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Zomer A, Ingham CJ, von Meijenfeldt FAB, Escobar Doncel Á, van de Kerkhof GT, Hamidjaja R, Schouten S, Schertel L, Müller KH, Catón L, Hahnke RL, Bolhuis H, Vignolini S, Dutilh BE. Structural color in the bacterial domain: The ecogenomics of a 2-dimensional optical phenotype. Proc Natl Acad Sci U S A 2024; 121:e2309757121. [PMID: 38990940 PMCID: PMC11260094 DOI: 10.1073/pnas.2309757121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 04/23/2024] [Indexed: 07/13/2024] Open
Abstract
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.
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Affiliation(s)
- Aldert Zomer
- Division of Infectious Diseases and Immunology, Utrecht University, Utrecht3584 CL, the Netherlands
| | - Colin J. Ingham
- Hoekmine Besloten Vennootschap, Utrecht3515 GJ, the Netherlands
| | - F. A. Bastiaan von Meijenfeldt
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht3584 CH, the Netherlands
- Department of Marine Microbiology & Biogeochemistry, Royal Netherlands Institute for Sea Research, ‘t Horntje1797 SZ, The Netherlands
| | | | - Gea T. van de Kerkhof
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | | | - Sanne Schouten
- Hoekmine Besloten Vennootschap, Utrecht3515 GJ, the Netherlands
| | - Lukas Schertel
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
- Department of Physics, University of Fribourg, FribourgCH-1700, Switzerland
| | - Karin H. Müller
- Department of Physiology, Development and Neuroscience, Cambridge Advanced Imaging Centre, University of Cambridge, CambridgeCB2 3DY, United Kingdom
| | - Laura Catón
- Hoekmine Besloten Vennootschap, Utrecht3515 GJ, the Netherlands
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Richard L. Hahnke
- Leibniz Institute, German Collection of Microorganisms and Cell Cultures, Braunschweig38124, Germany
| | - Henk Bolhuis
- Department of Marine Microbiology & Biogeochemistry, Royal Netherlands Institute for Sea Research, ‘t Horntje1797 SZ, The Netherlands
| | - Silvia Vignolini
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
- Sustainable and Bio-inspired Materials, Max Planck Institute of Colloids and Interfaces, Potsdam14476, Germany
| | - Bas E. Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht3584 CH, the Netherlands
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena07743, Germany
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2
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Frka-Petesic B, Parton TG, Honorato-Rios C, Narkevicius A, Ballu K, Shen Q, Lu Z, Ogawa Y, Haataja JS, Droguet BE, Parker RM, Vignolini S. Structural Color from Cellulose Nanocrystals or Chitin Nanocrystals: Self-Assembly, Optics, and Applications. Chem Rev 2023; 123:12595-12756. [PMID: 38011110 PMCID: PMC10729353 DOI: 10.1021/acs.chemrev.2c00836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Indexed: 11/29/2023]
Abstract
Widespread concerns over the impact of human activity on the environment have resulted in a desire to replace artificial functional materials with naturally derived alternatives. As such, polysaccharides are drawing increasing attention due to offering a renewable, biodegradable, and biocompatible feedstock for functional nanomaterials. In particular, nanocrystals of cellulose and chitin have emerged as versatile and sustainable building blocks for diverse applications, ranging from mechanical reinforcement to structural coloration. Much of this interest arises from the tendency of these colloidally stable nanoparticles to self-organize in water into a lyotropic cholesteric liquid crystal, which can be readily manipulated in terms of its periodicity, structure, and geometry. Importantly, this helicoidal ordering can be retained into the solid-state, offering an accessible route to complex nanostructured films, coatings, and particles. In this review, the process of forming iridescent, structurally colored films from suspensions of cellulose nanocrystals (CNCs) is summarized and the mechanisms underlying the chemical and physical phenomena at each stage in the process explored. Analogy is then drawn with chitin nanocrystals (ChNCs), allowing for key differences to be critically assessed and strategies toward structural coloration to be presented. Importantly, the progress toward translating this technology from academia to industry is summarized, with unresolved scientific and technical questions put forward as challenges to the community.
