Results for “Bacterial abundance” — Page 3

DOE OSTI2021

WA-Omic_LA.1.0 - Quantitative Lipidomics, Metabolomics, and Sequencing (16S/ITS) Publication Data DOI Package

Corresponding Data Publication: "Rapid remodeling of the soil lipidome in response to a drying-rewetting event." This study reveals specific changes in lipids and metabolites that are indicative of stress adaptation, substrate use, and cellular recovery during soil drying and subsequent rewetting. Drought induced nutrient limitation was reflected in the lipidome and polar metabalome, both of which rapidly shifted (within hours) upon rewet. Reduced nutrient access in dry soil caused the replacement of glycerophospholipids with phosphorus-free lipids and impeded resource-expensive osmolyte accumulation. Elevated levels of ceramides and lipids with long chain polyunsaturated fatty acids, in dry soil suggests that lipids play an important role in fungal drought tolerance. Increasing abundance of bacterial glycerophospholipids and triacylglycerols with fatty acids typical of bacteria and polar metabolites suggest metabolic recovery in representative bacteria once the environmental conditions are conducive for growth. These results underscore the importance of the soil lipidome as a robust indicator of microbial community responses, especially at the short time scales of cell-environment reactions. Data package contents reported here are the first version and contain pre- and post-processed data acquisition and subsequent downstream analysis files using various data source instrument method techniques and Mass Spectroscopy (MS) EMSL capabilities. This publication data package DOI is a comprehensive high-throughput multi-omics data lifecycle collection containing processed data method metadata. Support files include additional data download “Read Me” file containing data descriptor information and data source application ontologies (see data dictionary). Reported data download contents are structured for compliance with project data sharing guidelines, community standards initiatives, and sponsor stakeholder policies supporting FAIR data principles. For increased data availability and interoperability, GC-MS/LC-MS mass spectrometry datasets (Thermo .raw ) were deposited at the MassIVE database repository under the related data accession MSV000086931 and can be accessed by using the API. Statistical data processing software, analysis tools, and data workflows are listed below corresponding to the host repository long-term location.

Amplicon sequencing 16S ITS LC-MS/MS lipidomics mu↗

DOE OSTI2021

WA-Omic_LA.1.0 - Quantitative Lipidomics, Metabolomics, and Sequencing (16S/ITS) Publication Data DOI Package

Corresponding Data Publication: "Rapid remodeling of the soil lipidome in response to a drying-rewetting event." This study reveals specific changes in lipids and metabolites that are indicative of stress adaptation, substrate use, and cellular recovery during soil drying and subsequent rewetting. Drought induced nutrient limitation was reflected in the lipidome and polar metabalome, both of which rapidly shifted (within hours) upon rewet. Reduced nutrient access in dry soil caused the replacement of glycerophospholipids with phosphorus-free lipids and impeded resource-expensive osmolyte accumulation. Elevated levels of ceramides and lipids with long chain polyunsaturated fatty acids, in dry soil suggests that lipids play an important role in fungal drought tolerance. Increasing abundance of bacterial glycerophospholipids and triacylglycerols with fatty acids typical of bacteria and polar metabolites suggest metabolic recovery in representative bacteria once the environmental conditions are conducive for growth. These results underscore the importance of the soil lipidome as a robust indicator of microbial community responses, especially at the short time scales of cell-environment reactions. Data package contents reported here are the first version and contain pre- and post-processed data acquisition and subsequent downstream analysis files using various data source instrument method techniques and Mass Spectroscopy (MS) EMSL capabilities. This publication data package DOI is a comprehensive high-throughput multi-omics data lifecycle collection containing processed data method metadata. Support files include additional data download “Read Me” file containing data descriptor information and data source application ontologies (see data dictionary). Reported data download contents are structured for compliance with project data sharing guidelines, community standards initiatives, and sponsor stakeholder policies supporting FAIR data principles. For increased data availability and interoperability, GC-MS/LC-MS mass spectrometry datasets (Thermo .raw ) were deposited at the MassIVE database repository under the related data accession MSV000086931 and can be accessed by using the API. Statistical data processing software, analysis tools, and data workflows are listed below corresponding to the host repository long-term location.

