Bioaerosol field measurements: Challenges and perspectives in outdoor studies

Outdoor field measurements of bioaerosols are performed within a wide range of basic and applied scientific disciplines, each with its own goals, assumptions, and terminology. This paper contains brief reviews of outdoor field bioaerosol research from these diverse interests, with emphasis on perspectives from the atmospheric sciences. The focus is on a high level discussion of pressing scientific questions, grand challenges, and needs for cross-disciplinary collaboration. The research topics, in which bioaerosol field measurement are important, include (i) atmospheric physics, clouds, climate, and hydrological cycle; (ii) atmospheric chemistry; (iii) airborne allergen-containing particles; (iv) airborne human pathogens and national security; (v) airborne livestock and crop pathogens; and (vi) biogeography and biodiversity. We concisely review bioaerosol impacts and discuss properties that distinguish bioaerosols from abiological aerosols. We give extra focus to regions of specific interest, i.e. forests, polar regions, marine and coastal environments, deserts, urban and rural areas, and summarize key considerations related to bioaerosol measurements, such as of fluxes, long-range transport, and from both stationary and vessel-driven platforms. Keeping in mind a series of key scientific questions posed within the diverse communities, we suggest that pressing scientific questions include: (i) emission sources and flux estimates; (ii) spatial distribution; (iii) changes in distribution; (iv) atmospheric aging; (v) metabolic activity; (vi) urbanization of allergies; (vii) transport of human pathogens; and (viii) climate-relevant properties

A spatially explicit database of wind disturbances in European forests over the period 2000-2018

Strong winds may uproot and break trees and represent a major natural disturbance for European forests. Wind disturbances have intensified over the last decades globally and are expected to further rise in view of the effects of climate change. Despite the importance of such natural disturbances, there are currently no spatially explicit databases of wind-related impact at a pan-European scale. Here, we present a new database of wind disturbances in European forests (FORWIND). FORWIND is comprised of more than 80 000 spatially delineated areas in Europe that were disturbed by wind in the period 2000-2018 and describes them in a harmonized and consistent geographical vector format. The database includes all major windstorms that occurred over the observational period (e.g. Gudrun, Kyrill, Klaus, Xynthia and Vaia) and represents approximately 30% of the reported damaging wind events in Europe. Correlation analyses between the areas in FORWIND and land cover changes retrieved from the Landsat-based Global Forest Change dataset and the MODIS Global Disturbance Index corroborate the robustness of FORWIND. Spearman rank coefficients range between 0.27 and 0.48 (p value < 0.05). When recorded forest areas are rescaled based on their damage degree, correlation increases to 0.54. Wind-damaged growing stock volumes reported in national inventories (FORESTORM dataset) are generally higher than analogous metrics provided by FORWIND in combination with satellite-based biomass and country-scale statistics of growing stock volume. The potential of FORWIND is explored for a range of challenging topics and scientific fields, including scaling relations of wind damage, forest vulnerability modelling, remote sensing monitoring of forest disturbance, representation of uprooting and breakage of trees in large-scale land surface models, and hydrogeological risks following wind damage. Overall, FORWIND represents an essential and open-access spatial source that can be used to improve the understanding, detection and prediction of wind disturbances and the consequent impacts on forest ecosystems and the land-atmosphere system. Data sharing is encouraged in order to continuously update and improve FORWIND

Integrative Metabolomics for Assessing the Effect of Insect (Hermetia illucens) Protein Extract on Rainbow Trout Metabolism.

Nutrition of high trophic species in aquaculture is faced with the development of sustainable plant-based diets. Insects seem particularly promising for supplementing plant-based diets. However, the complex effect of whole insect meal on fish metabolism is not well understood, and even less is known about insect meal extracts. The purpose of this work was to decipher the metabolic utilization of a plant-based diet supplemented with the gradual addition of an insect protein extract (insect hydrolysate at 0%, 5%, 10% and 15%). 1H-NMR profiling was used to assess metabolites in experimental diets and in fish plasma, liver and muscle. A significant dose-dependent increase in growth and feed efficiency with increasing insect extract amounts was observed. The incremental incorporation of the insect extract in diet had a significant and progressive impact on the profile of dietary soluble compounds and trout metabolome. The metabolites modulated by dietary insect extracts in plasma and tissues were involved in protein and energy metabolism. This was associated with the efficient metabolic use of dietary free amino acids toward protein synthesis through the concomitant supply of balanced free amino acids and energy substrates in muscle. The findings provide new insights into how the dietary food metabolome affects fish metabolism

PaSiT: A novel approach based on short oligo-nucleotide frequencies for efficient bacterial identification and typing.