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Affiliation(s)
- Bruno Frka-Petesic
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- International
Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM), Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Thomas G. Parton
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Camila Honorato-Rios
- Department
of Sustainable and Bio-inspired Materials, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Aurimas Narkevicius
- B
CUBE − Center for Molecular Bioengineering, Technische Universität Dresden, 01307 Dresden, Germany
| | - Kevin Ballu
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Qingchen Shen
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Zihao Lu
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Yu Ogawa
- CERMAV-CNRS,
CS40700, 38041 Grenoble cedex 9, France
| | - Johannes S. Haataja
- Department
of Applied Physics, Aalto University School
of Science, P.O. Box
15100, Aalto, Espoo FI-00076, Finland
| | - Benjamin E. Droguet
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Richard M. Parker
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Silvia Vignolini
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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3
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Sullivan CJ, Brown K, Hung CS, Tang JKH, DeSimone M, Chen V, Lloyd PF, Gupta M, Juhl A, Crookes-Goodson W, Vasudev M, Dennis PB, Kelley-Loughnane N. Iridescent biofilms of Cellulophaga lytica are tunable platforms for scalable, ordered materials. Sci Rep 2023; 13:13192. [PMID: 37580360 PMCID: PMC10425352 DOI: 10.1038/s41598-023-38797-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 07/14/2023] [Indexed: 08/16/2023] Open
Abstract
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.
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Affiliation(s)
- Claretta J Sullivan
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, OH, 45433, USA.
| | - Kennedy Brown
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, OH, 45433, USA
| | - Chia-Suei Hung
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, OH, 45433, USA
| | - Joseph Kuo-Hsiang Tang
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, OH, 45433, USA
| | - Mark DeSimone
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, OH, 45433, USA
- Department of Bioengineering, University of Massachusetts Dartmouth, Dartmouth, MA, 02747, USA
| | - Vincent Chen
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, OH, 45433, USA
| | - Pamela F Lloyd
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, OH, 45433, USA
| | - Maneesh Gupta
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, OH, 45433, USA
| | - Abby Juhl
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, OH, 45433, USA
| | - Wendy Crookes-Goodson
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, OH, 45433, USA
| | - Milana Vasudev
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, OH, 45433, USA
- Department of Bioengineering, University of Massachusetts Dartmouth, Dartmouth, MA, 02747, USA
| | - Patrick B Dennis
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, OH, 45433, USA
| | - Nancy Kelley-Loughnane
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, OH, 45433, USA
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4
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Lu J, Şimşek E, Silver A, You L. Advances and challenges in programming pattern formation using living cells. Curr Opin Chem Biol 2022; 68:102147. [DOI: 10.1016/j.cbpa.2022.102147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 11/29/2022]
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5
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Datta B, Spero EF, Martin-Martinez FJ, Ortiz C. Socially-Directed Development of Materials for Structural Color. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2100939. [PMID: 35373398 DOI: 10.1002/adma.202100939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 10/14/2021] [Indexed: 06/14/2023]
Abstract
Advancing a socially-directed approach to materials research and development is an imperative to address contemporary challenges and mitigate future detrimental environmental and social impacts. This paper reviews, synergizes, and identifies cross-disciplinary opportunities at the intersection of materials science and engineering with humanistic social sciences fields. Such integrated knowledge and methodologies foster a contextual understanding of materials technologies embedded within, and impacting broader societal systems, thus informing decision making upstream and throughout the entire research and development process toward more socially responsible outcomes. Technological advances in the development of structural color, which arises due to the incoherent and coherent scattering of micro-and nanoscale features and possesses a vast design space, are considered in this context. Specific areas of discussion include material culture, narratives, and visual perception, material waste and use, environmental and social life cycle assessment, and stakeholder and community engagement. A case study of the technical and social implications of bio-based cellulose (as a source for structurally colored products) is provided. Socially-directed research and development of materials for structural color hold significant capacity for improved planetary and societal impact across industries such as aerospace, consumer products, displays and sensors, paints and dyes, and food and agriculture.
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Affiliation(s)
- Bianca Datta
- MIT Media Lab, Massachusetts Institute of Technology, 20 Ames Street, Cambridge, MA, 02139, USA
| | - Ellan F Spero
- Department of Materials Science & Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Station1, 280 Merrimack Street, Lawrence, MA, 01843, USA
| | - Francisco J Martin-Martinez
- Station1, 280 Merrimack Street, Lawrence, MA, 01843, USA
- Department of Chemistry, Swansea University, Singleton Park, Swansea, Wales, SA2 8PP, UK
| | - Christine Ortiz
- Department of Materials Science & Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Station1, 280 Merrimack Street, Lawrence, MA, 01843, USA
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6
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van de Kerkhof GT, Schertel L, Catòn L, Parton TG, Müller KH, Greer HF, Ingham CJ, Vignolini S. Polysaccharide metabolism regulates structural colour in bacterial colonies. J R Soc Interface 2022; 19:20220181. [PMID: 35611622 PMCID: PMC9131120 DOI: 10.1098/rsif.2022.0181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/13/2022] [Indexed: 12/17/2022] Open
Abstract
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.
