A5082704150- Plant-Microbe Interactions and Immunity
- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Legume Nitrogen Fixing Symbiosis
- Bacteriophages and microbial interactions
- Peatlands and Wetlands Ecology
- Advanced Proteomics Techniques and Applications
- Microbial Metabolic Engineering and Bioproduction
- Plant Parasitism and Resistance
- Mycorrhizal Fungi and Plant Interactions
- Gut microbiota and health
- Biofuel production and bioconversion
- Plant Pathogenic Bacteria Studies
- Nanoparticles: synthesis and applications
- Coastal wetland ecosystem dynamics
- Botany and Plant Ecology Studies
- Microbial bioremediation and biosurfactants
- Photosynthetic Processes and Mechanisms
- Plant Virus Research Studies
- Advanced Nanomaterials in Catalysis
- Bacterial biofilms and quorum sensing
- Plant tissue culture and regeneration
- Metabolomics and Mass Spectrometry Studies
- Bacterial Genetics and Biotechnology
- RNA and protein synthesis mechanisms
Oak Ridge National Laboratory
2016-2025
University of Tennessee at Knoxville
2004-2016
Pacific Northwest National Laboratory
2007-2008
Clemson University
2007
University of British Columbia
2006
Joint Genome Institute
2003
University of Iowa
1997-2000
Cornell University
1997
Novant Health Forsyth Medical Center
1996
A set of oligonucleotide primers capable initiating enzymatic amplification (polymerase chain reaction) on a phylogenetically and taxonomically wide range bacteria is described along with methods for their use examples. One pair amplifying nearly full-length 16S ribosomal DNA (rDNA) from many bacterial genera; the additional are useful various exceptional sequences. Methods purification amplified material, direct sequencing, cloning, transcription outlined. An obligate intracellular parasite...
Rhodopseudomonas palustris is among the most metabolically versatile bacteria known. It uses light, inorganic compounds, or organic for energy. acquires carbon from many types of green plant–derived compounds by dioxide fixation, and it fixes nitrogen. Here we describe genome sequence R. palustris, which consists a 5,459,213-base-pair (bp) circular chromosome with 4,836 predicted genes plasmid 8,427 bp. The reveals that confer remarkably large number options within given type metabolism,...
The root-rhizosphere interface of Populus is the nexus a variety associations between bacteria, fungi, and host plant an ideal model for studying interactions plants microorganisms. However, such studies have generally been confined to greenhouse plantation systems. Here we analyze microbial communities from root endophytic rhizospheric habitats deltoides in mature natural trees both upland bottomland sites central Tennessee. Community profiling utilized 454 pyrosequencing with separate...
ABSTRACT Interest in engineered nanostructures has risen recent years due to their use energy conservation strategies and biomedicine. To ensure prudent development of nanomaterials, the fate effects such structures on environment should be understood. Interactions nanomaterials with environmental microorganisms are inevitable, but general consequences interactions remain unclear, a lack standard methods for assessing interactions. Therefore, we have initiated multianalytical approach...
Microorganisms have long been known to develop resistance metal ions either by sequestering metals inside the cell or effluxing them into extracellular media. Here we report biosynthesis of silver-based single nanocrystallites well-defined composition and homogeneous morphology utilizing γ-proteobacterium, Shewanella oneidensis MR-1, upon incubation with aqueous silver nitrate solution. Further characterization these particles revealed that crystals consist small, reasonably monodispersed...
Due to their unique antimicrobial properties silver nanocrystallites have garnered substantial attention and are used extensively for biomedical applications as an additive wound dressings, surgical instruments bone substitute materials. They also released into unintended locations such the environment or biosphere. Therefore it is imperative understand potential interactions, fate transport of nanoparticles with environmental biotic systems. Numerous factors including composition, size,...
Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity functions and activities
Shewanella oneidensis MR-1 is a facultative Fe(III)- and Mn(IV)-reducing microorganism serves as model for studying microbially induced dissolution of Fe or Mn oxide minerals well biogeochemical cycles. In soil sediment environments, S. biofilms form on mineral surfaces are critical mediating the metabolic interaction between this microbe insoluble metal phases. order to develop an understanding molecular basis biofilm formation, we investigated developing glass in hydrodynamic flow chamber...
