Chapter 1: Biogenic Silica: Sources, Structure and Properties Free

Biogenic silica (bSi) can simply be demarcated as silica or silicon dioxide that is produced by living organisms. The other terms that are frequently used instead of bSi are opal, biogenic opal, and amorphous opaline silica.^1,2  Chemically bSi is hydrated silica (SiO₂·nH₂O) and it is noteworthy to mention that many plants and animals depend on bSi for their survival. For instance, grasses and other plants contain minute Si content known as phytoliths. Also, silicifiers play a very important role in silica deposition. These organisms can absorb dissolved silicon from their surroundings and convert it into glassy skeletons.³  Silicifiers, which include macro-organisms like siliceous sponges and other micro-organisms (silicoflagellates, diatoms, rhizarians) and several types of choanoflagellates, are among the most significant aquatic organisms.⁴  On a global scale, silicifying organisms such as diatoms that depend on photosynthesis effectively use large amounts of silicon in addition to nitrogen, phosphorus, and inorganic carbon. This interconnection influences the biogeochemistry of these elements and plays a crucial role in capturing atmospheric CO₂ within the ocean. The dissolved silicate, which is needed by the organisms to synthesize their amorphous silica frustules, strongly influences diatom productivity.^5–7  Rhizarians, choanoflagellates, and sponges that are heterotrophic organisms generate bSi without relying on the photoautotrophic processing of carbon (C) and nitrogen (N).

In aquatic ecosystems, the production of silicic acid arises from the weathering of the Earth’s crust by rainwater enriched with CO₂. This process plays a pivotal role in regulating atmospheric CO₂ levels.^6,8  The primary sources of bSi include diatoms, sponges, and grasses/plants. Diatoms, are an important group of algae, and they are also known for their intricate Si cell walls. These microscopic algae extract Si from their environment and use it to construct protective outer shells or frustules.⁹  In the case of sponges, certain types of sponges incorporate Si into their skeletons. Siliceous sponges are an example, and they often have intricate spicules made of Si.¹⁰  Some plants, particularly grasses, can accumulate Si in their tissues. This is often seen in grasses growing in environments with high Si concentrations in the soil.¹¹  In 1989, Wilding et al. estimated that bSi content ranges between 3 to 20% in most soils. These numbers indicate that opal can frequently surpass the concentrations of potassium, calcium, magnesium, sodium, and phosphate and make up a sizeable portion of the Si component of various types of soils. Currently, sodium silicate (Na₂SiO₃), a silica precursor, is produced by smelting sodium carbonate (Na₂CO₃) with quartz or sand to extract Si. Although Si has been successful in applications such as electrical components, however this approach is less practical because large amounts of energy is needed.^12–14  Hence, to avoid the limitations associated with the conventional techniques of Si extraction, innovative green techniques that are not only environmentally friendly but also cost-effective need to be explored.

Moreover, bSi is an adsorbent to eliminate heavy metal ions (such as lead, mercury, zinc, and nickel) from wastewater streams. Additionally, bSi is employed as a catalyst in the synthesis of zeolites and mesoporous silicon, as well as in drug delivery systems.^15,16  Moreover, Si particles are needed for various industrial applications, which require high purity and controllable textural properties. Different degrees of purities of bSi are needed, depending on the intended application. Generally, it is sufficient to have Si purity of at least 97% db (dry basis) for use as pozzolan in concrete. On the other hand, high-tech applications like solar applications and electronics demand a purity of Si almost equal to 99.9 wt% db.^17,18  For example, achieving synthesis of advanced materials requires low carbon content and high silicon purity.¹⁹  Similarly, for filler applications, desirable attributes include whiteness and suitable particle size,²⁰  while an amorphous structure and an optimized pore system (resulting in high specific surface area) are also important considerations.^19,21 

It is commonly known that Si serves as a precursor for a variety of applications, including chromatography, electronic coating, ceramics, concrete, and catalysts, optical materials as well as anticorrosion agents.^22–27  Also, there are many industrial uses for Si, such as anti-caking food additives, viscosity control, beverage clarification, anti-foaming agents, dough modifiers, and excipients in vitamins and medications.²⁸  Hence, there are several applications related to bSi but due to the high processing temperature, using high-purity Si in industrial applications is expensive. Therefore, using alternatives such as crop residues for Si synthesis has been identified as a good way to combat sustainability issues and lower the processing costs.²⁷  The subsequent sections address the possible sources, extraction methods and applications of bSi in detail, along with a brief discussion of the structure and general properties of bSi.

Numerous organisms, especially in the ocean, produce bSi, which is essential for marine ecosystems. Studying nutrient dynamics, carbon cycling, and ecosystem structure in both aquatic and terrestrial environments requires an understanding of the sources and cycling of bSi.^29,30  Furthermore, the accumulation of bSi in sediments adds to the geological record and can be examined to learn more about the environmental conditions that existed in ancient times. Both terrestrial and aquatic ecosystems are the sources of bSi. Diatoms are principally responsible for the production of bSi in aquatic ecosystems. Diatoms are a special kind of algae that have a Si cell wall known as a frustule.³¹  These fragments can gather in sediments to form deposits called diatomaceous earth. Plants, especially some kinds of grasses, are important for the accumulation and deposition of bSi in terrestrial ecosystems. The procedure entails the roots of plants absorbing dissolved silica (DSi) from the soil, moving it throughout the plant, and then depositing it in plant tissues. Plants require Si to grow, and different crops store differing amounts of Si in their tissues. Phytoliths are the most prevalent form of bSi in plants. Plant cells give rise to rigid, microscopic structures called phytoliths made of Si. They give structural support to the plant and aid in defending it against diseases and herbivores.^32–34  Genetic variables, environmental factors, and soil silicon availability all affect the buildup of Si in plant tissues. Therefore, it is possible to categorize the sources of bSi as terrestrial or aquatic as depicted in Figure 1.1.

