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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Complete genome sequence of Luteolibacter sp. strain Populi, a member of phylum Verrucomicrobiota isolated from the Populus trichocarpa rhizosphere

Luteolibacter sp. strain Populi is a bacterium from the phylum Verrucomicrobiota, isolated from the rhizosphere of a black cottonwood tree, Populus trichocarpa, from the Cascade mountains in Washington. Its 6.6-Mb chromosome was completely sequenced using Oxford Nanopore long-read sequencing and is predicted to encode 5,301 proteins and 60 RNAs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

RhizoGrid Indexed Sorghum Rhizosphere Multi-Omics

PerCon SFA project data dentification of spatially resolved biomarkers of drought in Sorghum bicolor rhizosphere molecular-microbe interactions using a novel root cartography "RhizoGrid" system for sampling plants under drought and control conditions across 10 equally sized root zone environments (4 quadrants each). Each quadrant was sampled and processed for 16S amplicon, metabolomics, and X-ray computed tomography (XCT). Data download includes experimental metadata and results files for 16S rRNA sequence analysis of microbial community assembly (processed data files), liquid chromatography mass spectrometry (LC-MS) metabolomics analysis of microbial community root exudates (processed data files), X-ray computed tomography (XCT) spatial gradient analysis (raw and processed data files) of microbial community composition, and related computational modeling outputs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Soil pore architecture and rhizosphere legacy define N 2 O production in root detritusphere

Root detritusphere is one of the most important sources of N 2 O, however, understanding of how N 2 O emission from the detritusphere is influenced by soil properties remains elusive. Here, we evaluated the effects of pore architecture and soil moisture on N 2 O emission during the decomposition of in-situ grown roots of switchgrass, an important bioenergy crop. We combined dual isotope labeling ( 15 C and 15 N) with zymography to gain insights into the location of the microbial N 2 O production in soils with contrasting pore architectures. In the studied soil, the effect of soil pore architecture on N 2 O emissions was 6 times greater than that of soil moisture. Soil dominated by > 30 μm Ø pores (i.e., large-pore soil) had higher chitinase activity than the soil dominated by < 10 μm Ø pores (i.e., small-pore soil), especially near the decomposing roots. The chitinase activity on the decomposing roots was positively correlated with emission of root-derived N 2 O, indicating that N released from root decomposition was an important source of N 2 O. Greater N 2 O and N2 emission was induced by switchgrass roots in soils dominated by the large- compared to the small-pore soils. Here, the microenvironment developed near decomposing roots of the large-pore soil also resulted in positive N 2 O priming. Our study challenged the traditional view on soil moisture as the main factor of N 2 O production. Production and emission of N 2 O was most intensive in microbial activity hotspots (i.e., rhizosphere legacy) in the large pores, where decomposed roots release mineral N as the main N 2 O source.

13C Pulse labeling↗
DOE OSTI2025

Molecular Imaging of Microbially Induced Corrosion of Synthetic Archeological Glasses by a Rhizosphere Bacterium

Microbially induced corrosion (MIC) focuses on the degradation of solid materials, such as glass or metal. Soil microbes are often associated with the corrosion of foreign objects in the rhizosphere. Paenibacillus polymyxa SCE2, a facultative anaerobic bacterium in soil, is of the same genus as bacteria found near nuclear waste disposal sites. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) was used for imaging surface changes induced by P. polymyxa SCE2 cultured on two synthetic glass coupons to represent natural analogs of materials that were studied in relation to the vitrification of nuclear waste. Multimodal imaging was used to verify bacterial coverage across the glass surface after long-term growth. ToF-SIMS spectral analysis showed detection of glass component ions, such as silicon oxide (m/z – 59.96 SiO 2 – ) and aluminum oxide (m/z – 101.95 Al 2 O 3 – ), and biofilm’s extracellular polymeric substance (EPS) components, such as pentadecanoic acid (m/z – 241.22 C 15 H 29 O 2 – ) and sterol lipids (m/z – 311.16 C 20 H 23 O 3 – ). ToF-SIMS spectral, imaging, and depth profiling analyses showed that the glass rich in silica and other light elements (“granite glass”) had more “corrosion related” peaks than the glass that was less silica-rich and contained more iron (“dike glass”). Furthermore, these surface and interface compositional and spatial differences observed in the mass spectra and imaging were attributed to bacterial metabolism and an electron transfer mechanism influenced by morphological and compositional differences between the two types of glasses. ToF-SIMS is effective in studying microbial effects, bringing new molecular insights into MIC in a broader context of materials degradation.

