Plant-environment microscopy tracks interactions of Bacillus subtilis with plant roots across the entire rhizosphere

Regulated cleavage and translocation of FERONIA control immunity in Arabidopsis roots

Plant roots exhibit localized immunity (LI) mainly in the transition zone (TZ) and elongation zone (EZ). Plasma membrane-localized receptor-like kinases (RLKs) can mediate the plant's response to rhizosphere bacteria. However, how RLKs are involved in triggering LI in roots remains unclear. Here we identified dual actions for the RLK FERONIA (FER) in the LI response of Arabidopsis (Arabidopsis thaliana). The FER cytoplasmic domain is cleaved and translocated to the nucleus (FERN) to activate LI in the TZ and EZ in response to colonization by beneficial and pathogenic bacteria. In the absence or cessation of bacterial infection, full-length FER is plasma membrane-localized to maintain growth. Upon colonization and invasion by a high titre of bacteria, mature RAPID ALKALINIZATION FACTOR23 peptide accumulates and activates the matrix metalloproteinase At2-MMP, which triggers FER cytoplasmic domain cleavage specifically in the TZ and EZ to activate LI. This work demonstrates that two molecular forms of a single RLK balance growth and immunity via LI activation in Arabidopsis roots.

Dynamic in situ detection in iRhizo-Chip reveals diurnal fluctuations of Bacillus subtilis in the rhizosphere

Effective colonization by microbe in the rhizosphere is critical for establishing a beneficial symbiotic relationship with the host plant. Bacillus subtilis, a soil-dwelling bacterium that is commonly found in association with plants and their rhizosphere, has garnered interest for its potential to enhance plant growth, suppress pathogens, and contribute to sustainable agricultural practices. However, research on the dynamic distribution of B. subtilis within the rhizosphere and its interaction mechanisms with plant roots remains insufficient due to limitations in existing in situ detection methodologies. To achieve dynamic in situ detection of the rhizosphere environment, we established iRhizo-Chip, a microfluidics-based platform. Using this device to investigate microbial behavior within the rhizosphere, we found obvious diurnal fluctuations in the growth of B. subtilis in the rhizosphere. Temporal dynamic analysis of rhizosphere dissolved oxygen (DO), pH, dissolved organic carbon, and reactive oxygen species showed that diurnal fluctuations in the growth of B. subtilis are potentially related to a variety of environmental factors. Spatial dynamic analysis also showed that the spatial distribution changes of B. subtilis and DO and pH were similar. Subsequently, through in vitro control experiments, we proved that rhizosphere DO and pH are the main driving forces for diurnal fluctuations in the growth of B. subtilis. Our results show that the growth of B. subtilis is driven by rhizosphere DO and pH, resulting in diurnal fluctuations, and iRhizo-Chip is a valuable tool for studying plant rhizosphere dynamics.

Whole proteome analysis of germinating and outgrowing Bacillus subtilis 168

In this study, we present a high-resolution dataset and bioinformatic analysis of the proteome of Bacillus subtilis 168 trp+ (BSB1) during germination and spore outgrowth. Samples were collected at 14 different time points (ranging from 0 to 130 min) in three biological replicates after spore inoculation into germination medium. A total of 2191 proteins were identified and categorized based on their expression kinetics. We observed four distinct clusters that were analyzed for functional categories and KEGG pathways annotations. The examination of newly synthesized proteins between successive time points revealed significant changes, particularly within the first 50 min. The dataset provides an information base that can be used for modeling purposes and inspire the design of new experiments.

