Network structure is often considered one of the most important features of a network, and various models exist to generate graphs having one of the most studied types of structures, such as blocks/communities or spatial structures. In this article, we introduce a framework for the generation of random graphs with a controlled size —number of nodes, edges— and a customizable structure, beyond blocks and spatial ones, based on node-pair rank and a tunable probability function allowing to control the amount of randomness. We introduce a structure zoo —a collection of original network structures— and conduct experiments on the small-world properties of networks generated by those structures. Finally, we introduce an implementation as a Python library named Structify-net.
{"title":"Structify-Net: Random Graph generation with controlled size and customized structure","authors":"Remy Cazabet, Salvatore Citraro, Giulio Rossetti","doi":"10.24072/pcjournal.335","DOIUrl":"https://doi.org/10.24072/pcjournal.335","url":null,"abstract":"Network structure is often considered one of the most important features of a network, and various models exist to generate graphs having one of the most studied types of structures, such as blocks/communities or spatial structures. In this article, we introduce a framework for the generation of random graphs with a controlled size —number of nodes, edges— and a customizable structure, beyond blocks and spatial ones, based on node-pair rank and a tunable probability function allowing to control the amount of randomness. We introduce a structure zoo —a collection of original network structures— and conduct experiments on the small-world properties of networks generated by those structures. Finally, we introduce an implementation as a Python library named Structify-net.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135778376","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}
Florian Taraveau, Thomas Pollet, Maxime Duhayon, Laëtitia Gardès, Hélène Jourdan-Pineau
Over the past decade, many studies have demonstrated the crucial role of the tick microbiome in tick biology. The soft tick Ornithodoros moubata is a hematophagous ectoparasite of Suidae, best known for transmitting the African swine fever virus. Its bacterial microbiota is characterized by a high prevalence of Francisella-like and Rickettsia endosymbionts. The present study aims to better understand the potential influence of these two major members of the tick microbiota on the reproductive fitness of O. moubata. A total of 132 adult female ticks were treated with antibiotics using gentamycin or rifampicin added to the blood meal. Half of the ticks were also supplemented with B vitamins to address the nutritional role of endosymbionts. Over two periods of 50 days, several traits related to the reproductive fitness were monitored to investigate the importance of Francisella and Rickettsia for these traits. It appeared that most of the reproductive parameters considered were not affected. However, antibiotic treatments induced an increase in the tick survival, indicating a potential fitness cost of harboring endosymbionts during the tick reproductive cycle. Similarly, 366 first stage nymphs of O. moubata were exposed to the same treatments for molecular quantification of both endosymbionts. Results from qPCR suggested that the treatments had a bacteriostatic effect on endosymbionts without completely eliminating neither Francisella-like endosymbiont nor Rickettsia.
{"title":"Influence of endosymbionts on the reproductive fitness of the tick Ornithodoros moubata","authors":"Florian Taraveau, Thomas Pollet, Maxime Duhayon, Laëtitia Gardès, Hélène Jourdan-Pineau","doi":"10.24072/pcjournal.334","DOIUrl":"https://doi.org/10.24072/pcjournal.334","url":null,"abstract":"Over the past decade, many studies have demonstrated the crucial role of the tick microbiome in tick biology. The soft tick Ornithodoros moubata is a hematophagous ectoparasite of Suidae, best known for transmitting the African swine fever virus. Its bacterial microbiota is characterized by a high prevalence of Francisella-like and Rickettsia endosymbionts. The present study aims to better understand the potential influence of these two major members of the tick microbiota on the reproductive fitness of O. moubata. A total of 132 adult female ticks were treated with antibiotics using gentamycin or rifampicin added to the blood meal. Half of the ticks were also supplemented with B vitamins to address the nutritional role of endosymbionts. Over two periods of 50 days, several traits related to the reproductive fitness were monitored to investigate the importance of Francisella and Rickettsia for these traits. It appeared that most of the reproductive parameters considered were not affected. However, antibiotic treatments induced an increase in the tick survival, indicating a potential fitness cost of harboring endosymbionts during the tick reproductive cycle. Similarly, 366 first stage nymphs of O. moubata were exposed to the same treatments for molecular quantification of both endosymbionts. Results from qPCR suggested that the treatments had a bacteriostatic effect on endosymbionts without completely eliminating neither Francisella-like endosymbiont nor Rickettsia.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"24 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135883688","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}
Gonché Danesh, Corentin Boennec, Laura Verdurme, Mathilde Roussel, Sabine Trombert-Paolantoni, Benoit Visseaux, Stéphanie Haim-Boukobza, Samuel Alizon
Phylodynamic analyses can generate important and timely data to optimise public health response to SARS-CoV-2 outbreaks and epidemics. However, their implementation is hampered by the massive amount of sequence data and the difficulty to parameterise dedicated software packages. We introduce the COVFlow pipeline, accessible at https://gitlab.in2p3.fr/ete/CoV-flow, which allows a user to select sequences from the Global Initiative on Sharing Avian Influenza Data (GISAID) database according to user-specified criteria, to perform basic phylogenetic analyses, and to produce an XML file to be run in the Beast2 software package. We illustrate the potential of this tool by studying two sets of sequences from the Delta variant in two French regions. This pipeline can facilitate the use of virus sequence data at the local level, for instance, to track the dynamics of a particular lineage or variant in a region of interest.
