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Background The plant microbiome represents one of the key determinants of plant health and productivity by providing a plethora of functional capacities such as access to low-abundance nutrients, suppression of phytopathogens, and resistance to biotic and/or abiotic stressors. However, a robust understanding of the structural composition of the bacterial microbiome present in different plant microenvironments and especially the relationship between below-ground and above-ground communities has remained elusive. In this work, we addressed hypotheses regarding microbiome niche differentiation and structural stability of the bacterial communities within different ecological plant niches. Methods We sampled the rhizosphere soil, root, stem, and leaf endosphere of field-grown poplar trees ( Populus tremula × Populus alba ) and applied 16S rRNA amplicon pyrosequencing to unravel the bacterial communities associated with the different plant habitats. Results We found that the structural variability of rhizosphere microbiomes in field-grown poplar trees ( P. tremula × P. alba ) is much lower than that of the endosphere microbiomes. Furthermore, our data not only confirm microbiome niche differentiation reports at the rhizosphere soil–root interface but also clearly show additional fine-tuning and adaptation of the endosphere microbiome in the stem and leaf compartment. Each plant compartment represents an unique ecological niche for the bacterial communities . Finally, we identified the core bacterial microbiome associated with the different ecological niches of Populus. Conclusions Understanding the complex host–microbe interactions of Populus could provide the basis for the exploitation of the eukaryote–prokaryote associations in phytoremediation applications, sustainable crop production (bio-energy efficiency), and/or the production of secondary metabolites.

Secondary metabolites of the flavonoid pathway participate in plant defense, and bHLH and MYB transcription factors regulate the synthesis of these metabolites. Here, we define the regulatory mechanisms in response to pathogens. Two transcription factors from var. , and , were overexpressed together in poplar, and transcriptome analysis revealed differences in response to pathogen infection. The transgenic plants showed elevated levels of several key flavonoid pathway components: total phenols, proanthocyanidins (PAs), and anthocyanins and intermediates quercetin and kaempferol. Furthermore, and overexpression in poplar enhanced antioxidase activities and H O release and also increased resistance to and infection. Gene expression profile analysis showed most genes involved in the flavonoid biosynthesis pathway or antioxidant response to be upregulated in / -OE poplar, but significant differential expression occurred in response to pathogen infection. Specifically, expression of (flavanone 3-hydroxylase), (dihydroflavonol 4-seductase), (anthocyanin synthase), and (anthocyanin reductase), which function in initial, middle, and final steps of anthocyanin and PA biosynthesis, respectively, was significantly upregulated in -infected / -OE poplar. Our results highlight that PalbHLH1 and PalMYB90 function as transcriptional activators of flavonoid pathway secondary-metabolite synthesis genes, with differential mechanisms in response to bacterial or fungal infection.

Intercellular communication mediated by CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) peptides and their receptors is crucial for plant development and environmental adaptation. In this study, 45 and 89 CLEs were identified in Populus tomentosa and Populus alba × Populus glandulosa, respectively, and, together with the 52 CLEs in Populus trichocarpa, the chromosome localization, gene and protein characteristics, collinearity and gene duplication events, cis-acting regulatory elements in promoters and evolutionary relationships of CLEs in these three poplar species were analyzed. The CLEs of three poplar species were divided into four subfamilies. Among them, the CLEs in subfamilies I, II and IV were A-type CLEs, while those in subfamily III were B-type CLEs. During the evolutionary process of poplar, the selection pressure faced by whole-genome duplication or segmental duplication was purifying selection, and the duplication events led to the expansion of the CLE family in poplar. The exogenous addition of a certain concentration of poplar CLE13 peptides inhibits the root growth of Arabidopsis thaliana and poplar and simultaneously reduces the expression levels of ARFs and LBDs in the roots. In addition, drought stress induces the expression of PtrCLE13A. The overexpression of preCLE13A significantly enhances the osmotic and drought tolerance in Populus tomentosa. These results have provided valuable information for further research on the molecular mechanisms of CLE peptide signaling pathways in the woody model plant poplar regarding plant growth and stress resistance.

