Publications

Names of students and past students are underlined.

Submitted

Pauvert C., Fort T., Calonnec A., Faivre d’Arcier J., Chancerel E., Massot M., Chiquet J., Robin S., Bohan D.A., Vallance J., Vacher C. Microbial association networks give relevant insights into plant pathobiomes. BioRxiv.

Accepted or published

2021

Faticov, M., Abdelfattah, A., Roslin, T., Vacher, C., Hambäck, P., Blanchet, G., Lindahl, B., Tack, A. Climate warming dominates over plant genotype in shaping the seasonal trajectory of foliar fungal communities on oak. New Phytologist, online (doi: 10.1111/nph.17434)

Ma Y., Fort T., Marais A., Lefebvre M., Theil S., Vacher C., Candresse T. 2021. Leaf-associated fungal and viral communities of wild plant populations differ between cultivated and natural ecosystems. Plant-Environment Interactions, online (doi: 10.1002/pei3.10043)

Vacher C., Castagneyrol B., Jousselin E., Schimann H. 2021. Trees and insects have microbiomes: consequences on forest health and management. Current Forestry Reports, in press

Fort T., Pauvert C., Zanne A. E., Ovaskainen O., Caignard T., Barret M., Compant S., Hampe A., Delzon S., Vacher C.  2021. Maternal effects shape the seed mycobiome in Quercus petraea. New Phytologist, 230: 1594–1608 (doi: 10.1111/nph.17153)

Barroso-Bergada D., Pauvert C., Vallance J., Delière L., Bohan D.A., Buée M., Vacher C. 2021. Microbial networks inferred from environmental DNA data for biomonitoring ecosystem change: strengths and pitfalls. Molecular Ecology Resources, 21: 762–780 (doi: 10.1111/1755-0998.13302)

Compant S., Cambon M., Vacher C., Mitter B., Samad A., Sessitch A. 2021. The plant endosphere world – bacterial life within plants Environmental Microbiology, 23(4): 18121829 (doi: 10.1111/1462-2920.15240)

2020

Makiola A, Compson ZG, Baird DJ, Barnes MA, Boerlijst SP, Bouchez A, Brennan G, Bush A, Canard E, Cordier T, Creer S, Curry RA, David P, Dumbrell AJ, Gravel D, Hajibabaei M, Hayden B, Hoorn B, Jarne P, Jones JI, Karimi B, Keck F, Kelly M, Knot IE, Krol L, Massol F, Monk WA, Murphy JF, Pawlowski J, Poisot T, Porter TM, Randall KC, Ransome E, Ravigné V, Raybould A, Robin S, Schrama M, Schatz B, Tamaddoni-Nezhad A, Trimbos KB, Vacher C, Vasselon V, Wood S, Woodward G, Bohan DA. 2020. Key questions for next-generation of biomonitoring. Frontiers in environmental science, 7: 197 (doi: 10.3389/fenvs.2019.00197)

Bohan DA, Gravel D, Tamaddoni-Nehzad A, Vacher C, Robin S. 2020. A next-generation of biomonitoring to detect global ecosystem change. E-Book. Frontiers in Ecology and Evolution & Frontiers in Environmental Science (doi: 10.3389/978-2-88966-027-8)

Arnaud-Haond S, Vacher C. 2020. Marine holobiont in the high throughput sequencing era. Recommendation for PCI Ecology (doi : 10.24072/pci.ecology.100045)

Barret M, Buée M, Mougel C, Vacher C. 2020. Le microbiote des plantes : diversité, transmission et fonction. In Fauvergue X, Malausa T, Rusch A, Jacquin-Joly E, Barret M, Bardin M, Lannou C. (eds). 2020. Biocontrôle : Éléments pour une protection agroécologique des cultures. Quae editions, collection : Savoir-Faire, Versailles, France

2019

Pauvert C., Buée M., Laval V., Edel-Hermann V., Fauchery L., Gautier A., Lesur I., Vallance J., Vacher C. 2019. Bioinformatics matters: the accuracy of plant and soil fungal community data is highly dependant on the metabarcoding pipeline. Fungal Ecology, 41: 23-33 (doi: 10.1016/j.funeco.2019.03.005)