Amorphous materials↗
DOE OSTI2024

Disentangling plant- and environment-mediated drivers of active rhizosphere bacterial community dynamics during short-term drought

Abstract Mitigating the effects of climate stress on crops is important for global food security. The microbiome associated with plant roots, the rhizobiome, can harbor beneficial microbes that alleviate stress, but the factors influencing their recruitment are unclear. We conducted a greenhouse experiment using field soil with a legacy of growing switchgrass and common bean to investigate the impact of short-term drought severity on the recruitment of active bacterial rhizobiome members. We applied 16S rRNA and 16S rRNA gene sequencing for both crops and metabolite profiling for switchgrass. We included planted and unplanted conditions to distinguish environment- versus plant-mediated rhizobiome drivers. Differences in community structure were observed between crops and between drought and watered and planted and unplanted treatments within crops. Despite crop-specific communities, drought rhizobiome dynamics were similar across the two crops. The presence of a plant more strongly explained the rhizobiome variation in bean (17%) than in switchgrass (3%), with a small effect of plant mediation during drought observed only for the bean rhizobiome. The switchgrass rhizobiome was stable despite changes in rhizosphere metabolite profiles between planted and unplanted treatments. We conclude that rhizobiome responses to short-term drought are crop-specific, with possible decoupling of plant exudation from rhizobiome responses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Abiotic Stress Reorganizes Rhizosphere and Endosphere Network Structure of Sorghum bicolor

Sorghum bicolor is a promising bioenergy feedstock with high biomass production and unusual tolerance for stresses, such as water and nutrient limitation. Although the membership of the sorghum microbiome in response to stress has been explored, relatively little is known about how microbe–microbe networks change under water- or nutrient-limited conditions. This is important because network changes can indicate impacts on the functionality and stability of microbial communities. We performed network-based analysis on the core bacterial and archaeal community of an agronomically promising high biomass bioenergy genotype, Grassl, grown under nitrogen and water stress. Stress caused relatively minor changes in bacterial abundances within soil, rhizosphere, and endosphere communities but led to significant changes in bacterial network structure and modularity. We found a complete reorganization of network roles in all plant compartments, as well as an increase in the modularity and proportion of positive associations, which potentially could represent coexistence and cooperation in the sorghum bacterial/archaeal community under stress. Although stressors are often believed to be destabilizing, we found stressed networks were as or more stable than non-stressed networks, likely due to their redundancy and compartmentalization. Together, these findings support the idea that both sorghum and its bacterial/archaeal community can be resilient to future environmental stressors.

09 BIOMASS FUELS↗
DOE OSTI2026

Draft Genome Sequences of 14 Bacterial Isolates from the Rhizosphere of Bioenergy Sorghum

We report the draft genomes of a collection of 15 bacteria, isolated from the rhizosphere soil of bioenergy sorghum (Sorghum bicolor (L.) Moench). These isolates belong to the genera, Acidovorax, Nocardioides, Agrobacterium, Peribacillus, Caulobacter, Cupriavidus, Pseudomonas, Rhizobium, Sphingomonas, Priestia, Dyadobacter, Roseomonas, Ideonella, and Bacillus.

Black, Grace S.↗
DOE OSTI2024

Bacterial isolate collection from switchgrass rhizosphere

ABSTRACT We provide a collection of 78 bacterial isolates from the rhizosphere of switchgrass ( Panicum virgatum L .) at the Lux Arbor Reserve in Delton, MI, a site of the Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, MI, USA. We include information on isolation conditions and full-length 16S rRNA sequences.

Grady, Keara L.↗
DOE OSTI2021

Data for Intra- and inter-annual variability of nitrification in the rhizosphere of field-grown bioenergy sorghum

These data were collected in 2018 and 2019 at the University of Illinois Energy Farm (N 40.063607, W 88.206926). During each growing season, bulk and rhizosphere soil were collected from replicate Sorghum bicolor nitrogen use efficiency trial plots at three separate time points (approximately July 1, August 1, and September 1). We measured soil moisture, pH, soil nitrate and ammonium, potential nitrification, potential denitrification, and extracted and sequenced the V4 region of the 16S rRNA gene for microbial community analysis. All microbial sequence data is archived in the National Center for Biotechnology Information’s (NCBI) Sequence Read Archive (accession number SRP326979, project number PRJNA741261).

bioenergy↗
DOE OSTI2023

Carbon Organisms Rhizosphere and Protection in Soil Environment model script and input data for soil moisture-respiration responses in tropical forests

