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Microbial biogeography and global change: Linking pyrosequencing, phy-logenetics and habitat modelling to study the ecogeography of soil fungal and bacterial communities along a wide elevation gradient in the Alps

Titel Englisch Microbial biogeography and global change: Linking pyrosequencing, phy-logenetics and habitat modelling to study the ecogeography of soil fungal and bacterial communities along a wide elevation gradient in the Alps
Gesuchsteller/in Guisan Antoine
Nummer 135129
Förderungsinstrument ProDoc (Forschungsmodul, FM)
Forschungseinrichtung Département d'Ecologie et d'Evolution Faculté de Biologie et de Médecine Université de Lausanne
Hochschule Universität Lausanne - LA
Hauptdisziplin Oekologie
Beginn/Ende 01.10.2011 - 30.09.2014
Bewilligter Betrag 202'424.00
Alle Daten anzeigen

Alle Disziplinen (2)

Disziplin
Oekologie
Genetik

Keywords (1)

microbial biogeography

Lay Summary (Französisch)

Lead
Lay summary

La Terre se réchauffe. Quel impact ces changements climatiques auront-ils sur la distribution de la biodiversité et des écosystèmes ? Ces dernières années, des modèles prédictifs ont été développés et utilisés pour évaluer l’impact des changements climatiques futurs sur la flore des Alpes vaudoises, mettant en évidence un risque accru pour les espèces de haute altitude. Ces modèles préliminaires ont cependant présenté des limites, qu’il est important aujourd’hui de surmonter pour produire des scénarios plus fiables. Une limite importante de ces modèles est qu’ils intégraient peu, jusqu’à présent, les interactions biotiques, par exemple entre plantes et micro-organismes du sol, alors que celles-ci pourraient changer dans un futur plus chaud et provoquer la rupture de certaines relations écologiques importantes. Les objectifs de ce nouveau projet sont premièrement d’étudier et de modéliser la distribution et la diversité des micro-organismes du sol (principalement champignons et bactéries, par des approches génétiques) le long d’un fort gradient d’altitude dans les Alpes vaudoises, puis de tester quel pourrait être l’impact des changements climatiques sur la distribution des micro-organismes eux-mêmes et, de par leur inclusion dans les modèles de plantes, sur les écosystèmes. Des données importantes ont déjà été collectées en 2009 et de nouvelles données seront collectées durant le projet qui permettront de mieux connaitre la biogéographie des micro-organismes du sol et de mieux comprendre les relations entre ceux-ci et les communautés végétales. Ce projet est aussi un véritable défi technologique quant à la quantité d’information génétique sur les micro-organismes qui devra être traitée, et un projet pionnier en termes de modélisation spatiale de données génétiques.

 

Direktlink auf Lay Summary Letzte Aktualisierung: 21.02.2013

Verantw. Gesuchsteller/in und weitere Gesuchstellende

Mitarbeitende

Publikationen

Publikation
Very high resolution environmental predictors in species distribution models: Moving beyond topography?
Pradervand Jean Nicolas, Dubuis Anne, Pellissier Loïc, Guisan Antoine, Randin Christophe F. (2014), Very high resolution environmental predictors in species distribution models: Moving beyond topography?, in Progress in Physical Geography, 38(1), 79-96.
A probabilistic approach to niche-based community models for spatial forecasts of assemblage properties and their uncertainties
Pellissier Loïc, Espíndola Anahí, Pradervand Jean Nicolas, Dubuis Anne, Pottier Julien, Ferrier Simon, Guisan Antoine (2013), A probabilistic approach to niche-based community models for spatial forecasts of assemblage properties and their uncertainties, in Journal of Biogeography, 40(10), 1939-1946.
Density-based hierarchical clustering of pyro-sequences on a large scale-the case of fungal ITS1
Pagni Marco, Niculita-Hirzel Helene, Pellissier Loic, Dubuis Anne, Xenarios Ioannis, Guisan Antoine, Sanders Ian R., Goudet Jerome, Guex Nicolas (2013), Density-based hierarchical clustering of pyro-sequences on a large scale-the case of fungal ITS1, in BIOINFORMATICS, 29(10), 1268-1274.
Plant species distributions along environmental gradients: Do belowground interactions with fungi matter?
Pellissier Loïc, Pinto-Figueroa Eric A., Niculita-Hirzel Hélène, Moora Mari, Villard Lucas, Goudét Jérôme, Guex Nicolas, Pagni Marco, Xenarios Loannis, Sanders Ian R., Guisan Antoine (2013), Plant species distributions along environmental gradients: Do belowground interactions with fungi matter?, in Frontiers in Plant Science, 4(DEC), 9p.
Soil fungal communities of grasslands are environmentally structured at a regional scale in the Alps
Pellissier Loïc, Niculita-Hirzel Hélène, Dubuis Anne, Pagni Marco, Guex Nicolas, Ndiribe Charlotte, Salamin Nicolas, Xénarios Ioannis, Goudét Jérôme, Sanders Ian R., Guisan Antoine (2013), Soil fungal communities of grasslands are environmentally structured at a regional scale in the Alps, in Molecular Ecology, 23(17), 4274-4290.
A framework for assessing the scale of influence of environmental factors on ecological patterns
Vicente J. Randin C.F. Pottier J. Gonçalves J. Broennimann O. Lomba A. Honrado J. Guisan A., A framework for assessing the scale of influence of environmental factors on ecological patterns, in Ecological Complexity .
Biotic interactions boost spatial models of species richness
Mod H.K. le Roux P.C. Guisan A. Luoto M., Biotic interactions boost spatial models of species richness, in Ecography.
What do we gain from simplicity versus complexity in species distribution models?
Merow C. Smith M.J. Edwards T.C. Guisan A. McMahon S. Normand S. Thuiller W. Wuest R. Zimmer, What do we gain from simplicity versus complexity in species distribution models?, in Ecography.