{"title":"COVFlow: phylodynamics analyses of viruses from selected SARS-CoV-2 genome sequences","authors":"Gonché Danesh, Corentin Boennec, Laura Verdurme, Mathilde Roussel, Sabine Trombert-Paolantoni, Benoit Visseaux, Stéphanie Haim-Boukobza, Samuel Alizon","doi":"10.24072/pcjournal.333","DOIUrl":"https://doi.org/10.24072/pcjournal.333","url":null,"abstract":"Phylodynamic analyses can generate important and timely data to optimise public health response to SARS-CoV-2 outbreaks and epidemics. However, their implementation is hampered by the massive amount of sequence data and the difficulty to parameterise dedicated software packages. We introduce the COVFlow pipeline, accessible at https://gitlab.in2p3.fr/ete/CoV-flow, which allows a user to select sequences from the Global Initiative on Sharing Avian Influenza Data (GISAID) database according to user-specified criteria, to perform basic phylogenetic analyses, and to produce an XML file to be run in the Beast2 software package. We illustrate the potential of this tool by studying two sets of sequences from the Delta variant in two French regions. This pipeline can facilitate the use of virus sequence data at the local level, for instance, to track the dynamics of a particular lineage or variant in a region of interest.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"76 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136114333","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}
Pea is a major pulse crop in temperate regions and a model plant in genetics. Large genetic marker resources are needed to assess the genetic diversity in the species genepool and to provide selection tools for breeders. In this study, we used second-generation sequencing to perform an exome-capture protocol using a diverse pea germplasm collection, and produced a resource of over 2 million Single Nucleotide Polymorphisms. This dataset was then used to characterize the genetic diversity present in the panel and compute phylogenetic and structure analyses. The development of this resource paves the way for Genome-wide association studies and the development of powerful genotyping tools.
