Diatom Morphogenesis E-Book

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Serie: Diatoms: Biology and Applications
• Sprache: Englisch

Seitenzahl: 854

Veröffentlichungsjahr: 2021

Beschreibung

DIATOM MORPHOGENESIS A unique book presenting the range of silica structures formed by diatoms, theories and hypotheses of how they are made, and applications to nanotechnology by use or imitation of diatom morphogenesis. There are up to 200,000 species of diatoms, each species of these algal cells bearing an ornate, amorphous silica glass shell. The silica is structured at 7 orders of magnitude size range and is thus the most complex multiscalar solid structure known. Recent research is beginning to unravel how a single cell marshals chemical, physical, biochemical, genetic, and cytoskeletal processes to produce these single-cell marvels. The field of diatom nanotechnology is advancing as this understanding matures. Diatoms have been actively studied over the recent 10-20 years with various modern equipment, experimental and computer simulation approaches, including molecular biology, fluorescence-based methods, electron, confocal, and AFM microscopy. This has resulted in a huge amount of information but the key stages of their silica morphogenesis are still not clear. This is the time to reconsider and consolidate the work performed so far and to understand how we can go ahead. The main objective of this book is to describe the actual situation in the science of diatom morphogenesis, to specify the most important unresolved questions, and to present the corresponding hypotheses. The following areas are discussed: * A tutorial chapter, with a glossary for newcomers to the field, who are often from outside of biology, let alone phycology; * Diatom Morphogenesis: general issues, including symmetry and size issues; * Diatom Morphogenesis: simulation, including analytical and numerical methods for description of the diatom valve shape and pore structure; * Diatom Morphogenesis: physiology, biochemistry, and applications, including the relationship between taxonomy and physiology, biosilicification hypotheses, and ideas about applications of diatoms. Audience Researchers, scientists, and graduate students in the fields of phycology, general biology, marine sciences, the chemistry of silica, materials science, and ecology.

Leseprobe

Table of Contents

Cover

Title page

Copyright

Preface

Part 1 GENERAL ISSUES

1 Introduction for a Tutorial on Diatom Morphology

1.1 Diatoms in Brief

1.2 Tools to Explore Diatom Frustule Morphology

1.3 Diatom Frustule 3D Reconstruction

1.4 Conclusion

Acknowledgements

References

2 The Uncanny Symmetry of Some Diatoms and Not of Others: A Multi-Scale Morphological Characteristic and a Puzzle for Morphogenesis

2.1 Introduction

2.2 Methods

2.3 Results

2.4 Discussion

References

3 On the Size Sequence of Diatoms in Clonal Chains

3.1 Introduction

3.2 Mathematical Analysis of the Size Sequence

3.3 Observations

3.4 Conclusions

Acknowledgements

Appendix 3A L-System for the Generation of the Sequence of Differences in Size Indices of Adjacent Diatoms

Appendix 3B Probability Consideration for Loss of Synchronicity

References

4 Valve Morphogenesis in

Amphitetras antediluviana

Ehrenberg

4.1 Introduction

4.2 Material and Methods

4.3 Observations

4.4 Conclusion

Acknowledgments

References

Glossary

Part 2 SIMULATION

5 Geometric Models of Concentric and Spiral Areola Patterns of Centric Diatoms

5.1 Introduction

5.2 Set of Common Rules Used in the Models

5.3 Concentric Pattern of Areolae

5.4 Spiral Patterns of Areolae

5.5 Conversion of an Areolae-Based Model Into a Frame-Based Model

5.6 Conclusion

Acknowledgements

References

6 Diatom Pore Arrays’ Periodicities and Symmetries in the Euclidean Plane: Nature Between Perfection and Imperfection

6.1 Introduction

6.2 Materials and Methods

6.3 Results and Discussion

6.4 Conclusion

Acknowledgment

Glossary

References

7 Quantified Ensemble 3D Surface Features Modeled as a Window on Centric Diatom Valve Morphogenesis

7.1 Introduction

7.2 Methods

7.3 Results

7.4 Discussion

7.5 Conclusions

Acknowledgment

References

8 Buckling: A Geometric and Biophysical Multiscale Feature of Centric Diatom Valve Morphogenesis

8.1 Introduction

8.2 Purpose of Study

8.3 Background: Multiscale Diatom Morphogenesis

8.4 Biophysics of Diatom Valve Formation and Buckling

8.5 Geometrical and Biophysical Aspects of Buckling and Valve Formation

8.6 Methods

8.7 Results

8.8 Conclusion

References

9 Are Mantle Profiles of Circular Centric Diatoms a Measure of Buckling Forces During Valve Morphogenesis?

9.1 Introduction

9.2 Methods

9.3 Results

9.4 Discussion

9.5 Conclusion

Acknowledgement

References

Part 3 PHYSIOLOGY, BIOCHEMISTRY AND APPLICATIONS

10 The Effect of the Silica Cell Wall on Diatom Transport and Metabolism

Publications by and about Mark Hildebrand

11 Diatom Plasticity: Trends, Issues, and Applications on Modern and Classical Taxonomy, Eco-Evolutionary Dynamics, and Climate Change

