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Biofilters have been broadly applied to degrade the odorous gases from industrial emissions. A industrial scale biofilter was set up to treat the odorous gases. To explore biofilter potentials, the microbial community structure and function must be well defined. Using of improved biofilter, the differences in microbial community structures and functions in biofilters before and after treatment were investigated by metagenomic analysis. Odorous gases have the potential to alter the microbial community structure in the sludge of biofilter. A total of 90,016 genes assigned into various functional metabolic pathways were identified. In the improved biofilter, the dominant phyla were Proteobacteria, Planctomycetes, and Chloroflexi, and the dominant genera were Thioalkalivibrio, Thauera, and Pseudomonas. Several xenobiotic biodegradation-related pathways showed significant changes during the treatment process. Compared with the original biofilter, Thermotogae and Crenarchaeota phyla were significantly enriched in the improved biofilter, suggesting their important role in nitrogen-fixing. Furthermore, several nitrogen metabolic pathway-related genes, such as nirA and nifA, and sulfur metabolic pathway-related genes, such as fccB and phsA, were considered to be efficient genes that were involved in removing odorous gases. Our findings can be used for improving the efficiency of biofilter and helping the industrial enterprises to reduce the emission of waste gases. [ABSTRACT FROM AUTHOR]

Key message: We employed both metabolomic and transcriptomic approaches to explore the accumulation patterns of physalins, flavonoids and chlorogenic acid in Physalis angulata and revealed the genes associated with the biosynthesis of bioactive compounds under methyl-jasmonate (MeJA) treatment. Physalis angulata L. is an annual Solanaceae plant with a number of medicinally active compounds. Despite the potential pharmacological benefits of P. angulata, the scarce genomic information regarding this plant has limited the studies on the mechanisms of bioactive compound biosynthesis. To facilitate the basic understanding of the main chemical constituent biosynthesis pathways, we performed both metabolomic and transcriptomic approaches to reveal the genes associated with the biosynthesis of bioactive compounds under methyl-jasmonate (MeJA) treatment. Untargeted metabolome analysis showed that most physalins, flavonoids and chlorogenic acid were significantly upregulated. Targeted HPLC–MS/MS analysis confirmed variations in the contents of two important representative steroid derivatives (physalins B and G), total flavonoids, neochlorogenic acid, and chlorogenic acid between MeJA-treated plants and controls. Transcript levels of a few steroid biosynthesis-, flavonoid biosynthesis-, and chlorogenic acid biosynthesis-related genes were upregulated, providing a potential explanation for MeJA-induced active ingredient synthesis in P. angulata. Systematic correlation analysis identified a number of novel candidate genes associated with bioactive compound biosynthesis. These results may help to elucidate the regulatory mechanism underlying MeJA-induced active compound accumulation and provide several valuable candidate genes for further functional study. [ABSTRACT FROM AUTHOR]

The GH3 genes play vital roles in auxin homeostasis by conjugating excess auxin to amino acids. However, how GH3 genes function during grafting in Chinese hickory (Carya cathayensis) is largely unknown. Here, based on the transcriptome database, a comprehensive identification and expression profiling analysis of 12 GH3 genes in Chinese hickory were performed. Phylogenetic analysis indicated that CcGH3-x exists in a specific subfamily. To understand the roles of CcGH3 genes, tissue-specific expression and the response to different phytohormones were determined. Expression profiles of GH3 genes of Chinese hickory during grafting were analysed. The data suggested that 10 CcGH3 genes were down-regulated at an early stage of grafting, indicating that auxin homeostasis regulated by the CcGH3 family might be inhibited at initial stages. At the completion of grafting, expression levels of members of the CcGH3 family were restored to normal levels. Endogenous auxin levels were also measured, and the data showed that free auxin decreased to the lowest level at an early stage of grafting, and then increased during grafting. Auxin amino acid conjugation increased at an early stage of grafting in rootstock, and then decreased with progression of the graft union. Our results demonstrate that the reduced expression of CcGH3 family genes during grafting might contribute to the release of free auxin, making an important contribution to the recovery of auxin levels after grafting. [ABSTRACT FROM AUTHOR]