Cytoplasmic incompatibility results in embryo mortality diploids, or all male offspring haplodiploids, when individuals carrying different cytoplasmic factors are crossed. have been identified as intracellular micro-organisms. Microbe-induced is found many insect taxa and may play a role reproductive isolation between populations. Such micro-organisms cause bidirectional species of the parasitoid wasp genus Nasonia. The phylogenetic relationship microorganisms (CIM) Nasonia was analysed...
To aid in the investigation of Populus deltoides microbiome, we generated draft genome sequences for 21 Pseudomonas strains and 19 other diverse bacteria isolated from roots. Genome isolates similar to Acidovorax, Bradyrhizobium, Brevibacillus, Caulobacter, Chryseobacterium, Flavobacterium, Herbaspirillum, Novosphingobium, Pantoea, Phyllobacterium, Polaromonas, Rhizobium, Sphingobium, Variovorax were generated.
Abstract Motivation: To assess the potential of different types sequence data combined with de novo and hybrid assembly approaches to improve existing draft genome sequences. Results: Illumina, 454 PacBio sequencing technologies were used generate assemblies for four bacteria, which assessed quality using summary statistics (e.g. number contigs, N50) in silico evaluation tools. Differences predictions multiple copies rDNA operons each respective bacterium evaluated by PCR Sanger sequencing,...
Adverse growth conditions can lead to decreased plant growth, productivity, and survival, resulting in poor yields or failure of crops biofeedstocks. In some cases, the microbial community associated with plants has been shown alleviate stress increase under suboptimal growing conditions. A systematic understanding how changes these is required understand contribution microbiome water utilization, nutrient uptake, ultimately yield. Using a inoculation strategy, we studied belowground Populus...
Sphagnum-dominated peatlands comprise a globally important pool of soil carbon (C) and are vulnerable to climate change. While peat mosses the genus Sphagnum known harbor diverse microbial communities that mediate C nitrogen (N) cycling in peatlands, effects change on microbiome composition functioning largely unknown. We investigated impacts experimental whole-ecosystem warming moss microbiome, focusing N2 fixing microorganisms (diazotrophs). To characterize response warming, we performed...
The biological function of the plant-microbiome system is result contributions from host plant and microbiome members. Populus root a diverse community that has high abundance β- γ-Proteobacteria, both classes which include multiple plant-growth promoting representatives. To understand contribution individual members in community, we studied simplified consisting Pseudomonas Burkholderia bacterial strains isolated hosts inoculated on axenic cutting controlled laboratory conditions. Both...
A reductive benzoate pathway is the central conduit for anaerobic biodegradation of aromatic pollutants and lignin monomers. Benzene ring reduction requires a large input energy this metabolic capability has, so far, been reported only in bacteria. To determine molecular basis environmentally important process, we cloned analyzed genes required degradation related compounds from phototrophic bacterium, Rhodopseudomonas palustris . cluster 24 was identified that includes twelve likely to be...
The bacterial genus Rhodopseudomonas is comprised of photosynthetic bacteria found widely distributed in aquatic sediments. Members the catalyze hydrogen gas production, carbon dioxide sequestration, and biomass turnover. genome sequence palustris CGA009 revealed a surprising richness metabolic versatility that would seem to explain its ability live heterogeneous environment like sediment. However, there considerable genotypic diversity among isolates. Here we report complete sequences four...
The application of systems biology tools holds promise for rational industrial microbial strain development. Here, we characterize a Zymomonas mobilis mutant (AcR) demonstrating sodium acetate tolerance that has potential importance in biofuel genome changes associated with AcR are determined using microarray comparative sequencing (CGS) and 454-pyrosequencing. Sanger analysis is employed to validate genomic differences investigate CGS 454-pyrosequencing limitations. Transcriptomics, genetic...
Colonization of plants by nonpathogenic Pseudomonas fluorescens strains can confer enhanced defense capacity against a broad spectrum pathogens. Few studies, however, have linked pathway regulation to primary metabolism and physiology. In this study, physiological data, metabolites, transcript profiles are integrated elucidate how molecular networks initiated at the root–microbe interface influence shoot whole-plant performance. Experiments with Arabidopsis thaliana were performed using...
Mycorrhiza helper bacteria (MHB) are known to increase host root colonization by mycorrhizal fungi but the molecular mechanisms and potential tripartite interactions poorly understood. Through an effort study Populus microbiome, we isolated 21 Pseudomonas strains from native deltoides roots. These bacterial isolates were characterized screened for MHB effectiveness on Populus-Laccaria system. Two additional (i.e., Pf-5 BBc6R8) existing collections included comparative purposes. We analyzed...