The impact of the rice production system (irrigated vs lowland) on root-associated microbiome from farmer's fields in western Burkina Faso.

Due to their potential applications for food safety, there is a growing interest in rice root-associated microbial communities, but some systems remain understudied. Here, we compare the assemblage of root-associated microbiota in rice sampled in 19 small farmer's fields from irrigated and rainfed lowlands in Burkina Faso, using an amplicon metabarcoding approach of the 16S rRNA gene (prokaryotes, three plant samples per field) and ITS (fungi, one sample per field). In addition to the expected structure by root compartments (root vs rhizosphere) and geographical zones, we showed that the rice production system is a major driver of microbiome structure. In irrigated systems, we found a higher diversity of prokaryotic communities from the rhizosphere and more complex co-occurrence networks, compared to rainfed lowlands, while fungal communities exhibited an opposite pattern (higher richness in rainfed lowlands). Core taxa were different between the two systems, and indicator species were identified: mostly within Bacillaceae in rainfed lowlands, and within Burkholderiaceae and Moraxellaceae in irrigated areas. Finally, a higher abundance in rainfed lowlands was found for mycorrhizal fungi (both compartments) and rhizobia (rhizosphere only). Our results highlight deep microbiome differences induced by contrasted rice production systems that should consequently be considered for microbial engineering applications.

Soil-microorganism-mediated invasional meltdown in plants.

While most alien species fail to establish, some invade native communities and become widespread. Our understanding of invasion success is derived mainly from pairwise interactions between aliens and natives, while interactions among more than two species remain largely unexplored. Here, we experimentally tested whether and how a third plant species, either native or alien, affected the competitive outcomes between alien and native plants through its soil legacy. We first conditioned soil with one of ten species (six natives and four aliens) or without plants. We then grew on these 11 soils five aliens and five natives without competition, or with intra- or interspecific competition. We found that aliens were not more competitive than natives when grown on soil conditioned by other natives or on non-conditioned soil. However, aliens were more competitive than natives on soil conditioned by other aliens (that is, invasional meltdown). Soil conditioning did not change competitive outcomes by affecting the strength of competition between later plants. Instead, soil conditioned by aliens pushed competitive outcomes towards later aliens by affecting the growth of aliens less negatively than that of natives. Microbiome analysis verified this finding, as we showed that the soil-legacy effects of a species on later species were less negative when their fungal endophyte communities were less similar, and that fungal endophyte communities were less similar between two aliens than between aliens and natives. Our study reveals invasional meltdown in multispecies communities and identifies soil microorganisms as a driver of the invasion success of alien plants.

Evidence for Elton's diversity-invasibility hypothesis from belowground.

Sixty year ago, Charles Elton posed that species-rich communities should be more resistant to biological invasion. Still, little is known about which processes could drive the diversity-invasibility relationship. Here we examined whether soil-microbe-mediated apparent competition on alien invaders is more negative when the soil originates from multiple native species. We trained soils with five individually grown native species and used amplicon sequencing to analyze the resulting bacterial and fungal soil communities. We mixed the soils to create trained soils from one, two or four native species. We then grew four alien species separately on these differently trained soils. In the soil-conditioning phase, the five native species built species-specific bacterial and fungal communities in their rhizospheres. In the test phase, it did not matter for biomass of alien plants whether the soil had been trained by one or two native species. However, the alien species achieved 11.7% (95% CI: 3.7-20.1%) less aboveground biomass when grown on soils trained by four native species than on soils trained by two native species. Our results revealed soil-microbes-mediated apparent competition as a mechanism underlying the negative relationship between diversity and invasibility.

Environmental Drivers of Microbial Functioning in Mediterranean Forest Soils.

