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Cropping systems based on carefully designed species mixtures reveal many potential advantages in terms of enhancing crop productivity, reducing pest and diseases, and enhancing ecological services. Associating cereals and legume production either through intercropping or rotations might be a relevant strategy of producing both type of culture, while benefiting from combined nitrogen fixed by the legume through its symbiotic association with nitrogen-fixing bacteria, and from a better use of P and water through mycorrhizal associations. These practices also participate to the diversification of agricultural productions, enabling to secure the regularity of income returns across the seasonal and climatic uncertainties. In this context, we designed a field experiment aiming to estimate the 2 years impact of these practices on wheat yield and on soil microbial activities as estimated through Substrate Induced Respiration method and mycorrhizal soil infectivity (MSI) measurement. It is expected that understanding soil microbial functionalities in response to these agricultural practices might allows to target the best type of combination, in regard to crop productivity. We found that the tested cropping systems largely impacted soil microbial functionalities and MSI. Intercropping gave better results in terms of crop productivity than the rotation practice after two cropping seasons. Benefits resulting from intercrop should be highly linked with changes recorded on soil microbial functionalities.

Soil fungi associated with plant roots, notably ectomycorrhizal (EcM) fungi, are central in above- and below-ground interactions in Mediterranean forests. They are a key component in soil nutrient cycling and plant productivity. Yet, major disturbances of Mediterranean forests, particularly in the Southern Mediterranean basin, are observed due to the greater human pressures and climate changes. These disturbances highly impact forest cover, soil properties and consequently the root-associated fungal communities. The implementation of efficient conservation strategies of Mediterranean forests is thus closely tied to our understanding of root-associated fungal biodiversity and environmental rules driving its diversity and structure. In our study, the root-associated fungal community of Q. suber was analyzed using high-throughput sequencing across three major Moroccan cork oak habitats. Significant differences in root-associated fungal community structures of Q. suber were observed among Moroccan cork oak habitats (Maâmora, Benslimane, Chefchaoun) subjected to different human disturbance levels (high to low disturbances, respectively). The fungal community structure changes correlated with a wide range of soil properties, notably with pH, C:N ratio (P = 0.0002), and available phosphorus levels (P = 0.0001). More than 90 below-ground fungal indicators (P < 0.01)-either of a type of habitat and/or a soil property-were revealed. The results shed light on the ecological significance of ubiquitous ectomycorrhiza (Tomentella, Russula, Cenococcum), and putative sclerotia-associated/ericoid mycorrhizal fungal taxa (Cladophialophora, Oidiodendron) in the Moroccan cork oak forest, and their intraspecific variability regarding their response to land use and soil characteristics.

Understanding the prevalence and polymorphism of antibiotic resistance genes in soil bacteria and their potential to be transferred horizontally is required to evaluate the likelihood and ecological (and possibly clinical) consequences of the transfer of these genes from transgenic plants to soil bacteria. In this study, we combined culture-dependent and -independent approaches to study the prevalence and diversity of bla genes in soil bacteria and the potential impact that a 10-successive-year culture of the transgenic Bt176 corn, which has a blaTEM marker gene, could have had on the soil bacterial community. The bla gene encoding resistance to ampicillin belongs to the beta-lactam antibiotic family, which is widely used in medicine but is readily compromised by bacterial antibiotic resistance. Our results indicate that soil bacteria are naturally resistant to a broad spectrum of beta-lactam antibiotics, including the third cephalosporin generation, which has a slightly stronger discriminating effect on soil isolates than other cephalosporins. These high resistance levels for a wide range of ntibiotics are partly due to the polymorphism of bla genes, which occur frequently among soil bacteria. The blaTEM116 gene of the transgenic corn Bt176 investigated here is among those frequently found, thus reducing any risk of introducing a new bacterial resistance trait from the transgenic material. In addition, no significant differences were observed in bacterial antibiotic-resistance levels between transgenic and nontransgenic corn fields, although the bacterial populations were different.