The CRISPR/Cas9 system has been used for genome editing in several plant species; however, there are few reports on its use in trees. Here, CRISPR/Cas9 was used to mutate a target gene in Populus alba × Populus glandulosa hybrid poplars. The hybrid poplar is routinely used in molecular biological studies due to the well-established Agrobacterium-mediated transformation method. A single guide RNA (sgRNA) with reported high mutation efficiency in other popular species was designed with a protospacer adjacent motif sequence for the phytoene desaturase 1 (PagPDS1) gene. The pHSE/Cas9-PagPDS1 sgRNA vector was delivered into hybrid poplar cells using Agrobacterium-mediated transformation. The transgenic plants were propagated and classified them into three groups according to their phenotypes. Among a total of 110 lines of transgenic hybrid poplars, 82 lines showed either an albino or a pale green phenotype, indicating around 74.5% phenotypic mutation efficiency of the PagPDS1 gene. The albino phenotypes were observed when the CRISPR/Cas9-mediated mutations in both PagPDS1 alleles in the transgenic plants. There was no off-target modification of the PagPDS2 gene, which has a potential sgRNA target sequence with two mismatches. The results confirmed that the sgRNA can specifically edit PagPDS1 rather than PagPDS2, indicating that CRISPR/Cas9-mediated genome editing can effectively induce target mutations in the hybrid poplar. This technique will be useful to improve tree quality in hybrid poplars (P. alba × P. glandulosa); for example, by enhancing biomass or stress tolerance.

The Ethylene Responsive Factor (ERF) transcription factor family is important for regulating plant growth and stress responses. Although the expression patterns of ERF family members have been reported in many plant species, their role in Populus alba × Populus glandulosa, an important model plant for forest research, remains unclear. In this study, we identified 209 PagERF transcription factors by analyzing the P. alba × P. glandulosa genome. We analyzed their amino acid sequences, molecular weight, theoretical pI (Isoelectric point), instability index, aliphatic index, grand average of hydropathicity, and subcellular localization. Most PagERFs were predicted to localize in the nucleus, with only a few PagERFs localized in the cytoplasm and nucleus. Phylogenetic analysis divided the PagERF proteins into ten groups, Class I to X, with those belonging to the same group containing similar motifs. Cis-acting elements associated with plant hormones, abiotic stress responses, and MYB binding sites were analyzed in the promoters of PagERF genes. We used transcriptome data to analyze the expression patterns of PagERF genes in different tissues of P. alba × P. glandulosa, including axillary buds, young leaves, functional leaves, cambium, xylem, and roots, and the results indicated that PagERF genes are expressed in all tissues of P. alba × P. glandulosa, especially in roots. Quantitative verification results were consistent with transcriptome data. When P. alba × P. glandulosa seedlings were treated with 6% polyethylene glycol 6000 (PEG6000), the results of RT-qRCR showed that nine PagERF genes responded to drought stress in various tissues. This study provides a new perspective on the roles of PagERF family members in regulating plant growth and development, and responses to stress in P. alba × P. glandulosa. Our study provides a theoretical basis for ERF family research in the future.

Summary Salt and drought impair plant osmotic homeostasis and greatly limit plant growth and development. Plants decrease stomatal aperture to reduce water loss and maintain osmotic homeostasis, leading to improved stress tolerance. Herein, we identified the C2H2 transcription factor gene OSMOTIC STRESS INDUCED C2H2 1 (OSIC1) from Populus alba var. pyramidalis to be induced by salt, drought, polyethylene glycol 6000 (PEG6000) and abscisic acid (ABA). Overexpression of OSIC1 conferred transgenic poplar more tolerance to high salinity, drought and PEG6000 treatment by reducing stomatal aperture, while its mutant generated by the CRISPR/Cas9 system showed the opposite phenotype. Furthermore, OSIC1 directly up‐regulates PalCuAOζ in vitro and in vivo, encoding a copper‐containing polyamine oxidase, to enhance H2O2 accumulation in guard cells and thus modulates stomatal closure when stresses occur. Additionally, ABA‐, drought‐ and salt‐induced PalMPK3 phosphorylates OSIC1 to increase its transcriptional activity to PalCuAOζ. This regulation of OSIC1 at the transcriptional and protein levels guarantees rapid stomatal closure when poplar responds to osmotic stress. Our results revealed a novel transcriptional regulatory mechanism of H2O2 production in guard cells mediated by the OSIC1‐PalCuAOζ module. These findings deepen our understanding of how perennial woody plants, like poplar, respond to osmotic stress caused by salt and drought and provide potential targets for breeding.

