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Exploring different methodological approaches to unlock paleobiodiversity in peat profiles using ancient DNA
No full textNatural and human-induced environmental changes deeply affected terrestrial ecosystems throughout the Holocene. Paleoenvironmental reconstructions provide information about the past and allow us to predict/model future scenarios. Among potential records, peat bogs are widely used because they present a precise stratigraphy and act as natural archives of highly diverse organic remains. Over the decades, several techniques have been developed to identify organic remains, including their morphological description. However, this is strongly constrained by the researcher's ability to identify residues at the species level, which typically requires many years of experience. In addition, potential contamination hampers using these techniques to obtain information from organisms such as fungi or bacteria. Environmental DNA metabarcoding and shotgun metagenome sequencing could represent a solution to detect specific groups of organisms without any a priori knowledge of their characteristics and/or to identify organisms that have rarely been considered in previous investigations. Moreover, shotgun metagenomics may allow the identification of bacteria and fungi (including both yeast and filamentous life forms), ensuring discrimination between ancient and modern organisms through the study of deamination/damage patterns. In the present review, we aim to i) present the state-of-the-art methodologies in paleoecological and paleoclimatic studies focusing on peat core analyses, proposing alternative approaches to the classical morphological identification of plant residues, and ii) suggest biomolecular approaches that will allow the use of proxies such as invertebrates, fungi, and bacteria, which are rarely employed in paleoenvironmental reconstruction
Prediction of blueberry sensory texture attributes by integrating multiple instrumental measurements
No full textBlueberry (Vaccinium spp.) texture contributes to consumer satisfaction, shelf-life, and machine harvestability and is now a critical goal in breeding for new fresh market cultivars. The industry commonly uses instrumental methods to phenotype texture, assuming that instrumental measurements correlate with sensory perceptions. However, the relationship between perceived sensory textures and mechanical parameters is not well established. In this study, we characterized the fruit texture profile of 43 blueberry cultivars using nine sensory descriptors and determined the predictability of the sensory attributes using mechanical parameters. The sensory study was done by a trained descriptive sensory analysis panel, and instrumental analysis was performed using flat probe penetration and texture profile analysis (TPA) methods. Differences in the perceived firmness of blueberries were mainly due to springiness, hardness, and snap/crisp attributes. Among the mechanical parameters, maximum force (FM; a flat probe penetration parameter) and gumminess (a TPA parameter) had the strongest correlations with these three sensory attributes. To develop predictive models for the nine sensory attributes, multivariate statistical methods were used. The highest level of prediction accuracy was achieved when all the penetration or TPA parameters were used for model development. The R2 values increased by up to 0.66 compared to using a single mechanical parameter. Springiness, hardness, and snap/crisp were predictable with R2 > 0.5, regardless of the instrumental method used. TPA parameters were more suitable for predicting juiciness while residual skin was only predictable using penetration parameters. Mealiness was not predictable with any instrumental measure (R2 < 0.05). For most of the sensory attributes, the models were able to effectively discern the cultivars with the highest or lowest intensity scores. This study provides a basis for breeding programs to utilize improved estimations of the sensorial texture using diverse mechanical parameters to enhance selection for desired blueberry texture
The Italian experience on the use of new breeding technologies in citrus: advanced and marker-free approaches to improve fruit quality and resistance to plant diseases
No full textCitrus improvement by conventional breeding is hampered by several factors, such as the high level of heterozygosity, polyembryony, partial or complete sterility, sexual (in)compatibility, and the long juvenility that imposes around 5 to 10 years to produce fruits. New breeding technologies (NBTs) might represent a complementary strategy for the development of improved new cultivars. However, there is still poor knowledge of genes controlling important horticultural traits and on the capacity to transform most of the cultivars of interest. The cisgenesis of Ruby (causative element for anthocyanin accumulation in citrus fruits) and the genome editing of β-LCY2 (converting lycopene in β-carotene) were successfully used at CREA (Italy) to improve citrus fruit quality, with the aim of enriching sweet orange and grapefruit cultivars in antioxidant compounds. The produced plants are marker-free thanks to the use of the FRT/Flp recombinase system and VvMYBA1 gene as phenotypic marker. Moreover, CRISPR/Cas9 was used to modify seed growth and development (to obtain seedless cultivars) and to speed up flowering. For most of the genotypes, the regeneration protocols were duly optimized considering different sources of material, either seeds, nucellar seedlings, and internodes of juvenile or mature tissues. The application of NBTs was possible thanks to the long history and experience in clonal selection and the large citrus germplasm available at CREA and Catania University, which offered a wide range of possibilities to select the best cultivar to improve. The expertise gained in the last 5 years and the new protocols developed for the NBTs applications on citrus are still employed for the improvement of new citrus quality traits and could now be used to generate resistant cultivars to diseases such as Huanglongbing and Alternaria brown spot
