Cotyledonary somatic embryo is one kind of intermediate material similar to callus in the process of in vitro tissue culture from Rosa hybrida 'John F. Kennedy'.

BACKGROUND: Rose is recognized as an important ornamental plant worldwide, and it is also one of the most widely used flowers in gardens. At present, the improvement of rose traits is still difficult and uncertain, and molecular breeding can provide new ideas for the improvement of modern rose varieties. Somatic embryos are quite good receptors for genetic transformation. However, little is known about the molecular mechanisms underlying during the regeneration process of rose somatic embryos. To elucidate the molecular regulation mechanism of somatic embryo plantlet regeneration, the relationship between the differences in traits of the two different regenerated materials and the significantly differentially expressed genes (DEGs) related to phytohormone pathways in the process of regeneration were be investigated. RESULTS: These representative two regenerated samples from single-piece cotyledonary somatic embryo (SPC) culture of Rosa hybrida 'John F. Kennedy', were harvested for transcriptome analysis, with the SPC explants at the initial culture (Day 0) as the control. The differentially expressed genes (DEGs) in the materials from two different types for regeneration approach (SBF type: the regeneration approach type of single bud formed from SPC explants; MBF type: the regeneration approach type of multiple buds formed from SPC explants) were be screened by means of the transcriptome sequencing technology. In this study, a total of about 396.24 million clean reads were obtained, of which 78.95-82.92% were localized to the reference genome, compared with the initial material (CK sample), there were 5594 specific genes in the material of SBF type and 6142 specific genes in the MBF type. The DEGs from the SBF type material were mainly concentrated in the biological processes of GO terms such as phytohormones, substance transport, cell differentiation, and redox reaction. The KEGG enrichment analysis revealed these DEGs were more active in ubiquinone and other terpenoid-quinone biosynthesis, fatty acid elongation, steroid biosynthesis, and glycosphingolipid biosynthesis-globo and isoglobo series. In contrast, the DEGs induced by the MBF type material were mainly associated with the biological processes such as phytohormones, phosphorylation, photosynthesis and signal transduction. According to KEGG analysis, these DEGs of MBF type were significantly enriched in the porphyrin and chlorophyll metabolism, brassinosteroid biosynthesis, carotenoid biosynthesis, and peroxisome. Furthermore, the results from the phytohormone pathways analysis showed that the auxin-responsive factor SAUR and the cell wall modifying enzyme gene XTH were upregulated for expression but the protein phosphatase gene PP2C was downregulated for expression in SBF type; the higher expression of the ethylene receptor ETR, the ethylene transduction genes EBF1/2, the transcription factor EIN3, and the ethylene-responsive transcription factor ERF1/2 were induced by MBF type. CONCLUSIONS: According to the GO and KEGG analysis, it indicated the DEGs between two different regenerated materials from somatic embryos were significantly different which might be causing morphological differences. That was somatic embryos from Rosa hybrida 'John F. Kennedy' could regenerate plantlet via both classic somatic embryogenesis (seed-like germination) and organogenesis, cotyledonary somatic embryos should be considered as one kind of intermediate materials similiar to callus, rather than the indicator materials for somatic embryogenesis.

Effects of combined microplastic and cadmium pollution on sorghum growth, Cd accumulation, and rhizosphere microbial functions.

The interaction between microplastics (MPs) and cadmium (Cd) poses a threat to agricultural soil environments, and their effects on plant growth and rhizosphere microbial community functions are not yet clear. In this study, energy sorghum was used as a test plant to investigate the effects of two types of MPs, polystyrene (PS) and polyethylene (PE), at different particle sizes (13 µm, 550 µm) and concentrations (0.1%, 1% w/w), and Cd, as well as their interactions, on the growth of sorghum in a soil-cultivation pot experiment. The results showed that the combined effects of MP and Cd pollution on the dry weight and Cd accumulation rate in sorghum varied depending on the type, concentration, and particle size of the MPs, with an overall trend of increasing stress from combined pollution with increasing Cd content and accumulation. High-throughput sequencing analysis revealed that combined MP and Cd pollution increased bacterial diversity, and the most significant increase was observed in the abundance-based coverage estimator (ACE), Shannon, and Sobs indices in the 13 µm 1% PS+Cd treatment group. Metagenomic analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways revealed that 19 groups of metabolic pathways, including microbial metabolism and methane metabolism, differed significantly under combined MP and Cd pollution. Hierarchical clustering results indicated that Cd treatment and combined MP and Cd treatment affected the abundances of sorghum rhizosphere soil nitrogen (N) and phosphorus (P) cycling genes and that the type of MP present was an important factor affecting N and P cycling genes. The results of this study provide a basis for exploring the toxic effects of combined MP and Cd pollution and for conducting soil environmental risk assessments.

