Biology subjects

Kuhl, M.

Publications and source records attributed to Kuhl, M..

15 recordsLinked to original sources

bioRxiv2026

From Coral Color to Tissue Heating: How Host Pigments Redirect Light Within the Tissue

Coral host pigments strongly modify the internal light environment of corals, yet their influence on heat dissipation in coral tissue remains poorly understood. Here, we combined scalar irradiance and temperature microsensor measurements with mechanistic multiphysics modelling to quantify how chromoproteins (CPs) and fluorescent proteins (FPs) regulate light propagation and tissue heating in corals. Measurement-informed simulations of coupled radiative and heat transfer showed that high host pigment concentrations increase broadband scattering while strongly absorbing light within their characteristic spectral bands, reducing light penetration into deeper tissue layers and producing localized energy deposition. Under high symbiont densities, tissue heating was governed by absorption by both symbionts and host pigments, whereas in bleached corals, host pigments became the dominant source of heat generation. Heat generated by CP absorption was concentrated within the epidermis, while symbiont absorption caused deeper heating within the gastrodermis. Unlike CPs, FPs additionally redistributed a fraction of the absorbed photons through lower energy fluorescence emission, increasing scalar irradiance at longer wavelengths and shifting energy deposition deeper into the tissue, thereby enhancing subsurface heating relative to the corresponding non-fluorescent CP scenario. In the model, this pathway changes scalar irradiance and predicted energy deposition relative to the same FP parameterization with fluorescence disabled. The magnitude of this effect varied with FP concentration, spatial organization (granular or diffuse), and symbiont density. Model outputs were supported by surface light and temperature microsensor measurements across sampled coral phenotypes and symbiont densities. Together, our results demonstrate distinct modeled optical pathways for CPs and FPs that regulate not only light propagation but also the spatial distribution of heat generation within coral tissues. By balancing light attenuation, spectral redistribution, and heat generation, host pigmentation is thus likely to influence photoacclimation, bleaching susceptibility, and recovery of the coral-algal symbiosis.

biophysics↗

bioRxiv2025

Enhancing Microalgal Growth through Integrated Computational Modeling and 3D Bioprinting

Efficient cultivation of microalgae for biofuel and bioproduct applications is often limited by suboptimal light distribution, poor mass transfer, and large land footprint requirements in conventional flat biofilm and open-pond systems. In this study, we combine computational modeling, 3D bioprinting, and experimental measurements to design and evaluate the role of different geometries for photosynthetic production in bioprinted microalgal constructs. Specifically, we investigate a perforated slab with channels (PS) and Vgroove structures, which show enhanced algal growth performance compared to flat slabs of the same volume and footprint. By integrating experimentally measured photosynthetic parameters into radiative transfer and oxygen diffusion-reaction simulations, we uncover the role of structure induced improvements in light penetration, surface area-to-volume ratio, and mass transfer dynamics driving increased algal growth and photosynthesis. Algal growth rates in printed PS and Vgroove geometries were 2.4 and 1.3 times higher, respectively, than in corresponding slab. These findings demonstrate the potential of engineered 3D bioprinted architectures to optimize photosynthetic efficiency and growth rates while minimizing spatial footprint, paving the way for compact, high-throughput bioreactors for sustainable algal cultivation. Beyond biofuel production, these microalgal systems enable sustainable CO2 capture and utilization.

bioengineering↗

bioRxiv2025

Chemical Microenvironment of the Coral Gastrovascular Cavity and Its Associated Bacterial Diversity

Coral gastrovascular cavities (GVCs) host diverse microorganisms and, as semi-closed compartments, are characterized by elevated nutrient concentrations and pronounced diel fluctuations in oxygen (O2) and pH. However, their broader chemical microenvironment and associated microbial activities remain poorly understood. Here, we provide direct evidence for active anaerobic metabolism in the GVC by measuring hydrogen (H2), nitric oxide (NO), and nitrous oxide (N2O) production, indicative of microbial fermentation, nitrogen fixation and denitrification. Changes in GVC H2 concentrations after feeding suggest that feeding modulates substrate availability, which in turn influences microbial activity in this compartment. In bleached corals, the GVC remained consistently hypoxic and acidic, and anaerobic metabolic processes persisted across the diel cycle. These patterns suggest a shift in energy and nutrient cycling pathways within the bleached coral holobiont. Together, our findings identify the GVC as a dynamic site of microbial activity that may play an important role in holobiont carbon and nitrogen cycling, with potential implications for nutrient balance and coral resilience.

