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In vitro metabolic interaction network of a rationally designed nasal microbiota community
Get PDFMounting evidence suggests that metabolite exchange between microbiota members is a key driver of microbiota composition. However, we still know little about the metabolic interaction networks within many microbiota. To tackle this issue, we developed the porcine nasal consortium (PNC8), which represents the most in vivo abundant genera in the nasal microbiota of healthy piglets, and used it to systematically map the in vitro metabolic interactions between its members. Spent media experiments, exometabolomics, and direct co-cultivation, revealed that most pairwise interactions between PNC8 strains are negative, with co-depletion of sugars acting as a key driver. This prevalence of negative interactions leads to a complex competition hierarchy in which only few strains are able to consistently outcompete all others. Overall, this work provides a valuable resource for studying the nasal microbiota under experimentally tractable in vitro conditions and is a key step toward mapping its metabolic interaction network.We thank Marcelo Gottschalk for kindly providing the bacterial strains S. suis P1/7 and A. pleuropneumoniae 4074. This work was supported by funding from the Spanish Ministry of Research and Innovation (RYC2021-033035-I and PID2023-152210NA-I00/AEI/10.13039/501100011033 to K.K., PID2019-106233RB-I00/AEI/10.13039/501100011033 to V.A. and F.C.-F., PID2022-138657OB-I00/AEI/10.13039/501100011033 to V.A. and M.S., RYC2019-028030-I to I.F.-S.). This work was co-funded by the European Union’s Horizon Europe Project 101136346 EUPAHW. Views and opinions expressed are those of the authors only and do not necessarily reflect those of the European Union or the European Research Executive Agency. Neither the European Union nor the granting authority can be held responsible for them. L.B.-L. and P.O.-G. are supported by FPI (PRE2020-096048/AEI/10.13039/501100011033) and FPU (FPU19/02126/AEI/10.13039/501100011033) fellowships from the Spanish Ministry of Research and Innovation, respectively. O.R.K. is supported by an intramural IRTA PhD fellowship.info:eu-repo/semantics/publishedVersio
ResynPy: a software for selecting pairs of complementary inbred lines to resynthesize valuable heterozygous genotypes
Get PDFBackground
Using cultivars based on a single, partly heterozygous, genotype is one of the bases of agriculture, frequently used in seed-propagated species such as vegetables and field crops (F1 hybrid varieties), and in most fruit trees and ornamentals (clonal varieties) that reproduce vegetatively. Producing two inbred lines that fully or partly reconstruct a given high-value heterozygous individual is now possible with the
Resynthesis method, which uses molecular markers to select pairs of complementary genotypes in the F2 and subsequent selfing generations. The objective of this paper was to develop a software to facilitate the selection of such complementary pairs from a large number of segregating genotyped individuals.
Results
The ResynPy tool we developed screens the genotyping data of a segregating population, originating from selfing a top-performing partly heterozygous individual, and detects pairs of individuals that could produce progeny containing individuals nearly identical to the initial elite genotype. Our software selects candidate pairs of individuals in a small timeframe window with a low memory footprint. ResynPy tool could be part of a breeding toolkit to accelerate breeding programs in any plant species of economic importance capable of producing self-pollinated progeny.
