Bioinformatics matters: The accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline C Pauvert, M Buée, V Laval, V Edel-Hermann… – Fungal Ecology, 2019
Fungal communities associated with plants and soilinfluence plant fitness and ecosystem functioning. They are frequently studied by metabarcoding approaches targeting the ribosomal internal transcribed spacer (ITS), but there is no consensusconcerning the most appropriate bioinformaticapproach for the analysis of these data. We sequenced an artificial fungal community composed of 189 strainscovering a wide range of Ascomycota and Basidiomycota, to compare the performance of 360 software and parameter combinations. The most sensitive approaches, based on the USEARCH and VSEARCH clustering algorithms, detected almost all fungal strains but greatly overestimated the total number of strains. By contrast, approaches using DADA2 to detect amplicon sequence variants were the most effective for recovering the richness and composition of the fungal community. Our results suggest that analyzing single forward (R1) sequences with DADA2 and no filter other than the removal of low-quality and chimeric sequences is a good option for fungal community characterization.
Plant intraspecific variation modulates nutrient cycling through its belowground rhizospheric microbiome L Pérez‐Izquierdo, M Zabal‐Aguirre… – Journal of Ecology
1.Plant genetic variation, through its phenotypic display, can determine the composition of belowground microbial communities. Variation within a species is increasingly acknowledged to have substantial ecological consequences, particularly through trophic cascades. We hypothesised that the intraspecific genotypic variation of the tree host might impact the phylogenetic composition of its rhizospheric microbial communities, by favouring particular clades, that might be further reflected in ecosystem process rates.
2.We tested whether the intraspecific genotypic variation of Pinus pinastermodulates nutrient cycling by determining the phylogenetic structure of its symbiotic ectomycorrhizal fungi and rhizospheric bacteria. We sequenced fungal and bacterial molecular markers and reconstructed phylogenies in the rhizosphere of P. pinaster trees belonging to three genotypic variants (Mediterranean, Atlantic, African) in three 45‐year‐old common garden experiments, and measured seven soil enzymatic activities.
3.Local effects, based on differences in elevation and soil conditions across sites, were strong predictors of the ectomycorrhizal and bacterial communities thriving in tree’s rhizosphere. Across‐site variation also explained differences in phosphorus cycling. We detected, however, a significant effect of the plant genotype on the phylogenetic structure of the root‐associated microbiota that was consistent across sites.
4.The most productive Mediterranean plant genotype sheltered the most distinct root microbiome, with the dominant Basidiomycetes and Proteobacteria having a strong influence on the phylogenetic microbial community structure and associating with an enhanced hydrolysis of celluloses, hemicelluloses and chitin. Beneath the less productive Atlantic genotype, the less abundant Ascomycetes and up to thirteen bacterial phyla shaped the phylogenetic microbial structure, and predicted the rates of peptidase. Ectomycorrhizal fungi explained the activity of cellulases and protease, and bacteria that of hemicellulases and chitinase, suggesting functional complementarity.
5.Synthesis: This is the first report using three‐replicated long‐term common gardens in mature forests to disentangle plant genotype‐ and site‐specific drivers of the rhizospheric microbiome and its enzymatic potential. We concluded that intraspecific variation in primary producers leaves a phylogenetic signature in mutualists and decomposers that further modulate key steps in carbon and nitrogen cycles. These results emphasise the ecological relevance of plant intraspecific diversity in determining essential plant‐soil feedbacks that control ecosystem productivity and performance.
Is there a role for glutaredoxins and BOLAs in the perception of the cellular iron status in plants? P Rey, M Taupin-Broggini, J Couturier, F Vignols, N Rouhier Frontiers in Plant Science 10, 712
Glutaredoxins (GRXs) have at least three major identified functions. In apoforms, they exhibit oxidoreductase activity controlling notably protein glutathionylation/deglutathionylation. In holoforms, i.e. iron-sulfur (Fe-S) cluster-bridging forms, they act as maturation factors for the biogenesis of Fe-S proteins or as regulators of iron homeostasis contributing directly or indirectly to the sensing of cellular iron status and/or distribution. The latter functions seem intimately connected with the capacity of specific GRXs to form [2Fe-2S] cluster-bridging homodimeric or heterodimeric complexes with BOLA proteins. In yeast species, both proteins modulate the localization and/or activity of transcription factors regulating genes coding for proteins involved in iron uptake and intracellular sequestration in response notably to iron deficiency. Whereas vertebrate GRX and BOLA isoforms may display similar functions, the involved partner proteins are different. We perform here a critical evaluation of the results supporting the implication of both protein families in similar signaling pathways in plants and provide ideas and experimental strategies to delineate further their functions.
