Single-cell transcriptome profiling of heterogeneous tissues can provide high-resolution windows into developmental dynamics and environmental responses, but its application to plants has been ...limited. Here, we used the high-throughput Drop-seq approach to profile >12,000 cells from Arabidopsis roots. This identified numerous distinct cell types, covering all major root tissues and developmental stages, and illuminated specific marker genes for these populations. In addition, we demonstrate the utility of this approach to study the impact of environmental conditions on developmental processes. Analysis of roots grown with or without sucrose supplementation uncovers changes in the relative frequencies of cell types in response to sucrose. Finally, we characterize the transcriptome changes that occur across endodermis development and identify nearly 800 genes with dynamic expression as this tissue differentiates. Collectively, we demonstrate that single-cell RNA-seq can be used to profile developmental processes in plants and show how they can be altered by external stimuli.
Display omitted
•RNA expression profiling of >12,000 single Arabidopsis root cells by Drop-seq•Recovered major tissue types and cell stages and identified specific marker genes•Sucrose alters cell type proportions but does not profoundly change cell identities•Identified ∼800 genes dynamically expressed across endodermis development
The application of single-cell transcriptome profiling to plants has been limited. Shulse et al. performed Drop-seq on Arabidopsis roots, generating a transcriptional resource for >12,000 cells across major populations. This revealed marker genes for distinct cell types, cell frequency changes resulting from sucrose addition, and genes dynamically regulated during development.
From bacteria to humans, individual cells within isogenic populations can show significant variation in stress tolerance, but the nature of this heterogeneity is not clear. To investigate this, we ...used single-cell RNA sequencing to quantify transcript heterogeneity in single Saccharomyces cerevisiae cells treated with and without salt stress to explore population variation and identify cellular covariates that influence the stress-responsive transcriptome. Leveraging the extensive knowledge of yeast transcriptional regulation, we uncovered significant regulatory variation in individual yeast cells, both before and after stress. We also discovered that a subset of cells appears to decouple expression of ribosomal protein genes from the environmental stress response in a manner partly correlated with the cell cycle but unrelated to the yeast ultradian metabolic cycle. Live-cell imaging of cells expressing pairs of fluorescent regulators, including the transcription factor Msn2 with Dot6, Sfp1, or MAP kinase Hog1, revealed both coordinated and decoupled nucleocytoplasmic shuttling. Together with transcriptomic analysis, our results suggest that cells maintain a cellular filter against decoupled bursts of transcription factor activation but mount a stress response upon coordinated regulation, even in a subset of unstressed cells.
The paper aims to investigate the influence of the characteristics of the strands on the properties of oriented strand boards (OSB). To solve this objective, some global synthetic characteristics of ...the strands (the slenderness ratio, the characteristics of thinness, and the specific surface) of four wood species currently used in this technology (spruce and pine for softwood, and poplar and willow for hardwood) were first studied. The characteristics of the OSB obtained from each species separately were also determined, and finally the correlations analysis was made between the characteristics of the strands and those of the corresponding OSB boards. The working methodology used the European tests regarding the physical and mechanical properties of the boards, but also algorithms for forecasting and evaluating the quality of the strands and boards. The conclusions regarding the characteristics of the strands have highlighted the role of the specific surface of the strand and the characteristics of the thickness; respectively, the conclusions regarding the characteristics of the boards showed that the fast-growing species of willow and poplar lead to obtaining higher quality OSB boards. The general conclusion of the paper is that the characteristics of the strands have a significant influence on the physical–mechanical properties of the OSB board.
The paper aims to analyze the biomass at one year growth, resulting from the cultivation of the INGER energy willow clone as a short rotation crop (SRC), in order to use it as a renewable fuel. The ...paper completes the data in the field of renewable energies in the context of decreasing fossil energy reserves worldwide and emphasizing the impact on renewable energies. The effect of a contaminated land on the survival rate of the planted seedlings and the effect of the energy willow culture on the composition of the contaminated soil are analyzed. The obtained results show that the biomass characteristics, such as the calorific power of about 18,21 kJ/g to18,90 kJ/g, and the ash content of about 2,25%, are comparable with the ones of other lignocellulosic energy materials. The results found in this study showed that the woody biomass in the first vegetation year of energy willow can be used directly as a renewable fuel without the need for compaction in the form of briquettes or pellets.
The paper aims to compare the oriented strand boards (OSBs) made in the laboratory from a mixture of softwood species to those made from hardwood species, followed by their comparison to European and ...industry standards. In this regard, the main properties of the panels made in the laboratory were determined, including density, absorption, and swelling in thickness, modulus of elasticity, modulus of rupture, and internal bond. The analysis of the properties of swelling (24 h) and absorption (24 h) revealed that the mixture of softwood species was slightly better thanthe hardwood one. It was also shown that the panels manufactured from the mixture of hardwood species had better mechanical properties than those made of the softwood mixture (modulus of rupture (MOR) = 43.48 N/mm2, modulus of elasticity (MOE) = 7253 N/mm, and internal bond (IB) = 1.57 N/mm2). Additionally, the comparative analysis of properties indicates that the density is highly significant in determining the MOE values of the OSBs. This will allow softwood speciestobe replaced with other species of soft and fast-growing deciduous trees such as willow, birch, and poplar in the manufacture of oriented strand boards.
