Estimating the complexity of bird song by using capture-recapture approaches from community ecology

Repertoire size, the number of unique song or syllable types in the repertoire, is a widely used measure of song complexity in birds, but it is difficult to calculate this exactly in species with large repertoires. A new method of repertoire size estimation applies species richness estimation procedures from community ecology, but such capture-recapture approaches have not been much tested. Here, we establish standardized sampling schemes and estimation procedures using capture-recapture models for syllable repertoires from 18 bird species, and suggest how these may be used to tackle problems of repertoire estimation. Different models, with different assumptions regarding the heterogeneity of the use of syllable types, performed best for different species with different song organizations. For most species, models assuming heterogeneous probability of occurrence of syllables (so-called detection probability) were selected due to the presence of both rare and frequent syllables. Capture-recapture estimates of syllable repertoire size from our small sample did not differ significantly from previous estimates using larger samples of count data. However, the enumeration of syllables in 15 songs yielded significantly lower estimates than previous reports. Hence, heterogeneity in detection probability of syllables should be addressed when estimating repertoire size. This is neglected using simple enumeration procedures, but is taken into account when repertoire size is estimated by appropriate capture-recapture models adjusted for species-specific song organization characteristics. We suggest that such approaches, in combination with standardized sampling, should be applied in species with potentially large repertoire size. On the other hand, in species with small repertoire size and homogenous syllable usage, enumerations may be satisfactory. Although researchers often use repertoire size as a measure of song complexity, listeners to songs are unlikely to count entire repertoires and they may rely on other cues, such as syllable detection probability.Communicated by A. Cockburn     

Determinants of local extinction and turnover rates in urban bird communities.

Studying the effects of urbanization on the dynamics of communities has become a priority for biodiversity conservation. The consequences of urbanization are mainly an increased fragmentation of the original landscapes associated with a decrease in the amount of favorable habitats and an increased pressure of human activities on the remaining patches suitable for wildlife. Patterns of bird species richness have been studied at different levels of urbanization, but little is known about the temporal dynamics of animal communities in urban landscapes. In particular, urbanization is expected to have stronger negative effects on migratory breeding bird communities than on sedentary ones, which should lead to different patterns of change in composition. Using an estimation method accounting for heterogeneity in species detection probability and data collected between 2001 and 2003 within a suburban area near the city of Paris, France, we tested whether these communities differ in their local extinction and turnover rates. We considered the potential effects of patch size and distance to Paris' center as a measure of the degree of urbanization around the patches. As expected, local rates of extinction and turnover were higher for migratory than for sedentary species, and they were negatively related to patch size for migratory species. Mean species richness of the sedentary species increased during the study period and their local turnover rate was negatively related to the distance to the urban core, showing a trend to colonize the most urban patches. These results highlight the very dynamic nature of the composition of some local bird communities in fragmented habitats and help to identify factors affecting colonization and extinction.     

Validating graph-based connectivity models with independent presence–absence and genetic data sets

Habitat connectivity is a key objective of current conservation policies and is commonly modeled by landscape graphs (i.e., sets of habitat patches [nodes] connected by potential dispersal paths [links]). These graphs are often built based on expert opinion or species distribution models (SDMs) and therefore lack empirical validation from data more closely reflecting functional connectivity. Accordingly, we tested whether landscape graphs reflect how habitat connectivity influences gene flow, which is one of the main ecoevolutionary processes. To that purpose, we modeled the habitat network of a forest bird (plumbeous warbler [Setophaga plumbea]) on Guadeloupe with graphs based on expert opinion, Jacobs’ specialization indices, and an SDM. We used genetic data (712 birds from 27 populations) to compute local genetic indices and pairwise genetic distances. Finally, we assessed the relationships between genetic distances or indices and cost distances or connectivity metrics with maximum-likelihood population-effects distance models and Spearman correlations between metrics. Overall, the landscape graphs reliably reflected the influence of connectivity on population genetic structure; validation R² was up to 0.30 and correlation coefficients were up to 0.71. Yet, the relationship among graph ecological relevance, data requirements, and construction and analysis methods was not straightforward because the graph based on the most complex construction method (species distribution modeling) sometimes had less ecological relevance than the others. Cross-validation methods and sensitivity analyzes allowed us to make the advantages and limitations of each construction method spatially explicit. We confirmed the relevance of landscape graphs for conservation modeling but recommend a case-specific consideration of the cost-effectiveness of their construction methods. We hope the replication of independent validation approaches across species and landscapes will strengthen the ecological relevance of connectivity models.     