Rhodanese domain-containing sulfurtransferases: multifaceted proteins involved in sulfur trafficking in plants B Selles, A Moseler, N Rouhier, J Couturier. Journal of Experimental Botany
Sulfur is an essential element for the growth and development of plants that synthesize cysteine and methionine residues from the reductive assimilation of sulfate. Besides its incorporation into proteins, cysteine is the building block for the biosynthesis of numerous sulfur-containing molecules and cofactors. The required sulfur atoms are extracted either directly from cysteine by cysteine desulfurases or indirectly after its catabolic transformation in 3-mercaptopyruvate, a substrate for sulfurtransferases (STRs). Both enzymes are transiently persulfidated in their reaction cycle, i.e. the abstracted sulfur atom is bound to a reactive cysteine residue in the form of a persulfide group. Trans-persulfidation reactions occur when sulfur atoms are transferred to nucleophilic acceptors such as glutathione, proteins or small metabolites. STRs form a ubiquitous, multigenic protein family. They are characterized by the presence of at least one rhodanese homology domain (Rhd), that usually contains the catalytic, persulfidated cysteine. In this review, we focused on Arabidopsis thaliana STRs presenting the sequence characteristics of all family members as well as their biochemical and structural features. Then, the physiological functions of peculiar STRs in the biosynthesis of molybdenum cofactor, thio-modification of cytosolic tRNAs, arsenate tolerance, cysteine catabolism and hydrogen sulfide formation are discussed.
Novel insights into the diversity of the sulfurtransferase family in photosynthetic organisms with emphasis on oak A Moseler, B Selles, N Rouhier, J Couturier. New Phytologist
Sulfurtransferases (STRs) constitute a large and complex protein family characterized by the presence of a rhodanese domain and implicated in diverse molecular and signaling processes as sulfur carriers. Although sulfurtransferases are present in the three domains of life and share evolutionary relationships, a high variability exists at different levels including the protein length and active site sequence, the presence of an indispensable catalytic cysteine residue, the domain arrangement, and the subcellular localization. Because only Arabidopsis thaliana sequences have been inventoried so far, this paper aims at providing a detailed classification and evolutionary features of this family in photosynthetic organisms using comparative genomics focusing on the oak genome. Based on the expansion of STRs in higher photosynthetic organisms, we classified the STR family in nine clusters depending on their primary sequence and domain arrangement. We found that oak possesses at least one isoform in all defined clusters and that clusters IV, V and VI contain plant‐specific isoforms that are mostly located in chloroplasts. The novel classification proposed here provides the basis for functional genomics approaches in order to dissect the biochemical characteristics and physiological functions of individual STR representatives.
Functional, structural and biochemical features of plant serinyl-glutathione transferases E Sylvestre-Gonon, S Law, M Schwartz, K Robe, O Keech, … Frontiers in Plant Science 10, 608
Glutathione transferases (GSTs) belong to a ubiquitous multigenic family of enzymes involved in diverse biological processes including xenobiotic detoxification and secondary metabolism. A canonical GST is formed by two domains, the N-terminal one adopting a thioredoxin-fold and the C-terminal one an all-helical structure. The most recent genomic and phylogenetic analysis based on this domain organization allowed the classification of the GST family into 14 classes in terrestrial plants. These GSTs are further distinguished based on the presence of the ancestral cysteine (Cys-GSTs) present in thioredoxin family proteins or on its substitution by a serine (Ser-GSTs). Cys-GSTs catalyse the reduction of dehydroascorbate and deglutathionylation reactions whereas Ser-GSTs catalyse glutathione conjugation reactions and eventually have peroxidase activity, both activities being important for stress tolerance or herbicide detoxification. Through non-catalytic, so-called ligandin properties, numerous plant GSTs also participate in the binding and transport of small heterocyclic ligands such as flavonoids including anthocyanins, and polyphenols. So far, this function has likely been underestimated compared to the other documented roles of GSTs. In this review, we first inventoried Ser-GSTs in various photosynthetic organisms including algae, before describing their reported biochemical and structural characteristics and associated cellular functions.
New insights into black truffle biology: discovery of the potential connecting structure between a Tuber aestivum ascocarp and its host root A Deveau, P Clowez, F Petit, JP Maurice, F Todesco, C Murat, M Harroué, … Mycorrhiza, 1-8
According to isotopic labeling experiments, most of the carbon used by truffle (Tuber sp.) fruiting bodies to develop underground is provided by host trees, suggesting that trees and truffles are physically connected. However, such physical link between trees and truffle fruiting bodies has never been observed. We discovered fruiting bodies of Tuber aestivum adhering to the walls of a belowground quarry and we took advantage of this unique situation to analyze the physical structure that supported these fruiting bodies in the open air. Observation of transversal sections of the attachment structure indicated that it was organized in ducts made of gleba-like tissue and connected to a network of hyphae traveling across soil particles. Only one mating type was detected by PCR in the gleba and in the attachment structure, suggesting that these two organs are from maternal origin, leaving open the question of the location of the opposite paternal mating type.