Genome editing of IKU1 to obtain citrus seedless fruits
No full textSeedlessness is a desired characteristic in citrus fruits and it is particularly requested by consumers; in the past years many efforts have been done to obtain seedless fruits using conventional breeding techniques, especially in mandarin and mandarin-like cultivars. The use of genome editing and new plant breeding techniques contributes to overcome some limits of conventional breeding and allows the modification of specific traits while maintaining the favourable genetic background of local cultivars. Here, CRISPR/Cas9 genome editing approach was applied to transform seedy citrus cultivars so to try to reduce seed presence by the editing of HAIKU1 (IKU1); this gene codes for a protein that is involved in the development of the seed zygotic tissue and thus in the regulation of the seed size. The construct pIKU-editing_GB was assembled using GoldenBraid 3.0 technology and consists of a dual single guide RNAs (sgRNA1 and sgRNA2) so to be able to induce different types of mutation in IKU1 gene in ‘Carrizo’ citrange. The editing consisted mostly in short insertions and deletions, and in some cases it was possible to recognize larger deletions between the two RNA guides. The deduced amino acid sequence of the edited IKU1 gene showed the introduction of stop codon responsible for the premature termination of the protein transduction. So far 8 citrange plantlets have been recovered and confirmed as edited. These transformed plantlets are now in the juvenile phase and further analysis of their flowers and fruits features would confirm the role of IKU1 gene in IKU pathway and its potential for the obtainment of seedless cultivar
Interpersonal differences in taste and flavor perception mirror gut microbial ecology and influence dietary habits
Get PDFHuman‐induced risk drives behavioural decisions in a recovering brown bear population
Get PDFIn human-dominated landscapes, rebounding bear populations share space with people, which may lead to bear–human conflicts and, consequently, a decrease in acceptance and an increase in bear mortality linked to human causes. Previous analyses of brown bear (Ursus arctos) movement data have shown that bears adopt a security-food trade-off strategy in response to variable human-related risk. However, brown bear flexibility to cope with these risky situations may be reduced when resting, mating or stocking fat in preparation for hibernation. In this study, we measured the multi-scale spatial response of brown bears to human-related risk and food resource distribution in a highly heterogeneous human-dominated landscape. We examined habitat selection both within the population range (‘second-order’ selection) and at bedding site locations (‘third-order’) for GPS-tagged brown bears of a recently reintroduced population in the Italian Alps. We identified resting locations by field-validated spatio-temporal cluster analysis of telemetry locations. We mapped food availability and distribution using dynamic geographic layers of fruiting wild berries, and human-related risk using human mobility data (Strava-based Cumulated Outdoor activity Index). Brown bears appeared to compromise their need for food resources for avoidance of anthropogenic disturbance when selecting home ranges, as they utilized areas richer in wild berries less when human use of outdoor tracks was higher. Furthermore, selection of resting site locations strongly depended on the avoidance of human-related risk only, with less frequented, more concealed and inaccessible sites being selected. We conclude that humans compete for space with bears beyond their infrastructural impact, that is, by actively occupying key areas for bear survival, thereby potentially restricting the bears' realized niche. We propose mitigating actions to promote bear–human coexistence by selectively restricting human access to key areas during sensitive annual physiological phases for bear surviva
There can be only one: the two-year spread of Procambarus clarkii in a Faxonius limosus infested small perialpine lake in Trentino (Northeast Italy)