ecology↗

bioRxiv2025

Subcellular assessment of algal carbon storage and chloroplasts across the microenvironmental landscape of a photosymbiotic coral

Light availability plays a central role in shaping the photophysiology and energy metabolism of photosymbiotic organisms such as reef-building corals. Although light varies greatly within coral colonies, the effects of this spatial heterogeneity on the subcellular organization and energy storage of symbiotic algae (Symbiodiniaceae) remain poorly understood. Here, we combined microscale measurements of light and oxygen across both light-exposed upper regions and shaded basal regions of a Favites abdita colony with three-dimensional subcellular imaging using Focused Ion Beam Scanning Electron Microscopy (FIB-SEM). Our multi-scale approach revealed subcellular heterogeneity among symbiont populations, suggesting different cell cycle stages and physiological states across a spatial stratification in the coral. Subcellular morphometrics revealed that symbiont cells at the top of the colony were twice more voluminous than those at the shaded base with similar plastid volume occupancy. Compared to symbionts at the top of the colony, symbionts in the basal region accumulated nearly three times more starch relative to their cell volume. These findings show that light gradients within coral colonies shape symbiont morphology and energy storage patterns, with important implications for coral stress tolerance and resilience.

cell biology↗

bioRxiv2025

Functional imaging of 3D bioprinted microalgal constructs and simulation of their photosynthetic performance

The intricate three dimensional architecture at different spatial length scales affects the functionality and growth performance of immobilized photosynthesizing cells in biofilms and bioprinted constructs. Despite the tremendous potential of 3D bioprinting in precisely defining sample heterogeneity and composition in spatial context, cell metabolism is mostly measured in media surrounding the constructs or by destructive sample analyses. The exploration and application of non-invasive techniques for monitoring physico-chemical microenvironments, growth and metabolic activity of cells in 3D printed constructs is thus in strong demand. Here, we present a pipeline for the fabrication of 3D bioprinted microalgal constructs with a functionalized gelatin methacryloyl (GelMA)-based bioink for imaging O2 dynamics within bioprinted constructs, as well as their characterization using various, non-invasive functional imaging techniques and numerical simulation of their photophysiological performance. This fabrication, imaging and simulation pipeline now enables investigation of the effect of structure and composition on photosynthetic efficiency of bioprinted constructs with microalgae or cyanobacteria. It can facilitate designing efficient construct geometries for enhanced light penetration and improved mass transfer of nutrients, CO2 or O2 between the 3D printed construct and the surrounding medium, thereby providing a mechanistic basis for the design of more efficient artificial photosynthetic systems.

bioengineering↗

bioRxiv2025

Metatranscriptomics sheds light on 'who is doing what' in the coral Porites lutea

Global decline of coral reefs due to climate change necessitates nature-based protection strategies for these crucial ecosystems. Developing such strategies requires a thorough understanding of the complex roles and interactions occurring within the coral holobiont. Using RNAseq, we investigated the active microbiome of healthy stony coral Porites lutea, focusing on the coral tissue, the green endolithic algal layer (Ostreobium layer), and the deeper coral skeleton. We identified distinct, metabolically active communities within these compartments and highlight substantial metabolic redundancy across carbon, nitrogen, and sulphur pathways. Our study provides first transcriptomic evidence of Ostreobiums ability to transfer fixed carbon to other holobiont members and the coral host. Additionally, we highlight critical roles of diverse coral holobiont members in nutrient cycling and maintaining homeostasis through scavenging of reactive oxygen and nitrogen species. This study provides novel molecular-level understanding of the functional roles played by diverse coral holobiont members in their respective compartments and underscores that corals harbour distinct microbiomes with wide-ranging functions.

microbiology↗

bioRxiv2023

Light management by algal aggregates in living photosynthetic hydrogels.