Linking soil’s volatilome to microbes and plant roots highlights the importance of microbes as emitters of belowground volatile signals D Schenkel, A Deveau, J Niimi, P Mariotte, A Vitra, A Meisser, A Buttler, … Environmental microbiology
Plants and microbes release a plethora of volatiles that act as signals in plant–microbe interactions. Characterizing soil’s volatilome and microbiome might shed light on the nature of relevant volatile signals and on their emitters. This hypothesis was tested by characterizing plant cover, soil’s volatilome, nutrient content and microbiomes in three grasslands of the Swiss Jura Mountains. The fingerprints of soil’s volatiles were generated by solid‐phase micro‐extraction gas chromatography/mass spectrometry, whereas high‐throughput sequencing was used to create a snapshot of soil’s microbial communities. A high similarity was observed in plant communities of two out of three sites, which was mirrored by the soil’s volatilome. Multiple factor analysis evidenced a strong association among soil’s volatilome, plant and microbial communities. The proportion of volatiles correlated to single bacterial and fungal taxa was higher than for plants. This suggests that those organisms might be major contributors to the volatilome of grassland soils. These findings illustrate that key volatiles in grassland soils might be emitted by a handful of organisms that include specific plants and microbes. Further work will be needed to unravel the structure of belowground volatiles and understand their implications for plant health and development.
The structure of Trametes versicolorGlutathione Transferase Omega 3S bound to its conjugation product GS‐PEITC reveals plasticity of its active site M Schwartz, T Perrot, M Morel‐Rouhier, G Mulliert, E Gelhaye, … Protein Science
Trametes versicolor glutathione transferase Omega 3S (TvGSTO3S) catalyzes the conjugation of isothiocyanates (ITC) with glutathione (GSH). Previously, this isoform was investigated in depth both biochemically and structurally. Structural analysis of complexes revealed the presence of a glutathione binding site (G site) and a deep hydrophobic binding site (H site) able to bind plant polyphenols. In the present study, crystals of apo TvGSTO3S were soaked with GS‐PEITC, the product of the reaction between glutathione (GSH) and phenethyl‐isothiocyanate (PEITC). On the basis of this crystal structure, we show that the phenethyl moiety binds in a new site at loop β2‐α2 while the glutathionyl part exhibits a particular conformation that occupies both the G site and the entrance to the H site. This binding mode is allowed by a conformational change of the loop β2‐α2 at the enzyme active site. It forms a hydrophobic slit that stabilizes the phenethyl group at a distinct site from the previously described H site. Structural comparison of TvGSTO3S with drosophila DmGSTD2 suggests that this flexible loop could be the region that binds PEITC for both isoforms. These structural features are discussed in a catalytic context.
Megaphylogeny resolves global patterns of mushroom evolution T Varga, K Krizsán, C Földi, B Dima, M Sánchez-García, … Nature Ecology & Evolution, 1
Mushroom-forming fungi (Agaricomycetes) have the greatest morphological diversity and complexity of any group of fungi. They have radiated into most niches and fulfil diverse roles in the ecosystem, including wood decomposers, pathogens or mycorrhizal mutualists. Despite the importance of mushroom-forming fungi, large-scale patterns of their evolutionary history are poorly known, in part due to the lack of a comprehensive and dated molecular phylogeny. Here, using multigene and genome-based data, we assemble a 5,284-species phylogenetic tree and infer ages and broad patterns of speciation/extinction and morphological innovation in mushroom-forming fungi. Agaricomycetes started a rapid class-wide radiation in the Jurassic, coinciding with the spread of (sub)tropical coniferous forests and a warming climate. A possible mass extinction, several clade-specific adaptive radiations and morphological diversification of fruiting bodies followed during the Cretaceous and the Paleogene, convergently giving rise to the classic toadstool morphology, with a cap, stalk and gills (pileate-stipitate morphology). This morphology is associated with increased rates of lineage diversification, suggesting it represents a key innovation in the evolution of mushroom-forming fungi. The increase in mushroom diversity started during the Mesozoic-Cenozoic radiation event, an era of humid climate when terrestrial communities dominated by gymnosperms and reptiles were also expanding.