Legeay J., Husson C., Cordier T., Vacher C., Marcais B., Buée M. 2019. Comparison and validation of Oomycetes metabarcoding primers for Phytophthora high-throughput sequencing. Journal of Plant Pathology, 101(3), 743-748 (doi: 10.1007/s42161-019-00276-9)

Compant, C., Vacher, C. Sources, niches and routes of colonization by beneficial bacterial endophytes. 2019. In: Endophyte biotechnology: promise for agriculture and pharmacology (Ed. A Schouten), CABI Biotechnology Series (doi: 10.1079/9781786399427.0032)

2018

Derocles, S.A.P., Bohan, D.A., Dumbrell, A.J., Kitson, J.J.N, Massol, F., Pauvert, C., Plantegenest, M., Vacher, C., Evans, D.M. 2018. Biomonitoring for the 21st Century: Integrating Next-Generation Sequencing Into Ecological Network Analysis. Advances in Ecological Research, 58: 1-62 (doi: 10.1016/bs.aecr.2017.12.001)

2017

Bohan, D. A., Vacher, C., Tamaddoni-Nezhad, A., Dumbrell, A.J., Woodward, G. 2017. Next-generation Biomonitoring: large-scale, automatic reconstruction of ecological networksTrends in Ecology and Evolution, 32(7): 477-487 (doi: 10.1016/j.tree.2017.03.001)

Lemanceau, P., Barret, M., Mazurier, S., Mondy, S., Pivato, B., Fort, T., Vacher C. 2017. Plant communication with associated microbiota in the spermosphere, rhizosphere and phyllosphere. Advances in Botanical Research, 82: 101-133 (doi: 10.1016/bs.abr.2016.10.007)

2016

REX Consortium. 2016. Combining selective pressures to enhance the durability of disease resistance genes. Frontiers in Plant Science 7:1916 (doi: 10.3389/fpls.2016.01916)

Fort, T., Robin, C., Capdevielle, X., Delière, L., Vacher C. 2016. Foliar fungal communities strongly differ between habitat patches in a landcape mosaic. PeerJ, 4:e2656 (doi: 10.7717/peerj.2656)

Jakuschkin, B., Fievet, V., Schwaller, L., Fort, T., Robin, C., Vacher, C. 2016. Deciphering the pathobiome: intra- and inter-kingdom interactions involving the pathogen Erysiphe alphitoides. Microbial Ecology, 72(4):870-880 (doi: 10.1007/s00248-016-0777-x)

Vacher, C., Hampe, A., Porté, A.J., Sauer, U., Compant, S., Morris, C.E. 2016. The phyllosphere: microbial jungle at the plant-climate interface. Annual Review of Ecology, Evolution, and Systematics, vol. 47, 1-24 (doi: 10.1146/annurev-ecolsys-121415-032238)

Vacher, C., Cordier, T., Vallance, J. 2016. Phyllosphere fungal communities differentiate more thoroughly than bacterial communities along an elevation gradient. Microbial Ecology, 72(1):1-3 (doi: 10.1007/s00248-016-0742-8)

QUINTESSENCE Consortium. 2016. Networking our way to better Ecosystem Service provison. Trends in Ecology and Evolution, 31(2):105-115 (doi: 10.1016/j.tree.2015.12.003)

Vacher, C., Tamaddoni-Nezhad A., Kamenova, S., Peyrard, N., Moalic, Y., Sabbadin, R., Schwaller, L., Chiquet, J., Smith, M. A., Vallance, J., Fievet, V., Jakuschkin, B., Bohan, D.A. 2016. Learning Ecological Networks from Next-Generation Sequencing Data. Advances in Ecological Research, 54, 1-39 (doi: 10.1016/bs.aecr.2015.10.004)

Plomion, C., Bastien, C., Bogeat-Triboulot, M.-B., Bouffier, L., Déjardin, A., Duplessis, S., Fady, B., Heuertz, M., Le Gac, A.-L., Le Provost, G., Legué, V., Lelu-Walter, M.-A., Leplé, J.-C., Maury, S., Morel, A., Oddou-Muratorio, S., Pilate, G., Sanchez, L., Scotti, I., Scotti-Saintagne, C., Segura, V., Trontin, J.-F., Vacher, C.. 2016. Forest tree genomics: 10 achievements from the past 10 years and future prospects. Annals of Forest Science, 73:77 (doi: 10.1007/s13595-015-0488-3)

