The rhizosphere microbiome of 51 potato cultivars with diverse plant growth characteristics.

Rhizosphere microbial communities play a substantial role in plant productivity. We studied the rhizosphere bacteria and fungi of 51 distinct potato cultivars grown under similar greenhouse conditions using a metabarcoding approach. As expected, individual cultivars were the most important determining factor of the rhizosphere microbial composition; however, differences were also obtained when grouping cultivars according to their growth characteristics. We demonstrated that plant growth characteristics were strongly related to deterministic and stochastic assembly processes of bacterial and fungal communities, respectively. The bacterial genera Arthrobacter and Massilia (known to produce IAA and siderophores) exhibited greater relative abundance in high- and medium performing cultivars. Bacterial co-occurrence networks were larger in the rhizosphere of these cultivars and were characterized by a distinctive combination of plant beneficial Proteobacteria and Actinobacteria along with a module of diazotrophs namely Azospira, Azoarcus, Azohydromonas. Conversely, the network within low performing cultivars revealed the lowest nodes, hub taxa, edges density, robustness and the highest average path length resulting in reduced microbial associations, which may potentially limit their effectiveness in promoting plant growth. Our findings established a clear pattern between plant productivity and the rhizosphere microbiome composition and structure for the investigated potato cultivars, offering insights for future management practices.

Homogalacturonan Pectins Tuned as an Effect of Susceptible rbohD, Col-0-Reactions, and Resistance rbohF-, rbohD/F-Reactions to TuMV.

The plant cell wall is an actively reorganized network during plant growth and triggered immunity in response to biotic stress. While the molecular mechanisms managing perception, recognition, and signal transduction in response to pathogens are well studied in the context of damaging intruders, the current understanding of plant cell wall rebuilding and active defense strategies in response to plant virus infections remains poorly characterized. Pectins can act as major elements of the primary cell wall and are dynamic compounds in response to pathogens. Homogalacturonans (HGs), a main component of pectins, have been postulated as defensive molecules in plant-pathogen interactions and linked to resistance responses. This research focused on examining the regulation of selected pectin metabolism components in susceptible (rbohD-, Col-0-TuMV) and resistance (rbohF-, rbohD/F-TuMV) reactions. Regardless of the interaction type, ultrastructural results indicated dynamic cell wall rebuilding. In the susceptible reaction promoted by RbohF, there was upregulation of AtPME3 (pectin methylesterase) but not AtPME17, confirmed by induction of PME3 protein deposition. Moreover, the highest PME activity along with a decrease in cell wall methylesters compared to resistance interactions in rbohD-TuMV were noticed. Consequently, the susceptible reaction of rbohD and Col-0 to TuMV was characterized by a significant domination of low/non-methylesterificated HGs. In contrast, cell wall changes during the resistance response of rbohF and rbohD/F to TuMV were associated with dynamic induction of AtPMEI2, AtPMEI3, AtGAUT1, and AtGAUT7 genes, confirmed by significant induction of PMEI2, PMEI3, and GAUT1 protein deposition. In both resistance reactions, a dynamic decrease in PME activity was documented, which was most intense in rbohD/F-TuMV. This decrease was accompanied by an increase in cell wall methylesters, indicating that the domination of highly methylesterificated HGs was associated with cell wall rebuilding in rbohF and rbohD/F defense responses to TuMV. These findings suggest that selected PME with PMEI enzymes have a diverse impact on the demethylesterification of HGs and metabolism as a result of rboh-TuMV interactions, and are important factors in regulating cell wall changes depending on the type of interaction, especially in resistance responses. Therefore, PMEI2 and PMEI3 could potentially be important signaling resistance factors in the rboh-TuMV pathosystem.

Cultivar-specific dynamics: unravelling rhizosphere microbiome responses to water deficit stress in potato cultivars.

