Protists in the soil food web of an arable field: Their density, taxonomic composition and functional role in carbon flux

Soil ecosystems are of fundamental importance for global carbon (C) cycling because they are the largest sinks and sources of terrestrial C. Therefore a detailed understanding of C fluxes through soil food webs is essential to predict ecosystem responses to anthropogenic CO2 enrichment of the atmosphere. Because organic C is also fundamental to the fertility of arable soils understanding of C cycling is inevitable to develop sustainable soil management strategies. Organic C enters the soil system via two different main routs: it is constantly released by plant roots in form of rhizodeposits and it enters the soil as dead organic matter (detritus). In both pathways C is directly acquired by diverse and highly active microorganisms. However, the C flux through microbial food webs is largely unknown predominantly due to the complex nature of trophic interactions. This PhD thesis is focusing on the functional role of protozoa in the rhizosphere and detritusphere of agricultural systems. Protozoa being at the base of soil food webs are assumed to be key-players in controlling the C flux from bacteria to higher trophic levels. Nevertheless the community composition in soil is largely unknown and the ecological importance of different protozoan taxa is even less understood. One aim of this thesis was to get deeper insights to the taxonomic composition and density of protozoan communities in arable soils. First the microbial food web was characterized at different soil depth and land management regimes. Further, the succession and functional roles of protozoan communities in controlling the flux of C in the rhizosphere and detritusphere was described in great detail and at high resolution. This study revealed highly dynamic and complex microbial food web interactions in soil and confirms the key-role of protozoa for the flow of C in agricultural soils

Disentangling carbon flow across microbial kingdoms in the rhizosphere of maize

Numerous 13CO2 labeling studies have traced the flow of carbon from fresh plant exudates into rhizosphere bacterial communities. However, the succession of the uptake of carbon leaving the roots by distinct rhizospheremicrobiota has rarely been resolved between microbial kingdoms. This can provide valuable insights on the niche partitioning of primary rhizodeposit consumption, as well as on community interactions in plant-derivedcarbon flows in soil. Here, we have traced the flow of fresh plant assimilates to rhizosphere microbiota of maize (Zea mays L.) by rRNA-stable isotope probing (SIP). Carbon flows involving bacteria, unicellular fungi, as well asprotists were observed over 5 and 8 days. Surprisingly, labeling of Paraglomerales and several bacteria including Opitutus, Mucliaginibacter and Massilia spp. was especially apparent in soil surrounding the strict rhizosphere after 5 d. This highlights the central role of arbuscular mycorrhizal fungi (AMF) as a shunt for fresh plant assimilates to soil microbes not directly influenced by root exudation. Distinct trophic webs involving different flagellates, amoeba and ciliates were also observed in rhizosphere and surrounding soil, while labeling of filamentous saprotrophic Ascomycota or Basidiomycota was not apparent. This challenges the proposed “sapro-rhizosphere” concept and demonstrates the utility of rRNA-SIP to disentangle inter-kingdom microbial relationships in the rhizosphere