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

Structural color in the bacterial domain: The ecogenomics of a 2-dimensional optical phenotype

Structural color is an optical phenomenon resulting from light interacting with nanostructured materials. Although structural color (SC) is widespread in the tree of life, the underlying genetics and genomics are not well understood. Here, we collected and sequenced a set of 87 structurally colored bacterial isolates and 30 related strains lacking SC. Optical analysis of colonies indicated that diverse bacteria from at least two different phyla (Bacteroidetes and Proteobacteria) can create two-dimensional packing of cells capable of producing SC. A pan-genome-wide association approach was used to identify genes associated with SC. The biosynthesis of uroporphyrin and pterins, as well as carbohydrate utilization and metabolism, was found to be involved. Using this information, we constructed a classifier to predict SC directly from bacterial genome sequences and validated it by cultivating and scoring 100 strains that were not part of the training set. We predicted that SCr is widely distributed within gram-negative bacteria. Analysis of over 13,000 assembled metagenomes suggested that SC is nearly absent from most habitats associated with multicellular organisms except macroalgae and is abundant in marine waters and surface/air interfaces. This work provides a large-scale ecogenomics view of SC in bacteria and identifies microbial pathways and evolutionary relationships that underlie this optical phenomenon.

Iridescent biofilms of Cellulophaga lytica are tunable platforms for scalable, ordered materials

Nature offers many examples of materials which exhibit exceptional properties due to hierarchical assembly of their constituents. In well-studied multi-cellular systems, such as the morpho butterfly, a visible indication of having ordered submicron features is given by the display of structural color. Detailed investigations of nature's designs have yielded mechanistic insights and led to the development of biomimetic materials at laboratory scales. However, the manufacturing of hierarchical assemblies at industrial scales remains difficult. Biomanufacturing aims to leverage the autonomy of biological systems to produce materials at lower cost and with fewer carbon emissions. Earlier reports documented that some bacteria, particularly those with gliding motility, self-assemble into biofilms with polycrystalline structures and exhibit glittery, iridescent colors. The current study demonstrates the potential of using one of these bacteria, Cellulophaga lytica, as a platform for the large scale biomanufacturing of ordered materials. Specific approaches for controlling C. lytica biofilm optical, spatial and temporal properties are reported. Complementary microscopy-based studies reveal that biofilm color variations are attributed to changes in morphology induced by cellular responses to the local environment. Incorporation of C. lytica biofilms into materials is also demonstrated, thereby facilitating their handling and downstream processing, as would be needed during manufacturing processes. Finally, the utility of C. lytica as a self-printing, photonic ink is established by this study. In summary, autonomous surface assembly of C. lytica under ambient conditions and across multiple length scales circumvent challenges that currently hinder production of ordered materials in industrial settings.

Gliding motility of a uranium-tolerant Bacteroidetes bacterium Chryseobacterium sp. strain PMSZPI: insights into the architecture of spreading colonies

Uranium-tolerant soil bacterium Chryseobacterium sp. strain PMSZPI moved over solid agar surfaces by gliding motility thereby forming spreading colonies which is a hallmark of members of Bacteroidetes phylum. PMSZPI genome harboured orthologs of all the gld and spr genes considered as core bacteroidetes gliding motility genes of which gldK, gldL, gldM and gldN were co-transcribed. Here, we present the intriguing interplay between gliding motility and cellular organization in PMSZPI spreading colonies. While nutrient deficiency enhanced colony spreading, high agar concentrations and presence of motility inhibitor like 5-hydroxyindole reduced the spreading. A detailed in situ structural analysis of spreading colonies revealed closely packed cells forming multiple layers at centre of colony while the edges showed clusters of cells periodically arranged in hexagonal lattices interconnected with each other. The cell migration within colony was visualized as branched structures wherein the cells were buried within extracellular matrix. PMSZPI colonies exhibited strong iridescence possibly as a result of periodicity within the cell population achieved through gliding motility. Presence of uranium reduced motility and iridescence and induced biofilm formation. The coordinated study of gliding motility and iridescence apparently influenced by uranium provides unique insights into the lifestyle of PMSZPI residing in uranium enriched environment.