BACKGROUND: Growing evidence suggests that soil microbes can improve plant fitness under drought. However, in potato, the world's most important non-cereal crop, the role of the rhizosphere microbiome under drought has been poorly studied. Using a cultivation independent metabarcoding approach, we examined the rhizosphere microbiome of two potato cultivars with different drought tolerance as a function of water regime (continuous versus reduced watering) and manipulation of soil microbial diversity (i.e., natural (NSM), vs. disturbed (DSM) soil microbiome). RESULTS: Water regime and soil pre-treatment showed a significant interaction with bacterial community composition of the sensitive (HERBST) but not the resistant cultivar (MONI). Overall, MONI had a moderate response to the treatments and its rhizosphere selected Rhizobiales under reduced watering in NSM soil, whereas Bradyrhizobium, Ammoniphilus, Symbiobacterium and unclassified Hydrogenedensaceae in DSM soil. In contrast, HERBST response to the treatments was more pronounced. Notably, in NSM soil treated with reduced watering, the root endophytic fungus Falciphora and many Actinobacteriota members (Streptomyces, Glycomyces, Marmoricola, Aeromicrobium, Mycobacterium and others) were largely represented. However, DSM soil treatment resulted in no fungal taxa and fewer enrichment of these Actinobacteriota under reduced watering. Moreover, the number of bacterial core amplicon sequence variants (core ASVs) was more consistent in MONI regardless of soil pre-treatment and water regimes as opposed to HERBST, in which a marked reduction of core ASVs was observed in DSM soil. CONCLUSIONS: Besides the influence of soil conditions, our results indicate a strong cultivar-dependent relationship between the rhizosphere microbiome of potato cultivars and their capacity to respond to perturbations such as reduced soil moisture. Our study highlights the importance of integrating soil conditions and plant genetic variability as key factors in future breeding programs aiming to develop drought resistance in a major food crop like potato. Elucidating the molecular mechanisms how plants recruit microbes from soil which help to mitigate plant stress and to identify key microbial taxa, which harbour the respective traits might therefore be an important topic for future research.

Glutathione Contribution in Interactions between Turnip mosaic virus and Arabidopsis thaliana Mutants Lacking Respiratory Burst Oxidase Homologs D and F.

Respiratory burst oxidase homologs (Rbohs) play crucial and diverse roles in plant tissue-mediated production of reactive oxygen species during the development, growth, and response of plants to abiotic and biotic stress. Many studies have demonstrated the contribution of RbohD and RbohF in stress signaling in pathogen response differentially modulating the immune response, but the potential role of the Rbohs-mediated response in plant-virus interactions remains unknown. The present study analyzed, for the first time, the metabolism of glutathione in rbohD-, rbohF-, and rbohD/F-transposon-knockout mutants in response to Turnip mosaic virus (TuMV) infection. rbohD-TuMV and Col-0-TuMV interactions were characterized by susceptible reaction to TuMV, associated with significant activity of GPXLs (glutathione peroxidase-like enzymes) and induction of lipid peroxidation in comparison to mock-inoculated plants, with reduced total cellular and apoplastic glutathione content observed at 7-14 dpi and dynamic induction of apoplast GSSG (oxidized glutathione) at 1-14 dpi. Systemic virus infection resulted in the induction of AtGSTU1 and AtGSTU24, which was highly correlated with significant downregulation of GSTs (glutathione transferases) and cellular and apoplastic GGT (γ-glutamyl transferase) with GR (glutathione reductase) activities. On the contrary, resistant rbohF-TuMV reactions, and especially enhanced rbohD/F-TuMV reactions, were characterized by a highly dynamic increase in total cellular and apoplastic glutathione content, with induction of relative expression of AtGGT1, AtGSTU13, and AtGSTU19 genes. Moreover, virus limitation was highly correlated with the upregulation of GSTs, as well as cellular and apoplastic GGT with GR activities. These findings clearly indicate that glutathione can act as a key signaling factor in not only susceptible rbohD reaction but also the resistance reaction presented by rbohF and rbohD/F mutants during TuMV interaction. Furthermore, by actively reducing the pool of glutathione in the apoplast, GGT and GR enzymes acted as a cell first line in the Arabidopsis-TuMV pathosystem response, protecting the cell from oxidative stress in resistant interactions. These dynamically changed signal transductions involved symplast and apoplast in mediated response to TuMV.

Biochemical and economical effect of application biostimulants containing seaweed extracts and amino acids as an element of agroecological management of bean cultivation.

The implementation of agronomic activities, based on the use of biostimulants, is an important element of agroecological practices. Therefore, comprehensive research was carried on the use of biostimulants. A field experiment was performed in 2016-2018 with common bean of Mexican Black cultivar. In particular growing seasons, bean plants were treated with Kelpak SL (seaweed extracts) and Terra Sorb Complex (free amino acids) in the form of single and double spraying with two solutions concentrations. According to the obtained data, application of biostimulants increased the yield of bean. Better results were observed after the use of Kelpak SL. The application of preparations influenced nutritional and nutraceutical quality of bean seeds. Terra Sorb Complex caused the highest increase in proteins level. In the light of achieved data, biostimulants in similar level decreased the starch accumulation. The most promising results, in the context of nutraceutical value of bean, were obtained in the case of increasing level of fiber. A positive impact of biostimulants on the seeds antioxidant potential was noted, expressed by the increased synthesis of phenolics, flavonoid, anthocyanins and antioxidant activities. Results of this study, directly indicate economic benefits from the use of biostimulants, which are extremely important to the farmers.

