Non-lethal rapid biodiversity assessment

For several animal taxa, non-lethal techniques that do not rely on collecting individuals are routinely used to assess biodiversity (e.g. point counts in birds). Identification often relies on the ability of the observer, are subjected to errors, but populations are not impacted. Thus, multiple counting sessions (MCS) that allow using robust analyses (e.g. unbiased Chao richness estimate) are available. However, for most species (e.g. arthropods), trap systems must be set up. Killed individuals are collected and later accurately identified in the laboratory, but unbiased MCS become unavailable. Environmental DNA bar-coding provides an alternative, yet it requires important technical support and is not designed for MCS. Lethal rapid biodiversity assessments (RBA), derived from classical trap surveys and based on less accurate identifications (morphospecies are used), have been successfully developed to relax technical constraints. In this study, we combined non-lethal and RBA approaches to address logistical, analytical and ethical issues. We tested five versions of a protocol to visually survey the macro-fauna of hedgerows. A large number of individuals were directly identified in the field, mostly arthropods but also vertebrates. Identification error varied with taxonomic level and lineage, but remained low at the morphospecies level. Importantly, estimates tended to reach asymptotes, suggesting that local richness was appropriately appraised. Like any technique, non-lethal RBA (NL-RBA) present both advantages and weaknesses, and may improve the toolbox to survey biodiversity.     

Evaluating the performance of sampling plans for phycotoxins in shellfish: Improvement of an existing method

According to the EU Regulation 854/2004, sampling plans must be set up to monitor production areas for the level of okadaic acid (OA) equivalents in live mussel. The level of these toxins, which are produced by harmful algal blooms, must not exceed 160 μg/kg of raw meat (Regulation 853/2004/EC). A sampling plan assessment consists in obtaining an OC (Operating Characteristic) curve showing both consumer and producer risks. The first risk is the risk of opening a shellfish area for harvest while the contamination level is above the threshold; whereas the second risk is the risk of closing a shellfish area having a contamination level under the threshold.For sampling plan validation purposes, a classical mathematical method was improved for the prediction of variance as function of the mean contamination level thanks to prior knowledge of the theoretical distribution fitting the observed OA levels among individual mussels. Indeed, knowing that, thanks to a regression analysis of literature data, for the lognormal distribution the scale parameter was observed to be directly proportional to the location parameter, the regression bias could be lowered. Literature data from Norway and Sweden showed different levels of variability between contamination events and depuration. However, the highest variability level was chosen to propose a best fit sampling plan in order to have a better approach of reality. It consisted of taking two samples of 50 mussels (Mytilus sp.) for this geographic location (Norway and Sweden).     

Topographic complexity and the power to detect structural and functional changes in temperate reef fish assemblages: The need for habitat-independent sample sizes

Functional approaches have shown promising results to detect degradation in marine fish assemblages. However, background variability significantly affects the amplitude of change that is detectable by a monitoring plan, and failing to detect such changes can have devastating consequences and carry aggravated recovery costs due to unnoticed degradation. The present study aimed to understand the relationship between topographic complexity in temperate reefs and the power to detect variations in fish-based metrics. Underwater visual census of fish assemblages was performed using strip transects and a Monte Carlo simulation approach was used to generate a large number of replicates and simulate three alternative hypotheses representing different magnitudes of change. Statistical power to detect differences between null and alternative hypotheses was estimated through 10,000 Mann–Whitney tests for numbers of replicates ranging from 2 to 15. Power tended to vary with topographic complexity particularly with small and medium changes in metric values and when using small sample sizes. While power increased with complexity for most metrics, some showed decreasing trends. With a large effect, 5–15 transects were needed, depending on the metric, to stabilise power above 0.80 independently of habitat features. A power of 0.95, however, could not be achieved for most metrics in all sites, even when using 15 transects. The observation that the power to detect degradation and recovery in temperate reef fish seems to vary with habitat features means that a monitoring programme that is correctly planned for a particular area may not be directly applicable in a nearby reef. Adding to the need to maximise power in monitoring, this study highlights the need to take into account habitat variability in these calculations and estimate habitat-independent sample sizes that are appropriate for the scale and location of interest.     

Advances in increment coring system for large tropical trees with high wood densities

Incremental coring of trees is the key method used in non-destructive dendrochronological sampling. Despite the advances in developing such methods, the sampling of large, high-density trees still poses a challenge in remote tropical forests. Manually operated incremental drills, while easy to transport across difficult terrain, limit sample size and can often get damaged in the sampling process, especially when trees have wood densities above 0.8 g/cm³. Here, we discuss the existing available alternatives and present an up-to-date incremental coring system composed of a borer coupled to a hand-held drilling machine and a support attached to the tree which can collect incremental cores of 1.5 mm in diameter and over 1.0 m in length. The support ensures stability for the drill throughout the sampling process. This system is relatively lightweight and portable, offering field flexibility and suitability for sampling in remote locations. It provides a core sample of an appropriate diameter and amount for carrying out ring-width measurements, stable isotope and radiocarbon analyses on some of the large, older trees which are now being found in the tropics. We expect that this methodology will broaden the possibilities in the now-blossoming sub-field of tropical dendrochronology.     