Conclusions
ResynPy is a software developed in Python language and is freely available on GitHub (HYPERLINK “https://github.com/kostasgalexiou/ResynPy/tree/main”). ResynPy automates the process of individual selection implemented by the Resynthesis method, in a highly efficient manner through parallelization, allowing to plant breeders for detection of pairs of complementary individuals in a selfing population that could be suitable parents to a plant variety with economically important agronomic traits. With ResynPy, breeders are provided with a fast and easyto-use tool that will aid them to advance their plant breeding programs.This research was supported by grants PID2019-110599RR-I00 funded by MICIU/AEI /10.13039/50110001103 and PID2022-140362OR-I00 funded by MICIU/AEI/ 10.13039/501100011033 and by “ERDF/EU”. This work was also supported by grants SEV‐2015‐0533 and CEX2019-000902-S funded by MICIU/AEI/10.13039/501100011033, and by the CERCA Programme / Generalitat de Catalunya.info:eu-repo/semantics/publishedVersio
Stakeholder-driven management strategies for recovering large herbivores
Get PDFIn modern landscapes, the sustainable coexistence of humans and wildlife depends on involving stakeholders in the development and implementation of management strategies. This is particularly important for species like the European bison (Bison bonasus) and Eurasian moose (Alces alces), which are reoccupying regions between Germany and Poland after a prolonged absence. The return of these species generates mixed emotions, as interactions with these species are associated with both costs and benefits to people. Addressing the apparent unpreparedness in managing these trade-offs, we implemented a digital participatory impact assessment in two steps. First, we engaged bison and moose experts to develop management scenarios and assessment criteria. Then, in a subsequent virtual workshop, stakeholders evaluated four scenarios along economic, social, and ecological dimensions. Quantitative and qualitative analyses revealed divergent perspectives and priorities, yet consensus emerged on the necessary future steps: formulating a comprehensive management strategy with guidelines and protocols for managing specific conflict scenarios, such as the incursion of large herbivores onto highways. Our approach underscores the importance of early stakeholder engagement in fostering a more equitable and sustainable management of human-wildlife interactions. Moreover, demonstrating the feasibility of remote stakeholder involvement, our study presents a robust model for enhancing coexistence, adaptable even where in-person meetings are challenging.This study was conducted as part of the EU Interreg Project (INT144) “LosBonasus—Crossing! Improving transboundary wildlife management for European bison and moose” and we extend our sincere appreciation for financing the project. Our gratitude extends to all project partners who contributed their expertise, to the working groups InterFAL of the Leibniz Centre for Agricultural Landscape Research (ZALF) and Plant Ecology and Nature Conservation of Potsdam University, along with their network, for their assistance in developing the evaluation matrix and testing the material. We express thanks to the stakeholders who participated in the study, dedicating their time, energy and open-mindedness. We also would like to thank Biodiversa+, the European Biodiversity Partnership, in the context of the TransWILD project for supporting the contribution of the coauthors CK, HJK and EFOM to this manuscript. Open Access funding enabled and organized by Projekt DEAL.info:eu-repo/semantics/publishedVersio
Comprehensive proteomic profling of Cucumber mosaic virus infection: identifying key proteins and pathways involved in resistance and susceptibility in melon
Get PDFBackground: Melon (Cucumis melo L.) is the model species of the Cucurbitaceae family and an important crop. However, its yield is primarily afected by viruses. Cucumber mosaic virus (CMV) is particularly signifcant due to its broad host range, capable of infecting over 100 plant families. Resistance to CMV in the melon accession Songwhan Charmi (SC) is controlled by the recessive gene cmv1, which encodes the Vacuolar Protein Sorting 41, involved in vesicle transport to the vacuole. cmv1 restricts the virus to the bundle sheath cells and impedes viral access to the phloem, preventing a systemic infection. This phenotype depends on the viral movement protein (MP). However, little is known about the broader cellular changes that CMV triggers in melon or the specifc biological responses that facilitate or restrict the virus entry into the phloem in susceptible and resistant varieties.
Result: We profled the proteomes of CMV-resistant or susceptible melon genotypes inoculated with CMV-LS or FNY strains. Analysis of co-abundance networks revealed the rewiring of central biological pathways during diferent stages of CMV infection. Upon inoculation, resistant varieties do not trigger any signalling event to the new leaves. Local infection triggers a general depletion in proteins related to translation, photosynthesis and intracellular transport, whereas only in resistant varieties CMV triggers an increase in lipid modifcation and phloem proteins. During the systemic infection of susceptible melon plants, there is a strong increase in proteins associated with stress responses, such as those involved in the ER-associated degradation (ERAD) and phenylpropanoid pathways, along with a decrease in translation and photosynthesis. Key hub proteins have been identifed in these processes.