Amplicon sequencing 16S ITS LC-MS/MS lipidomics mu↗

DOE OSTI2021

WA-Omic_LA.1.0 - Quantitative Lipidomics, Metabolomics, and Sequencing (16S/ITS) Publication Data DOI Package

Corresponding Data Publication: "Rapid remodeling of the soil lipidome in response to a drying-rewetting event." This study reveals specific changes in lipids and metabolites that are indicative of stress adaptation, substrate use, and cellular recovery during soil drying and subsequent rewetting. Drought induced nutrient limitation was reflected in the lipidome and polar metabalome, both of which rapidly shifted (within hours) upon rewet. Reduced nutrient access in dry soil caused the replacement of glycerophospholipids with phosphorus-free lipids and impeded resource-expensive osmolyte accumulation. Elevated levels of ceramides and lipids with long chain polyunsaturated fatty acids, in dry soil suggests that lipids play an important role in fungal drought tolerance. Increasing abundance of bacterial glycerophospholipids and triacylglycerols with fatty acids typical of bacteria and polar metabolites suggest metabolic recovery in representative bacteria once the environmental conditions are conducive for growth. These results underscore the importance of the soil lipidome as a robust indicator of microbial community responses, especially at the short time scales of cell-environment reactions. Data package contents reported here are the first version and contain pre- and post-processed data acquisition and subsequent downstream analysis files using various data source instrument method techniques and Mass Spectroscopy (MS) EMSL capabilities. This publication data package DOI is a comprehensive high-throughput multi-omics data lifecycle collection containing processed data method metadata. Support files include additional data download “Read Me” file containing data descriptor information and data source application ontologies (see data dictionary). Reported data download contents are structured for compliance with project data sharing guidelines, community standards initiatives, and sponsor stakeholder policies supporting FAIR data principles. For increased data availability and interoperability, GC-MS/LC-MS mass spectrometry datasets (Thermo .raw ) were deposited at the MassIVE database repository under the related data accession MSV000086931 and can be accessed by using the API. Statistical data processing software, analysis tools, and data workflows are listed below corresponding to the host repository long-term location.

Amplicon sequencing 16S ITS LC-MS/MS lipidomics mu↗

DOE OSTI2023

A comparison of free-living and sponge-associated bacterial communities from a remote oceanic island with a focus on calcareous sponges

Abstract Calcareous sponges are an often overlooked element of sponge communities. In contrast to most other sponges, calcareous sponges produce calcium carbonate spicules, as opposed to the siliceous spicules of most sponges. Here, we investigated the bacterial communities of 17 sponge species, including type and paratype specimens of recently described calcareous species, sampled off the remote island of Rodrigues, in the Indian Ocean. The main axis of variation in a PCO analysis of all samples separated noncalcareous sponge species, including Axinyssa aplysinoides, Cinachyrella aff. australiensis, Petrosia seychellensis, Ircinia aff. variabilis, Spongia ceylonensis, Plakinastrella aff. clipptertonensis, Agelas aff. ceylonica, Agelas aff. mauritiana, and Hyrtios erectus from calcareous sponges, the noncalcareous Biemna tubulata, sediment, and seawater. Overall, the bacterial communities of calcareous sponges revealed unique prokaryotic profiles with low abundances of several bacterial phyla, and relatively high abundances of other taxa, for example, the phyla Fibrobacterota, Proteobacteria, and the SAR324 clade, the class Alphaproteobacteria, and orders Cytophagales and Cyanobacteriales, although there was considerable variation among species. Calcareous sponges also had a high dominance of unknown bacterial operational taxonomic units (OTUs). Considering the unique nature of these communities, further studies are needed to better understand the environmental and ecological drivers of calcareous sponge-associated bacterial communities and their relevance as potential sources of novel microbes of biotechnological interest.

Cleary, D. F. R. (ORCID:0000000261433390)↗

DOE OSTI2022

Bacterial Community Assembly, Succession, and Metabolic Function during Outdoor Cultivation of Microchloropsis salina

