Bacterial biosilicification: a new insight into the global silicon cycle

Silicon: A valuable soil element for improving plant growth and CO2 sequestration

BACKGROUND

Silicon (Si), the second most abundant and quasi-essential soil element, is locked as a recalcitrant silicate mineral in the Earth's crust. The physical abundance of silicates can play an essential role in increasing plant productivity. Plants store Si as biogenic silica (phytoliths), which is mobilized through a chemical weathering process in the soil.

AIM OF REVIEW

Although Si is a critical element for plant growth, there is still a considerable need to understand its dissolution, uptake, and translocation in agroecosystems. Here, we show recent progress in understanding the interactome of Si, CO2, the microbiome, and soil chemistry, which can sustainably govern silicate dissolution and cycling in agriculture.

KEY SCIENTIFIC CONCEPTS OF THIS REVIEW

Si cycling is directly related to carbon cycling, and the resulting climate stability can be enhanced by negative feedback between atmospheric CO2 and the silicate uptake process. Improved Si mobilization in the rhizosphere by the presence of reactive elements (for example, Ca, Na, Al, Zn, and Fe) and Si uptake through genetic transporters in plants are crucial to achieving the dual objectives of (i) enhancing crop productivity and (ii) abiotic stress tolerance. Furthermore, the microbiome is a symbiotic partner of plants. Bacterial and fungal microbiomes can solubilize silicate minerals through intriguingly complex bioweathering mechanisms by producing beneficial metabolites and enzymes. However, the interaction of Si with CO2 and the microbiome's function in mobilization have been understudied. This review shows that enhancing our understanding of Si, CO2, the microbiome, and soil chemistry can help in sustainable crop production during climatic stress events.

Discovery of long-chain polyamines embedded in the biosilica on the Bacillus cereus spore coat

Biosilicification is the process by which organisms incorporate soluble, monomeric silicic acid, Si(OH)4, in the form of polymerized insoluble silica, SiO2. Although the mechanisms underlying eukaryotic biosilicification have been intensively investigated, prokaryotic biosilicification has only recently begun to be studied. We previously reported that biosilicification occurs in the gram-positive, spore-forming bacterium Bacillus cereus, and that silica is intracellularly deposited on the spore coat as a protective coating against acids, although the underlying mechanism is not yet fully understood. In eukaryotic biosilicifying organisms, such as diatoms and siliceous sponges, several relevant biomolecules are embedded in biogenic silica (biosilica). These biomolecules include peptides, proteins, and long-chain polyamines. In this study, we isolated organic compounds embedded in B. cereus biosilica to investigate the biomolecules involved in the prokaryotic biosilicification process and identified long-chain polyamines with a chemical structure of H2N-(CH2)4-[NH-(CH2)3]n-NH2 (n: up to 55). Our results demonstrate the common presence of long-chain polyamines in different evolutionary lineages of biosilicifying organisms, i.e., diatoms, siliceous sponges, and B. cereus, suggesting a common mechanism underlying eukaryotic and prokaryotic biosilicification.

Abiogenic silicon: Interaction with potentially toxic elements and its ecological significance in soil and plant systems

Abiogenic silicon (Si), though deemed a quasi-nutrient, remains largely inaccessible to plants due to its prevalence within mineral ores. Nevertheless, the influence of Si extends across a spectrum of pivotal plant processes. Si emerges as a versatile boon for plants, conferring a plethora of advantages. Notably, it engenders substantial enhancements in biomass, yield, and overall plant developmental attributes. Beyond these effects, Si augments the activities of vital antioxidant enzymes, encompassing glutathione (GSH), catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD), among others. It achieves through the augmentation of reactive oxygen species (ROS) scavenging gene expression, thus curbing the injurious impact of free radicals. In addition to its effects on plants, Si profoundly ameliorates soil health indicators. Si tangibly enhances soil vitality by elevating soil pH and fostering microbial community proliferation. Furthermore, it exerts inhibitory control over ions that could inflict harm upon delicate plant cells. During interactions within the soil matrix, Si readily forms complexes with potentially toxic metals (PTEs), encapsulating them through Si-PTEs interactions, precipitative mechanisms, and integration within colloidal Si and mineral strata. The amalgamation of Si with other soil amendments, such as biochar, nanoparticles, zeolites, and composts, extends its capacity to thwart PTEs. This synergistic approach enhances soil organic matter content and bolsters overall soil quality parameters. The utilization of Si-based fertilizers and nanomaterials holds promise for further increasing food production and fortifying global food security. Besides, gaps in our scientific discourse persist concerning Si speciation and fractionation within soils, as well as its intricate interplay with PTEs. Nonetheless, future investigations must delve into the precise functions of abiogenic Si within the physiological and biochemical realms of both soil and plants, especially at the critical juncture of the soil-plant interface. This review seeks to comprehensively address the multifaceted roles of Si in plant and soil systems during interactions with PTEs.

