Photosymbiotic giant clams are transformers of solar flux

The genome of a giant clam zooxanthella (Cladocopium infistulum) offers few clues to adaptation as an extracellular symbiont with high thermotolerance

BACKGROUND

Cladocopium infistulum (Symbiodiniaceae) is a dinoflagellate specialized to live in symbiosis with western Pacific giant clams (Tridacnidae). Unlike coral-associated symbionts, which reside within the host cells, C. infistulum inhabits the extracellular spaces of the clam's digestive diverticula. It is phylogenetically basal to a large species complex of stress-tolerant Cladocopium, many of which are associated with important reef-building corals in the genus Porites. This close phylogenetic relationship may explain why C. infistulum exhibits high thermotolerance relative to other tridacnid symbionts. Moreover, past analyses of microsatellite loci indicated that Cladocopium underwent whole-genome duplication prior to the adaptive radiations that led to its present diversity.

RESULTS

A draft genome assembly of C. infistulum was produced using long- and short-read sequences to explore the genomic basis for adaptations underlying thermotolerance and extracellular symbiosis among dinoflagellates and to look for evidence of genome duplication. Comparison to three other Cladocopium genomes revealed no obvious over-representation of gene groups or families whose functions would be important for maintaining C. infistulum's unique physiological and ecological properties. Preliminary analyses support the existence of partial or whole-genome duplication among Cladocopium, but additional high-quality genomes are required to substantiate these findings.

CONCLUSION

Although this investigation of Cladocopium infistulum revealed no patterns diagnostic of heat tolerance or extracellular symbiosis in terms of overrepresentation of gene functions or genes under selection, it provided a valuable genomic resource for comparative analyses. It also indicates that ecological divergence among Cladocopium species, and potentially among other dinoflagellates, is partially governed by mechanisms other than gene content. Thus, additional high-quality, multiomic data are needed to explore the molecular basis of key phenotypes among symbiotic microalgae.

Measuring Photonics in Photosynthesis: Combined Micro-Fourier Image Spectroscopy and Pulse Amplitude Modulated Chlorophyll Fluorimetry at the Micrometre-Scale

Natural photonic structures are common across the biological kingdoms, serving a diversity of functionalities. The study of implications of photonic structures in plants and other phototrophic organisms is still hampered by missing methodologies for determining in situ photonic properties, particularly in the context of constantly adapting photosynthetic systems controlled by acclimation mechanisms on the cellular scale. We describe an innovative approach to determining spatial and spectral photonic properties and photosynthesis activity, employing micro-Fourier Image Spectroscopy and Pulse Amplitude Modulated Chlorophyll Fluorimetry in a combined microscope setup. Using two examples from the photosynthetic realm, the dynamic Bragg-stack-like thylakoid structures of Begonia sp. and complex 2.5 D photonic crystal slabs from the diatom Coscinodiscus granii, we demonstrate how the setup can be used for measuring self-adapting photonic-photosynthetic systems and photonic properties on single-cell scales. We suggest that the setup is well-suited for the determination of photonic–photosynthetic systems in a diversity of organisms, facilitating the cellular, temporal, spectral and angular resolution of both light distribution and combined chlorophyll fluorescence determination. As the catalogue of photonic structure from photosynthetic organisms is rich and diverse in examples, a deepened study could inspire the design of novel optical- and light-harvesting technologies.

Genomic Survey and Resources for the Boring Giant Clam Tridacna crocea

The boring giant clam Tridacna crocea is an evolutionary, ecologically, economically, and culturally important reef-dwelling bivalve targeted by a profitable ornamental fishery in the Indo-Pacific Ocean. In this study, we developed genomic resources for T. crocea. Using low-pass (=low-coverage, ~6×) short read sequencing, this study, for the first time, estimated the genome size, unique genome content, and nuclear repetitive elements, including the 45S rRNA DNA operon, in T. crocea. Furthermore, we tested if the mitochondrial genome can be assembled from RNA sequencing data. The haploid genome size estimated using a k-mer strategy was 1.31–1.39 Gbp, which is well within the range reported before for other members of the family Cardiidae. Unique genome content estimates using different k-mers indicated that nearly a third and probably at least 50% of the genome of T. crocea was composed of repetitive elements. A large portion of repetitive sequences could not be assigned to known repeat element families. Taking into consideration only annotated repetitive elements, the most common were classified as Satellite DNA which were more common than Class I-LINE and Class I-LTR Ty3-gypsy retrotransposon elements. The nuclear ribosomal operon in T. crocea was partially assembled into two contigs, one encoding the complete ssrDNA and 5.8S rDNA unit and a second comprising a partial lsrDNA. A nearly complete mitochondrial genome (92%) was assembled from RNA-seq. These newly developed genomic resources are highly relevant for improving our understanding of the biology of T. crocea and for the development of conservation plans and the fisheries management of this iconic reef-dwelling invertebrate.

Assessment of the juvenile vulnerability of symbiont-bearing giant clams to ocean acidification

Ocean acidification (OA) severely affects marine bivalves, especially their calcification processes. However, very little is known about the fate of symbiont-bearing giant clams in the acidified oceans, which hinders our ability to develop strategies to protect this ecologically and economically important group in coral reef ecosystems. Here, we explored the integrated juvenile responses of fluted giant clam Tridacna squamosa (Lamarck, 1819) to acidified seawater at different levels of biological organization. Our results revealed that OA did not cause a significant reduction in survival and shell growth performance, indicating that T. squamosa juveniles are tolerated to moderate acidification. Yet, significantly reduced net calcification rate demonstrated the calcifying physiology sensitivity to OA, in line with significant declines in symbiont photosynthetic yield and zooxanthellae density which in turn lowered the amount of energy supply for energetically expensive calcification processes. Subsequent transcriptome sequencing and comparative analysis of differentially expressed genes revealed that the regulation of calcification processes, such as transport of calcification substrates, acid-base regulation, synthesis of organic matrix in the calcifying fluid, as well as metabolic depression were the major response to OA. Taken together, the integration of physiological and molecular responses can provide a comprehensive understanding of how the early life history stages of giant clams respond to OA and make an important leap forward in assessing their fate under future ocean conditions.

