Engineering topics

Jansson, Georg C.

Publications and source records attributed to Jansson, Georg C..

9 records

DOE OSTI2025

Holo-Omics disentangle drought response and biotic interactions among plant, endophyte and pathogen

Holo-omics provide a novel opportunity to study the interactions among fungi from different functional guilds in host plants in field conditions. We address the entangled responses of plant pathogenic and endophytic fungi associated with sorghum when droughted through the assembly of the most abundant fungal, endophyte genome from rhizospheric metagenomic sequences followed by a comparison of its metatranscriptome with the host plant metabolome and transcriptome. The rise in relative abundance of endophytic Acremonium persicinum (operational taxonomic unit 5 (OTU5)) in drought co-occurs with a rise in fungal membrane dynamics and plant metabolites, led by ethanolamine, a key phospholipid membrane component. The negative association between endophytic A. persicinum (OTU5) and plant pathogenic fungi co-occurs with a rise in expression of the endophyte's biosynthetic gene clusters coding for secondary compounds. Endophytic A. persicinum (OTU5) and plant pathogenic fungi are negatively associated under preflowering drought but not under postflowering drought, likely a consequence of variation in fungal fitness responses to changes in the availability of water and niche space caused by plant maturation over the growing season. Our findings suggest that the dynamic biotic interactions among host, beneficial and harmful microbiota in a changing environment can be disentangled by a blending of field observation, laboratory validation, holo-omics and ecological modelling.

Chen, Peilin↗

DOE OSTI2021

Molecular imaging of plant-microbe interactions on the Brachypodium seed surface

Plant growth-promoting rhizobacteria (PGPR) play a crucial role in biological control and pathogenic defense on and with-in plant tissues, however the mechanism(s) by which plants associate with PGPR to elicit such beneficial effects needs further study. Here, we present high mass resolution time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging of Brachypodium distachyon (Brachypodium) seeds with and without exposure to two model PGPR, i.e., Gram-negative Pseudomonas fluorescens SBW25::GFP (P.) and Gram-positive Arthrobacter chlorophenolicus A6::GFP (A.). Delayed image extraction was used to image PGPB-treated seed sections to reveal morphological changes. ToF-SIMS spectral compari-son, principal component analysis (PCA), and two-dimensional (2D) imaging show that the selected PGPR have different effects on the host seed surface, resulting in changes in chemical composition and morphology. Metabolite prod-ucts and biomarkers, such as flavonoids, phenolic com-pounds, fatty acids, and indole-3-acetic acid (IAA), were ob-served on the PGPR-treated seed surfaces. These compounds had different distributions on the Brachypodium seed surface for the two PGPR, indicating that the different bacteria elicited distinct responses from the host. Our results illustrate that ToF-SIMS is an effective tool to study plant-microbe interac-tions and to provide insightful information with submicrome-ter lateral resolution of the chemical distributions associated with morphological features, potentially offering a new way to study the mechanisms underlying beneficial roles of PGPR.

PGPR, Brachypodium distachyon, ToF-SIMS, metabolit↗

DOE OSTI2021

Molecular level characterization of wildfire aerosol induced changes to plant health and value

The potential impacts of wildfire smoke on plant health and value are of increasing concern, due both to increasing awareness, and more frequent wildfire events. Wildfires produce substantial amounts of atmospheric pollution in smoke and particulate matter which can travel thousands of miles. These smoke events can blanket entire agricultural regions and cause impacts to plant development. One notable example of this is ‘smoke taint’ in wine, where vines, exposed to smoke, absorb many small volatile phenolic (VP) compounds. These VPs can be metabolized (glycosylated) and transported throughout the plant. Later, during downstream processing (fermentation of the grape musts), these glycosylated VPs can be hydrolyzed to re-release and volatilize the aroma-active phenolic compounds. The final product, thus, smells of smoke. Despite the obvious commercial and general research interests here, the nature of wildfire impacts on plant health are incompletely understood. Using established metabolomics and organic matter (aerosol) characterization methods, the overall aim of this proposal is thus to study wildfire smoke impacts on plant health and value, in the context of a model system (V. vinifera). This project closed early, and this report reflects some of the limited work conducted prior to conclusions. Specifically, this report discusses some sample preparation and initial MALDI-mass spectrometry analysis.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Isolation of Histone from Sorghum Leaf Tissue for Top Down Mass Spectrometry Profiling of Potential Epigenetic Markers

