Microbial biogeography



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.


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.


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.


Eric Pinto (PhD student), Erika Yashiro (Post-Doc), Jan Roelof Van der Meer (Prof), Antoine Guisan (Prof)

Follow us:  
Biophore - CH-1015 Lausanne
Tel. +41 21 692 41 60
Fax +41 21 692 41 65