Outdoor cultivation of microalgae has promising potential for renewable bioenergy, but there is a knowledge gap on the structure and function of the algal microbiome that coinhabits these ecosystems. Here, we describe the assembly mechanisms, taxonomic structure, and metabolic potential of bacteria associated with Microchloropsis salina cultivated outdoors. Open mesocosms were inoculated with algal cultures that were either free of bacteria or coincubated with one of two different strains of alga-associated bacteria and were sampled across five time points taken over multiple harvesting rounds of a 40-day experiment. Using quantitative analyses of metagenome-assembled genomes (MAGs), we tracked bacterial community compositional abundance and taxon-specific functional capacity involved in algal-bacterial interactions. One of the inoculated bacteria (Alteromonas sp.) persisted and dispersed across mesocosms, whereas the other inoculated strain (Phaeobacter gallaeciensis) disappeared by day 17 while a taxonomically similar but functionally distinct Phaeobacter strain became established. The inoculated strains were less abundant than 6 numerically dominant newly recruited taxa with functional capacities for mutualistic or saprophytic lifestyles, suggesting a generalist approach to persistence. This includes a highly abundant unclassified Rhodobacteraceae species that fluctuated between 25% and 77% of the total community. Overall, we did not find evidence for priority effects exerted by the distinct inoculum conditions; all mesocosms converged with similar microbial community compositions by the end of the experiment. Instead, we infer that the 15 total populations were retained due to host selection, as they showed high metabolic potential for algal-bacterial interactions such as recycling alga-produced carbon and nitrogen and production of vitamins and secondary metabolites associated with algal growth and senescence, including B vitamins, tropodithietic acid, and roseobacticides.

rhodobacteraceae↗

DOE OSTI2026

Data for Impacts of Legacy and Contemporary Nitrogen Inputs on N2O and CO2 Emissions in Miscanthus and Maize Cultivated Soils

Nutrient inputs influence the sustainability of bioenergy crop production through contemporary (shortly after addition) and legacy effects (persisting over years) on microbial nitrogen (N) and carbon cycling, which contribute to greenhouse gas emissions. However, the relative importance of contemporary and legacy effects and how that could vary by crop functional types is poorly understood. Considering its rhizomatous roots and perennial growth, we hypothesized that Miscanthus × giganteu s ( M × g ) would be more sensitive to legacy N fertilization and the historical context of its environment than an annual crop like maize. To test this hypothesis, we examined the effects of legacy and contemporary N inputs on nitrous oxide (N2O) and carbon dioxide (CO2) emissions, as well as key N cycling genes in soils where M × g and maize were grown. A 150-day soil incubation experiment was conducted using soils from a long-term M × g and maize fertility experiment with three historic N fertilization rates (0, 112, and 336 kg N ha−1 year−1) and a contemporary amendment (60 mg N kg−1) with negative control (0 mg N kg−1). We observed significant increases in cumulative N2O emissions in M × g soils relative to maize soils, particularly at higher legacy fertilization rates, while contemporary N had no significant effect. Bacterial amoA gene abundance, which plays a significant role in nitrification in nutrient-rich soils, also increased with higher legacy fertilization rates in M × g soils but was unaffected by the contemporary N. In maize soils, legacy and contemporary N did not significantly affect N2O emissions, but cumulative CO2 emissions and amoA gene abundance significantly increased. The abundances of norB genes were not significantly influenced by either legacy fertilization or contemporary N amendments in either soil. Our findings demonstrate the greater importance of fertilization history over contemporary N in mediating soil N2O emissions, particularly for perennial bioenergy crops.

Carbon↗

DOE OSTI2022

Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean

Enzymes catalyze key reactions within Earth’s life-sustaining biogeochemical cycles. Here, we use metaproteomics to examine the enzymatic capabilities of the microbial community (0.2 to 3 µm) along a 5,000-km-long, 1-km-deep transect in the central Pacific Ocean. Eighty-five percent of total protein abundance was of bacterial origin, with Archaea contributing 1.6%. Over 2,000 functional KEGG Ontology (KO) groups were identified, yet only 25 KO groups contributed over half of the protein abundance, simultaneously indicating abundant key functions and a long tail of diverse functions. Vertical attenuation of individual proteins displayed stratification of nutrient transport, carbon utilization, and environmental stress. The microbial community also varied along horizontal scales, shaped by environmental features specific to the oligotrophic North Pacific Subtropical Gyre, the oxygen-depleted Eastern Tropical North Pacific, and nutrient-rich equatorial upwelling. Some of the most abundant proteins were associated with nitrification and C1 metabolisms, with observed interactions between these pathways. The oxidoreductases nitrite oxidoreductase (NxrAB), nitrite reductase (NirK), ammonia monooxygenase (AmoABC), manganese oxidase (MnxG), formate dehydrogenase (FdoGH and FDH), and carbon monoxide dehydrogenase (CoxLM) displayed distributions indicative of biogeochemical status such as oxidative or nutritional stress, with the potential to be more sensitive than chemical sensors. Enzymes that mediate transformations of atmospheric gases like CO, CO 2 , NO, methanethiol, and methylamines were most abundant in the upwelling region. Here, we identified hot spots of biochemical transformation in the central Pacific Ocean, highlighted previously understudied metabolic pathways in the environment, and provided rich empirical data for biogeochemical models critical for forecasting ecosystem response to climate change.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Sweet Sorghum Genotypes Tolerant and Sensitive to Nitrogen Stress Select Distinct Root Endosphere and Rhizosphere Bacterial Communities