Polysaccharide metabolism regulates structural colour in bacterial colonies

The brightest colours in nature often originate from the interaction of light with materials structured at the nanoscale. Different organisms produce such coloration with a wide variety of materials and architectures. In the case of bacterial colonies, structural colours stem for the periodic organization of the cells within the colony, and while considerable efforts have been spent on elucidating the mechanisms responsible for such coloration, the biochemical processes determining the development of this effect have not been explored. Here, we study the influence of nutrients on the organization of cells from the structurally coloured bacteria Flavobacterium strain IR1. By analysing the optical properties of the colonies grown with and without specific polysaccharides, we found that the highly ordered organization of the cells can be altered by the presence of fucoidans. Additionally, by comparing the organization of the wild-type strain with mutants grown in different nutrient conditions, we deduced that this regulation of cell ordering is linked to a specific region of the IR1 chromosome. This region encodes a mechanism for the uptake and metabolism of polysaccharides, including a polysaccharide utilization locus (PUL operon) that appears specific to fucoidan, providing new insight into the biochemical pathways regulating structural colour in bacteria.

On the Explicit Function of Life within a Physical Universe

To describe the meaning of functionality in a universe before life evolved, existing etiological and systemic accounts of function are evaluated. Since the theory of function is only applicable in context with living beings and artifacts used by living beings and therefore cannot predict how a prebiotic form of functionality could evolve, a maintenance account for functionality is proposed. This account ascribes functionality to a structurally disposed property that increases the probability of maintenance or recurrence of the property in the surrounding selective environment. With the help of the maintenance account and a concept of physical information comprising kinetic and structural types of information, possible evolutionary processes preceding the evolution of life are explored. As important mechanisms in abiotic and prebiotic evolution, linear and non-linear mixing processes, as well as dynamics of solitary waves, are identified. Before the question of the meaning of life in prebiotic environments is renewed and an educated guess based on the elaborated arguments is made on the progress of evolution under the influencing impression of the living state, the evolution of functionality in different selective contexts is analyzed.

Ecological and Biotechnological Aspects of Pigmented Microbes: A Way Forward in Development of Food and Pharmaceutical Grade Pigments

Microbial pigments play multiple roles in the ecosystem construction, survival, and fitness of all kinds of organisms. Considerably, microbial (bacteria, fungi, yeast, and microalgae) pigments offer a wide array of food, drug, colorants, dyes, and imaging applications. In contrast to the natural pigments from microbes, synthetic colorants are widely used due to high production, high intensity, and low cost. Nevertheless, natural pigments are gaining more demand over synthetic pigments as synthetic pigments have demonstrated side effects on human health. Therefore, research on microbial pigments needs to be extended, explored, and exploited to find potential industrial applications. In this review, the evolutionary aspects, the spatial significance of important pigments, biomedical applications, research gaps, and future perspectives are detailed briefly. The pathogenic nature of some pigmented bacteria is also detailed for awareness and safe handling. In addition, pigments from macro-organisms are also discussed in some sections for comparison with microbes.

Does Structural Color Exist in True Fungi?

Structural color occurs by the interaction of light with regular structures and so generates colors by completely different optical mechanisms to dyes and pigments. Structural color is found throughout the tree of life but has not, to date, been reported in the fungi. Here we give an overview of structural color across the tree of life and provide a brief guide aimed at stimulating the search for this phenomenon in fungi.

Draft Genome Sequence of the Free-Living, Iridescent Bacterium Tenacibaculum mesophilum Strain ECR

Here, we report the genome sequence of Tenacibaculum mesophilum strain ECR, which was isolated from the river/ocean interface at Trunk River, Falmouth, Massachusetts, USA. The isolation and sequencing were performed as part of the 2016 and 2018 Microbial Diversity courses at the Marine Biological Laboratory in Woods Hole, Massachusetts, USA.

Here, we report the genome sequence of Tenacibaculum mesophilum strain ECR, which was isolated from the river/ocean interface at Trunk River in Falmouth, Massachusetts. The isolation and sequencing were performed as part of the 2016 and 2018 Microbial Diversity courses at the Marine Biological Laboratory in Woods Hole, Massachusetts.

Quo vadis biophotonics? Wearing serendipity and slow science as a badge of pride, and embracing biology

This article is a reflection on the themes of the Faraday Discussion meeting on 'Biological and bio-inspired optics' held from 20 to 22 July 2020. It is a personal perspective on the nature of this field as a broad and interdisciplinary field that has led to a sound understanding of the material properties of biological nanostructured and optical materials. The article describes how the nature of the field and the themes of the conference are reflected in particular in work on the 3D bicontinuous biophotonic nanostructures known as single gyroids and in bicontinuous structures more broadly. Such single gyroid materials are found for example in the butterfly Thecla opisena, where the questions of biophotonic response, of bio-inspired optics, of the relationship between structure and function, and of the relationship between natural and synthetic realisations are closely interlinked. This multitude of facets of research on single gyroid structures reflects the beauty of the broader field of biophotonics, namely as a field that lives through embracing the serendipitous discovery of the biophotonic marvels that nature offers to us as seeds for in-depth analysis and understanding. The meandering nature of its discoveries, and the need to accept the slowness that comes from exploration of intellectually new or foreign territory, mean that the field shares some traits with biological evolution itself. Looking into the future, I consider that a closer engagement with living tissue and with the biological questions of function and formation, rather than with the materials science of biological materials, will help ensure the continuing great success of this field.