Plant growth-promoting bacteria improve the Cd phytoremediation efficiency of soils contaminated with PE-Cd complex pollution by influencing the rhizosphere microbiome of sorghum.

Composite pollution by microplastics and heavy metals poses a potential threat to the soilplant system and has received increasing attention. Plant growth-promoting bacteria (PGPB) have good application potential for the remediation of combined microplastic and heavy metal pollution, but few related studies exist. The present study employed a pot experiment to investigate the effects of inoculation with the PGPB Bacillus sp. SL-413 and Enterobacter sp. VY-1 on sorghum growth and Cd accumulation under conditions of combined cadmium (Cd) and polyethylene (PE) pollution. Cd+PE composite contamination led to a significant reduction in sorghum length and biomass due to increased toxicity. Inoculation with Bacillus sp. SL-413 and Enterobacter sp. VY-1 alleviated the stress caused by Cd+PE complex pollution, and the dry weight of sorghum increased by 25.7% to 46.1% aboveground and by 12.3% to 45.3% belowground. Bacillus sp. SL-413 and Enterobacter sp. VY-1 inoculation increased the Cd content and accumulation in sorghum and improved the phytoremediation efficiency of Cd. The inoculation treatment effectively alleviated the nutrient stress caused by the reduction in soil mineral nutrients due to Cd+PE composite pollution. The composition of the soil bacterial communities was also affected by the Cd, Cd+PE and bacterial inoculation treatments, which affected the diversity of the soil bacterial communities. Network analyses indicated that bacterial inoculation regulated the interaction of rhizospheric microorganisms and increased the stability of soil bacterial communities. The Mantel test showed that the changes in the soil bacterial community and function due to inoculation with Bacillus sp. SL-413 and Enterobacter sp. VY-1 were important factors influencing sorghum growth and Cd remediation efficiency. The results of this study will provide new evidence for the research on joint plantmicrobe remediation of heavy metal and microplastic composite pollution.

First Report of Colletotrichum fructicola Causing Anthracnose on Rosa chinensis in China.

China rose (Rosa chinensis Jacq.) is a popular ornamental plant grown widely in China. In September 2021, a serious leaf spot disease was observed on R. chinensis in Rose plantation of Nanyang Academy of Agricultural Sciences in Nanyang (112°25'41″N, 32°54'28″E), Henan Province, causing severe defoliation of infected plants with a foliar disease incidence of 50 to 70% (n = 100). The early symptoms were irregular brown specks on the leaves, mostly at the tip and margin of the leaves. Then the specks gradually expanded into round amorphous and became dark brown, eventually leading to large irregular or circular lesions. Twenty symptomatic samples were collected from several individual plants, and the junction areas between infected and healthy tissues were cut into 3×3 mm pieces. These tissues were sterilized in 75% ethanol for 30 seconds and 1% HgCl solution for 3 min, rinsed thrice in sterile water, and placed on potato dextrose agar (PDA) plates, incubated at 25°C for 3 days. The edges of the colony were cut and transferred to new PDA plates for purification. These isolates were isolated from the original diseased leaves and showed similar phenotypes in morphological characters. Three representative purified strains (YJY20, YJY21, and YJY30) were used for further study. Colonies were villiform, initially white, later turning gray and greyish-green. Conidia were unitunicate, clavate, and averaged 17.36 (11.61 to 22.12) - 5.29 (3.92 to 7.04) µm in diameter (n=100). The characteristics were close to those of Colletotrichum spp. (Weir et al. 2012). The genomic DNA was extracted, and the rDNA internal transcribed spacer (ITS), glyceraldehyde-3-phosphate dehydrogenase (GADPH), calmodulin genes (CAL), actin genes (ACT), chitin synthase 1 genes (CHS-1), manganesesuperoxide dismutase (SOD2), and ß-tubulin 2 genes (TUB2) were amplified from genomic DNA by primers ITS1/ITS4, GDF/GDR, CL1C/CL2C, ACT-512F/ACT-783R, CHS-79F/CHS-345R, SODglo2-F/SODglo2-R, and Bt2a/Bt2b, respectively (Weir et al. 2012). Sequences were submitted to GenBank with accession numbers OP535983, OP535993, OP535994(ITS), OP554748, OP546349, OP546350(GAPDH), OP546351-OP546353(CAL), OP546354-OP546356(ACT), OP554742-OP554744(CHS-1), OP554745-OP554747(SOD2), and OP554749-OP554751(TUB2). BLASTn analyses of ITS, GAPDH, CAL, ACT, CHS-1, SDO2 and TUB2 sequences exhibited 99.62%, 98.40%, 99.72%-99.86%, 96.85%-96.86%, 99.26%-100%, 100% and 99.33% similarity to the sequences of Colletotrichum fructicola strain ICMP 18581, respectively in GenBank. These morphological features and molecular identification indicated that the pathogen possessed identical characteristics as C. fructicola (Weir et al. 2012). Pathogenicity was tested through in vivo experiments. Six 1-year-old intact plants were used per isolate. The test leaves of plants were gently scratched with a sterilized needle. Conidial suspension of the pathogen strains were inoculated on the wounded leaves at a concentration of 107 conidial/mL. The control leaves were inoculated with distilled water. The inoculated plants were placed in greenhouse at 28℃ and 90% humidity. After 3-6 days，anthracnose-like symptoms were observed on inoculated leaves of five plants while the control plants remained healthy. The strains of C. fructicola were reisolated from the symptomatic inoculated leaves, confirming Koch's postulates. To our knowledge, this is the first report of C. fructicola causing anthracnose on Rosa chinensis in China. C. fructicola has been reported to affect numerous plants worldwide, including grape, citrus, apple, cassava, mango （Qili Li et al. 2019）, and tea-oil tree (X. G. Chen et al. 2022), among others (Oliveira et al. 2018). This identification research will facilitate subsequent assistance with disease control and field management of plants.