{"title":"SNP discovery by exome capture and resequencing in a pea genetic resource collection","authors":"Grégoire Aubert, Jonathan Kreplak, Magalie Leveugle, Hervé Duborjal, Anthony Klein, Karen Boucherot, Emilie Vieille, Marianne Chabert-Martinello, Corinne Cruaud, Virginie Bourion, Isabelle Lejeune-Hénaut, Marie-Laure Pilet-Nayel, Yanis Bouchenak-Khelladi, Nicolas Francillonne, Nadim Tayeh, Jean-Philippe Pichon, Nathalie Rivière, Judith Burstin","doi":"10.24072/pcjournal.332","DOIUrl":"https://doi.org/10.24072/pcjournal.332","url":null,"abstract":"Pea is a major pulse crop in temperate regions and a model plant in genetics. Large genetic marker resources are needed to assess the genetic diversity in the species genepool and to provide selection tools for breeders. In this study, we used second-generation sequencing to perform an exome-capture protocol using a diverse pea germplasm collection, and produced a resource of over 2 million Single Nucleotide Polymorphisms. This dataset was then used to characterize the genetic diversity present in the panel and compute phylogenetic and structure analyses. The development of this resource paves the way for Genome-wide association studies and the development of powerful genotyping tools.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"57 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135858683","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}
Phenotypic plasticity has important ecological and evolutionary consequences. In particular, behavioural phenotypic plasticity such as plastic foraging (PF) by consumers, may enhance community stability. Yet little is known about the ecological conditions that favor the evolution of PF, and how the evolutionary dynamics of PF may modulate its effects on community stability. In order to address these questions, we constructed an eco-evolutionary model in which resource and consumer niche traits underwent evolutionary diversification. Consumers could either forage randomly, only as a function of resources abundance, or plastically, as a function of resource abundance, suitability and consumption by competitors. PF evolved when the niche breadth of consumers with respect to resource use was large enough and when the ecological conditions allowed substantial functional diversification. In turn, PF promoted further diversification of the niche traits in both guilds. This suggests that phenotypic plasticity can influence the evolutionary dynamics at the community-level. Faced with a sudden environmental change, PF promoted community stability directly and also indirectly through its effects on functional diversity. However, other disturbances such as persistent environmental change and increases in mortality, caused the evolutionary regression of the PF behaviour, due to its costs. The causal relationships between PF, community stability and diversity are therefore intricate, and their outcome depends on the nature of the environmental disturbance, in contrast to simpler models claiming a direct positive relationship between PF and stability.
{"title":"The evolutionary dynamics of plastic foraging and its ecological consequences: a resource-consumer model","authors":"Léo Ledru, Jimmy Garnier, Océane Guillot, Erwan Faou, Camille Noûs, Sébastien Ibanez","doi":"10.24072/pcjournal.330","DOIUrl":"https://doi.org/10.24072/pcjournal.330","url":null,"abstract":"Phenotypic plasticity has important ecological and evolutionary consequences. In particular, behavioural phenotypic plasticity such as plastic foraging (PF) by consumers, may enhance community stability. Yet little is known about the ecological conditions that favor the evolution of PF, and how the evolutionary dynamics of PF may modulate its effects on community stability. In order to address these questions, we constructed an eco-evolutionary model in which resource and consumer niche traits underwent evolutionary diversification. Consumers could either forage randomly, only as a function of resources abundance, or plastically, as a function of resource abundance, suitability and consumption by competitors. PF evolved when the niche breadth of consumers with respect to resource use was large enough and when the ecological conditions allowed substantial functional diversification. In turn, PF promoted further diversification of the niche traits in both guilds. This suggests that phenotypic plasticity can influence the evolutionary dynamics at the community-level. Faced with a sudden environmental change, PF promoted community stability directly and also indirectly through its effects on functional diversity. However, other disturbances such as persistent environmental change and increases in mortality, caused the evolutionary regression of the PF behaviour, due to its costs. The causal relationships between PF, community stability and diversity are therefore intricate, and their outcome depends on the nature of the environmental disturbance, in contrast to simpler models claiming a direct positive relationship between PF and stability.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136013097","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}
Thibaut Ferraille, Christian Kerbiriou, Charlotte Bigard, Fabien Claireau, John D. Thompson
Strategic Environmental Assessment (SEA) of land-use planning is a fundamental tool to minimize environmental impacts of artificialization. In this context, Systematic Conservation Planning (SCP) tools based on Species Distribution Models (SDM) are frequently used for the elaboration of spatially exhaustive biodiversity diagnostics. Despite the paradigm of “garbage in - garbage out” that emphasises the importance of testing the suitability of data for SDM and priority conservation areas, the assessment of database sources remains relatively rare. In addition, the lack of practical recommendations for the use of open-access databases by SEA stakeholders remains a problem. The aim of this study is to explore the quality of data sources that can be used in SEA to assess priority conservation areas in SEA. The study used data for nine taxonomic groups (commonly used in inventories for environmental impact assessment) and three databases available to SEA stakeholders. Three local administrative entities in very different socio-ecological contexts were used to examine three main issues : (i) the suitability of local versus regional or country databases for assessing conservation priorities, (ii) differences among taxonomic groups or territories in terms of the suitability of databases, (iii) the importance of the quality of databases for the application of SDM to assess priority conservation areas. Our study provides several clear messages for potential users of open-access databases. First, the need for prudence in the interpretation of biodiversity maps. Second, the collection of individual databases at the country scale is necessary to complete local data and ensure the suitability of SDM in a local context. Third, a data driven approach can lead to the use of notably different species communities to identify priority conservation areas when compared to the community in the original database. Finally, we propose a workflow to guide SEA stakeholders through the process of data rationalization and use in conservation planning.