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Affiliation(s)
- Gea T. van de Kerkhof
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Lukas Schertel
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Laura Catòn
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Hoekmine BV, Room 1.091 (iLab), Kenniscentrum Technologie en Innovatie, Hogeschool Utrecht, Heidelberglaan 7, 3584 CS, Utrecht, The Netherlands
| | - Thomas G. Parton
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Karin H. Müller
- Cambridge Advanced Imaging Centre, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Heather F. Greer
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Colin J. Ingham
- Hoekmine BV, Room 1.091 (iLab), Kenniscentrum Technologie en Innovatie, Hogeschool Utrecht, Heidelberglaan 7, 3584 CS, Utrecht, The Netherlands
| | - Silvia Vignolini
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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7
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Patinios C, Creutzburg SCA, Arifah AQ, Adiego-Pérez B, Gyimah E, Ingham C, Kengen SWM, van der Oost J, Staals RHJ. Streamlined CRISPR genome engineering in wild-type bacteria using SIBR-Cas. Nucleic Acids Res 2021; 49:11392-11404. [PMID: 34614191 PMCID: PMC8565351 DOI: 10.1093/nar/gkab893] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
CRISPR-Cas is a powerful tool for genome editing in bacteria. However, its efficacy is dependent on host factors (such as DNA repair pathways) and/or exogenous expression of recombinases. In this study, we mitigated these constraints by developing a simple and widely applicable genome engineering tool for bacteria which we termed SIBR-Cas (Self-splicing Intron-Based Riboswitch-Cas). SIBR-Cas was generated from a mutant library of the theophylline-dependent self-splicing T4 td intron that allows for tight and inducible control over CRISPR-Cas counter-selection. This control delays CRISPR-Cas counter-selection, granting more time for the editing event (e.g. by homologous recombination) to occur. Without the use of exogenous recombinases, SIBR-Cas was successfully applied to knock-out several genes in three wild-type bacteria species (Escherichia coli MG1655, Pseudomonas putida KT2440 and Flavobacterium IR1) with poor homologous recombination systems. Compared to other genome engineering tools, SIBR-Cas is simple, tightly regulated and widely applicable for most (non-model) bacteria. Furthermore, we propose that SIBR can have a wider application as a simple gene expression and gene regulation control mechanism for any gene or RNA of interest in bacteria.
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Affiliation(s)
- Constantinos Patinios
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Sjoerd C A Creutzburg
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Adini Q Arifah
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Belén Adiego-Pérez
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Evans A Gyimah
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Colin J Ingham
- Hoekmine Besloten Vennootschap, Kenniscentrum Technologie en Innovatie, Hogeschool Utrecht, 3584 CS, Utrecht, The Netherlands
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Raymond H J Staals
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
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8
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McCoy DE, Shneidman AV, Davis AL, Aizenberg J. Finite-difference Time-domain (FDTD) Optical Simulations: A Primer for the Life Sciences and Bio-Inspired Engineering. Micron 2021; 151:103160. [PMID: 34678583 DOI: 10.1016/j.micron.2021.103160] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 10/20/2022]
Abstract
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.
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Affiliation(s)
- Dakota E McCoy
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA; Department of Materials Science and Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Anna V Shneidman
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, 9 Oxford Street, Cambridge, MA, 02138, USA.
