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Windsor FM, Armenteras D, Assis APA, Astegiano J, Santana PC, Cagnolo L, Carvalheiro LG, Emary C, Fort H, Gonzalez XI, Kitson JJ, Lacerda AC, Lois M, Márquez-Velásquez V, Miller KE, Monasterolo M, Omacini M, Maia KP, Palacios TP, Pocock MJ, Poggio SL, Varassin IG, Vázquez DP, Tavella J, Rother DC, Devoto M, Guimarães PR, Evans DM. Network science: Applications for sustainable agroecosystems and food security. Perspect Ecol Conserv 2022. [DOI: 10.1016/j.pecon.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Ravigné V, Becker N, Massol F, Guichoux E, Boury C, Mahé F, Facon B. Fruit fly phylogeny imprints bacterial gut microbiota. Evol Appl 2022; 15:1621-1638. [PMID: 36330298 PMCID: PMC9624087 DOI: 10.1111/eva.13352] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 11/30/2022] Open
Abstract
One promising avenue for reconciling the goals of crop production and ecosystem preservation consists in the manipulation of beneficial biotic interactions, such as between insects and microbes. Insect gut microbiota can affect host fitness by contributing to development, host immunity, nutrition, or behavior. However, the determinants of gut microbiota composition and structure, including host phylogeny and host ecology, remain poorly known. Here, we used a well‐studied community of eight sympatric fruit fly species to test the contributions of fly phylogeny, fly specialization, and fly sampling environment on the composition and structure of bacterial gut microbiota. Comprising both specialists and generalists, these species belong to five genera from to two tribes of the Tephritidae family. For each fly species, one field and one laboratory samples were studied. Bacterial inventories to the genus level were produced using 16S metabarcoding with the Oxford Nanopore Technology. Sample bacterial compositions were analyzed with recent network‐based clustering techniques. Whereas gut microbiota were dominated by the Enterobacteriaceae family in all samples, microbial profiles varied across samples, mainly in relation to fly identity and sampling environment. Alpha diversity varied across samples and was higher in the Dacinae tribe than in the Ceratitinae tribe. Network analyses allowed grouping samples according to their microbial profiles. The resulting groups were very congruent with fly phylogeny, with a significant modulation of sampling environment, and with a very low impact of fly specialization. Such a strong imprint of host phylogeny in sympatric fly species, some of which share much of their host plants, suggests important control of fruit flies on their gut microbiota through vertical transmission and/or intense filtering of environmental bacteria.
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Affiliation(s)
| | | | - François Massol
- Univ. Lille CNRS Inserm CHU Lille Institut Pasteur de Lille U1019 ‐ UMR 9017 ‐ CIIL ‐ Center for Infection and Immunity of Lille F‐59000 Lille France
| | | | | | - Frédéric Mahé
- PHIM Plant Health Institute Univ Montpellier CIRAD, INRAE Institut Agro IRD Montpellier France
| | - Benoit Facon
- INRAE UMR CBGP Campus International de Baillarguet F‐349988 Montferrier/Lez France
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Poggi S, Vinatier F, Hannachi M, Sanz Sanz E, Rudi G, Zamberletti P, Tixier P, Papaïx J. How can models foster the transition towards future agricultural landscapes? ADV ECOL RES 2021. [DOI: 10.1016/bs.aecr.2020.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Karimi B, Dequiedt S, Terrat S, Jolivet C, Arrouays D, Wincker P, Cruaud C, Bispo A, Chemidlin Prévost-Bouré N, Ranjard L. Biogeography of Soil Bacterial Networks along a Gradient of Cropping Intensity. Sci Rep 2019; 9:3812. [PMID: 30846759 PMCID: PMC6405751 DOI: 10.1038/s41598-019-40422-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/13/2019] [Indexed: 12/18/2022] Open
Abstract
Although land use drives soil bacterial diversity and community structure, little information about the bacterial interaction networks is available. Here, we investigated bacterial co-occurrence networks in soils under different types of land use (forests, grasslands, crops and vineyards) by sampling 1798 sites in the French Soil Quality Monitoring Network covering all of France. An increase in bacterial richness was observed from forests to vineyards, whereas network complexity respectively decreased from 16,430 links to 2,046. However, the ratio of positive to negative links within the bacterial networks ranged from 2.9 in forests to 5.5 in vineyards. Networks structure was centered on the most connected genera (called hub), which belonged to Bacteroidetes in forest and grassland soils, but to Actinobacteria in vineyard soils. Overall, our study revealed that soil perturbation due to intensive cropping reduces strongly the complexity of bacterial network although the richness is increased. Moreover, the hub genera within the bacterial community shifted from copiotrophic taxa in forest soils to more oligotrophic taxa in agricultural soils.