11.1 Introduction

11.2 Model Species:

Phaeodactylum tricornutum

11.3 Transformation Mechanisms of

P. tricornutum

11.4 Future Advances in the Phenotypic Plasticity on

P. tricornutum

11.5 Conclusion

References

12 Frustule Photonics and Light Harvesting Strategies in Diatoms

12.1 Introduction

12.2 Light Spectral Characteristics and Signaling

12.3 Photosynthesis and Photo-Protection in Diatoms

12.4 Frustule Photonics Related to Diatom Photobiology

12.5 Frustule Photonics in Light of Niche Differentiation

12.6 Conclusion

References

13 Steps of Silicic Acid Transformation to Siliceous Frustules: Main Hypotheses and Discoveries

13.1 Introduction

13.2 Penetration of the Boundary Layer: The Diatom as an Antenna for Silica

13.3 Getting Past the Cloud of Extracellular Material

13.4 Adsorption of Silica Onto the Outer Organic Coat of the Diatom

13.5 Getting Past the Silica Frustule or Through Its Pores

13.6 Getting Past the Inner Organic Coat, the Diatotepum

13.7 Transport of Silica Across the Cell Membrane

13.8 Cytoplasm Storage and Trafficking of Silica to the Places of Synthesis of the Frustule Parts

13.9 Transport and Patterning of Silica Across the Silicalemma

13.10 Precipitation and Morphogenesis of the Nascent Valve Within the Silicalemma

13.11 Thickening of the Valve Within the Silicalemma

13.12 Exteriorization of the Valve

13.13 Future Work Needed

13.14 Conclusion

References

14 The Effects of Cytoskeletal Inhibitors on Diatom Valve Morphogenesis

14.1 Introduction

14.2 Cytoskeleton and Its Role in Cell Morphogenesis

14.3 Abnormalities of Diatom Valve Morphogenesis Induced by Cytoskeleton Inhibitors

14.4 Conclusion

Acknowledgment

References

15 Modeling Silicon Pools in Diatoms Using the Chemistry Toolbox

15.1 Diatoms

15.2 “Silicon Pools” Biology

15.3 Silica Particle Formation From Silicic Acid

15.4 Stabilization of “Soluble” Silica Species (Monosilicic and Disilicic Acids)

15.5 Chemical Mechanisms

15.6 Conclusions/Perspectives

Acknowledgments

References

16 The Mesopores of Raphid Pennate Diatoms: Toward Natural Controllable Anisotropic Mesoporous Silica Microparticles

16.1 Introduction

16.2 Morphology and Very Fine Ultrastructure of Diatom Frustules

16.3 Synthetic Mesoporous Silica

16.4 The Potential of Raphid Pennates’ Mesoporous Bio-Silica, Similarities, and Dissimilarities Compared With Synthetic MSM/Ns

16.5 Our Ability to Control the Diatom Frustule’s Ultrastructure

16.6 Conclusion

Acknowledgment

References

Glossary

Index

Also of Interest

End User License Agreement

Guide

Cover

Table of Contents

Title page

Copyright

Preface

Begin Reading

Index

End User License Agreement

List of Tables

Chapter 1

Table 1.1 A summary of the major tools used to study diatom frustule morphology ...

Chapter 2

Table 2.1 List of species considered and thumbnail, masked image examples for al...

Table 2.2 Valve formation simulation for eight centric diatom taxa and character...

Chapter 6

Table 6.1 The comparison of the bare hand measurements of 2D lattice parameters,...

Table 6.2 The comparison of the bare hand measurements of 2D lattice parameters...

Table 6.3 The comparison of the bare hand measurements of 2D lattice parameters...

Table 6.4 The lattice parameters and lattice types found in some of the studied ...

Table 6.5 A comparison between different 2D group arrays within the same microg...

Chapter 7

Table 7.1 Terms with parameters and coefficients of the

z

-equations for centric ...

Table 7.2 Ensemble surface features, mathematical operator, and numerical result...

Chapter 8

Table 8.1 Parametric 3D equations on the interval for a non-buckled disk and e...

Table 8.2 Parametric 2D equations on the interval for non-buckled and buckled ...

Table 8.3 Eigenvalues from upper Hessenberg matrices for centric diatom exemplar...

Chapter 9

Table 9.1 Circular centric diatom

Stephanodiscus

sp. and surfaces of revolution.

Table 9.2 Polynomials and coefficients of determination for centric valve profil...

Table 9.3 Polynomials and coefficients of determination for one valve profile fo...

Table 9.4 Length profiles normalized to 1 for nth-order polynomial curve fits in...

Chapter 12

Table 12.1 Summary of studies on the optical properties of different diatoms and...

Chapter 13

Table 13.1 Chemical composition of

Ulnaria ferefusiformis

[13.196] frustules cle...

Chapter 14

Table 14.1 Effects of various cytoskeleton inhibitors on valve morphogenesis of ...

Chapter 16

Table 16.1 Major classes of microorganisms with porous siliceous structures. Exa...

