A5040034865- Microbial Community Ecology and Physiology
- Legume Nitrogen Fixing Symbiosis
- Plant-Microbe Interactions and Immunity
- Metabolomics and Mass Spectrometry Studies
- Plant nutrient uptake and metabolism
- Microbial Metabolic Engineering and Bioproduction
- Gut microbiota and health
- Soil Carbon and Nitrogen Dynamics
- Soybean genetics and cultivation
- Bacteriophages and microbial interactions
- Genomics and Phylogenetic Studies
- Phytase and its Applications
- Plant Pathogenic Bacteria Studies
- Photosynthetic Processes and Mechanisms
- Allelopathy and phytotoxic interactions
- Marine and coastal ecosystems
- Genomics, phytochemicals, and oxidative stress
- Phytoplasmas and Hemiptera pathogens
- Gene Regulatory Network Analysis
- Algal biology and biofuel production
- Plant Molecular Biology Research
- CRISPR and Genetic Engineering
- Microbial Natural Products and Biosynthesis
- Biocrusts and Microbial Ecology
- Microbial bioremediation and biosurfactants
Lawrence Berkeley National Laboratory
2016-2025
Joint Genome Institute
2018-2021
Cornell University
2008-2013
Abstract Root exudates are plant-derived, exported metabolites likely shaping root-associated microbiomes by acting as nutrients and signals. However, root exudation dynamics unclear thus also, if changes in reflected microbiome structure. Here, we assess commonalities differences between of different plant species, diurnal dynamics, well the accompanying methodological aspects exudate sampling. We find that should be collected for hours rather than days many metabolite abundances saturate...
QS-21 is a potent vaccine adjuvant and remains the only saponin-based that has been clinically approved for use in humans
Understanding plant-microbe interactions requires examination of root exudation under nutrient stress using standardized and reproducible experimental systems. We grew
Abstract Microorganisms play vital roles in modulating organic matter decomposition and nutrient cycling soil ecosystems. The enzyme latch paradigm posits microbial degradation of polyphenols is hindered anoxic peat leading to polyphenol accumulation, consequently diminished activity. This model assumes that are microbially unavailable under anoxia, a supposition has not been thoroughly investigated any type. Here, we use reactors amended with without chemically defined test this hypothesis,...
Soil organic matter (SOM) is comprised of a diverse array reactive carbon molecules, including hydrophilic and hydrophobic compounds, that impact rates SOM formation persistence. Despite clear importance to ecosystem science, little known about broad-scale controls on diversity variability in soil. Here, we show microbial decomposition drives significant the molecular richness between soil horizons across continental-scale gradient climate type (arid shrubs, coniferous, deciduous, mixed...
There is a dynamic reciprocity between plants and their environment: soil physiochemical properties influence plant morphology metabolism, root exudates shape the environment surrounding roots. Here, we investigate reproducibility of trait changes in response to three growth environments. We utilized fabricated ecosystem (EcoFAB) devices grow model grass Brachypodium distachyon distinct media across four laboratories: phosphate-sufficient -deficient mineral allowed assessment effects...
Abstract Root morphology and exudation define a plants’ sphere of influence in soils. In turn, soil characteristics plant growth, morphology, root microbiome, rhizosphere chemistry. Collectively, all these parameters have significant implications on the major biogeochemical cycles, crop yield, ecosystem health. However, how plants are shaped by physiochemistry particles is still not well understood. We explored particle size chemistry growth substrates affect model grass. grew Brachypodium...
Chemical signalling in the plant microbiome can have drastic effects on microbial community structure, and host growth development. Previously, we demonstrated that auxin metabolic signal interference performed by bacterial genus Variovorax via an degradation locus was essential for maintaining stereotypic root development ecologically relevant synthetic community. Here, dissect to define genes iadDE as necessary sufficient indole-3-acetic acid (IAA) interference. We determine crystal...
Roles of different ecological classes algal exometabolites in regulating microbial community composition are not well understood. Here, we identify from the model diatom Phaeodactylum tricornutum and demonstrate their potential to influence bacterial abundances. We profiled across a time course axenic growth using liquid chromatography-tandem mass spectrometry. then investigated 12 isolates on individual-identified exometabolites. Lastly, compared responses P. tricornutum-adapted enrichment...
Biocrusts are phototroph-driven communities inhabiting arid soil surfaces. Like plants, most photoautotrophs (largely cyanobacteria) in biocrusts thought to exchange fixed carbon for essential nutrients like nitrogen with cyanosphere bacteria. Here, we aim compare beneficial interactions rhizosphere and environments, including finding growth-promoting strains hosts from both environments. To examine this, performed a retrospective analysis of 16S rRNA gene sequencing datasets, host-microbe...
