Project description:Gene expression patterns of the plant colonizing bacterium,Pseudomonas putida KT2440 were evaluated as a function of growth in the Arabidopsis thaliana rhizosphere. Gene expression in rhizosphere grown P. putida cells was compared to gene expression in non-rhizosphere grown cells. Keywords: Gene expression
Project description:Maize (Zea mays L.) is one of the major cereal crops worldwide. Increasing planting density is an effective way to improve crop yield. However, plants grown under high-density conditions compete for water, nutrients, and light, which often leads to changes in productivity. To date, few studies have determined the transcriptomic differences in maize leaves in response to different planting densities. This study examined the whole-genome expression patterns in the leaves of maize planted under high and low densities to identify density-regulated genes. Leaves at upper, ear, and lower stem nodes were collected at the grain-filling stage of the maize hybrid Xianyu335 grown under low-density planting and high-density planting. In total, 72, 733, and 1,739 differentially expressed genes (DEGs) were identified in the respective upper, ear, and lower leaves under HDP. Upregulated and downregulated DEGs in the upper and lower leaves were similar in number, whereas upregulated DEGs in the ear leaves were significantly higher in number than the downregulated DEGs. Functional analysis indicated that genes responding to HDP-related stresses were mediated by pathways involving four phytohormones responsible for metabolism and signaling, osmoprotectant biosynthesis, transcription factors, and fatty acid biosynthesis and protein kinases, which suggested that these pathways are affected by the adaptive responses mechanisms underlying the physiological and biochemical responses of the leaves of maize planted at high density.
Project description:Arsenic (As) bioavailability in the rice rhizosphere is influenced by many microbial interactions, particularly by metal-transforming functional groups at the root-soil interface. This study was conducted to examine As-transforming microbes and As-speciation in the rice rhizosphere compartments, in response to two different water management practices (continuous and intermittently flooded), established on fields with high to low soil-As concentration. Microbial functional gene composition in the rhizosphere and root-plaque compartments were characterized using the GeoChip 4.0 microarray. Arsenic speciation and concentrations were analyzed in the rhizosphere soil, root-plaque, porewater and grain samples. Results indicated that intermittent flooding significantly altered As-speciation in the rhizosphere, and reduced methyl-As and AsIII concentrations in the pore water, root-plaque and rice grain. Ordination and taxonomic analysis of detected gene-probes indicated that root-plaque and rhizosphere assembled significantly different metal-transforming functional groups. Taxonomic non-redundancy was evident, suggesting that As-reduction, -oxidation and -methylation processes were performed by different microbial groups. As-transformation was coupled to different biogeochemical cycling processes establishing functional non-redundancy of rice-rhizosphere microbiome in response to both rhizosphere compartmentalization and experimental treatments. This study confirmed diverse As-biotransformation at root-soil interface and provided novel insights on their responses to water management, which can be applied for mitigating As-bioavailability and accumulation in rice grains.
Project description:We sequenced mRNA of G. biloba leaves from different planting densities using the Illumina HiSeq4000 platform. We identified the transcriptome changes in leaves , which provided valuable information for uncovering the molecular mechanisms of flavonoid accumulation in G. biloba under different densities.
Project description:Microbial communities in the rhizosphere make significant contributions to crop health and nutrient cycling. However, their ability to perform important biogeochemical processes remains uncharacterized. Important functional genes, which characterize the rhizosphere microbial community, were identified to understand metabolic capabilities in the maize rhizosphere using GeoChip 3.0-based functional gene array method.
Project description:Subjects with different allergic phenotypes showed distinct gut microbial patterns and functions. AD+FA subjects showed the mixtures of gut microbial patterns of FA and AD, while gut microbial pattern of FA seems to dominate in subjects with AD+FA
Project description:Microbial communities in the rhizosphere make significant contributions to crop health and nutrient cycling. However, their ability to perform important biogeochemical processes remains uncharacterized. Important functional genes, which characterize the rhizosphere microbial community, were identified to understand metabolic capabilities in the maize rhizosphere using GeoChip 3.0-based functional gene array method. Triplicate samples were taken for both rhizosphere and bulk soil, in which each individual sample was a pool of four plants or soil cores. To determine the abundance of functional genes in the rhizosphere and bulk soils, GeoChip 3.0 was used.