bioRxiv - Ecology最新文献

{"title":"Assessing the risk of highly pathogenic avian influenza H5 viruses spread within French broiler and layer production networks","authors":"Claire Hautefeuille, Facundo Munoz, Gwenaelle Dauphin, Mathilde Paul, Marisa Peyre, Flavie Goutard","doi":"10.1101/2024.09.11.612235","DOIUrl":"https://doi.org/10.1101/2024.09.11.612235","url":null,"abstract":"Since 2015, French poultry production is threatened almost every year by a reintroduction of highly pathogenic avian influenza H5 viruses. The duck sector was the most concerned by this crisis but other sectors such as broiler, layer and turkey were also affected by outbreaks. The objective of this work was to assess the risk of highly pathogenic avian influenza H5 virus transmission from one farm to another within the French broiler and layer production network.\u0000This study used the WOAH risk assessment framework. After drawing up a scenario tree of virus transmission from one farm to another, data were collected through a literature review or through experts' elicitation. Three questionnaires were developed according to the experts' field of expertise: avian influenza, broiler and layer sectors. The experts' estimates were combined using a beta distribution weighted by their confidence level. A Monte Carlo iteration process was used to combine the different probabilities of the scenario tree and to assess the transmission risk. In the broiler sector, the highest transmission probabilities were observed if the exposed farm was an indoor broiler farm and the source a broiler farm (indoor or free-range). The high transmission probability between broiler farm integrated within the same company highlighted the role of integration in this probability. In the layer sector, the highest transmission probabilities were observed if the source farm was a free-range farm and the exposed farm a production farm (indoor or free-range). The sensitivity analysis showed that the exposed farm's biosecurity had a significant impact on the transmission probability. Our results provide an insight on the role of each type of farms in the virus spread within the French broiler and layer production network and will be useful for the implementation of control measures such as movement restriction or vaccination.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":"34 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142269609","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Using correlative and mechanistic species distribution models to predict vector-borne disease risk for the current and future environmental and climatic change: a case study of West Nile Virus in the UK.","authors":"Amy J. Withers, Simon Croft, Richard Budgey, Daniel Warren, Nicholas Johnson","doi":"10.1101/2024.09.12.612656","DOIUrl":"https://doi.org/10.1101/2024.09.12.612656","url":null,"abstract":"Globally, vector-borne diseases have significant impacts on both animal and human health, and these are predicted to increase with the effects of climate change. Understanding the drivers of such diseases can help inform surveillance and control measures to minimise risks both now and in the future. In this study, we illustrate a generalised approach for assessing disease risk combining species distribution models of vector and wildlife hosts with data on livestock and human populations using the potential emergence of West Nile Virus (WNV) in the UK as a case study. Currently absent in the UK, WNV is an orthoflavivirus with a natural transmission cycle between Culex mosquitos (Cx. pipiens and Cx. modestus) and birds. It can spread into non-target hosts (e.g., equids, humans) via mosquito bites where it can cause febrile disease with encephalitis and mortality in severe cases. We compared six correlative species distribution models and selected the most appropriate for each vector based on a selection of performance measures and compared this to mechanistic species distribution models and known distributions. We then combined these with correlative species distribution models of representative avian hosts, equines, and human population data to predict risk of WNV occurrence. Our findings highlighted areas at greater risk of WNV due to higher habitat suitability for both avian hosts and vectors, and considered how this risk could change by 2100 under a best-case Shared Socioeconomic Pathway (SSP1) and worst-case (SSP5) future climate scenario. Generally, WNV risk in the future was found to increase in south-eastern UK and decrease further north. Overall, this paper presents how current and future vector distributions can be modelled and combined with projected host distributions to predict areas at greater risk of novel diseases. This is important for policy decision making and contingency preparedness to enable adaptation to changing environments and the resulting shifts in vector-borne diseases that are predicted to occur.