Finite-difference Time-domain (FDTD) Optical Simulations: A Primer for the Life Sciences and Bio-Inspired Engineering

Light influences most ecosystems on earth, from sun-dappled forests to bioluminescent creatures in the ocean deep. Biologists have long studied nano- and micro-scale organismal adaptations to manipulate light using ever-more sophisticated microscopy, spectroscopy, and other analytical equipment. In combination with experimental tools, simulations of light interacting with objects can help researchers determine the impact of observed structures and explore how variations affect optical function. In particular, the finite-difference time-domain (FDTD) method is widely used throughout the nanophotonics community to efficiently simulate light interacting with a variety of materials and optical devices. More recently, FDTD has been used to characterize optical adaptations in nature, such as camouflage in fish and other organisms, colors in sexually-selected birds and spiders, and photosynthetic efficiency in plants. FDTD is also common in bioengineering, as the design of biologically-inspired engineered structures can be guided and optimized through FDTD simulations. Parameter sweeps are a particularly useful application of FDTD, which allows researchers to explore a range of variables and modifications in natural and synthetic systems (e.g., to investigate the optical effects of changing the sizes, shape, or refractive indices of a structure). Here, we review the use of FDTD simulations in biology and present a brief methods primer tailored for life scientists, with a focus on the commercially available software Lumerical FDTD. We give special attention to whether FDTD is the right tool to use, how experimental techniques are used to acquire and import the structures of interest, and how their optical properties such as refractive index and absorption are obtained. This primer is intended to help researchers understand FDTD, implement the method to model optical effects, and learn about the benefits and limitations of this tool. Altogether, FDTD is well-suited to (i) characterize optical adaptations and (ii) provide mechanistic explanations; by doing so, it helps (iii) make conclusions about evolutionary theory and (iv) inspire new technologies based on natural structures.

The colorful mantle of the giant clam Tridacna squamosa expresses a homolog of electrogenic sodium: Bicarbonate cotransporter 2 that mediates the supply of inorganic carbon to photosynthesizing symbionts

Giant clams live in symbiosis with phototrophic dinoflagellates, which reside extracellularly inside zooxanthellal tubules located mainly in the colourful and extensible outer mantle. As symbiotic dinoflagellates have no access to the ambient seawater, they need to obtain inorganic carbon (C_i) from the host for photosynthesis during illumination. The outer mantle has a host-mediated and light-dependent carbon-concentrating mechanism to augment the supply of C_i to the symbionts during illumination. Iridocytes can increase the secretion of H⁺ through vacuolar H⁺-ATPase to dehydrate HCO₃⁻ present in the hemolymph to CO₂. CO₂ can permeate the basolateral membrane of the epithelial cells of the zooxanthellal tubules, and rehydrated back to HCO₃⁻ in the cytoplasm catalysed by carbonic anhydrase 2. This study aimed to elucidate the molecular mechanism involved in the transport of HCO₃⁻ across the apical membrane of these epithelial cells into the luminal fluid surrounding the symbionts. We had obtained the complete cDNA coding sequence of a homolog of electrogenic Na⁺-HCO₃⁻cotransporter 2 (NBCe2-like gene) from the outer mantle of the fluted giant clam, Tridacna squamosa. NBCe2-like gene comprised 3,399 bp, encoding a protein of 1,132 amino acids of 127.3 kDa. NBCe2-like protein had an apical localization in the epithelial cells of zooxanthellal tubules, denoting that it could transport HCO₃⁻ between the epithelial cells and the luminal fluid. Furthermore, illumination augmented the transcript level and protein abundance of NBCe2-like gene/NBCe2-like protein in the outer mantle, indicating that it could mediate the increased transport of HCO₃⁻ into the luminal fluid to support photosynthesis in the symbionts.

Cytoklepty in the plankton: A host strategy to optimize the bioenergetic machinery of endosymbiotic algae

Endosymbioses have shaped the evolutionary trajectory of life and remain ecologically important. Investigating oceanic photosymbioses can illuminate how algal endosymbionts are energetically exploited by their heterotrophic hosts and inform on putative initial steps of plastid acquisition in eukaryotes. By combining three-dimensional subcellular imaging with photophysiology, carbon flux imaging, and transcriptomics, we show that cell division of endosymbionts (Phaeocystis) is blocked within hosts (Acantharia) and that their cellular architecture and bioenergetic machinery are radically altered. Transcriptional evidence indicates that a nutrient-independent mechanism prevents symbiont cell division and decouples nuclear and plastid division. As endosymbiont plastids proliferate, the volume of the photosynthetic machinery volume increases 100-fold in correlation with the expansion of a reticular mitochondrial network in close proximity to plastids. Photosynthetic efficiency tends to increase with cell size, and photon propagation modeling indicates that the networked mitochondrial architecture enhances light capture. This is accompanied by 150-fold higher carbon uptake and up-regulation of genes involved in photosynthesis and carbon fixation, which, in conjunction with a ca.15-fold size increase of pyrenoids demonstrates enhanced primary production in symbiosis. Mass spectrometry imaging revealed major carbon allocation to plastids and transfer to the host cell. As in most photosymbioses, microalgae are contained within a host phagosome (symbiosome), but here, the phagosome invaginates into enlarged microalgal cells, perhaps to optimize metabolic exchange. This observation adds evidence that the algal metamorphosis is irreversible. Hosts, therefore, trigger and benefit from major bioenergetic remodeling of symbiotic microalgae with potential consequences for the oceanic carbon cycle. Unlike other photosymbioses, this interaction represents a so-called cytoklepty, which is a putative initial step toward plastid acquisition.