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Scrivener Publishing100 Cummings Center, Suite 541JBeverly, MA 01915-6106

Diatoms: Biology and Applications

Series Editors: Richard Gordon ([email protected]) and Joseph Seckbach ([email protected])

Scope: The diatoms are a single-cell algal group, with each cell surrounded by a silica shell. The shells have beautiful attractive shapes with multiscalar structure at 8 orders of magnitude, and have several uses. 20% of the oxygen we breathe is produced by diatom photosynthesis, and they feed most of the aquatic food chain in freshwaters and the oceans. Diatoms serve as sources of biofuel and electrical solar energy production and are impacting on nanotechnology and photonics. They are important ecological and paleoclimate indicators. Some of them are extremophiles, living at high temperatures or in ice, at extremes of pH, at high or low light levels, and surviving desiccation. There are about 100,000 species and as many papers written about them since their discovery over three hundred years ago. The literature on diatoms is currently doubling every ten years, with 50,000 papers during the last decade (2006-2016). In this context, it is timely to review the progress to date, highlight cutting-edge discoveries, and discuss exciting future perspectives. To fulfill this objective, this new Diatom Series is being launched under the leadership of two experts in diatoms and related disciplines. The aim is to provide a comprehensive and reliable source of information on diatom biology and applications and enhance interdisciplinary collaborations required to advance knowledge and applications of diatoms.

Publishers at Scrivener

Martin Scrivener ([email protected])Phillip Carmical ([email protected])

Diatom Morphogenesis

Edited by

Vadim Annenkov,

Limnological Institute, Siberian Branch of Russian Academy of Sciences

Joseph Seckback

The Hebrew University of Jerusalem, Israel

and

Richard Gordon

Gulf Specimen Marine Laboratory & Aquarium, Panacea, FL, USA and Wayne State University, Detroit, MI, USA

This edition first published 2022 by John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, USA and Scrivener Publishing LLC, 100 Cummings Center, Suite 541J, Beverly, MA 01915, USA© 2022 Scrivener Publishing LLC

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Library of Congress Cataloging-in-Publication Data

ISBN 978-1-119-487951

Cover image: Colored scanning electron micrographs (SEMs) of a morphogenetic sequence of the diatom Fragillaria capucina var. mesolepta by Dr. Mary Ann Tiffany, Biology Department, San Diego State University, USA Sample taken from Lake Murray (a freshwater San Diego Reservoir) on 3/18/2000.

Cover design by Russell Richardson

Set in size of 11pt and Minion Pro by Manila Typesetting Company, Makati, Philippines

Printed in the USA

10 9 8 7 6 5 4 3 2 1

Preface

Diatoms comprise a large, unicellular eukaryotic algal group that thrives mainly in aqueous environments: in fresh water, and in ponds, lakes and oceans. They may be attached to benthic substrates, in moist habitats or in floating debris and on macrophytes, and as phytoplankton; they form a substantial basis of aquatic food webs. They are ubiquitous, being distributed among various ecological locations. Among this group are some extremophiles with varying features, such as living in high temperatures, surviving desiccation, or in ice and at extreme ranges of pH. Some 20%-30% of the oxygen we breath is produced by diatom photosynthesis.

Vegetative cells of diatoms are diploid (2N), and meiosis can take place, producing male and female gametes fusing to zygotes which grow to auxospores.

One of their specific features is that their chemical composition includes siliceous (glassy) cell walls (frustules). Their exoskeleton is made of two halves called “valves” that fit inside one another, secured by silica “girdle bands”.

Diatoms’ fine structure is very impressive as revealed by transmission electron microscope, scanning microscope, and atomic force micrographs. The appearance of their cells is strikingly unique, and their shells are beautiful attractive shapes, with 60,000 to 200,000 species.

Why Valve Morphogenesis is Important?

Because there is so much detail in their silica wall shapes, spanning 8 orders of magnitude, diatoms are model organisms for single-cell morphogenesis. The problem of single cell morphogenesis has a long history, as yet unsolved, and perhaps diatoms rather than desmids and ciliates will now lead the way, especially given their 200 million years fossil record. This may further be because diatoms serve as a source of biofuel, food supplements and lipids and serve as significant material for nanotechnology. Thus, they are of very wide interest.

This volume focuses on the morphogenesis of diatoms, namely, the formation of their shape and the initial developmental steps.

The chapters were contributed by experts on morphological diatoms. The authors stem from the USA, Russia, Denmark, Germany, Greece, Israel, and Portugal.

Topics Addressed in This Volume

Topics include computer simulation of morphogenesis, silicic acid to silica frustules, inhibition in valve morphogenesis, pores within frustules, mesopores of pennate diatoms, frustule photonics and light harvesting, clonal chains, silica cell wall, geometric models of centric diatoms, morphology, surface features, buckling of valve morphogenesis, on mantle profiles, genetic-biochemical approaches, modeling silicon pools, valve morphogenesis, diatom teratology in taxonomy, phenotypic plasticity, geometric and morphometric analysis, silica morphogenesis in sister algae, and the uncanny symmetry of some diatoms.

This volume is the third book in the series Diatoms: Biology and Applications. The first book, Diatoms: Fundamentals and Applications appeared in 2019, and was edited by Joseph Seckbach and Richard Gordon. The second book, Diatom Gliding Motility, was published in September 2021 and is edited by Stanley A. Cohn, Kalina M. Manoylov and Richard Gordon.