NAC domain genes belong to a large plant-specific transcription factor family, which is well-known to be associated with multiple stress responses and plant developmental processes. In this study, we screened differentially expressed genes (DEGs) and detected mRNA abundance of NAC family by RNA-Seq in the poplar leaves under salt stress condition. A total of 276 up-regulated DEGs and 159 down-regulated DEGs were identified to be shared in × and × . Among 170 NAC members, gene was significantly up-regulated in response to salt stress in the two species. Tissue-specific and salt-responsive analyses indicated the expression pattern of gene was spatial and temporal in poplar under salt stress. Particle bombardment results showed subcellular localization of NAC57 was not solely nucleus-targeted. Full-length cDNA sequence of the gene was cloned from × and transformed into . Under salt stress, transgenic overexpressing showed higher seed germination rate, root length, and fresh weight than wild type plants. In addition, the transgenic plants displayed higher superoxide dismutase activity and peroxidase activity, and lower malondialdehyde content and relative electrical conductivity than the wild type under salt stress condition. Furthermore, histochemical staining indicated reactive oxygen species accumulation was lower in the transgenic plants than that in the wild type under salt stress. All the results indicated that the gene plays an important role in salt stress responses.

For many clonally propagated species, the accumulation of somatic mutations is the principal driver of declines in yield and quality. However, somatic mutations may also promote genetic diversification. Thus, elucidating somatic mutation rates and patterns is important to understand the genetic basis undergirding the emergence of commercially valuable traits and developmental processes. In this study, we studied the effect of short‐time clonal domestication of Populus alba var. pyramidalis, a species that has been propagated by cutting for the last 67 years. We found that: (1) the somatic mutation rate for P. alba var. pyramidalis is 9.24 × 10−9, which is higher than rates observed in related species; (2) there were more mutations near heterozygous regions, and a larger proportion of CpG and CHG sites were associated with somatic mutations, which may be related to the blocking of DNA repair by methylation; and (3) deleterious mutations were not shared by multiple individuals, and all occurred in heterozygous states, demonstrating the strong selective pressures that act against deleterious mutations. Taken together, the results of our study provide a global view of somatic mutation that will aid efforts to understand the genetic basis of commercially valuable traits and to improve clonally breeding species.

In order to investigate the effects of heavy metal stress on woody plant defense against phytophagous insects, we studied development and reproduction traits of the gypsy moth, Lymantria dispar that were separately fed with leaves plucked from poplar seedlings ( Populus alba berolinensis ) grown in either non-contaminated soil (control), Cd-contaminated soil (1.5 mg/kg), Zn-contaminated soil (500 mg/kg) or Pb-contaminated soil (500 mg/kg). The results showed that feeding on Cd or Pb stressed poplar leaves significantly decreased L. dispar larval weights, body lengths and head capsule widths, pupal weights and female fecundity, and delayed the duration of larval development. Similar effects from the Zn stressed poplar leaves were also observed on all the above mentioned variables except male pupal weight and larval development duration that showed no differences from the control. Cd, Zn, or Pb stressed poplar leaves had no significant effects on L. dispar larval survival, pupation and emergence rates; in fact, both larval survival and pupation rates reached 100%. These results suggest that Cd, Zn or Pb stress in P. alba berolinensis might help the trees defend against the defoliator, however; L. dispar may in turn have an effective detoxification mechanism for lessening the effects of plant-mediated defenses and heavy metals in leaves on larval survival, pupation and eclosion.

Mixed inorganic and organic contaminations are one of the main challenges in phytoremediation, due to the higher complexity derived by pollutant interactions and the increase of phytotoxicity. The cultivation of fast-growing poplars for removing contaminants from water could be a low-cost and flexible choice. The main objective of this study was to evaluate the tolerance of a poplar species (Populus alba ‘Villafranca’ clone) to irrigation with water contaminated with zinc (Zn) and caffeine (CFN). Poplars were maintained in hydroponic and exposed to four different treatments (Control, CFN, Zn and Zn + CFN) over 7 days. Poplar showed a good tolerance to Zn and CFN treatments, without any symptom of phytotoxicity. However, the type of treatment affected the contaminant dynamics in the plant-water system and a pollutant partitioning was observed among organs, with a higher accumulation of Zn in root (472 ± 128.7 mg kg− 1 DW) and CFN in shoot (30 ± 4.5 µg g− 1 FW). Under mixed condition, the CFN uptake significantly increased in root (+ 40%) and stem (+ 28%) while the Zn concentration decreased in leaves (-19%). A focus on the potential role of natural resistance-associated macrophage proteins (NRAMPs) in divalent metal transport has been performed. A down-regulation of NRAMP1.3 was detected in roots of plants exposed to CFN treatment in relation to an increase of Mn concentration. Data confirmed the suitability of Populus alba for the remediation of multi contaminated water.