Alleviative mechanisms of silicon solubilizing Bacillus amyloliquefaciens mediated diminution of arsenic toxicity in rice

Insight into the genome of an arsenic loving and plant growth-promoting strain of Micrococcus luteus isolated from arsenic contaminated groundwater

Contamination of arsenic in drinking water and foods is a threat for human beings. To achieve the goal for the reduction of arsenic availability, besides conventional technologies, arsenic bioremediation by using some potent bacteria is one of the hot topics for researchers. In this context, bacterium, AKS4c was isolated from arsenic contaminated water of Purbasthali, West Bengal, India, and through draft genome sequence; it was identified as a strain of Micrococcus luteus that comprised of 2.4 Mb genome with 73.1% GC content and 2256 protein coding genes. As the accessory genome, about 22 genomic islands (GIs) associated with many metal-resistant genes were identified. This strain was capable to tolerate more than 46,800 mg/L arsenate and 390 mg/L arsenite salts as well as found to be tolerable to multi-metals such as Fe, Pb, Mo, Mn, and Zn up to a certain limit of concentrations. Strain AKS4c was able to oxidize arsenite to less toxic arsenate, and its arsenic adsorption property was qualitatively confirmed through X-ray fluorescence (XRF) and Fourier transform infrared spectroscopy (FTIR) analysis. Quantitative estimation of plant growth-promoting attributes like Indole acetic acid (IAA), Gibberellic acid (GA), and proline production and enhancement of rice seedling growth in laboratory condition leads to its future applicability in arsenic bioremediation as a plant growth-promoting rhizobacteria (PGPR).

Modifying humus-phosphorus-arsenic interactions in sludge composting: The strengthening of phosphorus availability and arsenic efflux detoxification mechanisms

Arsenic (As) in sewage sludge poses a significant threat to environmental and human health, which has attracted widespread attention. This study investigated the value of adding sodium percarbonate (SP) on phosphorus (P) availability and As efflux detoxification through HS-P-As interactions. Due to the unique structure of humus (HS) and the similar chemical properties of P and As, the conditions for HS-P-As interaction are provided. This study discussed the content, morphology and microbial communities of HS, P and As by using metagenomic and correlation analysis. The results showed that the humification index in the experiment group (SPC) was 2.34 times higher than that in the control group (CK). The available phosphorus (AP) content of SPC increased from 71.09 mg/kg to 126.14 mg/kg, and SPC was 1.11 times that of CK. The relative abundance of ACR3/ArsB increased. Pst, Actinomyces and Bacillus commonly participated in P and As conversion. The correlation analysis revealed that the humification process was enhanced, the AP was strengthened, and the As was efflux detoxified after SP amendment. All in all, this study elucidated the key mechanism of HS-P-As interaction and put forward a new strategy for sewage sludge resource utilization and detoxification.

Integrated genome-transcriptome analysis unveiled the mechanism of Debaryomyces hansenii-mediated arsenic stress amelioration in rice

Globally, rice is becoming more vulnerable to arsenic (As) pollution, posing a serious threat to public food safety. Previously Debaryomyces hansenii was found to reduce grain As content of rice. To better understand the underlying mechanism, we performed a genome analysis to identify the key genes in D. hansenii responsible for As tolerance and plant growth promotion. Notably, genes related to As resistance (ARR, Ycf1, and Yap) were observed in the genome of D. hansenii. The presence of auxin pathway and glutathione metabolism-related genes may explain the plant growth-promoting potential and As tolerance mechanism of this novel yeast strain. The genome annotation of D. hansenii indicated that it contains a repertoire of genes encoding antioxidants, well corroborated with the in vitro studies of GST, GR, and glutathione content. In addition, the effect of D. hansenii on gene expression profiling of rice plants under As stress was also examined. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database revealed 307 genes, annotated in D. hansenii-treated rice, related to metabolic pathways (184), photosynthesis (12), glutathione (10), tryptophan (4), and biosynthesis of secondary metabolite (117). Higher expression of regulatory elements like AUX/IAA and WRKY transcription factors (TFs), and defense-responsive genes dismutases, catalases, peroxiredoxin, and glutaredoxins during D. hansenii+As exposure was also observed. Combined analysis revealed that D. hansenii genes are contributing to stress mitigation in rice by supporting plant growth and As-tolerance. The study lays the foundation to develop yeast as a beneficial biofertilizer for As-prone areas.

