Effect of scale on trait predictors of species responses to agriculture

Species persistence in human‐altered landscapes can depend on factors operating at multiple spatial scales. To understand anthropogenic impacts on biodiversity, it is useful to examine relationships between species traits and their responses to land‐use change. A key knowledge gap concerns whether these relationships vary depending on the scale of response under consideration. We examined how local‐ and large‐scale habitat variables influence the occupancy dynamics of a bird community in cloud forest zones in the Colombian Chocó‐Andes. Using data collected across a continuum of forest and agriculture, we examined which traits best predict species responses to local variation in farmland and which traits best predict species responses to isolation from contiguous forest. Global range size was a strong predictor of species responses to agriculture at both scales; widespread species were less likely to decline as local habitat cover decreased and as distance from forest increased. Habitat specialization was a strong predictor of species responses only at the local scale. Open‐habitat species were particularly likely to increase as pasture increased, but they were relatively insensitive to variation in distance to forest. Foraging plasticity and flocking behavior were strong predictors of species responses to distance from forest, but not their responses to local habitat. Species with lower plasticity in foraging behaviors and obligate flock‐following species were more likely to decline as distance from contiguous forest increased. For species exhibiting these latter traits, persistence in tropical landscapes may depend on the protection of larger contiguous blocks of forest, rather than the integration of smaller‐scale woodland areas within farmland. Species listed as threatened or near threatened on the International Union for Conservation of Nature Red List were also more likely to decline in response to both local habitat quality and isolation from forest relative to least‐concern species, underlining the importance of contiguous forests for threatened taxa.     

Improving credibility and transparency of conservation impact evaluations through the partial identification approach

The fundamental challenge of evaluating the impact of conservation interventions is that researchers must estimate the difference between the outcome after an intervention occurred and what the outcome would have been without it (counterfactual). Because the counterfactual is unobservable, researchers must make an untestable assumption that some units (e.g., organisms or sites) that were not exposed to the intervention can be used as a surrogate for the counterfactual (control). The conventional approach is to make a point estimate (i.e., single number along with a confidence interval) of impact, using, for example, regression. Point estimates provide powerful conclusions, but in nonexperimental contexts they depend on strong assumptions about the counterfactual that often lack transparency and credibility. An alternative approach, called partial identification (PI), is to first estimate what the counterfactual bounds would be if the weakest possible assumptions were made. Then, one narrows the bounds by using stronger but credible assumptions based on an understanding of why units were selected for the intervention and how they might respond to it. We applied this approach and compared it with conventional approaches by estimating the impact of a conservation program that removed invasive trees in part of the Cape Floristic Region. Even when we used our largest PI impact estimate, the program's control costs were 1.4 times higher than previously estimated. PI holds promise for applications in conservation science because it encourages researchers to better understand and account for treatment selection biases; can offer insights into the plausibility of conventional point‐estimate approaches; could reduce the problem of advocacy in science; might be easier for stakeholders to agree on a bounded estimate than a point estimate where impacts are contentious; and requires only basic arithmetic skills.     

Assessment of the applicability of a “toolbox” designed for microbially assisted phytoremediation: the case study at Ingurtosu mining site (Italy)

The paper describes the fieldwork at the Italian test site of the abandoned mine of sphalerite and galena in Ingurtosu (Sardinia), with the aim to assess the applicability of a “toolbox” to establish the optimized techniques for remediation of soils contaminated by mining activities. A preliminary characterization—including (hydro)geochemistry, heavy metal concentration and their mobility in soil, bioprospecting for microbiology and botany—provided a data set for the development of a toolbox to deliver a microbially assisted phytoremediation process. Euphorbia pithyusa was selected as an endemic pioneer plant to be associated with a bacterial consortium, established with ten selected native strains, including metal-tolerant bacteria and producers of plant growth factors. The toolbox was firstly assessed in a greenhouse pot experiment. A positive effect of bacterial inoculum on E. pithyusa germination and total plant survival was observed. E. pithyusa showed to be a well-performing metallophyte species, and only inoculated soil retained a microbial activity with a high functional diversity, expanding metabolic affinity also towards root exudates. These results supported the decision to proceed with a field trial, investigating different treatments used singly or in combination: bioaugmentation with bacterial consortia, mycorrhizal fungi and a commercial mineral amendment. Microbial activity in soil, plant physiological parameters and heavy metal content in plants and in soil were monitored. Five months after the beginning, an early assessment of the toolbox under field conditions was carried out. Despite the cold season (October–March), results suggested the following: (1) the field setup as well as the experimental design proved to be effective; (2) plant survival was satisfactory; (3) soil quality was increased and bioaugmentation improved microbial activity, expanding the metabolic competences towards plant interaction (root exudates); and (4) multivariate analysis supported the data provided that the proposed toolbox can be established and the field trial can be carried forward.     