The 3' Untranslated Region of a Plant Viral RNA Directs Efficient Cap-Independent Translation in Plant and Mammalian Systems.

Many plant viral RNA genomes lack a 5' cap, and instead are translated via a cap-independent translation element (CITE) in the 3' untranslated region (UTR). The panicum mosaic virus-like CITE (PTE), found in many plant viral RNAs, binds and requires the cap-binding translation initiation factor eIF4E to facilitate translation. eIF4E is structurally conserved between plants and animals, so we tested cap-independent translation efficiency of PTEs of nine plant viruses in plant and mammalian systems. The PTE from thin paspalum asymptomatic virus (TPAV) facilitated efficient cap-independent translation in wheat germ extract, rabbit reticulocyte lysate, HeLa cell lysate, and in oat and mammalian (BHK) cells. Human eIF4E bound the TPAV PTE but not a PTE that did not stimulate cap-independent translation in mammalian extracts or cells. Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) footprinting revealed that both human and wheat eIF4E protected the conserved guanosine (G)-rich domain in the TPAV PTE pseudoknot. The central G plays a key role, as it was found to be required for translation and protection from SHAPE modification by eIF4E. These results provide insight on how plant viruses gain access to the host's translational machinery, an essential step in infection, and raise the possibility that similar PTE-like mechanisms may exist in mRNAs of mammals or their viruses.

Optimization of a magnetic capture RT-LAMP assay for fast and real-time detection of potato virus Y and differentiation of N and O serotypes.

Potato virus Y (PVY) infection has been a global challenge for potato production and the leading cause of downgrading and rejection of seed crops for certification. Accurate and timely diagnosis is a key for effective disease control. Here, we have optimized a reverse transcription loop-mediated amplification (RT-LAMP) assay to differentiate the PVY O and N serotypes. The RT-LAMP assay is based on isothermal autocyclic strand displacement during DNA synthesis. The high specificity of this method relies heavily on the primer sets designed for the amplification of the targeted regions. We designed specific primer sets targeting a region within the coat protein gene that contains nucleotide signatures typical for O and N coat protein types, and these primers differ in their annealing temperature. Combining this assay with total RNA extraction by magnetic capture, we have established a highly sensitive, simplified and shortened RT-LAMP procedure as an alternative to conventional nucleic acid assays for diagnosis. This optimized procedure for virus detection may be used as a preliminary test for identifying the viral serotype prior to investing time and effort in multiplex RT-PCR tests when a specific strain is needed.

Removal of Phenol from Synthetic and Industrial Wastewater by Potato Pulp Peroxidases.

Plant peroxidases have strong potential utility for decontamination of phenol-polluted wastewater. However, large-scale use of these enzymes for phenol depollution requires a source of cheap, abundant, and easily accessible peroxidase-containing material. In this study, we show that potato pulp, a waste product of the starch industry, contains large amounts of active peroxidases. We demonstrate that potato pulp may serve as a tool for peroxidase-based remediation of phenol pollution. The phenol removal efficiency of potato pulp was over 95 % for optimized phenol concentrations. The potato pulp enzymes maintained their activity at pH 4 to 8 and were stable over a wide temperature range. Phenol solutions treated with potato pulp showed a significant reduction in toxicity compared with untreated phenol solutions. Finally we determined that this method may be employed to remove phenol from industrial effluent with over 90 % removal efficiency under optimal conditions.

Cation-dependent folding of 3' cap-independent translation elements facilitates interaction of a 17-nucleotide conserved sequence with eIF4G.

The 3'-untranslated regions of many plant viral RNAs contain cap-independent translation elements (CITEs) that drive translation initiation at the 5'-end of the mRNA. The barley yellow dwarf virus-like CITE (BTE) stimulates translation by binding the eIF4G subunit of translation initiation factor eIF4F with high affinity. To understand this interaction, we characterized the dynamic structural properties of the BTE, mapped the eIF4G-binding sites on the BTE and identified a region of eIF4G that is crucial for BTE binding. BTE folding involves cooperative uptake of magnesium ions and is driven primarily by charge neutralization. Footprinting experiments revealed that functional eIF4G fragments protect the highly conserved stem-loop I and a downstream bulge. The BTE forms a functional structure in the absence of protein, and the loop that base pairs the 5'-untranslated region (5'-UTR) remains solvent-accessible at high eIF4G concentrations. The region in eIF4G between the eIF4E-binding site and the MIF4G region is required for BTE binding and translation. The data support the model in which the eIF4F complex binds directly to the BTE which base pairs simultaneously to the 5'-UTR, allowing eIF4F to recruit the 40S ribosomal subunit to the 5'-end.

