PhD Project

Soils host a huge biodiversity, but our understanding of the organisms and their functions is still very limited. Soil organisms include microbes (archaea, bacteria, fungi) and fauna (protozoa, microarthropods, nematodes, oligochaeta). Soil organisms are small due to the small pore space of their habitat, they are extremely diverse due to their many functions and great heterogeneity of their habitats, and most organisms can not be cultured. This is especially true for the "microfauna" with less than 1 mm body size. However, recent progress in the molecular characterization of soil organisms offers the exciting prospect of exploring this hidden biodiversity which is so important for the functioning of our terrestrial ecosystems.

In the framework of the EU-project EcoFinders, my project investigates the diversity and functions of protozoa in soils, with special emphasis on amoeba.

Despite their functional importance, we have only a vague idea of the taxonomic identity and diversity of protozoan taxa in soil. For example amoebae repeatedly originated from very different protistan branches during the evolution of unicellular Eukaryotes. Naked amoebae are found in at least tree very distinct phyla: Amoebozoa, Cercozoa and Heterolobosea. The large evolutionary distance can explain the striking relative absence of Protists from eukaryote-targetted environmental studies: the "universal primers", mostly designed on fungal, plant and animal ribosomal sequences, cannot amplify such divergent groups. One aim of my studies is to identify the diversity of amoebae in soil by linking taxonomic and molecular methods. For this purpose I am developing methods for barcoding and high throughput sequencing of soil amoebae, but also for quantifying protozoa in soil by real-time qPCR.

EcoFinders
Ecological Function and Biodiversity Indicators in European Soils

Soil ecosystem services

Soils provide numerous essential ecosystem services such as:

• primary production (including agricultural and forestry products);
• regulation of biogeochemical cycles (with consequences for the climate);
• water filtration; resistance to diseases and pests;
• and regulation of above-ground biodiversity.

However, soils are subjected to many threats, so there is an urgent need to preserve this resource which is not renewable within Human time scale.

Perspectives

Scientific and technological knowledge on soil biodiversity and functioning in relation with the ecosystem services is required to define and adopt a Soil Framework Directive by the European Commission. This European project, coordinated by INRA, France, gathers together 23 partners from 10 European countries plus China, to harness expertise in ecology, biodiversity, environmental economy, modeling, bioinformatics and database management.