Cooperation involving Plant Growth-Promoting Rhizobacteria results in improvements of plant growth and health. While pathogenic and symbiotic interactions are known to induce transcriptional changes for genes related to plant defense and development, little is known about the impact of phytostimulating rhizobacteria on plant gene expression. This study aims at identifying genes significantly regulated in rice roots upon Azospirillum inoculation, considering possible favored interaction between a strain and its original host cultivar. Genome-wide analyzes of Oryza sativa japonica cultivars Cigalon and Nipponbare were performed, by using microarrays, seven days post-inoculation with Azospirillum lipoferum 4B (isolated from Cigalon) or Azospirillum sp. B510 (isolated from Nipponbare) and compared to the respective non-inoculated condition. A total of 7384 genes were significantly regulated, which represent about 16% of total rice genes. A set of 34 genes is regulated by both Azospirillum strains in both cultivars, including a gene orthologous to PR10 of Brachypodium, and these could represent plant markers of Azospirillum-rice interactions. The results highlight a strain-dependent response of rice, with 83% of the differentially expressed genes being classified as combination-specific. Whatever the combination, most of the differentially expressed genes are involved in primary metabolism, transport, regulation of transcription and protein fate. When considering genes involved in response to stress and plant defense, it appears that strain B510, a strain displaying endophytic properties, leads to the repression of a wider set of genes than strain 4B. Individual genotypic variations could be the most important driving force of rice roots gene expression upon Azospirillum inoculation. Strain-dependent transcriptional changes observed for genes related to auxin and ethylene signaling highlight the complexity of hormone signaling networks in the Azospirillum-rice cooperation.

Despite the strong ecological importance of ectomycorrhizal (ECM) fungi, their vertical distribution remains poorly understood. To our knowledge, ECM structures associated with trees have never been reported in depths below 2 meters. In this study, fine roots and ECM root tips were sampled down to 4-m depth during the digging of two independent pits differing by their water availability. A meta-barcoding approach based on Illumina sequencing of internal transcribed spacers (ITS1 and ITS2) was carried out on DNA extracted from root samples (fine roots and ECM root tips separately). ECM fungi dominated the root-associated fungal community, with more than 90% of sequences assigned to the genus Pisolithus. The morphological and barcoding results demonstrated, for the first time, the presence of ECM symbiosis down to 4-m. The molecular diversity of Pisolithus spp. was strongly dependent on depth, with soil pH and soil water content as primary drivers of the Pisolithus spp. structure. Altogether, our results highlight the importance to consider the ECM symbiosis in deep soil layers to improve our understanding of fine roots functioning in tropical soils.

Background This work aimed at characterizing 12 isolates of the genus Tuber including Tuber melanosporum (11 isolates) and Tuber brumale (one isolate). This was done using internal transcribed spacer (ITS) sequences, confirming their origin. Results Analysis of their mating type revealed that both MAT1 - 1 and MAT1 - 2 exist within these isolates (with 3 and 8 of each, respectively). We observed that each of these cultures was consistently associated with one bacterium that was intimately linked to fungal growth. These bacterial associates failed to grow in the absence of fungus. We extracted DNA from bacterial colonies in the margin of mycelium and sequenced a nearly complete 16S rDNA gene and a partial ITS fragment. We found they all belonged to the genus Rhodopseudomonas , fitting within different phylogenetic clusters. No relationships were evidenced between bacterial and fungal strains or mating types. Rhodopseudomonas being a sister genus to Bradyrhizobium , we tested the nodulation ability of these bacteria on a promiscuously nodulating legume ( Acacia mangium ), without success. We failed to identify any nif H genes among these isolates, using two different sets of primers. Conclusions While the mechanisms of interaction between Tuber and Rhodopseudomonas remain to be elucidated, their interdependency for in vitro growth seems a novel feature of this fungus.

Climate change may impose severe challenges to coffee farmers to maintain agricultural production levels especially in smallholder farmers, who produce 90% Uganda’s coffee. In Uganda, Robusta coffee, which accounts for 80% of the total coffee production is predicted to be significantly affected. Climate adaptation and mitigation measures are required to moderate some of the worst predicted scenarios. Agroforestry has been highlighted as a cost-effective and sustainable strategy for modulating the effects of climate change in coffee farms given its contribution to carbon sequestration, reducing greenhouse gas emissions, diversification of tree and forest products, and reduction in the susceptibility of land-use systems to extreme weather events, among others. However, various research gaps need to be addressed, for deriving optimal benefits from agroforestry for climate change adaptation and mitigation in coffee. Paradoxically, while nearly all Robusta coffee is historically conducted using agroforestry methods, the growing negative view of the role of trees, especially the possibility of shade tree species serving as a reservoir for pests calls for concerted research efforts to guide the promotion of agroforestry methods to curb the development of monocultures. The review, therefore, highlights; (i) current knowledge relating to agroforestry tree choice, (ii) knowledge on above/below-ground interactions between trees and Robusta coffee from plot to landscape scales, and (iii) research areas that need to be addressed for building climate resilient Robusta coffee agroforestry (CAF) systems. Selecting appropriate agroforestry tree species and managing above and below-ground resources appear to be key factors for optimizing Robusta coffee production, but most of the information is missing in the context of Uganda’s Robusta coffee-agroforestry systems. In the face of climate change that is likely to affect the biophysical environments and social structures, approaching the research activities through living laboratories, to collaboratively co-create, develop, and test new technologies, products and services in real-life environments could yield more practical solutions.