We would like to thank the authors, the reviewers, the guest editor (Vadim V. Annenkov), and our publisher Martin Scrivener of Massachusetts, USA.

Joseph SeckbachHebrew University Jerusalem, Israel September 2021

Part 1GENERAL ISSUES

1Introduction for a Tutorial on Diatom Morphology

Kalina Manoylov1* and Mohamed Ghobara2

1Dept. of Biological & Environmental Sciences, Georgia College and State University, Milledgeville, GA, United States

2Department of Physics, Freie Universitat Berlin, Berlin, Germany

Abstract

Diatoms are an exceptionally successful group of unicellular microalgae with a large contribution of global primary production in aquatic environments and contributing a significant amount of oxygen to both hydro- and atmospheres. They are fascinating throughout their life and even after death, thanks to their unique cell walls made from ornamented silica. The diatoms include centric species, which may have radial or polar symmetry, and pennates, which include araphid, monoraphid, and biraphid species. Several applications have utilized diatomite, i.e., the fossil form of diatom frustules. To date, many diatoms’ secrets have been understood; however, there are still more hidden. Thus, there is a need for more research on diatom basic biology and applications. Seeking this goal, more people should be encouraged to work on diatoms. Often novice researchers are overwhelmed by the terminology associated with the diverse morphology, the discrepancy between expected features for published descriptions, and the actual observation of those complex 3D organisms, which can be a barrier for more progress. Here, we provide a brief introduction to the beginners with a guide to approach the complex diatom morphology focusing on the tools that can be used for its study.

Keywords: Diatom morphology, tutorial, LM and SEM, frustule morphology

1.1 Diatoms in Brief

Diatoms are unicellular, eukaryotic, microscopic algae (range from 1.5 μm to 5 mm in length, or diameter [1.9]), which maintain large population numbers and contribute considerably to the carbon and oxygen cycle on a global scale [1.8]. This ecologically successful group of algae is present in all aquatic habitats e.g. [1.1, 1.2] and even extends to humid terrestrial places. In aquatic habitats, diatoms are present in the photic zone, i.e., the region of water that light strongly penetrates, as well as in the benthic zone, i.e., the lowest level of water adjacent to the bottom with dim light conditions, depending on water column height and water’s turbidity. Diatoms can exist as planktonic (i.e., suspended in the water column), benthic (i.e., living near the bottom), epiphytic (i.e., adhered to aquatic plants [1.19], Figures 1.2c–d), or epizoic (i.e., adhered to a wide range of marine organisms such as crustaceans, mollusks, and vertebrates [1.19, 1.38]), or epilithic (i.e., attached completely or partially to submerged rocks). The adhesion ability of some diatoms is related to their mucilage secretion from specialized areas within their rigid cell walls (such as examples shown in Figures 1.1d and 1.2c–d). Some diatoms can form colonies in different arrangements such as chains and ribbons (examples shown in Figures 1.1 and 1.2).

Diatoms are a unique group of microalgae for several reasons, but one of the most notable and unique differences is the glass cell walls they possess [1.45]. This cell wall is called the “frustule” and is composed of amorphous hydrated silica that gives it unique properties. In general, the frustule is composed of two pieces that fit together like a petri-dish, meaning that the lower part of the frustule, called the hypotheca, sits inside of the upper part of the frustule, called the epitheca. The frustule volume extends by adding strips of silica called girdle bands (cingulum) to the mantle, i.e., the curved edge of the valve. It should be noted that there are plenty of frustule morphologies that vary between taxa.

Diatoms reproduce both asexually (visible in Figure 1.6) and sexually. Most of the time, they reproduce asexually via binary fission through adding new hypovalves to the parent valves. Those new hypovalves are synthesized inside the silica deposition vesicle (SDV). Only after the new hypovalves have completely synthesized and the protoplast cleavage, as well as the exocytosis of siliceous parts, has occurred, the final splitting apart will occur, leaving two daughter diatoms in place. Because the SDV forms inside of each new cell before splitting into two, each new cell creates a new interior of the petri-dish structure. What this means is that the cell that originally contained the upper part of the petri dish (the epitheca) remains the same size, whereas the cell that originally contained the lower part of the petri-dish (the hypotheca) becomes smaller, since it has now built a smaller hypovalve to fit into it. Repeated cell division, therefore, leads to some part of the resulting population becoming smaller and smaller. Were asexual reproduction the only method by which diatoms reproduces, this could lead the population eventually to become vulnerable to dying out, but diatoms are ingenious and have gotten around this problem. At some point, sexual reproduction is initiated by a number of steps, including meiotic divisions to produce male and female gametes. These cells can find each other, fuse to form a zygote and create a structure known as an auxospore, out of which a new large cell of the diatom species will form, restoring its optimal size, which also depends on the environmental circumstances surrounding the auxospores. Some new research proposes chemical communication with pheromones between the male and female gametes [1.20].

