Using metataxonomics to evaluate interactions between soil fauna and microorganism composition along an elevational gradient

<p>Almost 40% of terrestrial organisms depend directly or indirectly on soil during their life cycle. In particular, the soils of Alpine pastures have been managed for centuries and therefore, harbor specific soil fauna and microbial communities. In fact, the below-ground biomass in pastures is estimated to be much greater than the above-ground biomass, even including livestock. Excluding roots and algae, the below-ground biomass is mainly composed of microorganisms, which play a central role in fertility and carbon cycles. Moreover, soil bacteria and fungi interact with components of soil microfauna and mesofauna such as nematodes and collembolans, as well as soil macrofauna (i.e., earthworms, insects, spiders), and plants through the rhizosphere soil. To add to the complexity, each invertebrate taxa hosts its own microbiota, crucial for development, survival and reproduction,. &#160;Although many aspects of this biodiversity have already been described, the complex interactions between the microbiota of soil, rhizosphere soil, and soil fauna are almost unknown.</p><p>Given the importance of soil biodiversity for the sustainability of Alpine agro-ecosystems, and the possible impact of climate change scenarios on the complex network of interactions, there is an urgent need to fill the fundamental knowledge gap concerning microbial and soil fauna diversity, their composition, function and interaction in Alpine soils. Recent advances in next generation DNA sequencing technologies now make it possible to characterize the composition of microorganisms present in a soil, fecal or gut sample through the amplification and sequencing of the 16S rRNA bacterial and ITS fungal genes &#160;(&#8216;metataxonomics&#8217;). However, the comparison of microbiota composition of various matrices has been limited.</p><p>In MICROVALU: Evaluating microbiodiversity in alpine pastures (a EUREGIO - Interregional Project Network project), we optimized laboratory protocols that, for the first time, will allow the comparison of microbiota from different sample types. In three replicate sites, we sampled soil microfauna (nematodes), mesofauna (collembolans) and macrofauna (earthworms, ground beetles and rove beetles), as well as rhizosphere soil and fecal pellets deposited by wild mammals and domestic livestock. Sampling was repeated at four different altitudes (1000, 1500, 2000, 2500 m asl) to investigate how microclimate could effect microbiota interactions.&#160;</p><p>After metataxonomic and bioinformatics analysis, our results indicate that each soil type and faunal taxa has a unique microbiota, overlapping to different degrees depending on life cycle, as well as phylogenetic and tropic relationships. In combination with climatic and soil chemistry data, our results will an important step towards a more complete understanding of the relationships between soil organisms and their effect on soil processes.</p>