Traditionally, it has been believed that soil/geological processes fuelled by Si weathering are primarily responsible for the transfer of Si from the land and also for the cycling of Si on land. Thus, the final export of DSi crucial for eutrophication and carbon sequestration in oceans and coastal zones is regulated by the comparatively gradual weathering processes involving both primary and secondary silicate minerals.^29,35  However, a growing body of research now indicates how crucial biological activities are for both global Si cycle and terrestrial Si mobilisation. Soil microbiota and land plants promote the weathering of silicate minerals. Consequently, vegetation takes up DSi as orthosilicic acid (H₄SiO₄), released through weathering. This leads to significant accumulations of silicon stored as amorphous bSi within ecosystem biomass and soils, predominantly in the structure of plant siliceous bodies known as phytoliths as shown in Table 1.1.^36,37  After plant decomposition and litterfall, the highly soluble bSi in biomass returns to the topsoil. Significant amounts of bSi have been discovered in wetlands, woods, and grassland soils.³⁸ 

The realization that silicon is biologically necessary for plants is one of the foremost results of the data accumulated through numerous studies conducted on plants. Also, plants lacking in Si are frequently structurally weaker than those with sufficient Si, exhibit unusual growth, development, viability, reproduction, and are more vulnerable to abiotic and biotic stresses. Plants readily assimilate silicon in the dissolved form (i.e., DSi), precipitating as solid amorphous silicon. Silicon is present in diverse tissues, including the epidermis of leaves, stems, roots, and reproductive organs of plants. Additionally, specialized silicon cells are found in grasses, along with hairs or trichomes.^36,39  These accumulations come in various forms and embellishments, some of which are unique in terms of taxonomy. These silicon structures, varying in size from a few to several tens of micrometers, are commonly known as opal phytoliths, plant phytoliths, opaline Si, or bSi. Silicon’s function is similar to lignin’s in plants as it is a structural element of the cell wall that provides resistance toward compression. It can be incorporated with low energy expenditure and is essential for plant growth and energy-related processes. The enduring presence of fossil phytoliths in both terrestrial and aquatic paleoenvironments has been utilized to reconstruct historical ecosystems and human activities. Si is present in significant amounts in terrestrial plants, varying from less than 1 to 5% of the dry matter, and in some cases, up to 10% or even more.^36,40,41 

For example, Chauhan et al. analyzed the Laser-Induced Breakdown Spectroscopy (LIBS) spectra for various components (leaf blade, leaf sheath, and stem) of freshly harvested C. dactylon plants. The aim was to investigate the distribution pattern of silicon deposition across different plant segments. Leaf blades have a higher Si concentration than leaf sheaths and stems, according to a detailed examination of the LIBS spectra of the various plant parts. The findings from the LIBS analysis are compared with the density of phytoliths deposited in different locations of C. dactylon. In LIBS analysis, it is observed that leaf blades have the highest frequency of silicified cells, followed by leaf sheaths and stems.⁴²  Aside from calcium, aluminium, magnesium, sodium, and potassium oxides, rice residues such as straw and husk are recognized for containing SiO₂ in an amorphous state, with SiO₂ content being notably higher compared to other crops. Approximately 200 kg of rice husk (RH), yielding nearly 40 kg of ash with an 85–98% silicon content, is generated from one tonne of rice.⁴³  Using biomass as a renewable energy source for the production of biogenic materials has recently gained significant attention. Combining these techniques enables the production of high-quality bSi with purities exceeding 98 wt% using combustion residues, particularly from RH and rice straw (RS) characterized by elevated silicon contents in the fuel ash. In terms of global warming and CO₂ emissions, the entire process can be regarded as nearly neutral, but it can also solve the problems associated with disposing of RH and RS. Numerous cutting-edge uses for the resulting bSi are possible, including as drug delivery systems, catalysts, adsorbents, and more.¹⁵ 

In another study conducted by Porrang and others, bSi was extracted from cereals husk using acid leaching and it was further converted to sodium silicate as a Si precursor. For drug delivery, mesoporous Si nanocarriers were created in this study using natural materials like rice and wheat husk.⁴⁴  Similarly, in a different study bSi was obtained from rice hull ash (RHA). This study also suggests that RH, one of the many sources of bSi, is considered a valuable agricultural biomass material and an affordable source that can provide bSi for biomedical applications.⁴⁵  RH ash can yield extremely pure bSi if ash melting and agglomeration during combustion are prevented.⁴⁶  A different investigation supports the idea that RH is a valuable reservoir of biogenic silicon nanoparticles (Si NPs) characterized by remarkable physicochemical attributes and a wide range of potential applications. Several factors may affect the yield of extracted biogenic Si NPs. This study delves into the morphology and examines how the choice of solvent (sodium hydroxide, potassium hydroxide) and aging time (0, 6, 12, 18, 24 hours) influence the extraction yield and properties of specific biogenic Si NPs derived from Indonesian RH.⁴⁷  Using RHA as a source of bSi, the production of polycrystalline silicon was achieved, exhibiting impurity levels lower than those stipulated by the SEMI III standard for solar grade silicon feedstock, which is approximately 99.99% pure. To refine the RHA, cost-effective and energy-efficient techniques such as acid milling, boiling water wash purification, pelletization, and carbothermal reduction were employed. These processes were conducted using an experimental 50 kW electric arc furnace in batch mode, maintaining temperatures between 1700–2100 °C.⁴⁸  Setiawan and coworkers also demonstrated that RH is a good source of bSi.⁴⁹  In this work, three distinct molecular structure amine groups were used to functionalize bSi, which was extracted from RH. Grimm et al. endeavoured to propose an energy-optimized method for synthesizing metal oxide-supported bSi. Their proposed synthesis approach involves the integration of metal salts into the lignocellulosic matrix of biomass, aiming to reduce the pyrolysis steps. By calcining the modified RH or RS, the targeted metal oxide supported on bSi can be obtained directly.⁵⁰  Recently, a novel form of mesoporous, highly hierarchical fibrillar bSi was derived from the perennial plant Equisetum fluviatile. The inherent highly ordered structure of the plant stems can be largely preserved in the bSi skeleton by removing organic compounds through a combination of chemical and heat treatment.⁵¹  It has also been proposed that Si, a physical barrier and component for improving mechanical properties, exists in plant tissues. Pineapples present in their shells, along with bracts that resemble rosette-shaped microparticles may be related to bSi. In a previous work, it is demonstrated that Si-based microparticles are co-purified while pineapple (Ananas comosus) nanocellulose is being extracted.⁵²  A different study focuses on the sophisticated textural characterization of bSi derived from various biomasses that accumulate Si, as well as agricultural waste materials like horsetail, rice, oat, and spelt husk. Thus, it is clear that plant-based biomass is a good source for bSi. Furthermore, the findings suggested that various plant species and origins would result in different textural characteristics and interconnections between the pores in bSi.⁵³  The fibrous material known as sugarcane bagasse is a great source of bSi. Additionally, sugarcane bagasse is an environmentally friendly precursor for synthesizing Si NPs with cost-effective production.⁵⁴  Moreover, it was found that the extracted bSi constituted between 0.01 and 5.9% of the dry biomass of leaves and wood in samples collected from 28 alpine plant species in the Swiss Alps (Valais). This observation extends to arborescent dicotyledons from 43 diverse families in temperate regions, showcasing a broad range of opal silicon content. Also, compared to woodlands, grassland communities produce significantly more opal Si, which increases the amount of bSi added to the soil.⁵⁵ 