Mobility and growth in confined spaces are important mechanisms for the establishment of Bacillus subtilis in the rhizosphere

The rhizosphere hosts complex and abundant microbiomes whose structure and composition are now well described by metagenomic studies. However, the dynamic mechanisms that enable micro-organisms to establish along a growing plant root are poorly characterized. Here, we studied how a motile bacterium utilizes the microhabitats created by soil pore space to establish in the proximity of plant roots. We have established a model system consisting of Bacillus subtilis and lettuce seedlings co-inoculated in transparent soil microcosms. We carried out live imaging experiments and developed image analysis pipelines to quantify the abundance of the bacterium as a function of time and position in the pore space. Results showed that the establishment of the bacterium in the rhizosphere follows a precise sequence of events where small islands of mobile bacteria were first seen forming near the root tip within the first 12-24 h of inoculation. Biofilm was then seen forming on the root epidermis at distances of about 700-1000 µm from the tip. Bacteria accumulated predominantly in confined pore spaces within 200 µm from the root or the surface of a particle. Using probabilistic models, we could map the complete sequence of events and propose a conceptual model of bacterial establishment in the pore space. This study therefore advances our understanding of the respective role of growth and mobility in the efficient colonization of bacteria in the rhizosphere.

Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers?

Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.

Effects of plant growth-promoting rhizobacteria on blueberry growth and rhizosphere soil microenvironment

Background

Plant growth-promoting rhizobacteria (PGPR) have a specific symbiotic relationship with plants and rhizosphere soil. The purpose of this study was to evaluate the effects of PGPR on blueberry plant growth, rhizospheric soil nutrients and the microbial community.

Methods

In this study, nine PGPR strains, belonging to the genera Pseudomonas and Buttiauxella, were selected and added into the soil in which the blueberry cuttings were planted. All the physiological indexes of the cuttings and all rhizospheric soil element contents were determined on day 6 after the quartic root irrigation experiments were completed. The microbial diversity in the soil was determined using high-throughput amplicon sequencing technology. The correlations between phosphorus solubilization, the auxin production of PGPR strains, and the physiological indexes of blueberry plants, and the correlation between rhizospheric microbial diversity and soil element contents were determined using the Pearson's correlation, Kendall's tau correlation and Spearman's rank correlation analysis methods.

Results

The branch number, leaf number, chlorophyllcontentand plant height of the treated blueberry group were significantly higher than those of the control group. The rhizospheric soil element contents also increased after PGPR root irrigation. The rhizospheric microbial community structure changed significantly under the PGPR of root irrigation. The dominant phyla, except Actinomycetota, in the soil samples had the greatest correlation with phosphorus solubilization and the auxin production of PGPR strains. The branch number, leaf number, and chlorophyllcontent had a positive correlation with the phosphorus solubilization and auxin production of PGPR strains and soil element contents. In conclusion, plant growth could be promoted by the root irrigation of PGPR to improve rhizospheric soil nutrients and the microenvironment, with modification of the rhizospheric soil microbial community.

Discussion

Plant growth could be promoted by the root irrigation of PGPR to improve rhizospheric soil nutrients and the microenvironment, with the modification of the rhizospheric soil microbial community. These data may help us to better understand the positive effects of PGPR on blueberry growth and the rhizosphere soil microenvironment, as well as provide a research basis for the subsequent development of a rhizosphere-promoting microbial fertilizer.

Emerging sensing, imaging, and computational technologies to scale nano-to macroscale rhizosphere dynamics - Review and research perspectives