Illumina MiSeq sequencing and network analysis the distribution and co-occurrence of bacterioplankton in Danjiangkou Reservoir, China.

Network analysis has contributed to studies of the interactions of microorganisms and the identification of key populations. However, such analysis has rarely been conducted in the study of reservoir bacterioplankton communities. This study investigated the bacterioplankton community composition in the surface water of the Danjiangkou Reservoir using the Illumina MiSeq sequencing platform. We observed that the bacterioplankton community primarily consisted of 27 phyla and 336 genera, including Actinobacteria, Proteobacteria, and Bacteroidetes, demonstrating the richness of the community composition. Redundancy analysis of the bacterioplankton communities and environmental variables showed that the total nitrogen (TN), pH, chemical oxygen demand (COD), and permanganate index (CODMn) were important factors affecting the bacterioplankton distribution. Network analysis was performed using the relative abundances of bacterioplankton based on the phylogenetic molecular ecological network (pMEN) method. The connectivity of node i within modules (Zi), the connectivity of node i among modules (Pi), and the number of key bacteria were high at the Taizishan and Heijizui sites, which were associated with higher TN contents than at the other sites. Among the physicochemical properties of water, TN, ammonia nitrogen (NH4-N), pH, COD, and dissolved oxygen (DO) might have great influences on the functional units of the bacterial communities in bacterioplankton molecular networks. This study improves the understanding of the structure and function of bacterioplankton communities in the Danjiangkou Reservoir.

[Community Structure and Predictive Functional Analysis of Surface Water Bacterioplankton in the Danjiangkou Reservoir].

Bacterioplankton are important components of aquatic ecosystems, and play a crucial role in the global biogeochemical cycle of nitrogen. In this study, surface-water samples were collected from Kuxin (the center of Danjiangkou Reservoir) and Qushou (the Middle Route of the South-to-North Water Diversion Project's canal head) in the Danjiangkou Reservoir in May 2016. Total DNA was isolated, and high-throughput sequencing was performed to analyze the community structure and diversity of bacteria. Phylogenetic analyses of 16S rDNA sequences showed that bacterial communities included species from 12 major phylogenetic groups. The predominant phylogenetic groups included Proteobacteria, Bacteroidetes, Firmicutes, Cyanobacteria, and Verrucomicrobia. The microbial biodiversity of Danjiangkou Reservoir bacterioplankton was greater in water samples from Qushou than in those from Kuxin. PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states) was used to determine the metabolic and functional abilities of the observed bacterial communities. Our results revealed a wide genetic diversity of organisms involved in various essential processes, such as Amino acid transport and metabolism, Transcription, Energy production and conversion, and Carbohydrate transport and metabolism. Thirty-five metabolic pathways involving nitrogen were detected. Key genes impacting the nitrogen cycle were detected in both the Kuxin and Qushou samples, and these encoded enzymes involved in nitrogen fixation (nifH), nitrification (hao), denitrification (narG、nirK、norB、nosZ), and assimilatory and dissimilatory nitrogen reduction to ammonia (nasA、narB、napA、nirA、nirB、nrfA). Copy numbers of 16S rRNA genes of each detected phylotype of Danjiangkou Reservoir bacterioplankton were uniformly higher in water samples from Kuxin than in water samples from Qushou. Our analyses of differences in nitrogen abatement potential between water samples, based on bacterial community composition and function, provide a foundation for setting water environmental protection policies in the Danjiangkou Reservoir.