Figure 1.1 Living diatoms as observed under LM, brightfield. (a) Two living cells of Actinoptychus senarius (Ehrenberg) Ehrenberg at the valve view. (b) The valve view of a single living cell of Coscinodiscus wailesii Gran and Angst. (c) The girdle view of a single living cell of Coscinodiscus granii L.F. Gough. (d) Two living cells of Achnanthes brevipes C. Agardh at the girdle view attached to each other with a prolonged stalk for the attachment to the substrate. (e) A living colony of Stephanopyxis turris (Greville) Ralfs with visible linking spines. (f) A living colony of Odontella longicruris (Greville) M.A. Hoban with discoid chloroplasts. Copyright reserved Mary Ann Tiffany, used with her permission. The identification was carried out by Mary Ann Tiffany. All the scale bars are 50 μm.

Figure 1.2 Live centric (a, b) and pennate (c–h) diatoms. (a, b) Pleurosira laevis (Ehrenberg) Compère shown from girdle view, frustules with numerous girdle bands in straight filaments with discoid chloroplasts, chains connected with mucilage pads released from ocelli; in (b), visible diameter size restoration within the chain; (c, d) Epiphytic diatoms on Cladophora glomerata (Linnaeus) Kützing, in (c) focus on Cocconeis spp. With visible one flat C-shaped plastid; in (d) focus on Rhoicosphenia spp.; (e) Cymbella sp. partial valve and girdle views, visible chloroplast bridge connecting the chloroplast plates; (f) Eunotia cf. camelus Ehrenberg in girdle view with visible discoid chloroplasts; (g) Amphora ovalis (Kützing) Kützing with H shaped chloroplast; (h) Rhoicosphenia sp. girdle view with visible lobes of the plastid. Scale bars, 10 μm. These micrographs were obtained and identified by KMM.

Figure 1.3 Specific diatom morphology gleaned from images with whole and partial valves views of Navicula oblonga (Kützing) Kützing; (a) live linear-lanceolate cell with visible two plates like brown chloroplasts, visible linear striae, and proximal raphe ends deflected slightly toward the secondary side. (b) Valve view after cleaning, axial area is linear, widening toward the central area and about twice the width of the raphe. The central area orbicular. The raphe is lateral, becoming filiform near the proximal ends, which are simple. Central striae do not reach valve edge. These micrographs were obtained and identified by KMM.

Details shown:

Central area is more or less orbicular and two to three times wider than the axial area. Proximal raphe ends are simple and barely wider than the raphe. Striae are finely lineate and the individual areolae are difficult to distinguish.

Round, subsidiary vacuoles on each side of the nucleus visible behind the glass cell wall and chloroplasts; axial area outlines by lineate striae.

Terminal bent striae (terminal striae convergent at the margins and bent back toward the central area). Striae are radiate next to the axial area.

Voigt discontinuity identifies the secondary side of the valve morphogenesis. Ontogeny in diatoms varies with morphology; in Naviculoid diatoms, the secondary side shows the completion of silica deposition around the raphe.

Distal raphe positioned on the broad, rounded apices and curved toward the primary side of the valve in the opposite direction when compared to the proximal raphe ends. Scale bars, 10 μm.

Frustule morphogenesis, deposits SDVs and needs more research with new tools. However, it has been established that the silica morphogenesis of centric species will begin at the center of the valve, and it begins by creating a primary rib in pennate species [1.21]. Completion of the sternum around the raphe slit morphologically can be identified with the Voight discontinuity (Figure 1.3b). From that onset within the mother frustule, the silica will continue to form outward to complete the shape as well as inward to create more layers, with the oldest silica being on the most outside layer [1.46]. The silicic acid (or its anions) is taken from the environment, condensed, associated with proteins synthesized by the endoplasmic reticulum and packaged in a globular vesicle in the Golgi apparatus. Then finally, these vesicles (silica deposition vesicles) are transported by microtubules, likely in a genetically predetermined pattern, and delivered to the new valve interface. These are not the only groups that pull silicic acid (an inorganic compound contains silicon) out of the water and use it to make a frustule, but diatoms do it uniquely.

Diatom frustules are porous with multilayer, multiscalar porosity, a property that is unique for each species, giving frustules their beautiful ornamentation [1.17]. The major bigger pores within the valves are called “areolae” and usually arranged in rows known as “striae”, which could be either branched or not. In the most general way, diatoms can be divided into centric and pennate diatoms, which are classified based on the valve symmetry. Centric diatoms are radially symmetric and lack raphes. Pennate diatoms usually have bilateral symmetry and there can be no, one, or two raphes. Pennate diatoms can further be classified based on variations in the position of the raphe on valve. The raphe is used for motility [1.4] and attachment [1.12]. Sometimes, the frustules are also covered in spines, which can allow some species to hook together and form chains (Figure 1.1e).

The frustule’s morphological features of diatoms are required for identification. Specialized terminology has been collected in [1.5–1.7, 1.15, 1.16], and a general guide to the literature is in [1.10]. Characters continue to be discovered and new descriptive terminologies are proposed [1.23].