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.

The cell organization underlying structural colour is involved in Flavobacterium IR1 predation

Flavobacterium IR1 is a gliding bacterium with a high degree of colonial organization as a 2D photonic crystal, resulting in vivid structural coloration when illuminated. Enterobacter cloacae B12, an unrelated bacterium, was isolated from the brown macroalga Fucus vesiculosus from the same location as IR1. IR1 was found to be a predator of B12. A process of surrounding, infiltration, undercutting and killing of B12 supported improved growth of IR1. A combination of motility and capillarity facilitated the engulfment of B12 colonies by IR1. Predation was independent of illumination. Mutants of IR1 that formed photonic crystals less effectively than the wild type were reduced in predation. Conversely, formation of a photonic crystal was not advantageous in resisting predation by Rhodococcus spp. PIR4. These observations suggest that the organization required to create structural colour has a biological function (facilitating predation) but one that is not directly related to the photonic properties of the colony. This work is the first experimental evidence supporting a role for this widespread type of cell organization in the Flavobacteriia.

Complex photonic response reveals three-dimensional self-organization of structural coloured bacterial colonies

Vivid colours found in living organisms are often the result of scattering from hierarchical nanostructures, where the interplay between order and disorder in their packing defines visual appearance. In the case of Flavobacterium IR1, the complex arrangement of the cells in polycrystalline three-dimensional lattices is found to be a distinctive fingerprint of colony organization. By combining analytical analysis of the angle-resolved scattering response of in vivo bacterial colonies with numerical modelling, we show that we can assess the inter-cell distance and cell diameter with a resolution below 10 nm, far better than what can be achieved with conventional electron microscopy, suffering from preparation artefacts. Retrieving the role of disorder at different length scales from the salient features in the scattering response enables a precise understanding of the structural organization of the bacteria.

The cellular and genetic basis of structural colour in plants

While the pathways that produce plant pigments have been well studied for decades, the use by plants of nanoscale structures to produce colour effects has only recently begun to be studied. A variety of plants from across the plant kingdom have been shown to use different mechanism to generate structural colours in tissues as diverse as leaves, flowers and fruits. In this review we explore the cellular mechanisms by which these nanoscale structures are built and discuss the first insights that have been published into the genetic pathways underpinning these traits.

Quantitative characterization of iridescent colours in biological studies: a novel method using optical theory

Iridescent colours are colours that change with viewing or illumination geometry. While they are widespread in many living organisms, most evolutionary studies on iridescence do not take into account their full complexity. Few studies try to precisely characterize what makes iridescent colours special: their angular dependency. Yet, it is likely that this angular dependency has biological functions and is therefore submitted to evolutionary pressures. For this reason, evolutionary biologists need a repeatable method to measure iridescent colours as well as variables to precisely quantify the angular dependency. In this study, we use a theoretical approach to propose five variables that allow one to fully describe iridescent colours at every angle combination. Based on the results, we propose a new measurement protocol and statistical method to reliably characterize iridescence while minimizing the required number of time-consuming measurements. We use hummingbird iridescent feathers and butterfly iridescent wings as test cases to demonstrate the strengths of this new method. We show that our method is precise enough to be potentially used at intraspecific level while being also time-efficient enough to encompass large taxonomic scales.

Intercellular adhesion promotes clonal mixing in growing bacterial populations

Dense bacterial communities, known as biofilms, can have functional spatial organization driven by self-organizing chemical and physical interactions between cells, and their environment. In this work, we investigated intercellular adhesion, a pervasive property of bacteria in biofilms, to identify effects on the internal structure of bacterial colonies. We expressed the self-recognizing ag43 adhesin protein in Escherichia coli to generate adhesion between cells, which caused aggregation in liquid culture and altered microcolony morphology on solid media. We combined the adhesive phenotype with an artificial colony patterning system based on plasmid segregation, which marked clonal lineage domains in colonies grown from single cells. Engineered E. coli were grown to colonies containing domains with varying adhesive properties, and investigated with microscopy, image processing and computational modelling techniques. We found that intercellular adhesion elongated the fractal-like boundary between cell lineages only when both domains within the colony were adhesive, by increasing the rotational motion during colony growth. Our work demonstrates that adhesive intercellular interactions can have significant effects on the spatial organization of bacterial populations, which can be exploited for biofilm engineering. Furthermore, our approach provides a robust platform to study the influence of intercellular interactions on spatial structure in bacterial populations.