Effects of elevated temperature and pCO2 on the respiration, biomineralization and photophysiology of the giant clam Tridacna maxima

Many reef organisms, such as the giant clams, are confronted with global change effects. Abnormally high seawater temperatures can lead to mass bleaching events and subsequent mortality, while ocean acidification may impact biomineralization processes. Despite its strong ecological and socio-economic importance, its responses to these threats still need to be explored. We investigated physiological responses of 4-year-old Tridacna maxima to realistic levels of temperature (+1.5°C) and partial pressure of carbon dioxide (pCO₂) (+800 μatm of CO₂) predicted for 2100 in French Polynesian lagoons during the warmer season. During a 65-day crossed-factorial experiment, individuals were exposed to two temperatures (29.2°C, 30.7°C) and two pCO₂ (430 μatm, 1212 μatm) conditions. The impact of each environmental parameter and their potential synergetic effect were evaluated based on respiration, biomineralization and photophysiology. Kinetics of thermal and/or acidification stress were evaluated by performing measurements at different times of exposure (29, 41, 53, 65 days). At 30.7°C, the holobiont O₂ production, symbiont photosynthetic yield and density were negatively impacted. High pCO₂ had a significant negative effect on shell growth rate, symbiont photosynthetic yield and density. No significant differences of the shell microstructure were observed between control and experimental conditions in the first 29 days; however, modifications (i.e. less-cohesive lamellae) appeared from 41 days in all temperature and pCO₂ conditions. No significant synergetic effect was found. Present thermal conditions (29.2°C) appeared to be sufficiently stressful to induce a host acclimatization response. All these observations indicate that temperature and pCO₂ are both forcing variables affecting T. maxima's physiology and jeopardize its survival under environmental conditions predicted for the end of this century.

Using glutamine synthetase 1 to evaluate the symbionts' potential of ammonia assimilation and their responses to illumination in five organs of the giant clam, Tridacna squamosa

Nitrogen-deficient symbiotic dinoflagellates (zooxanthellae) living inside the fluted giant clam, Tridacna squamosa, need to obtain nitrogen from the host. Glutamine synthetase 1 (GS1) is a cytosolic enzyme that assimilates ammonia into glutamine. We determined the transcript levels of zooxanthellal GS1 (Zoox-GS1), which represented comprehensively GS1 transcripts of Symbiodinium, Cladocopium and Durusdinium, in five organs of T. squamosa. The outer mantle had significantly higher transcript level of Zoox-GS1 than the inner mantle, foot muscle, hepatopancreas and ctenidium, but the transcript ratios of Zoox-GS1 to zooxanthellal form II ribulose-1,5-bisphosphate carboxylase/oxygenase (Zoox-rbcII), which represented the potential of ammonia assimilation relative to the phototrophic potential, were comparable among these five organs. Based on transcript ratios of Zoox-GS1 to zooxanthellal Urease (Zoox-URE), the outer mantle had the highest potential of urea degradation relative to ammonia assimilation among the five organs, probably because urea degradation could furnish CO₂ and NH₃ for photosynthesis and amino acid synthesis, respectively, in the symbionts therein. The protein abundance of Zoox-GS1 was upregulated in the outer mantle and the inner mantle during illumination. Zoox-GS1 could catalyze light-enhanced glutamine formation using ammonia absorbed from the host or ammonia released through urea degradation in the cytoplasm. The glutamine produced could be used to synthesize other nitrogenous compounds, including amino acids in the cytoplasm or in the plastid of the dinoflagellates. Some of the amino acids synthesized by the symbionts in the inner mantle and foot muscle could be donated to the host to support shell organic matrix formation and muscle production, respectively.

Symbiodiniaceae Dinoflagellates Express Urease in Three Subcellular Compartments and Upregulate its Expression Levels in situ in Three Organs of a Giant Clam (Tridacna squamosa) During Illumination

Giant clams harbor three genera of symbiotic dinoflagellates (Symbiodinium, Cladocopium, and Durusdinium) as extracellular symbionts (zooxanthellae). While symbiotic dinoflagellates can synthesize amino acids to benefit the host, they are nitrogen-deficient. Hence, the host must supply them with nitrogen including urea, which can be degraded to ammonia and carbon dioxide by urease (URE). Here, we report three complete coding cDNA sequences of URE, one for each genus of dinoflagellate, obtained from the colorful outer mantle of the giant clam, Tridacna squamosa. The outer mantle had higher transcript level of Tridacna squamosa zooxanthellae URE (TSZURE) than the whitish inner mantle, foot muscle, hepatopancreas, and ctenidium. TSZURE was immunolocalized strongly and atypically in the plastid, moderately in the cytoplasm, and weakly in the cell wall and plasma membrane of symbiotic dinoflagellates. In the outer mantle, illumination upregulated the protein abundance of TSZURE, which could enhance urea degradation in photosynthesizing dinoflagellates. The urea-nitrogen released could then augment synthesis of amino acids to be shared with the host for its general needs. Illumination also enhanced gene and protein expression levels of TSZURE/TSZURE in the inner mantle and foot muscle, which contain only small quantities of symbiotic dinoflagellate, have no iridocyte, and lack direct exposure to light. With low phototrophic potential, dinoflagellates in the inner mantle and foot muscle might need to absorb carbohydrates in order to assimilate the urea-nitrogen into amino acids. Amino acids donated by dinoflagellates to the inner mantle and the foot muscle could be used especially for synthesis of organic matrix needed for light-enhanced shell formation and muscle protein, respectively.

Optical costs and benefits of disorder in biological photonic crystals

Photonic structures in ordered, quasi-ordered or disordered forms have evolved across many different animal and plant systems. They can produce complex and often functional optical responses through coherent and incoherent scattering processes, often too, in combination with broadband or narrowband absorbing pigmentation. Interestingly, these systems appear highly tolerant of faults in their photonic structures, with imperfections in their structural order appearing not to impact, discernibly, the systems' optical signatures. The extent to which any such biological system deviates from presenting perfect structural order can dictate the optical properties of that system and, thereby, the optical properties that system delivers. However, the nature and extent of the optical costs and benefits of imperfect order in biological systems demands further elucidation. Here, we identify the extent to which biological photonic systems are tolerant of defects and imperfections. Certainly, it is clear that often significant inherent variations in the photonic structures of these systems, for instance a relatively broad distribution of lattice constants, can consistently produce what appear to be effective visual appearances and optical performances. In this article, we review previously investigated biological photonic systems that present ordered, quasi-ordered or disordered structures. We discuss the form and nature of the optical behaviour of these structures, focusing particularly on the associated optical costs and benefits surrounding the extent to which their structures deviate from what might be considered ideal systems. Then, through detailed analyses of some well-known 1D and 2D structurally coloured systems, we analyse one of the common manifestations of imperfect order, namely, the extent and nature of positional disorder in the systems' spatial distribution of layers and scattering centres. We use these findings to inform optical modelling that presents a quantitative and qualitative description of the optical costs and benefits of such positional disorder among ordered and quasi-ordered 1D and 2D photonic systems. As deviation from perfectly ordered structures invariably limits the performance of technology-oriented synthetic photonic processes, we suggest that the use of bio-inspired fault tolerance principles would add value to applied photonic technologies.

