In production of cereals like maize ( Zea mays L.) and barley ( Hordeum vulgare L.), seeds are often treated with pesticides and/or commercial products of plant beneficial microorganisms (PBM) to reduce possible root damage from insect pests and soil borne root diseases. In a field experiment with maize and barley under conservation agriculture, we examined how such seed treatments affected the resident root and soil microbiota. The seed treatments included a pesticide mixture and different commercial products of common PBM based on the biocontrol agents (BCA) Trichoderma harzianum and Metarhizium anisopliae alone and in combination and a mix of plant growth promoting rhizobacteria (PGPR), which were compared to a negative control without seed treatment. Soil and root samples were taken at two and three sampling times during the crop cycles for barley and maize, respectively, to measure root biomass, root colonization with mycorrhizal fungi and pathogens, soil microbial communities at a general taxonomic level using biomarker fatty acids, and ecological guilds of soil nematodes. Root health was monitored with observations of the presence of insect feeding larvae and root disease symptoms, which in general showed healthy roots during the full crop cycle. Overall, most of the root and soil biota variables measured changed during the crop cycle. However, for both crops, the seed treatments had no effects on the soil and root microbiota measured, except in the case of barley root infection with Polymyxa sp., which was reduced by all treatments. In conclusion, the pesticide and PBM seed treatments evaluated in the present study for maize and barley under conservation agriculture, in general, had limited effects on the resident root and soil microbiota. However, future studies should include complementary high-resolution sequencing methods when examining non-target effects of pesticides and microbial inoculants on the root and soil microbiota.

Millet/cowpea intercropping is a promoted practice in Sub-Saharan agriculture. However, because cowpea is known as a host for plant-parasitic nematodes that may also infect millet, we examined whether intercropping may increase the risk of nematode-mediated millet damage, and if this risk may be controlled by organic amendments. In twelve Senegalese farmers' fields which had been either non-manured or regularly manured over the past 10 years at least, we assessed the effects of intercropping millet and cowpea on the abundance of free-living and plant-parasitic nematodes, ecological indices, and land equivalent ratios (LER). Six fields were manured, and six non-manured. Each field included four plots: millet and cowpea as pure stands, and two plots with millet intercropped with cowpea sown at two densities. Soil nematofauna was evaluated before sowing and at cowpea flowering. Soil nematofauna was dominated by plant-parasitic nematodes. Before manure application and crop sowing, regularly manured fields had higher structure indices of nematofauna than non-manured ones, and Pratylenchus was almost absent. At crop flowering, abundance of Pratylenchus increased and was drastically higher in pure cowpea (149 individuals 100 g(-1) dry soil) than in intercropping and pure millet (18 and 17 individuals 100 g(-1) dry soil, respectively), regardless of the manuring regime. Manuring had significant positive effects on various bacterivorous families, on fungivorous and plant-parasitic trophic groups, but not on Pratylenchus. Millet and cowpea yields of manured fields were the highest, regardless of cropping pattern. LER averaged 1.7 and 1.5 in manured and non-manured intercropping, respectively. Regardless of the treatments, ecological indices indicated that the soil food web was undisturbed, with moderate enrichment, and suppressive against crop pests. Intercropping millet with cowpea, even in poorly manured fields and with high cowpea density, constitutes an appropriate way to improve productivity without increasing Pratylenchus pressure in nutrient-poor soils of central Senegal.