Histones belong to a family of highly conserved proteins in eukaryotes. They pack DNA into nucleosomes as functional units of chromatin. Post-translational modifications (PTMs) of histones, which are highly dynamic and can be added or removed by enzymes, play critical roles in regulating gene expression. In plants, epigenetic factors including histone PTMs are related to their adaptive responses to the environment. Understanding the molecular mechanisms of epigenetic control can bring unprecedented opportunities for engineering solutions to increase the resilience of crops to climate change. Herein, we describe a protocol to isolate the nuclei and purify histones from sorghum leaf tissue. The extracted histones can be analyzed as their intact forms by top-down mass spectrometry (MS) coupled to online reversed-phase (RP) liquid chromatography (LC). Combinations and stoichiometry of multiple PTMs on the same histone proteoform can be readily identified. In addition, histone tail clipping can be detected using the top-down LC-MS workflow thus yielding the global PTM profile of core histones (H4, H2A, H2B, H3). By comparing the PTM profile among samples corresponding to different conditions (e.g. drought vs. control), potential epigenetic marks can be discovered as targets for further characterization using approaches such as chromatin immunoprecipitation – sequencing (ChIP-seq).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Metabolic Interactions between Brachypodium and Pseudomonas fluorescens under Controlled Iron-Limited Conditions

Plant iron (Fe) nutritional status has a significant impact on rhizosphere microbial communities. While this effect has been attributed to alterations in the composition of root exudates, the underlying mechanisms are not known. Here, we investigated the effect of Fe deficiency on the interactions between the grass Brachypodium distachyon and the common soil bacteria Pseudomonas fluorescens SBW25. Increased phytosiderophore production was the most significant response of Brachypodium root exudation to Fe deficiency. We observed upregulated expression of phytosiderophore biosynthesis genes but lower accumulated exudate concentrations in the presence of Pseudomonas, indicating that the bacteria degrade these phytosiderophores. Pseudomonas did not produce endogenous siderophores under the low Fe conditions. Rather, the bacterial transcriptome revealed upregulation of four genes in response to Fe deficiency that contain motifs associated with cellular uptake of small molecules. Collectively, these results suggest that rhizosphere Pseudomonas fluorescens may take up phytosiderophores produced by grasses in response to Fe deficiency, and we propose target genes that may be involved. Our findings provide insight into the molecular basis for the exchange of C, N, and Fe between plants and bacteria under Fe deficient conditions. These interactions may contribute to differences in the rhizosphere microbial community structure across soil pH regimes.

Boiteau, Rene M.↗

DOE OSTI2020

The Consortium for Advanced Sorghum Phenomics (CASP). Final report

The goal of CASP was to accelerate breeding of biomass sorghum [Sorghum bicolor (L.) Moench] by identifying genotypes exhibiting high yield under well-watered, pre- or post-drought and/or salinity-stress conditions. We did this by combining high-throughput, non-invasive drone phenotyping with genomics and molecular profiling. Field-based phenotyping utilized a multi-modal sensor suite of LiDAR, multispectral cameras, and thermal cameras mounted on a commercial drone to detect traits required for yield prediction and selection of drought and saline tolerant lines of sorghum. Traits of interest included plant height (PH), leaf area index (LAI), wet biomass (BMW), and biomass at 65% moisture (BM65) and were measured from emergence to harvest on a weekly basis over three growing seasons. The final output were measurements of traits on a plot-by-plot basis, identified by the plot ID used by the Proprietary data processing software enabled raw field data to be turned into plant traits and delivered to the PNNL and JGI within the same workday.