Violet-light suppression of thermogenesis by opsin 5 hypothalamic neurons

The opsin family of G-protein-coupled receptors are used as light detectors in animals. Opsin 5 (also known as neuropsin or OPN5) is a highly conserved opsin that is sensitive to visible violet light1,2. In mice, OPN5 is a known photoreceptor in the retina3 and skin4 but is also expressed in the hypothalamic preoptic area (POA)5. Here we describe a light-sensing pathway in which POA neurons that express Opn5 regulate thermogenesis in brown adipose tissue (BAT). We show that Opn5 is expressed in glutamatergic warm-sensing POA neurons that receive synaptic input from several thermoregulatory nuclei. We further show that Opn5 POA neurons project to BAT and decrease its activity under chemogenetic stimulation. Opn5-null mice show overactive BAT, increased body temperature, and exaggerated thermogenesis when cold-challenged. Moreover, violet photostimulation during cold exposure acutely suppresses BAT temperature in wild-type mice but not in Opn5-null mice. Direct measurements of intracellular cAMP ex vivo show that Opn5 POA neurons increase cAMP when stimulated with violet light. This analysis thus identifies a violet light-sensitive deep brain photoreceptor that normally suppresses BAT thermogenesis.

The fluted giant clam (Tridacna squamosa) increases the protein abundance of the host's copper-zinc superoxide dismutase in the colorful outer mantle, but not the whitish inner mantle, during light exposure

The colorful outer mantle of giant clams contains abundance of symbiotic dinoflagellates (zooxanthellae) and iridocytes, and has direct exposure to light. In light, photosynthesizing dinoflagellates produce O₂, and the host cells in the outer mantle would be confronted with hyperoxia-related oxidative stress. In comparison, the whitish inner mantle contains few symbiotic dinoflagellates and no iridocytes. It is involved in shell formation, and is shaded from light. CuZnSOD is a cytosolic enzyme that scavenges intracellular O₂^-. We had obtained from the outer mantle of the fluted giant clam, Tridacna squamosa, the complete cDNA coding sequence of a host-derived copper zinc superoxide dismutase (CuZnSOD), which comprised 462 bp and encoded for 154 amino acids with a calculated MW of 15.6 kDa. CuZnSOD was expressed strongly in the outer mantle, ctenidium, hepatopancreas and kidney. The transcript level of CuZnSOD remained unchanged in the outer mantle during light exposure, but the protein abundance of CuZnSOD increased ~3-fold after exposure to light for 6 or 12 h. By contrast, 12 h of light exposure had no significant effects on the gene and protein expression levels of CuZnSOD/CuZnSOD in the inner mantle. Hence, the increased expression of CuZnSOD in the outer mantle of T. squamosa was probably a host's response to ameliorate oxidative stress related to photosynthesis in the symbionts, and not simply due to increased metabolic rate in the host cells. Evidently, the host clam must possess light- or O₂-responsive anti-oxidative defenses in order to align with the light-dependent photosynthetic activity of its symbionts.

Shedding light: a phylotranscriptomic perspective illuminates the origin of photosymbiosis in marine bivalves

BACKGROUND

Photosymbiotic associations between metazoan hosts and photosynthetic dinoflagellates are crucial to the trophic and structural integrity of many marine ecosystems, including coral reefs. Although extensive efforts have been devoted to study the short-term ecological interactions between coral hosts and their symbionts, long-term evolutionary dynamics of photosymbiosis in many marine animals are not well understood. Within Bivalvia, the second largest class of mollusks, obligate photosymbiosis is found in two marine lineages: the giant clams (subfamily Tridacninae) and the heart cockles (subfamily Fraginae), both in the family Cardiidae. Morphologically, giant clams show relatively conservative shell forms whereas photosymbiotic fragines exhibit a diverse suite of anatomical adaptations including flattened shells, leafy mantle extensions, and lens-like microstructural structures. To date, the phylogenetic relationships between these two subfamilies remain poorly resolved, and it is unclear whether photosymbiosis in cardiids originated once or twice.

RESULTS

In this study, we establish a backbone phylogeny for Cardiidae utilizing RNASeq-based transcriptomic data from Tridacninae, Fraginae and other cardiids. A variety of phylogenomic approaches were used to infer the relationship between the two groups. Our analyses found conflicting gene signals and potential rapid divergence among the lineages. Overall, results support a sister group relationship between Tridacninae and Fraginae, which diverged during the Cretaceous. Although a sister group relationship is recovered, ancestral state reconstruction using maximum likelihood-based methods reveals two independent origins of photosymbiosis, one at the base of Tridacninae and the other within a symbiotic Fraginae clade.

CONCLUSIONS

The newly revealed common ancestry between Tridacninae and Fraginae brings a possibility that certain genetic, metabolic, and/or anatomical exaptations existed in their last common ancestor, which promoted both lineages to independently establish photosymbiosis, possibly in response to the modern expansion of reef habitats.

Marine-Derived Polymeric Materials and Biomimetics: An Overview

The review covers recent literature on the ocean as both a source of biotechnological tools and as a source of bio-inspired materials. The emphasis is on marine biomacromolecules namely hyaluronic acid, chitin and chitosan, peptides, collagen, enzymes, polysaccharides from algae, and secondary metabolites like mycosporines. Their specific biological, physicochemical and structural properties together with relevant applications in biocomposite materials have been included. Additionally, it refers to the marine organisms as source of inspiration for the design and development of sustainable and functional (bio)materials. Marine biological functions that mimic reef fish mucus, marine adhesives and structural colouration are explained.