{"title":"Integrating biodiversity assessments into local conservation planning: the importance of assessing suitable data sources","authors":"Thibaut Ferraille, Christian Kerbiriou, Charlotte Bigard, Fabien Claireau, John D. Thompson","doi":"10.24072/pcjournal.331","DOIUrl":"https://doi.org/10.24072/pcjournal.331","url":null,"abstract":"Strategic Environmental Assessment (SEA) of land-use planning is a fundamental tool to minimize environmental impacts of artificialization. In this context, Systematic Conservation Planning (SCP) tools based on Species Distribution Models (SDM) are frequently used for the elaboration of spatially exhaustive biodiversity diagnostics. Despite the paradigm of “garbage in - garbage out” that emphasises the importance of testing the suitability of data for SDM and priority conservation areas, the assessment of database sources remains relatively rare. In addition, the lack of practical recommendations for the use of open-access databases by SEA stakeholders remains a problem. The aim of this study is to explore the quality of data sources that can be used in SEA to assess priority conservation areas in SEA. The study used data for nine taxonomic groups (commonly used in inventories for environmental impact assessment) and three databases available to SEA stakeholders. Three local administrative entities in very different socio-ecological contexts were used to examine three main issues : (i) the suitability of local versus regional or country databases for assessing conservation priorities, (ii) differences among taxonomic groups or territories in terms of the suitability of databases, (iii) the importance of the quality of databases for the application of SDM to assess priority conservation areas. Our study provides several clear messages for potential users of open-access databases. First, the need for prudence in the interpretation of biodiversity maps. Second, the collection of individual databases at the country scale is necessary to complete local data and ensure the suitability of SDM in a local context. Third, a data driven approach can lead to the use of notably different species communities to identify priority conservation areas when compared to the community in the original database. Finally, we propose a workflow to guide SEA stakeholders through the process of data rationalization and use in conservation planning.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"63 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135141360","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}
Next generation sequencing offers several ways to study microbial communities. For agri-food sciences, identifying species in diverse food ecosystems is key for both food sustainability and food security. The aim of this study was to compare metabarcoding pipelines and markers to determine fungal diversity in food ecosystems, from Illumina short reads. We built mock communities combining the most representative fungal species in fermented meat, cheese, wine and bread. Four barcodes (ITS1, ITS2, D1/D2 and RPB2) were tested for each mock and on real fermented products. We created a database, including all mock species sequences for each barcode to compensate for the lack of curated data in available databases. Four bioinformatics tools (DADA2, QIIME, FROGS and a combination of DADA2 and FROGS) were compared. Our results clearly showed that the combined DADA2 and FROGS tool gave the most accurate results. Most mock community species were not identified by the RPB2 barcode due to unsuccessful barcode amplification. When comparing the three rDNA markers, ITS markers performed better than D1/D2, as they are better represented in public databases and have better specificity to distinguish species. Between ITS1 and ITS2, differences in the best marker were observed according to the studied ecosystem. While ITS2 is best suited to characterize cheese, wine and fermented meat communities, ITS1 performs better for sourdough bread communities. Our results also emphasized the need for a dedicated database and enriched fungal-specific public databases with novel barcode sequences for 118 major species in food ecosystems.