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Affiliation(s)
- Battle Karimi
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, F- 21000, Dijon, France
| | - Samuel Dequiedt
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, F- 21000, Dijon, France
| | - Sébastien Terrat
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, F- 21000, Dijon, France
| | | | | | - Patrick Wincker
- CEA/Institut de Génomique/Genoscope, 91057, Evry cedex, France
| | - Corinne Cruaud
- CEA/Institut de Génomique/Genoscope, 91057, Evry cedex, France
| | - Antonio Bispo
- INRA, US 1106, Unité INFOSOL, 45075, Orléans, France
- ADEME, Service Agriculture et Forêt, 49000, Angers, France
| | | | - Lionel Ranjard
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, F- 21000, Dijon, France.
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Biomonitoring for the 21st Century: Integrating Next-Generation Sequencing Into Ecological Network Analysis. ADV ECOL RES 2018. [DOI: 10.1016/bs.aecr.2017.12.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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Schiesari L, Leibold MA, Burton GA. Metacommunities, metaecosystems and the environmental fate of chemical contaminants. J Appl Ecol 2017. [DOI: 10.1111/1365-2664.13054] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Luis Schiesari
- Escola de Artes, Ciências e Humanidades Universidade de São Paulo São Paulo Brazil
- Departamento de Ecologia Instituto de Biociências Universidade de São Paulo São Paulo Brazil
| | - Mathew A. Leibold
- Department of Integrative Biology University of Texas at Austin Austin TX USA
| | - G. Allen Burton
- School for Environment and Sustainability University of Michigan Ann Arbor MI USA
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Massol F, Altermatt F, Gounand I, Gravel D, Leibold MA, Mouquet N. How life-history traits affect ecosystem properties: effects of dispersal in meta-ecosystems. OIKOS 2017. [DOI: 10.1111/oik.03893] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- François Massol
- CNRS, Univ. de Lille, UMR 8198 Evo-Eco-Paleo, SPICI group; FR-59000 Lille France
| | - Florian Altermatt
- Dept of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology; Dübendorf, Switzerland, and: Dept of Evolutionary Biology and Environmental Studies, Univ. of Zürich; Zürich Switzerland
| | - Isabelle Gounand
- Dept of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology; Dübendorf, Switzerland, and: Dept of Evolutionary Biology and Environmental Studies, Univ. of Zürich; Zürich Switzerland
| | - Dominique Gravel
- Dépt de biologie; Univ. de Sherbrooke, Sherbrooke, Canada, and: Québec Center for Biodiversity Science; Quebec Canada
| | - Mathew A. Leibold
- Dept of Integrative Biology; Univ. of Texas at Austin; Austin TX USA
| | - Nicolas Mouquet
- 7 UMR MARBEC (MARine Biodiversity, Exploitation and Conservation); Univ. de Montpellier; Montpellier France
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Astegiano J, Guimarães PR, Cheptou PO, Vidal MM, Mandai CY, Ashworth L, Massol F. Persistence of Plants and Pollinators in the Face of Habitat Loss. ADV ECOL RES 2015. [DOI: 10.1016/bs.aecr.2015.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Bohan DA, Raybould A, Mulder C, Woodward G, Tamaddoni-Nezhad A, Bluthgen N, Pocock MJ, Muggleton S, Evans DM, Astegiano J, Massol F, Loeuille N, Petit S, Macfadyen S. Networking Agroecology. ADV ECOL RES 2013. [DOI: 10.1016/b978-0-12-420002-9.00001-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Loeuille N, Barot S, Georgelin E, Kylafis G, Lavigne C. Eco-Evolutionary Dynamics of Agricultural Networks. ADV ECOL RES 2013. [DOI: 10.1016/b978-0-12-420002-9.00006-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Tamaddoni-Nezhad A, Milani GA, Raybould A, Muggleton S, Bohan DA. Construction and Validation of Food Webs Using Logic-Based Machine Learning and Text Mining. ADV ECOL RES 2013. [DOI: 10.1016/b978-0-12-420002-9.00004-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Traugott M, Kamenova S, Ruess L, Seeber J, Plantegenest M. Empirically Characterising Trophic Networks. ADV ECOL RES 2013. [DOI: 10.1016/b978-0-12-420002-9.00003-2] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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