13004 research outputs found
Sort by
Bacterial and fungal diversity of Alpine pastures
Get PDFAlpine pastures are a complex, multidimensional terrestrial habitat in which animal and plant species interact with each other and with large numbers of bacteria and fungi (microbiota), forming an ecological network that extends both above ground and within the soil. Although soil-, plant-, and animal-associated microbiota are known to provide fundamental services for their hosts, microbial diversity of ecosystems in general, and Alpine pastures in particular, is still largely unexplored. In addition, the extent to which climate changes in Europe and especially in the Alpine space will impact such micro-biodiversity is completely unknown. Here, we investigated changes in bacterial and fungal diversity associated with more than 900 samples of soil, rhi- zosphere (Carex spp. and Festuca spp.), invertebrates (nematodes, collembolans, earthworms, beetles) and vertebrates (using faecal eDNA of hares, wild ungulates and livestock) along an elevational gradient spanning 1,500 metres (a proxy for climate change). Characterization of bacterial and fungal communities of each sample was performed by targeting the bacterial 16S rRNA gene V3-V4 region and the fungal ITS2 loci as barcodes for amplicon sequencing-based meta-taxonomics. Diversity metrics of ASVs (amplicon sequence variants) and phylogenetic distances (Bray-Curtis, Unifrac) were used in redundancy analyses (db-RDA) to compare microbiota composition across sample types and elevation gradient. We found that soil, plant, invertebrate, and vertebrate microbiota were characterized by only partially overlapping bacterial and fungal communities, displaying specific associations with host, elevation, temperature, nutrient availability, and plant community composition. Fae- cal microbiota of wild and farmed animals revealed different patterns across bacterial and fungal microbiota, with bacterial communities being markedly shaped by host-interaction dynamics, and fungal communities showing closer associations with habitat and elevation. Analyses of fungal and bacterial taxa shared between sample types established greater overlaps between soil, rhizosphere and soil-dwelling invertebrates, compared to other invertebrates and vertebrates, highlighting above/ belowground and host/habitat-specific associations in the Alpine meta-community
More than meets the eye: unraveling anthropic land use impacts on skin microbiota of an opportunistic amphibian species
No full textAs amphibians continue to register population declines worldwide due to human-driven habitat modifications and emerging diseases, their skin microbiota has attracted major interest as both a possible means of adaptation to the changing environment and a barrier against pathogens. Here we focussed on Bombina variegata, a small anuran colonizing both natural and artificial water bodies, to investigate differences in skin microbiota composition between individuals living in different habitats across the Province of Trento, Italy. Fourteen populations were sampled, including those of natural ponds, seasonal ponds on agricultural land, water tanks, and farm ponds. Skin and water microbiota were investigated using metataxonomics by targeting the bacterial V3-V4 16S rRNA gene and fungal ITS1 loci. Our results highlight a significant association between skin and water microbiota across all investigated habitats. Composition and diversity of skin microbiota changed between habitats, with the skin microbiota of animals collected from natural ponds being characterized by lower alpha diversity and distinct bacterial and fungal composition. Furthermore, observed variation in skin microbial diversity could be partially explained by the water parameters: pH, dissolved oxygen, and temperature. Implication of human-driven habitat modifications and water composition on B. variegata skin microbiota for the conservation of this species are discussed
GWAS analysis of an almond germplasm collection unravels the genetic regulation of aroma in fresh and roasted kernels
No full textAlmond (Prunus dulcis Mill. D.A. Webb) cultivation rapidly spread throughout the Mediterranean area from central Asia, reaching Sicily while it was under Greek colonization. The long history of cultivation resulted in the selection and propagation of hundreds of selections characterized by a wide variability in terms of kernel quality, ripening period, and resistance to biotic and abiotic stress. Kernel quality is one of the leading aspects influencing the marketability of the product. Almonds are particularly priced for their sensory, nutritional, and health attributes and kernels are often consumed fresh, toasted and/or as ingredient in food productions. To decipher the genetic mechanism of the aroma, a germplasm collection of 140 almond accessions (including Sicilian accessions and Italian and international varieties) was genotyped using the AxiomTM 60K almond SNP array leading to the selection of 47,946 robust SNPs. The SNP-genotyped individuals of the almond collection were also phenotyped for the production of volatile organic compounds (VOCs) using a proton-transfer time-of-flight mass spectrometer (PTR-TOF-MS). This analysis was carried out both on fresh and roasted (15 min at 150°C) kernels, resulting in the detection of 165 mass peaks. Some peaks, such as those related with sulfur compounds, furan containing compounds, and aldehydes formed by Strecker degradation, significantly increased during roasting, while VOCs belonging mostly to alcohols and terpenes, significantly decreased. The GWAS analysis enabled the identification of 85 and 130 mass peaks characterized by an association with one or more SNPs for raw and toasted almond kernel aroma, respectively. The detection of molecular markers linked to different VOCs will help both the understanding of their regulation and the selection of novel varieties with enhanced aromatic profile through marker-assisted selectio