1.2 Tools to Explore Diatom Frustule Morphology

The beauty of diatoms was missed until the early, curious microscopists started observing ambiguous glassy microorganisms under their optical microscopes in the 18th century [1.22, 1.38]. Although the light microscope (LM) helped us to reveal the diatoms’ world, diatom frustules also helped the microscopists in developing and testing the quality and resolution of their optical microscopes [1.24, 1.25]. Since the nineteenth century, several works have been published on diatoms, its morphology, and taxonomy by remarkable workers including Kützing, Schmidt, Ehrenberg, Grunow, Hustedt, Krammer, Lange-Bertalot, and more (see references in Round et al. [1.38]). They described both living cells and clean frustules extensively using LM. The unique structure of diatom frustules under LM, with a variety of shapes and symmetries, has captured a wide interest; however, most of the diatom’s real art, at the nanoscale, was kept hidden. The limitations for observing frustule ultrastructure, especially details below 200 nm, were solved after the invention of the electron microscope [1.26]. In 1936, the transmission electron microscope (TEM) was used to capture the first micrograph of a diatom frustule [1.26, 1.27], using it as a test object for the quality and resolution of TEM. After that TEM was used to explore diatom ultrastructure. Following, the scanning electron microscope (SEM) was invented and used extensively as a more effective tool for exploring frustules morphology and ultrastructure [1.24, 1.28, 1.36, 1.38].

The details observed using the SEM and TEM reflected the beauty of diatoms when many hidden details became observable. For instance, some bright striae under an optical microscope appear as arrays of fine pores under the electron microscope (Figure 1.5a). It was, to some extent, a kind of revolution for diatom classification and taxonomy with the morphological details that became available down to 15 nm with SEM and below 10 nm with TEM (Figure 1.5b). Nowadays, the observation of diatom frustule morphology and ultrastructure using LM, SEM, and TEM became routine work for people working on ecology, environment, forensic, nanotechnological, and other applications that concern frustule ultrastructure, monitoring diatom species, and taxonomy.

Although 2D information can be collected from LM and TEM and the 3D-shape appeared under SEM, the information about the surface topology, internal ultrastructure, and siliceous element relationships within diatom frustules was missing. Therefore, more tools were evolved and involved in the exploration and understanding of the 3D complex ultrastructure of the frustule, which could be the reason for their various natural features, including unique photonic, mechanical, and hydrokinetic properties [1.9, 1.45]. The new tools include the atomic force microscope (AFM) and the focused ion beam SEM (FIBSEM) [1.32, 1.34, 1.35, 1.41].

Figure 1.4 Cleaned diatoms in valve (g, h–j, m–r, u, v) and girdle views (a–f, k, l, s, t, w, x). (a–e, g) Rhoicosphenia spp., frustules are clavate and strongly flexed, one valve is concave with long raphe branches and the other valve convex with shortened raphe, different depth pseudosepta visible; (f, k, l) Gomphonema spp. showing valve heterogeneity; (h) Gomphonella olivacea (Hornemann) Raben. (i) Planothidium lanceolatum (Bréb. Ex Kütz.) Lange-Bert, rapheless valve shown with asymmetrical central area containing depression; (j) Geissleria cascadensis (Sovereign) Stancheva and S. A. Spaulding, valves elliptic, with cuneate apices, coarse areolae, three pairs of annulae are present at each apex; (m) Planothidium delicatulum (Kütz.) Round and Bukht. Rapheless valve shown, lacking a central area and two middle striae spaced distantly. Cleaned diatoms in valve (g, h–j, m–r, u, v) and girdle views (a–f, k, l, s, t, w, x). (n) Gomphonema sp. valve heteropolar wider in the middle, axial area narrow, central area irregular outlined by two shortened striae and opposite to a single striae finishing with an isolated pore, striae parallel toward the headpole, radiate toward the foot pole; (o) Amphora ovalis, dorsal fascia visible and dorsal striae interrupted transapically by intercostal ribs; (p) Gomphonema micropus Reichardt lanceolate valve with headpole widely drawn out and wider than foot pole, striae radiate, central area unilaterally rectangular with shortened central stria, on the opposite side longer striae finishing with a stigmoid; (q) Navicula genovefae Fusey valve linear-lanceolate with rostrate broadly rounded apices, punctate striae radiate and curved, becoming nearly parallel at the apices, less dense around the well-defined central area; (r) Cocconeis placentula Ehrenb. Valves elliptic, striae radiate and interrupted by a hyaline ring positioned close to the valve margin, siliceous bridges (imbriae extending from valvocopula) visible; (s) Amphora pediculus (Kütz.) Grunow focus from dorsal site of two frustules; (t, u) Caloneis sp. on girdle view striae continue on valve mantle, on the linear valve view with rounded apices, axial area is narrow, broadening to a transverse fascia; (v) Navicula cryptocephala Kütz. Valve lanceolate with protracted apices and visible large, circular central area; (w) Mastogloia pseudosmithii Sylvia S. Lee, E. E. Gaiser, Van de Vijver, Edlund, and S. A. Spaulding, evenly sized partecta (chambers on the valvocopula) on both valves; (x) Navicula cf. tripunctata (O.F. Müll.) Bory. Scale bar, 10 μm. These micrographs were obtained and identified by KMM.