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142269853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"How does co-occurrence of Daphnia species affect their gut microbiome?","authors":"Shira Houwenhuyse, Francois Massol, Emilie Macke, Luc De Meester, Isabel Vanoverberghe, Robby Stoks, Ellen Decaestecker","doi":"10.1101/2024.09.10.612237","DOIUrl":"https://doi.org/10.1101/2024.09.10.612237","url":null,"abstract":"Species co occurrence can lead to competitive interactions that influence fitness. Competition is typically assumed to be modulated by species niche, especially food acquisition related traits. The influence of interspecific interactions on host microbiome communities has rarely been considered, and yet may provide an alternative mechanism regarding the effect of host species co occurrence on their fitness. Here, we investigated whether the composition of the gut microbial community differs between two Daphnia species (D. magna and D. pulex), and whether the gut microbiome of one species depends on the presence of the other. We hypothesized the stronger filter feeder D. magna to have a larger effect on the gut microbiome of the weaker filter feeder D. pulex than vice versa. To this purpose, three D. magna and three D. pulex genotypes were first made axenic and then grown in monocultures or in cocultures in natural environmental bacterioplankton-enriched water, before assessing the community composition of the gut microbiomes and bacterioplankton. We found that the composition of the gut microbiome of the two Daphnia species did not significantly differ overall. However, subtle differences between mono- and cocultures were found at the Daphnia genotype level. For most genotype combinations (six out of nine), the microbiome of D. pulex changed more when grown in cocultures with D. magna than in monocultures. This provides limited support for our hypothesis that the stronger competitor has a larger effect on the gut microbiome of the weaker one than vice versa, and that this effect is possibly mediated via the bacterioplankton community.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":"17 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260204","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"No enhancement of soil carbon persistence by sheep grazing in a long-term calcareous grassland experiment","authors":"David Encarnation, Deborah Ashworth, Richard Bardgett, Mona Edwards, Clive Hambler, Jeppe Kristensen, Andrew Hector","doi":"10.1101/2024.09.11.611980","DOIUrl":"https://doi.org/10.1101/2024.09.11.611980","url":null,"abstract":"Soils hold a globally important carbon pool that is generally more persistent than the carbon stored in plant biomass. However, this carbon is becoming increasingly vulnerable to disturbances such as soil warming, fire, and erosion. Managing land to increase soil carbon sequestration and persistence may therefore improve long-term soil carbon storage and contribute to climate change mitigation. It has been hypothesized that grazing by large herbivores may enhance the persistence of soil carbon by increasing the amount of soil organic matter forming more stable associations with mineral particles (mineral-associated organic matter). We compared sheep-grazed and ungrazed plots within the Gibson Grazing and Successional Experiment located in the Upper Seeds calcareous grassland in Wytham Woods, Oxfordshire, using organic matter fractionation to estimate the surface (0-5 cm) carbon stocks in the mineral-associated and particulate organic matter fractions. Counter to predictions, after 35 years sheep grazing had not increased mineral-associated organic matter carbon stocks relative to ungrazed plots. We hypothesize that this indicates the saturation of mineral surfaces in both grazed and ungrazed treatments and the inability of grazing to increase soil nitrogen stocks and decrease pH to levels conducive for mineral-associated carbon sequestration. Only one of twelve soil properties examined showed statistically detectable responses to grazing: spring-grazing increased the C:N ratio in the mineral-associated organic matter. While the number of tests performed (24) means this may be a false-positive result, if genuine it would be consistent with a more direct pathway from plant exudates to mineral-associated organic matter formation due to compensatory growth in response to spring grazing. Overall, the results of this long-term experiment do not support the hypothesis that grazing can improve the persistence of the soil carbon pool.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142269854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The resilience of the oral microbiome and lability of the hair microbiome across host environments in wild and captive lemurs","authors":"Rachel Bell Burten, Richard R Lawler, Joelisoa Ratsirarson, Jeannin Ranaivonasy, Rebecca C Leduc, Ankita Bhagat, Amelia Lopez, Jason M. Kamilar","doi":"10.1101/2024.09.09.612164","DOIUrl":"https://doi.org/10.1101/2024.09.09.612164","url":null,"abstract":"Microbiome diversity and composition in mammals is affected by the host’s environment and has been linked to important immune and physiological host functions, yet most of these data come from the gut microbiome. Research on the oral and hair microbiome in nonhuman primates has been far less common, and information from wild primates is even rarer. These overlooked patterns of environmental effects on microbial communities across the body may have important implications for a range of host functions. Therefore, in this study we characterized the gut, oral, and