Metagenomic and biochemical analyses reveal the potential of silicon to alleviate arsenic toxicity in rice (Oryza sativa L.)

Arsenic (As) pollution in agricultural systems poses a serious threat to crop productivity and food safety. Silicon (Si) has been reported to mitigate toxic effects of heavy metals in plants. However, the mechanisms behind Si-mediated alleviation of As toxicity in rice (Oryza sativa L.) remain poorly understood. Here, we performed metagenomic and biochemical analyses to investigate the potential of Si in alleviating As toxicity to rice plants. As exposure reduced plant growth, chlorophyll contents, antioxidant enzyme levels and soil enzymes activity, while increasing reactive oxygen species (ROS) activity and inducing alterations in the rhizosphere microbiome of rice seedlings. Silicon amendments enhanced rice growth (24%), chlorophyll a (25%), and chlorophyll b (26.7%), indicating enhanced photosynthetic capacity. Si amendments also led to the upregulation of antioxidant enzymes viz., superoxide dismutase (15.4%), and peroxidase (15.6%), resulting in reduced ROS activity and oxidative stress compared to the As-treated control. Furthermore, Si treatment reduced uptake and translocation of As in rice plants, as evidenced by the analysis of elemental contents. Microscopic examination of leaf and root ultrastructure showed that Si mitigated As-induced cellular damage and maintained normal morphology. Metagenomic analysis of the rice rhizosphere microbiome revealed that Si application modulated composition and diversity of microbial communities e.g., Proteobacteria, Actinobacteria, and Firmicutes. Additionally, Si amendments upregulated the relative expression levels of OsGSH, OsPCs, OsNIP1;1 and OsNIP3;3 genes, while the expression levels of the OsLis1 and OsLis2 genes were significantly downregulated compared with As-treated rice plants. Overall, these findings contribute to our understanding of Si-mediated plant resilience to As stress and offer potential strategies for sustainable agriculture in As-contaminated regions.

Endophytic biofungicide Bacillus subtilis (NBRI-W9) reshapes the metabolic homeostasis disrupted by the chemical fungicide, propiconazole in tomato plants to provide sustainable immunity against non-target bacterial pathogens

Chemical and microbial fungicides (Bio/fungicide) act differentially on plant systems. The present work assessed the metabolic profile of tomato plants vis-a-vis endophytic diversity after spraying of Propiconazole (PCZ) and endophytic biofungicide Bacillus subtilis (W9). Bio/fungicides were sprayed on tomato plants and evaluated for phenotypic, biochemical, and metabolic profiles after one week. In W9 treatment, a significant increase in relative abundance of several metabolites was observed including sugars, sugar alcohols, fatty-acids, organic-acids, and amino-acids. Polysaccharides and fatty acids showed a significant positive correlation with Rhizobiales, Burkholderiales, Bacillales, and Lactobacillales, respectively (p < 0.05). The PCZ and W9 treated plant's metabolic status significantly affected their resistance to non-target, bacterial pathogen P. syringae. Compared to PCZ and control, W9 treatment reduced the ROS deposition and expression of antioxidants gene GPx, PO (~0.1-1.7fold). It enhanced the genes related to the Phenylpropanoid pathway (∼1.6-5.2 fold), PR protein (~1.2-3.4 fold), and JA biosynthesis (~1.7-4.3 fold), resulting in reduced disease incidence. The results provide novel insights into the effects of endophytic biofungicide and chemical fungicides on the plant's metabolic status, its relation to the endophytes, and role in altering the plant's immune system.