The belowground microbiomes have many beneficial functions that assist plant growth, including nutrient cycling, acquisition and transport, as well as alleviation of stresses caused by nutrient limitations such as nitrogen (N). Here we analyzed the root endosphere, rhizosphere and soil bacterial communities of seven sweet sorghum genotypes differing in sensitivity to N-stress. Sorghum genotypes were grown in fields with no (low-N) or sufficient (high-N) N. The dry shoot weight ratio (low-N/high-N) was used to determine N-stress sensitivity. Our hypothesis was that genotypes tolerant and sensitive to N-stress select distinct bacterial communities. The endosphere and rhizosphere bacterial community structure were significantly different between the N-stress sensitive and tolerant genotypes in the high-N field, but not in the low-N field. However, significant changes in the relative abundance of specific bacterial taxa were observed in both fields. Streptomyces, a bacterial genus known to alleviate plant abiotic stresses, was enriched in the endosphere and rhizosphere of the tolerant genotypes in the low-N field. Our study indicates that sweet sorghum genotypes tolerant to N-stress select taxa that can potentially mitigate the N-stress, suggesting that the interactions between N-stress tolerant lines and the root-associated microbiome might be vital for coping with N-stress.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Hidden Allies: Decoding the Core Endohyphal Bacteriome of Aspergillus fumigatus

ABSTRACT Bacterial–fungal interactions that influence the behaviour of one or both organisms are common in nature. Well‐studied systems include endosymbiotic relationships that range from transient to long‐term associations. Diverse endohyphal bacteria associate with fungal hosts, emphasising the need to better comprehend the fungal bacteriome. We evaluated the hypothesis thatAspergillus fumigatusharbours an endohyphal community of bacteria that influence the host phenotype. We analysed whether 38A. fumigatusstrains show stable association with diverse endohyphal bacteria; all derived from single‐conidium cultures that were subjected to antibiotic and heat treatments. The fungal bacteriome, inferred through analysis of bacterial diversity within the fungal strains (short‐ and long‐ read sequencing methods), revealed the presence of core endohyphal bacterial genera. Microscopic analysis further confirmed the presence of endohyphal bacteria. The fungal strains exhibited high genetic diversity and phenotypic heterogeneity in drug susceptibility and in vivo virulence. No correlations were observed between genomic or functional traits and bacteriome diversity, but the abundance of some bacterial genera correlated with fungal virulence or posaconazole susceptibility. The observed endobacteriome may play functional roles, for example, nitrogen fixation. Our study emphasises the existence of complex interactions between fungi and endohyphal bacteria, possibly impacting the phenotype of the fungal host, including virulence.

Environmental Sciences & Ecology↗

DOE OSTI2021

Colonization of Naive Roots from Populus tremula × alba Involves Successive Waves of Fungi and Bacteria with Different Trophic Abilities