Assessing Cd,Pb, Zn human bioaccessibility in smelter-contaminated agricultural topsoils (northern France)

The extractability of Cd, Pb, and Zn was investigated in contaminated agricultural topsoils located in an area highly affected by the past atmospheric emissions of two smelters in northern France in order to assess their mobility and human bioaccessibility. The determination of Cd, Pb, and Zn bioaccessibility (Unified Barge Method, in vitro test) was made to evaluate the absolute trace element (TE) bioavailability. The results highlighted differences in bioaccessibility between Cd, Pb, and Zn (Cd > Pb > Zn). The mean values of the bioaccessible fractions of Cd, Pb, and Zn during the gastric phase were 82, 55, and 33%, respectively, of the pseudototal concentrations, whereas during the gastrointestinal phase, the bioaccessible fractions of metals decreased to 45, 20, and 10%, respectively. Stepwise multiple regression analysis showed that human bioaccessibility was affected by various physicochemical parameters (i.e., sand, carbonates, organic matter, assimilated P, free Al oxides, and pseudototal Fe contents). Sequential extractions were performed as an indication of the TE availability in these soils. Cadmium occurred in the more available fractions, Pb was mostly present as bound by oxides, and a significant contribution to the pseudototal Zn concentration was defined as the unavailable residual form related to the crystalline structures of minerals. The concepts of bioavailability and bioaccessibility are important for quantifying the risks associated with exposure to environmental pollutants and providing more realistic information for human health.     

Characterization of the toxic effects of cadmium and 3.5-dichlorophenol on nitrifying activity and mortality in biologically activated sludge systems—effect of low temperature

Background, aims, and scope  Sometimes, urban wastewaters convey a more or less significant part of toxic products from industries or the craft industry. Nitrifying activity can be affected by these substances, implying higher ammonia concentrations in the outlet effluent and contributing to toxicity for the aquatic environment. Moreover, the more stringently treated wastewater standards now require a reliable treatment for nitrogen. One of the key issues is the identification of the inhibition behavior of nitrifying bacteria facing a toxic substance. This new understanding could then finally be integrated into models in order to represent and to optimize wastewater treatment plants (WWTP) operation in cases involving ‘toxic scenarios’. Materials and methods  The toxic substances studied in this work, cadmium and 3.5-dichlorophenol (3.5-DCP), are representative of chemical substances commonly found in municipal sewage and industrial effluents and symbolize two different contaminant groups. The effects of Cd and 3.5-DCP on nitrification kinetics have been investigated using respirometry techniques. Results  IC50 values determination gives concentrations of 3.1 mg/L for 3.5-DCP and 45.8 mg/L for Cd at 21 ± 1°C. The variation to low temperature seems to have no real effect on IC50 for DCP, but induces a decrease of cadmium IC50 to 27.5 mg/L at 14°C. Finally, specific respirometric tests have been carried out in order to determine the potential effect of these toxic substances on the nitrifying decay rate b _a . No significant effect has been noticed for Cd, whereas the presence of 3.5-DCP (at IC50 concentration) induced a dramatic increase of b _a at 20°C. The same behavior has been confirmed by experiments performed in winter periods with a sludge temperature around 12°C. Discussion  The target substances have different modes of action on activity and mortality, notably due to the abilities of the contaminant to be precipitated, accumulated, or even to be progressively degraded. Studies realized at low temperature confirmed this assumption, and put in evidence the effect of temperature on toxic substances capable of being biosorbed. However, the change in the sludge sample characteristics can be pointed out as a problem in the investigation of the temperature effect on nitrification inhibition, as biosorption, bioaccumulation, and predation are directly linked to the sludge characteristics (VSS concentration, temperature) and the plant operating conditions (loading rates, sludge age, etc.). Conclusions  This work brings new understandings concerning the action mode of these specific contaminants on nitrifying bacteria and, in particular, on the role of temperature. The experiments lead to the determination of the IC50 values for both toxic substances on biological nitrification. The inhibition mechanisms of Cd and 3.5-DCP on nitrifying activity have been simply represented by a non-competitive inhibition model. Recommendations and perspectives  Other experiments carried out in a continuous lab-scale pilot plant should be done with a proper control of the operating conditions and of the sludge characteristics in order to better understand the mechanisms of nitrification inhibition for each contaminant. Finally, these first results show that toxic substances can have an effect on the growth rate but also on the decay rate, depending on the characteristics of the toxic substance and the sludge. This eventual double effect would imply different strategies of WWTP operation according to the behavior of the contaminant on the bacteria.     

The Effect of Heat and Free Chlorine Treatments on the Surface Properties of Murine Norovirus

Heat and free chlorine are among the most efficient and commonly used treatments to inactivate enteric viruses, but their global inactivation mechanisms have not been elucidated yet. These treatments have been shown to affect at least the capsid proteins of viruses and thus may affect the surface properties (i.e. electrostatic charge and hydrophobicity) of such particles. Our aim was to study the effects of heat and free chlorine on surface properties for a murine norovirus chosen as surrogate for human norovirus. No changes in the surface properties were observed with our methods for murine norovirus exposed to free chlorine. Only the heat treatment led to major changes in the surface properties of the virus with the expression of hydrophobic domains at the surface of the particles after exposure to a temperature of 55 °C. No modification of the expression of hydrophobic domains occurred after exposure to 60 °C, and the low hydrophobic state exhibited by infectious and inactivated particles after exposure to 60 °C appeared to be irreversible for inactivated particles only, which may provide a means to discriminate infectious from inactivated murine noroviruses. When exposed to a temperature of 72 °C or to free chlorine at a concentration of 50 mg/L, the genome became available for RNases.     