Plants are not the only creatures that can biomineralize, that is, absorb minerals into their tissues. Certain fungi and insects that live on land are also capable of producing bSi. For instance, some ant species add Si particles to their exoskeletons, which increases the resilience and hardness of their outermost layer of defense. When discussing terrestrial organisms, testate amoeba, along with a few bacteria and fungi, are one of the main sources of bSi. Testate amoebae, a polyphyletic group of unicellular eukaryotes (protists) characterized by a test (shell) ranging in size from approximately 5 to 300 µm, constitute the primary origin of protozoic Si in soils.^56,57  Two supergroups can be used to classify testate amoebae: (1) Amorphea, which includes the order Arcellinida, and (2) TSAR, which includes the order Euglyphida. Arcellinida, an order encompassing testate amoebae with lobose pseudopodia and shells, exhibits shells formed through either the agglutination of foreign materials gathered from the environment (xenogenous shells) or a combination of agglutination and secretion (autogenous shells). Testate amoebae possessing filose pseudopodia are classified within the order Euglyphida, and most existing species in this order are characterized by siliceous shells comprised of self-synthesized Si platelets, also known as idiosomes.⁵⁶  Sommer et al. looked specifically at bSi, which is produced by testate amoebae and trees, while studying Si cycling in a beech forest in northeastern Germany. They observed that phytogenic Si pools amounted to 660 kg Si per hectare, with an average Si uptake by plants of 35 kg Si per hectare per year. Protozoic Si pools were significantly smaller, weighing 1.9 kg Si per hectare, but the Si uptake by trees was similar to that of the silicification process in disomic testate amoebae, reaching 17 kg Si per hectare per year.⁵⁸  It is known that at least certain fungi and bacteria, like Proteus mirabilis, can accumulate Si inside their cells. Additionally, by releasing acidic metabolites, these organisms can accelerate the dissolution of both crystalline and amorphous Si (bioweathering). To comprehensively grasp the importance of biota in Si cycling within agricultural plant–soil systems, there is a pressing need for additional research on bSi produced by sponges, fungi, and bacteria.^59,60 

Ocean surface planktonic organisms are the main producers of bSi. Within the top 100 meters of the water column, a sizable portion (60 per cent on average) of the bSi production is recycled through dissolution.⁵  Also, one essential element of the global oceanic Si cycle is silicifying organisms. The silicic acid found in seawater can be used by diatoms, silicoflagellates, sponges, and siliceous rhizarians to construct complex skeletons that are thought to enhance vital functions like mechanical protection for the cell, armour against predators, an efficient pH buffer, or an enhancement for the absorption or accumulation of bio essential elements.^61,62  Previous research has indicated that the unique optical characteristics of the frustule may provide diatoms with an advantage.⁶³  Diatoms are thought to be the primary global contributors to the Si cycle, controlling the rate at which bSi is produced as well as its standing stock in the water column.⁶⁴  Hence, it is noteworthy to mention that over 20 billion tons of bSi produced worldwide each year are essential to the carbon cycle and have the power to influence atmospheric CO₂ concentrations. A quarter of this amount is produced in seawater by tiny photosynthetic algae called diatoms and, to a much lesser extent, by sponges and radiolarians of the zooplankton,⁶⁵  which is quite evident by looking at Table 1.1. Considering that diatoms make up between 35 and 75% of marine net primary production and roughly 20% of Earth’s photosynthetic activity, it is clear that bSi is important to the planet’s ecosystem. Various research initiatives, including the use of sediment traps and environmental molecular surveys, have further emphasized the importance of rhizarians in biogeochemical cycles and the transport of carbon and bSi to the deep continental ocean.⁶⁶ 

Rivers receive a significant amount of phytolith bSi from vegetation and soils. Thus, alterations in land use may impact the composition and concentrations of bSi in neighboring rivers. An investigation explored into the origin and characteristics of bSi present in rivers of the Asian tropical region, along with the phenomenon of reverse weathering observed in these fluvial systems. The study utilized samples collected from rivers in Peninsular Malaysia.^41,67  The findings revealed that the bSi samples obtained from sediments included phytoliths, diatoms, and sponge spicules. Elongate-form phytoliths constituted 92.8–98.3% of the total bSi in the Pahang River. Despite representing a minor fraction of the overall bSi volume, pennate diatoms dominated the diatom-derived bSi in this river. In contrast to the Pahang River, the Pontian and Endau rivers exhibited elevated concentrations of diatom-derived bSi, primarily of the Centricae form, making up 68.8% and 79.3% of the total bSi volumes, respectively. The bSi particulates had an average carbon content of 4.79%, ranging from 1.85% to 10.8%.⁶⁷ 

According to the findings of Ran et al. for the rivers Changjiang (Yangtze) and Huanghe (Yellow), phytoliths and diatoms make up most of the riverine bSi. River bSi concentrations are dependent on in-stream primary production and terrestrial inputs.⁶⁸  If there was a bSi tracer, one could monitor the differences in bSi derived from freshwater and marine environments, establishing a connection between terrestrial and aquatic ecosystems. Tracking the origin of bSi in aquatic environments has traditionally involved identifying particles once bSi has been separated from other particles.^68,69  The vegetation and sediment in tidal marshes have the capacity to accumulate substantial quantities of bSi. Throughout the entire year, an investigation was conducted to assess the bSi content in prevalent freshwater marsh plants, including Salix sp., Impatiens glandulifera, Urtica dioica, Phragmites australis, and Epilobium hirsutum. It was seen that P. australis had the highest concentration of bSi (accumulating from 6 to 55 mg g⁻¹) among the living plants. The dead stems of P. australis exhibited the highest bSi content at 72.2 mg g⁻¹. In contrast, considerably lower levels of bSi were observed in U. dioica (<11.1 mg g⁻¹), I. glandulifera (<1.1 mg g⁻¹), E. hirsutum (<1.2 mg g⁻¹), and Salix sp. (<1.9 mg g⁻¹). Low concentrations of bSi (<6 mg g⁻¹) were found in underground biomass, with the exception of P. australis rhizomes (<15 mg g⁻¹). From the surface (9 to 10 mg g⁻¹) to deeper layers (5 to 7 mg g⁻¹), the sediment bSi content decreased. It was observed that in the biogeochemical cycling of Si, P. australis wetlands may be a crucial sink for bSi.⁷⁰ 