Desprez-Loustau, M-L., Agayo, J. Dutech, C., Hayden, K.J., Husson, C., Jakuschkin, B., Marçais, B., Piou, D., Robin, C.,  Vacher, C. 2016. An evolutionary ecology perspective to address forest pathology challenges of today and tomorrow. Annals of Forest Science, 73:45 (doi: 10.1007/s13595-015-0487-4)

2015

Mulder, C., Bennett, E.M., Bohan, D.A., Bonkowski, M., Carpenter, S.R., Chalmers, R., Cramer, W., Durance, I., Eisenhauer, N., Fontaine, C., Haughton, A.J., Hettelingh, J-P., Hines, J., Ibanez, S., Jeppesen, E., Krumins, J.A., Ma, A., Mancinelli, G., Massol, F., McLaughlin, O., Naeem, S., Pascual, U., Peñuelas, J., Pettorelli, N., Pocock, M.J.O., Raffaelli, D., Rasmussen, J.J., Rusch, G.M., Scherber, C., Setälä, H., Sutherland, W.J., Vacher, C., Voigt, W., Vonk, J.A., Wood, S.A., Woodward, G. 2015. 10 Years Later: Revisiting Priorities for Science and Society a Decade after the Millennium Assessment. Advances in Ecological Research, 53, 1-53 (doi: 10.1016/bs.aecr.2015.10.005)

Leger, J-B., Daudin, J-J., Vacher, C. 2015. Clustering methods differ in their ability to detect patterns in ecological networks. Methods in Ecology and Evolution 6(4): 474-481 (doi: 10.1111/2041-210X.12334)

2014

Coince, A., Cordier, T., Lengellé, J., Defossez, E., Vacher, C., Robin, C., Buée, M., Marçais, C. 2014.  Leaf and root-associated fungal assemblages do not follow similar elevational diversity patterns. PLOS ONE 9(6): e100668 (doi: 10.1371/journal.pone.0100668)

Leger, J-B., Vacher C, Daudin, J-J. 2014. Detection of structurally homogeneous subsets in graphs. Statistics & Computing 24: 675-692 (doi: 10.1007/s11222-013-9395-3)

Castagneyrol, B., Jactel, H., Vacher, C., Koricheva, J., Brockerhoff, E. 2014. Effects of plant phylogenetic diversity on herbivory depend on herbivore specialization. Journal of Applied Ecology 54: 675-692 (doi: 10.1111/1365-2664.12175)

2013

Lagache, L., Leger, J-B., Daudin, J-J., Petit, R., Vacher C. 2013. Putting the biological species concept to the test: using mating networks to delimit species. PLOS ONE, 8(6): e68267 (doi: 10.1371/journal.pone.0068267)

REX Consortium. 2013. Heterogeneity of selection pressures and the evolution of resistance. Trends in Ecology and Evolution 28(2):110-118 (doi: 10.1016/j.tree.2012.09.001)

REX Consortium. 2013. Gestion des résistances: l’importance des modalités de déploiement des substances. Phytoma 669: 10-14

2012

Cordier, T., Robin, C., Capdevielle, X., Fabreguettes, O., Desprez-Loustau, M-L., Vacher C. 2012. The composition of phyllosphere fungal assemblages of European beech (Fagus sylvatica L.) varies significantly along an elevation gradient. New Phytologist 196: 510-519 (doi: 10.1111/j.1469-8137.2012.04284.x)

Cordier, T., Robin, C., Capdevielle, X., Desprez-Loustau, M-L., Vacher C. 2012. Spatial variability of phyllosphere fungal assemblages: genetic distance predominates over geographic distance in a European beech stand (Fagus sylvatica). Fungal Ecology 5: 509-520 (doi: 10.1016/j.funeco.2011.12.004)