The soil region influenced by plant roots, i.e., the rhizosphere, is one of the most complex biological habitats on Earth and significantly impacts global carbon flow and transformation. Understanding the structure and function of the rhizosphere is critically important for maintaining sustainable plant ecosystem services, designing engineered ecosystems for long-term soil carbon storage, and mitigating the effects of climate change. However, studying the biological and ecological processes and interactions in the rhizosphere requires advanced integrated technologies capable of decoding such a complex system at different scales. Here, we review how emerging approaches in sensing, imaging, and computational modeling can advance our understanding of the complex rhizosphere system. Particularly, we provide our perspectives and discuss future directions in developing in situ rhizosphere sensing technologies that could potentially correlate local-scale interactions to ecosystem scale impacts. We first review integrated multimodal imaging techniques for tracking inorganic elements and organic carbon flow at nano- to microscale in the rhizosphere, followed by a discussion on the use of synthetic soil and plant habitats that bridge laboratory-to-field studies on the rhizosphere processes. We then describe applications of genetically encoded biosensors in monitoring nutrient and chemical exchanges in the rhizosphere, and the novel nanotechnology-mediated delivery approaches for introducing biosensors into the root tissues. Next, we review the recent progress and express our vision on field-deployable sensing technologies such as planar optodes for quantifying the distribution of chemical and analyte gradients in the rhizosphere under field conditions. Moreover, we provide perspectives on the challenges of linking complex rhizosphere interactions to ecosystem sensing for detecting biological traits across scales, which arguably requires using the best-available model predictions including the model-experiment and image-based modeling approaches. Experimental platforms relevant to field conditions like SMART (Sensors at Mesoscales with Advanced Remote Telemetry) soils testbed, coupled with ecosystem sensing and predictive models, can be effective tools to explore coupled ecosystem behavior and responses to environmental perturbations. Finally, we envision that with the advent of novel high-resolution imaging capabilities at nano- to macroscale, and remote biosensing technologies, combined with advanced computational models, future studies will lead to detection and upscaling of rhizosphere processes toward ecosystem and global predictions.

Construction and characterisation of a structured, tuneable, and transparent 3D culture platform for soil bacteria

We have developed a tuneable workflow for the study of soil microbes in an imitative 3D soil environment that is compatible with routine and advanced optical imaging, is chemically customisable, and is reliably refractive index matched based on the carbon catabolism of the study organism. We demonstrate our transparent soil pipeline with two representative soil organisms, Bacillus subtilis and Streptomyces coelicolor, and visualise their colonisation behaviours using fluorescence microscopy and mesoscopy. This spatially structured, 3D approach to microbial culture has the potential to further study the behaviour of bacteria in conditions matching their native environment and could be expanded to study microbial interactions, such as competition and warfare.

Characterizing a Cost-Effective Hydrogel-Based Transparent Soil

Transparent soil (TS) was specifically designed to support root growth in the presence of air, water, and nutrients and allowed the time-resolved phenotyping of roots in vivo. Nevertheless, it is imperative to further optimize the reagent cost of TS to enable its wider utilization. We substituted the costly Phytagel obtained from Sigma with two more economical alternatives, namely Biodee and Coolaber. TS beads from each brand were prepared using 12 different polymer concentrations and seven distinct crosslinker concentrations. A comprehensive assessment encompassing transparency, mechanical characteristics, particle size, porosity, and stability of TS was undertaken. Compared to the Sigma Phytagel brand, both Biodee and Coolaber significantly reduced the transparency and collapse stress of the TS they produced. Consequently, this led to a significant reduction in the allowable width and height of the growth box, although they could still simultaneously exceed 20 cm and 19 cm. There was no notable difference in porosity and stability among the TS samples prepared using the three Phytagel brands. Therefore, it is feasible to consider replacing the Phytagel brand to reduce TS production costs. This study quantified the differences in TS produced using three Phytagel brands at different prices that will better promote the application of TS to root phenotypes.

Spatiotemporal control of root immune responses during microbial colonization

The entire evolutionary trajectory of plants towards large and complex multi-cellular organisms has been accompanied by incessant interactions with omnipresent unicellular microbes. This led to the evolution of highly complex microbial communities, whose members display the entire spectrum of pathogenic to mutualistic behaviors. Plant roots are dynamic, fractally growing organs and even small Arabidopsis roots harbor millions of individual microbes of diverse taxa. It is evident that microbes at different positions on a root surface could experience fundamentally different environments, which, moreover, rapidly change over time. Differences in spatial scales between microbes and roots compares to humans and the cities they inhabit. Such considerations make it evident that mechanisms of root-microbe interactions can only be understood if analyzed at relevant spatial and temporal scales. This review attempts to provide an overview of the rapid recent progress that has been made in mapping and manipulating plant damage and immune responses at cellular resolution, as well as in visualizing bacterial communities and their transcriptional activities. We further discuss the impact that such approaches will have for a more predictive understanding of root-microbe interactions.