Among Si-forming organisms, siliceous sponges are unique in that they can enzymatically synthesize bSi, which has growing applications in nanobiotechnology, biomedicine, and biooptics.⁷¹  The identification of an enzymatically active protein within the axial filaments of spicules (structural components of sponges such as demosponges and hexactinellids), responsible for synthesizing polymeric silicate known as bSi, marked a noteworthy progression in comprehending the formation of siliceous spicules. The enzyme, referred to as silicatein, has been observed to catalyze and polycondense bSi during both the axial and radial expansion phases of the spicules. In contrast to the deposition of bSi onto organic templates from a super-saturated solution, as observed in diatom frustules and plant phytoliths, the siliceous spicules of sponges undergo formation within an intra organism environment characterized by hypo-saturation. This occurs through an enzymatic mechanism that reduces the activation energy of the polycondensation reaction. Orthosilicic acid, also recognized as TEOS (tetraethyl orthosilicate), has been utilized as a substrate or precursor for bSi in enzymatic reactions within in vitro systems.⁷²  A different study suggests that the amorphous hydrated Si spicules that make up the skeleton of Euplectella aspergillum are held together by additional layers of Si.⁷³ 

The bSi that reaches the seafloor primarily comprises siliceous hard parts from siliceous sponges, silicoflagellates, radiolaria, and diatoms. The main sources of bSi in marine sediments are typically diatom valves, radiolaria, and sponge spicules.⁷⁴  About half of the bSi deposited in the marine environment comes from sediments found in the Southern Ocean, and diatoms are mostly responsible for this siliceous material.³⁴  However, the findings of a different study suggest that, during the period when the Larsen ice shelf covered the sea surface, sponge spicules rather than diatoms were the primary source of bSi in this region’s sedimentary record.⁷⁵  It has been documented that diatom-derived bSi possesses a unique chemical structure featuring exposed free hydroxyl groups that can be altered to attach chemical or biological entities.⁷⁶  A group of researchers recently revealed exciting potential applications of an alternate Si porous material derived from diatoms as a readily available, naturally occurring, multifunctional material for regenerative medicine.⁷⁷  Rembauville et al. demonstrated a robust correlation between wintertime bSi and particulate organic carbon export, primarily linked to Fragilariopsis kerguelensis in the Indian sector, employing sediment traps.⁷⁸  Another investigation proposes that valuable three-dimensional, nanoporous, hollow-structured bSi can be obtained alongside organic components such as lipids, proteins, and bioactives with minimal chemical input by utilizing diatoms as a tool.⁷⁹ 

Despite not having silicon-dependent cellular structures, recent research has shown that some smaller marine organisms (such as the picocyanobacterium Synechococcus) can also absorb silicic acid, or DSi, and accumulate Si. That said, it was demonstrated that the five strains of picoeukaryotes grown in cultures supplemented with added dSi accumulate bSi. These strains include two marine species (Ostreococcus tauri and Micromonas commoda) and three novel isolates from the Baltic Sea.⁸⁰  A study proposed that the low-latitude South China Sea’s bSi fluxes are primarily caused by radiolarians, as evidenced by the relatively strong bSi correlation for radiolarian abundance and weak for diatom abundance.⁸¹  Open-ocean planktonic protists, known as siliceous polycystines and phaeodarians, are distributed all over the water column. These protists are characterized by intricate siliceous skeletons primarily developed through the absorption of silicic acid. While their role in the Si biogeochemical cycle remains somewhat obscure, these protists do play a part in the marine pools of organic carbon and bSi.⁶⁵ 

Other than the above-mentioned sources of bSi, it is perceivable that soil and vegetation are good sources of bSi. In certain regions of Brazil, lake bed sediments contain high concentrations of short fibers of bSi along with organic matter, sand, and clay.⁸²  On a global scale, there is a wealth of biomass residues readily accessible from agricultural food production. These biomass residues have important uses as feedstock for bioenergy and as starting points for producing materials with added value. The assessment involved the production of bSi from diverse biomass residues in Africa, including cornhusk, corncob, yam peelings, cassava peelings, and coconut husks.⁸³  The weathering of continental silicates is the primary source of DSi in rivers. Based on volume-weighted averaging, 16% of the suspended Si load from rivers is delivered to the ocean as bSi. In most cases, hot alkaline solutions are used to measure bSi in sediments.⁴¹ 

It is notable to mention that bSi is characterized by various structural shapes, including sheet-like, globular, fibrillar, helical, tubular, and folded sheets. It also displays variations in density, content, and structure. There are many degrees of biosilica structural organization found in the natural world.⁸⁴ 

Due to its inherent amorphous nature, bSi is a biomineral with infinitely adaptable morphology. At locations of mineralization, the mechanisms governing structural organization and the resultant morphological forms involve spatial constraints, ordered particle aggregation, and chemical regulation.⁸⁵  The fundamental unit of most silicon-containing minerals is the SiO₄ tetrahedron as shown in Figure 1.2, where silicon is situated at its center, and oxygen atoms are in contact with each other. Additionally, it is known that minerals like stishovite and coesite, incorporating SiO₆ octahedral units, display sixfold coordination for silicon.^85,86  The Si–O bond measures approximately 0.162 nm in all these structures, significantly smaller than the sum of the covalent radii of silicon and oxygen atoms (0.191 nm). This size difference contributes to the remarkable stability of the siloxane bond. Central to the chemistry of silicon crystals is the arrangement of SiO₄ and SiO₆ units, along with their inclination to create three-dimensional framework structures.⁸⁷ 