Rapid progress in algal biotechnology has triggered a growing interest in hydrogel-encapsulated microalgal cultivation, especially for the engineering of functional photosynthetic materials and biomass production. An overlooked characteristic of gel-encapsulated cultures is the emergence of cell aggregates, which are the result of the mechanical confinement of the cells. Such aggregates have a dramatic effect on the light management of gel-encapsulated photobioreactors and hence strongly affect the photosynthetic outcome. In order to evaluate such an effect, we experimentally studied the optical response of hydrogels containing algal aggregates and developed optical simulations to study the resultant light intensity profiles. The simulations are validated experimentally via transmittance measurements using an integrating sphere and aggregate volume analysis with confocal microscopy. Specifically, the heterogeneous distribution of cell aggregates in a gel matrix can increase light penetration while alleviating photoinhibition compared to a flat biofilm. Finally, we demonstrate that light harvesting efficiency can be further enhanced with the introduction of scattering particles within the hydrogel matrix, leading to a four-fold increase in biomass growth. Our study, therefore, highlights a new strategy for the design of spatially efficient photosynthetic living materials that have important implications for the engineering of future algal cultivation systems. Significance StatementThe ability to cultivate microalgae at scale efficiently would allow more sustainable production of food and food additives. However, efficient growth of microalgae requires optimised light conditions, which are usually challenging to obtain using biofilm cultivations mode: as the outer layer of cells are necessarily more exposed to incoming light than the inner layer, posing the problem of photoinhibition on the outer cells receiving too much light, and shading the ones below. Here we study both experimentally and numerically, how microalgae aggregates growing in the confinement of a hydrogel can provide an improved light distribution and therefore biomass growth is maximised. This study proposes new strategies on how to engineer future photobioreactors.

plant biology↗

bioRxiv2023

Modeling the radiative, thermal and chemical microenvironment of 3D scanned corals

O_LIReef building corals are efficient biological collectors of solar radiation and consist of a thin stratified tissue layer spread over a light scattering calcium carbonate skeleton surface that together construct complex three dimensional (3D) colony structures forming the foundation of coral reefs. They exhibit a vast diversity of structural forms to maximize photosynthesis of their dinoflagellate endosymbionts (Symbiodiniaceae), while simultaneously minimizing photodamage. The symbiosis takes place in the presence of dynamic gradients of light, temperature and chemical species that are affected by the interaction of incident irradiance and water flow with the coral colony. C_LIO_LIWe developed a multiphysics modelling approach to simulate microscale spatial distribution of light, temperature and O2 in coral fragments with accurate morphology determined by 3D scanning techniques. C_LIO_LIModel results compared well with spatial measurements of light, O2 and temperature under similar flow and light conditions. The model enabled us to infer the effect of coral morphology and light scattering in tissue and skeleton on the internal light environment experienced by the endosymbionts, as well as the combined contribution of light, water flow and ciliary movement on O2 and temperature distributions in the coral. C_LIO_LIThe multiphysics modeling approach is general enough to enable simulation of external and internal light, O2 and temperature microenvironments in 3D scanned coral species with varying degrees of branching and morphology under different environmental conditions. This approach is also relevant for simulating structure-function relationships in other benthic systems such as photosynthetic biofilms and aquatic plant tissue, and can also be adapted to other sessile organisms such as symbiont-bearing giant clams, ascidians, jellyfish or foraminifera. The model could also be useful in more applied research such as optimization of 3D bioprinted constructs where different designs can be evaluated and optimized. C_LI

biophysics↗

bioRxiv2021

Photosynthesis from stolen chloroplasts increases sea slug reproductive fitness

Some sea slugs are able to steal functional chloroplasts (kleptoplasts) from their algal food sources, but the role and relevance of photosynthesis to the animal host remain controversial. While some researchers claim that kleptoplasts are slowly digestible snacks, others advocate that they enhance the overall fitness of sea slugs much more profoundly. Our analysis show light-dependent incorporation of 13C and 15N in the albumen gland and gonadal follicles of the sea slug Elysia timida, representing translocation of photosynthates to kleptoplast-free reproductive organs. Long-chain polyunsaturated fatty acids with reported roles in reproduction were produced in the sea slug cells using labelled precursors translocated from the kleptoplasts. Finally, we report reduced fecundity of E. timida by suppressing kleptoplast photosynthesis. The present study provides the first thorough experimental evidence that photosynthesis enhances the reproductive fitness of kleptoplast-bearing sea slugs, confirming the biological relevance of this remarkable association between a metazoan and an algal-derived organelle. TeaserSea slugs incorporate functional chloroplasts from algae and use products of photosynthesis to maximize reproductive output.