Engineered microbial ecosystems in biofilters have been widely applied to treat odorous gases from industrial emissions. Variations in microbial community structure and function associated with the removal of odorous gases by biofilters are largely unknown. This study performed a metagenomic analysis to discover shifts in microbial community structures in a commercial scale biofilter after treating odorous gas. Our study identified 175,675 functional genes assigned into 43 functional KEGG pathways. Based on the unigene sequences, there were significant changes in microbial community structures in the biofilter after treating odorous gas. The dominant genera were Thiobacillus and Oceanicaulis before the treatment, and were Acidithiobacillus and Ferroplasma after the treatment. A clustering analysis showed that the number of down-regulated microbes exceeded the number of up-regulated microbes, suggesting that odorous gas treatment reduced in microbial community structures. A differential expression analysis identified 29,975 up- and 452,599 down-regulated genes. An enrichment analysis showed 17 classic types of xenobiotic biodegradation pathways. The results identified 16 and 15 genes involved in ammonia and sulfite metabolism, respectively; an analysis of their relative abundance identified several up-regulated genes, which may be efficient genes involved in removing odorous gases. The data provided in this study demonstrate the changes in microbial communities and help identify the dominant microflora and genes that play key roles in treating odorous gases. [ABSTRACT FROM AUTHOR]

Downy mildew is one of the most prevalent diseases that cause destructive damages to the production of cucumber worldwide. To understand the regulation mechanism underlying the responses of cucumber leaves to P. cubensis infection, a proteomic approach was used to profile protein variations in cucumber leaves during a incubation period of up to 72 h. Differentially accumulated proteins (DAPs) at different time points after inoculation were investigated. A total of 90 DAP spots were identified using an integrated approach involving two-dimensional gel electrophoresis and MALDI-TOF-TOF mass spectrometer. Functional classification showed that most DAPs were putatively involved in metabolic reaction, transportation, protein folding, proteolysis, cell proliferation, photosynthesis, glucose metabolism, translation elongation, damage response, and other closely related biological processes. Several antioxidants, such as Cu/Zn-superoxide dismutase and 2-cysteine peroxiredoxins, were significantly up-regulated under P. cubensis infection. These antioxidants may play roles in regulating potentially harmful reactive oxygen species under pathogen infections. Furthermore, changes in the photosynthetical system-related proteins and heat shock proteins were observed under P. cubensis infection. Our data provides fundamental resources for identifying candidate proteins and metabolic pathways involved in the responses of cucumber plants to P. cubensis infection. [ABSTRACT FROM AUTHOR]

Dendrobium officinale is a traditional medicinal herb with a variety of bioactive components. Alkaloid is one of the major active ingredients of Dendrobium plants, and its immune regulatory effects have been well-studied. Although a number of genes involved in the biosynthetic pathway of alkaloids have been elucidated, the regulation mechanism underlying the methyl-jasmonate (MeJA)-induced accumulation of alkaloids in D. officinale is largely unknown. In our study, a total of 4,857 DEGs, including 2,943 up- and 1,932 down-regulated genes, were identified between the control and MeJA-treated groups. Kyoto Encyclopedia of Genes and Genomes annotation showed that a number of DEGs were associated with the putative alkaloid biosynthetic pathway in D. officinale. The main group of Dendrobium alkaloids are sesquiterpene alkaloids, which are the downstream products of mevalonate (MVA) and methylerythritol 4-phosphate (MEP) pathway. Several MVA and MEP pathway genes were significantly up-regulated by the MeJA treatment, suggesting an active precursor supply for the alkaloid biosynthesis under MeJA treatment. A number of MeJA-induced P450 family genes, aminotransferase genes and methyltransferase genes were identified, providing several important candidates to further elucidate the sesquiterpene alkaloid biosynthetic pathway of D. officinale. Furthermore, a large number of MeJA-induced transcript factor encoding genes were identified, suggesting a complex genetic network affecting the sesquiterpene alkaloid metabolism in D. officinale. Our data aids to reveal the regulation mechanism underlying the MeJA-induced accumulation of sesquiterpene alkaloids in D. officinale. [ABSTRACT FROM AUTHOR]

Taxus media is an important species in the family Taxaceae with high medicinal and commercial value. Overexploitation and illegal trade have led T. media to a severe threat of extinction. In addition, T. media and other Taxus species have similar morphological traits and are easily misidentified, particularly during the seedling stage. The purpose of this study is to develop a species-specific marker for T. media. Through a screening of 36 start codon targeted (SCoT) polymorphism primers, among 15 individuals of 4 Taxus species (T. media, T. chinensis, T. cuspidate and T. fuana), a clear species-specific DNA fragment (amplified by primer SCoT3) for T. media was identified. After isolation and sequencing, a DNA sequence with 530 bp was obtained. Based on this DNA fragment, a primer pair for the sequence-characterized amplified region marker was designed and named MHSF/MHSR. PCR analysis with primer pair MHSF/MHSR revealed a clear amplified band for all individuals of T. media but not for T. chinensis, T. cuspidate and T. fuana. Therefore, this marker can be used as a quick, efficient and reliable tool to identify T. media among other related Taxus species. The results of this study will lay an important foundation for the protection and management of T. media as a natural resource. [ABSTRACT FROM AUTHOR]