Thalassiosira pseudonana (Cyclotella nana) (Hustedt) Hasle et Heimdal (Bacillariophyceae): A genetically tractable model organism for studying diatom biology, including biological silica formation

In 2004, Thalassiosira pseudonana was the first eukaryotic marine alga to have its genome sequenced. Since then, this species has quickly emerged as a valuable model species for investigating the molecular underpinnings of essentially all aspects of diatom life, particularly bio-morphogenesis of the cell wall. An important prerequisite for the model status of T. pseudonana is the ongoing development of increasingly precise tools to study the function of gene networks and their encoded proteins in vivo. Here, we briefly review the current toolbox for genetic manipulation, highlight specific examples of its application in studying diatom metabolism, and provide a peek into the role of diatoms in the emerging field of silica biotechnology.

Microbe-Mineral Interactions between Asbestos and Thermophilic Chemolithoautotrophic Anaerobes

The Fe content and the morphometry of asbestos are two major factors linked to its toxicity. This study explored the use of microbe-mineral interactions between asbestos (and asbestos-like) minerals and thermophilic chemolithoautotrophic microorganisms as possible mineral dissolution treatments targeting their toxic properties. The removal of Fe from crocidolite was tested through chemolithoautotrophic Fe(III) reduction activities at 60°C. Chrysotile and tremolite-actinolite were tested for dissolution and potential release of elements like Si and Mg through biosilicification processes at 75°C. Our results show that chemolithoautotrophic Fe(III) reduction activities by Deferrisoma palaeochoriense were supported with crocidolite as the sole source of Fe(III) used as a terminal electron acceptor during respiration. Microbial Fe(III) reduction activities resulted in higher Fe release rates from crocidolite in comparison to previous studies on Fe leaching from crocidolite through Fe assimilation activities by soil fungi. Evidence of biosilicification in Thermovibrio ammonificans did not correspond with increased Si and Mg release from chrysotile or tremolite-actinolite dissolution. However, overall Si and Mg release from chrysotile into our experimental medium outmatched previously reported capabilities for Si and Mg release from chrysotile by fungi. Differences in the profiles of elements released from chrysotile and tremolite-actinolite during microbe-mineral experiments with T. ammonificans underscored the relevance of underlying crystallochemical differences in driving mineral dissolution and elemental bioavailability. Experimental studies targeting the interactions between chemolithoautotrophs and asbestos (or asbestos-like) minerals offer new access to the mechanisms behind crystallochemical mineral alterations and their role in the development of tailored asbestos treatments. IMPORTANCE We explored the potential of chemosynthetic microorganisms growing at high temperatures to induce the release of key elements (mainly iron, silicon, and magnesium) involved in the known toxic properties (iron content and fibrous mineral shapes) of asbestos minerals. We show for the first time that the microbial respiration of iron from amphibole asbestos releases some of the iron contained in the mineral while supporting microbial growth. Another microorganism imposed on the two main types of asbestos minerals (serpentines and amphiboles) resulted in distinct elemental release profiles for each type of asbestos during mineral dissolution. Despite evidence of microbially mediated dissolution in all minerals, none of the microorganisms tested disrupted the structure of the asbestos mineral fibers. Further constraints on the relationships between elemental release rates, amount of starting asbestos, reaction volumes, and incubation times will be required to better compare asbestos dissolution treatments studied to date.

