The rhizosphere microbiota of the zinc and cadmium hyperaccumulators Arabidopsis halleri and Noccaea caerulescens is highly convergent in Prayon (Belgium)

The Prayon site is known as a zinc-polluted area where two zinc and cadmium hyperaccumulator plant species currently coexist, although Arabidopsis halleri was introduced more recently than Noccaea caerulescens . While soil microorganisms may influence metal uptake, the microbial community present in the rhizosphere of hyperaccumulators remains poorly known. Plants of both species were sampled with their bulk and rhizosphere soil from different plots of the Prayon site. Soil components (ionome, pH, water composition, temperature) were analyzed, as well as shoot ionome and expression levels of metal transporter genes ( HMA3 , HMA4 , ZIP4 / ZNT1 , ZIP6 , MTP1 ). The taxonomic diversity of the microorganisms in soil samples was then determined by 16S rRNA metabarcoding and compared at the Operational Taxonomy Unit (OTU) level and across different taxonomic levels. Our elemental analyses confirmed that the site is still highly contaminated with zinc and cadmium and that both plant species indeed hyperaccumulate these elements in situ . Although the pollution is overall high, it is heterogenous at the site scale and correlates with the expression of some metal transporter genes. Metabarcoding analyses revealed a decreasing gradient of microbial diversity, with more OTUs discovered in the rhizosphere than in the soil bulk, especially at the bottom of the cores. However, the variability gradient increases with the distance from roots. Using an ad hoc pseudo-taxonomy to bypass the biases caused by a high proportion of unclassified and unknown OTUs, we identified Chloroflexi, Armatimonadetes, Pirellulaceae, Gemmatimonadetes and Chitinophagaceae as the drivers of the differences in the gradient along the cores. In contrast, no significant difference was identified between the rhizosphere composition of A. halleri and N. caerulescens . This suggests that, despite their distinct colonization history in Prayon, the two plant species have now recruited highly convergent microbial communities in the rhizosphere

Growth and metal bioconcentration by conspecific freshwater macroalgae cultured in industrial waste water

The bioremediation of industrial waste water by macroalgae is a sustainable and renewable approach to the treatment of waste water produced by multiple industries. However, few studies have tested the bioremediation of complex multi-element waste streams from coal-fired power stations by live algae. This study compares the ability of three species of green freshwater macroalgae from the genus Oedogonium, isolated from different geographic regions, to grow in waste water for the bioremediation of metals. The experiments used Ash Dam water from Tarong power station in Queensland, which is contaminated by multiple metals (Al, Cd, Ni and Zn) and metalloids (As and Se) in excess of Australian water quality guidelines. All species had consistent growth rates in Ash Dam water, despite significant differences in their growth rates in “clean” water. A species isolated from the Ash Dam water itself was not better suited to the bioremediation of that waste water. While there were differences in the temporal pattern of the bioconcentration of metals by the three species, over the course of the experiment, all three species bioconcentrated the same elements preferentially and to a similar extent. All species bioconcentrated metals (Cu, Mn, Ni, Cd and Zn) more rapidly than metalloids (As, Mo and Se). Therefore, bioremediation in situ will be most rapid and complete for metals. Overall, all three species of freshwater macroalgae had the ability to grow in waste water and bioconcentrate elements, with a consistent affinity for the key metals that are regulated by Australian and international water quality guidelines. Together, these characteristics make Oedogonium a clear target for scaled bioremediation programs across a range of geographic regions

Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes

International audienceBackground: Transposable elements (TEs) are genomic parasites with major impacts on host genome architecture and host adaptation. A proper evaluation of their evolutionary significance has been hampered by the paucity of short scale phylogenetic comparisons between closely related species. Here, we characterized the dynamics of TE accumulation at the micro-evolutionary scale by comparing two closely related plant species, Arabidopsis lyrata and A. halleri. Results: Joint genome annotation in these two outcrossing species confirmed that both contain two distinct populations of TEs with either 'recent' or 'old' insertion histories. Identification of rare segregating insertions suggests that diverse TE families contribute to the ongoing dynamics of TE accumulation in the two species. Orthologous TE fragments (i.e. those that have been maintained in both species), tend to be located closer to genes than those that are retained in one species only. Compared to non-orthologous TE insertions, those that are orthologous tend to produce fewer short interfering RNAs, are less heavily methylated when found within or adjacent to genes and these tend to have lower expression levels. These findings suggest that long-term retention of TE insertions reflects their frequent acquisition of adaptive roles and/or the deleterious effects of removing nearly neutral TE insertions when they are close to genes. Conclusion: Our results indicate a rapid evolutionary dynamics of the TE landscape in these two outcrossing species, with an important input of a diverse set of new insertions with variable propensity to resist deletion