Predictive model for areas with illegal landfills using logistic regression

The existence of illegal landfills is an environmental problem in most countries. However, research on this issue is scarce and limited by the availability and quality of data on the subject. Thus, most illegal landfill studies have only been conducted in a partial manner, focusing on geographical aspects or the causes of these landfills (lack of environmental awareness, inadequate waste management systems, and the role of local government). This research analyses a sample of 120 possible areas with illegal landfills in Andalusia using logistic regression in order to obtain a predictive model for the occurrence of these landfills, including both types of variables (geographical and behavioural) jointly. The results confirm that the variables that most influence the occurrence of illegal landfills are spatial (“Industrial Land”, “Plains” and “Rural Land”); whilst the variables that most reduce the likelihood of illegal landfills are those related to certain characteristics of the municipal waste management system and environmental awareness, such as “Availability of Recycling Facilities”, “Punitive Policies”, “Supervision” and “Awareness-raising Campaigns”. The model obtained shows that variables of very different nature and magnitude interact in the occurrence of illegal landfills, each of which contributes a series of features characteristic of its scale. It is advisable, therefore, to perform an analysis using a multi-scale approach in order to gain an overall understanding of the phenomenon.     

Detection of Norovirus GII.17 Kawasaki 2014 in Shellfish,Marine Water and Underwater Sewage Discharges in Italy

Norovirus (NoV) is a major cause of non-bacterial acute gastroenteritis worldwide, and the variants of genotype GII.4 are currently the predominant human strains. Recently, a novel variant of NoV GII.17 (GII.P17_GII.17 NoV), termed Kawasaki 2014, has been reported as the cause of gastroenteritis outbreaks in Asia, replacing the pandemic strain GII.4 Sydney 2012. The GII.17 Kawasaki 2014 variant has also been reported sporadically in patients with gastroenteritis outside of Asia, including Italy. In this study, 384 shellfish samples were subjected to screening for human NoVs using real-time PCR and 259 (67.4%) tested positive for Genogroup II (GII) NoV. Of these, 52 samples, selected as representative of different areas and sampling dates, were further amplified by conventional PCR targeting the capsid gene, using broad-range primers. Forty shellfish samples were characterized by amplicon sequencing as GII.4 (n = 29), GII.2 (n = 4), GII.6 (n = 2), GII.12 (n = 2), and GII.17 (n = 3). Sixty-eight water samples (39 seawater samples from the corresponding shellfish production areas and 29 water samples from nearby underwater sewage discharge points) were also tested using the above broad-range assay: eight NoV-positive samples were characterized as GII.1 (n = 3), GII.2 (n = 1), GII.4 (n = 2), and GII.6 (n = 2). Based on full genome sequences available in public databases, a novel RT-PCR nested assay specific for GII.17 NoVs was designed and used to re-test the characterized shellfish (40) and water (8) samples. In this second screening, the RNA of GII.17 NoV was identified in 17 additional shellfish samples and in one water sample. Upon phylogenetic analysis, these GII.17 NoV isolates were closely related to the novel GII.17 Kawasaki 2014. Interestingly, our findings chronologically matched the emergence of the Kawasaki 2014 variant in the Italian population (early 2015), as reported by hospital-based NoV surveillance. These results, showing GII.17 NoV strains to be widespread in shellfish samples collected in 2015 in Italy, provide indirect evidence that this strain has started circulating in the Italian population. Notably, using a specific assay, we were able to detect many more samples positive for GII.17 NoV, indicating that, in food and water matrices, broad-range assays for NoV may grossly underestimate the prevalence of some, less common, NoVs. The detection of the GII.17 strain Kawasaki 2014 in clinical, water and food samples in Italy highlights the need for more systematic surveillance for future disease control and prevention.     

