Auteurs, date et publication :
Auteurs Hannah Loranger , Gerhard Zotz , Maaike Y. Bader
Publication : Oikos
Date : 2025
Volume : 126
Issue : 11
Pages : 1625-1636
Catégorie(s)
#CNRS #Lautaret #UGAAuteurs, date et publication :
Auteurs Nicolas Legay , F. Grassein , T. M. Robson , Emmanuelle Personeni , Marie-Paule Bataillé , S. Lavorel , J.-C. Clement
Publication : Biogeosciences
Date : 2025
Volume : 10
Issue : 11
Catégorie(s)
#CNRS #Lautaret #UGARésumé
Abstract Metabarcoding of bulk or environmental DNA has great potential for biomonitoring of freshwater environments. However, successful application of metabarcoding to biodiversity monitoring requires universal primers with high taxonomic coverage that amplify highly variable, short metabarcodes with high taxonomic resolution. Moreover, reliable and extensive reference databases are essential to match the outcome of metabarcoding analyses with available taxonomy and biomonitoring indices. Benthic invertebrates, particularly insects, are key taxa for freshwater bioassessment. Nevertheless, few studies have so far assessed markers for metabarcoding of freshwater macrobenthos. Here we combined in silico and laboratory analyses to test the performance of different markers amplifying regions in the 18S rDNA (Euka02), 16S rDNA (Inse01) and COI (BF1_BR2-COI) genes, and developed an extensive database of benthic macroinvertebrates of France and Europe, with a particular focus on key insect orders (Ephemeroptera, Plecoptera and Trichoptera). Analyses on 1,514 individuals representing different taxa of benthic macroinvertebrates showed very different amplification success across primer combinations. The Euka02 marker showed the highest universality, while the Inse01 marker showed excellent performance for the amplification of insects. BF1_BR2-COI showed the highest resolution, while the resolution of Euka02 was often limited. By combining our data with GenBank information, we developed a curated database including sequences representing 822 genera. The heterogeneous performance of the different primers highlights the complexity in identifying the best markers, and advocates for the integration of multiple metabarcodes for a more comprehensive and accurate understanding of ecological impacts on freshwater biodiversity.
Auteurs, date et publication :
Auteurs Gentile Francesco Ficetola , Frédéric Boyer , Alice Valentini , Aurélie Bonin , Albin Meyer , Tony Dejean , Coline Gaboriaud , Philippe Usseglio-Polatera , Pierre Taberlet
Publication : Molecular Ecology
Date : 2025
Volume : 30
Issue : 13
Pages : 3189–3202
Catégorie(s)
#CNRS #eDNARésumé
Targeted sequencing of 16S rDNA amplicons is routinely used for microbial community profiling but this method suffers several limitations such as bias affinity of universal primers and short read size. Gene capture by hybridization represents a promising alternative. Here we used a metagenomic extract from the pea aphid Acyrthosiphon pisum to compare the performances of two widely used PCR primer pairs with DNA capture, based on solution hybrid selection. All methods produced an exhaustive description of the 8 bacterial taxa known to be present in this sample. In addition, the methods yielded similar quantitative results, with the number of reads strongly correlating with quantitative PCR controls. Both methods can thus be considered as qualitatively and quantitatively robust on such a sample with low microbial complexity.
Auteurs, date et publication :
Auteurs Marie Cariou , Céline Ribière , Stéphanie Morlière , Jean-Pierre Gauthier , Jean-Christophe Simon , Pierre Peyret , Sylvain Charlat
Publication : BMC Research Notes
Date : 2018
Volume : 11
Issue : 1
Pages : 1-5
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
Abstract The rapidly growing field of molecular diet analysis is becoming increasingly popular among ecologists, especially when investigating methodologically challenging groups, such as invertebrate generalist predators. Prey DNA detection success is known to be affected by multiple factors; however, the type of dietary sample has rarely been considered. Here, we address this knowledge gap by comparing prey DNA detection success from three types of dietary samples. In a controlled feeding experiment, using the carabid beetle Pterostichus melanarius as a model predator, we collected regurgitates, faeces and whole consumers (including their gut contents) at different time points postfeeding. All dietary samples were analysed using multiplex PCR, targeting three different length DNA fragments (128, 332 and 612 bp). Our results show that both the type of dietary sample and the size of the DNA fragment contribute to a significant part of the variation found in the detectability of prey DNA. Specifically, we observed that in both regurgitates and whole consumers, prey DNA was detectable significantly longer for all fragment sizes than for faeces. Based on these observations, we conclude that prey DNA detected from regurgitates and whole consumers DNA extracts are comparable, whereas prey DNA detected from faeces, though still sufficiently reliable for ecological studies, will not be directly comparable to the former. Therefore, regurgitates and faeces constitute a useful, nonlethal source for dietary information that could be applied to field studies in situations when invertebrate predators should not be killed.