Genetic manipulation of structural color in bacterial colonies

Naturally occurring photonic structures are responsible for the bright and vivid coloration in a large variety of living organisms. Despite efforts to understand their biological functions, development, and complex optical response, little is known of the underlying genes involved in the development of these nanostructures in any domain of life. Here, we used Flavobacterium colonies as a model system to demonstrate that genes responsible for gliding motility, cell shape, the stringent response, and tRNA modification contribute to the optical appearance of the colony. By structural and optical analysis, we obtained a detailed correlation of how genetic modifications alter structural color in bacterial colonies. Understanding of genotype and phenotype relations in this system opens the way to genetic engineering of on-demand living optical materials, for use as paints and living sensors.

Colony analysis and deep learning uncover 5-hydroxyindole as an inhibitor of gliding motility and iridescence in Cellulophaga lytica

Iridescence is an original type of colouration that is relatively widespread in nature but has been either incompletely described or entirely neglected in prokaryotes. Recently, we reported a brilliant 'pointillistic' iridescence in agar-grown colony biofilms of Cellulophaga lytica and some other marine Flavobacteria that exhibit gliding motility. Bacterial iridescence is created by a unique self-organization of sub-communities of cells, but the mechanisms underlying such living photonic crystals are unknown. In this study, we used Petri dish assays to screen a large panel of potential activators or inhibitors of C. lytica's iridescence. Derivatives potentially interfering with quorum-sensing and other communication or biofilm formation processes were tested, as well as metabolic poisons or algal exoproducts. We identified an indole derivative, 5-hydroxyindole (5HI, 250 µM) which inhibited both gliding and iridescence at the colonial level. 5HI did not affect growth or cell respiration. At the microscopic level, phase-contrast imaging confirmed that 5HI inhibits the gliding motility of cells. Moreover, the lack of iridescence correlated with a perturbation of self-organization of the cell sub-communities in both the WT and a gliding-negative mutant. This effect was proved using recent advances in machine learning (deep neuronal networks). In addition to its effect on colony biofilms, 5HI was found to stimulate biofilm formation in microplates. Our data are compatible with possible roles of 5HI or marine analogues in the eco-biology of iridescent bacteria.

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.

Draft Genome Sequence of the Iridescent Marine Bacterium Cellulophaga lytica CECT 8139

Some species of the genus Cellulophaga have been reported as having biotechnological interests and noteworthy physiological properties. We report here the draft genome sequence of Cellulophaga lytica CECT 8139, a bacterium that produces an intensely iridescent colony biofilm on agar surfaces.

On the colour of wing scales in butterflies: iridescence and preferred orientation of single gyroid photonic crystals

Lycaenid butterflies from the genera Callophrys, Cyanophrys and Thecla have evolved remarkable biophotonic gyroid nanostructures within their wing scales that have only recently been replicated by nanoscale additive manufacturing. These nanostructures selectively reflect parts of the visible spectrum to give their characteristic non-iridescent, matte-green appearance, despite a distinct blue–green–yellow iridescence predicted for individual crystals from theory. It has been hypothesized that the organism must achieve its uniform appearance by growing crystals with some restrictions on the possible distribution of orientations, yet preferential orientation observed in Callophrys rubi confirms that this distribution need not be uniform. By analysing scanning electron microscope and optical images of 912 crystals in three wing scales, we find no preference for their rotational alignment in the plane of the scales. However, crystal orientation normal to the scale was highly correlated to their colour at low (conical) angles of view and illumination. This correlation enabled the use of optical images, each containing up to 10⁴–10⁵ crystals, for concluding the preferential alignment seen along the at the level of single scales, appears ubiquitous. By contrast, orientations were found to occur at no greater rate than that expected by chance. Above a critical cone angle, all crystals reflected bright green light indicating the dominant light scattering is due to the predicted band gap along the direction, independent of the domain orientation. Together with the natural variation in scale and wing shapes, we can readily understand the detailed mechanism of uniform colour production and iridescence suppression in these butterflies. It appears that the combination of preferential alignment normal to the wing scale, and uniform distribution within the plane is a near optimal solution for homogenizing the angular distribution of the band gap relative to the wings. Finally, the distributions of orientations, shapes, sizes and degree of order of crystals within single scales provide useful insights for understanding the mechanisms at play in the formation of these biophotonic nanostructures.