Nature exhibits various levels of hierarchically structured three-dimensional organization, ranging from the siliceous skeletons of marine glass sponges that can reach up to 2 m in height and 70 cm in width, to bSi nanogranules found in bacteria and mitochondria.⁸⁴  Also, most of the time, the nanostructure of bSi is described as nanospheres made of colloidal SiO₂ with diameters varying from 10 to 100 nm. The highly-branched polysilicic acid (general formula [SiO _X (OH)_4−2X ] _n ) that grows into these Si nanospheres is absorbed by the cells (microorganisms such as diatoms, radiolarians, silicoflagellates, and siliceous sponges) through active transport and functions as a Si nucleus.^87,88  The Si nanospheres frequently establish a three-dimensional network, giving rise to branched particle chains interconnected by siloxane linkages (Si–O–Si).^87,88  As is commonly observed in the diatom cell wall, flocculation (a process that almost closes and unites Si spheres and provides the surface a smooth appearance), fills the spaces between the nanospheres with Si in many situations. The Si deposited between the nanospheres usually dissolves first when the bSi dissolves, producing a porous structure. Both modern and ancient bSi have pore spaces with a mean diameter of 5–10 nm and an overall porosity range from 35–50%.⁸⁹ 

The robust stability of Si–O–Si units significantly limits the reactivity of silicon in water at neutral pH, leading to the formation of condensed phases with potential crystalline or amorphous structures. Low temperature and pressure are preferred for amorphous phases where the Si–O–Si bond angle can vary greatly because of the large kinetic barrier to crystallization. Thus, one would anticipate that any bSi generated from scratch would be non-crystalline and subject to kinetic control regarding energetics.^84,85 

When discussing the marine environment, the mechanical strength of Si frustules of diatoms helps them fend off grazers.⁹⁰  Due to its enhanced solubility, bSi assumes a crucial role as a readily available source of Si (H₄SiO₄) for plants in soils. This aspect holds particular significance in agricultural biogeosystems.⁹¹  In addition, bSi has exceptional absorption capacity, chemical inertness, thermostability, and a reasonably low cost.⁹²  Also, in comparison with synthetic Si, bSi is a much more biocompatible and nontoxic material which seems to be some of the most dependable properties of bSi.⁹³ 

Porous Si is typically created by precipitating alkaline silicates on an industrial scale. Alkaline silicates, or water glass, are generally produced by the very energy-intensive and high temperature (approximately 1400 °C) reaction of carbonate powders with Si sand.¹⁵  Industrial processes include (i) hydrolyzing mineral precursors like TEOS, (ii) acidifying sodium silicate solutions, and (iii) smelting quartz sand with sodium carbonate at high temperatures (>1200 °C) to produce Si products like precipitated Si, fumed Si, arc Si, Si xerogels, and xerogels.⁹³  These synthesis routes all share energy-intensive characteristics and the emission of CO₂ along with the release of hazardous byproducts. To be precise the conventional method is not only costly but also environmentally dangerous since it produces 20 tons of wastewater, 0.23 tons of CO₂, and 0.74 tons of sodium sulfate for every ton of Si produced. This goes against the idea of sustainable development.^15,94  Because of these drawbacks, industrialized Si products are now less desirable in terms of cost and environmental impact, which restricts their widespread use in various industrial sectors. Thus, an alternative approach that is both environmentally friendly and commercially viable is needed to produce Si.^15,95  For this purpose, several different approaches such as biological, chemical and thermal methods are included.

Chemicals including acids, bases, and other agents are employed in this process to raise the quality of the Si by eliminating impurities as shown in Figure 1.3(a) and (b).⁹⁶  In addition, contaminants can be changed into ions that can dissolve by acid leaching.⁹⁷  Given that RH is abundant in plants used for grain cleaning and can be utilized to produce various organic compounds like furfural, xylose, and polysaccharides, its potential as a renewable raw material for generating high-quality amorphous SiO₂ is highly promising.⁹⁸  One such study reported that chemical procedures were used to extract Si from RH. HFA was dissolved in 15% (1 : 4.5) NaOH solution by weight, then the mixture was kept at 100 °C for two hours before being filtered. Additionally, NaOH was added to separate the Si from the impurities and create a sodium silicate solution. This solution was then converted to hydrosol Si by using an ultrasonication-assisted method to get the pH of the solution down to 6 or 7. Consequently, the impact of pH on the purity of Si was generated, and upon dehydrogenation, gelation, and drying, powdered SiO₂ was acquired.⁹⁹ 

Alyosef et al. exhibited two methods for producing amorphous Si from Egyptian RHs that are low-cost and least detrimental to the environment. The first method entails leaching with citric acid (CA), dry milling, and thorough washing of the husk sample with water. Two stages of the leaching procedure were used: first, for 180 minutes at 323 K and then for 60 minutes at 353 K. The leached sample underwent four successive stages of heat treatment in a muffle furnace following washing and drying.¹⁰⁰  All of the previously listed steps are included in the second route, with the exception of the CA leaching. The findings demonstrate that there are numerous benefits to CA leaching in terms of Si yield and porosity as well.¹⁰⁰  Utilising a combustion process in conjunction with pre-treatment techniques can yield superior bSi from RH. A study demonstrates the comparison of applicability of CA, and gluconic acid (GA) for the preparation of bSi from RH. The results showed that, with a small amount of Si loss, both GA and CA could remove the majority of the metal alkali impurities in RH. The results also indicate that GA is a great new environmentally friendly carboxylic acid that can be used to produce bSi from RH.¹⁰¹ 

The thermal extraction process involves the valorization of agricultural biomass into ash using various methods such as a muffle furnace, fixed bed furnace, inclined step-grate furnace, cyclonic furnace, fluidized bed reactor, rotary kiln, or tubular reactor, with a specified time period typically ranging from 2 to 8 hours.¹⁰²  The thermal approach employs either pyrolysis or calcination as a form of heating. With the increasing interest in environmentally friendly methods for Si production, there is a demand for novel and dependable extraction techniques. One such technique was used by Park et al., in which a pilot-scale one-pot alkali hydrothermal and ball-milling method was established for the continuous Si extraction.¹⁰³  In a different study, a thermal approach was used to extract Si from RHs, which effectively eliminated the majority of organic contaminants. The heating temperature was changed in this investigation to observe its impact on the percentage of Si that was achieved. Furthermore, the acid-treated RHs were utilized for the direct extraction of Si following dehydration with a NaOH solution. Then, Si is extracted from the sodium silicate that is left behind by adding the right quantity of mineral acid and heating it for 5–6 hours. This process produces RHA, which is then pyrolyzed in a muffle furnace at temperatures ranging from 500 to 850 °C.¹⁰⁴ 