Mediterranean forests own distinct characteristics resulting from climate, soil, and vegetation that affect soil microbial communities' assembly and their associated functions. We initiated a multi-scalar analysis of environmental drivers of soil functioning to (1) identify pertinent factorial scales and (2) determine the relative importance of soil, vegetation, and geoclimate influences in shaping soil microbial functions across the French Mediterranean forests. Soil samples (0-15 cm) were collected from 60 forest sites and soil physicochemical and microbiological properties were assessed across different factorial scales i.e., bioclimates, slope exposures, and forest stands. Patterns in microbial catabolic potential (i.e., extracellular enzymes and microbial respiration) and carbon (C) source utilization (i.e., catabolic-level physiological profiling) were partitioned between vegetation cover, soil characteristics, and geoclimate components. Our results reveal that the catabolic potential of soil microbes was strongly influenced by the forest stands and mainly relied on ammonium and nitrate contents. In contrast, variation in C source utilization was mainly explained by vegetation cover. Soil metabolic capacities of microorganisms and resulting C dynamics were largely constrained by climate parameters, which suggests potentially important consequences for soil C storage. Our study revealed diverse structuration patterns between the catabolic potential and the carbon source utilization of soil microbial communities, and gives insights into the underlying mechanisms of soil microbial functioning in Mediterranean forests.

Towards Unraveling Macroecological Patterns in Rhizosphere Microbiomes.

It is generally accepted that plants locally influence the composition and activity of their rhizosphere microbiome, and that rhizosphere community assembly further involves a hierarchy of constraints with varying strengths across spatial and temporal scales. However, our knowledge of rhizosphere microbiomes is largely based on single-location and time-point studies. Consequently, it remains difficult to predict patterns at large landscape scales, and we lack a clear understanding of how the rhizosphere microbiome forms and is maintained by drivers beyond the influence of the plant. By synthesizing recent literature and collating data on rhizosphere microbiomes, we point out the opportunities and challenges offered by advances in molecular biology, bioinformatics, and data availability. Specifically, we highlight the use of exact sequence variants, coupled with existing and newly generated data to decipher the rules of rhizosphere community assembly across large spatial and taxonomic scales.

Responses of Rhizospheric Microbial Communities of Native and Alien Plant Species to Cuscuta Parasitism.

Parasitic plants have major impacts on host fitness. In the case of species of the holoparasitic Cuscuta genus, these impacts were shown to be particularly strong in some invasive alien plants, which has raised interest in the underlying mechanism. We hypothesized that Cuscuta parasitization may exert strong influence in shaping the diversity patterns in the host rhizosphere microbiome and that this may vary between native (coevolved) and alien (non-coevolved) plants. Here, we report on a field study exploring the effect of parasitization by Cuscuta australis on the rhizosphere microbiota (16S and ITS rDNA) of four plant species sharing and three plant species not sharing the parasite's native range. Despite a predominant role of the host species in shaping the rhizosphere microbiota, the role of host origin and of parasitization still appeared important in structuring microbial communities and their associated functions. Bacterial communities were more strongly influenced than fungi by the native range of the host plant, while fungi were slightly more affected than bacteria by parasitization. About 7% of bacterial phylotypes and 11% of fungal phylotypes were sensitive to Cuscuta parasitization. Parasitization also reduced the abundance of arbuscular mycorrhizal fungi by ca. 18% and of several genes related to plant growth promoting functions (e.g., nitrogen metabolism and quorum sensing). Both fungi and bacteria differentially responded to host parasitization depending on host origin, and the extent of these shifts suggests that they may have more dramatic consequences for alien than for native plants.

Infrared spectroscopy as a useful tool to predict land use depending on Mediterranean contrasted climate conditions: A case study on soils from olive-orchards and forests.