| | - Alexander L Davis
- Department of Biology, Duke University, Campus Box 90338, Durham, NC, 27708, USA
| | - Joanna Aizenberg
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, 9 Oxford Street, Cambridge, MA, 02138, USA; Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
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9
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Yamashita K, Kunitsu K, Hattori T, Kuwahara Y, Saito A. Demonstration of a diffraction-based optical diffuser inspired by the Morpho butterfly. OPTICS EXPRESS 2021; 29:30927-30936. [PMID: 34614808 DOI: 10.1364/oe.436193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Optical diffusers are widely used in a variety of light sources to create uniform illumination over a wide field of view. Inspired by the diffraction-based light diffusion of the Morpho butterfly, here we demonstrate a novel diffuser which fulfils (i) high transmittance, (ii) wide angular spread, and (iii) low color dispersion. Two-dimensional nanopatterns were designed using optical simulations to enable simple fabrication. By introducing anisotropy into the surface nanopatterns, we achieved control of anisotropic light diffusion, which has been challenging for conventional diffusers. Next, the designed diffuser was implemented over a large area (100 × 100 mm2) via nanoimprint lithography. The obtained diffuser demonstrated a high transmittance of ∼85% and full width at half maximum (FWHM) of >60° with low color dispersion, outperforming conventional diffusers. Since the presented diffuser has the controllable diffusion properties with low light loss, it has many applications including LED lighting, displays, and daylight harvesting systems.
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10
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Heins A, Amann RI, Harder J. Cultivation of particle-associated heterotrophic bacteria during a spring phytoplankton bloom in the North Sea. Syst Appl Microbiol 2021; 44:126232. [PMID: 34399113 DOI: 10.1016/j.syapm.2021.126232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/21/2021] [Accepted: 07/05/2021] [Indexed: 11/29/2022]
Abstract
Seawater contains free-living and particle-attached bacteria. Only a small fraction is cultivable on plates. As free-living and particle-associated bacteria differ in their physiological traits, their cultivability on plates may coincide with particle association. Using filtration and Imhoff sedimentation cones, particles were collected during a spring phytoplankton bloom off Helgoland (North Sea) in order to obtain particle-associated bacteria as inocula. Direct dilution plating resulted in 526 strains from 3 µm filtration retentates and 597 strains from settled particles. Motile Gammaproteobacteria from the genera Pseudoalteromonas, Shewanella, Psychrobacter, Vibrio and Colwellia, as well as particle-attached Flavobacteriia affiliating with the genera Tenacibaculum and Gramella, were frequently isolated. As a result, a diverse collection comprised of 266 strains was deposited. Two strains were most likely to represent novel genera and 78 strains were probably novel species. Recently, a high-throughput cultivation study from the same site using seawater as an inoculum had retrieved 271 operational phylogenetic units (OPUs) that represented 88% of the 4136 characterized strains at the species level. A comparison of 16S rRNA gene sequences revealed that the collection obtained matched 104 of the 271 seawater OPUs at the species level and an additional 113 at the genus level. This large overlap indicated a significant contribution of particle-associated bacteria to the cultivable microbiome from seawater. The presence of 49 genera not identified in the larger seawater study suggested that sample fractionation was an efficient strategy to cultivate rare members of the planktonic microbiome. The diverse collection of heterotrophic bacteria retrieved in this study will be a rich source for future studies on the biology of particle-associated bacteria.
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Affiliation(s)
- Anneke Heins
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf I Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jens Harder
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.
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11
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Does Structural Color Exist in True Fungi? J Fungi (Basel) 2021; 7:jof7020141. [PMID: 33669274 PMCID: PMC7920071 DOI: 10.3390/jof7020141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/12/2021] [Accepted: 02/12/2021] [Indexed: 12/25/2022] Open
Abstract
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.
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12
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Mouchet SR, Luke S, McDonald LT, Vukusic P. Optical costs and benefits of disorder in biological photonic crystals. Faraday Discuss 2020; 223:9-48. [PMID: 33000817 DOI: 10.1039/d0fd00101e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
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.
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Affiliation(s)
- Sébastien R Mouchet
- School of Physics, University of Exeter, Physics Building, Stocker Road, Exeter EX4 4QL, UK. and Department of Physics, Namur Institute of Structured Matter (NISM), University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Stephen Luke
- School of Physics, University of Exeter, Physics Building, Stocker Road, Exeter EX4 4QL, UK.
| | - Luke T McDonald
- School of Physics, University of Exeter, Physics Building, Stocker Road, Exeter EX4 4QL, UK.
| | - Pete Vukusic
- School of Physics, University of Exeter, Physics Building, Stocker Road, Exeter EX4 4QL, UK.
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The cell organization underlying structural colour is involved in Flavobacterium IR1 predation. ISME JOURNAL 2020; 14:2890-2900. [PMID: 32873891 PMCID: PMC7784876 DOI: 10.1038/s41396-020-00760-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 08/14/2020] [Accepted: 08/24/2020] [Indexed: 12/03/2022]
Abstract
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.
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