Isolation and the interaction between a mineral-weathering Rhizobium tropici Q34 and silicate minerals

Exploring the potential: Can arsenic (As) resistant silicate-solubilizing bacteria manage the dual effects of silicon on As accumulation in rice?

Rice (Oryza sativa L.) cultivation in regions marked by elevated arsenic (As) concentrations poses significant health concerns due to As uptake by the plant and its subsequent entry into the human food chain. With rice serving as a staple crop for a substantial share of the global population, addressing this issue is critical for food security. In flooded paddy soils, where As availability is pronounced, innovative strategies to reduce As uptake and enhance agricultural sustainability are mandatory. Silicon (Si) and Si nanoparticles have emerged as potential candidates to mitigate As accumulation in rice. However, their effects on As uptake exhibit complexity, influenced by initial Si levels in the soil and the amount of Si introduced through fertilization. While low Si additions may inadvertently increase As uptake, higher Si concentrations may alleviate As uptake and toxicity. The interplay among existing Si and As availability, Si supplementation, and soil biogeochemistry collectively shapes the outcome. Adding water-soluble Si fertilizers (e.g., Na2SiO3 and K2SiO3) has demonstrated efficacy in mitigating As toxicity stress in rice. Nonetheless, the expense associated with these fertilizers underscores the necessity for low cost innovative solutions. Silicate-solubilizing bacteria (SSB) resilient to As hold promise by enhancing Si availability by accelerating mineral dissolution within the rhizosphere, thereby regulating the Si biogeochemical cycle in paddy soils. Promoting SSB could make cost-effective Si sources more soluble and, consequently, managing the intricate interplay of Si's dual effects on As accumulation in rice. This review paper offers a comprehensive exploration of Si's nuanced role in modulating As uptake by rice, emphasizing the potential synergy between As-resistant SSB and Si availability enhancement. By shedding light on this interplay, we aspire to shed light on an innovative attempt for reducing As accumulation in rice while advancing agricultural sustainability.

Impact of Silicon on Plant Nutrition and Significance of Silicon Mobilizing Bacteria in Agronomic Practices

Globally, rejuvenation of soil health is a major concern due to the continuous loss of soil fertility and productivity. Soil degradation decreases crop yields and threatens global food security. Improper use of chemical fertilizers coupled with intensive cultivation further reduces both soil health and crop yields. Plants require several nutrients in varying ratios that are essential for the plant to complete a healthy growth and development cycle. Soil, water, and air are the sources of these essential macro- and micro-nutrients needed to complete plant vegetative and reproductive cycles. Among the essential macro-nutrients, nitrogen (N) plays a significant in non-legume species and without sufficient plant access to N lower yields result. While silicon (Si) is the 2nd most abundant element in the Earth’s crust and is the backbone of soil silicate minerals, it is an essential micro-nutrient for some plants. Silicon is just beginning to be recognized as an important micronutrient to some plant species and, while it is quite abundant, Si is often not readily available for plant uptake. The manufacturing cost of synthetic silica-based fertilizers is high, while absorption of silica is quite slow in soil for many plants. Rhizosphere biological weathering processes includes microbial solubilization processes that increase the dissolution of minerals and increases Si availability for plant uptake. Therefore, an important strategy to improve plant silicon uptake could be field application of Si-solubilizing bacteria. In this review, we evaluate the role of Si in seed germination, growth, and morphological development and crop yield under various biotic and abiotic stresses, different pools and fluxes of silicon (Si) in soil, and the bacterial genera of the silicon solubilizing microorganisms. We also elaborate on the detailed mechanisms of Si-solubilizing/mobilizing bacteria involved in silicate dissolution and uptake by a plant in soil. Last, we discuss the potential of silicon and silicon solubilizing/mobilizing to achieve environmentally friendly and sustainable crop production.