Prioritising riparian ecotones to sustain and connect multiple biodiversity and functional components in river networks
Get PDFThe Biodiversa+ RIPARIANET project aims to optimize the spatial biodiversity conservation of natural stream-riparian networks in order to provide practitioners with evidence-based guidance and approaches to conservation by mainly exploiting the increasing resolution of remote sensing information. The main purpose of the project is to assess riparian integrity and connectivity along the watercourse. To reach this goal, we investigate riparian networks within six river basins in Europe, along a geographical and climatic gradient to assess multiple biodiversity and stressors at the local scale, and scale-up this information to the network scale using geostatistical tools and advanced modelling. The conservation status and threats on riparian habitats will be evaluated along the Sävar River basin (Sweden), Queich River basin (Germany), Noce Stream and Tiber River basins (Northern and Southern Italy), Saja River basin (Spain), and Cávado River basin (Portugal). Particularly, data on river functionality (i.e., hydrology, decomposition, biofilm biomass accrual, and metabolism), diversity (i.e., microbes and fungi, macroinvertebrates, bats, and riparian vegetation) and stressors (i.e., pesticides, microplastics, and macroplastics) will be evaluated in different abiotic and biotic matrices. We expect to (i) identify protection gaps and ecological hotspots along riparian networks, based on multiple biodiversity, functional and connectivity criteria, and (ii) provide decision-support tools for decision-makers at local and EU level
Assessing predictability of post-storage texture and appearance characteristics in blueberry at breeding population level
No full textThe shelf-life of blueberry (Vaccinium corymbosum L.) fruits depends on changes in multiple fruit characteristics during storage, including texture, appearance of wrinkles and mold, and loss of water. These changes result in softening, decay, and change in flavor, which can negatively affect consumer acceptance. Therefore, understanding how breeders can select for new cultivars with extended shelf-life is crucial. In this study, 20 mechanical texture parameters and four fruit appearance traits (fruit weight, fruit scar diameter, fruit height and wrinkle) were measured at harvest and six weeks post-storage in two very large (N>2000) collections of northern and southern highbush blueberry (NHB, SHB, respectively) genotypes. The study is the first to assess shelf-life at the scale resembling the number, genetic structure and diversity of populations used in blueberry breeding programs. The results highlighted that post-storage changes are positively correlated with initial texture. The low storage temperature for SHB best explained a notable lower rate of changes for all parameters. Correlation analysis indicated that three main texture components representing the Young Modulus parameters (YMs), ‘Distance to Maximum Force’ (DFM) and ‘Mean Internal Firmness’ (MIF) contributed to blueberry texture. YMs and DFM likely represent textural characteristics of the external fruit structural components. Also, texture parameters YMs and DFM explained most of the phenotypic changes observed between harvest and post-storage, suggesting that changes during storage largely occurs in the more external layers of the berry. Changes for parameters correlated to size were highly predictable, while most of the texture parameters had a low to moderate predictability. The contribution of fruit chemistry parameters to predict texture and appearance traits at harvest and post-storage was very limited or not significant. The rate of water loss and appearance of wrinkles was higher in small size berries and was not affected by the size of the stem scar. Overall, selecting for high YMs, DFM, F1mm (Force at 1 mm), Maximum Force (FM), and large size at harvest can contribute to select berries with better mechanical texture and appearance in post-storag
Welfare of rainbow trout at slaughter: Integrating behavioural, physiological, proteomic and quality indicators and testing a novel fast-chill stunning method