Motivation: One of the most widespread methods used in taxonomy studies to distinguish between strains or taxa is the calculation of average nucleotide identity. It requires a computationally expensive alignment step and is therefore not suitable for large-scale comparisons. Short oligonucleotide-based methods do offer a faster alternative but at the expense of accuracy. Here, we aim to address this shortcoming by providing a software that implements a novel method based on short-oligonucleotide frequencies to compute inter-genomic distances. Results: Our tetranucleotide and hexanucleotide implementations, which were optimized based on a taxonomically well-defined set of over 200 newly sequenced bacterial genomes, are as accurate as the short oligonucleotide-based method TETRA and average nucleotide identity, for identifying bacterial species and strains, respectively. Moreover, the lightweight nature of this method makes it applicable for large-scale analyses. Availability and implementation: The method introduced here was implemented, together with other existing methods, in a dependency-free software written in C, GenDisCal, available as source code from https://github.com/LMUGent/ GenDisCal. The software supports multithreading and has been tested on Windows and Linux (CentOS). In addition, a Java-based graphical user interface that acts as a wrapper for the software is also available

L’impact des attributs et indicateurs de qualité sur le comportement d’achat d’un produit alimentaire : une approche exploratoire, par la valeur perçue et l’authenticité perçue : cas de l’huile d’olive d’Algérie

Cette recherche s’interroge sur la relation entre la valeur perçue et l’authenticité perçue, deux variables perceptuelles clés du processus décisionnel du consommateur. Une étude exploratoire appliquée au cas de l’huile d’olive d’Algérie a été menée. Trente entretiens individuels conduits auprès d’experts de la filière oléicole algérienne et des consommateurs ont permis d’identifier : 1) les facteurs qui contribuent à construire la valeur perçue d’un produit alimentaire ainsi que ceux qui contribuent à construire son authenticité perçue ; 2) le rôle de l’authenticité perçue dans la formation de la valeur perçue ; 3) et les conséquences de cette relation en termes de comportements d’achat et post-achat. En conclusion, un modèle théorique reprenant ces concepts et leurs liens est proposé pour être testé.This research questions the relationship between perceived value and perceived authenticity, two key perceptual variables of consumer decision-making. An exploratory study applied to the case of olive oil from Algeria was conducted. Thirty individual interviews conducted with experts from the Algerian olive oil sector and consumers have identified: 1) the factors that contribute to building the perceived value of a food product as well as those that contribute to its perceived authenticity; 2) the role of perceived authenticity in the formation of perceived value; 3) and the consequences of this relationship in terms of purchasing and post-purchase behavior.[br/] In conclusion, a theoretical model presenting these concepts and their links is proposed to be tested

How effective are strategies to control the dissemination of antibiotic resistance in the environment? A systematic review

Background: Antibiotic resistance is a major concern for public and environmental health. The role played by the environment in disseminating resistance is increasingly considered, as well as its capacity for mitigation. We reviewed the literature on strategies to control dissemination of antibiotic-resistant bacteria (ARB), antibiotic resistance genes (ARG) and mobile genetic elements (MGE) in the environment. Methods: This systematic review focused on three main strategies: (i) restriction of antibiotic use (S1), (ii) treatments of liquid/solid matrices (S2) and (iii) management of natural environment (S3). Articles were collected from seven scientific databases until July 2017 and from Web of Science until June 2018. Only studies reporting measurements of ARB, ARG or MGE in environmental samples were included. An evidence map was drawn from metadata extracted from all studies eligible for S1, S2 and S3. Subsets of studies were assessed for internal and external validity to perform narrative and quantitative syntheses. A meta-analysis was carried out to assess the effects of organic waste treatments (random-effect models). Review findings: Nine hundred and thirty-one articles representing 1316 individual studies (n) were eligible for S1 (n = 59), S2 (n = 781) and S3 (n = 476) strategies, respectively. Effects of interventions to control the dissemination of antibiotic resistance in the environment were primarily studied in strategy S2. A partial efficiency of wastewater treatment plants (WWTPs) to reduce antibiotic resistance in treated effluent was reported in 118 high validity studies. In spite of the heterogeneity in published results, the meta-analysis showed that composting and drying were efficient treatments to reduce the relative abundance of ARG and MGE in organic waste, by 84% [65%; 93%] and 98% [80%; 100%], respectively. The effect of anaerobic digestion was not statistically significant (51% reduction [− 2%; 77%]) when organic waste treatments were compared together in the same model. Studies in strategies S1 and S3 mainly assessed the effects of exposure to sources of contamination. For instance, 28 medium/high validity studies showed an increase of antibiotic resistance in aquatic environments at the WWTP discharge point. Some of these studies also showed a decrease of resistance as the distance from the WWTP increases, related to a natural resilience capacity of aquatic environments. Concerning wildlife, nine medium/high validity studies showed that animals exposed to anthropogenic activities carried more ARB. Conclusions and implications : Knowledge gaps were identified for the relationship between restriction of antibiotic use and variation of antibiotic resistance in the environment, as well as on possible interventions in situ in natural environment. Organic waste treatments with thermophilic phase (> 50 °C) should be implemented before the use/release of organic waste in the environment. More investigation should be conducted with the datasets available in this review to determine the treatment efficiency on ARG carried by specific bacterial communities

