Environmental Soil Microbiology

Lots of digging. Lots of bioinformatics. Alpine soil is still a black box but now we better understand why. This line of research was initiated with the ANR project MicroAlpes (ANR-06-BLAN-0301) led by Roberto Gérémia.

  • Geremia, R. A., M. Pușcaș, L. Zinger, J.-M. Bonneville, and P. Choler. 2016. Contrasting microbial biogeographical patterns between anthropogenic subalpine grasslands and natural alpine grasslands. The New phytologist 209:1196-1207. [pdf]

  • Pansu, J., R. C. Winkworth, F. Hennion, L. Gielly, P. Taberlet, and P. Choler. 2015. Long-lasting modification of soil fungal diversity associated with the introduction of rabbits to a remote sub-Antarctic archipelago. Biology Letters 11.[pdf]

  • Pansu, J., S. De Danieli, J. Puissant, J.-M. Gonzalez, L. Gielly, T. Cordonnier, L. Zinger, J.-J. Brun, P. Choler, P. Taberlet, and L. Cecillon. 2015. Landscape-scale distribution patterns of earthworms inferred from soil DNA. Soil Biology & Biochemistry 83:100-105. [pdf]

  • Roy, J., C. H. Albert, S. Ibanez, P. Saccone, L. Zinger, P. Choler, J. C. Clement, S. Lavergne, and R. A. Geremia. 2013. Microbes on the cliff: alpine cushion plants structure bacterial and fungal communities. Frontiers in Microbiology 4:14. [pdf]

  • Taberlet, P., S. M. Prud'homme, E. Campione, J. Roy, C. Miquel, W. Shehzad, L. Gielly, D. Rioux, P. Choler, J. C. Clement, C. Melodelima, F. Pompanon, and E. Coissac. 2012. Soil Sampling and Isolation of Extracellular DNA from Large Amount of Starting Material Suitable for Metabarcoding Studies. Molecular Ecology 21:1816-1820. [pdf]

  • Bouasria, A., T. Mustapha, F. De Bello, L. Zinger, G. Lemperiere, R. A. Gérémia, and P. Choler. 2012. Effect of Plant Species Identity, Drought Stress and Defoliation on the Diversity of Bacterial and Fungal Communities Associated with Grass Roots. European Journal of Soil Biology 52:59-66. [pdf]

  • Shahnavaz, B., L. Zinger, S. Lavergne, P. Choler, and R. Geremia. in press. Phylogenetic Clustering Reveals Selective Events Driving the Turnover of Bacterial Community in Alpine Tundra Soils. Arctic, Antarctic, and Alpine Research 44:232-238. [pdf]

  • Lentendu, G., L. Zinger, S. Manel, E. Coissac, P. Choler, R. A. Geremia, and C. Melodelima. 2011. Assessment of Soil Fungal Diversity in Different Alpine Tundra Habitats by Means of Pyrosequencing. Fungal Diversity 49:113-123. DOI:10.1007/s13225-011-0101-5. [pdf]

  • Zinger, L., D. P. H. Lejon, F. Baptist, A. Bouasria, S. Aubert, R. A. Geremia, and P. Choler. 2011. Contrasting Diversity Patterns of Crenarchaeal, Bacterial and Fungal Soil Communities in an Alpine Landscape. Plos One 6: e19950. DOI:10.1371/journal.pone.0019950. [pdf]

  • Zinger, L., B. Shahnavaz, F. Baptist, R. A. Geremia, and P. Choler. 2009. Microbial diversity in alpine tundra soils correlates with snow cover dynamics. Isme Journal 3:850-859. DOI:10.1038/ismej.2009.20. [pdf]

  • Zinger, L., E. Coissac, P. Choler, and R. A. Geremia. 2009. Assessment of Microbial Communities by Graph Partitioning in a Study of Soil Fungi in Two Alpine Meadows. Applied and Environmental Microbiology 75:5863-5870. DOI:10.1128/aem.00748-09. [pdf]

  • Baptist, F., L. Zinger, J. C. Clement, C. Gallet, R. Guillemin, J.M.F. Martins, L. Sage, B. Shahnavaz, P. Choler, and R. Geremia. 2008. Tannin impacts on microbial diversity and the functioning of alpine soils: a multidisciplinary approach. Environmental Microbiology 10: 799–809. [pdf]

"You see, in this world there's two kinds of people, my friend... those with loaded guns, and those who dig. You dig...."
...a 2.5 m deep snowpack to collect soil samples in full winter.