Conclusions: This study is the frst comprehensive high-throughput proteomic analysis of CMV-infected melon plants, providing a novel and detailed understanding of the proteomic changes associated with CMV infection, highlighting the diferential responses between resistant and susceptible genotypes and identifying key proteins that could be potential targets for future research and CMV management strategies.This work was supported by the grants RTI2018-097665-B-C21 and PID2021-125998OB-C21, funded by MCIN/AEI/10.13039/501100011033, CEX2019-000902-S funded by MICIU/AEI/10.13039/501100011033 through the “Severo Ochoa Program for Centres of Excellence in R&D” and the CERCA Program/Generalitat de Catalunya.info:eu-repo/semantics/publishedVersio
The role of human–pig interactions in modulating gut microbiota, stress, and performance
Get PDFBackground
The microbiota‒gut‒brain axis modulates pigs’ stress response, behavior, and overall welfare. Stressful management practices can disrupt gut microbiota (GM), negatively impacting pigs' health and welfare. This study evaluated how the quality of human handling influences stress-related physiological responses, productive performance, and gut microbiota (GM) composition in pigs during the nursery phase.
Results
Female pigs (n= 36, 21 days old) were randomly assigned to three experimental groups (12 pigs/group, four pens per treatment): positive human handling (PHH), negative human handling (NHH), and a control group (CG). The PHH group experienced gentle tactile interactions, whereas the NHH group was subjected to chronic intermittent stress through acute stressors, and the CG group received minimal handling for routine practices. Hair cortisol concentrations were measured as an indicator of chronic stress (days 15 and 64). Productive performance was assessed through body weight (BW), average daily gain (ADG), average daily feed intake (ADFI), and feed conversion (FC). Fecal samples were collected at baseline (T0, day 16), mid-study (T1, day 37), and end of the study (T2, day 65) and analyzed using 16S rRNA gene amplicon sequencing to assess GM changes over time. Pigs in the PHH group showed a significant reduction in cortisol levels from baseline to post-treatment (P < 0.0001), while no significant changes were observed in the NHH group (P = 0.26). A smaller but significant decrease was also detected in the CG group (P = 0.001). PHH pigs had higher BW (P = 0.0009) and ADG (P = 0.03) during the later growth phase compared to NHH pigs. At T2, PHH pigs exhibited greater diversity and richness compared to NHH pigs, indicating a restorative effect on GM composition. Differential abundance analyses identified four bacterial genera that distinguished treatment groups: Blautia, Megasphaera, and Subdoligranulum were enriched in PHH pigs, while Terrisporobacter was enriched in NHH pigs. Additionally, bacterial interaction networks exhibited the least complex network in the NHH group, with ecological associations primarily involving Clostridium and Terrisporobacter.