3D structured materials and devices for artificial photosynthesis

Artificial photosynthesis is an effective way to convert solar energy into fuels, which is of great significance to energy production and reduction of atmospheric CO₂ content. In recent years, 3D structured artificial photosynthetic system has made great progress as an effective design strategy. This review first highlights several typical mechanisms for improved artificial photosynthesis with 3D structures: improved light harvesting, mass transfer and charge separation. Then, we summarize typical examples of 3D structured artificial photosynthetic systems, including bioinspired structures, photonic crystals (PC), designed photonic structures (PC coupling structure, plasmon resonance structure, optical resonance structure, metamaterials), 3D-printed systems, nanowire integrated systems and hierarchical 3D structures. Finally, we discuss the problems and challenges to the application and development of 3D artificial photosynthetic system and the possible trends of future development. We hope this review can inspire more progress in the field of artificial photosynthesis.

Molecular mechanisms of acclimation to long-term elevated temperature exposure in marine symbioses

Seawater temperature rise in French Polynesia has repeatedly resulted in the bleaching of corals and giant clams. Because giant clams possess distinctive ectosymbiotic features, they represent a unique and powerful model for comparing molecular pathways involved in (a) maintenance of symbiosis and (b) acquisition of thermotolerance among coral reef organisms. Herein, we explored the physiological and transcriptomic responses of the clam hosts and their photosynthetically active symbionts over a 65 day experiment in which clams were exposed to either normal or environmentally relevant elevated seawater temperatures. Additionally, we used metabarcoding data coupled with in situ sampling/survey data to explore the relative importance of holobiont adaptation (i.e., a symbiont community shift) versus acclimation (i.e., physiological changes at the molecular level) in the clams' responses to environmental change. We finally compared transcriptomic data to publicly available genomic datasets for Symbiodiniaceae dinoflagellates (both cultured and in hospite with the coral Pocillopora damicornis) to better tease apart the responses of both hosts and specific symbiont genotypes in this mutualistic association. Gene module preservation analysis revealed that the function of the symbionts' photosystem II was impaired at high temperature, and this response was also found across all holobionts and Symbiodiniaceae lineages examined. Similarly, epigenetic modulation appeared to be a key response mechanism for symbionts in hospite with giant clams exposed to high temperatures, and such modulation was able to distinguish thermotolerant from thermosensitive Cladocopium goreaui ecotypes; epigenetic processes may, then, represent a promising research avenue for those interested in coral reef conservation in this era of changing global climate.

Adaptive Thermogenesis in Mice Is Enhanced by Opsin 3-Dependent Adipocyte Light Sensing

Almost all life forms can detect and decode light information for adaptive advantage. Examples include the visual system, in which photoreceptor signals are processed into virtual images, and the circadian system, in which light entrains a physiological clock. Here we describe a light response pathway in mice that employs encephalopsin (OPN3, a 480 nm, blue-light-responsive opsin) to regulate the function of adipocytes. Germline null and adipocyte-specific conditional null mice show a light- and Opn3-dependent deficit in thermogenesis and become hypothermic upon cold exposure. We show that stimulating mouse adipocytes with blue light enhances the lipolysis response and, in particular, phosphorylation of hormone-sensitive lipase. This response is Opn3 dependent. These data establish a key mechanism in which light-dependent, local regulation of the lipolysis response in white adipocytes regulates energy metabolism.

Interfacial Assembly of Amphiphilic Tiles for Reconfigurable Photonic Surfaces

Nature has created photonic structures in cells and assembled them to make photonic layers for a living. Inspired from nature, we design amphiphilic photonic tiles and assemble them at air-water interface to compose highly reconfigurable photonic layers. The photonic tiles are prepared by photolithographically defining the shape of the disc using a photocurable dispersion of repulsive particles. The tiles are further treated by directional dry etching to selectively render top and side surfaces of the discs hydrophobic. The amphiphilic photonic tiles deform the air-water interface by gravity, which causes a strong attractive force driven by capillarity. Therefore, the tiles form two-dimensional (2D) dense-packing, which rapidly adapts dynamic fluctuation and shape change of the interface, providing highly reconfigurable photonic layers. In addition, the assembly can be transferred into target solid surfaces through the Langmuir-Blodgett method to make photonic coatings. Moreover, the amphiphilic tiles can be assembled on the surface of water drops, forming a photonic shell on liquid marbles which resembles photonic structures in nature. We believe that our strategy based on a 2D tile assembly at the free interface will provide a simple yet useful means to create photonic layers on various purposes.

Core-shell nanospheres behind the blue eyes of the bay scallop Argopecten irradians

The bay scallop Argopecten irradians (Mollusca: Bivalvia) has dozens of iridescent blue eyes that focus light using mirror-based optics. Here, we test the hypothesis that these eyes appear blue because of photonic nanostructures that preferentially scatter short-wavelength light. Using transmission electron microscopy, we found that the epithelial cells covering the eyes of A. irradians have three distinct layers: an outer layer of microvilli, a middle layer of random close-packed nanospheres and an inner layer of pigment granules. The nanospheres are approximately 180 nm in diameter and consist of electron-dense cores approximately 140 nm in diameter surrounded by less electron-dense shells 20 nm thick. They are packed at a volume density of approximately 60% and energy-dispersive X-ray spectroscopy indicates that they are not mineralized. Optical modelling revealed that the nanospheres are an ideal size for producing angle-weighted scattering that is bright and blue. A comparative perspective supports our hypothesis: epithelial cells from the black eyes of the sea scallop Placopecten magellanicus have an outer layer of microvilli and an inner layer of pigment granules but lack a layer of nanospheres between them. We speculate that light-scattering nanospheres help to prevent UV wavelengths from damaging the internal structures of the eyes of A. irradians and other blue-eyed scallops.

