A Comprehensive Insight of Current and Future Challenges in Large-Scale Soil Microbiome Analyses.

In the last decade, various large-scale projects describing soil microbial diversity across large geographical gradients have been undertaken. However, many questions remain unanswered about the best ways to conduct these studies. In this review, we present an overview of the experience gathered during these projects, and of the challenges that future projects will face, such as standardization of protocols and results, considering the temporal variation of microbiomes, and the legal constraints limiting such studies. We also present the arguments for and against the exhaustive description of soil microbiomes. Finally, we look at future developments of soil microbiome studies, notably emphasizing the important role of cultivation techniques.

Surprising low diversity of the plant pathogen Phytophthora in Amazonian forests.

The genus Phytophthora represents a group of plant pathogens with broad global distribution. The majority of them cause the collar and root-rot of diverse plant species. Little is known about Phytophthora communities in forest ecosystems, especially in the Neotropical forests where natural enemies could maintain the huge plant diversity via negative density dependence. We characterized the diversity of soil-borne Phytophthora communities in the North French Guiana rainforest and investigated how they are structured by host identity and environmental factors. In this little-explored habitat, 250 soil cores were sampled from 10 plots hosting 10 different plant families across three forest environments (Terra Firme, Seasonally Flooded and White Sand). Phytophthora diversity was studied using a baiting approach and metabarcoding (High-Throughput Sequencing) on environmental DNA extracted from both soil samples and baiting-leaves. These three approaches revealed very similar communities, characterized by an unexpected low diversity of Phytophthora species, with the dominance of two cryptic species close to Phytophthora heveae. As expected, the Phytophthora community composition of the French Guiana rainforest was significantly impacted by the host plant family and environment. However, these plant pathogen communities are very small and are dominated by generalist species, questioning their potential roles as drivers of plant diversity in these Amazonian forests.

Phenotyping Thermal Responses of Yeasts and Yeast-like Microorganisms at the Individual and Population Levels: Proof-of-Concept, Development and Application of an Experimental Framework to a Plant Pathogen.

Deciphering the responses of microbial populations to spatiotemporal changes in their thermal environment is instrumental in improving our understanding of their eco-evolutionary dynamics. Recent studies have shown that current phenotyping protocols do not adequately address all dimensions of phenotype expression. Therefore, these methods can give biased assessments of sensitivity to temperature, leading to misunderstandings concerning the ecological processes underlying thermal plasticity. We describe here a new robust and versatile experimental framework for the accurate investigation of thermal performance and phenotypic diversity in yeasts and yeast-like microorganisms, at the individual and population levels. In addition to proof-of-concept, the application of this framework to the fungal wheat pathogen Zymoseptoria tritici resulted in detailed characterisations for this yeast-like microorganism of (i) the patterns of temperature-dependent changes in performance for four fitness traits; (ii) the consistency in thermal sensitivity rankings of strains between in planta and in vitro growth assessments; (iii) significant interindividual variation in thermal responses, with four principal thermotypes detected in a sample of 66 strains; and (iv) the ecological consequences of this diversity for population-level processes through pairwise competition experiments highlighting temperature-dependent outcomes. These findings extend our knowledge and ability to quantify and categorise the phenotypic heterogeneity of thermal responses. As such, they lay the foundations for further studies elucidating local adaptation patterns and the effects of temperature variations on eco-evolutionary and epidemiological processes.

The rhizosphere of a drought-tolerant plant species in Morocco: A refuge of high microbial diversity with no taxon preference.

Arid and semi-arid areas are facing increasingly severe water deficits that are being intensified by global climate changes. Microbes associated with plants native to arid regions provide valuable benefits to plants, especially in water-stressed environments. In this study, we used 16S rDNA metabarcoding analysis to examine the bacterial communities in the bulk soil, rhizosphere and root endosphere of the plant Malva sylvestris L. in Morocco, along a gradient of precipitation. We found that the rhizosphere of M. sylvestris did not show significant differences in beta-diversity compared to bulk soil, although, it did display an increased degree of alpha-diversity. The endosphere was largely dominated by the genus Rhizobium and displayed remarkable variation between plants, which could not be attributed to any of the variables observed in this study. Overall, the effects of precipitation level were relatively weak, which may be related to the intense drought in Morocco at the time of sampling. The dominance of Rhizobium in a non-leguminous plant is particularly noteworthy and may permit the utilization of this bacterial taxon to augment drought tolerance; additionally, the absence of any notable selection of the rhizosphere of M. sylvestris suggests that it is not significatively affecting its soil environment.

Multicomponent synthesis of unsymmetrical unsaturated N-heterocyclic carbene precursors and their related transition-metal complexes.

A low-cost, modular, and easily scalable multicomponent procedure affording access in good yields and excellent selectivity (up to 93%) to a wide range of (a)chiral unsymmetrical 1-aryl-3-cycloalkyl-imidazolium salts is disclosed. Electronic and steric properties of the corresponding unsymmetrical unsaturated N-heterocyclic carbene (U2-NHC) ligands were evaluated and evidenced strong electron donor ability, high steric discrimination, and modular steric demand.

Combining two-directional synthesis and tandem reactions: new access to 3,5-disubstituted pyrrolizidines and first total synthesis of alkaloid cis-223B.

Two new tandem reactions for the synthesis of 3,5-disubstituted pyrrolizidines and the first total synthesis of alkaloid cis-223B (in 7 steps and 43% overall yield), involving a double cross metathesis and double Michael addition as key steps, are presented.

Two-directional cross-metathesis.

Two-directional cross-metathesis of a range of alpha,omega dienes with a variety of electron deficient alkenes has been accomplished. It was found that the process is quite general and gives complete selectivity for the E,E-dienes, making this a very useful and high yielding protocol for two-directional chain elongation.

Two-directional ring-opening cross-metathesis.

Two-directional ring-opening cross-metathesis of a range of cyclic alkenes with a variety of electron deficient alkenes has been accomplished; it was found that the process is quite general and gives complete selectivity for the E,E-dienes, making this a very useful and high-yielding protocol for two-directional chain synthesis.

Nitrone [2+3]-cycloadditions in stereocontrolled synthesis of a potent proteasome inhibitor: (-)-omuralide.

A new stereocontrolled synthetic route to omuralide has been developed from methyl pyroglutamate. This route involves regio- and stereoselective N-methylnitrone 1,3-dipolar cycloadditions to appropriate pyrrolinones, beta-eliminations, and highly selective hydrogenations as the main steps.

Liquid-phase synthesis of polyhydroquinoline using task-specific ionic liquid technology.

A new strategy for the synthesis of polyhydroquinolines from task-specific ionic liquids (TSIL) as a soluble support was developed. The preparation of the polyhydroquinolines by a three-component reaction was achieved by using ionic liquid-phase bound beta-oxo esters. These starting functionalized esters were synthesized by a solventless transesterification without catalyst under microwave irradiation. The structure of the intermediates in each step was verified routinely by spectroscopic analysis, and after oxidation of the polyhydroquinolines grafted on the TSIL with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone or after cleavage (transesterification, saponification-acidification), the target compounds were obtained in good yields and high purities.