2011

Vacher, C., Kossler, T. M., Hochberg, M., Weis, A.E. 2011. Impact of interspecific hybridization between crops and weedy relatives on the evolution of flowering time in weedy phenotypes. PLOS ONE 6(2): e14649 (doi: 10.1371/journal.pone.0014649)

Philibert, A., Desprez-Loustau, M-L., Fabre, B., Frey, P., Halkett, F., Husson, C., Lung-Escarmant, B., Marçais, B. Robin, C., Vacher, C., Makowski, D. 2011. Predicting invasion success of forest pathogenic fungi from species traits. Journal of Applied Ecology 48(6): 1381-1390 (doi: 10.1111/j.1365-2664.2011.02039.x)

2010

REX Consortium. 2010. The skill and style to model the evolution of resistance to pesticide and drugs. Evolutionary Applications 3(4): 375-390 (doi: 10.1111/j.1752-4571.2010.00124.x)

Mariadassou, M., Robin, S., Vacher, C. 2010. Uncovering latent structure in valued graphs: a variational approach. Annals of Applied Statistics 4(2):715-742 (doi : 10.1214/10-AOAS361)

Vacher, C., Daudin, J-J., Piou, D., Desprez-Loustau, M-L. 2010. Ecological integration of alien species into a tree-parasitic fungus network. Biological Invasions 12:3249-3259 (doi: 10.1007/s10530-010-9719-6)

Daudin, J-J., Pierre, L., Vacher, C. 2010. Model for heterogeneous random networks using continuous variables and an application to a tree-fungus networkBiometrics 66:1043-1051 (doi: 10.1111/j.1541-0420.2009.01378.x)

2008

Vacher, C., Piou, D., Desprez-Loustau, M-L. 2008. Architecture of an antagonistic tree/fungus network: the asymmetric influence of past evolutionary history. PLOS ONE 3(3):e1740 (doi: 10.1371/journal.pone.0001740)

Vacher, C., Vile, D., Helion, M. Piou, D., Desprez-Loustau, M-L. 2008. Distribution of parasitic fungal species richness: influence of climate versus host species diversity. Diversity and Distributions 14(5):786-798 (doi: 10.1111/j.1472-4642.2008.00479.x)

2007

REX Consortium. 2007. Structure of the scientific community modelling the evolution of resistance. PloS ONE 2(12):e1275 (doi: 10.1371/journal.pone.0001275)

2006 and before (PhD thesis)

Vacher, C., Bourguet, D., Desquilbet, M., Lemarié, M., Ambec, S. and M.E. Hochberg. 2006. Fees or refuges: which is better for the sustainable management of insect resistance to transgenic Bt corn? Biology Letters 2: 198-202 (doi: 10.1098/rsbl.2005.0418)

Vacher, C., Brown, S. and M.E. Hochberg. 2005.  Avoid, attack or do both? Behavioral and physiological adaptations in natural enemies faced with novel hosts. BMC Evolutionary Biology 5: 60 (doi: 10.1186/1471-2148-5-60)

Weis, A.E., Winterer, J. A., Vacher, C., Freshwater, M., Kossler, T.M., Young, C.A. and G. LeBuhn. 2005. Phenological assortative mating in flowering plants: the nature and consequences of its frequency-dependance. Evolutionary Ecology Research 7: 161-181

Vacher, C., Weis, A.E., Hermann, D., Kossler, T.M., Young, C. and M.E. Hochberg. 2004. Impact of ecological factors on the initial invasion of Bt transgenes into wild populations. Theoretical and Applied Genetics 109: 806-814 (doi: 10.1007/s00122-004-1696-7)

Vacher, C., Bourguet, D., Rousset, F., Chevillon, C. and M.E. Hochberg. 2004. High dose refuge strategies and genetically modified crops – Reply to Tabashnik et al. Journal of Evolutionary Biology 17: 913-918 (doi: 10.1111/j.1420-9101.2004.00730.x)

Vacher, C., Bourguet, D., Rousset, F., Chevillon, C. and M.E. Hochberg. 2003. Modelling the spatial configuration of refuges for a sustainable control of pests: a case study of Bt cotton. Journal of Evolutionary Biology 16: 378-387 (doi: 10.1046/j.1420-9101.2003.00553.x)