ABSTRACT Through their roots, trees interact with a highly complex community of microorganisms belonging to various trophic guilds and contributing to tree nutrition, development, and protection against stresses. Tree roots select for specific microbial species from the bulk soil communities. The root microbiome formation is a dynamic process, but little is known on how the different microorganisms colonize the roots and how the selection occurs. To decipher whether the final composition of the root microbiome is the product of several waves of colonization by different guilds of microorganisms, we planted sterile rooted cuttings of gray poplar obtained from plantlets propagated in axenic conditions in natural poplar stand soil. We analyzed the root microbiome at different time points between 2 and 50 days of culture by combining high-throughput Illumina MiSeq sequencing of the fungal ribosomal DNA internal transcribed spacer and bacterial 16S rRNA amplicons with confocal laser scanning microscopy observations. The microbial colonization of poplar roots took place in three stages, but bacteria and fungi had different dynamics. Root bacterial communities were clearly different from those in the soil after 2 days of culture. In contrast, if fungi were also already colonizing roots after 2 days, the initial communities were very close to that in the soil and were dominated by saprotrophs. They were slowly replaced by endophytes and ectomycorhizal fungi. The replacement of the most abundant fungal and bacterial community members observed in poplar roots over time suggest potential competition effect between microorganisms and/or a selection by the host. IMPORTANCE The tree root microbiome is composed of a very diverse set of bacterial and fungal communities. These microorganisms have a profound impact on tree growth, development, and protection against different types of stress. They mainly originate from the bulk soil and colonize the root system, which provides a unique nutrient-rich environment for a diverse assemblage of microbial communities. In order to better understand how the tree root microbiome is shaped over time, we observed the composition of root-associated microbial communities of naive plantlets of poplar transferred in natural soil. The composition of the final root microbiome relies on a series of colonization stages characterized by the dominance of different fungal guilds and bacterial community members over time. Our observations suggest an early stabilization of bacterial communities, whereas fungal communities are established following a more gradual pattern.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Carbon dioxide (CO2) flux, amplicon sequencing and liquid chromatography–mass spectrometry (LC-MS) data for pyrogenic organic matter (PYOM) amended soil incubations in lab, Madison, WI, 2021-22

This dataset comprises soil-pyrogenic organic matter (PyOM) incubation experiments conducted in a laboratory setting. The focus was on measuring carbon dioxide (CO2) flux emitted in the headspace of incubation jars over a one-month period. The aim was to estimate carbon mineralization from two different carbon fractions in PyOM, as well as carbon mineralization from soil organic carbon (SOC). Bacterial and fungal community profiles were tracked at various time points during the incubation to observe changes in the overall community and specific responders to PyOM. LC-MS analysis of soil samples was also performed to monitor changes in the soil's chemical composition.The provided dataset includes processed CO2 flux measurements obtained from the Picarro-multiplexer measurement setup for each sample incubation jar. This data is available in the "CO2Flux.csv" file. Additionally, the dataset includes CO2 flux data partitioned to estimate mean carbon mineralization from the two PyOM carbon fractions, bulk PyOM, and SOC. The cumulative carbon mineralization data is provided in "cml_respired.csv," while the rate of carbon mineralization data is in "rate_respired.csv." The file "cml_respired_lastcyc.csv" contains cumulative carbon mineralization data for the PyOM carbon fractions, bulk PyOM, and SOC throughout the entire incubation period.For the LC-MS analysis, the raw data can be found in the "20220721_NZ_PeakHeights_FinalAnalysis.csv" file, while sample metadata is provided in "20220721_NZpilot_Metadata.csv". Processed LC-MS data is available in the file "20220721_NZ_FINAL_msdat_sub3.csv". Lastly, the dataset includes the relative abundance data for bacterial genera that exhibited a significant positive response to the addition of PyOM produced at 350 degrees Celsius, which can be found in "resp_genera_350.csv".

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Chemical composition of cold‐pressed blackberry seed flour extract and its potential health‐beneficial properties

Abstract The blackberry seed flour was cold‐extracted using 50% acetone and examined for its phytochemical composition and health‐beneficial properties including in vitro gut microbiota modulatory, free radical scavenging, anti‐inflammatory, and antiproliferative capacities. Among identified thirteen components of blackberry seed flour extract through UHPLC‐MS analysis, sanguiin H6 was the primary component and followed by ellagic acid and pedunculagin. For health‐beneficial properties, the blackberry seed flour extract increased the total number of gut bacteria and shifted the abundance of specific bacterial phylum, family, or genus. The extract had RDSC, ORAC, HOSC, and ABTS •+ scavenging capacities of 362, 304, 2,531, and 267 μmol Trolox equivalents (TE)/g, respectively. In addition, the blackberry seed flour extract showed capacities for anti‐inflammation and antiproliferation by suppressing LPS induced IL‐1β mRNA expressions in the cultured J774A.1 mouse macrophages and the proliferation of LNCaP prostate cancer cells. The results suggest potential health benefits and further utilization of blackberry seed flour as functional foods.

