Bacterivores, mostly represented by protists and nematodes, are a key component of soil biodiversity involved in soil fertility and plant productivity. In the current context of global change and soil biodiversity erosion, it becomes urgent to suitably recognize and quantify their ecological importance in ecosystem functioning.

Priming effect (PE) is defined as a stimulation of the mineralization of soil organic matter (SOM) following a supply of fresh organic matter. This process can have important consequences on the fate of SOM and on the management of residues in agricultural soils, especially in tropical regions where soil fertility is essentially based on the management of organic matter. Earthworms are ecosystem engineers known to affect the dynamics of SOM. Endogeic earthworms ingest large amounts of soil and assimilate a part of organic matter it contains. During gut transit, microorganisms are transported to new substrates and their activity is stimulated by (i) the production of readily assimilable organic matter (mucus) and (ii) the possible presence of fresh organic residues in the ingested soil. The objective of our study was to see (i) whether earthworms impact the PE intensity when a fresh residue is added to a tropical soil and (ii) whether this impact is linked to a stimulation/inhibition of bacterial taxa, and which taxa are affected. A tropical soil from Madagascar was incubated in the laboratory, with a ¹³C wheat straw residue, in the presence or absence of a peregrine endogeic tropical earthworm, Pontoscolex corethrurus. Emissions of ¹²CO₂ and ¹³CO₂ were followed during 16 days. The coupling between DNA-SIP (stable isotope probing) and pyrosequencing showed that stimulation of both the mineralization of wheat residues and the PE can be linked to the stimulation of several groups especially belonging to the Bacteroidetes phylum.

Conventional agriculture strongly alters soil quality due to industrial practices that often have negative effects on soil life. Alternative systems such as conservation agriculture and organic farming could restore better conditions for soil organisms. Improving soil life should in turn improve soil quality and farming sustainability. Here, we have compared for the first time the long-term effects of conservation agriculture, organic farming, and conventional agriculture on major soil organisms such as microbes, nematofauna, and macrofauna. We have also analyzed functional groups. Soils were sampled at the 14-year-old experimental site of La Cage, near Versailles, France. The microbial community was analyzed using molecular biology techniques. Nematofauna and macrofauna were analyzed and classified into functional groups. Our results show that both conservation and organic systems increased the abundance and biomass of all soil organisms, except predaceous nematodes. For example, macrofauna increased from 100 to 2,500 %, nematodes from 100 to 700 %, and microorganisms from 30 to 70 %. Conservation agriculture showed a higher overall improvement than organic farming. Conservation agriculture increased the number of many organisms such as bacteria, fungi, anecic earthworms, and phytophagous and rhizophagous arthropods. Organic farming improved mainly the bacterial pathway of the soil food web and endogeic and anecic earthworms. Overall, our study shows that long-term, no-tillage, and cover crops are better for soil biota than periodic legume green manures, pesticides, and mineral fertilizers.