hair microbiomes across nine different captive and wild lemur species: <em>Eulemur collaris, Eulemur coronatus, Eulemur mongoz, Lemur catta, Microcebus griseorufus, Microcebus murinus, Propithecus coquereli</em>, and <em>Varecia rubra</em>. We explored how host environment affects the microbiome diversity of these three body regions using 16S rRNA sequencing and found significant differences in microbiome composition, diversity, and environmental influence across body regions. The oral microbiome was least diverse and most resilient to different environmental effects; conversely, the hair microbiome was both most diverse and most labile. Differentially abundant bacterial taxa across oral, gut, and hair microbiota may also reflect selective regimes unique to each body region. These results emphasize the importance of accounting for body region when conducting microbiome studies.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":"1 1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260250","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cost-benefit analysis across smallholder rice farmers reveals that existing fertilization practices severely compromise their income","authors":"Junjiang Chen, Magkdi Mola, Xing Liu, Tien Ming Lee, Nikolaos Monokrousos, Stavros D Veresoglou","doi":"10.1101/2024.09.10.612194","DOIUrl":"https://doi.org/10.1101/2024.09.10.612194","url":null,"abstract":"Modernizing agricultural practices of smallholder farmers can increase considerably global food produce. Smallholder farmers are, nevertheless, often unwilling to adopt practices unfamiliar to them. Increases in the cost of fertilizers, can nonetheless render existing practices unsustainable, raising concerns of food injustice. We addressed here the potential to which we can increase yield through popularizing existing best practice agricultural approaches. We worked over a network of 40 smallholder farmers in the Danxia Mountain region, Guangdong province, China. We divided them into two crop-rotation treatments and gave them the freedom to implement agricultural management practices the way they usually do. We subsequently clustered them into three groups based on the management history. Over the final growth season, on which the clustering was based, there was an over 30% increase in crop yield between the most and the least efficient clusters. More importantly we show that the use of fertilizers not only did not promote rice production but it also had adverse effects. We finally present a cost-benefit analysis. Through familiarizing of the smallholder farmers` existing management practices, policy makers could make integrating new farming guidelines easier to adopt than purely dishing out modern farming practice recommendations. We thus propose that any attempts to transition agricultural practices should involve the extensive monitoring of existing practices at the very beginning. This should effectively close existing yield gaps in relation to industrial farmers.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":"35 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The effect of nitrogen on the growth of Calluna vulgaris and Avenella flexuosa in a dune heath ecosystem: competition and frequency-dependence","authors":"Christian Damgaard, Mathias Emil Kaae, Jesper L Bak","doi":"10.1101/2024.09.12.612621","DOIUrl":"https://doi.org/10.1101/2024.09.12.612621","url":null,"abstract":"Nitrogen was manipulated in a dune heath ecosystem and using time-series pin-point data it was demonstrated that both Lotka-Volterra type interspecific competition and frequency dependency play significant roles in determining plant growth. For modelling simplicity, plant taxa were divided into heather, wavy hair-grass, and all other vascular species. Significant interspecific competition was observed among all species, except wavy hair-grass on the growth of all other vascular species, and nitrogen addition was found to increase the competitive effect of heather on the growth of all other vascular species. Both heather and wavy hair-grass showed positive feedback dynamics on growth when they were relatively dominant at the plot scale and the effect increased with added nitrogen. Such positive feedback dynamics may lead to the formation of patches, which are a characteristic feature of heath ecosystems. Oppositely, there was a beneficial effect of being relatively rare on the growth of all other vascular species in plots with added nitrogen. The study highlights the importance of the combined effects of interspecific competition and frequency dependency in regulating plant communities, and consequently undermine both theoretical and empirical conclusions of modern coexistence theory.