Conclusions
The quality of human handling influenced stress physiology, performance, and gut microbiota in pigs. Positive handling reduced cortisol levels, improved growth, and promoted microbial diversity, while negative handling was linked to decreased performance and reduced microbial network complexity. These results highlight the potential of positive interactions to enhance welfare and productivity, and identify specific bacterial genera as potential biomarkers differentiating negative and positive handling conditions.This research was funded by the National Research and Development Agency (ANID) of Chile, through the Programme FONDECYT Iniciación (project number 11220280), and by the Research Office of FAVET.info:eu-repo/semantics/publishedVersio
Insights Into the Almond Domestication History
Get PDFUnderstanding crop domestication offers crucial insights into the evolutionary processes that drive population divergence and adaptation. It also informs the identification of genetically diverse wild germplasm, which is essential for breeding and conservation efforts. While domestication has been extensively studied in many Mediterranean fruit trees, the evolutionary history of the almond (Prunus dulcis) remains comparatively underexplored. To address this, we analyzed 209 wild and cultivated almond accessions sampled across Eurasia and genotyped with 23 microsatellite markers. Using population genetics and coalescentbased inference, we reconstructed the domestication history of P. dulcis and its relationships with wild relatives. Bayesian clustering revealed four genetically distinct clusters of cultivated almonds: Turkish, Caucasian–Central Asian, Southern Spanish, and European/North American. These groups were differentiated from wild almond species—including Prunus turcomanica,
Prunus orientalis, Prunus fenzliana, and Prunus spinosissima—each forming its gene pool across the Middle East and Central Asia. Approximate Bayesian Computation (ABC) supported a single domestication event in the Middle East, originating from either P. orientalis or P. turcomanica, with subsequent gene flow from P. fenzliana and P. spinosissima into the Turkish and Central Asian cultivated gene pools, respectively. We also inferred reciprocal introgression from cultivated almonds back into wild populations. Notably, sharka resistance—caused by plum pox virus (PPV)—was identified in three P. dulcis clusters and P. fenzliana, suggesting that resistance may have arisen independently or been maintained through crop–wild introgression. Together, our results highlight a complex and protracted domestication history for almond, shaped by contributions from multiple wild relatives and recurrent gene flow. These findings enhance our understanding of perennial crop evolution and underscore the value
of wild germplasm in breeding programs aimed at increasing resilience in fruit trees.We acknowledge funding from the FP7 MCSA STONE, PRIMA (FREECLIMB ANR-18-PRIM-000, 10.13039/100014439), the Grant PCI2019-103670 funded by MCIN/AEI/ 10.13039/501100011033 and co-financed by the European Union, and the current support from Horizon Europe (FRUITDIV 101133964) project. European FP7 IFPT-PEOPLE-2009-PIRSES STONE (246795).info:eu-repo/semantics/publishedVersio
European Union green deal in action: Harnessing consumer preferences to drive pesticide reduction in winegrowing
Get PDFThis study determines consumers' willingness to pay (WTP) for wines with reduced pesticide use in the EU Mediterranean region in the context of the European Commission's Green Deal objective to halve pesticide use by 2030, a goal that has faced significant political and practical challenges. A dynamic reference-dependent discrete choice experiment (DCE) involving over 4000 wine consumers from France, Greece, Italy, Portugal, and Spain was conducted. This innovative pivot design incorporates consumer-specific reference points based on previous purchases into a two-stage choice framework, enabling a more realistic estimation of willingness to pay in a market characterized by diverse wine attributes and price ranges. The study tests eight hypotheses related to WTP for pesticide reduction, certification type, and personal factors influencing consumer decisions. The results show that conventional winegrowers who reduce pesticide use by up to 40 % could command price premiums of approximately 26 % in France, 29 % in Greece, 30 % in Italy and Portugal, and 28 % in Spain compared with standard conventional practices. Certification by EU-approved third-party entities consistently generated the highest consumer trust and WTP. Furthermore, sociodemographics, subjective knowledge, environmental attitudes, economic capacity, consumer involvement, and exploratory behavior significantly influence consumers' WTP. The findings reveal a market opportunity for pesticide-reduced conventional wines and demonstrate that consumer preferences could serve as a viable incentive for the voluntary adoption of sustainable practices in viticulture. While generalizability may be influenced by sampling, as well as cultural and institutional differences, the results provide practical insights into untapped market-based incentives that could be leveraged to drive pesticide reduction in the absence of binding EU regulations.This study was supported by the NOVATERRA project under research grant agreement number 101000554. The NOVATERRA project has received funding from the European Union’s Horizon 2020. We gratefully acknowledge Cristina Poyato Santiago and Filippo Alfonso Baldaro for their invaluable administrative and technical support. We also extend our sincere thanks to the team of reviewers for their constructive feedback and guidance.info:eu-repo/semantics/publishedVersio