{"title":"Comparison of metabarcoding taxonomic markers to describe fungal communities in fermented foods","authors":"Olivier Rué, Monika Coton, Eric Dugat-Bony, Kate Howell, Françoise Irlinger, Jean-Luc Legras, Valentin Loux, Elisa Michel, Jérôme Mounier, Cécile Neuvéglise, Delphine Sicard","doi":"10.24072/pcjournal.321","DOIUrl":"https://doi.org/10.24072/pcjournal.321","url":null,"abstract":"Next generation sequencing offers several ways to study microbial communities. For agri-food sciences, identifying species in diverse food ecosystems is key for both food sustainability and food security. The aim of this study was to compare metabarcoding pipelines and markers to determine fungal diversity in food ecosystems, from Illumina short reads. We built mock communities combining the most representative fungal species in fermented meat, cheese, wine and bread. Four barcodes (ITS1, ITS2, D1/D2 and RPB2) were tested for each mock and on real fermented products. We created a database, including all mock species sequences for each barcode to compensate for the lack of curated data in available databases. Four bioinformatics tools (DADA2, QIIME, FROGS and a combination of DADA2 and FROGS) were compared. Our results clearly showed that the combined DADA2 and FROGS tool gave the most accurate results. Most mock community species were not identified by the RPB2 barcode due to unsuccessful barcode amplification. When comparing the three rDNA markers, ITS markers performed better than D1/D2, as they are better represented in public databases and have better specificity to distinguish species. Between ITS1 and ITS2, differences in the best marker were observed according to the studied ecosystem. While ITS2 is best suited to characterize cheese, wine and fermented meat communities, ITS1 performs better for sourdough bread communities. Our results also emphasized the need for a dedicated database and enriched fungal-specific public databases with novel barcode sequences for 118 major species in food ecosystems.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135435013","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}
Barbara Viginier, Lucie Cappuccio, Céline Garnier, Edwige Martin, Carine Maisse, Claire Valiente Moro, Guillaume Minard, Albin Fontaine, Sébastian Lequime, Maxime Ratinier, Frédérick Arnaud, Vincent Raquin
Arbovirus emergence and epidemic potential, as approximated by the vectorial capacity formula, depends on host and vector parameters, including the vector’s intrinsic ability to replicate then transmit the pathogen known as vector competence. Vector competence is a complex, time-dependent, quantitative phenotype influenced by biotic and abiotic factors. A combination of experimental and modelling approaches is required to assess arbovirus intra-vector dynamics and estimate epidemic potential. In this study, we measured infection, dissemination, and transmission dynamics of chikungunya virus (CHIKV) in a field-derived Aedes albopictus population (Lyon, France) after oral exposure to a range of virus doses spanning human viraemia. Statistical modelling indicates rapid and efficient CHIKV progression in the vector mainly due to an absence of a dissemination barrier, with 100% of the infected mosquitoes ultimately exhibiting a disseminated infection, regardless of the virus dose. Transmission rate data revealed a time-dependent, but overall weak, transmission barrier, with individuals transmitting as soon as 2 days post-exposure (dpe) and >50% infectious mosquitoes at 6 dpe for the highest dose. Based on these experimental intra-vector dynamics data, epidemiological simulations conducted with an agent-based model showed that even at low mosquito biting rates, CHIKV could trigger outbreaks locally. Together, this reveals the epidemic potential of CHIKV upon transmission by Aedes albopictus in mainland France.
{"title":"Chikungunya intra-vector dynamics in Aedes albopictus from Lyon (France) upon exposure to a human viremia-like dose range reveals vector barrier’s permissiveness and supports local epidemic potential","authors":"Barbara Viginier, Lucie Cappuccio, Céline Garnier, Edwige Martin, Carine Maisse, Claire Valiente Moro, Guillaume Minard, Albin Fontaine, Sébastian Lequime, Maxime Ratinier, Frédérick Arnaud, Vincent Raquin","doi":"10.24072/pcjournal.326","DOIUrl":"https://doi.org/10.24072/pcjournal.326","url":null,"abstract":"Arbovirus emergence and epidemic potential, as approximated by the vectorial capacity formula, depends on host and vector parameters, including the vector’s intrinsic ability to replicate then transmit the pathogen known as vector competence. Vector competence is a complex, time-dependent, quantitative phenotype influenced by biotic and abiotic factors. A combination of experimental and modelling approaches is required to assess arbovirus intra-vector dynamics and estimate epidemic potential. In this study, we measured infection, dissemination, and transmission dynamics of chikungunya virus (CHIKV) in a field-derived Aedes albopictus population (Lyon, France) after oral exposure to a range of virus doses spanning human viraemia. Statistical modelling indicates rapid and efficient CHIKV progression in the vector mainly due to an absence of a dissemination barrier, with 100% of the infected mosquitoes ultimately exhibiting a disseminated infection, regardless of the virus dose. Transmission rate data revealed a time-dependent, but overall weak, transmission barrier, with individuals transmitting as soon as 2 days post-exposure (dpe) and >50% infectious mosquitoes at 6 dpe for the highest dose. Based on these experimental intra-vector dynamics data, epidemiological simulations conducted with an agent-based model showed that even at low mosquito biting rates, CHIKV could trigger outbreaks locally. Together, this reveals the epidemic potential of CHIKV upon transmission by Aedes albopictus in mainland France.