Metal contamination of riverine sediments below the Avoca mines, south east Ireland

The River Avoca is severely polluted by discharges of acid mine drainage (AMD) from the abandoned sulphur and copper mines at Avoca. The riverine sediments were studied during a low flow period to establish the degree of contamination and to identify the major processes affecting sediment metal concentrations. pH plays a major role in the regulation of zinc adsorption and desorption in sediments, showing a significant correlation (p&0.001). The zinc concentration in the sediment falls below background levels after the input of AMD. However, the metal precipitated when the pH increased downstream of a fertiliser factory (pH8.0), some 7 km below the mine. In contrast Cu and Fe significantly increased (p0.001) both in the sediment (0--30 mm depth) and the surface ochre immediately below the mixing zone. Copper removal appears to be primarily by co-precipitation. Higher sediment enrichment factors for all metals were obtained in the surface sediment layer (ochre) deposited on larger stones and in floc material collected in sediment traps, compared with the subsurface sediment. Cadmium was not recorded in any of the sediment collected at the detection limit used (0.01 g g-1). Metal deposition in the sediments was found to be spacially variable, so sub-sampling is required, although replicates show little variation. Results indicate that short term variation in metal inputs is identified by sampling the surface layer only, whereas sampling of the subsurface layer (<63 m fraction) is more suitable for identifying long-term trends in sediment quality. The implication of sediment analysis in assessing environmental impact is discussed.     

Lactation performance of guinea pigs (Cavia porcellus) does not respond to experimental manipulation of pup demands

To ensure proper development of young, mothers should react to offspring signals of need. Studies of such parent-offspring interaction often manipulated litter size to measure effects of changed offspring food demand. We used the extreme precociality of guinea pig (Cavia porcellus) pups to increase offspring demand without changing any other litter characteristic. As pups contribute to their own energy demands from birth by independent feeding, their food demand can be increased by withholding solid food early in lactation. We studied whether mothers reacted to increased food demand of offspring by enhanced parental care, especially by changes in the pattern of milk production and nursing. Pups deprived of solid food early in lactation grew more slowly and were in poorer body condition than pups in control litters, even after the former had access to solid food in late lactation. Mothers of deprived young reacted to offspring long-term need by maintaining nursing behaviour for longer than control mothers. However, this change in behaviour did not occur early in lactation when pup short-term need was greatest nor did it result in increased milk transfer at any time. Energy allocation of mothers measured by changes in their food intake, maternal body reserves, and milk production stayed the same whether offspring had early access to solid food or not. Thus mothers did not increase energy allocation to pups even though they apparently had information about the pups' poor state.     

Acoustical signals in the dance language of the giant honeybee,Apis dorsata

Summary Acoustical signals emitted by dancing bees have recently been shown to transmit information about the location of food sources in the western honeybee, Apis mellifera. Towne (1985) reported that in the Asian honeybee species Apis dorsata, which builds a single comb in the open under overhanging rocks or tree branches, sound signals were not emitted by the dancers. This led to the conclusion that acoustical communication is restricted to bees that nest in the dark, like A. mellifera. Here we show that in fact A. dorsata produces dance sounds similar to those emitted by A. mellifera, and that these acoustical signals contain information about distance, direction and profitability of food sources. The acoustical transfer of information has thus evolved independently of nesting in dark cavities. The significance of nocturnal activity in Apis dorsata for the evolution of sound communication is discussed. Correspondence to: W.H. Kirchner