In 1992, the first observation of diatoms using an AFM has been done [1.33]. In general, AFM is used as an advanced tool to explore diatom ultrastructure providing information in the Z-direction, with the ability to understand the surface topology of the frustule parts with a nanoresolution. For instance, AFM observations of Coscinodiscus sp. clean valves revealed a distinct dome topology for the cribellum, which was not observed before [1.34]. At the beginning of the current century, AFM was used in several works for understanding the nanoscale ultrastructure and topology of frustule surfaces in a 3D manner. Today, AFM is also used to explore the organic envelope, micromechanical properties, and to understand the biomineralization processes of diatom frustules [1.35]. Luis et al. [1.35] can be considered a good review for starting AFM studies on diatom frustules.

Figure 1.5 (a) SEM of a single cleaned partially open frustule, two overlapping valves, of Nitzschia palea(Kützing) W. Smith, and scale bar is 5 μm. The rows of pores (striae) that observed here cannot be observed under LM for this species. (b) TEM of a close-up in Navicula sp. valve showing the hymenate pore occlusions that will not be observed under SEM; scale bar is 200 nm. These micrographs were obtained and identified by MG.

Figure 1.6 A cross-section at the center of Coscinodiscus sp. cell collected and treated while binary fission process was in progress, fabricated and captured by FIB-SEM. Reproduced from Xing et al. [1.42] under a Creative Commons Attribution 4.0 International license.

Furthermore, diatom valves seem to have a complex inner ultrastructure that cannot be understood completely by observing the internal and external view of a given valve surface using the previously mentioned tools. Although the multilayer, multiscalar porosity can be observed easily using such techniques, the internal anatomy and relations of the siliceous elements of the frustule cannot be understood [1.41]. It was usual to wish that the observation of a broken valve or girdle band at the right site and right angle would help, otherwise, the complex inner structure remained unseen [1.41].

Thus, another advanced method was required for understanding the inner structures and spatial relationships of the siliceous elements of a given diatom frustule. The FIB-SEM was introduced as a solution for such a problem by cutting the diatom frustule parts at nanoresolution to reveal the inner complex ultrastructure of a given valve or frustule (Figure 1.6) [1.41]. Suzuki et al. [1.40] was the first work introduced using FIB-SEM for making a cross-section in diatoms. Only a few articles are available using FIB-SEM and the field is still growing. The acquired data using FIB-SEM could be used to reconstruct the overall 3D geometry of diatoms to carry out further computational simulations necessary for diatom nanotechnology applications.

Table 1.1 A summary of the major tools used to study diatom frustule morphology and its ultrastructure.

LM

TEM

SEM

AFM

FIB-SEM

The date of first known observation of diatoms using the tool

Anonymous, 1703 [1.22]

Krause, 1936 [1.27]

Mid of 1960s [1.24]

Linder

et al

., 1992 [1.33]

Suzuki

et al

., 2001 [1.40]

Up-to-date resolution

The maximum resolution of the common compound optical microscope can be around 200 nm. Recently, the resolution was enhanced (down to 97 nm) using special kind of lenses [1.37].

Up-to-date, the highest TEM resolution could be down to 50 picometer or even lower [1.29].

The details less than 15 nm was not resolved under most of SEMs. Recently, an outbreak has been achieved, and the resolution of SEM could be below 1 nm [1.39].

Recently, the resolution can be below 1 nm.

Having SEM as the microscope part of the device. Thus, the resolution is dependent on this SEM.

When we should use?

Observation of the presence or absence of diatoms in a sample. Identification of diatoms on the genus level. Enumeration of diatom frustules for different purposes.

Observation of the fine porosity (mesopores) present in some genera, like raphid pennates (

Figure 1.5b

).Observation of thin cross-sections in a valve or a girdle band.Observation of the cytoplasmic components of thin cross-sections of living cells (living cells anatomy).

Observation of the outer ultrastructure including most porosity.Observation of the overall 3D ultrastructure of the frustule or different parts.Identification at the species and subspecies level.

Observation of the 3D topology of a diatom frustule or its components.Measuring forces related with both living diatoms and its cleaned frustules.

Understanding the inner ultrastructure of diatom frustule or its parts by cutting cross-sections through it.Observation of the siliceous elements structural relations within the frustule.Observation of the whole 3D ultrastructure of the frustule via the 3D reconstruction.

The disadvantages

The observations for most of the ultrastructure details will be limited. Either the girdle view or the valve view will be available.

Only the tiniest parts of the valve, like pore occlusions, will be observed.The high energy electron beam may damage some sensitive samples, so it should be used wisely.

The samples must be coated with a conductive layer, which in turn could change the nano texture of the frustule silica and probably pore sizes, thus the thickness and smoothness of the conductive layer should be optimized and be thin as possible without getting nanoparticles on the top.The high energy electron beam may also damage some sensitive samplesThe regular resolution keep the pore occlusions of very fine porosity (below 10 nm) hidden.

The frustules must fix to the substrate before measuring.A very sensitive tool with complicated precautions to follow to get the desired results.

This technique sometimes needs more sophisticated preparation of the samples and more sophisticated work to reconstruct the frustule or its parts, however it worth.Related with the presence of the device, which usually is not available for all research groups.

Finally, all the techniques mentioned were summarized in Table 1.1 to help beginners and students choose between different tools on-demand.