Progress in sequencing, microfluidics, and analysis strategies has revolutionized the granularity at which multicellular organisms can be studied. In particular, single-cell transcriptomics has led ...to fundamental new insights into animal biology, such as the discovery of new cell types and cell type-specific disease processes. However, the application of single-cell approaches to plants, fungi, algae, or bacteria (environmental organisms) has been far more limited, largely due to the challenges posed by polysaccharide walls surrounding these species' cells. In this perspective, we discuss opportunities afforded by single-cell technologies for energy and environmental science and grand challenges that must be tackled to apply these approaches to plants, fungi and algae. We highlight the need to develop better and more comprehensive single-cell technologies, analysis and visualization tools, and tissue preparation methods. We advocate for the creation of a centralized, open-access database to house plant single-cell data. Finally, we consider how such efforts should balance the need for deep characterization of select model species while still capturing the diversity in the plant kingdom. Investments into the development of methods, their application to relevant species, and the creation of resources to support data dissemination will enable groundbreaking insights to propel energy and environmental science forward.
Generating sequence data of a defined community composed of organisms with complete reference genomes is indispensable for the benchmarking of new genome sequence analysis methods, including assembly ...and binning tools. Moreover the validation of new sequencing library protocols and platforms to assess critical components such as sequencing errors and biases relies on such datasets. We here report the next generation metagenomic sequence data of a defined mock community (Mock Bacteria ARchaea Community; MBARC-26), composed of 23 bacterial and 3 archaeal strains with finished genomes. These strains span 10 phyla and 14 classes, a range of GC contents, genome sizes, repeat content and encompass a diverse abundance profile. Short read Illumina and long-read PacBio SMRT sequences of this mock community are described. These data represent a valuable resource for the scientific community, enabling extensive benchmarking and comparative evaluation of bioinformatics tools without the need to simulate data. As such, these data can aid in improving our current sequence data analysis toolkit and spur interest in the development of new tools.
Strict planetary protection practices are implemented during spacecraft assembly to prevent inadvertent transfer of earth microorganisms to other planetary bodies. Therefore, spacecraft are assembled ...in cleanrooms, which undergo strict cleaning and decontamination procedures to reduce total microbial bioburden. We wanted to evaluate if these practices selectively favor survival and growth of hardy microorganisms, such as pathogens. Three geographically distinct cleanrooms were sampled during the assembly of three NASA spacecraft: The Lockheed Martin Aeronautics' Multiple Testing Facility during DAWN, the Kennedy Space Center's Payload Hazardous Servicing Facility (KSC-PHSF) during Phoenix, and the Jet Propulsion Laboratory's Spacecraft Assembly Facility during Mars Science Laboratory. Sample sets were collected from the KSC-PHSF cleanroom at three time points: before arrival of the Phoenix spacecraft, during the assembly and testing of the Phoenix spacecraft, and after removal of the spacecraft from the KSC-PHSF facility. All samples were subjected to metagenomic shotgun sequencing on an Illumina HiSeq 2500 platform. Strict decontamination procedures had a greater impact on microbial communities than sampling location Samples collected during spacecraft assembly were dominated by Acinetobacter spp. We found pathogens and potential virulence factors, which determine pathogenicity in all the samples tested during this study. Though the relative abundance of pathogens was lowest during the Phoenix assembly, potential virulence factors were higher during assembly compared to before and after assembly, indicating a survival advantage. Decreased phylogenetic and pathogenic diversity indicates that decontamination and preventative measures were effective against the majority of microorganisms and well implemented, however, pathogen abundance still increased over time. Four potential pathogens, Acinetobacter baumannii, Acinetobacter lwoffii, Escherichia coli and Legionella pneumophila, and their corresponding virulence factors were present in all cleanroom samples. This is the first functional metagenomics study describing presence of pathogens and their corresponding virulence factors in cleanroom environments. The results of this study should be considered for microbial monitoring of enclosed environments such as schools, homes, hospitals and more isolated habitation such the International Space Station and future manned missions to Mars.
We describe environmental microbial eukaryotes (EMEs) sample collection, single-cell isolation, lysis, and genome amplification, followed by the rDNA amplification and OTU screening for recovery of ...high-quality species-specific genomes for de novo assembly. These protocols are part of our pipeline that also includes bioinformatic methods. The pipeline and its application on a wide range of phyla of different sample complexity are described in our complementary paper. In addition, this protocol describes optimized lysis, genome amplification, and OTU screening steps of the pipeline.
For complete details on the use and execution of this protocol, please refer to Ciobanu et al. (2021).
Display omitted
•We describe EME sample-collection, single-cell isolation, lysis, genome amplification•These protocols are suitable for mining single-cell EME genomes•These protocols are directed towards recovery of high-quality genomes•The genomes are suitable for species-specific de novo genome assembly
We describe environmental microbial eukaryotes (EMEs) sample collection, single-cell isolation, lysis, and genome amplification, followed by the rDNA amplification and OTU screening for recovery of high-quality species-specific genomes for de novo assembly. These protocols are part of our pipeline that also includes bioinformatic methods. The pipeline and its application on a wide range of phyla of different sample complexity are described in our complementary paper. In addition, this protocol describes optimized lysis, genome amplification, and OTU screening steps of the pipeline.
PDF