Choe, Uyory↗

DOE OSTI2023

Microbial Drivers of Plant Performance during Drought Depend upon Community Composition and the Greater Soil Environment

The increasing occurrence of drought is a global challenge that threatens food security through direct impacts to both plants and their interacting soil microorganisms. Plant growth promoting microbes are increasingly being harnessed to improve plant performance under stress. However, the magnitude of microbiome impacts on both structural and physiological plant traits under water limited and water replete conditions are not well-characterized. Using two microbiomes sourced from a ponderosa pine forest and an agricultural field, we performed a greenhouse experiment that used a crossed design to test the individual and combined effects of the water availability and the soil microbiome composition on plant performance. Specifically, we studied the structural and leaf functional traits of maize that are relevant to drought tolerance. We further examined how microbial relationships with plant phenotypes varied under different combinations of microbial composition and water availability. We found that water availability and microbial composition affected plant structural traits. Surprisingly, they did not alter leaf function. Maize grown in the forest-soil microbiome produced larger plants under well-watered and water-limited conditions, compared to an agricultural soil community. Although leaf functional traits were not significantly different between the watering and microbiome treatments, the bacterial composition and abundance explained significant variability in both plant structure and leaf function within individual treatments, especially water-limited plants. Our results suggest that bacteria-plant interactions that promote plant performance under stress depend upon the greater community composition and the abiotic environment.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

germs-lab/PAPER_miscanthus_soil_response

Nutrient inputs influence the sustainability of bioenergy crop production through contemporary (shortly after addition) and legacy effects (persisting over years) on microbial nitrogen (N) and carbon cycling, which contribute to greenhouse gas emissions. However, the relative importance of contemporary and legacy effects and how that could vary by crop functional types is poorly understood. Considering its rhizomatous roots and perennial growth, we hypothesized that Miscanthus × giganteus (M×g) would be more sensitive to legacy N fertilization and the historical context of its environment than an annual crop like maize. To test this hypothesis, we examined the effects of legacy and contemporary N inputs on nitrous oxide (N2O) and carbon dioxide (CO2) emissions, as well as key N cycling genes in soils where M×g and maize were grown. A 150-day soil incubation experiment was conducted using soils from a long-term M×g and maize fertility experiment with three historic N fertilization rates (0, 112, and 336 kg N ha−1 year−1) and a contemporary amendment (60 mg N kg−1) with negative control (0 mg N kg−1). We observed significant increases in cumulative N2O emissions in Mxg soils relative to maize soils, particularly at higher legacy fertilization rates, while contemporary N had no significant effect. Bacterial amoA gene abundance, which plays a significant role in nitrification in nutrient-rich soils, also increased with higher legacy fertilization rates in M×g soils but was unaffected by the contemporary N. In maize soils, legacy and contemporary N did not significantly affect N2O emissions, but cumulative CO2 emissions and amoA gene abundance significantly increased. The abundances of norB genes were not significantly influenced by either legacy fertilization or contemporary N amendments in either soil. Our findings demonstrate the greater importance of fertilization history over contemporary N in mediating soil N2O emissions, particularly for perennial bioenergy crops.

Lee, Jaejin↗

DOE OSTI2022

Molecular simulation of lignin-related aromatic compound permeation through gram-negative bacterial outer membranes

Lignin, an abundant aromatic heteropolymer in secondary plant cell walls, is the single largest source of renewable aromatics in the biosphere. Leveraging this resource for renewable bioproducts through targeted microbial action depends on lignin fragment uptake by microbial hosts and subsequent enzymatic action to obtain the desired product. Recent computational work has emphasized that bacterial inner membranes are permeable to many aromatic compounds expected from lignin depolymerization processes. In this study, we expand on these findings through simulations for 42 lignin-related compounds across a gram-negative bacterial outer membrane model. Unbiased simulation trajectories indicate that spontaneous crossing for the full outer membrane is relatively rare at molecular simulation timescales, primarily due to preferential membrane partitioning and slow diffusion within the lipopolysaccharide layer within the outer membrane. Membrane partitioning and permeability coefficients were determined through replica exchange umbrella sampling simulations to overcome sampling limitations. We find that the glycosylated lipopolysaccharides found in the outer membrane increase the permeation barrier to many lignin-related compounds, particularly the most hydrophobic compounds. However, the effect is relatively modest; at industrially relevant concentrations, uncharged lignin-related compounds will readily diffuse across the outer membrane without the need for specific porins. Together, our results provide insight into the permeability of the bacterial outer membrane for assessing lignin fragment uptake and the future production of renewable bioproducts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Intraspecific variability in root traits and edaphic conditions influence soil microbiomes across 12 switchgrass cultivars

