Imaging O2 dynamics and microenvironments in the seagrass leaf phyllosphere with magnetic optical sensor nanoparticles

In Vivo Lifetime Imaging of the Internal O2 Dynamics in Corals with near-Infrared-Emitting Sensor Nanoparticles

Mapping of O2 with luminescent sensors within intact animals is challenging due to attenuation of excitation and emission light caused by tissue absorption and scattering as well as interfering background fluorescence. Here we show the application of luminescent O2 sensor nanoparticles (∼50-70 nm) composed of the O2 indicator platinum(II) tetra(4-fluoro)phenyltetrabenzoporphyrin (PtTPTBPF) immobilized in poly(methyl methacrylate-co-methacrylic acid) (PMMA-MA). We injected the sensor nanoparticles into the gastrovascular system of intact colony fractions of reef-building tropical corals that harbor photosynthetic microalgae in their tissues. The sensor nanoparticles are excited by red LED light (617 nm) and emit in the near-infrared (780 nm), which enhances the transmission of excitation and emission light through biological materials. This enabled us to map the internal O2 concentration via time-domain luminescence lifetime imaging through the outer tissue layers across several coral polyps in flowing seawater. After injection, nanoparticles dispersed within the coral tissue for several hours. While luminescence intensity imaging showed some local aggregation of sensor particles, lifetime imaging showed a more homogeneous O2 distribution across a larger area of the coral colony. Local stimulation of symbiont photosynthesis in corals induced oxygenation of illuminated tissue areas and formation of lateral O2 gradients toward surrounding respiring tissues, which were dissipated rapidly after the onset of darkness. Such measurements are key to improving our understanding of how corals regulate their internal chemical microenvironment and metabolic activity, and how they are affected by environmental stress such as ocean warming, acidification, and deoxygenation. Our experimental approach can also be adapted for in vivo O2 imaging in other natural systems such as biofilms, plant and animal tissues, as well as in organoids and other cell constructs, where imaging internal O2 conditions are relevant and challenging due to high optical density and background fluorescence.

Nitrogen Fixation and Microbial Communities Associated with Decomposing Seagrass Leaves in Temperate Coastal Waters

Seagrass meadows play pivotal roles in coastal biochemical cycles, with nitrogen fixation being a well-established process associated with living seagrass. Here, we tested the hypothesis that nitrogen fixation is also associated with seagrass debris in Danish coastal waters. We conducted a 52-day in situ experiment to investigate nitrogen fixation (proxied by acetylene reduction) and dynamics of the microbial community (16S rRNA gene amplicon sequencing) and the nitrogen fixing community (nifH DNA/RNA amplicon sequencing) associated with decomposing Zostera marina leaves. The leaves harboured distinct microbial communities, including distinct nitrogen fixers, relative to the surrounding seawater and sediment throughout the experiment. Nitrogen fixation rates were measurable on most days, but highest on days 3 (dark, 334.8 nmol N g-1 dw h-1) and 15 (light, 194.6 nmol N g-1 dw h-1). Nitrogen fixation rates were not correlated with the concentration of inorganic nutrients in the surrounding seawater or with carbon:nitrogen ratios in the leaves. The composition of nitrogen fixers shifted from cyanobacterial Sphaerospermopsis to heterotrophic genera like Desulfopila over the decomposition period. On the days with highest fixation, nifH RNA gene transcripts were mainly accounted for by cyanobacteria, in particular by Sphaerospermopsis and an unknown taxon (order Nostocales), alongside Proteobacteria. Our study shows that seagrass debris in temperate coastal waters harbours substantial nitrogen fixation carried out by cyanobacteria and heterotrophic bacteria that are distinct relative to the surrounding seawater and sediments. This suggests that seagrass debris constitutes a selective environment where degradation is affected by the import of nitrogen via nitrogen fixation.

