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:Stable isotope probing (SIP) has been used to track nu- trient flows in microbial communities, but existing pro- tein-based SIP methods capable of quantifying the degree of label incorporation into peptides and proteins have been demonstrated only by targeting usually less than 100 proteins per sample. Our method automatically (i) identi- fies the sequence of and (ii) quantifies the degree of heavy atom enrichment for thousands of proteins from microbial community proteome samples. These features make our method suitable for comparing isotopic differences be- tween closely related protein sequences, and for detect- ing labeling patterns in low-abundance proteins or pro- teins derived from rare community members. The proteomic SIP method was validated using proteome samples of known stable isotope incorporation levels at 0.4%, 50%, and 98%. The method was then used to monitor incorporation of 15 N into established and regrow- ing microbial biofilms. The results indicate organism-spe- cific migration patterns from established communities into regrowing communities and provide insights into me- tabolism during biofilm formation. The proteomic SIP method can be extended to many systems to track fluxes of 13 C or 15 N in microbial communities. Molecular and Cellular Proteomics 10: 10.1074/mcp.M110.006049, 1–11, 2011.
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.
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.
Project description:Background: The soil environment is responsible for sustaining most terrestrial plant life on earth, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. Understanding the microbial metagenome of the detritusphere and how it responds to agricultural management such as crop rotations and soil tillage will be vital for improving global food production. Methods: The rhizosphere soils of wheat and chickpea growing under + and - decaying root were collected for metagenomics sequencing. A gene catalogue was established by de novo assembling metagenomic sequencing. Genes abundance was compared between bulk soil and rhizosphere soils under different treatments. Conclusions: The study describes the diversity and functional capacity of a high-quality soil microbial metagenome. The results demonstrate the contribution of the microbiome from decaying root in determining the metagenome of developing root systems, which is fundamental to plant growth, since roots preferentially inhabit previous root channels. Modifications in root microbial function through soil management, can ultimately govern plant health, productivity and food security.