Project description:Many trees form ectomycorrhizal symbiosis with fungi. During symbiosis, the tree roots supply sugar to the fungi in exchange for nitrogen, and this process is critical for the nitrogen and carbon cycles in forest ecosystems. However, the extents to which ectomycorrhizal fungi can liberate nitrogen and modify the soil organic matter and the mechanisms by which they do so remain unclear since they have lost many enzymes for litter decomposition that were present in their free-living, saprotrophic ancestors. Using time-series spectroscopy and transcriptomics, we examined the ability of two ectomycorrhizal fungi from two independently evolved ectomycorrhizal lineages to mobilize soil organic nitrogen. Both species oxidized the organic matter and accessed the organic nitrogen. The expression of those events was controlled by the availability of glucose and inorganic nitrogen. Despite those similarities, the decomposition mechanisms, including the type of genes involved as well as the patterns of their expression, differed markedly between the two species. Our results suggest that in agreement with their diverse evolutionary origins, ectomycorrhizal fungi use different decomposition mechanisms to access organic nitrogen entrapped in soil organic matter. The timing and magnitude of the expression of the decomposition activity can be controlled by the below-ground nitrogen quality and the above-ground carbon supply.
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:The association between soil microbes and plant roots is present in all natural and agricultural environments. Microbes can be beneficial, pathogenic, or neutral to the host plant development and adaptation to abiotic or biotic stresses. Progress in investigating the functions and changes in microbial communities in diverse environments have been rapidly developing in recent years, but the changes in root function is still largely understudied. The aim of this study was to determine how soil bacteria influence maize root transcription and microRNAs (miRNAs) populations in a controlled inoculation of known microbes over a defined time course. At each time point after inoculation of the maize inbred line B73 with ten bacterial isolates, DNA and RNA were isolated from roots. The V4 region of the 16S rRNA gene was amplified from the DNA and sequenced with the Illumina MiSeq platform. Amplicon sequencing of the 16S rRNA gene indicated that most of the microbes successfully colonized maize roots. The colonization was dynamic over time and varied with the specific bacterial isolate. Small RNA sequencing and mRNA-Seq was done to capture changes in the root transcriptome from 0.5 to 480 hours after inoculation. The transcriptome and small RNA analyses revealed epigenetic and transcriptional changes in roots due to the microbial inoculation. This research provides the foundational data needed to understand how plant roots interact with bacterial partners and will be used to develop predictive models for root response to bacteria.