Zusammenarbeit

Gruppe / Person Land
Formen der Zusammenarbeit
Dr. M. Pagni & Prof. I. Xenarios, Swiss Institute of Bioinformatics - VITAL-IT platform, Lausanne Schweiz (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Forschungsinfrastrukturen
Prof. Ian Sanders & J. Goudet / DEE / University of Lausanne Schweiz (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Forschungsinfrastrukturen
Prof. E. Verecchia & Dr. Thierry Adatte, Earth Science Institute, GSE Faculty, UNIL Schweiz (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
- Forschungsinfrastrukturen

Wissenschaftliche Veranstaltungen

Aktiver Beitrag

Titel Art des Beitrags Titel des Artikels oder Beitrages Datum Ort Beteiligte Personen
International Society for Microbial Ecology, ISME 15 Poster Biogeography of Fungal communities along and environmental gradient in the Swiss Alps  24.08.2014 Seoul, Korea, Republik (Südkorea) Guisan Antoine; van der Meer Jan Roelof; Hirzel-Niculita Hélène; Pinto Eric;
International Society for Microbial Ecology, ISME 14 Poster Fungal barcoding along an altitudinal gradient 19.08.2014 Copenhagen, Dänemark Pinto Eric; van der Meer Jan Roelof; Guisan Antoine; Hirzel-Niculita Hélène;
International Society for Microbial Ecology, ISME 14 Poster Examination of the biases in soil bacterial and archaeal community analysis using paired-end Illumina sequencing (by E. Yashiro) 19.08.2014 copenhagen, Dänemark Guisan Antoine; van der Meer Jan Roelof; Hirzel-Niculita Hélène;
Eukaryotic-omics Symposium Vortrag im Rahmen einer Tagung Predicting the distribution of soil fungal amplicons on a changing planet  24.04.2014 Geneva, Schweiz Hirzel-Niculita Hélène; van der Meer Jan Roelof; Pinto Eric; Guisan Antoine;
Doctoral Program in Population Genomics Meeting 2014 Vortrag im Rahmen einer Tagung Environmental, edaphic drivers and spatial distribution of fungal communities 23.01.2014 Lausanne, Schweiz van der Meer Jan Roelof; Pinto Eric; Guisan Antoine; Hirzel-Niculita Hélène;
D-BSSE ETH-Zurich Einzelvortrag Fungal community analysis in the Swiss Alps 01.01.2014 Lausanne, Schweiz Pinto Eric; Hirzel-Niculita Hélène; van der Meer Jan Roelof; Guisan Antoine;
DMF department seminar Einzelvortrag Biogeography of alpine soil bacteria using ultra-high throughput sequencing (by E. Yashiro) 01.01.2014 Lausanne, Schweiz van der Meer Jan Roelof; Hirzel-Niculita Hélène; Guisan Antoine;
Symposium on Soil Metagenomics Poster Expanding the soil fungal diversity through barcoding and illumina paired-end of the ITS1 region 11.12.2013 Thünen, Deutschland van der Meer Jan Roelof; Guisan Antoine; Pinto Eric; Hirzel-Niculita Hélène; Buri Aline;
Thunen Soil Metagenomics Meeting Poster Soil bacterial biogeography in the western Swiss Alps (by E. Yashiro) 11.12.2013 Thünen, Deutschland Pinto Eric; Guisan Antoine; Hirzel-Niculita Hélène; van der Meer Jan Roelof;
Host-Associated Microbiota Poster Spatial distribution models for micro-organisms in the Swiss Alps 12.09.2012 Thünen, Deutschland Guisan Antoine; Buri Aline; Pinto Eric; van der Meer Jan Roelof; Hirzel-Niculita Hélène;
Host-Associated Microbiota Poster Soil bacterial biogeography in the western Swiss Alps (by E. Yashiro) 01.01.2012 Basel, Schweiz Hirzel-Niculita Hélène; van der Meer Jan Roelof; Guisan Antoine;
Swiss Microbiology Society annual meeting Poster Soil bacterial biogeography in the western Swiss Alps (by E. Yashiro) 01.01.2012 Fribourg, Schweiz Hirzel-Niculita Hélène; Pinto Eric; Guisan Antoine;
DMF department seminar by Dr. E. Yashiro Einzelvortrag Microbial biogeography in the Swiss Alps: Community analysis by high throughput sequencing 01.01.2012 Lausanne, Schweiz Hirzel-Niculita Hélène; van der Meer Jan Roelof; Guisan Antoine;