Untranslated regions of diverse plant viral RNAs vary greatly in translation enhancement efficiency.

BACKGROUND: Whole plants or plant cell cultures can serve as low cost bioreactors to produce massive amounts of a specific protein for pharmacological or industrial use. To maximize protein expression, translation of mRNA must be optimized. Many plant viral RNAs harbor extremely efficient translation enhancers. However, few of these different translation elements have been compared side-by-side. Thus, it is unclear which are the most efficient translation enhancers. Here, we compare the effects of untranslated regions (UTRs) containing translation elements from six plant viruses on translation in wheat germ extract and in monocotyledenous and dicotyledenous plant cells. RESULTS: The highest expressing uncapped mRNAs contained viral UTRs harboring Barley yellow dwarf virus (BYDV)-like cap-independent translation elements (BTEs). The BYDV BTE conferred the most efficient translation of a luciferase reporter in wheat germ extract and oat protoplasts, while uncapped mRNA containing the BTE from Tobacco necrosis virus-D translated most efficiently in tobacco cells. Capped mRNA containing the Tobacco mosaic virus omega sequence was the most efficient mRNA in tobacco cells. UTRs from Satellite tobacco necrosis virus, Tomato bushy stunt virus, and Crucifer-infecting tobamovirus (crTMV) did not stimulate translation efficiently. mRNA with the crTMV 5' UTR was unstable in tobacco protoplasts. CONCLUSIONS: BTEs confer the highest levels of translation of uncapped mRNAs in vitro and in vivo, while the capped omega sequence is most efficient in tobacco cells. These results provide a basis for understanding mechanisms of translation enhancement, and for maximizing protein synthesis in cell-free systems, transgenic plants, or in viral expression vectors.

Structure of a viral cap-independent translation element that functions via high affinity binding to the eIF4E subunit of eIF4F.

RNAs of many positive strand RNA viruses lack a 5' cap structure and instead rely on cap-independent translation elements (CITEs) to facilitate efficient translation initiation. The mechanisms by which these RNAs recruit ribosomes are poorly understood, and for many viruses the CITE is unknown. Here we identify the first CITE of an umbravirus in the 3'-untranslated region of pea enation mosaic virus RNA 2. Chemical and enzymatic probing of the approximately 100-nucleotide PEMV RNA 2 CITE (PTE), and mutagenesis revealed that it forms a long, bulged helix that branches into two short stem-loops, with a possible pseudoknot interaction between a C-rich bulge at the branch point and a G-rich bulge in the main helix. The PTE inhibited translation in trans, and addition of eIF4F, but not eIFiso4F, restored translation. Filter binding assays revealed that the PTE binds eIF4F and its eIF4E subunit with high affinity. Tight binding required an intact cap-binding pocket in eIF4E. Among many PTE mutants, there was a strong correlation between PTE-eIF4E binding affinity and ability to stimulate cap-independent translation. We conclude that the PTE recruits eIF4F by binding eIF4E. The PTE represents a different class of translation enhancer element, as defined by its structure and ability to bind eIF4E in the absence of an m(7)G cap.

The 3' cap-independent translation element of Barley yellow dwarf virus binds eIF4F via the eIF4G subunit to initiate translation.

The 3' cap-independent translation element (BTE) of Barley yellow dwarf virus RNA confers efficient translation initiation at the 5' end via long-distance base pairing with the 5'-untranslated region (UTR). Here we provide evidence that the BTE functions by recruiting translation initiation factor eIF4F. We show that the BTE interacts specifically with the cap-binding initiation factor complexes eIF4F and eIFiso4F in a wheat germ extract (wge). In wge depleted of cap-interacting factors, addition of eIF4F (and to a lesser extent, eIFiso4F) allowed efficient translation of an uncapped reporter construct (BLucB) containing the BTE in its 3' UTR. Translation of BLucB required much lower levels of eIF4F or eIFiso4F than did a capped, nonviral mRNA. Both full-length eIF4G and the carboxy-terminal half of eIF4G lacking the eIF4E binding site stimulated translation to 70% of the level obtained with eIF4F, indicating a minor role for the cap-binding protein, eIF4E. In wge inhibited by either BTE in trans or cap analog, eIF4G alone restored translation nearly as much as eIF4F, while addition of eIF4E alone had no effect. The BTE bound eIF4G (Kd = 177 nm) and eIF4F (Kd = 37 nm) with high affinity, but very weakly to eIF4E. These interactions correlate with the ability of the factors to facilitate BTE-mediated translation. These results and previous observations are consistent with a model in which eIF4F is delivered to the 5' UTR by the BTE, and they show that eIF4G, but not eIF4E, plays a major role in this novel mechanism of cap-independent translation.