Get PDFA containment campaign to prevent the spread of Faxonius limosus was conducted in June, July and September 2023 and repeated in 2024, in Costa Lake, a Special Area of Conservation of about 1 hectare surface area, where this IAS was first recorded in spring 2021. Unexpectedly, in June 2023 we trapped 38 adult Procambarus clarkii in the NW part of the lake, suggesting a recent point of introduction. Procambarus clarkii showed a high invasive potential, spreading quickly in 2023 to the whole lake perimeter and its emissary canal; its body size was much larger than that of F. limosus, with two main size classes, one (50-60 mm cephalothorax length) corresponding to the individuals introduced most likely in the fall 2022 (2 years old), and a second class (40-50 mm) representing the new generation born in the lake. In July 2024, we recorded three main size classes: about half of the P. clarkii population belonged to the 50-60 mm size class (2 years old), while the remaining was evenly distributed between the size classes of 40-50 mm (new generation) and 60-70 mm, i.e., older individuals (4 years old). F. limosus did not show significant shifts in size: in both years the majority of the individuals belonged to the 30-40 mm size class. The much larger size of P. clarkii, longer time span, fast dispersion ability, suggest a future dominance of P. clarkii and possible disappearance of F. limosus, with relevant risk of spread of this new, more invasive species to the upstream, hydrologically connected, water bodies
A protocol for assessing bias and robustness of social network metrics using GPS based radio-telemetry data
Get PDFBackground: Social network analysis of animal societies allows scientists to test hypotheses about social evolution, behaviour, and dynamic processes. However, the accuracy of estimated metrics depends on data characteristics like sample proportion, sample size, and frequency. A protocol is needed to assess for bias and robustness of social network metrics estimated for the animal populations especially when a limited number of individuals are monitored. Methods: We used GPS telemetry datasets of five ungulate species to combine known social network approaches with novel ones into a comprehensive five-step protocol. To quantify the bias and uncertainty in the network metrics obtained from a partial population, we presented novel statistical methods which are particularly suited for autocorrelated data, such as telemetry relocations. The protocol was validated using a sixth species, the fallow deer, with a known population size where ∼85% of the individuals have been directly monitored. Results: Through the protocol, we demonstrated how pre-network data permutations allow researchers to assess non-random aspects of interactions within a population. The protocol assesses bias in global network metrics, obtains confidence intervals, and quantifies uncertainty of global and node-level network metrics based on the number of nodes in the network. We found that global network metrics like density remained robust even with a lowered sample size, while local network metrics like eigenvector centrality were unreliable for four of the species. The fallow deer network showed low uncertainty and bias even at lower sampling proportions, indicating the importance of a thoroughly sampled population while demonstrating the accuracy of our evaluation methods for smaller samples. Conclusions: The protocol allows researchers to analyse GPS-based radio-telemetry or other data to determine the reliability of social network metrics. The estimates enable the statistical comparison of networks under different conditions, such as analysing daily and seasonal changes in the density of a network. The methods can also guide methodological decisions in animal social network research, such as sampling design and allow more accurate ecological inferences from the available data. The R package aniSNA enables researchers to implement this workflow on their dataset, generating reliable inferences and guiding methodological decisions
Unravel the underlying mechanisms of delaying ripening techniques in grapevine
Get PDFIn a scenario of changing climate conditions, grapevine is significantly affected at multiple levels. Advancements in phenology and berry ripening, however, are the major dynamics of the generalized increase in average temperature and evaporative demand, negatively affecting berry quality and productivity. The aim of this work was to unravel the underlying mechanisms of bunch-zone auxin application (NAA; 1-Naphthaleneacetic acid) and source-limiting canopy management approaches in delaying berry ripening. In randomized block design experiments, control vines were compared to vines treated with NAA, subjected to apical-to-bunch defoliation or antitranspirant application (n=10-to-42 plants per treatment). Juice chemical analysis, berry ripening kinetics and physiological traits were monitored every week from pre-veraison over multiple vineyards, years (2021, 2022, 2023) and varieties (Chardonnay, Pinot gris, Syrah, Merlot). Overall, all the treatments delayed berry ripening, and in particular °Brix build up, by 7 to up 15 days. Opposite trends were observed for total acidity, particularly malic acid concentration that displayed a slower degradation kinetic post-veraison. Time course expression profile of ripening-associated transcription factors revealed a significant and consistent repression for VviNAC60, VviNAC33, VviBHLH75, VviWRKY19, VviERF45 following the application of delaying ripening techniques. Similarly, abscisic acid and Indole-3-acetic acid concentration in the berry were modulated by treatments, with specific variation for their free and conjugated forms. This work enlightens, for the first time, the mechanistic framework of berry ripening dynamics following specific treatments with different mechanisms of action and provides novel avenues to harmonize management approaches in grapevine in the context of climate change