Selber organisiert

Titel Datum Ort
Introductory course to bash for biological data manipulations 17.11.2014 Lausanne, Schweiz
Retreat Symposium of ProDoc program 22.03.2013 Charmey, Schweiz

Veranstaltungen zum Wissenstransfer

Aktiver Beitrag

Titel Art des Beitrags Titel des Artikels oder Beitrages Datum Ort Beteiligte Personen
Mystères de l'UNIL 2014 (open doors at the University of Lausanne) 22.05.2014 University of Lausanne, Schweiz


Kommunikation mit der Öffentlichkeit

Kommunikation Titel Medien Ort Jahr
Medienarbeit: Radio, Fernsehen CQFD (27.02.2014) RTS 1ère Westschweiz 2014
Medienarbeit: Radio, Fernsehen CQFD (29.08.2014) RTS 1ère Westschweiz 2014
Referate/Veranstaltungen/Ausstellungen LabLife - exposition des 10 ans de la Faculté de Biologie et Médecine (Musée de la Main, Lausanne) Westschweiz 2014

Verbundene Projekte

Nummer Titel Start Förderungsinstrument
126393 Population Genomics 01.02.2010 ProDoc (Ausbildungsmodul, AM)

Abstract

Background. A project is currently under way that investigates community assembly and biotic interactions in mountain meadows communities, and how these could be integrated into predictions of species distributions. More than 900 plots were sampled for plants and among these >150 for butterflies and bumblebees across a 700 km2 mountainous study area in the Western Swiss Alps. Species traits and phylogeny data are additionally available for the >250 most abundant plant species and >130 butterfly species. This study should improve our understanding of how plant and insect communities assemble in geographic space, under current and future climate. In this context, soils were also surveyed in the same plant communities (2008-2009), resulting in soil being sampled in >250 distinct sites along a wide elevation gradient. For 205 of these soil samples, DNA extractions were conducted in addition to standard biogeochemical analyses, yielding a set of soil DNA samples of unprecedented large size. To our knowledge, no other dataset exists that is as exhaustive, and spatially-explicit at such very high spatial resolution (potentially <1m) and large extent (>700km2). Pyrosequencing of soil DNA is currently ongoing only for fungal communities, but other biotic groups could also be investigated.Aim. Here, we intend to extend the pyrosequencing of soil DNA to microbial communities and then test several hypotheses on the geographic distribution and ecology of fungal and microbial soil communities, and their relationship to macro-organisms (plants, insects). We intend more particularly to answer the main, still largely unanswered question: Do soil fungi and bacteria taxa exhibit biogeographic patterns? Or alternatively, are all taxa everywhere? If they do exhibit non-random geographic and environmental patterns, are these similar to those of macro-organisms? If similar, then how interdependent are distributions of micro- and macro-organisms? If distinct, then what factors are responsible for the divergence? And more specifically, which factors explains the distribution of microbial taxa in such mountain landscape? Do they affect - and if so how - the assembly of macro-organisms like plants? Finally, we will use all findings to assess the potential impact of climate and landuse changes on microbial communities.Methods. The DNA samples already extracted for the 205 2 m x 2 m plots described above will be used as initial input. A first PhD project (subproject 1) will focus on obtaining high-throughput sequencing data of bacterial communities, using high-depth phylogenetic analysis to obtain genus and species level classifications and microbial community composition. Together with data on fungal communities, it will then be to analyze their distribution and ecology with computer intensive bioinformatic and advanced statistical methods, in combination with vegetation composition, soil conditions, and topo-climatic and landuse characteristics. If needed, complementary field sampling may be performed. A second PhD project (subproject 2) will focus on developing a very high-resolution spatial modelling framework and use it to assess and predict the distribution of microbial operational taxonomic units and their assemblages under current and future climate. Funding requested. Funding is only requested for the PhD student of subproject 1 and for lab consumables including ultra high throughput sequencing. The second PhD student in subproject 2 will be entirely granted by UNIL as matching funds to this ProDoc project.Expected value of the proposed project. With this project, we aim at providing a better understanding of: (i) the biogeography and ecology of soil microorganisms, especially on factors - environmental or historic - shaping soil microbial communities in the Alps; (ii) the relation between soil microorganisms and plant species assemblages; (iii) how climate and land use changes may impact on micro-organisms distribution and communities. Coupled with results from the separate BioAssemble project (plants, soils, insects), these results will additionally be used to provide a comprehensive assessment of biodiversity distribution and ecosystem functioning in such mountain environments, with huge implications for assessing the sensitivity of these systems to ongoing anthropogenic global change.
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