1.3 Diatom Frustule 3D Reconstruction

Toward the complete understanding of the 3D structure of a given diatom frustule, a comprehensive 3D model can be created from the data collected from different characterization techniques. This approach, which is designated as the 3D reconstruction of diatom frustules, can be used for different purposes but is mainly for computer modeling. Oncoming tools for the 3D reconstruction of diatom frustules are FIB-SEM [1.32, 1.42] and digital holographic microscopy (DHM) combined with SEM [1.30]. The combination of DHM and SEM or AFM might give the ability to model and visualize microscopic 3D objects with a high resolution in all directions [1.30]. Hildebrand et al. [1.32] introduced the ability for the 3D reconstruction of subcellular architecture using FIB-SEM with new insights into the architecture and synthesis process of both the siliceous and organic components inside the cell. Xing et al. [1.42] is an inspiring reference for the 3D reconstruction of diatom frustule using the 2D image series resulting from FIB-SEM.

1.3.1 Recommended Steps to Understand the Complex Diatom Morphology: A Guide for Beginners

1. Fresh samples, if available, which means the sample is not diatomite (i.e., the fossil form of diatom frustules) [1.31], allow evaluation of the physiological state of the population at the time of collection. The features of living cells might help in the identification process, through the descriptions of colonial forms, cell attachment, extruded materials, plastids, and nucleus position (for instance see Figures 1.1 and 1.2). Since diatom frustules are rigid silica, they appear from two different viewpoints, the girdle view (from the side) and the valve view (from the front) under LM Figure 1.4. Some genera are easily identifiable in girdle view, such as Mastogloia and Amphora pediculus (Kütz.) Grunow, others are not. Lately, confocal microscopy uses are very promising [1.3, 1.13], also combining microscopic and molecular information allowed reclassification of a population in culture annotated as a radial centric species related to Leptocylindrus danicus Cleve, as an araphid pennate species in the staurosiroid lineage, within the genus Plagiostriata [1.14].

2. The selection of the suitable cleaning procedure, depending on the source of diatoms, is a crucial step to extract the siliceous frustule parts. Routinely, diatoms are identified and enumerated without their protoplasts where striae morphology & number, raphe shape, and other morphological characteristics could be verified for identification (details in Figures 1.3b and 1.4). Among the best guides for the cleaning process could be Wang et al. [1.43]. More gentle cleaning methods (e.g., H2O2 method) should be considered in case we need to preserve mesopores (i.e., fine pores with diameters ranging from 50 to 3 nm that present on pore occlusions, which cover the areolae from inside or outside [1.48]) especially within genera, such as raphid pennate diatoms (Figure 1.5b).

3. Preparation of permanent slides should be carried out for LM observations using a suitable high refractive index mounting medium such as Naphrax and Hyrax [1.44]. Figure 1.4 considers a good example of observing cleaned frustules fixed in a permanent slide under LM.

4. Using LM to observe the 2D morphology of the cleaned valve and girdle bands to assign the most similar genus and, if possible, the species. The overall morphology, striae, valve symmetry, ribs, and the presence of raphe will be clear under LM; however, the pores, the spines, and special structures within the valve and girdle band might be not observable due to their smaller size. Though, in other few cases, the areolae might be observable even before the frustule cleaning procedure, especially for large taxa (Figure 1.1b). Valve outline, valve ends, shapes of sturdy, and hyaline silica (not penetrated with striae or other openings) should be recorded. Classical diameter in centric diatoms from valve view or length and frustule depth form girdle view allows verifications of descriptions from literature. Moreover, the frustule silicification rate can be observed under LM reflects information about the environmental condition that surrounds the living cells.

5. Using SEM, after suitable sample preparation and coating with a conductive material [1.38], to observe the ultrastructure of the valve and girdle bands and define the species accordingly. Under SEM, the valve will have two different viewpoints, the internal and external view. Some important criteria should be recorded using SEM including:

• the areolae structure from the internal and external valve view,

• striae (the periodic rows of areolae) shape,

• striae count in 10 microns or fibulae (in Nitzschioid diatoms [1.11], folds in Surirelloid diatoms [1.18]),

• sternum size and shape (in Fragilaroid and Naviculoid pennate diatoms),

• nodule zone or annulus shape and its number (if more than one present),

• raphe structure and shape of raphe at the end and in the middle of a valve,

• the pore occlusions (if observable),

• the presence of spine or other projections like fultoportulae and labiate processes,

• the shape and porosity of the girdle bands should also be recorded.

* For calculating the averages and ranges of the measured morphological data at least 10 specimens should be measured. Acid cleaned material allows observation of details but often causes change or collapse of the frustule’s three-dimensional ultrastructure, thus the selection of the most suitable cleaning procedure might be a crucial step to observe the diatom ultrastructure properly. It worthy to be noted that the observation of the frustule parts using SEM might be sufficient for genus and species identification without the need of LM; however, some important descriptions for identification are based on the LM appearance of the valve.

6. Observing the ultrastructure using TEM [1.38], if necessary and missing details did not appear under SEM, such as the hymenate pore occlusions of raphid pennate (see, for example, Figure 1.5b).