Objectives: Climatic drying is predicted for many tropical forests, yet models remain poorly parameterized for tropical forests, hampering predictions of forest-climate feedbacks. We applied an integrated model–experiment approach, parameterizing an ecosystem model Carbon Organisms Rhizosphere and Protection in the Soil Environment (CORPSE) with tropical forest observational data, and comparing model predictions with a field drying manipulation. We hypothesized that drying would suppress soil CO2 fluxes (i.e., respiration) in already-drier tropical forests, but increases CO2 fluxes in wetter tropical forests by alleviating anaerobiosis. We measured soil CO2 fluxes, soil moisture, soil temperature, and forest floor biomass during wet-dry cycles (2015 – 2022) in four Panamanian forests that vary in rainfall and soil fertility. We used the field data to parameterize and run tests in the model.Results: Measured CO2 fluxes declined in the dry season and peaked in the early wet season ahead of peak soil moisture, resulting in a lower soil moisture optimum for respiration than previously modeled. We used this data to parameterize the model, which then predicted increased soil CO2 fluxes in wetter and fertile forests with drying, and decreased fluxes in drier, infertile forests. In contrast to model predictions, a chronic throughfall exclusion experiment in the forests initially suppressed soil CO2 fluxes across forests, with sustained suppression after four years in the wettest forest only (-28 ± 4% during the dry season), but elevated soil CO2 fluxes in a fertile forest after four years (+75 ± 28% during the late wet season), as predicted by the model. The unexpected negative drying effect in the wettest, most infertile forest could have resulted from reduced vertical flushing of nutrients into soils. Including hydro-nutrient interactions in ecosystem models could improve predictions of tropical forest-climate feedbacks (results presented in Cusack et al. 2023). Datasets included: Code files:CORPSE_array.py: Defines the equations of the CORPSE modelCORPSE_solvers: Functions for running the CORPSE model using either iterative or ordinary differential equation (ODE) solversrun_Panama_sims.py: Read in datasets and run the model simulations for this studyInput data:PanamaGradientEcosystemChem_BT_CPools_20152016CO2_DC_20190615.xlsx: Plot characteristics used in running model simulationsLiCor compiled surface flux only to 2020_03 DC_20200825.xlsx: Surface gas exchange fluxes used in model-data comparisonsPARCHED litterfall data for Ben Sulman LD 20200902.xlsx: Litterfall data used to drive model simulationsInitialization data:state_500y_20190823.csv: Initial state of model pools based on previous spinup runsOutput data:Outputs/prev_moisture_response.csv: Simulations of multiple sites using original model moisture response function.Outputs/updated_moisture_response.csv: Simulations of multiple sites using updated model moisture response function.Outputs/dry15_prev_moisture_response.csv: Simulations with soil moisture reduced by 15%, using original moisture response function.Outputs/dry15_updated_moisture_response.csv: Simulations with soil moisture reduced by 15%, using updated moisture response function.Outputs/dry30_prev_moisture_response.csv: Simulations with soil moisture reduced by 30%, using original moisture response function.Outputs/dry30_updated_moisture_response.csv: Simulations with soil moisture reduced by 30%, using updated moisture response function.Outputs/latestart_prev_moisture_response.csv: Simulations with extended dry season, using original moisture response function.Outputs/latestart_updated_moisture_response.csv: Simulations with extended dry season, using updated moisture response function.Outputs/[site name]_oneyear.csv: One-year simulation for each site in expanded site list using original moisture response function.Outputs/[site name]_oneyear_dried.csv: One-year simulation for each site in expanded site list using original moisture response function, with soil moisture reduced by 25%.Outputs/[site name]_oneyear_updated_moisture_response.csv: One-year simulation for each site in expanded site list using updated moisture response function.Outputs/[site name]_oneyear_updated_moisture_response_dried.csv: One-year simulation for each site in expanded site list using updated moisture response function, with soil moisture reduced by 25%.Field plot location data:There is also a .kml file that includes coordinates for all 32 plots included in the study of four forests (n = 4 throughfall reduction and n = 4 control plots per site).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Mechanisms of regulation of the rhizosphere, roots and shoots of naive poplars

Trees are associated with a broad range of microorganisms colonising the diverse tissues of their host. However, the early dynamics of the microbiota assembly microbiota from the root to shoot axis and how it is linked to root exudates and metabolite contents of tissues remain unclear. Here, we characterised how fungal and bacterial communities are altering root exudates as well as root and shoot metabolomes in parallel with their establishment in poplar cuttings (Populus tremula x tremuloides clone T89) over 30 days of growth. Sterile poplar cuttings were planted in natural or gamma irradiated soils. Bulk and rhizospheric soils, root and shoot tissues were collected from day 1 to day 30 to track the dynamic changes of fungal and bacterial communities in the different habitats by DNA metabarcoding. Root exudates and root and shoot metabolites were analysed in parallel by gas chromatography-mass spectrometry.