The impact of global change on the intraguild predation among three predatory mites of Tetranychus urticae in citrus orchards
Get PDFThe two-spotted spider mite, Tetranychus urticae, is a key pest of clementine mandarin orchards in the Mediterranean basin. Efective biological control, vital for managing T. urticae populations, involves the phytoseiid mites Euseius stipulatus, Neoseiulus californicus, and Phytoseiulus persimilis. The Mediterranean region is highly susceptible to climate change, with predicted increases in average temperatures and reduced rainfall, with potentially negative consequences for agro-ecosystem dynamics. Given the often-overlooked complexity of species interactions in climate change models, this study investigates into the potential impact of climate change, specifcally extreme events like heatwaves, on intraguild interactions among these key predatory mite species. Our fndings reveal that N. californicus is the most robust intraguild predator under forecasted climate change conditions, outperforming the other two. Conversely, E. stipulatus showed reduced performance under future climatic conditions, further afected by intraguild predation from the other two phytoseiids. Notably, P. persimilis fails to maintain its biological parameters in interactions with both intraguild prey under anticipated climatic conditions, suggesting a low tolerance to global warming in the presence of E. stipulatus and N. californicus, the primary predators of T. urticae in our citrus system. These insights are essential for biological control, as they provide crucial data on the biological paràmetres of natural enemies crucial that are critical to efective pest control in the expected global warming scenarios.This study was partially funded by the Spanish Ministry of Economy and Competitiveness, MINECO, (Grants AGL2011-30538-C03-01 and AGL2014-55616-C3-3-R) and the Spanish Ministry of Science and Innovation, MCINN, (Grant EEBB-I-14-08555).info:eu-repo/semantics/publishedVersio
Toxicity and toxin profile of La Réunion (Indian Ocean) fish containing CTX-like compounds
Get PDFSeveral outbreaks of ciguatera poisoning have been recorded in La Réunion (SW Indian Ocean) since 1986. Toxicities and toxin profiles of fish from the Indian Ocean are poorly documented. In this work, a multidisciplinary study on the toxicity of fish from the Indian Ocean by neuro-2a cell-based assay was assessed, and the CTX-like compounds were evaluated by a magnetic bead-based immunoassay. The toxin profile is described by liquid chromatography coupled to tandem mass spectrometry and high-resolution mass spectrometry. The liver, muscle, and viscera of four fish specimens of three different species (one Lutjanus bohar, two Variola louti and one Carcharinus leucas) caught in the waters of La Réunion were analysed. One of the V. louti specimens was obtained after a CP incident. Their toxicity values ranged between 0.01 and 2.69 μg CTX1B equiv.·kg-1 in flesh, 1.60 and 6.50 μg CTX1B equiv.·kg-1 in liver and 0.07 and 4.77 μg CTX1B equiv.·kg-1 in viscera. In general, liver and viscera showed higher concentrations of CTX-like compounds than flesh. Several potential CTX congeners were identified. LC-MS/MS confirmed the presence of CTX1B, 52-epi-54-deoxyCTX1B and 54-deoxyCTX1B in the flesh of the V. louti specimen involved in the CP incident. CTX1B was identified in the three tissues of the other V. louti individual and in the L. bohar. The C. leucas samples revealed the presence of a complex CTXs profile showing congeners of the CTX3C-group. The strategy used within this research work could be a valuable tool for future food safety monitoring in the Indian Ocean area.The research leading to these results has received funding from the Direction de l'Alimentation, de l'Agriculture et de la Forêt (DAAF), Ministry of Agriculture and Food, which supports the action plan on marine biotoxins of Réunion Island; CIGUATOXRUN financed by Europe and la Région Réunion; Ministerio de Ciencia e Innovación (MICIN) and Agencia Estatal de Investigación (AEI) through the CIGUARISK project (PID2019-108781RR-C21), CELLECTRA project (PID2020-112976RB-C21) and CIGUAADAPT project (PID2022-137174OR-C21); and the EFSA FRAMEWORK PARTNERSHIP AGREEMENT NUMBER –EUROCIGUA II (GP/EFSA/KNOW/2022/03).info:eu-repo/semantics/publishedVersio