Chemical communication in plant-microbe beneficial interactions: a toolbox for precise management of beneficial microbes

Harnessing the power of beneficial microbes in the rhizosphere to improve crop performance is a key goal of sustainable agriculture. However, the precise management of rhizosphere microbes for crop growth and health remains challenging because we lack a comprehensive understanding of the plant-rhizomicrobiome relationship. In this review, we discuss the latest research progress on root colonisation by representative beneficial microbes (e.g. Bacillus spp. and Pseudomonas spp.). We also highlight the bidirectional chemical communication between microbes and plant roots for precise functional control of beneficial microbes in the rhizosphere, as well as advances in understanding how beneficial microbes overcome the immune system of plants. Finally, we propose future research objectives that will help us better understand the complex network of plant-microbe interactions.

Scaling up and down: movement ecology for microorganisms

Movement is critical for the fitness of organisms, both large and small. It dictates how individuals acquire resources, evade predators, exchange genetic material, and respond to stressful environments. Movement also influences ecological and evolutionary dynamics at higher organizational levels, such as populations and communities. However, the links between individual motility and the processes that generate and maintain microbial diversity are poorly understood. Movement ecology is a framework linking the physiological and behavioral properties of individuals to movement patterns across scales of space, time, and biological organization. By synthesizing insights from cell biology, ecology, and evolution, we expand theory from movement ecology to predict the causes and consequences of microbial movements.

Quantifying bacterial concentration in water and sand media during flow-through experiments using a non-invasive, real-time, and efficient method

Monitoring the dynamics of bacteria in porous media is of great significance to understand the bacterial transport and the interplay between bacteria and environmental factors. In this study, we reported a non-invasive, real-time, and efficient method to quantify bioluminescent bacterial concentration in water and sand media during flow-through experiments. First, 27 column experiments were conducted, and the bacterial transport was monitored using a real-time bioluminescent imaging system. Next, we quantified the bacterial concentration in water and sand media using two methods-viable count and bioluminescent count. The principle of the bioluminescent count in sand media was, for a given bioluminescence image, the total number of bacteria was proportionally allocated to each segment according to its bioluminescence intensity. We then compared the bacterial concentration for the two methods and found a good linear correlation between the bioluminescent count and viable count. Finally, the effects of porous media surface coating, pore water velocity, and ionic strength on the bioluminescent count in sand media were investigated, and the results showed that the bioluminescence counting accuracy was most affected by surface coating, followed by ionic strength, and was hardly affected by pore water velocity. Overall, the study proved that the bioluminescent count was a reliable method to quantify bacterial concentration in water (10⁶ to 2 × 10⁸ cell mL^-1) or sand media (5 × 10⁶-5 × 10⁸ cell cm^-3). This approach also offers a new way of thinking for in situ bacterial enumeration in two-dimensional devices such as 2D flow cells, microfluidic devices, and rhizoboxes.

Novel form of collective movement by soil bacteria

Although migrations are essential for soil microorganisms to exploit scarce and heterogeneously distributed resources, bacterial mobility in soil remains poorly studied due to experimental limitations. In this study, time-lapse images collected using live microscopy techniques captured collective and coordinated groups of B. subtilis cells exhibiting "crowd movement". Groups of B. subtilis cells moved through transparent soil (nafion polymer with particle size resembling sand) toward plant roots and re-arranged dynamically around root tips in the form of elongating and retracting "flocks" resembling collective behaviour usually associated with higher organisms (e.g., bird flocks or fish schools). Genetic analysis reveals B. subtilis flocks are likely driven by the diffusion of extracellular signalling molecules (e.g., chemotaxis, quorum sensing) and may be impacted by the physical obstacles and hydrodynamics encountered in the soil like environment. Our findings advance understanding of bacterial migration through soil matrices and expand known behaviours for coordinated bacterial movement.