Metal accumulation in tobacco expressing Arabidopsis halleri metal hyperaccumulation gene depends on external supply

Engineering enhanced transport of zinc to the aerial parts of plants is a major goal in bio-fortification. In Arabidopsis halleri, high constitutive expression of the AhHMA4 gene encoding a metal pump of the P1B-ATPase family is necessary for both Zn hyperaccumulation and the full extent of Zn and Cd hypertolerance that are characteristic of this species. In this study, an AhHMA4 cDNA was introduced into N. tabacum var. Xanthi for expression under the control of its endogenous A. halleri promoter known to confer high and cell-type specific expression levels in both A. halleri and the non-hyperaccumulator A. thaliana. The transgene was expressed at similar levels in both roots and shoots upon long-term exposure to low Zn, control, and increased Zn concentrations. A down-regulation of AhHMA4 transcript levels was detected with 10 μM Zn resupply to tobacco plants cultivated in low Zn concentrations. In general, a transcriptional regulation of AhHMA4 in tobacco contrasted with the constitutively high expression previously observed in A. halleri. Differences in root/shoot partitioning of Zn and Cd between transgenic lines and the wild type were strongly dependent on metal concentrations in the hydroponic medium. Under low Zn conditions, an increased Zn accumulation in the upper leaves in the AhHMA4-expressing lines was detected. Moreover, transgenic plants exposed to cadmium accumulated less metal than the wild type. Both modifications of zinc and cadmium accumulation are noteworthy outcomes from the biofortification perspective and healthy food production. Expression of AhHMA4 may be useful in crops grown on soils poor in Zn

Tandem quadruplication of HMA4 in the zinc (Zn) and cadmium (Cd) hyperaccumulator noccaea caerulescens

Zinc (Zn) and cadmium (Cd) hyperaccumulation may have evolved twice in the Brassicaceae, in Arabidopsis halleri and in the Noccaea genus. Tandem gene duplication and deregulated expression of the Zn transporter, HMA4, has previously been linked to Zn/Cd hyperaccumulation in A. halleri. Here, we tested the hypothesis that tandem duplication and deregulation of HMA4 expression also occurs in Noccaea. A Noccaea caerulescens genomic library was generated, containing 36,864 fosmid pCC1FOSTM clones with insert sizes ~20–40 kbp, and screened with a PCR-generated HMA4 genomic probe. Gene copy number within the genome was estimated through DNA fingerprinting and pooled fosmid pyrosequencing. Gene copy numbers within individual clones was determined by PCR analyses with novel locus specific primers. Entire fosmids were then sequenced individually and reads equivalent to 20-fold coverage were assembled to generate complete whole contigs. Four tandem HMA4 repeats were identified in a contiguous sequence of 101,480 bp based on sequence overlap identities. These were flanked by regions syntenous with up and downstream regions of AtHMA4 in Arabidopsis thaliana. Promoter-reporter b-glucuronidase (GUS) fusion analysis of a NcHMA4 in A. thaliana revealed deregulated expression in roots and shoots, analogous to AhHMA4 promoters, but distinct from AtHMA4 expression which localised to the root vascular tissue. This remarkable consistency in tandem duplication and deregulated expression of metal transport genes between N. caerulescens and A. halleri, which last shared a common ancestor >40 mya, provides intriguing evidence that parallel evolutionary pathways may underlie Zn/Cd hyperaccumulation in Brassicaceae

Development of a bioinformatic tool for the treatment of WGS data for dermatophytes typing and characterization: Focus on squalene epoxidase mutations and terbinafine resistance.