Aggregation of omic data and secretome prediction enable the discovery of candidate plasma biomarkers for beef tenderness

Beef quality is a complex phenotype that can be evaluated only after animal slaughtering. Previous research has investigated the potential of genetic markers or muscle-derived proteins to assess beef tenderness. Thus, the use of low-invasive biomarkers in living animals is an issue for the beef sector. We hypothesized that publicly available data may help us discovering candidate plasma biomarkers. Thanks to a review of the literature, we built a corpus of articles on beef tenderness. Following data collection, aggregation, and computational reconstruction of the muscle secretome, the putative plasma proteins were searched by comparison with a bovine plasma proteome atlas and submitted to mining of biological information. Of the 44 publications included in the study, 469 unique gene names were extracted for aggregation. Seventy-one proteins putatively released in the plasma were revealed. Among them 13 proteins were predicted to be secreted in plasma, 44 proteins as hypothetically secreted in plasma, and 14 additional candidate proteins were detected thanks to network analysis. Among these 71 proteins, 24 were included in tenderness quantitative trait loci. The in-silico workflow enabled the discovery of candidate plasma biomarkers for beef tenderness from reconstruction of the secretome, to be examined in the cattle plasma proteome

From refugia to contact: Pine processionary moth hybrid zone in a complex biogeographic setting

Contact zones occur at the crossroad between specific dispersal routes and are facilitated by biogeographic discontinuities. Here, we focused on two Lepidoptera sister species that come in contact near the Turkish Straits System (TSS). We aimed to infer their phylogeographic histories in the Eastern Mediterranean and finely analyze their co-occurrence and hybridization patterns in this biogeographic context. We used molecular mitochondrial and nuclear markers to study 224 individuals from 42 localities. We used discordances between markers and complementary assignment methods to identify and map hybrids and parental individuals. We confirmed the parapatric distribution of Thaumetopoea pityocampa (Lepidoptera: Notodontidae) in the west and Thaumetopoea wilkinsoni in the east and identified a narrow contact zone. We identified several glacial refugia of T. wilkinsoni in southern Turkey with a strong east-west differentiation in this species. Unexpectedly, T. pityocampa crossed the TSS and occur in northern Aegean Turkey and some eastern Greek islands. We found robust evidence of introgression between the two species in a restricted zone in northwestern Turkey, but we did not identify any F-1 individuals. The identified hybrid zone was mostly bimodal. The distributions and genetic patterns of the studied species were strongly influenced both by the Quaternary climatic oscillations and the complex geological history of the Aegean region. T. pityocampa and T. wilkinsoni survived the last glacial maximum in disjoint refugia and met in western Turkey at the edge of the recolonization routes. Expanding population of T. wilkinsoni constrained T. pityocampa to the western Turkish shore. Additionally, we found evidence of recurrent introgression by T. wilkinsoni males in several T. pityocampa populations. Our results suggest that some prezygotic isolation mechanisms, such as differences in timing of the adult emergences, might be a driver of the isolation between the sister species

Applicability of an unmedicated feeding program aimed to reduce the use of antimicrobials in nursery piglets: impact on performance and fecal microbiota

This study aimed to assess the impact of two different feeding programs, including or not antimicrobials, on gut microbiota development at early ages in commercial pigs. For this, 21-day-old weaned piglets were distributed into 12 pens (6 replicates with 26 pigs each) and fed ad libitum until fattening with: standard commercial formula with antibiotics and zinc oxide (2400 ppm) (AB), and alternative unmedicated feed formula (UN). Subsequently, the animals were moved to the fattening unit (F) receiving a common diet. Pigs were weighed, and feed consumption and diarrhea scores registered. Feces were collected on days 9 (pre-starter), 40 (starter) and 72 (fattening) post-weaning and microbial DNA extracted for 16S rDNA sequencing. Piglets fed UN diets had a worse feed efficiency (p < 0.05) than AB during nursery; however, UN pigs spent less time scouring after weaning (p = 0.098). The structure of fecal community evolved with the age of the animals (p = 0.001), and diet also showed to have a role, particularly in the starter period when UN microbiomes clustered apart from AB, resembling the ecosystems found in the fattening animals. Fibrolytic genera (Fibrobacter, Butyrivibrio, Christellansellaceae) were enriched in UN piglets whereas Lactobacillus characterized AB piglets (adjusted p < 0.05). Overall, this alternative feeding program could anticipate the gut development of piglets despite a lower feed efficiency compared to standard medicalized programs