A5028031668- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Bioenergy crop production and management
- Plant-Microbe Interactions and Immunity
- Gut microbiota and health
- Legume Nitrogen Fixing Symbiosis
- Mycorrhizal Fungi and Plant Interactions
- Biofuel production and bioconversion
- Soil Carbon and Nitrogen Dynamics
- Peatlands and Wetlands Ecology
- Botany and Plant Ecology Studies
- Ocular Infections and Treatments
- Ocular Surface and Contact Lens
- Plant Disease Resistance and Genetics
- Health, Environment, Cognitive Aging
- RNA modifications and cancer
- Genetic diversity and population structure
- Molecular Biology Techniques and Applications
- SARS-CoV-2 detection and testing
- SARS-CoV-2 and COVID-19 Research
- COVID-19 diagnosis using AI
- Species Distribution and Climate Change
- Connexins and lens biology
- Soybean genetics and cultivation
- Plant nutrient uptake and metabolism
Michigan State University
2016-2023
Diversitech (United States)
2016-2021
Great Lakes Bioenergy Research Center
2018
Michigan United
2016-2018
Argonne National Laboratory
2010-2011
Purpose.: Ocular surface (OS) microbiota contributes to infectious and autoimmune diseases of the eye. Comprehensive analysis microbial diversity at OS has been impossible because limitations conventional cultivation techniques. This pilot study aimed explore true human using DNA sequencing-based detection identification bacteria. Methods.: Composition bacterial community was characterized deep sequencing 16S rRNA gene amplicon libraries generated from total conjunctival swab DNA. The...
Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity functions and activities
Abstract Global climate change and shifting land‐use are increasing plant stress due to abiotic factors such as drought, heat, salinity cold, well via the intensification of biotic stressors herbivores pathogens. The ability plants tolerate stresses is modulated by bacteria fungi that live on or inside tissues comprise microbiome. However, impacts diverse classes beneficial members microbiome contrasting impact most commonly studied independently each other. Our meta‐analysis 288 experiments...
A database of curated genomes is needed to better assess soil microbial communities and their processes associated with differing land management environmental impacts. Interpreting metagenomic datasets existing sequence databases challenging because these are biased towards medical biotechnology research can result in misleading annotations. We have a 922 soil-associated organisms (888 bacteria 34 archaea). Using this database, we evaluated phyla functions that enriched soils as well those...
Associative N fixation (ANF), the process by which dinitrogen gas is converted to ammonia bacteria in casual association with plants, has not been well-studied temperate ecosystems. We examined ANF potential of switchgrass (Panicum virgatum L.), a North American prairie grass whose productivity often unresponsive fertilizer addition, via separate short-term 15N2 incubations rhizosphere soils and excised roots four times during growing season. Measurements occurred along fertilization...
To establish and spread in a new location, an invasive species must be able to carry out its life cycle novel environmental conditions. A key trait underlying fitness is the shift from vegetative reproductive growth through floral development. In this study, we used common garden experiment genotyping-by-sequencing test whether latitudinal flowering cline of North American plant Medicago polymorpha was translocated European native range multiple introductions, or rapidly established due...
Sequencing of the 16S rRNA gene (16S) has long been a go-to method for microbiome characterization due to its accessibility and lower cost compared shotgun metagenomic sequencing (SMS). However, rarely provides species-level resolution cannot provide direct assessment other taxa (e.g., viruses fungi) or functional content. Shallow (SSMS) emerged as an approach bridge gap between deep sequencing. SSMS is cost-competitive with sequencing, while also providing content insights. In present...
Switchgrass (Panicum virgatum L.) remains the preeminent American perennial (C4) bioenergy crop for cellulosic ethanol, that could help displace over a quarter of US current petroleum consumption. Intriguingly, there is often little response to nitrogen fertilizer once stands are established. The rhizosphere microbiome plays critical role in cycling and overall plant nutrient uptake. We used high-throughput metagenomic sequencing characterize switchgrass microbial community before after...
Abstract A database of curated genomes is needed to better assess soil microbial communities and their processes associated with differing land management environmental impacts. Interpreting metagenomic datasets existing sequence databases challenging because these are biased towards medical biotechnology research can result in misleading annotations. We have a 922 soil-associated organisms (888 bacteria 34 archaea). Using this database, we evaluated phyla functions that enriched soils as...
ABSTRACT The most recent virus from the Coronaviridae family infecting humans, SARS-CoV-2, has resulted in a global pandemic. As part of surveillance efforts, SARS-CoV-2 genomes are increasingly being made publicly available. Methods that include both short- and long-read sequencing have been used to elucidate genomes; however, many these untargeted approaches may require deeper for greater genome coverage. For this reason, sequence capture or amplicon-based developed. present study...
Bradyrhizobium sp. strain USDA 3456 is a historic from the United States Department of Agriculture (USDA) Agricultural Research Service (ARS) National Rhizobium Germplasm Collection isolated Vigna unguiculata (cowpea) in 1966. Strain has been utilized global agricultural applications, including improving soil nitrogen fertility. The draft genome sequence here provides genetic reference novel diazotroph.
Pairing plants with plant growth-promoting bacteria is critical to the future of agriculture. Bradyrhizobium sp. strain USDA 3458 isolated from Vigna unguiculata (cowpea) paired cowpea genotype IT82E-16 represents a novel combination in arid regions. Here, we report draft genome sequence 3458.
Here, we report the draft genome sequence of type strain Ideonella azotifigens DSMZ21438T (formally 1a22T = JCM15503T). a novel betaproteobacterial non-symbiotic nitrogen-fixing grass rhizosphere dwelling microbe. The 891,561 paired-end shotgun reads were quality filtered and decontaminated with ATLAS pipeline, then assembled Unicycler. size is 6,257,981 bp, an N50 7,849 G+C content 66.71%, 5,882 predicted protein-coding genes. I. represents first member genus isolated from soil, providing...
Switchgrass (Panicum virgatum L.) remains the preeminent American perennial (C4) bioenergy crop for cellulosic ethanol that could help displace over a quarter of US current petroleum consumption. Intriguingly, there is often little response to nitrogen fertilizer once stands are established. The rhizosphere microbiome plays critical role in cycling and overall plant nutrient uptake. We used high-throughput metagenomic sequencing characterize switchgrass microbial community (5.37 billion...
Paenibacillus sp. tmac-D7 was isolated from coastline growing Trifolium macraei (double-head clover) root nodules Bodega Bay, California. The draft genome is 5,567,337 bp with a G+C% of 52.4%, an N50 114,261 bp, and 5,282 predicted protein-coding genes. Paenibacillus, while found in many other environments, frequently nodules, acting as plant pathogen antagonists. the first non-rhizobial endophyte isolate wild clover).