Summary• Here we characterized the effect of the ectomycorrhizal symbiosis on the genotypic and functional diversity of soil Pseudomonas fluorescens populations and analysed its possible consequences in terms of plant nutrition, development and health.• Sixty strains of P. fluorescens were isolated from the bulk soil of a forest nursery, the ectomycorrhizosphere and the ectomycorrhizas of the Douglas fir ( Pseudostuga menziesii ) seedlings-Laccaria bicolor S238N. They were characterized in vitro with the following criteria: ARDRA, phosphate solubilization, siderophore, HCN and AIA production, genes of N 2 -fixation and antibiotic synthesis, in vitro confrontation with a range of phytopathogenic and ectomycorrhizal fungi, effect on the Douglas fir-L. bicolor symbiosis.• For most of these criteria, we demonstrated that the ectomycorrhizosphere significantly structures the P. fluorescens populations and selects strains potentially beneficial to the symbiosis and to the plant.• This prompts us to propose the ectomycorrhizal symbiosis as a true microbial complex where multitrophic interactions take place. Moreover it underlines the fact that this symbiosis has an indirect positive effect on plant growth, via its selective pressure on bacterial communities, in addition to its known direct positive effect.

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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.

Nine isolates from Argyrolobium uniflorum, Lotus creticus, Medicago sativa (Tunisia) and Lotus arabicus (Senegal) were analysed by multilocus sequence analysis (MLSA) of five housekeeping genes (recA, atpD, glnA, gltA and thrC), the 16S rRNA gene and the nodulation gene nodA. Analysis of the individual and concatenated gene sequences demonstrated that the nine new strains constituted three stable, well-supported (bootstrap and gene sequence similarity values) monophyletic clusters, A, B and C, all belonging to the branch of the genus Ensifer, regardless of the phylogenetic reconstruction method used (maximum likelihood, maximum-parsimony, neighbour-joining). The three groups were further characterized by API 100 auxanographic tests, host specificity and nodA gene sequence analysis. On the basis of these data, clusters A and C are suggested as representing two novel species within the genus Ensifer, for which the names Ensifer numidicus sp. nov. (type strain ORS 1407T=LMG 24690T=CIP 109850T) and Ensifer garamanticus sp. nov. (type strain ORS 1400T=LMG 24692T=CIP 109916T) are proposed. The cluster B strains were assigned to Ensifer adhaerens genomovar A.

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Nodulated legume trees comprised 43% of the stand basal area in the low, most frequently flooded microsites, and 23% in higher, drier microsites in a tropical freshwater swamp forest in French Guiana. Dinitrogen fixation in Pterocarpus officinalis, Hydrochorea corymbosa and Inga pilosula was confirmed by acetylene reduction assay (ARA), presence of leghaemoglobin in nodules and the N-15 natural abundance method. The results for Zygia cataractae were inconclusive but suggested N-2 fixation in drier microsites. Nodulated Inga disticha had a N-15-to-N-14 ratio similar to non-N-2-fixing trees, but ARA indicated nitrogenase activity and leghaemoglobin was present in nodules. All bacterial strains were identified as Bradyrhizobium spp. according to the partial 16S rDNA sequences, and they were infective in vitro in the model species Macroptilium atropurpuretan. About 35-50% of N in the leaves of P. officinalis, H. corymbosa and I. pilosula was fixed from the atmosphere. Dinitrogen fixation was estimated to contribute at least 8-13% and 1728% to whole-canopy N in high and low microsites, respectively. Symbiotic N, fixation appears to provide both a competitive advantage to legume trees under N-limited, flooded conditions and an important N input to neotropical freshwater swamp forests

Little is known regarding how the increased diversity of nitrogen-fixing bacteria contributes to the productivity and diversity of plants in complex communities. However, some authors have shown that the presence of a diverse group of nodulating bacteria is required for different plant species to coexist. A better understanding of the plant symbiotic organism diversity role in natural ecosystems can be extremely useful to define recovery strategies of environments that were degraded by human activities. This study used ARDRA, BOX-PCR fingerprinting and sequencing of the 16S rDNA gene to assess the diversity of root nodule nitrogen-fixing bacteria in former bauxite mining areas that were replanted in 1981, 1985, 1993, 1998, 2004 and 2006 and in a native forest. Among the 12 isolates for which the 16S rDNA gene was partially sequenced, eight, three and one isolate(s) presented similarity with sequences of the genera Bradyrhizobium, Rhizobium and Mesorhizobium, respectively. The richness, Shannon and evenness indices were the highest in the area that was replanted the earliest (1981) and the lowest in the area that was replanted most recently (2006).

Inga edulis Mart. is a tropical legume tree used for shade in coffee and cacao plantations and as a hedgerow in alley-cropping practices. Little information can be found concerning N 2 fixation in this species. This study was conducted to characterize the rhizobia of I. edulis and determine if it is capable of fixing substantial amounts of N 2 . Four strains of fast-growing, Gram-negative rhizobia-type bacteria were isolated from I. edulis nodules. The strains were identified by sequencing of partial 16S-23S rDNA internal spacer region. Nitrogenase activity was determined using acetylene reduction assay (ARA). Dinitrogen fixation was measured under controlled conditions by the 15 N isotope dilution technique using two non-N 2 -fixing reference species, Vochysia guatemalensis Donn. Sm, and Gmelina arborea Roxb. ex. Sm. Seedlings were grown in three growth media: native soil and naturally N-depleted sand amended to a low and high N level. The four strains of symbiotic bacteria were closely related to Bradyrhizobium japonicum and to Bradyrhizobium liaoningense. Nodules demonstrated nitrogenase activity as measured by ARA. Vochysia guatemalensis was a better non-N 2 -fixing reference than G. arborea. When V. guatemalensis was used as the non-N 2 -fixing reference, the estimate of the percentage of N fixed from atmosphere out of total N in I. edulis seedlings was ca. 40% in the two sand media treatments and 10% in the native soil.