Also, using residues from South African sugarcane and maize, biogenic amorphous Si was created through a thermo-chemical technique. To produce Si, various sugarcane fractions (such as the leaves, pith, and fiber) from South Africa were processed. The biomass samples were leached for two hours at 353 K with either 7 wt% H₂SO₄ or 7 wt% CA. Subsequently, the samples were subjected to a four-step program in a furnace, involving drying, rinsing, and burning, with temperatures ranging from room temperature to 873 K. Sugarcane leaves were used to produce high-quality amorphous bSi, with up to 99.3 wt% Si content and 0.1 wt% residual carbon. In addition to its outstanding textural characteristics, the produced bSi exhibited a surface area of up to 323 m² g⁻¹, a pore volume of 0.41 cm³ g⁻¹, and an average pore diameter of 5.0 nm.¹⁰⁵ 

Biological or microbiological approaches employ microorganisms like bacteria, fungi, cyanobacteria, chrysophytes like diatoms, and Porifera (also known as Californian red worms) to produce bSi in a more environmentally friendly and cleaner manner.¹⁰⁶  These organisms may utilize materials containing Si as a source of food, which causes a process called bio-silicification (the buildup of Si inside the cells). To obtain above 90% purity of bSi, the resultant product can be removed by disrupting the cells, then precipitating, purifying, and drying.^105,106  A study has reported employing enzymatic fluids comprising lipase, amylase, trypsinogen, and other digestive enzymes to extract Si from RHs that have been wet and digested in the mouths of California worms. Si NPs were produced with sizes ranging from 55 to 250 nm, and a Si recovery rate of 88% was achieved through the bio-digestion process of RH by worms after a 5-month processing period.¹⁰⁷  In a distinct study, Rohatgi et al. explored the potential use of white-rot fungus species, specifically Cyathus, to extract high-grade Si from RHs. The microbial fermentation process occurred over a span of 60 days, following which the material underwent drying at 80 °C, sieving to a specific size, and burning at 450 °C. According to the findings, this method resulted in diminished organic matter and a heightened concentration of inorganic material, specifically SiO₂.¹⁰⁸ 

Scientists have been fascinated by bSi’s remarkable structures and properties for a decade now, and they have been using it to create new devices and technologies. In addition to its chemical inertness, which makes bSi extremely demanding in terms of science, it also demonstrated some of its remarkable inherent qualities that could be used to advance technology.⁷⁶  Regarding applications in nanotechnology, bSi is superior to synthetic nanoporous Si materials because it can be produced more affordably through in vivo biomineralization, which avoids the need for hazardous chemicals.^76,109  The following section highlights the various fields where bSi finds its application (Figure 1.4) and also gives a brief overview of the research work being conducted where bSi is the focal point as listed out in Table 1.2.

The unique properties of bSi enhance its applicability in catalysis and photocatalysis as shown in Figure 1.5 for various environmental applications, including the removal of organophosphate pesticides, extraction of heavy metals from wastewater, treatment of textile effluents, and decolorization of dyes.¹⁰⁹  Photocatalytic degradation of methylene blue (MB) using Si NPs derived from RS was explored in a particular research work conducted by Singh et al.¹⁰⁹  The potential and effectiveness of surface-modified polyacrylonitrile nanofibers/bSi composites for the photocatalytic degradation of malachite green dye were investigated.¹¹⁰  Some studies have reported that forming nanostructures when Fe₃O₄ is dissolved into Si results in increased stability and photocatalytic activity enhancement.¹¹¹  On this basis Purwiandono et al. aimed to assess the photocatalytic potential of Fe₃O₄ dispersed in bSi (Fe₃O₄@SiO₂) derived from snake fruit (Salaccazalacca) leaf ash (SLA) from the standpoint of developing magnetite nanostructures and using agricultural waste. The study aimed to investigate the physicochemical characterization of Fe₃O₄@SiO₂ synthesized by SLA. Additionally, the research sought to provide mechanistic insights into the photocatalytic activity of Fe₃O₄@SiO₂ in the photocatalytic wet peroxidation and adsorption processes related to pollutants and Rhodamine B in batik wastewater.¹¹² 

A novel photocatalyst based on diatom bSi doped with palladium(ii) chloride nanoparticles was produced and tested for effective methyl orange degradation in water solution.¹¹³  The biological immobilization of titanium dioxide (TiO₂) in the porous 3D architecture of the frustules was achieved through a controlled culture of the diatom Pinnularia sp. on soluble titanium in a batch procedure. The extracted Pinnularia cells were treated with either high-temperature treatment or nitric acid (65%) to isolate the silica–titania frustules. The silica–titania material that is formed is assessed for its potential to reduce acetaldehyde (C₂H₄O) through photocatalysis.¹¹⁴  In a different study set, bSi from bamboo leaves was extracted, and titanium tetraisopropoxide was used as a titania precursor using a sol–gel mechanism to create TiO₂/SiO₂ composite photocatalysts. The MB photocatalytic degradation process was used to assess the relationship between physicochemical parameters and photocatalytic performance under UV irradiation, both with and without adding H₂O₂ as an oxidant.¹¹⁵  Similarly, RH was used in another study to synthesize biogenic hierarchical TiO₂/SiO₂ for the degradation of MB.¹¹⁶ 