09 BIOMASS FUELS↗
DOE OSTI2024

Continuous cropping of potato changed the metabolic pathway of root exudates to drive rhizosphere microflora

For potato production, continuous cropping (CC) could lead to autotoxicity buildup and microflora imbalance in the field soil, which may result in failure of crops and reduction in yield. In this study, non-targeted metabolomics (via liquid chromatography with tandem mass spectrometry (LC–MS/MS)) combined with metagenomic profiling (via high-throughput amplicon sequencing) were used to evaluate correlations between metabolomics of potato root exudates and communities of bacteria and fungi around potato plants to illustrate the impacts of CC. Potato plants were grown in soil collected from fields with various CC years (0, 1, 4, and 7 years). Metabolomic analysis showed that the contents and types of potential autotoxins in potato root exudates increased significantly in CC4 and CC7 plants (i.e., grown in soils with 4 and 7 years of CC). The differentially expressed metabolites were mainly produced via alpha-linolenic acid metabolism in plant groups CC0 and CC1 (i.e., no CC or 1 year CC). The metabolomics of the groups CC4 and CC7 became dominated by styrene degradation, biosynthesis of siderophore group non-ribosomal peptides, phenylpropanoid biosynthesis, and biosynthesis of various plant secondary metabolites. Continuous cropping beyond 4 years significantly changed the bacterial and fungal communities in the soil around the potato crops, with significant reduction of beneficial bacteria and accumulation of harmful fungi. Correlations between DEMs and microflora biomarkers were established with strong significances. These results suggested that continuous cropping of potato crops changed their metabolism as reflected in the plant root exudates and drove rhizosphere microflora to directions less favorable to plant growth, and it needs to be well managed to assure potato yield.

Xing, Yanhong↗
DOE OSTI2025

Purification and expression of a novel bacteriocin, JUQZ-1, against Pseudomonas syringae pv. Actinidiae (PSA), secreted by Brevibacillus laterosporus Wq-1, isolated from the rhizosphere soil of healthy kiwifruit

Kiwifruit canker, caused by Pseudomonas syringae pv. actinidiae (PSA), has led to significant losses in the kiwifruit industry each year. Due to the drug resistance feature of PSA, biological control is currently the most promising method. Developing biocontrol bacteria against PSA could help solve the issue of drug resistance generated during the chemical control of PSA to a certain extent. In this research, a Wq-1 strain that demonstrated excellent inhibitory activity against PSA was isolated from the rhizosphere soil of healthy kiwifruit. Based on the morphological characteristics and phylogenetic analysis of the 16S rRNA gene sequence, the isolated strain was identified as Brevibacillus laterosporus Wq-1. Bacteriostatic proteins were isolated from the cell-free culture filtrate of strain Wq-1 and were found to have a molecular weight of approximately 12 kDa, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Liquid chromatography–tandem mass spectrometry (LC–MS/MS) detection revealed that there were several peptides in the target band that were consistent with protein 01021 in the genome. The gene of the 01021 protein was cloned into the plasmid pPICZa, and the recombinant bacteriocin was successfully expressed using the Pichia pastoris X33 expression system. The recombinant protein 01021 effectively inhibited the growth of PSA. This is the first report of the protein’s antimicrobial activity, distinguishing it from previously identified bacteriocins. Therefore, we named this bacteriocin JUQZ-1. In addition, our results showed that the protein JUQZ-1 not only exhibited a broad bacteriostatic spectrum but also high thermal and pH stability suitable for harsh environmental conditions., JUQZ-1, a protein with antimicrobial properties and strong environmental tolerance, may serve as a promising alternative to antibiotics.

Shuai, Yang↗
DOE OSTI2021

Influence of Tall Fescue Epichloë Endophytes on Rhizosphere Soil Microbiome

Tall fescue (Lolium arundinaceum (Schreb.) S.J. Darbyshire) often forms a symbiotic relationship with fungal endophytes (Epichloë coenophiala), which provides increased plant performance and greater tolerance to environmental stress compared to endophyte-free tall fescue. Whether this enhanced performance of tall fescue exclusively results from the grass–fungus symbiosis, or this symbiosis additionally results in the recruitment of soil microbes in the rhizosphere that in turn promote plant growth, remain a question. We investigated the soil bacterial and fungal community composition in iron-rich soil in the southeastern USA, and possible community shifts in soil microbial populations based on endophyte infection in tall fescue by analyzing the 16s rRNA gene and ITS specific region. Our data revealed that plant-available phosphorus (P) was significantly (p < 0.05) influenced by endophyte infection in tall fescue. While the prominent soil bacterial phyla were similar, a clear fungal community shift was observed between endophyte-infected (E+) and endophyte-free (E−) tall fescue soil at the phylum level. Moreover, compared to E− soil, E+ soil showed a greater fungal diversity at the genus level. Our results, thus, indicate a possible three-way interaction between tall fescue, fungal endophyte, and soil fungal communities resulting in improved tall fescue performance.

Mahmud, Kishan↗