Microbial communities help plants access nutrients and tolerate stress. Some microbiomes are specific to plant genotypes and, therefore, may contribute to intraspecific differences in plant growth and be a promising target for plant breeding. Switchgrass (Panicum virgatum L.) is a potential bioenergy crop with broad variation in yields and environmental responses; recent studies suggest that associations with distinct microbiomes may contribute to variation in cultivar yields. We used a common garden experiment to investigate variation in 12 mature switchgrass cultivar soil microbiomes and, further, to examine how root traits and soil conditions influence microbiome structure. Here, we found that average root diameter varied up to 33% among cultivars and that they associated with distinct soil microbiomes. Cultivar had a larger effect on the soil bacterial than fungal community, but both were strongly influenced by soil properties. Root traits had a weaker effect on microbiome structure, but root length contributed to variation in the fungal community. Unlike the soil communities, the root bacterial communities did not group by cultivar, based on a subset of samples. Microbial biomass carbon and nitrogen and the abundance of several dominant bacterial phyla varied between ecotypes, but overall the differences in soil microbiomes were greater among cultivars than between ecotypes. Our findings show that there is not one soil microbiome that applies to all switchgrass cultivars, or even to each ecotype. These subtle but significant differences in root traits, microbial biomass, and the abundance of certain soil bacteria could explain differences in cultivar yields and environmental responses.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Root-associated bacterial communities and root metabolite composition are linked to nitrogen use efficiency in sorghum

ABSTRACT The development of cereal crops with high nitrogen use efficiency (NUE) is a priority for worldwide agriculture. In addition to conventional plant breeding and genetic engineering, the use of the plant microbiome offers another approach to improving crop NUE. To gain insight into the bacterial communities associated with sorghum lines that differ in NUE, a field experiment was designed comparing 24 diverse Sorghum bicolor lines under sufficient and deficient nitrogen (N). Amplicon sequencing and untargeted gas chromatography–mass spectrometry were used to characterize the bacterial communities and the root metabolome associated with sorghum genotypes varying in sensitivity to low N. We demonstrated that N stress and sorghum type (energy, sweet, and grain sorghum) significantly impacted the root-associated bacterial communities and root metabolite composition of sorghum. We found a positive correlation between sorghum NUE and bacterial richness and diversity in the rhizosphere. The greater alpha diversity in high NUE lines was associated with the decreased abundance of a dominant bacterial taxon, Pseudomonas . Multiple strong correlations were detected between root metabolites and rhizosphere bacterial communities in response to low N stress. This indicates that the shift in the sorghum microbiome due to low N is associated with the root metabolites of the host plant. Taken together, our findings suggest that host genetic regulation of root metabolites plays a role in defining the root-associated microbiome of sorghum genotypes differing in NUE and tolerance to low N stress. IMPORTANCE The development of crops that are more nitrogen use-efficient (NUE) is critical for the future of the enhanced sustainability of agriculture worldwide. This objective has been pursued mainly through plant breeding and plant molecular engineering, but these approaches have had only limited success. Therefore, a different strategy that leverages soil microbes needs to be fully explored because it is known that soil microbes improve plant growth through multiple mechanisms. To design approaches that use the soil microbiome to increase NUE, it will first be essential to understand the relationship among soil microbes, root metabolites, and crop productivity. Using this approach, we demonstrated that certain key metabolites and specific microbes are associated with high and low sorghum NUE in a field study. This important information provides a new path forward for developing crop genotypes that have increased NUE through the positive contribution of soil microbes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Single-cell RNA sequencing reveals plasmid constrains bacterial population heterogeneity and identifies a non-conjugating subpopulation

Transcriptional heterogeneity in isogenic bacterial populations can play various roles in bacterial evolution, but its detection remains technically challenging. Here, we use microbial split-pool ligation transcriptomics to study the relationship between bacterial subpopulation formation and plasmid-host interactions at the single-cell level. We find that single-cell transcript abundances are influenced by bacterial growth state and plasmid carriage. Moreover, plasmid carriage constrains the formation of bacterial subpopulations. Plasmid genes, including those with core functions such as replication and maintenance, exhibit transcriptional heterogeneity associated with cell activity. Notably, we identify a cell subpopulation that does not transcribe conjugal plasmid transfer genes, which may help reduce plasmid burden on a subset of cells. Our study advances the understanding of plasmid-mediated subpopulation dynamics and provides insights into the plasmid-bacteria interplay.

59 BASIC BIOLOGICAL SCIENCES↗