Designing Structural-Color Patterns Composed of Colloidal Arrays

Structural coloration provides a great potential for various applications due to unique optical properties distinguished from conventional pigment colors. Structural colors are nonfading, iridescent, and tunable, which is difficult to achieve with pigments. In addition, structural color is potentially less toxic than pigments. However, it is challenging to develop structural colors because elaborate nanostructures are a prerequisite for the coloration. Furthermore, it is highly suggested the nanostructures be patterned at various length scales on a large area to provide practical formats. There have been intensive studies to develop pragmatic methods for producing structural-color patterns in a controlled manner using either colloidal crystals or glasses. This article reviews the current state of the art in the structural-color patterning based on the colloidal arrays. We first discuss common and different features between colloidal crystals and glasses. We then categorize colloidal arrays into six distinct structures of 3D opals, inverse opals, non-close-packed arrays, 2D colloidal crystals, 1D colloidal strings, and 3D amorphous arrays and study various methods to make them patterned from recent key contributions. Finally, we outline the current challenges and future perspectives of the structural-color patterns.

Functional nanomaterials to augment photosynthesis: evidence and considerations for their responsible use in agricultural applications

At the current population growth rate, we will soon be unable to meet increasing food demands. As a consequence of this potential problem, considerable efforts have been made to enhance crop productivity by breeding, genetics and improving agricultural practices. While these techniques have traditionally been successful, their efficacy since the 'green revolution' has begun to significantly plateau. This stagnation of gains combined with the negative effects of climate change on crop yields has prompted researchers to develop novel and radical methods to increase crop productivity. Recent work has begun exploring the use of nanomaterials as synthetic probes to augment how plants use light. Photosynthesis in crops is often limited by their ability to absorb and exploit solar energy for photochemistry. The capacity to interact with and optimize how plants use light has the potential to increase the productivity of crops and enable the tailoring of crops for different environments and to compensate for predicted climate changes. Advances in the synthesis and surface modification of nanomaterials have overcome previous drawbacks and renewed their potential use as synthetic probes to enhance crop yields. Here, we review the current applications of functional nanomaterials in plants and will make an argument for the continued development of promising new nanomaterials and future applications in agriculture. This will highlight that functional nanomaterials have the clear potential to provide a much-needed route to enhanced future food security. In addition, we will discuss the often-ignored current evidence of nanoparticles present in the environment as well as inform and encourage caution on the regulation of nanomaterials in agriculture.

Characterization of chloroplast iridescence in Selaginella erythropus

Iridescence in shade-dwelling plants has previously been described in only a few plant groups, and even fewer where the structural colour is produced by intracellular structures. In contrast with other Selaginella species, this work reports the first example in the genus of structural colour originating from modified chloroplasts. Characterization of these structures determines that they form one-dimensional photonic multilayers. The Selaginella bizonoplasts present an analogous structure to recently reported Begonia iridoplasts; however, unlike Begonia species that produce iridoplasts, this Selaginella species was not previously described as iridescent. This therefore raises the possibility of widespread but unobserved and uncharacterized photonic structures in plants.

Symbiont photosynthesis in giant clams is promoted by V-type H+-ATPase from host cells

Giant clams (genus Tridacna) are the largest living bivalves and, like reef-building corals, host symbiotic dinoflagellate algae (Symbiodinium) that significantly contribute to their energy budget. In turn, Symbiodinium rely on the host to supply inorganic carbon (C_i) for photosynthesis. In corals, host 'proton pump' vacuolar-type H⁺-ATPase (VHA) is part of a carbon-concentrating mechanism (CCM) that promotes Symbiodinium photosynthesis. Here, we report that VHA in the small giant clam (Tridacna maxima) similarly promotes Symbiodinium photosynthesis. VHA was abundantly expressed in the apical membrane of epithelial cells of T. maxima's siphonal mantle tubule system, which harbors Symbiodinium Furthermore, application of the highly specific pharmacological VHA inhibitors bafilomycin A1 and concanamycin A significantly reduced photosynthetic O₂ production by ∼40%. Together with our observation that exposure to light increased holobiont aerobic metabolism ∼5-fold, and earlier estimates that translocated fixed carbon exceeds metabolic demand, we conclude that VHA activity in the siphonal mantle confers strong energetic benefits to the host clam through increased supply of C_i to algal symbionts and subsequent photosynthetic activity. The convergent role of VHA in promoting Symbiodinium photosynthesis in the giant clam siphonal mantle tubule system and coral symbiosome suggests that VHA-driven CCM is a common exaptation in marine photosymbioses that deserves further investigation in other taxa.

Structure-based optics of centric diatom frustules: modulation of the in vivo light field for efficient diatom photosynthesis

The optical properties of diatom silicate frustules inspire photonics and nanotechnology research. Whether light interaction with the nano-structure of the frustule also affects diatom photosynthesis has remained unclear due to lack of information on frustule optical properties under more natural conditions. Here we demonstrate that the optical properties of the frustule valves in water affect light harvesting and photosynthesis in live cells of centric diatoms (Coscinodiscus granii). Microscale cellular mapping of photosynthesis around localized spot illumination demonstrated optical coupling of chloroplasts to the valve wall. Photonic structures of the three-layered C. granii valve facilitated light redistribution and efficient photosynthesis in cell regions distant from the directly illuminated area. The different porous structure of the two sides of the valve exhibited photon trapping and forward scattering of blue light enhancing photosynthetic active radiation inside the cell. Photonic structures of diatom frustules thus alter the cellular light field with implications on diatom photobiology.

Living Light 2018: Conference Report

Living Light is a biennial conference focused on all aspects of light–matter interaction in biological organisms with a broad, interdisciplinary outlook. The 2018 edition was held at the Møller Centre in Cambridge, UK, from April 11th to April 14th, 2018. Living Light’s main goal is to bring together researchers from different backgrounds (e.g., biologists, physicists and engineers) in order to discuss the current state of the field and sparkle new collaborations and new interdisciplinary projects. With over 90 national and international attendees, the 2018 edition of the conference was strongly multidisciplinary: oral and poster presentations encompassed a wide range of topics ranging from the evolution and development of structural colors in living organisms and their genetic manipulation to the study of fossil photonic structures.