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"54 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134977963","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}
Marie Simonin, Anne Préveaux, Coralie Marais, Tiffany Garin, Gontran Arnault, Alain Sarniguet, Matthieu Barret
Seed-borne microorganisms can be pioneer taxa during germination and seedling emergence. Still, the identity and phenotypic effects of these taxa that constitute a primary inoculum of plant microbiota is mostly unknown. Here, we studied the transmission of bacteria from radish seeds to seedlings using the inoculation of individual seed-borne strains and synthetic communities (SynComs) under in vitro conditions. The SynComs were composed of highly abundant and prevalent, sub-dominant, or rare bacterial seed taxa. We monitored the transmission of each strain alone or in communities using gyrB gene amplicon sequencing and assessed their impacts on germination and seedling phenotype. All strains and SynComs successfully colonized seedlings and we were able to reconstruct a richness gradient (6, 8 and 12 strains) on both seeds and seedlings. Stenotrophomonas rhizophila became dominant on seedlings of the three SynComs but most strains had variable transmission success (i.e increasing, stable or decreasing during seed to seedling transition) that also depended on the SynCom richness. Most individual strains had no effect on seedling phenotypes, with the exception of Pseudomonas viridiflava and Paenibacillus sp. which had detrimental effects on germination and seedling development. Abnormal seedling morphologies were also observed with SynComs but their proportions decreased at the highest richness level. Interestingly, some bacterial strains previously identified as core taxa of radish seeds (Pseudomonas viridiflava, Erwinia persicina) were associated with detrimental effects on seedling phenotypes either in isolation or in SynComs. These results confirm that the plant core microbiome includes pathogenic and not only commensal or mutualistic taxa. Altogether, these results show that SynCom inoculation can effectively manipulate seed and seedling microbiota diversity and thus represents a promising tool to better understand the early stages of plant microbiota assembly. This study also highlights strong differences between native seed-borne taxa in the colonization and survival on plant habitats.
{"title":"Transmission of synthetic seed bacterial communities to radish seedlings: impact on microbiota assembly and plant phenotype","authors":"Marie Simonin, Anne Préveaux, Coralie Marais, Tiffany Garin, Gontran Arnault, Alain Sarniguet, Matthieu Barret","doi":"10.24072/pcjournal.329","DOIUrl":"https://doi.org/10.24072/pcjournal.329","url":null,"abstract":"Seed-borne microorganisms can be pioneer taxa during germination and seedling emergence. Still, the identity and phenotypic effects of these taxa that constitute a primary inoculum of plant microbiota is mostly unknown. Here, we studied the transmission of bacteria from radish seeds to seedlings using the inoculation of individual seed-borne strains and synthetic communities (SynComs) under in vitro conditions. The SynComs were composed of highly abundant and prevalent, sub-dominant, or rare bacterial seed taxa. We monitored the transmission of each strain alone or in communities using gyrB gene amplicon sequencing and assessed their impacts on germination and seedling phenotype. All strains and SynComs successfully colonized seedlings and we were able to reconstruct a richness gradient (6, 8 and 12 strains) on both seeds and seedlings. Stenotrophomonas rhizophila became dominant on seedlings of the three SynComs but most strains had variable transmission success (i.e increasing, stable or decreasing during seed to seedling transition) that also depended on the SynCom richness. Most individual strains had no effect on seedling phenotypes, with the exception of Pseudomonas viridiflava and Paenibacillus sp. which had detrimental effects on germination and seedling development. Abnormal seedling morphologies were also observed with SynComs but their proportions decreased at the highest richness level. Interestingly, some bacterial strains previously identified as core taxa of radish seeds (Pseudomonas viridiflava, Erwinia persicina) were associated with detrimental effects on seedling phenotypes either in isolation or in SynComs. These results confirm that the plant core microbiome includes pathogenic and not only commensal or mutualistic taxa. Altogether, these results show that SynCom inoculation can effectively manipulate seed and seedling microbiota diversity and thus represents a promising tool to better understand the early stages of plant microbiota assembly. This study also highlights strong differences between native seed-borne taxa in the colonization and survival on plant habitats.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135590824","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}