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":"190 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142269855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Crop productivity of Central European Permaculture is within the range of organic and conventional agriculture.","authors":"Julius Reiff, Hermann F Jungkunst, Nicole Antes, Martin H Entling","doi":"10.1101/2024.09.09.611985","DOIUrl":"https://doi.org/10.1101/2024.09.09.611985","url":null,"abstract":"Permaculture is a promising framework to design and manage sustainable food production systems. However, there is still a lack of scientific evidence especially on the crop productivity of permaculture systems. In this first study on permaculture yield, we collected yield data of eleven permaculture sites, that work according to organic guidelines, in Germany and surrounding countries. We used the Land Equivalent Ratio (LER) as index to compare mixed cropping systems of permaculture sites with average monoculture yield data of total and organic German agriculture. An LER of 1 indicates equal yields of the compared polyculture and monoculture. Mean permaculture LER as compared to total German agriculture was 0.80 ± 0.27 and 1.44 ± 0.52 as compared to German organic agriculture, both with no significant difference to 1. Our results imply, that yields of permaculture sites are comparable to predominant industrial agriculture. Provided that future studies will support our findings, permaculture could combine soil, biodiversity and climate protection with agricultural productivity. Most importantly, the variables that determine the difference in crop productivity amoung permaculture sites need to be identified and evaluated.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":"215 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Systematic review and meta-analysis of Hyalomma marginatum vertebrate hosts in the EU","authors":"Madiou Thierno Bah, Laurence Vial, Luca Busani, Lea Souq, Vladimir Grosbois, Celia Bernard, Ferran Jori","doi":"10.1101/2024.09.11.612300","DOIUrl":"https://doi.org/10.1101/2024.09.11.612300","url":null,"abstract":"Host choice is a determining component of tick population and pathogen transmission dynamics. In Europe, ticks of the genus Hyalomma, which are involved in the transmission of several pathogens such as the Crimean Congo Haemorrhagic fever (CCHF) virus, are suspected to be spreading into new territories where they were previously unreported. Therefore, we performed a systematic review of the tick-host relationship of Hyalomma spp in Europe with a focus on Hyalomma marginatum, combined with a meta-analysis and meta-regression to describe its host preference pattern using three outcome values. Our initial qualitative analysis highlighted an increase in tick-host interaction rate in the last decades mostly in South-eastern and Central Europe. H. marginatum also appeared as the species holding the highest citation rate in terms of its association with hosts, and for which the largest number of host species were reported. The meta-analysis on Hyalomma marginatum host choice revealed preferential interactions for horses in the adult stage and birds of the Emberizidae and Strigidae families, in immature stages. Nevertheless, most of the heterogeneity of tick-host interactions remained unexplained suggesting the involvement of multiple drivers such as environmental or climatic conditions. Our results suggest that H. marginatum is a generalist tick whose distribution depends primarily on environmental conditions such as climate and habitat. Current limitations of our meta-analysis approach to identify hosts preference for H. marginatum and suggestions ways for improvement are further discussed.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":"85 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142180905","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Wilting Wildflowers and Bummed-Out Bees: Climate Change Threatens U.S. State Symbols","authors":"Xuezhen Ge, Ya Zou, Heather A Hager, Jonathan A Newman","doi":"10.1101/2024.09.08.611901","DOIUrl":"https://doi.org/10.1101/2024.09.08.611901","url":null,"abstract":"Species designated as state symbols in the United States carry cultural importance and embody historical heritage. However, they are threatened by climate change and even face the risk of local or global extinction. The responses of these species to climate change have received little attention. In this study, we examine the effects of climate change on state flowers and insects in the United States by employing correlative species distribution models (SDMs). We select a variety of commonly used SDM algorithms to construct an ensemble forecasting framework aimed at predicting the potential habitats for each species under both historical and future climate scenarios, and how these changes might influence the distributions of state flower and insect species. Our results show that more than half of the state flowers (～66%) and insects (51%) are predicted to experience a substantial decrease in regions with favorable climates within the states they represent. Conversely, only a small number (Flowers: ～2%; Insects: ～10%) are projected to see an increase in habitat suitability in the future. Certain states may no longer possess suitable habitats for their state-designated species. Our findings indicate that cultural heritage might be at risk due to reduced habitat suitability and local extinctions driven by climate change. These findings can provide guidance regarding the protection or replacement of state species to preserve cultural heritage.","PeriodicalId":501320,"journal":{"name":"bioRxiv - Ecology","volume":"19 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142260253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}