Efficacy of created and restored nesting sites for the conservation of colonial Laridae in the South of France

By rapidly modifying key habitat components, habitat restoration is at risk of producing attractive cues for animals without providing habitats of sufficient quality. As such, individual fitness components, such as reproduction, could be reduced and restored habitats could become ecological traps. This risk notably appears by using artificial constructions in restoration projects, yet few studies have evaluated their efficacy in a robust way. We investigated this by analyzing 154 islets that were created or restored to improve the conservation status of 7 colonial Laridae species in the South of France. From 2007 to 2016, we compared occupancy dynamics and breeding parameters of these species between the restored sites and 846 unmanaged nesting sites. We also explored species’ preference for different nesting site characteristics and their respective effect on breeding parameters. Restored nesting sites were 2–9 times as attractive as unmanaged sites for all species except the Black-headed Gull (Chroicocephalus ridibundus). Colonization probability was up to 100 times higher in sites already used by other species the previous year and increased with distance to the shore until >0.2 when distance was over 250 m. Abandonment probability was 29–70% lower when breeding was successful the previous year in all species except the Sandwich Tern (Thalasseus sandvicensis). Productivity and breeding success probability were 2 times higher on managed sites. Distance from the shore was an important attractive characteristic of artificial nesting sites in all species. Other nesting site characteristics had species-specific effects on colonization, abandonment, and breeding success. Our results indicate that managed nesting sites are successful conservation tools for colonial Laridae in the Mediterranean and do not act as ecological traps. Our study showed that testing the ecological trap hypothesis is a robust way to evaluate the success of restoration projects of breeding habitats.     

Biosorption of heavy metals using rice milling by-products. Characterisation and application for removal of metals from aqueous effluents

The morphological characteristics as well as chemical composition of rice husks were evaluated by different techniques such as spectroscopy and thermogravimetry. The material, which is considered a by-product obtained from rice milling, was then investigated as a potential decontaminant of toxic heavy metals present in laboratory effluents. Studies using glass columns were carried out at room temperature employing 100 ml of synthetic solutions containing Cd(II) and Pb(II) at 100 mg l(-1) in order to study the effects of pH, flow rate and particle size on Cd(II) and Pb(II) adsorption. After establishing the optimised conditions, the potentiality of rice husks for removing Cd(II) and Pb(II) ions from 100 ml of laboratory effluent, presenting concentrations before treatment of 22 and 12 mg l(-1), respectively, was evaluated. The ability to take up other metals species, such as Al(III), Cu(II) and Zn(II), present in this effluent was also studied. According to the data obtained, under the optimised conditions (pH=4.0, flow rate of 8.0 ml min(-1) and < or =355 microm rice husk particle size), 30 g of husks were necessary to attain the permissible limits for effluent release, as recommend by the EPA, for those species evolved in this work (Al, Cd, Cu, Pb and Zn).     

FMEA and consideration of real work situations for safer design of production systems

Production equipment designers must ensure the health and safety of future users; in this regard, they augment requirements for standardizing and controlling operator work. This contrasts with the ergonomic view of the activity, which recommends leaving operators leeway (margins for manoeuvre) in performing their task, while safeguarding their health. Following a brief analysis of design practices in the car industry, we detail how the Failure Modes and Effects Analysis (FMEA) approach is implemented in this sector. We then suggest an adaptation that enables designers to consider real work situations. This new protocol, namely, work situation FMEA, allows experience feedback to be used to defend the health standpoint during designer project reviews, which usually only address quality and performance issues. We subsequently illustrate the advantage of this approach using two examples of work situations at car parts manufacturers: the first from the literature and the second from an in-company industrial project.     

Indicators of deforestation in the Southern Brazilian Pre-Amazon

In recent years, Amazonian deforestation has become a question of global concern. Deforestation in Amazon is a complex phenomenon in nature and has been related to traditional agriculture expansion. In this work, land use, socioeconomic and conservation indicators, combined with statistical analysis, were used to understand forces associated with patterns of deforestation. This approach was applied in Southern Brazilian Pre-Amazon in Mato Grosso State, which represents an extensive rain forest-savanna ecotone, located in the south border of Amazon biome. Based on data from the last two agricultural censuses (1995/1996–2006), we compared agricultural expansion in this area and Mato Grosso state. Results have shown that 85 % of state deforestation was concentrated in Southern Pre-Amazon and was closely related to increase in number of cattle and pasture area. PCA results pointed that population (92 %), number of cattle (86.5 %), pastures (84.2 %) and tractors (78.4 %) were variables with highest positive correlation to deforestation. It showed that GDP contributes to an individual axis and has a low correlation to deforestation (37.8 %). Conservation units and indigenous reserves also contribute to a single axis and were negatively correlated to temporary crops area. Results revealed a significant reduction in production and commercialization of extractive products in the region, revealing that the main, almost only conservation policy in Mato Grosso remains the creation of Special Areas. We suggest that further studies are necessary to screen development alternatives to simple cutting trees down. It is important to diversify strategies for deforestation control, and development aspects must be more seriously considered to reach a sustainable deforestation control policy.