Light-induced dynamic structural color by intracellular 3D photonic crystals in brown algae

Natural photonic crystals are responsible for strong reflectance at selective wavelengths in different natural systems. We demonstrate that intracellular opal-like photonic crystals formed from lipids within photosynthetic cells produce vivid structural color in the alga Cystoseira tamariscifolia. The reflectance of the opaline vesicles is dynamically responsive to environmental illumination. The structural color is present in low light-adapted samples, whereas higher light levels produce a slow disappearance of the structural color such that it eventually vanishes completely. Once returned to low-light conditions, the color re-emerges. Our results suggest that these complex intracellular natural photonic crystals are responsive to environmental conditions, changing their packing structure reversibly, and have the potential to manipulate light for roles beyond visual signaling.

Light-dependent expression of a Na+/H+ exchanger 3-like transporter in the ctenidium of the giant clam, Tridacna squamosa, can be related to increased H+ excretion during light-enhanced calcification

Na⁺/H⁺ exchangers (NHEs) regulate intracellular pH and ionic balance by mediating H⁺ efflux in exchange for Na⁺ uptake in a 1:1 stoichiometry. This study aimed to obtain from the ctenidium of the giant clam Tridacna squamosa (TS) the complete cDNA sequence of a NHE3‐like transporter (TSNHE3), and to determine the effect of light exposure on its mRNA expression level and protein abundance therein. The coding sequence of TSNHE3 comprised 2886 bp, encoding 961 amino acids with an estimated molecular mass of 105.7 kDa. Immunofluorescence microscopy revealed that TSNHE3 was localized to the apical membrane of epithelial cells of the ctenidial filaments and the tertiary water channels. Particularly, the apical immunofluorescence of the ctenidial filaments was consistently stronger in the ctenidium of clams exposed to 12 h of light than those of the control kept in darkness. Indeed, light induced significant increases in the transcript level and protein abundance of TSNHE3/TSNHE3 in the ctenidium, indicating that the transcription and translation of TSNHE3/TSNHE3 were light‐dependent. As light‐enhanced calcification generates H⁺, the increased expression of TSNHE3/TSNHE3 in the ctenidium could be a response to augment H⁺ excretion in pursuance of whole‐body acid‐base balance during light exposure. These results signify that shell formation in giant clams requires the collaboration between the ctenidium, which is a respiratory and iono‐regulatory organ, and the inner mantle, which is directly involved in the calcification process, and provide new insights into the mechanisms of light‐enhanced calcification in giant clams.

Progress and Opportunities in Soft Photonics and Biologically Inspired Optics

Optical components made fully or partially from reconfigurable, stimuli-responsive, soft solids or fluids-collectively referred to as soft photonics-are poised to form the platform for tunable optical devices with unprecedented functionality and performance characteristics. Currently, however, soft solid and fluid material systems still represent an underutilized class of materials in the optical engineers' toolbox. This is in part due to challenges in fabrication, integration, and structural control on the nano- and microscale associated with the application of soft components in optics. These challenges might be addressed with the help of a resourceful ally: nature. Organisms from many different phyla have evolved an impressive arsenal of light manipulation strategies that rely on the ability to generate and dynamically reconfigure hierarchically structured, complex optical material designs, often involving soft or fluid components. A comprehensive understanding of design concepts, structure formation principles, material integration, and control mechanisms employed in biological photonic systems will allow this study to challenge current paradigms in optical technology. This review provides an overview of recent developments in the fields of soft photonics and biologically inspired optics, emphasizes the ties between the two fields, and outlines future opportunities that result from advancements in soft and bioinspired photonics.

Geometric Design of Scalable Forward Scatterers for Optimally Efficient Solar Transformers

It will be ideal to deliver equal, optimally efficient "doses" of sunlight to all cells in a photobioreactor system, while simultaneously utilizing the entire solar resource. Backed by the numerical scattering simulation and optimization, here, the design, synthesis, and characterization of the synthetic iridocytes that recapitulated the salient forward-scattering behavior of the Tridacnid clam system are reported, which presents the first geometric solution to allow narrow, precise forward redistribution of flux, utilizing the solar resource at the maximum quantum efficiency possible in living cells. The synthetic iridocytes are composed of silica nanoparticles in microspheres embedded in gelatin, both are low refractive index materials and inexpensive. They show wavelength selectivity, have little loss (the back-scattering intensity is reduced to less than ≈0.01% of the forward-scattered intensity), and narrow forward scattering cone similar to giant clams. Moreover, by comparing experiments and theoretical calculation, it is confirmed that the nonuniformity of the scatter sizes is a "feature not a bug" of the design, allowing for efficient, forward redistribution of solar flux in a micrometer-scaled paradigm. This method is environmentally benign, inexpensive, and scalable to produce optical components that will find uses in efficiency-limited solar conversion technologies, heat sinks, and biofuel production.

The inner mantle of the giant clam, Tridacna squamosa, expresses a basolateral Na+/K+-ATPase α-subunit, which displays light-dependent gene and protein expression along the shell-facing epithelium

Na+/K+-ATPase (NKA) is essential for maintaining the Na+ and K+ gradients, and supporting the secondary active transport of certain ions/molecules, across the plasma membrane of animal cells. This study aimed to clone the NKA α-subunit (NKAα) from the inner mantle adjacent to the extrapallial fluid of Tridacna squamosa, to determine its subcellular localization, and to examine the effects of light exposure on its transcript level and protein abundance. The cDNA coding sequence of NKAα from T. squamosa comprised 3105 bp, encoding 1034 amino acids with an estimated molecular mass of 114 kDa. NKAα had a basolateral localization along the shell-facing epithelium of the inner mantle. Exposure to 12 h of light led to a significantly stronger basolateral NKAα-immunofluorescence at the shell-facing epithelium, indicating that NKA might play a role in light-enhanced calcification in T. squamosa. After 3 h of light exposure, the transcript level of NKAα decreased transiently in the inner mantle, but returned to the control level thereafter. In comparison, the protein abundance of NKAα remained unchanged at hour 3, but became significantly higher than the control after 12 h of light exposure. Hence, the expression of NKAα in the inner mantle of T. squamosa was light-dependent. It is probable that a higher expression level of NKA was needed in the shell-facing epithelial cells of the inner mantle to cope with a rise in Na+ influx, possibly caused by increases in activities of some Na+-dependent ion transporters/channels involved in light-enhanced calcification.