The use of soil microbial potassium solubilizers in potassium nutrient availability in soil and its dynamics

Background

An increase in population has led to a higher demand for food. Meeting up this demand has necessitated the use of chemical fertilizers. However, utilization of these fertilizers has a considerable deleterious effect on the soil, plant, human, environmental sustainability, and only increase the cost and reduced profitability. With these identified problems, there is a need for efficient and sustainable methods regarding managing natural resources to enhance food production. Naturally, potassium (K) is an abundant element present in the soil but in an inaccessible form. There is therefore a need to seek an alternative method to improve the K availability to plants noting that K is an essential plant nutrient that plays a major role in plant physiological and metabolic processes. Subsequently, employing microbial potassium solubilizers is an efficient method to enhance the potassium availability in the soil, which in turn improves productivity. Therefore, this review discusses the various types of potassium solubilizing microorganisms in soil, their mechanism of action, and their importance in sustainable crop production.

Main body

Potassium solubilizing microorganisms (KSM) such as bacteria and fungi can solubilize K from an insoluble form to a soluble form to enhance uptake by plants. These microorganisms solubilize K through the production of organic acids such as tartaric acid, citric acid, and oxalic acid to release K from its minerals. Apart from making potassium available, these microbes can improve soil health and crop yield and act as bio-control agents by producing antibiotics. Potassium solubilizing microbes also produce hormones that help plants withstand both biotic and abiotic stresses. Hence, the application of KSM to agricultural soils will reduce the use of chemical fertilizers and enhance the sustainability of food production.

Conclusion

One of the most efficient ways of improving plant utilization of potassium in the soil is to use potassium solubilizing microbes, which can make potassium ions available from minerals of both igneous and sedimentary origins. The use of potassium solubilizing microbes as biofertilizers may be the awaited solution to increasing crop productivity, concerns linked to chemical fertilizer application, and earth resource diminution.

The Multiple Role of Silicon Nutrition in Alleviating Environmental Stresses in Sustainable Crop Production

In addition to the application of macronutrients (N, P, K), there has been an increasing interest in studying the effects of different micronutrients on growth and development in plant populations under abiotic and biotic stresses. Experimental results have demonstrated the role of silicon in mitigating environmental stresses on plants (especially in silicon accumulating plant species). Furthermore, as the silicon content of soils available to plants can vary greatly depending on soil type, the many positive results have led to increased interest in silicon as a nutrient in sustainable agriculture over the last decade. The grouping of plant species according to silicon accumulation is constantly changing as a result of new findings. There are also many new research results on the formation of phytoliths and their role in the plants. The use of silicon as a nutrient is becoming more widespread in crop production practices based on research results reporting beneficial effects. Controversial results have also been obtained on the use of different Si-containing materials as fertilizers. Many questions remain to be clarified about the uptake, transport, and role of silicon in plant life processes, such as stress management. Future research is needed to address these issues. This review discusses the role and beneficial effects of silicon in plants as a valuable tool for regulating biological and abiotic stresses. Our aim was to provide an overview of recent research on the role and importance of silicon in sustainable crop production and to highlight possible directions for further research.

Exploration of silicate solubilizing bacteria for sustainable agriculture and silicon biogeochemical cycle

Silicon (Si), a quasi-essential element for plants, is abundant in the soil typically as insoluble silicate forms. However, plants can uptake Si only in the soluble form of monosilicic acid. Production of monosilicic acid by rock-weathering mostly depends on temperature, pH, redox-potential, water-content, and microbial activities. In the present review, approaches involved in the efficient exploration of silicate solubilizing bacteria (SSB), its potential applications, and available technological advances are discussed. Present understanding of Si uptake, deposition, and subsequent benefits to plants has also been discussed. In agricultural soils, pH is found to be one of the most critical factors deciding silicate solubilization and the formation of different Si compounds. Numerous studies have predicted the role of Indole-3-Acetic Acid (IAA) and organic acids produced by SSB in silicate solubilization. In this regard, approaches for the isolation and characterization of SSB, quantification of IAA, and subsequent Si solubilization mechanisms are addressed. Phylogenetic evaluation of previously reported SSB showed a highly diverse origin which provides an opportunity to study different mechanisms involved in Si solubilization. Soil biochemistry in concern of silicon availability, microbial activity and silicon mediated changes in plant physiology are addressed. In addition, SSB's role in Si-biogeochemical cycling is summarized. The information presented here will be helpful to explore the potential of SSB more efficiently to promote sustainable agriculture.

