"Visualizing the Hidden Half: Plant-Microbe Interactions in the Rhizosphere" Plant roots and the associated rhizosphere constitute a dynamic environment that fosters numerous intra- and interkingdom interactions, including metabolite exchange between plants and soil mediated by root exudates and the...
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Pending Review Microbiomes contribute to multiple ecosystem services by transforming organic matter in soil. Extreme shifts in the environment, such as drying-rewetting cycles during drought, can impact microbial metabolism of organic matter by altering their physiology and function. These...
Elmore JR, Dexter GN, Baldino H, Huenemann JD, Francis R, Peabody GL 5th, Martinez-Baird J, Riley LA, Simmons T, Coleman-Derr D, Guss AM, Egbert RG. High-throughput genetic engineering of nonmodel and undomesticated bacteria via iterative site-specific genome integration. Sci Adv. 2023 Mar 10;9(10)...
The rhizosphere represents a dynamic and complex interface between plant hosts and the microbial community found in the surrounding soil. While it is recognized that manipulating the rhizosphere has the potential to improve plant fitness and health, engineering the rhizosphere microbiome through...
Agriculture is the largest source of greenhouse gases (GHG) production. Conversion of nitrogen fertilizers into more reduced forms by microbes through a process known as biological nitrification drives GHG production, enhances proliferation of toxic algal blooms, and increases cost of crop...
Metabolite exchange between plant roots and their associated rhizosphere microbiomes underpins plant growth promotion by microbes. Sorghum bicolor is a cereal crop that feeds animals and humans and is used for bioethanol production. Its root tips exude large amounts of a lipophilic benzoquinone...
A major challenge in biotechnology and biomanufacturing is the identification of a set of biomarkers for perturbations and metabolites of interest. Here, we develop a data-driven, transcriptome-wide approach to rank perturbation-inducible genes from time-series RNA sequencing data for the discovery...
The Sequel II System Sequencer is a high-throughput DNA sequencer machine developed and manufactured by PacBio , and is designed for high throughput, production-scale sequencing laboratories. Originally released in 2015, the Sequel system provides Single Molecule, Real-Time (SMRT) sequencing core...
"Moisture modulates soil reservoirs of active DNA and RNA viruses" Soil is known to harbor viruses, but the majority are uncharacterized and their responses to environmental changes are unknown. Here, we used a multi-omics approach (metagenomics, metatranscriptomics and metaproteomics) to detect...
Two factors that are well-known to influence soil microbiomes are the depth of the soil as well as the level of moisture. Previous works have demonstrated that climate change will increase the incidence of drought in soils, but it is unknown how fluctuations in moisture availability affect soil...
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The year 2014 solution files are based on model calibration effort based on inputs and data from Year 2014 as described in Khangaonkar et al. 2018). It includes water surface elevation, currents, temperature and salinity at an hourly interval. These netcdf files with 24 hourly records include...
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This data set provides ITS fungal community composition via DNA sequence analysis at the time of peat coring at the South End bog in 2013. These samples were collected outside the experimental enclosures and are pre-treatment with no experimental manipulation. These are part of the Spruce and...
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The year 2014 solution files are based on model calibration effort based on inputs and data from Year 2014 as described in Khangaonkar et al. 2018). It includes water surface elevation, currents, temperature and salinity at an hourly interval. These netcdf files with 24 hourly records include...
Category
This data set provides the 16S microbial community composition via DNA sequence analysis from ingrowth peat and sand cores at the South End bog in 2013. These samples were collected outside the experimental enclosures and are pre-treatment with no experimental manipulation. These are part of the...
Category
This data set provides the ITS fungal community composition via DNA sequence analysis from sand and peat ingrowth cores at the South End bog in 2013. These samples were collected outside the experimental enclosures and are pre-treatment with no experimental manipulation. These are part of the Spruce...