Background: Tremendous progress has been made in understanding the functions of the GLUTAMATE RECEPTOR-LIKE (GLR) family in Arabidopsis. Still, the functions of OsGLRs in rice, especially the ion channel activities, are largely unknown. Results: Using the aequorin-based luminescence imaging system, we screened the specificity of amino acids involved in the induction of Ca flux in rice roots. Of all the amino acids tested, glutamate (Glu) was the only one to trigger Ca flux significantly in rice roots. Detailed analysis showed a dose response of Ca increase to different concentrations of Glu. In addition, the Ca spike response to Glu was rapid, within 20 s after the application. A desensitization assay and pharmacological tests showed that the Glu-triggered Ca flux is mediated by OsGLRs. Whole genome analysis identified 13 OsGLR genes in rice, and these genes have various expression patterns in different tissues. Subcellular localization studies showed that all the OsGLRs examined are likely localized to the plasma membrane. Bacteria growth assays showed that at least OsGLR2.1 and OsGLR3.2 have the potential to mediate ion uptake in bacteria. Further analysis using Fura-2-based Ca imaging revealed a Glu-triggered Ca increase in OsGLR2.1-expressing human embryonic kidney (HEK) cells. Conclusions: Our work provides a molecular basis for investigating mechanisms of Glu-triggered Ca flux in rice. [ABSTRACT FROM AUTHOR]

Background and aims: Our recent research revealed that several key enzymes involved in flavonoid biosynthesis played vital roles in soybean's tolerance to salinity. Since the flavonoids also act as important signals mediating the establishment of symbiosis between rhizobium and leguminous plants, the Sinorhizobium meliloti 1021 was tested to find out whether it had any impact on soybean's tolerance to salt stress. Methods: The roots of soybean seedling ( Glycine max cultivar Union85140) were inoculated by soak in diluted S. meliloti 1021 suspension and then the seedlings were transferred in sphagnum peat and pearlite soil. Five days after inoculation, the seedlings were treated with salt solutions every four days until harvest. Results: Soybean seedlings inoculated with S. meliloti 1021 demonstrated significantly stronger lodging-resistance and the fresh weight of the whole plants increased by 10.95-30.95 % compared with that of the non-inoculated plants. These changes in soybean seedlings might be resulted from: 1. S. meliloti 1021 playing a role in helping soybean plant to exclude Na while absorb K, reducing ionic stress caused by salts; 2. S. meliloti 1021 enhancing the antioxidant enzymes' activities on reducing oxidative stress caused by salts; 3. S. meliloti 1021 increasing the content of osmotic compounds, thus reducing osmotic stress caused by salts. In addition, S. meliloti 1021 played significant roles in regulating the transcription of several key enzymes related to flavonoids metabolism (cytochrome P450 monooxygenase, chalcone synthase and chalcone isomerase), ROS scavenging (catalases, ascorbate peroxidase, glutathione S-transferase and superoxide dismutase), and other salt-responsive genes (Stress-induced protein SAM22, PR10-like protein and Phosphatidylinositol-specific phospholipase C) in soybean seedlings. Conclusion: These results showed that S. meliloti 1021 significantly enhanced soybean's ability to adapt to saline soil, mostly due to its effect on flavonoids metabolism in plants. [ABSTRACT FROM AUTHOR]

In recent years, a novel family of calmodulin-binding transcription activators (CAMTAs) has been reported in various species. The CAMTAs share a conserved domain organization, with a CG-1 DNA-binding domain, a transcription factor immunoglobulin domain, several ankyrin repeats, a calmodulin-binding domain, and a varying number of IQ motifs. CAMTAs participate in transcriptional regulation by recognizing and binding to a specific cis-element: (G/A/C) CGCG(C/G/T). Plants suffer from the environmental challenges, including abiotic and biotic stresses. Investigations in various plant species indicate a broad range of CAMTA functions involved in developmental regulation, environmental stress response, and hormone cross talk. In this review, we focus on the expression patterns and biological functions of CAMTAs to explore their probable applications in biotechnology. Furthermore, the identification and phylogenetic analysis of CAMTAs in crops could open new perspectives for enhancing stress tolerance, which could lead to improved crop production. [ABSTRACT FROM AUTHOR]