BACKGROUND AND AIMS: Plant growth is frequently limited by the availability of inorganic phosphorus (P) in the soil. In most soils, a considerable amount of the soil P is bound to organic molecules. Of these, phytate is the most abundant identifiable organic P form, but is not readily available to plants. In contrast, microorganisms have been shown to degrade phytate with high efficiency. The current study aims to characterize the members of the phytate-hydrolysing bacterial community in rhizosphere, and the molecular and enzymatic ability of these bacteria to degrade phytate. METHODS AND RESULTS: The phytate-hydrolysing bacterial community was characterized from the rhizosphere of plants cultivated in the presence or absence of phytate supplementation. Major changes in the bacterial community structure were observed with both culture-dependent and -independent methods, which highlighted the predominance of Proteobacteria and Actinobacteria. Phytase activity was detected for a range of rhizobacterial isolates as well as the presence of, β-propeller phytases (BPP) for both isolates and directly in a soil sample. CONCLUSION: A wide taxonomic range of functional phytate utilizers have been discovered, in soil bacterial taxa that were previously not well known for their ability to utilise phytate as P or C sources. This study provides new insights into microbial carbon and phosphorus cycling in soil.

The intensification of biological processes coping with salt stress became a major issue to mitigate land degradation. The Sine-Saloum Delta in Senegal is characterized by salt-affected soils with vegetation dominated by salt-tolerant grass Sporobolus robustus and shrubs like Prosopis juliflora. Plant experiments in controlled conditions suggested that arbuscular mycorrhizal (AM) fungi might be the key actors of facilitation process observed between S. robustus and P. juliflora, but the AM fungal community determinants are largely unknown. The current field-based study aimed at (1) characterizing the environmental drivers (rhizosphere physico-chemical properties, plant type and season) of the AM fungal community along an environmental gradient and (2) identifying the AM fungal taxa that might explain the S. robustus–mediated benefits to P. juliflora. Glomeraceae predominated in the two plants, but a higher richness was observed for S. robustus. The pH and salinity were the main drivers of AM fungal community associated with the two plants, negatively impacting richness and diversity. However, while a negative impact was also observed on mycorrhizal colonization for S. robustus, P. juliflora showed opposite colonization patterns. Furthermore, no change was observed in terms of AM fungal community dissimilarity between the two plants along the environmental gradient as would be expected according to the stress-gradient and complementary hypotheses when a facilitation process occurs. However, changes in intraspecific diversity of shared AM fungal community between the two plants were observed, highlighting 23 AM fungal OTUs associated with both plants and the highest salinity levels. Consequently, the increase of their abundance and frequency along the environmental gradient might suggest their potential role in the facilitation process that can take place between the two plants. Their use in ecological engineering could also represent promising avenues for improving vegetation restoration in saline Senegalese’s lands.

Background and aims Plant-bacterial interactions in the rhizosphere are important in mediating soil nutrient transformations. Plants supply carbon-rich substrates to rhizobacteria as root exudates and bacteria mobilise soil-bound phosphate for plant nutrition. This study aimed to probe the specificity of the plant effect on bacterial gene expression in P-starved rhizosphere conditions. Methods DNA microarrays were employed to study gene expression in the rhizosphere of Lolium perenne grown under high and low phosphate regimes (330 μM vs. 3–6 μM phosphate). Root exudation under these regimes was also quantified. Phosphate-regulated gene expression of a panel of 22 genes was compared in rhizosphere, planktonic culture and during biofilm growth on an artificial root. Results Plant growth and root exudation were affected by P-availability. P-limited conditions induced increased expression of bacterial genes of an aromatic degradation pathway (catA), heavy metal sensing (PA2523), and membrane proteins (glpM, crcB), while genes involved in cell motility and amino acid uptake/ metabolism were downregulated. A crcB mutant was impaired in rhizosphere survival under low phosphate conditions, though glpM and catA mutants were not affected. Several of the genes studied were induced by phosphate limitation in all three lifestyles studied. Conclusions Our results show the importance of the plant-microbe interaction in controlling the bacterial transcriptional response in a phosphate-limited rhizosphere.