The Whitish Inner Mantle of the Giant Clam, Tridacna squamosa, Expresses an Apical Plasma Membrane Ca2+-ATPase (PMCA) Which Displays Light-Dependent Gene and Protein Expressions

Giant clams live in symbiosis with extracellular zooxanthellae and display high rates of growth and shell formation (calcification) in light. Light-enhanced calcification requires an increase in the supply of Ca²⁺ to, and simultaneously an augmented removal of H⁺ from, the extrapallial fluid where shell formation occurs. We have obtained the complete coding cDNA sequence of Plasma Membrane Ca²⁺-ATPase (PMCA) from the thin and whitish inner mantle, which is in touch with the extrapallial fluid, of the giant clam Tridacna squamosa. The deduced PMCA sequence consisted of an apical targeting element. Immunofluorescence microscopy confirmed that PMCA had an apical localization in the shell-facing epithelium of the inner mantle, whereby it can actively secrete Ca²⁺ in exchange for H⁺. More importantly, the apical PMCA-immunofluorescence of the shell-facing epithelium of the inner mantle increased significantly after 12 h of exposure to light. The transcript and protein levels of PMCA/PMCA also increased significantly in the inner mantle after 6 or 12 h of light exposure. These results offer insights into a light-dependable mechanism of shell formation in T. squamosa and a novel explanation of light-enhanced calcification in general. As the inner mantle normally lacks light sensitive pigments, our results support a previous proposition that symbiotic zooxanthellae, particularly those in the colorful and extensible outer mantle, may act as light-sensing elements for the host clam.

Photonic multilayer structure of Begonia chloroplasts enhances photosynthetic efficiency

Enhanced light harvesting is an area of interest for optimizing both natural photosynthesis and artificial solar energy capture^1,2. Iridescence has been shown to exist widely and in diverse forms in plants and other photosynthetic organisms and symbioses^3,4, but there has yet to be any direct link demonstrated between iridescence and photosynthesis. Here we show that epidermal chloroplasts, also known as iridoplasts, in shade-dwelling species of Begonia⁵, notable for their brilliant blue iridescence, have a photonic crystal structure formed from a periodic arrangement of the light-absorbing thylakoid tissue itself. This structure enhances photosynthesis in two ways: by increasing light capture at the predominantly green wavelengths available in shade conditions, and by directly enhancing quantum yield by 5-10% under low-light conditions. These findings together imply that the iridoplast is a highly modified chloroplast structure adapted to make best use of the extremely low-light conditions in the tropical forest understorey in which it is found^5,6. A phylogenetically diverse range of shade-dwelling plant species has been found to produce similarly structured chloroplasts^7-9, suggesting that the ability to produce chloroplasts whose membranes are organized as a multilayer with photonic properties may be widespread. In fact, given the well-established diversity and plasticity of chloroplasts^10,11, our results imply that photonic effects may be important even in plants that do not show any obvious signs of iridescence to the naked eye but where a highly ordered chloroplast structure may present a clear blue reflectance at the microscale. Chloroplasts are generally thought of as purely photochemical; we suggest that one should also think of them as a photonic structure with a complex interplay between control of light propagation, light capture and photochemistry.

Wavelength-specific forward scattering of light by Bragg-reflective iridocytes in giant clams

A surprising recent discovery revealed that the brightly reflective cells ('iridocytes') in the epithelia of giant clams actually send the majority of incident photons 'forward' into the tissue. While the intracellular Bragg reflectors in these cells are responsible for their colourful back reflection, Mie scattering produces the forward scattering, thus illuminating a dense population of endosymbiotic, photosynthetic microalgae. We now present a detailed micro-spectrophotometric characterization of the Bragg stacks in the iridocytes in live tissue to obtain the refractive index of the high-index layers (1.39 to 1.58, average 1.44 ± 0.04), the thicknesses of the high- and low-index layers (50-150 nm), and the numbers of pairs of layers (2-11) that participate in the observed spectral reflection. Based on these measurements, we performed electromagnetic simulations to better understand the optical behaviour of the iridocytes. The results open a deeper understanding of the optical behaviour of these cells, with the counterintuitive discovery that specific combinations of iridocyte diameter and Bragg-lamellar spacing can produce back reflection of the same colour that is also scattered forward, in preference to other wavelengths that are scattered at higher angles. We find for all values of size and wavelength investigated that more than 90% of the incident energy is carried by the photons that are scattered in the forward direction; while this forward scattering from each iridocyte shows very narrow angular dispersion (ca ±6°), the multiplicative scattering from a layer of ca 20 iridocytes broadens this dispersion to a cone of approximately ±90°. This understanding of the complex biophotonic dynamics enhances our comprehension of the physiologically, ecologically and evolutionarily significant light environment inside the giant clam, which is diffuse and nearly white at small tissue depths and downwelling, relatively monochromatic, and can be the same colour as the back-reflected light at greater depths in the tissue. Originally thought to be unique, cells of similar structure and photonic activity are now recognized in other species, where they serve other functions. The behaviour of the iridocytes opens possible new considerations for conservation and management of the valuable giant clam resource and new avenues for biologically inspired photonic applications.

A unique self-organization of bacterial sub-communities creates iridescence in Cellulophaga lytica colony biofilms

Iridescent color appearances are widespread in nature. They arise from the interaction of light with micron- and submicron-sized physical structures spatially arranged with periodic geometry and are usually associated with bright angle-dependent hues. Iridescence has been reported for many animals and marine organisms. However, iridescence has not been well studied in bacteria. Recently, we reported a brilliant "pointillistic" iridescence in colony biofilms of marine Flavobacteria that exhibit gliding motility. The mechanism of their iridescence is unknown. Here, using a multi-disciplinary approach, we show that the cause of iridescence is a unique periodicity of the cell population in the colony biofilm. Cells are arranged together to form hexagonal photonic crystals. Our model highlights a novel pattern of self-organization in a bacterial biofilm. "Pointillistic" bacterial iridescence can be considered a new light-dependent phenomenon for the field of microbiology.