ecology↗

bioRxiv2019

Bionic 3D printed corals

Symbiotic corals have evolved as a highly optimised photon augmentation system leading to space-efficient microalgal growth and photosynthetic quantum efficiencies that approach theoretical limits1-3. Corals are characterized by an elastic animal tissue hosting microalgae and a light scattering calcium carbonate skeleton that maximizes light delivery towards otherwise shaded algal-containing tissues4,5. Rapid light attenuation due to algal self-shading is a key limiting factor for the upscaling of microalgal cultivation6,7. Coral-inspired light management systems could overcome this limitation and facilitate scalable bioenergy and bioproduct generation8,9. Here, we developed 3D printed bionic corals capable of growing various types of microalgae with cell densities approaching 109 cells mL-1, up to 100 times greater than in liquid culture. The hybrid photosynthetic biomaterials are produced with a new 3D bioprinting platform which mimics morphological features of living coral tissue and the underlying skeleton with micron resolution, including their optical and mechanical properties. The programmable synthetic microenvironment thus allows for replicating both structural and functional traits of the coral-algal symbiosis. Our work defines a new class of bionic materials capable of interacting with living organisms, that can be exploited for the design of next generation photobioreactors7 and disruptive approaches for coral reef conservation10.

bioengineering↗

bioRxiv2019

Optical properties of living corals determined with diffuse reflectance spectroscopy

The internal light field and thus light exposure of the photosymbiotic microalgae (Symbiodinium sp.) in corals is strongly modulated by the optical properties of coral tissue and skeleton. While there are numerous studies documenting the light microenvironment in corals, there are only few measurements of the inherent optical properties of corals in the literature, and this has hampered a more quantitative understanding of coral optics. Here we present a study of the optical properties of 26 live coral samples, representative of 11 coral species and spanning a variety of morphotypes. We employed well-established fiber-optic reflectance spectroscopy techniques from biomedical optics using two methods: (1) A source and a detection fiber separated by a variable distance measured the lateral spread of light in corals, dominated by the skeleton; (2) A fiber-optic field radiance probe measured the diffuse reflectance from the coral surface, dominated by the living coral tissue. Analysis based on diffusion theory and Monte Carlo simulation yielded estimates of the bulk scattering and absorption coefficients of the coral tissue and skeleton, in the 750-1030 nm wavelength range. Extrapolating into the spectral region of photosynthetically active radiation (PAR, 400-700 nm) allowed estimation of the optical depth of absorption by the main Symbiodinium photopigment chlorophyll a. Coral tissue scattering was on average ~1.9x stronger than the scattering of the skeleton, consistent with the model that corals trap photons by high scattering to enhance absorption by algal pigments, while the lower scattering of the skeleton allows spread of light to otherwise shaded coral tissue areas.

plant biology↗

bioRxiv2018

Microscale light management and inherent optical properties of intact corals studied with optical coherence tomography

Coral reefs are highly productive photosynthetic systems and coral optics studies suggest that such high efficiency is due to optimised light scattering by coral tissue and skeleton. Here, we characterise the inherent optical properties, i.e., the scattering coefficient, s, and the anisotropy of scattering, g, of 8 intact coral species using optical coherence tomography (OCT). Specifically, we describe light scattering by coral skeletons, coenoarc tissues, polyp tentacles and areas covered by fluorescent pigments (FP). Our results reveal that light scattering between coral species ranges from s = 3 mm-1 (Stylophora pistillata) to s= 25 mm-1 (Echinopora lamelosa). For Platygyra pini, s was 10-fold higher for tissue vs skeleton, while in other corals (e.g. Hydnophora pilosa) no difference was found between tissue and skeletal scattering. Tissue scattering was 3-fold enhanced in coenosarc tissues (s = 24.6 mm-1) vs polyp tentacles (s = 8.3 mm-1) in Turbinaria reniformis. FP scattering was almost isotropic when FP were organized in granule chromatophores (g=0.34) but was forward directed when FP were distributed diffusely in the tissue (g=0.96). Our study provides detailed measurements of coral scattering and establishes a rapid approach for characterising optical properties of photosynthetic soft tissues via OCT in vivo.