Soil chemical properties depend on various environmental factors such as above ground vegetation, climate and the parent rock substratum. Land use, and the associated management practices, is one of the major drivers which can deeply impact soil properties. To better understand the dynamics of soil chemical properties and to assess potential impact of land use, an improved monitoring of chemical signature in organo-mineral topsoils is necessary. Here, we explored how land use (forests or agrosystems i.e. olive-tree orchards) may shape soil chemical signature and whether it depends i) on the type of agricultural or sylvicultural practices, ii) on contrasted Mediterranean climate conditions at different spatial scales. We measured variations in soils properties by FTIR-ATR (Fourier-Transformed Infrared - Attenuated Total Reflectance) spectroscopy and elemental concentrations. FTIR showed that the aromatic fraction of organic matter and CaCO3 discriminated soils under different land uses (orchards or forests) and this depended on climate (sub-humid vs humid climate). Moreover, the chemical signatures of soils varied with the practices applied. For agrosystems, soils complemented with olive-mill wastes were characterized by aromatics compared to soils under natural grass or tillage. For forests, soils from Pinus spp. stands and Quercus spp. stands were discriminated by CaCO3 and aromatics respectively. Contrasted climate conditions at local scale, i.e. northern vs southern slopes for forests and distance from the sea (coastal vs inland area) for agrosystems, had an effect on soil chemical signature. The AcomDIM interpretation of FTIR-ATR signals showed that factors "land use", "practices" and "climate" and their interactions could have a significant impact on soil chemical signature. PLS modeling also confirmed that FTIR-ATR is a useful tool to predict a type of land use depending on climate.

Additive or non-additive effect of mixing oak in pine stands on soil properties depends on the tree species in Mediterranean forests.

This study investigated how oak abundance in pine stands (using relative Oak Basal Area %, OBA%) may modulate soil microbial functioning. Forests were composed of sclerophyllous species i.e. Quercus ilex mixed with Pinus halepensis Miller or of Q. pubescens mixed with P. sylvestris. We used a series of plots with OBA% ranging from 0 to 100% in the two types of stand (n=60) and both OLF and A-horizon compartments were analysed. Relations between OBA% and either soil chemical (C and N contents, quality of organic matter via solid-state NMR, pH, CaCO3) or microbial (enzyme activities, basal respiration, biomass and catabolic diversity via BIOLOG) characteristics were described. OBA% increase led to a decrease in the recalcitrant fraction of organic matter (OM) in OLF and promoted microbial growth. Catabolic profiles of microbial communities from A-horizon were significantly modulated in Q. ilex and P. halepensis stand by OBA% and alkyl C to carboxyl C ratio (characteristic of cutin from Q. ilex tissues) and in Q. pubescens and P. sylvestris stands, by OBA% and pH. In A-horizon under Q. ilex and P. halepensis stands, linear regressions were found between catabolic diversity, microbial biomass and OBA% suggesting an additive effect. Conversely, in A-horizon Q. pubescens and P. sylvestris stands, the relationship between OBA% and either cellulase activities, polysaccharides or ammonium contents, suggested a non-additive effect of Q. pubescens and P. sylvestris, enhancing mineralization of the OM labile fraction for plots characterized by an OBA% ranging from 40% to 60%. Mixing oak with pine thus favored microbial dynamics in both type of stands though OBA% print varied with tree species and consequently sustainable soil functioning depend strongly on the composition of mixed stands. Our study indeed revealed that, when evaluating the benefits of forest mixed stand on soil microbial functioning and OM turnover, the identity of tree species has to be considered.

Importance of competition mechanisms in successive invasions by polyphagous tephritids in La Reunion.

Understanding the strength and modes of interspecific interactions between introduced and resident species (native or previously introduced) is necessary to predict invasion success. We evaluated different mechanisms of interspecific competition among four species of polyphagous fruit flies (Diptera: Tephritidae) from the island of La Reunion: one endemic species, Ceratitis catoirii, and three exotic species, C. capitata, C. rosa, and Bactrocera zonata, that have successively invaded the island. Larval competition experiments, i.e., co-infestations of the same fruit, and behavioral interference experiments measuring the ability of one female to displace another from a fruit, were performed among all pairs of the four species. We observed asymmetric and hierarchical interactions among species in both larval and adult interference competition. In agreement with the hypothesis that invasion is competition-limited, the competitive hierarchy coincided with the temporal sequence of establishment on the island, i.e., each newly established species tended to be competitively dominant over previously established ones.