While non-marine turtles are almost ubiquitous in the archaeological record of Southeast Asia, their zooarchaeological examination has been inadequately pursued within this tropical region. This gap in research hinders a complete comprehension of past human subsistence strategies and economies, as only a limited number of comprehensive studies encompassing all the taxa found in archaeological sites have been conducted thus far. This constraint becomes particularly significant in relation to prehistoric hunter-gatherer populations, who might have extensively utilized inland chelonian taxa. In order to initiate a new approach to the study of past human-turtle interactions in Southeast Asia, we propose an in-depth zooarchaeological analysis of turtle bone remains recovered from four Hoabinhian Hunter-gatherer archaeological assemblages located in Thailand and Cambodia, dating from the Late Pleistocene to the first half of the Holocene. Our study focuses on the bone remains attributed to the Yellow-headed Tortoise (Indotestudo elongata) as it is the most represented taxon in archaeological assemblages in the region of study. For this species, we developed osteometric equations enabling the estimation of the carapace size of the archaeological individuals. This allowed us to study the size structure of the archaeological populations at different sites and to reveal the human exploitation strategies of these animals. We observed a significant taphonomic homogeneity among the studied assemblages, along with similarities in the diversity of hunted reptile and amphibian taxa as well as the size of the exploited tortoises. These findings suggest consistent subsistence behaviors across distinct sites, despite their varying environmental conditions, and raise the possibility of cultural similarities across different periods and regions. Additionally, we provide a baseline for future zooarchaeological studies and a methodological framework for the detailed analysis of archaeological turtle bones in continental Southeast Asia.
{"title":"Zooarchaeological investigation of the Hoabinhian exploitation of reptiles and amphibians in Thailand and Cambodia with a focus on the Yellow-headed Tortoise (Indotestudo elongata (Blyth, 1854))","authors":"Corentin Bochaton, Sirikanya Chantasri, Melada Maneechote, Julien Claude, Christophe Griggo, Wilailuck Naksri, Hubert Forestier, Heng Sophady, Prasit Auertrakulvit, Jutinach Bowonsachoti, Valéry Zeitoun","doi":"10.24072/pcjournal.328","DOIUrl":"https://doi.org/10.24072/pcjournal.328","url":null,"abstract":"While non-marine turtles are almost ubiquitous in the archaeological record of Southeast Asia, their zooarchaeological examination has been inadequately pursued within this tropical region. This gap in research hinders a complete comprehension of past human subsistence strategies and economies, as only a limited number of comprehensive studies encompassing all the taxa found in archaeological sites have been conducted thus far. This constraint becomes particularly significant in relation to prehistoric hunter-gatherer populations, who might have extensively utilized inland chelonian taxa. In order to initiate a new approach to the study of past human-turtle interactions in Southeast Asia, we propose an in-depth zooarchaeological analysis of turtle bone remains recovered from four Hoabinhian Hunter-gatherer archaeological assemblages located in Thailand and Cambodia, dating from the Late Pleistocene to the first half of the Holocene. Our study focuses on the bone remains attributed to the Yellow-headed Tortoise (Indotestudo elongata) as it is the most represented taxon in archaeological assemblages in the region of study. For this species, we developed osteometric equations enabling the estimation of the carapace size of the archaeological individuals. This allowed us to study the size structure of the archaeological populations at different sites and to reveal the human exploitation strategies of these animals. We observed a significant taphonomic homogeneity among the studied assemblages, along with similarities in the diversity of hunted reptile and amphibian taxa as well as the size of the exploited tortoises. These findings suggest consistent subsistence behaviors across distinct sites, despite their varying environmental conditions, and raise the possibility of cultural similarities across different periods and regions. Additionally, we provide a baseline for future zooarchaeological studies and a methodological framework for the detailed analysis of archaeological turtle bones in continental Southeast Asia.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"28 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135829385","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}
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