Auteurs, date et publication :
Auteurs Stefaniya Kamenova , Rebecca Mayer , Oskar R Rubbmark , Eric Coissac , Manuel Plantegenest , Michael Traugott
Publication : Molecular Ecology Resources
Date : 2018
Volume : 18
Issue : 5
Pages : 966–973
Catégorie(s)
#CNRS #eDNARésumé
Flowing surface waters (rivers, creeks, streams) are integrators of biological, chemical and physical processes occurring in a catchment and they link catchment land cover from the headwaters to the outlet. The dynamics of human and animal pathogens in catchments have been widely studied in a large variety of contexts allowing the optimization of disease risk reduction. In parallel, there is an emerging awareness that crop pathogens might also be disseminated via surface waters especially when they are used for irrigation. However, there are no studies on the extent to which potential plant pathogens are present - nor about their dynamics - along the full course of a catchment. We do not know if they are confined to regions close to crops or if they are present throughout a catchment. Here we have compared the seasonal dynamics of populations of the Pseudomonas syringae (Psy) and the Soft Rot Pectobacteriaceae (SRP) species complexes along a 270 km stretch of the Durance River from the upstream alpine reaches to the downstream agricultural production areas at the confluence with the Rhone River at Avignon. Among 168 samples collected at 21 sites in fall, winter, spring and summer of 2016 and 2017, Psy strains were detected at all sampling sites and in 156 of the samples at population densities up to 10e5 bacteria/L. In contrast, SRP strains were detected in 98 of the samples, mostly from the southern part of the river, at population densities that did not exceed 3 x 10e4 bacteria/L. Among the aquatic parameters that were characterized at each sampling site (total culturable bacteria, temperature, conductivity, concentrations of dissolved organic carbon (DOC), PO43-, NH4+, NO2- and NO3-), temperature was the only factor that explained a significant amount of the variability in population size for both species complexes. Psy densities decreased with increasing temperature whereas SRP densities increased with increasing temperature. River-borne populations of SRP were composed mainly of Pectobacterium versatile and P. aquaticum that have little known epidemiological importance. Only a few strains of Pectobacterium and Dickeya species reputed for their epidemiological impact were observed. In contrast, Psy populations at all sites were dominated by a genetic lineage of phylogroup 2 known from other studies for its broad host range and its geographic and habitat ubiquity. These results suggest that strains of SRP with pathogenic potential to plants have lower competence for saprophytic survival (in freshwaters) than do potentially pathogenic strains of Psy and that their presence in river water is probably much more dependent on specific vegetative sources than are pathogenic strains of Psy. Nevertheless, their vegetative sources have not yet been identified. We discuss how to incorporate knowledge of the abundance and diversity of these two groups of plant pathogens in river water into a strategy for anticipating risk for disease outbreaks on crops in a catchment.
Auteurs, date et publication :
Auteurs Cindy E. Morris , Christelle Lacroix , Charlotte Chandeysson , Caroline Guilbaud , Cécile Monteil , Sylvain Piry , Emma Rochelle-Newall , Sarah Fiorini , Frédérique Van Gijsegem , Marie-Anne Barny , Odile Berge
Date : 2022
Catégorie(s)
#CNRS #PLANAQUAAuteurs, date et publication :
Auteurs Antoine Fouquet , Killian Leblanc , Anne-Claire Fabre , Miguel T Rodrigues , Marcelo Menin , Elodie A Courtois , Maël Dewynter , Monique Hölting , Raffael Ernst , Pedro Peloso
Publication : Zoologischer Anzeiger
Date : 2025
Volume : 293
Pages : 46-73
Catégorie(s)
#CNRS #FORET NouraguesAuteurs, date et publication :
Auteurs Kaïna Privet , Julien Pétillon
Publication : Ecology and evolution
Date : 2025
Volume : 10
Issue : 23
Pages : 13165-13172
Catégorie(s)
#CNRS #FORET NouraguesAuteurs, date et publication :
Auteurs Adriana de Almeida , Sandra Bos Mikich
Publication : Oikos
Date : 2025
Volume : 127
Issue : 2
Pages : 184-197
Catégorie(s)
#CNRS #FORET NouraguesRésumé
Assessing trait responses to environmental gradients requires the simultaneous analysis of the information contained in three tables: L (species distribution across samples), R (environmental characteristics of samples), and Q (species traits). Among the available methods, the so-called fourth-corner and RLQ methods are two appealing alternatives that provide a direct way to test and estimate trait–environment relationships. Both methods are based on the analysis of the fourth-corner matrix, which crosses traits and environmental variables weighted by species abundances. However, they differ greatly in their outputs: RLQ is a multivariate technique that provides ordination scores to summarize the joint structure among the three tables, whereas the fourth-corner method mainly tests for individual trait–environment relationships (i.e., one trait and one environmental variable at a time). Here, we illustrate how the complementarity between these two methods can be exploited to promote new ecological knowledge and to improve the study of trait–environment relationships. After a short description of each method, we apply them to real ecological data to present their different outputs and provide hints about the gain resulting from their combined use.
Auteurs, date et publication :
Auteurs Stéphane Dray , Philippe Choler , Sylvain Dolédec , Pedro R. Peres-Neto , Wilfried Thuiller , Sandrine Pavoine , Cajo J. F. ter Braak
Publication : Ecology
Date : 2025
Volume : 95
Issue : 1
Pages : 14-21