Contribution of Arbuscular Mycorrhizal Fungi, Phosphate-Solubilizing Bacteria, and Silicon to P Uptake by Plant

Phosphorus (P) availability is usually low in soils around the globe. Most soils have a deficiency of available P; if they are not fertilized, they will not be able to satisfy the P requirement of plants. P fertilization is generally recommended to manage soil P deficiency; however, the low efficacy of P fertilizers in acidic and in calcareous soils restricts P availability. Moreover, the overuse of P fertilizers is a cause of significant environmental concerns. However, the use of arbuscular mycorrhizal fungi (AMF), phosphate-solubilizing bacteria (PSB), and the addition of silicon (Si) are effective and economical ways to improve the availability and efficacy of P. In this review the contributions of Si, PSB, and AMF in improving the P availability is discussed. Based on what is known about them, the combined strategy of using Si along with AMF and PSB may be highly useful in improving the P availability and as a result, its uptake by plants compared to using either of them alone. A better understanding how the two microorganism groups and Si interact is crucial to preserving soil fertility and improving the economic and environmental sustainability of crop production in P deficient soils. This review summarizes and discusses the current knowledge concerning the interactions among AMF, PSB, and Si in enhancing P availability and its uptake by plants in sustainable agriculture.

Silicon-Solubilizing Media and Its Implication for Characterization of Bacteria to Mitigate Biotic Stress

Silicon (Si), the second most abundant element on earth, remains unavailable for plants' uptake due to its poor solubility. Microbial interventions to convert it in soluble forms are well documented. However, studies on discrimination of Si and P solubilizing microbes due to common estimation method and sharing of solubilization mechanism are still obscure. A defined differential media, i.e. silicon-solubilizing media (NBRISSM) is developed to screen Si solubilizers. NBRISN13 (Bacillus amyloliquefaciens), a Si solubilizer, exhibiting antagonistic property against Rhizoctonia solani, was further validated for disease resistance. The key finding of the work is that NBRISSM is a novel differential media for screening Si solubilizers, distinct from P solubilizers. Dominance of Pseudomonas and Bacillus spp. for the function of Si solubilization was observed during diversity analysis of Si solubilizers isolated from different rhizospheres. Sphingobacterium sp., a different strain has been identified for silicon solubilization other than Pseudomonas and Bacillus sp. Role of acidic phosphatase during Si solubilization has been firstly reported in our study in addition to other pH dependent phenomenon. Study also showed the combinatorial effect of feldspar and NBRISN13 on elicited immune response through (i) increased Si uptake, (ii) reduced disease severity, (iii) modulation of cell wall degrading and antioxidative enzyme activities, and (iv) induced defense responsive gene expression.

Distinct biotite-weathering activities of Arthrobacter pascens F74 under different contact conditions

Bacteria play important roles in mineral weathering and soil formation. However, little is known regarding the interactions between biotite and Arthrobacter strains. In this study, the mineral-mineral activities of the Arthrobacter pascens F74 isolated from a weathered rock surface were evaluated for its weathering behavior under direct contact and no contact with biotite. No contact was obtained by using dialysis bags. When directly in contact with biotite, Al and Fe concentrations increased by 9- to 47-fold compared with the controls in the presence of strain F74. Furthermore, strain F74 increased mobilized Al by 106% to 175% and Fe by 29% to 123% under direct contact than under no contact conditions. During biotite dissolution, significantly higher cell numbers and lower pH in the culture medium were observed in the presence of strain F74 under direct contact conditions than under no contact conditions. Significantly higher gluconic acid concentration and glucose dehydrogenase activity were found under direct contact conditions than under no contact and no biotite conditions. Scanning electron microscopy analysis showed cell adhesion on the biotite surface. These results demonstrated that strain F74 behaved differently with respect to biotite-weathering effectiveness and mechanisms under different contact conditions. The results also suggested that direct contact between biotite and strain F74 was important for the production of gluconic acid, cell adhesion on the mineral surface, and the mineral dissolution of the strain.