Chemical cues mediate interactions between marine phytoplankton and bacteria, underpinning ecosystem-scale processes including nutrient cycling carbon fixation. Phage infection alters host metabolism, stimulating the release of chemical from intact plankton, but how these dynamics impact ecology biogeochemistry is poorly understood. Here we determine phage on dissolved metabolite pools cyanobacteria subsequent chemotactic response heterotrophic bacteria using time-resolved metabolomics...
ABSTRACT Soybean [ Glycine max (L.) Merr.] seeds accumulate sucrose, raffinose family oligosaccharides (RFO), phytin, and small amounts of galactopinitols fagopyritols during normal seed maturation. RFO phytin are indigestible by non‐ruminant animals contribute to decreased feed efficiency, reduced mineral adsorption, phosphorous pollution in manure. Low raffinose, stachyose, may have imbibitional chilling sensitivity field emergence. The objective was characterize the profiles soluble...
Healthcare associated infections (HAI) with multidrug-resistant (MDR) bacteria continue to be a global threat, highlighting an urgent need for novel antibiotics. In this study, we assessed the potential of free fatty acids and cholesteryl esters that form part innate host defense as antibacterial agents use against MDR bacteria. Liposomes six different phospholipid mixtures were employed carrier four esters. Using modified MIC assay based on DNA quantification fluoroprobe Syto9, formulations...
With the advent of genome sequencing and mining technologies, secondary metabolite biosynthetic gene clusters (BGCs) within bacterial genomes are becoming easier to predict. For subsequent BGC characterization, clustered regularly interspaced short palindromic repeats (CRISPR) has contributed knocking out target genes and/or modulating their expression; however, CRISPR is limited strains for which robust genetic tools available. Here we present a strategy that combines with...
Microorganisms have evolved various life-history strategies to survive fluctuating resource conditions in soils. However, it remains elusive how the of microorganisms influence their processing organic carbon, which may affect microbial interactions and carbon cycling Here, we characterized genomic traits, exometabolite profiles, soil bacteria representing copiotrophic oligotrophic strategists. Isolates were selected based on differences ribosomal RNA operon (
Exometabolomics is an approach to assess how microorganisms alter, or react their environments through the depletion and production of metabolites. It allows examination soil microbes transform small molecule metabolites within environment, which can be used study resource competition cross-feeding. This most powerful when with defined media that enable tracking all However, microbial growth have traditionally been developed for isolation but not metabolite utilization profiling Liquid...
Summary Bacteria colonize plants and contribute to their health. Despite advances in our understanding of bacterial plant colonization, the extent which growth substrate influences molecular mechanisms enabling bacteria efficiently remains poorly understood. To evaluate if genes important for colonization are influenced by substrate, we used randomly barcoded transposon mutagenesis sequencing (RB-TnSeq) Paraburkholderia graminis OAS925, an efficient rhizosphere colonizer, Brachypodium...
ABSTRACT Bacteriophages impact soil bacteria through lysis, altering the availability of organic carbon and plant nutrients. However, magnitude nutrient uptake by plants from lysed remains unknown, partly because this process is challenging to investigate in field. In study, we extend ecosystem fabrication (EcoFAB 2.0) approaches study plant−bacteria−phage interactions comparing virocell (phage‐lysed) uninfected 15 N‐labelled bacterial necromass on nitrogen acquisition rhizosphere...
Mixed cultures of different microbial species are increasingly being used to carry out a specific biochemical function in lieu engineering single microbe do the same task. However, knowing how species’ metabolisms will integrate reach desired outcome is difficult problem that has been studied great detail using steady-state models. many biotechnological processes, as well natural habitats, represent more dynamic system. Examining individual use resources their growth medium or environment...
Synthetic microbial ecology has the potential to enhance productivity and resiliency of biotechnology processes compared approaches using single isolates. Engineering consortia is challenging; however, one approach that attracted significant attention creation synthetic obligate mutualism auxotrophic mutants depend on each other for exchange or cross-feeding metabolites. Here, we describe integration mutant library fitness profiling with mass spectrometry based exometabolomics as a method...
Domestication and breeding have affected interactions between plants their microbiomes in ways that are only beginning to be understood but may important implications for recruitment of rhizosphere microorganisms, particularly under stress conditions. We investigated the responses a modern maize (Zea mays subsp. mays) cultivar its wild relative, teosinte (Z. parviglumis), different phosphate availabilities. appraised plant-microbial holobiont stresses by profiling root exudate metabolomes,...
Solar panels can be found practically all over the world and represent a standard surface that colonized by microbial communities are resistant to harsh environmental conditions, including high irradiation, temperature fluctuations desiccation. These properties make them not only ideal sources of stress-resistant bacteria, but also devices study their colonization process from different areas Earth. We report here comprehensive description associated with solar in Berkeley, California....