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The occurrence of Pseudomonas aeruginosa was monitored at a broad spatial scale in French agricultural soils, from various soil types and under various land uses to evaluate the ability of soil to be a natural habitat for that species. To appreciate the impact of agricultural practices on the potential dispersion of P. aeruginosa, we further investigated the impact of organic amendment at experimental sites in France and Burkina Faso. A real-time quantitative PCR (qPCR) approach was used to analyze a set of 380 samples selected within the French RMQS (“Réseau de Mesures de la Qualité des Sols”) soil library. In parallel, a culture-dependent approach was tested on a subset of samples. The results showed that P. aeruginosa was very rarely detected suggesting a sporadic presence of this bacterium in soils from France and Burkina Faso, whatever the structural and physico-chemical characteristics or climate. When we analyzed the impact of organic amendment on the prevalence of P. aeruginosa, we found that even if it was detectable in various manures (at levels from 103 to 105 CFU or DNA targets (g drywt)−1 of sample), it was hardly ever detected in the corresponding soils, which raises questions about its survival. The only case reports were from a vineyard soil amended with a compost of mushroom manure in Burgundy, and a few samples from two fields amended with raw urban wastes in the sub-urban area of Ouagadougou, Burkina Faso. In these soils the levels of culturable cells were below 10 CFU (g drywt)−1.

Droplet digital PCR (ddPCR) allows absolute quantification and tolerance to inhibitors and has been proposed as the method of choice to overcome limitations of qPCR. The aim of this study was to evaluate ddPCR and qPCR performances to detect low copy number and copy number variation of antibiotic resistance genes (sul1 and qnrB genes encoding for resistance to sulfonamides and quinolones, respectively) using bacterial genomic DNA (gDNA) and metagenomic DNA extracted from soil and organic residue samples. With gDNA, qPCR showed a better range of quantification but the lower limit of quantification was at 15 copies of qnrB target vs. 1.6 in ddPCR. In the presence of background DNA or inhibitors, we observed a high loss of sensitivity in qPCR and an overestimation of target sequences. When using high amount of environmental DNA templates (70 ng per reaction), ddPCR was still allowing accurate quantification without adding PCR facilitator (i.e., T4 Gene 32 protein). Sensitivity to detect copy number variation was tenfold higher in ddPCR than in qPCR. Finally, the advantages of using ddPCR in environmental studies were confirmed with the quantification of sul1 and qnrB in soils, manures, or urban wastes.

Aims: To develop a qPCR approach for the detection of Pseudomonas aeruginosa in soil and manure and explore its efficacy and limitations compared with that of a classical culture-dependent approach. Methods and Results: A Ps. aeruginosa ecfX qPCR assay was developed. This assay was optimized for soils of contrasting physico-chemical properties and evidenced a three-log dynamic range of detection [5 9 10 4 -5 9 10 6 cells (g drywt soil)À1

Erratum paru dans Agroforestry Systems = ISSN 0167-4366. - (2015)vol.89:n°1 p. 95-96. In Sudano-Sahelian agriculture, organic amendments are often limited by resource availability. Small branches (ramial wood, RW) represent an organic resource found in many landscapes but little is known about their effects. This field trial (2007-2009) studied the effects of RW or straw at low application rate (0.69 Mg C ha?1 year?1) on topsoil carbon (C), nitrogen (N) and available phosphorus (P, Pav), termite cast abundance, and sorghum yield. Straw and RW were chopped and either buried (StBu, WoBu) or mulched (StMu, WoMu). Mineral fertilizers were added to straw so that RW- and straw-amended plots received similar applications of C, N, P, and potassium. Another treatment had RW buried with additional N (WoBuN), and there was a control (Ctrl). Branches came from Piliostigma reticulatum, very common in the area. The treatments had little significant effect on topsoil and crop, owing to the low application rate and spatial variability. However, Pav was significantly lower with buried than mulched amendments in 2009, and decreased significantly over time in Ctrl and with buried amendments. Topsoil C also decreased significantly with time in WoMu. Significantly more termite casts were observed with RW. The sorghum yield averaged 0.87 Mg DM ha?1 in 2007 and then decreased. The treatments affected yield significantly in 2008 only: it was higher in WoBuN and StBu than in Ctrl. In 2009, the yield was mainly affected by initial topsoil Pav. These results suggest that RW stimulated biological activity, leading to P immobilization and C mineralization, but had little effect on yields. (Résumé d'auteur

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Restoring degraded soils to support food production is a major challenge for West African smallholders who have developed local innovations to counter further degradation. The objective of this study was to evaluate a local farmer's technique that uses ramial wood (RW) as soil amendment (Piliostigma reticulatum shrub). Three treatments were applied in an experimental plot in Burkina Faso: control (no amendment), low RW (3 Mg fresh mass·ha−1·yr−1), and high RW (12 Mg fresh mass·ha−1·yr−1). RW was chipped to <5‐cm pieces and either buried or mulched. Topsoil carbon (C), nitrogen (N), and phosphorus (P) in control and low‐RW treatments declined after 7 years of continuous sorghum cultivation. Use of high‐RW amendment stabilized soil C content while N and P declined, thus not replenishing nutrient exports. Net contribution to soil C in the layer measuring 0–15 cm was 15% of the applied C in the high‐RW amendments. Although biomass and grain yields were higher in high‐RW treatments, crop productivity declined throughout the experiment for all treatments. Termite casts on RW treatments evidenced the potential role of wood‐foraging termites in diluting the impact of RW on soil fertility build‐up and soil water content. We conclude that mitigating soil degradation under semiarid conditions in Burkina Faso would require large amounts of woody amendments, particularly if the level of termite activity is high. Additional nutrient sources would be needed to compensate for removal in exported products so that biomass and grain production can be stabilized or increased.

Dynamique des compartiments du carbone et de l'azote dans le sol cultivé en niébé et sorgho dans le système zaï en zone Nord soudanienne du Burkina Faso RESUME La gestion appropriée des sols cultivés peut permettre un stockage de carbone, en plus de l'avantage supplémentaire du maintien du niveau de fertilité qui en résulte. L'objectif de cette étude est d'appréhender l'influence réelle de pratiques culturales sous niébé ou sorgho dans le système zaï, sur l'évolution et l'organisation des teneurs de carbone (C) et d'azote (N) du sol à l'échelle de la parcelle. Un dispositif factoriel en blocs de Fisher a été utilisé. Les traitements comprenant des apports de fumier seul ou associé au burkina phosphate avec exportation des résidus de cultures ont été testés. Le fractionnement granulométrique de la matière organique du sol a été utilisé, séparant trois fractions. Les résultats révèlent que la répartition de C et N dans les fractions granulométriques n'a pas été affectée par les espèces cultivées. Quelle que soit la culture, le carbone et l'azote se trouvent essentiellement sous forme de matière organique stable dans la fraction 0-20 µm, soit respectivement 64% et 73% pour C et N. L'apport du fumier seul ou combiné au phosphate, entraîne une augmentation de la matière organique labile ; 38% de C et 31% de N sont stockés dans la fraction 50-2000 µm. La dynamique de la matière organique du sol à l'échelle de la parcelle est plus influencée par les amendements que par les espèces cultivées.