09 BIOMASS FUELS↗

DOE OSTI2020

Microanalysis of Primary Biological Particles from Model Grass over Its Life Cycle

Airborne biological aerosols are an integral part of the atmosphere–biosphere interface and significantly impact the environment and Earth’s climate. Primary biological particles such as fungal spores, bacteria, and fragments of plant debris are emitted directly from the biosphere into the atmosphere. The phyllosphere (aboveground plant surfaces) is one of the major habitats for different microbes. Here, atmospheric emissions of primary biological particles from model grass Brachypodium distachyon were monitored by online particle number concentration counting at eight principal growth stages starting from leaf development to senescence. Particles collected at each of the growth stages were then characterized using microspectroscopy techniques. Our findings indicate that the morphological and compositional characteristics of emitted biological particles are highly variable at the different growth stages. We identified fungal spores as the most abundant biological particles in the heading stage, while bacteria were most abundant in the flowering and fruit development stages. Understanding differences in the composition and morphology of biological particles during the plant life cycle provides more accurate and reliable insights on structural, functional, and biochemical properties of plant systems, as well as their interactions with microbial communities. This study also provides insights into Earth geoscience system models that represent primary biological particle emissions from the biosphere.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Correlative Surface Imaging Reveals Chemical Signatures for Bacterial Hotspots on Plant Roots

The rhizosphere is arguably the most complex microbial habitat on earth, comprising an integrated network of plant roots, soil and a highly diverse microbial community (the rhizosphere microbiome)1. Understanding, predicting and controlling plant-microbe interactions in the rhizosphere will allow us to harness the plant microbiome as a means to increase or restore plant ecosystem productivity, improve plant responses to a wide range of environmental perturbations, and mitigate effects of climate change by designing ecosystems for long-term soil carbon storage1. To this end, it is imperative to develop new molecular approaches with high spatial resolution to capture interactions at the plant-microbe, microbe-microbe, and plant-plant interfaces. In this work, we designed an imaging sample holder that allows integrated surface imaging tools to map the same locations of a plant root-microbe interface with submicron lateral resolutions, providing novel in vivo analysis of root-microbe interactions. Specifically, confocal fluorescence microscopy, time-of-flight secondary ion mass spectrometry (ToF-SIMS), X-ray photoelectron spectroscopy (XPS), and scanning electron microscope (SEM) were used for the first time for correlative imaging of the Brachypodium distachyon root and its interaction with Pseudomonas SW25, a typical plant growth-promoting soil bacterium. Imaging data suggest that the root surface is inhomogeneous and that the interaction between Pseudomonas and Brachypodium roots was confined to only few spots along the sampled root segments and that the bacterial attachment spots were enriched in Na- and S-related and high-mass organic species. We conclude that attachment of the Pseudomonas cells to the root surface is outcompeted by strong root-soil mineral interactions but facilitated by formation of extracellular polymeric substances (EPS).

Plant root, Plant growth-promoting bacteria, soil,↗

DOE OSTI2020

Sedimentation of ballasted cells-free EPS in meromictic Fayetteville Green Lake

Fayetteville Green Lake (FGL) is a recognized, extensively studied present-day model of the stratified Proterozoic Ocean. Nonetheless, biomass sedimentation in FGL remains hard to explain: Whilst virtually all sediment pigments belong to photosynthetic sulfur bacteria (PSB) from a chemocline, the isotopic carbon signature of the bulk biomass suggests its epilimnetic phytoplankton origin. Here we present experimental evidence that FGL Synechococci produce copious extracellular polysacchrides (EPS), which become impregnated with Ca, Mg and Na cations and are release to the environment as ballasted cell coverings. We propose that sedimentation of these cell-free EPS can constitute the bulk of pigment-less organic material in FGL sediment. Because increased availability of inorganic carbon (Ci) stimulates accumulation of ballasted EPS, we propose the universal role of cyanobacterial EPS in biomass sedimentation in the high-Ci Paleoproterozoic Ocean as well as in modern aquatic systems like FGL.

Kamennaya, Nina A.↗