Because of their biological characteristics, Si NPs have drawn a lot of attention recently for a variety of biomedical applications, such as protein adsorption and separation, nucleic acid detection, molecular imaging, gene therapy, drug delivery, and scaffolds.¹¹⁷  Particularly, tissue engineering and regenerative medicine applications use nanomaterials based on Si. Dietary intake was suggested by Jugdaohsingh and coworkers to significantly increase bone mineral density in men and premenopausal women.¹¹⁸  In a different study, the authors used sugarcane bagasse as a bio-precursor to create Si NPs. The evaluation of Si NPs biocompatibility in human lung fibroblast cell (hLFCs) revealed that there are no appreciable cytotoxic effects of Si NPs. Additionally, Si NPs to some extent affect gene expression and the course of the cell cycle. According to this research, Si NPs and hLFC are biocompatible and can be used for bone tissue engineering, scaffolds for in vitro lung cell culture, along with other applications.¹¹⁹  On a similar basis another study presents a novel and straightforward method to synthesize high-purity Si NPs from RHs and assess their biocompatible characteristics using in vitro cell-based techniques. Using a viability assay and evaluations of cellular morphological alterations, intracellular ROS production, mitochondrial transmembrane potential, and oxidative stress-related gene expression, the biocompatibility of the Si NPs with hLFCs was explored. According to the findings, there was no discernible incompatibility between the Si NPs in these in vitro cell-based methods. According to these initial results, Si NPs are biocompatible, may be the greatest substitute for synthetic Si, and can be used in biomedical applications.¹²⁰ 

RH was used as a precursor to create Si NPs and using human mesenchymal stem cells (hMSc) and the MTT assay, the biological characteristics of bSi NPs were investigated. The results of the cell viability studies demonstrated the high level of biocompatibility between Si NPs and hMSc. These Si NPs can be used in bone tissue engineering, according to the findings of this study.¹²¹  In another study, the authors valorized Sorghum bicolor seed head with the production of a biocompatible bSi nanostructure (BSN). Furthermore, because bone marrow hMSc can differentiate into a variety of lineages, the authors have evaluated the role of BSN on osteogenic differentiation using hMSc in an in vitro model.¹²²  In another study, RH was used as a Si source to create bSi–metal phosphate nanocomposites. A cell viability test and the examination of microscopy images were used to investigate the in vitro biological characteristics of the nanocomposites. The material was shown to be nontoxic and to have excellent biocompatibility with hMSc through cytocompatibility studies. These nanocomposites can be employed in bone tissue engineering, as per these findings.¹²³ 

The biogenic polyphosphate (bio-polyP) and bSi, two naturally occurring polymers produced by deep-sea sponges, have also been found in recent years to promote morphogenetic on both osteoblasts and osteoclasts. The discoveries of this research have led to the development of novel bioinspired methods using 3D printing technology to create bone biomimetic templates.⁷²  In a different study, a green chemistry method was used to create the silica dioxide nanoparticles using the Allium cepa bulb aqueous extract. This work also indicates that the synthesis of Si NPs mediated by A. cepa may find use in biomedical applications.¹²⁴ 

Tailored biogenic Si NPs have been shown by Capeletti et al. to have antibacterial qualities and less cellular toxicity when applied to cell lines.¹²⁵  Furthermore, human cell lines tend to exhibit biocompatibility with biogenic Si NPs.¹²¹  The study conducted by Sharma et al. created bSi nanopowder from RHA using a chemical process and assessed their toxicity and compatibility with bacteria. Microorganisms classified as Gram-positive (Escherichia coli) and Gram-negative (Staphylococcus aureus) were used to test the bSi nanopowders’ antibacterial activity. This work highlights the significance and utility of RHA-mediated synthesized bSi in the fields of medicine, biomedicine, clinical, and biology.¹²⁶  In a different study, the antibacterial activity of bSi rosettes derived from leftover pineapple peels against Escherichia coli as well as the bSi rosette films’ anti-adhesive qualities on polydimethylsiloxane (PDMS) were assessed. The study also suggests that because of its high porosity, this coating may be used as a platform for encapsulating active compounds. Therefore, to enhance its antifouling properties, various bSi rosette arrangements could be investigated.¹²⁷ 

Punica granatum leaf extract was used as a capping and stabilizing agent for the synthesis of Si NPs. The antibacterial activity of P. granatum assisted Si NPs was evaluated against two Gram-negative bacterial pathogens, namely Salmonella sp. and E. coli. The antibacterial experiments demonstrate the good antibacterial activities of Si NPs aided by P. granatum.¹²⁸  The invasive species Lantana camara was used to produce Si NPs which were then chemically altered utilizing nitrogen-containing moieties, such as CTAB and APTES. The modified Si NPs were employed as electrostatic cross-linking agents to create hydrogels made of tragacanth gum (TG). When compared to TG hydrogels, the cytocompatible CTAB@SiNP-TG hydrogels showed an approximately 10- to 12-fold increase in antibacterial activity against Pseudomonas aeruginosa and Staphylococcus aureus.¹²⁹ 

Enzymes are naturally occurring catalysts with various intriguing qualities, including high activity, specificity, stereo selectivity, etc. However, before they can be used on an industrial scale, some properties need to be modified.⁷⁶  Enzyme application in an industrial process is determined by its capacity to endure hazardous industrial circumstances and its ability to recover efficiently from catalytic reactions at industrial reactors. Soluble enzymes can be made more reusable, have improved thermal and storage durability, and have increased catalytic efficacy through immobilization.⁷⁶  The use of porous Si materials for enzyme immobilization has advanced significantly, but depending on the biomolecule, the Si source, and the intended application, a proper immobilization strategy is needed. In a recent study, the potential of bSi extracted from a rarely studied plant (E. Myriochaetum), its conversion to silicon and possible applications of both biogenic materials as supports for enzyme immobilization were investigated.¹³⁰  Also, using RH as a renewable source for synthesizing Si NPs, PersiXyn2 (recombinant xylanase enzyme) was immobilized to improve its stability and recyclability.¹³¹ 

In a different study, raw oil palm leaves (OPL) were used to extract nanocrystalline cellulose (NC) and SiO₂, which were then used as nano-fillers in polyethersulfone (PES) to create NC-SiO₂-PES, a platform for immobilizing Candida rugosa lipase (CRL).¹³²  Onoja et al. described the synthesis of butyl butyrate using a composite made of magnetite (Fe₃O₄) coated in nanosilica that was extracted from the ash of OPL as nanosupports for immobilizing CRL.¹³³  On a similar basis bSi was obtained from OPL and was used as an enzyme support. Its qualities could be enhanced by adding graphene oxide (GO) and Fe₃O₄ to produce a better ternary support for immobilizing enzymes, such as CRL which was further used to produce ethyl valerate.¹³⁴  Also, using a straightforward hydrothermal method, Si was extracted from RHs and functionalized with triethoxy(octyl)silane-OCTES (octyl-SiO₂) and (3-aminopropyl)triethoxysilane-3-APTES (amino-SiO₂) in order to use it as a support for the adsorption-based immobilization of lipase from Thermomyces lanuginosus.¹³⁵ 