biophysics↗

bioRxiv2017

Radiative energy budgets of phototrophic surface-associated microbial communities and their photosynthetic efficiency under diffuse and collimated light

We investigated the radiative energy budgets of a heterogeneous photosynthetic coral reef sediment and a compact uniform cyanobacterial biofilm on top of coastal sediment. By combining electrochemical, thermocouple and fiber-optic microsensor measurements of O2, temperature and light, we could calculate the proportion of the absorbed light energy that was either dissipated as heat or conserved by photosynthesis. We show, across a range of different incident light regimes, that such radiative energy budgets are highly dominated by heat dissipation constituting up to 99.5% of the absorbed light energy. Highest photosynthetic energy conservation efficiency was found in the coral sediment under light-limiting conditions and amounted to ~13% of the absorbed light energy. Additionally, the effect of light directionality, i.e., diffuse or collimated light, on energy conversion efficiency was tested on the two surface-associated systems. The effects of light directionality on the radiative energy budgets of these phototrophic communities were not unanimous but, resulted in local spatial differences in heat-transfer, gross photosynthesis and light distribution. The light acclimation index, Ek was >2 times higher in the coral sediment compared to the biofilm and changed the pattern of photosynthetic energy conservation under light-limiting conditions. At moderate to high incident 45 irradiances, the photosynthetic conservation of absorbed energy was highest in collimated light; a tendency that changed in the biofilm under sub-saturating incident irradiances, where higher photosynthetic efficiencies were observed under diffuse light. Our results suggest that the optical properties and the structural organization of phytoelements are important traits affecting the photosynthetic efficiency of biofilms and sediments.

ecology↗

bioRxiv2016

Diffusion or advection? Mass transfer and diffusive boundary layer landscapes of the brown alga Fucus vesiculosus

The role of hyaline hairs on the thallus of brown-algae in the genus Fucus is long debated and several functions have been proposed. We used a novel motorized setup for 2D-and 3D-mapping with O2-microsensors to investigate the spatial heterogeneity of the diffusive boundary layer (DBL) and O2 flux around single and multiple tufts of hyaline hairs on the thallus of Fucus vesiculosus. Flow was a major determinant of DBL thickness, where higher flow decreased DBL thickness and increased O2 flux between algal thallus and the surrounding seawater. However, the topography of the DBL varied and did not directly follow the contour of the underlying thallus. Areas around single tufts of hyaline hairs exhibited both increased and decreased DBL thickness as compared to areas over smooth thallus surfaces. Over thallus areas with several hyaline hair tufts, the overall effect was a local increase in the DBL thickness. We also found indications for advective O2 transport driven by pressure gradients or vortex-shedding downstream from dense tufts of hyaline hairs alleviating local mass-transfer resistance imposed by thickened DBL. Mass-transfer dynamics around hyaline hair tufts are thus more complex than hitherto assumed and may have important implications for algal physiology and plant-microbe interactions.

biophysics↗

bioRxiv2016

In vivo imaging of coral tissue and skeleton with optical coherence tomography

Optical coherence tomography (OCT) is a non-invasive three-dimensional imaging technique with micrometer resolution allowing microstructural characterization of tissues in vivo and in real time. We present the first application of OCT for in vivo imaging of tissue and skeleton structure of intact living corals spanning a variety of morphologies and tissue thickness. OCT visualized different coral tissue layers (e.g. endoderm vs ectoderm), special structures such as mesenterial filaments and skeletal cavities, as well as mucus release from living corals. We also developed a new approach for non-invasive imaging and quantification of chromatophores containing green fluorescent protein (GFP)-like host pigment granules in coral tissue. The chromatophore system is hyper-reflective and can thus be imaged with good optical contrast in OCT, enabling quantification of chromatophore size, distribution and abundance. Because of its rapid imaging speed, OCT can also be used to quantify coral tissue movement showing that maximal linear contraction velocity was ~120 m per second upon high light stimulation. Based on OCT imaging of tissue expansion and contraction, we made first estimates of dynamic changes in the coral tissue surface area, which varied by a factor of 2 between the contracted and expanded state of the coral Pocillopora damicornis. We conclude that OCT is an excellent novel tool for in vivo tomographic imaging of corals that can reveal tissue and skeleton organization as well as quantify dynamic changes in tissue structure and coral surface area non-invasively and at high spatio-temporal resolution.

biophysics↗