Distinct Mineral Weathering Behaviors of the Novel Mineral-Weathering Strains Rhizobium yantingense H66 and Rhizobium etli CFN42

Bacteria play important roles in mineral weathering, soil formation, and element cycling. However, little is known about the interaction between silicate minerals and rhizobia. In this study, Rhizobium yantingense H66 (a novel mineral-weathering rhizobium) and Rhizobium etli CFN42 were compared with respect to potash feldspar weathering, mineral surface adsorption, and metabolic activity during the mineral weathering process. Strain H66 showed significantly higher Si, Al, and K mobilization from the mineral and higher ratios of cell numbers on the mineral surface to total cell numbers than strain CFN42. Although the two strains produced gluconic acid, strain H66 also produced acetic, malic, and succinic acids during mineral weathering in low- and high-glucose media. Notably, higher Si, Al, and K releases, higher ratios of cell numbers on the mineral surface to total cell numbers, and a higher production of organic acids by strain H66 were observed in the low-glucose medium than in the high-glucose medium. Scanning electron microscope analyses of the mineral surfaces and redundancy analysis showed stronger positive correlations between the mineral surface cell adsorption and mineral weathering, indicated by the dissolved Al and K concentrations. The results showed that the two rhizobia behaved differently with respect to mineral weathering. The results suggested that Rhizobium yantingense H66 promoted potash feldspar weathering through increased adsorption of cells to the mineral surface and through differences in glucose metabolism at low and high nutrient concentrations, especially at low nutrient concentrations.

IMPORTANCE

This study reported the potash feldspar weathering, the cell adsorption capacity of the mineral surfaces, and the metabolic differences between the novel mineral-weathering Rhizobium yantingense H66 and Rhizobium etli CFN42 under different nutritional conditions. The results showed that Rhizobium yantingense H66 had a greater ability to weather the mineral in low- and high-glucose media, especially in the low-glucose medium. Furthermore, Rhizobium yantingense H66 promoted mineral weathering through the increased adsorption of cells to the mineral surface and through increased organic acid production. Our results allow us to better comprehend the roles of different rhizobia in silicate mineral weathering, element cycling, and soil formation in various soil environments, providing more insight into the geomicrobial contributions of rhizobia to these processes.

Complete genome sequence and comparative genome analysis of the Paenibacillus mucilaginosus K02

AIM

Paenibacillus mucilaginosus (P. mucilaginosus) K02 is implicated in mineral weathering. However, relevant molecular mechanisms remain obscure. The study aims to uncover the bacterium's physiological processes using genomic approaches.

METHODS AND RESULTS

Genomic DNA from P. mucilaginosus K02 was sequenced using high-throughput Solexa sequencing technology and then conducted for Clusters of Orthologous Group (COG) annotation. Thereafter, genome sequences of K02 were compared with two strains, 3016 and KNP414. Mummer was applied for collinearity analysis of three P. mucilaginosus genomes. BLAST was used to identify pan and core genes in these strains. Finally, a phylogenetic tree was constructed using the maximum likelihood method by TreeBeST. Complete genome sequence of P. mucilaginosus K02 indicated the strain comprises one circular chromosome with 8,819,200 bases containing 58.3% GC content and 84.75% coding regions. A total of 7299 predicted ORFs were identified in the genome, among them, several genes were related to carbonic anhydrase (CA), and exopolysaccharide biosynthesis and secretion. Moreover, proteins of the predicted genes were annotated in COG categories such as "Carbohydrate transport and metabolism" and "Inorganic ion transport and metabolism." In comparison with KNP414 and 3016, K02 exhibited chromosomal recombination or transposition. A total of 6662 core genes were identified among three P. mucilaginosus strains. The phylogenomic study indicated that P. mucilaginosus K02 was clustered with P. mucilaginosus strains 3016 and KNP414.

CONCLUSIONS

In P. mucilaginosus K02, genes related to CA and exopolysaccharide biosynthesis and secretion, and that involved in metabolism-related processes might play significant roles in mineral weathering.