Sampling in aerobiology. Differences between traverses along the length of the slide in Hirst sporetraps

Two years of data from four longitudinal traverses along each day's slide prepared from a continuously running Burkard sporetrap have been analyzed statistically. Using the Friedman test, a statistically significant difference was found between the four traverses, with a greater than 7% loss of pollen grains in the two outer traverses in relation to the inner. Four slides were then selected for more detailed analysis, using 18 longitudinal traverses with a 1-mm separation from the upper to the lower edge of the Melinex tape. There was found to be a progressive decline from the centre to the outside, and more than 4% of pollen grains were found outside the typical 14 mm width of the impaction orifice. There was no correlation between pollen grain size and the decline in counts from the centre to the outside. For the complete data set, there was a general rise in the diversity of pollen types with increasing sample counts, but above about 1000 pollen grains per sample there were no more than 27 pollen types found, often even fewer. A discussion is presented of whether four traverses really should be a fixing sample size, or whether it might be better to fix the total pollen count beginning with a traverse in the middle of the slide and ending with a variable number of traverses when that count is reached.     

Solution NMR views of dynamical ordering of biomacromolecules

Background

To understand the mechanisms related to the ‘dynamical ordering’ of macromolecules and biological systems, it is crucial to monitor, in detail, molecular interactions and their dynamics across multiple timescales. Solution nuclear magnetic resonance (NMR) spectroscopy is an ideal tool that can investigate biophysical events at the atomic level, in near-physiological buffer solutions, or even inside cells.

Sampling efficiency of the pale grass blue butterfly Zizeeria maha (Lepidoptera: Lycaenidae): A versatile indicator species for environmental risk assessment in Japan

The pale grass blue butterfly, Zizeeria maha (Lepidoptera, Lycaenidae), has successfully been employed as an indicator species to evaluate acute biological changes in polluted human-living environments after the Fukushima nuclear accident. Here, we quantitatively examined the field sampling efficiency of the butterfly and its associated sexual sampling bias under different conditions, which may provide important information for environmental risk assessment. Sampling data were obtained in 2014 and 2015 from 87 localities across Japan. Across the localities, the mean capture rate was 17 individuals per hour per person, and males represented approximately 80% of the collected butterflies. No significant difference was detected in the capture rate under different weather conditions. Among the four habitats, the riverside showed a significantly higher capture rate than the city park. A shorter sampling time tended to yield a higher capture rate. Comparisons among prefectures and districts of collection localities revealed that the Kanto district had significantly higher percentages of collected males than 4 other districts. Fukushima prefecture also had high percentage, although not significant. A generalized linear mixed model indicated that the capture rate was significantly negatively affected by the agricultural village, the city park, the rainy weather, and latitude and positively by longitude. Together, the present study showed high sampling efficiency and versatility of this butterfly as an indicator for environmental risk assessment but simultaneously suggested preferable conditions for a field sampling design. This study also suggested a possibility that the Fukushima nuclear accident or other factors might have affected behavioral or population dynamics of the butterfly.     

Line transect methods for plant surveys

Interest in surveys for monitoring plant abundance is increasing, due in part to the need to quantify the rate of loss of biodiversity. Line transect sampling offers an efficient way to monitor many species. However, the method does not work well in some circumstances, for example on small survey plots, when the plant species has a strongly aggregated distribution, or when plants that are on the line are not easily detected. We develop a crossed design, together with methods that exploit the additional information from such a design, to address these problems. The methods are illustrated using data on a colony of cowslips.     

Monitoring of occupational exposure to cyclohexanone by diffusive sampling and urinalysis

The present study was initiated in order to identify the best marker of occupational exposure to cyclohexanone among cyclohexanone and its metabolites in urine. To examine if diffusive samplers are applicable to personal monitoring of exposure to cyclohexanone in workroom air, the performance of carbon cloth to adsorb cyclohexanone in air was studied by experimental exposure of the cloth to cyclohexanone at 5, 10, 25 or 50 ppm (i.e. 20, 40, 100 or 200 mg m-3) for up to 8 h. Cyclohexanone in the exposed cloth was extracted with carbon disulphide followed by gas chromatographic (GC) analysis. The cloth adsorbed cyclohexanone in proportion to the concentration (up to 50 ppm) and the duration (up to 8 h), and responded quantitatively to a 15 min exposure at 100 ppm. In a field survey, end-of-shift urine samples were collected from 24 factory workers occupationally exposed to cyclohexanone (up to 9 ppm) in combination with toluene and other solvents. Urine samples were also collected from 10 subjects with no occupational exposure to solvents. The urine samples were treated with acid or an enzyme preparation for hydrolysis, and extracted with dichloromethane or ethyl acetate. The extracts were analysed by GC for cyclohexanone, cyclohexanol, and trans- and cis-isomers of 1,2- and 1,4-cyclohexanediol. Both cyclohexanol and trans-1,2-cyclohexanediol in urine correlated significantly with time-weighted average intensity of exposure to cyclohexanone. Although trans -1,4-isomer was also excreted, its quantitative relation with cyclohexanone exposure could not be established, because the solvent extraction rate was low and unstable. Excretion of cis-isomers was not confirmed. The two analytes, cyclohexanol and trans-1,2-cyclohexanediol, appeared to be equally valid as exposure markers, but the latter may be superior to the former in the sense that it is sensitive enough to separate the exposed from the non-exposed at 1 ppm or less cyclohexanone exposure.