Even though the as-synthesized silicon material’s electrochemical performances still require development, producing silicon anode materials from biomass resources permits the battery industry to utilize subsidiary agricultural products effectively.¹³⁶  A group of authors report for the first time the fabrication of silicon/nitrogen-doped carbon/carbon nanotube (SNCC) nano/micro-hierarchical structured spheres using a simple electrospray method, using RH as the Si source. The inexpensive silicon composites derived from RH that were created using an easy-to-scale synthetic technique show promise for the next generation of rechargeable lithium-ion batteries (LiBs).¹³⁶  In a different work set, Si from RH was utilized to create Si NPs using a magnesiothermic reduction process. Moreover, the Si NPs were utilized to create a binder-free composite system with graphene and Si NPs for use as the anode material in LiBs.¹³⁷  Similarly, using a magnesiothermic reduction process, RHs were utilized as a source of raw materials to create porous Si. Also, a new technique was presented for creating a porous Si composite with reduced GO for LiBs anodes.¹³⁸ 

ZnCl₂ was used as an activating agent during a simple carbonization process to create RHs into micro-sized porous C/SiO₂ composites in an Ar atmosphere. This porous C/SiO₂ composite shows good rate-capability, good cycling stability, and a high discharge specific capacity when tested as anode material for LiBs. This C/SiO₂ composite anode material’s ease of use and inexpensive cost make it a viable substitute for the conventional graphite anode.¹³⁹  In a similar fashion a different study has investigated the use of SiO _x /C composite material as an anode for rechargeable lithium batteries, which is directly produced from agricultural RH byproducts using a financially feasible and ecologically friendly method.¹⁴⁰ 

Because bSi is porous, it can be used in various ways. For example, it can be used as an affordable, non-traditional adsorbent and a good substitute for more expensive activated carbon in treating effluents to get rid of harmful metal ions or dyes.¹⁴¹  In reference to this a study was conducted to develop a time and cost-effective method to increase the specific surface area and mesopore volume of bSi by partial pseudomorphic transformation in a microwave reactor using a low-cost surfactant.¹⁴¹  Because of its high specific surface area and porous nature, bSi may find application in low-cost biocide delivery systems that provide controlled, sustained biocide release to protect wood and crops.¹⁴²  In addition, bSi can be used to make water glass at much lower temperatures (353–373 K) and under much milder conditions than in the traditional method of furnace roasting with sand and sodium carbonate (∼1670 K) and additional hydrothermal treatment. Without a carbothermal reduction at 2173 K, high-purity Si can also be utilized to synthesis silicon tetrachloride (SiCl₄), silicon carbide (SiC), and silicon nitride (Si₃N₄).^142,143 

The sedimentary record of bSi and its generally good preservation efficiency all suggest that bSi is a potentially significant paleoproductivity proxy.¹⁴⁴  Consequently, variations in the abundance of bSi in sedimentary records are frequently very valuable for reconstructing paleoenvironments. With significant worldwide ramifications, bSi records have been utilized over time to reconstruct paleoproductivity and paleoclimatic changes based on variations in their regional distribution.⁸¹  And, since bSi is a major regulator of Si fluxes from terrestrial to aquatic ecosystems, it has been discovered to be a basic component of the global Si and carbon cycles. Since diatom reproduction is highly dependent on Si bioavailability (for the synthesis of diatom frustules), these Si fluxes regulate marine diatom production globally. Because marine diatoms make up to 54% of the biomass in the oceans, they can fix large amounts of CO₂ through photosynthesis.⁶⁴  The application of silicaceous biodeposition by diatoms as a waterproofing surface treatment for recycled concrete is the research subject for Maldonado and coworkers.¹⁴⁵ 

One of the main biogenic elements of oceanic sediments bSi, can also be used to reconstruct historical fluctuations in the effectiveness of the biological pump of CO₂.¹⁴⁶  According to the research conducted by Schneider and others, bSi can be used to synthesize MCM-41/-48 and MFI-type zeolites, offering a sustainable method of producing high-performance materials for a variety of uses, including adsorption and catalysis.¹⁴⁷  Thus, either by its biological function or as a material, bSi offers a dual interest. A study demonstrated that bSi could be used to fabricate bioplastic films and ultimately in packaging. The goal of the study was to prepare Si-reinforced cellulose-based composite bioplastic films via a casting method, which could be evaluated in packaging applications, and to simultaneously extract cellulose fiber and crystal bSi from the same RHs.¹⁴⁸ 

Living things have been chosen by nature to have the best potential to produce certain functional components that are essential to their survival, development, and procreation. These functional elements with highly replicable properties, have attracted a lot of interest from researchers as a very potential alternative to synthetic materials, particularly bSi. In particular, the unique properties of bSi, in terms of composition and structure have been used in a variety of applications.⁷⁶  Also, the wide diversity in the sources of bSi, be it terrestrial or aquatic has increased the bioavailability and utilisation of bSi in recent times. The use of agricultural biomass as a renewable source for the production of bSi has been highlighted in contemporary research which surely helps in resolving emerging issues of sustainability and waste management. In addition to this, the emerging extraction techniques of bSi are designed so that it is environmentally friendly and commercially viable.

Applications for bSi are abound, as they possess an unmatched diversity in form and structure. The primary benefit of bSi over other synthetic mesoporous materials is its ability to produce Si structures in vivo without the need for intricate chemical processes, making it an incredibly affordable material for analytical sciences. Scientists have been fascinated by bSi’s remarkable structures and properties for a decade now, and they have been using it to create new devices and technologies. In addition to its chemical inertness, which makes bSi extremely demanding in terms of science, it also demonstrated some of its remarkable inherent qualities that could be used to advance technology.^76,149 

The number of research work carried out in recent times calls attention to the fact that bSi is fascinating in terms of its formation, structure, sources and application. Despite the fact that bSi has been investigated in a variety of fields, including the creation of novel materials and the development of new devices, it would not be surprising if their many characteristics were designed to demonstrate their utility in previously unexplored fields. An examination of the growing number of bSi applications may reveal new characteristics in them, leading to the development of fresh approaches to use them in unexplored fields.