Get PDFA critical point in the life of a captive fish is the final stages of production, not only in welfare terms but also due to effects on meat quality, carcass appearance and derived economic impacts. The most common method to slaughter fish is by asphyxia either in ice-water or in the open air. In humane slaughter procedures, however, a stunning method needs to be implemented to render the fish immediately unconscious (within one second) until death. The objective of this research was to evaluate and compare the effectiveness and welfare effects of four types of stunning methods in rainbow trout (O. mykiss): cold shock by fast-chilling as a novel method, where the fish were immersed in liquid water at − 8 ◦C, asphyxia (as the currently used method), electrical stunning, and anaesthesia with MS-222. We used a total of 176 trout (mean weight 524 ± 138 g), combining behavioural (individual swimming activity, equilibrium, opercular movement and eye-roll), physiological (heart rate and electrocardiogram amplitude) and circulating (plasma cortisol and osmolality) indicators with brain proteomic signatures. We also analysed the effects on fillet shelf-life and quality in each method (rigor mortis, water content, fillet colour, pH and ATP degradation). Anaesthesia effectively induced unconsciousness, with regular and strong heartbeat and low cortisol. Quality indicators were the best among all the methods assessed. Electric shock was found to be an effective and irreversible method for inducing unconsciousness, with strong heartbeat and large variation in cortisol response and quality indicators similar to anaesthesia. On the contrary, asphyxia presented indicators of poor welfare (e.g., long-lasting consciousness throughout the slaughter process, high cortisol levels), with very low flesh quality parameters. Fast-chilling also resulted in extreme signs of stress (intense mucus release, haemorrhage and no loss of consciousness), low ATP content and the worst proteomic signatures, along with an early onset and resolution of rigor mortis (6 and 48 h, respectively). Our results reinforce the idea that electric stunning is a promising humane method to stun farmed trout. In contrast, the fast-chilling method showed very poor results both in welfare and in quality, indicating that it is not a viable humane alternative to asphyxia. Moreover, the proteome analysis provided valuable insights into the brain mechanisms of rainbow trout at slaughter, offering potential fine-scale biomarkers of welfar
Metabarcoding analysis of the bacterial and fungal communities during the maturation of preparation 500, used in biodynamic agriculture, suggests a rational link between horn and manure
Get PDFHorn manure (Preparation 500) is a product used in the practice of biodynamic agriculture. It is obtained by an underground fermentation of cow fecal material incubated in cow horns for several months. The product is used as spray treatment meant to increase soil fertility. In the present report, we analyzed the successional changes in bacterial and fungal communities throughout the process of horn manure maturation by high throughput sequencing of ribosomal 16S (bacterial) and ITS (fungal) gene markers. Marked shifts in the microbial community were seen involving a general decrease from a Firmicutes dominated material to a product transiently enriched in Proteobacteria and later in Actinobacteria, mostly within the Nocardioidaceae family. In the fungal community evolution, the most abundant taxon in the starting fecal material resulted a member of the Onygenales order, known to specifically degrade keratin. Its abundance in the intestine is explained by the fact that keratin, which is also the structural component of hairs and horns, is found in all epithelial layers, including gut mucosae. This occurrence suggests a link of enzymatic/catabolic nature between manure and horn
Shotgun metagenomic sequencing for conservation genomics: rock ptarmigan as a case study
Get PDFThe rock ptarmigan (Lagopus muta) inhabits alpine and arctic tundra throughout the northern hemisphere with its current distribution mainly determined by the last glacial maximum. In southern Europe this species is only found in fragmented populations on the main mountain ranges, where numbers are decreasing due to habitat loss, degradation and fragmentation, climate warming and human disturbance. This decline could be mitigated through conservation measures, but these require fundamental information on the evolutionary ecology, distribution and genetic diversity. Such data is difficult to collect in a species which is particularly elusive and living in extreme environments. Thanks to the technological and computational advances of recent years, understanding of species’ biology has been greatly enhanced by analyzing fecal samples, collected non-invasively in the field, using shotgun metagenomics sequencing. Although this approach is still poorly tested in wild species, ongoing studies highlight its potential for conservation and biomonitoring that should be further explored. In the present study, this approach was applied to 30 rock ptarmigan from three different areas of the Paneveggio-Pale di San Martino Natural Park, characterized by contrasting rocky substrates. The shotgun metagenomic sequencing method does not require the enrichment or targeted amplification of specific molecular markers, thus allowing both qualitative and quantitative evaluation of data on different aspects related to the species. In particular, the ongoing analyses aimed to determine: i) the genomic relationships between individuals and population, ii) the fundamental resources for the species through the study of the diet, iii) the health status of individuals through the analysis of gut microbiota and parasites. First results confirmed the utility of shotgun metagenomic sequencing for conservation purposes and provides fundamental data for improving conservation strategies for this species