Organosilica Nanosensors for Monitoring Spatiotemporal Changes in Oxygen Levels in Bacterial Cultures

Oxygen plays a central role in aerobic metabolism, and while many approaches have been developed to measure oxygen concentration in biological environments over time, monitoring spatiotemporal changes in dissolved oxygen levels remains challenging. To address this, we developed a ratiometric core-shell organosilica nanosensor for continuous, real-time optical monitoring of oxygen levels in biological environments. The nanosensors demonstrate good steady state characteristics (KpSV = 0.40 L/mg, R2 = 0.95) and respond reversibly to changes in oxygen concentration in buffered solutions and report similar oxygen level changes in response to bacterial cell growth (Escherichia coli) in comparison to a commercial bulk optode-based sensing film. We further demonstrated that the oxygen nanosensors could be distributed within a growing culture of E. coli and used to record oxygen levels over time and in different locations within a static culture, opening the possibility of spatiotemporal monitoring in complex biological systems.

Two-dimensional, high-resolution imaging of pH dynamics in the phyllosphere of submerged macrophyte using a new Nano-optode

The phyllosphere pH helps shape the plant microbiome and strongly influences aboveground interactions in plant canopies. Yet little is known about the distribution of pH at a microscale within the macrophyte phyllosphere and the factors promoting them because achieving high-resolution quantitative imaging of phyllosphere pH is a great challenge. Here, new ratiometric pH nano-optodes were prepared by firstly encapsulating the self-synthesized lipophilic dyes (8-acetoxypyrene-N1, N3, N6-trioctadecyl-1, 3, 6-tri-trisulfonamide) to poly(1-vinylpyrrolidone-co-styrene) nanoparticles, and then immobilizing the resulting nanoparticles in polyurethane hydrogel on transparent foils. The nano-optodes presented reversible and fast response (t95 < 80 s) to the pH range from 7.0 to 11.0, with merits of good spatial resolution, photobleaching/leaching resistance and negligible cross-sensitives toward temperature, O2 and ionic strength (< 100 mM). The nano-optodes together with a self-designed phyllosphere chamber were further applied to directly measure the pH distributions at a microscale around single leaves of V. spiralis grown in natural sediment. The pronounced pH microheterogeneity and leaf basification within the V. spiralis phyllosphere were quantitatively visualized. We also provided direct empirical evidence that the dynamic of the phyllosphere pH at high resolution was significantly controlled by the shifting light intensity and temperature. Implementation of the nano-optodes holds great potential for various laboratory applications, which will provide an in-depth insight into phyllosphere activities on the microscale.

Influence of nutrient enrichment on colonisation and photosynthetic parameters of hard substrate marine microphytobenthos

This study aimed to assess the influence of nutrient enrichment on the development of microalgal biofilm on concrete and PVC cubes. Three mesocosms were utilized to create a nutrient gradient over a period of 28 days. Various parameters including biomass, photosynthetic activity, microtopography, and extracellular polymeric substances (EPS) were measured. Imaging PAM techniques were employed to obtain surface-wide data. Results revealed that nutrient availability had no significant impact on Chl a biomass and the maximum quantum efficiency of PSII (F v /F m ). The photosynthetic capacity and efficiency were minimally affected by nutrient availability. Interestingly, the relationship between microphytobenthic (MPB) biomass and photosynthesis and surface rugosity exhibited distinct patterns. Negative reliefs showed a strong correlation with F v /F m , while no clear pattern emerged for biomass on rough concrete structures. Overall, our findings demonstrate that under conditions of heightened eutrophication, biofilm photosynthesis thrives in the fissures and crevasses of colonized structures regardless of nutrient levels. This investigation provides valuable insights into the interplay between nutrient availability and surface rugosity.

Complexity of Abiotic Stress Stimuli: Mimicking Hypoxic Conditions Experimentally on the Basis of Naturally Occurring Environments

Plants require oxygen to respire and produce energy. Plant cells are exposed to low oxygen levels (hypoxia) in different contexts and have evolved conserved molecular responses to hypoxia. Both environmental and developmental factors can influence intracellular oxygen concentrations. In nature, plants can experience hypoxic conditions when the soil becomes saturated with water following heavy precipitation (i.e., waterlogging). Hypoxia can also arise in specific tissues that have poor gas exchange with atmospheric oxygen. In this case, hypoxic niches that are physiologically and developmentally relevant may form. To dissect the molecular mechanisms underlying the regulation of hypoxia response in plants, a wide range of hypoxia-inducing methods have been used in the laboratory setting. Yet, the different characteristics, pros and cons of each of these hypoxia treatments are seldom compared between methods, and with natural forms of hypoxia. In this chapter, we present both environmental and developmental forms of hypoxia that plants encounter in the wild, as well as the different experimental hypoxia treatments used to mimic them in the laboratory setting, with the aim of informing on what experimental approaches might be most appropriate to the questions addressed, including stress signaling and regulation.