peer reviewedObjectives: The present work aims to use the Whole Genome Sequencing (WGS) as a tool to characterize dermatophytes strains. Data generated by WGS are analyzed by using a bioinformatic tool called “WGS typer” and several markers are highlighted, such as genes implicated in resistance to antifungals or genes linked with high virulence in dermatophytes. The tool will also permit to analyze dermatophytes following their genetic diversity and provide similarity dendrograms. The present work focus on squalene epoxidase (SQLE) gene characterization among T. rubrum and T. indotineae strains by the WGS typer. Material and methods: 15 strains of T. rubrum (7 resistant to terbinafine and 8 susceptible) and 19 strains of T. indotineae (8 resistant to terbinafine and 11 susceptible) from a multicenter study, previously characterized by Eucast E.Def.11.0 method (Arendrup et al., 2020) were used for SQLE characterization by WGS.WGS has been performed by the GIGA genomics platform using the Illumina technology. The WGS Typer is a commercial bioinformatics tool developed by Hedera-22 (http://www.hedera22.com) and licensed to the Department of Clinical Microbiology of the University of Liège. This tool enables high-throughput typing of pathogen isolates based on raw sequencing data and a collection of relevant markers (single genes, gene variants, gene clusters, MLST). The analysis reports the presence/absence of targeted markers or genotypes from a sequence homology search against the assembled sequencing data according to a set of sequence identity/coverage thresholds. Results: We evaluated the ability of the tool to detect mutations in the SQLE gene that are responsible for terbinafine resistance in dermatophytes. Seven T. rubrum showed a resistant profile to terbinafine (MIC values >0.25µg/µl) with the microdilution method. Among these, four shared the F397L mutation on SQLE, one was wearing L393F mutation while two other shared the L393S mutation. All these mutations were efficiently highlighted by the WGS typer. Among the eight strains presenting a MIC value under 0.25µg/µl, no mutation was found on SQLE gene. Regarding T. indotineae, 8 strains were previously characterized to be resistant to terbinafine with the microdilution method (MIC values >0,25µg/µl). Among them, the WGS typer detected seven strains with the mutation F397L and one strain with the mutation L393F on the SQLE gene. Among the eleven strains presenting a MIC value under 0.25µg/µl by microdilution, no mutation was found on SQLE. The study was completed with genetic similarity comparisons and dendrogram creation. No clear separation into clusters was observed between resistant/susceptible strains neither in the T. rubrum group nor in the T. indotineae group. T. rubrum and T. indotineae species were well separated into two distinct clusters. Conclusion: We present here a valuable and innovative tool for the analysis of dermatophytes. The tool permits to easily and accurately detect mutations on the SQLE gene responsible for terbinafine resistance. A dendrogram of similarity based on WGS data can also be generated

Genomics of Divergence along a Continuum of Parapatric Population Differentiation

MM received funding from the Max Planck innovation funds for this project. PGDF was supported by a Marie Curie European Reintegration Grant (proposal nr 270891). CE was supported by German Science Foundation grants (DFG, EI 841/4-1 and EI 841/6-1)

AtHMA4 drives natural variation in leaf Zn concentration of Arabidopsis thaliana

Zinc (Zn) is an essential element for plant growth and development, and Zn derived from crop plants in the diet is also important for human health. Here, we report that genetic variation in Heavy Metal-ATPase 4 (HMA4) controls natural variation in leaf Zn content. Investigation of the natural variation in leaf Zn content in a world-wide collection of 349 Arabidopsis thaliana wild collected accessions identified two accessions, Van-0 and Fab-2, which accumulate significantly lower Zn when compared with Col-0. Both quantitative trait loci (QTL) analysis and bulked segregant analysis (BSA) identified HMA4 as a strong candidate accounting for this variation in leaf Zn concentration. Genetic complementation experiments confirmed this hypothesis. Sequence analysis revealed that a 1-bp deletion in the third exon of HMA4 from Fab-2 is responsible for the lose of function of HMA4 driving the low Zn observed in Fab-2. Unlike in Fab-2 polymorphisms in the promoter region were found to be responsible for the weak function of HMA4 in Van-0. This is supported by both an expression analysis of HMA4 in Van-0 and through a series of T-DNA insertion mutants which generate truncated HMA4 promoters in the Col-0 background. In addition, we also observed that Fab-2, Van-0 and the hma4-2 null mutant in the Col-0 background show enhanced resistance to a combination of high Zn and high Cd in the growth medium, raising the possibility that variation at HMA4 may play a role in environmental adaptation

A mitochondrial half-size ABC transporter is involved in cadmium tolerance in Chlamydomonas reinhardtii

Five cadmium-sensitive insertional mutants, all affected at the CDS1 ('cadmium-sensitive 1') locus, have been previously isolated in the unicellular green alga Chlamydomonas reinhardtii. We here describe the cloning of the Cds1 gene (8314 bp with 26 introns) and the corresponding cDNA. The Cds1 gene, strongly induced by cadmium, encodes a putative protein (CrCds1) of 1062 amino acid residues that belongs to the ATM/HMT subfamily of half-size ABC transporters. This subfamily includes both vacuolar HMT-type proteins transporting phytochelatin-cadmium complexes from the cytoplasm to the vacuole and mitochondrial ATM-type proteins involved in the maturation of cytosolic Fe/S proteins. Unlike the Delta sphmt1 cadmium-sensitive mutant of Schizosaccharomyces pombe that lacks a vacuolar HMT-type transporter, the cds1 mutant accumulates a high amount of phytochelatin-cadmium complexes. By epitope tagging, the CrCds1 protein was localized in the mitochondria. Even though mitochondria of cds1 do not accumulate important amounts of 'free' iron, the mutant cells are hypersensitive to high iron concentrations. Our data show for the first time that a mitochondrial ATM-like transporter plays a major role in tolerance to cadmium.Peer reviewe