Iron deficiency is one of the most serious nutrient limiting factors that affect rice plant growth and photosynthesis. Several phytohormones, including auxin, participate in iron uptake and homeostasis. However, how auxin signaling is involved in iron deficiency-induced inhibition of shoot growth and photosynthetic efficiency is largely unknown. The Nipponbare (NIP) seedlings displayed typical chlorotic symptoms, biomass reduction and photosynthesis depression when subjected to iron deficiency. We measured the soluble Fe content in the shoots under different conditions. The soluble Fe content in the shoots under Fe deficiency was increased by 1-naphthoxyaceticacids (1-NOA) treatment and was decreased by 1-naphthaleneacetic acid (NAA) treatment. Blocking (1-NOA treatment) or enhancement (NAA treatment) of auxin signaling also affects photosynthetic parameters under Fe deficiency conditions. Furthermore, rice microarray data (GSE17245 and GSE39429) were used to analyze the relationship between iron deficiency responses and auxin signaling in shoots. Most iron deficiency response gene expression levels in the shoots increased under exogenous auxin treatment, and most auxin early response gene expression levels responded to iron deficiency. It suggested that there is a crosstalk between iron deficiency signaling and auxin signaling. Our results indicated that iron deciencyinduced growth inhibition and photosynthesis depression were mediated by systemic auxin signaling. [ABSTRACT FROM AUTHOR]

Auxin plays a pivotal role in the regulation of plant growth and development by controlling the expression of auxin response genes rapidly. As one of the major auxin early response gene families, Gretchen Hagen 3 ( GH3) genes are involved in auxin homeostasis by conjugating excess auxins to amino acids. However, how GH3 genes function in environmental stresses and rhizobial infection responses in Medicago truncatula are largely unknown. Here, based on the latest updated M. truncatula genome, a comprehensive identification and expression profiling analysis of MtGH3 genes were performed. Our data showed that most of MtGH3 genes were expressed in tissue-specific manner and were responsive to environmental stress-related hormones. To understand the possible roles of MtGH3 genes involved in symbiosis establishment between M. truncatula and symbiotic bacteria, quantitative real-time polymerase chain reaction (qRT-PCR) was used to test the expressions of MtGH3 genes during the early phase of Sinorhizobium meliloti infection. The expression levels of most MtGH3 genes were upregulated in shoots and downregulated in roots by S. meliloti infection. The differences in expression responses to S. meliloti infection between roots and shoots were in agreement with the results of free indoleacetic acid (IAA) content measurements. The identification and expression analysis of MtGH3 genes at the early phase of S. meliloti infection may help us to understand the role of GH3-mediated IAA homeostasis in the regulation of nodule formation in model legumes M. truncatula. [ABSTRACT FROM AUTHOR]

Background and aims: Environmental stresses are major hurdles for the production of soybean ( Glycine max), a major food crop that is able to acquire N and P nutrients through symbiotic association with rhizobia and arbuscular mycorhizal fungi. The calmodulin-binding transcription activators (CAMTA) belong to a transcription factor family that plays critical roles in plant responses to both abiotic and biotic stresses such as drought, cold and attacks from pathogens and insects. Our current knowledge about CAMTA genes in soybean is scarce, but is of critical significance to the improvement of stress tolerance and production of soybean, a worldwide major protein-rich food crop. Methods: In this study, we first searched for all the CAMTA homologous genes in the whole genome of soybean. We then surveyed the distribution of stress-related cis-regulatory elements in the −1.5 kb promoter regions of all GmCAMTA genes. Next, we analyzed the expression patterns of all these GmCAMTAs in root and leaf tissues and studied how they respond to various stress treatments by quantitative RT-PCR. Results: Fifteen genes in the soybean genome were identified to encode CAMTA proteins, and their gene structures and protein sequences were highly similar to that in Arabidopsis. Like their counterparts in other plants and animals, all GmCAMTAs contain a CG-1 DNA-binding domain in the N terminal region, followed by a TIG domain, ankyrin repeats, IQ motifs and a calmodulin binding site. All GmCAMTA genes were found to be expressed in root and leaf tissues. The expression of all GmCAMTAs was induced by salinity. Most of the GmCAMTA genes were induced by several stresses and hormone signals including dehydration, cold, HO, abscisic acid, salicylic acid, and methyl jasmonate. Only four GmCAMTAs ( GmCAMTA5, 6, 7 and 10) were found to be repressed by HO treatment. Consistent with their responsiveness to all these stimuli, many stress-related cis-elements were found in the promoter regions of all the GmCAMTA genes. Conclusions: These results indicate that GmCAMTA genes are responsive to various stress and hormone signals, and likewise, GmCAMTAs could act as critical components in regulating soybean tolerances to various environmental stresses. [ABSTRACT FROM AUTHOR]