Picocyanobacteria-A non-negligible group for the export of biomineral silica to ocean depth

Diatoms have long been thought to dominate the marine silicon (Si) cycle, as well as play an important role in the ocean's carbon (C) export, due to density-driven particle sedimentation. Research in the past decade has shed new light on the potential importance of picocyanobacteria to C export, although the sinking mechanism is still unclear. Interestingly, the recent discovery of Si accumulation by picocyanobacteria of the genus Synechococcus has strong implications for the marine Si cycle, which may also have profound influence on the oceanic C export. Understanding the mechanisms of Synechococcus Si accumulation and its ecological effects are therefore critical for addressing wider issues such as Si and C exports by small cells via biological pump. Here, we show that recent advances in process studies indicate that the presence of Si within picocyanobacteria may be a common and universal feature. Subsequently, we generalize four biochemical forms of Si potentially present in picocyanobacterial cells, which are all different from diatomaceous opal-A, and hypothesize that these various structures of Si phases may be several stage products of Si precipitation. At the same time, several aspects of Si dynamics in Synechococcus are also discussed emphatically. In addition, we provide a first estimate of picocyanobacteria Si stock and production for the global ocean, accounting for 12% of the global Si inventory and 45% of the global annual Si production in the surface ocean, respectively. The implication is that picocyanobacteria may exert a significant influence on the marine Si cycle, which is likely to alter our understanding of the long-term control of the oceanic Si cycling by diatoms. Finally, we summarize three possible mechanisms and pathways through which picocyanobacteria-derived Si can be transported to the deep ocean. Altogether, marine picocyanobacteria, despite very small in cell size, are a non-negligible group for the export of biomineral Si to deeper waters and ocean sediments.

Integrative effects of morphology, silicification, and light on diatom vertical movements

Diatoms represent the most abundant and diversified class of primary producers in present oceans; their distinctive trait is the ability to incorporate silicic acid in a silica outer shell called frustule. Numerous adaptative functions are ascribed to frustules, including the control of vertical movements through the water column; this indirectly determines cell access to fundamental resources such as light and nutrients, and favors diatom escape from predators. At the same time, light guides phototroph movements in the water column by affecting cell density (e.g., by modulating Si deposition in diatoms, vacuole volume, and/or solution). We investigated how the tremendous diversity in morphology and silicification that characterizes the frustule and the crucial role of light in diatom spatial distribution govern diatom sinking capacity. To test their integrative effects, we acclimated four diatoms distinguished by frustule traits (Chaetoceros muelleri, Conticribra weissflogii, Phaeodactylum tricornutum, and Cylindrotheca fusiformis) to different light conditions and evaluated their physiological performance in terms of growth, elemental composition, morphological changes, and their in vivo sinking capacity. What emerged from this study was that silicification, more than other morphological characteristics, controls species vertical movements, while a higher energy availability enhances cell floating independently from the silica content.

Intracellular silicification by early-branching magnetotactic bacteria

Biosilicification-the formation of biological structures composed of silica-has a wide distribution among eukaryotes; it plays a major role in global biogeochemical cycles, and has driven the decline of dissolved silicon in the oceans through geological time. While it has long been thought that eukaryotes are the only organisms appreciably affecting the biogeochemical cycling of Si, the recent discoveries of silica transporter genes and marked silicon accumulation in bacteria suggest that prokaryotes may play an underappreciated role in the Si cycle, particularly in ancient times. Here, we report a previously unidentified magnetotactic bacterium that forms intracellular, amorphous silica globules. This bacterium, phylogenetically affiliated with the phylum Nitrospirota, belongs to a deep-branching group of magnetotactic bacteria that also forms intracellular magnetite magnetosomes and sulfur inclusions. This contribution reveals intracellularly controlled silicification within prokaryotes and suggests a previously unrecognized influence on the biogeochemical Si cycle that was operational during early Earth history.