Planktonic fungal community structures and their relationship to water quality in the Danjiangkou Reservoir, China.

Planktonic fungi are important components of aquatic ecosystems, and analyses of their community composition and function have far-reaching significance for the ecological management and maintenance of reservoir environments. However, few studies have investigated the composition, distribution, and function of planktonic fungi in reservoir ecosystems and their relationship with water quality. Here, the composition of the planktonic fungal community in the surface water layer of the Danjiangkou Reservoir is investigated using Illumina MiSeq sequencing. According to the results, the reservoir community is primarily composed of 7 phyla, including Ascomycota, Rozellomycota, Basidiomycota, Chytridiomycota, and Zygomycota, comprising 294 genera, demonstrating the rich diversity of this community. Redundancy analysis (RDA) of the planktonic fungal community and environmental factors showed dissolved oxygen (DO), chemical oxygen demand (COD), total nitrogen (TN), chlorophyll a (Chl a), and permanganate (CODMn) to be important factors influencing the distribution of planktonic fungi. Spearman correlation analysis of the planktonic fungal community composition and diversity indices with physical and chemical water quality parameters showed that the impacts of TN, COD and DO were the most significant. The results of this study on the planktonic fungal community in the Danjiangkou Reservoir area using high-throughput sequencing revealed that the community is sensitive to water quality parameters. This result provides a reference for studying the composition and distribution of the planktonic fungal community in Danjiangkou Reservoir and its role in the biogeochemical cycle.

Integrated metagenomics and molecular ecological network analysis of bacterial community composition during the phytoremediation of cadmium-contaminated soils by bioenergy crops.

Two energy crops (maize and soybean) were used in the remediation of cadmium-contaminated soils. These crops were used because they are fast growing, have a large biomass and are good sources for bioenergy production. The total accumulation of cadmium in maize and soybean plants was 393.01 and 263.24µg pot-1, respectively. The rhizosphere bacterial community composition was studied by MiSeq sequencing. Phylogenetic analysis was performed using 16S rRNA gene sequences. The rhizosphere bacteria were divided into 33 major phylogenetic groups according to phyla. The dominant phylogenetic groups included Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Bacteroidetes. Based on principal component analysis (PCA) and unweighted pair group with arithmetic mean (UPGMA) analysis, we found that the bacterial community was influenced by cadmium addition and bioenergy cropping. Three molecular ecological networks were constructed for the unplanted, soybean- and maize-planted bacterial communities grown in 50mgkg-1 cadmium-contaminated soils. The results indicated that bioenergy cropping increased the complexity of the bacterial community network as evidenced by a higher total number of nodes, the average geodesic distance (GD), the modularity and a shorter geodesic distance. Proteobacteria and Acidobacteria were the keystone bacteria connecting different co-expressed operational taxonomic units (OTUs). The results showed that bioenergy cropping altered the topological roles of individual OTUs and keystone populations. This is the first study to reveal the effects of bioenergy cropping on microbial interactions in the phytoremediation of cadmium-contaminated soils by network reconstruction. This method can greatly enhance our understanding of the mechanisms of plant-microbe-metal interactions in metal-polluted ecosystems.

[Expression and functional analyses of the Arabidopsis QUA1 gene in light signal transduction].

Plants not only use light as an energy source for photosynthesis, but also have to monitor the light quality and quantity input to execute appropriate physiological and developmental responses, such as cell differentiation, structural and functional changes, as well as the formation of tissues and organs. The process is referred to as photomorphogenesis. Arabidopsis QUA1 (QUASIMODO1), which functions in pectin synthesis, is identified as a member of glycosyltransferases. Previously, the hypocotyl elongation of the qua1-1 mutant was shown to be inhibited under dark conditions. In this study, we used the qua1-1/cry1 and qua1-1/phyB double mutants as the materials to study the function of the QUA1 gene in light signal transduction. The results showed that QUA1 not only participated in hypocotyl elongation under dark conditions, but also in blue light, red light and far red light conditions. In qua1-1 mutant seedlings, both the cell length of hypocotyl and the light-regulated gene expression were affected. Compared with cry1 and phyB mutants, qua1-1/cry1 and qua1-1/phyB double mutants had the shorter hypocotyl. Light-regulated gene expression was also affected in the double mutants. These data indicated that QUA1 might participate in the light signal transduction regulated by CRY1 and PHYB. Hence, the QUA1 gene may play multiple roles in light signal transduction by regulating the cell elongation and light-regulated gene expression.