How plants recruit their microbiome? New insights into beneficial interactions

•

Plant-microbiome interaction occurs at the rhizosphere, endosphere, and phyllosphere.

•

Root exudates can favor the recruitment of a beneficial microbiome in the rhizosphere.

•

Plant topology and phytochemistry influence the recruitment of the phyllosphere microbiome.

•

Diverse plant strategies selectively recruit beneficial microbiomes.

•

Multiple plant mechanisms displace potential pathogens from the rhizosphere.

•

The beneficial microbiome helps plants to recruit other beneficial microbiota.

Background

Research on beneficial mechanisms by plant-associated microbiomes, such as plant growth stimulation and protection from plant pathogens, has gained considerable attention over the past decades; however, the mechanisms used by plants to recruit their microbiome is largely unknown.

Aim of Review

Here, we review the latest studies that have begun to reveal plant strategies in selectively recruiting beneficial microbiomes, and how they manage to exclude potential pathogens.

Key Scientific concepts of Review: We examine how plants attract beneficial microbiota from the main areas of interaction, such as the rhizosphere, endosphere, and phyllosphere, and demonstrate that such process occurs by producing root exudates, and recognizing molecules produced by the beneficial microbiota or distinguishing pathogens using specific receptors, or by triggering signals that support plant-microbiome homeostasis. Second, we analyzed the main environmental or biotic factors that modulate the structure and successional dynamics of microbial communities. Finally, we review how the associated microbiome is capable of engaging with other synergistic microbes, hence providing an additional element of selection. Collectively, this study reveals the importance of understanding the complex network of plant interactions, which will improve the understanding of bioinoculant application in agriculture, based on a microbiome that interacts efficiently with plant organs under different environmental conditions.

Optode Based Chemical Imaging-Possibilities, Challenges, and New Avenues in Multidimensional Optical Sensing

Seeing is believing, as the saying goes, and optical sensors (so-called optodes) are tools that can make chemistry visible. Optodes react reversibly and quickly (seconds to minutes) to changing analyte concentrations, enabling the spatial and temporal visualization of an analyte in complex environments. By being available as planar sensor foils or in the form of nano- or microparticles, optodes are flexible tools suitable for a wide array of applications. The steadily grown applications of in particular oxygen (O₂) and pH optodes in fields as diverse as medical, environmental, or material sciences is proof for the large demand of optode based chemical imaging. Nevertheless, the full potential of this technology is not exhausted yet, challenges have to be overcome, and new avenues wait to be taken. Within this Perspective, we look at where the field currently stands, highlight several successful examples of optode based chemical imaging and ask what it will take to advance current state-of-the-art technology. It is our intention to point toward some potential blind spots and to inspire further developments.

Luminescence lifetime imaging of three-dimensional biological objects

A major focus of current biological studies is to fill the knowledge gaps between cell, tissue and organism scales. To this end, a wide array of contemporary optical analytical tools enable multiparameter quantitative imaging of live and fixed cells, three-dimensional (3D) systems, tissues, organs and organisms in the context of their complex spatiotemporal biological and molecular features. In particular, the modalities of luminescence lifetime imaging, comprising fluorescence lifetime imaging (FLI) and phosphorescence lifetime imaging microscopy (PLIM), in synergy with Förster resonance energy transfer (FRET) assays, provide a wealth of information. On the application side, the luminescence lifetime of endogenous molecules inside cells and tissues, overexpressed fluorescent protein fusion biosensor constructs or probes delivered externally provide molecular insights at multiple scales into protein-protein interaction networks, cellular metabolism, dynamics of molecular oxygen and hypoxia, physiologically important ions, and other physical and physiological parameters. Luminescence lifetime imaging offers a unique window into the physiological and structural environment of cells and tissues, enabling a new level of functional and molecular analysis in addition to providing 3D spatially resolved and longitudinal measurements that can range from microscopic to macroscopic scale. We provide an overview of luminescence lifetime imaging and summarize key biological applications from cells and tissues to organisms.