SummaryIt is known that environmental factors can affect the biosynthesis of leaf metabolites. Similarly, specific pairwise plant-microbe interactions modulate the plant's metabolome by stimulating production of phytoalexins and other defense-related compounds. However, there is no information about how different soil microbiomes could affect the plant growth and the leaf metabolome.We analyzed experimentally how diverse soil microbiomes applied to the roots of Arabidopsis thaliana were able to modulate plant growth and the leaf metabolome, as assessed by GC-MS analyses. Further, we determined the effects of soil microbiome-driven changes in leaf metabolomics on the feeding behavior of Trichopulsia ni larvae.Soil microbiomes differentially impacted plant growth patterns as well as leaf metabolome composition. Similarly, most microbiome-treated plants showed inhibition to larvae feeding, compared with unamended control plants. Pyrosequencing analysis was conducted to determine the soil microbial composition and diversity of the soils used in this study.Correlation analyses were performed to determine relationships between various factors (soil microbial taxa, leaf chemical components, plant growth patterns and insect feeding behavior) and revealed that leaf amino acid content was positively correlated with both microbiome composition and insect feeding behavior.

Plant roots exhibit remarkable developmental plasticity in response to local soil conditions. It is shown here that mild salt stress stimulates a stress-induced morphogenic response (SIMR) in Arabidopsis thaliana roots characteristic of several other abiotic stresses: the proliferation of lateral roots (LRs) with a concomitant reduction in LR and primary root length. The LR proliferation component of the salt SIMR is dramatically enhanced by the transfer of seedlings from a low to a high NO3− medium, thereby compensating for the decreased LR length and maintaining overall LR surface area. Increased LR proliferation is specific to salt stress (osmotic stress alone has no stimulatory effect) and is due to the progression of more LR primordia from the pre-emergence to the emergence stage, in salt-stressed plants. In salt-stressed seedlings, greater numbers of LR primordia exhibit expression of a reporter gene driven by the auxin-sensitive DR5 promoter than in unstressed seedlings. Moreover, in the auxin transporter mutant aux1-7, the LR proliferation component of the salt SIMR is completely abrogated. The results suggest that salt stress promotes auxin accumulation in developing primordia thereby preventing their developmental arrest at the pre-emergence stage. Examination of ABA and ethylene mutants revealed that ABA synthesis and a factor involved in the ethylene signalling network also regulate the LR proliferation component of the salt SIMR.

Abiotic stresses are a primary cause of crop loss worldwide. The convergence of stress signalling pathways to a common set of transcription factors suggests the existence of upstream regulatory genes that control plant responses to multiple abiotic stresses. To identify such genes, data from published Arabidopsis thaliana abiotic stress microarray analyses were combined with our presented global analysis of early heat stress-responsive gene expression, in a relational database. A set of Multiple Stress (MST) genes was identified by scoring each gene for the number of abiotic stresses affecting expression of that gene. ErmineJ overrepresentation analysis of the MST gene set identified significantly enriched gene ontology biological processes for multiple abiotic stresses and regulatory genes, particularly transcription factors. A subset of MST genes including only regulatory genes that were designated 'Multiple Stress Regulatory' (MSTR) genes, was identified. To validate this strategy for identifying MSTR genes, mutants of the highest-scoring MSTR gene encoding the circadian clock protein CCA1, were tested for altered sensitivity to stress. A double mutant of CCA1 and its structural and functional homolog, LATE ELONGLATED HYPOCOTYL, exhibited greater sensitivity to salt, osmotic and heat stress than wild-type plants. This work provides a reference data set for further study of MSTR genes.

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SUMMARYDEAD-box RNA helicases are involved in many aspects of RNA metabolism and in diverse biological processes in plants. Arabidopsis thaliana mutants of two DEAD-box RNA helicases, STRESS RESPONSE SUPPRESSOR1 (STRS1) and STRS2 were previously shown to exhibit tolerance to abiotic stresses and upregulated stress-responsive gene expression. Here, we show that Arabidopsis STRS-overexpressing lines displayed a less tolerant phenotype and reduced expression of stress-induced genes confirming the STRSs as attenuators of Arabidopsis stress responses. GFP-STRS fusion proteins exhibited localization to the nucleolus, nucleoplasm and chromocenters and exhibited relocalization in response to abscisic acid (ABA) treatment and various stresses. This relocalization was reversed when stress treatments were removed. The STRS proteins displayed mis-localization in specific gene-silencing mutants and exhibited RNA-dependent ATPase and RNA-unwinding activities. In particular, STRS2 showed mis-localization in three out of four mutants of the RNA-directed DNA methylation (RdDM) pathway while STRS1 was mis-localized in the hd2c mutant that is defective in histone deacetylase activity. Furthermore, heterochromatic RdDM target loci displayed reduced DNA methylation and increased expression in the strs mutants. Taken together, our findings suggest that the STRS proteins are involved in epigenetic silencing of gene expression to bring about suppression of the Arabidopsis stress response.

Capirona (Calycophyllum spruceanum (Benth.) K. Schum.) and Bolaina (Guazuma crinita Lam.) are fast-growing Amazonian trees with increasing demand in timber industry. Therefore, it is necessary to determine the content of cellulose, hemicellulose, holocellulose and lignin in juvenile trees to accelerate forest breeding programs. The aim of this study was to identify chemical differences between apical and basal stem of Capirona and Bolaina to develop models for estimating the chemical composition using Fourier transform infrared (FTIR) spectra. FTIR-ATR spectra were obtained from 150 samples for each species that were 1.8 year-old. The results showed significant differences between the apical and basal stem for each species in terms of cellulose, hemicellulose, holocellulose and lignin content. This variability was useful to build partial least squares (PLS) models from the FTIR spectra and they were evaluated by root mean squared error of predictions (RMSEP) and ratio of performance to deviation (RPD). Lignin content was efficiently predicted in Capirona (RMSEP = 0.48, RPD > 2) and Bolaina (RMSEP = 0.81, RPD > 2). In Capirona, the predictive power of cellulose, hemicellulose and holocellulose models (0.68 < RMSEP < 2.06, 1.60 < RPD < 1.96) were high enough to predict wood chemical composition. In Bolaina, model for cellulose attained an excellent predictive power (RMSEP = 1.82, RPD = 6.14) while models for hemicellulose and holocellulose attained a good predictive power (RPD > 2.0). This study showed that FTIR-ATR together with PLS is a reliable method to determine the wood chemical composition in juvenile trees of Capirona and Bolaina.

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RuBisCO is the most abundant enzyme on earth; it regulates the organic carbon cycle in the biosphere. Studying its structural evolution will help to develop new strategies of genetic improvement in order to increase food production and mitigate CO2 emissions. In the present work, we evaluate how the evolution of sequence and structure among isoforms I, II and III of RuBisCO defines their intrinsic flexibility and residue-residue interactions. To do this, we used a multilevel approach based on phylogenetic inferences, multiple sequence alignment, normal mode analysis, and molecular dynamics. Our results show that the three isoforms exhibit greater fluctuation in the loop between αB and βC, and also present a positive correlation with loop 6, an important region for enzymatic activity because it regulates RuBisCO conformational states. Likewise, an increase in the flexibility of the loop structure between αB and βC, as well as Lys330 (form II) and Lys322 (form III) of loop 6, is important to increase photosynthetic efficiency. Thus, the cross-correlation dynamics analysis showed changes in the direction of movement of the secondary structures in the three isoforms. Finally, key amino acid residues related to the flexibility of the RuBisCO structure were indicated, providing important information for its enzymatic engineering.