection of the different subsets was made in terms of the notion of toxic ratio (TR), a parameter based on the ratio between predicted and experimental values. The robustness of QR and QSVMR to outliers was clearly observed, thus demonstrating that this approach represents a major interest for QSAR associated with a diverse set of chemicals. We focused particularly on descriptors related to molecular surface properties.

Field chronobiology of a molluscan bivalve: how the moon and sun cycles interact to drive oyster activity rhythms.

The present study reports new insights into the complexity of environmental drivers in aquatic animals. The focus of this study was to determine the main forces that drive mollusc bivalve behavior in situ. To answer this question, the authors continuously studied the valve movements of permanently immersed oysters, Crassostrea gigas, during a 1-year-long in situ study. Valve behavior was monitored with a specially build valvometer, which allows continuously recording of up to 16 bivalves at high frequency (10 Hz). The results highlight a strong relationship between the rhythms of valve behavior and the complex association of the sun-earth-moon orbital positions. Permanently immersed C. gigas follows a robust and strong behavior primarily driven by the tidal cycle. The intensity of this tidal driving force is modulated by the neap-spring tides (i.e., synodic moon cycle), which themselves depend of the earth-moon distance (i.e., anomalistic moon cycle). Light is a significant driver of the oysters' biological rhythm, although its power is limited by the tides, which remain the predominant driver. More globally, depending where in the world the bivalves reside, the results suggest their biological rhythms should vary according to the relative importance of the solar cycle and different lunar cycles associated with tide generation. These results highlight the high plasticity of these oysters to adapt to their changing environment.

Serial analysis of gene expression in the skeletal muscles of zebrafish fed with a methylmercury-contaminated diet.

Mercury (Hg) is a widespread environmental contaminant and its organic form, methylmercury (MeHg), has been known as a potent neurotoxic since the Minamata tragedy. In the Amazonian basin, gold mining leads to MeHg biomagnification all along the food web, culminating in piscivorous fish, ultimately responsible for contamination of human beings through fish consumption. In order to assess the biological impact of dietary MeHg on fish at the genome scale, we contaminated zebrafish with MeHg-contaminated food for 25 days (13.5 microg of Hg/g of food). A serial analysis of gene expression (SAGE) was conducted on the skeletal muscle because this tissue does not perform MeHg demethylation, and 19171 SAGE tags were sequenced from the control library versus 22 261 from the MeHg-contaminated library, corresponding to 5280 different transcripts. Among those identified, 60 genes appeared up-regulated and 15 down-regulated by more than 2 times. A net impact of MeHg was noticed on 14 ribosomal protein genes, indicating a perturbation of protein synthesis. Several genes involved in mitochondrial metabolism, the electron transport chain, endoplasmic reticulum (ER) function, detoxification, and general stress responses were differentially regulated, suggesting an onset of oxidative stress and ER stress. Several other genes for which expression varied with MeHg contamination could be clustered in various compartments of the cell's life, such as lipid metabolism, calcium homeostasis, iron metabolism, muscle contraction, and cell cycle regulation. This study reveals the effectiveness of the SAGE approach to acquire a better understanding of the MeHg global effects. Furthermore, this is the first time that the SAGE was used to characterize the effect of a toxicant at the genome scale in an aquatic organism.

Novel approach for genome scan meta-analysis of rheumatoid arthritis: a kernel-based estimation procedure.

Genome scan meta-analysis (GSMA) can prove very useful in detecting genetic effects too small to be detected in an individual linkage study and can also lead to more consistent results. In this paper, we propose a new kernel-based estimation procedure for GSMA. Instead of estimating identity by descent between markers, as performed in interval mapping approaches, we estimated directly the nonparametric linkage score between markers using a kernel procedure. The GSMA is then extended to take into account the kernel estimate of the nonparametric linkage score and its variance at a given chromosomal position. The method is applied to the rheumatoid arthritis genome scan data (Genetic Analysis Workshop 15 Problem 2).