Advances in the Involvement of Metals and Metalloids in Plant Defense Response to External Stress

Plants, as sessile organisms, uptake nutrients from the soil. Throughout their whole life cycle, they confront various external biotic and abiotic threats, encompassing harmful element toxicity, pathogen infection, and herbivore attack, posing risks to plant growth and production. Plants have evolved multifaceted mechanisms to cope with exogenous stress. The element defense hypothesis (EDH) theory elucidates that plants employ elements within their tissues to withstand various natural enemies. Notably, essential and non-essential trace metals and metalloids have been identified as active participants in plant defense mechanisms, especially in nanoparticle form. In this review, we compiled and synthetized recent advancements and robust evidence regarding the involvement of trace metals and metalloids in plant element defense against external stresses that include biotic stressors (such as drought, salinity, and heavy metal toxicity) and abiotic environmental stressors (such as pathogen invasion and herbivore attack). We discuss the mechanisms underlying the metals and metalloids involved in plant defense enhancement from physiological, biochemical, and molecular perspectives. By consolidating this information, this review enhances our understanding of how metals and metalloids contribute to plant element defense. Drawing on the current advances in plant elemental defense, we propose an application prospect of metals and metalloids in agricultural products to solve current issues, including soil pollution and production, for the sustainable development of agriculture. Although the studies focused on plant elemental defense have advanced, the precise mechanism under the plant defense response still needs further investigation.

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.

Arsenic stress management through arsenite and arsenate-tolerant growth-promoting bacteria in rice

Arsenic (As) contamination is a major problem affecting soil and groundwater in India, harming agricultural crops and human health. Plant growth-promoting rhizobacteria (PGPR) have emerged as promising agents for reducing As toxicity in plants. This study aimed to isolate and characterize As-tolerant PGPR from rice field soils with varying As levels in five districts of West Bengal, India. A total of 663 bacterial isolates were obtained from the different soil samples, and 10 bacterial strains were selected based on their arsenite (As-III) and arsenate (As-V) tolerant ability and multiple PGP traits, including phosphate solubilization, production of siderophore, indole acetic acid, biofilm formation, alginate, and exopolysaccharide. These isolates were identified by 16S rRNA gene sequencing analysis as Staphylococcus sp. (4), Niallia sp. (2), Priestia sp. (1), Bacillus sp. (1), Pseudomonas sp. (1), and Citricoccus sp. (1). Among the selected bacterial strains, Priestia flexa NBRI4As1 and Pseudomonas chengduensis NBRI12As1 demonstrated significant improvement in rice growth by alleviating arsenic stress under greenhouse conditions. Both strains were also able to modulate photosynthetic pigments, soluble sugar content, proline concentration, and defense enzyme activity. Reduction in As-V accumulation inoculated with NBRI4As1 was recorded highest by 53.02% and 31.48%, while As-III by NBRI12As1 38.84% and 35.98% in the roots and shoots of rice plants, respectively. Overall, this study can lead to developing efficient As-tolerant bacterial strains-based bioinoculant application packages for arsenic stress management in rice.

A critical analysis of various post-harvest arsenic removal treatments of rice and their impact on public health due to nutrient loss

Rice (Oryza sativa L.) is particularly susceptible to arsenic (As) accumulation. Currently, to decrease the level of As accumulated in rice, various post-harvest methods, i.e., polishing, parboiling, pH-dependent soaking, washing, and cooking at different rice-to-water ratios (r/w), are being focused, because it removes significant amount of As from rice grain. Depending upon the rice variety and type, i.e., rough (with husk), husked (without husk/brown), or polished rice, these methods can remove 39-54% As by parboiling, 38-55% by polishing, 37-63% by soaking, and 6-80% by washing and cooking. Infants are highly vulnerable to As exposure; thus, these methods can be helpful for the production of rice-based infant foods. Although concern arises during the use of these methods that apart from decreasing the level of As in rice grain, they also lead to a significant loss of nutrients, such as macro- and micro-elements present in rice. Among these discussed methods, parboiling curtails 5-59%, polishing curtails 6-96%, soaking curtails 33-83%, and washing and cooking in different r/w reduce 8-81% of essential nutrients resulting in 2-90% reduction in contribution to the RDI of these nutrients through rice-based diet. Thus, these post-harvest arsenic removal methods, although reduce arsenic induced health hazard, but may also lead to malnutrition and compromised health in the population based on rice diet. There is a need to explore another way to reduce As from rice without compromising the nutrient availability or to supplement these nutrients through grain enrichment or by introducing additional dietary sources by changing eating habits; however, this may impose an extra economic burden on people.

Wheat PHT1;9 acts as one candidate arsenate absorption transporter for phytoremediation

Arsenate (AsV) is one of the most common forms of arsenic (As) in environment and plant high-affinity phosphate transporters (PHT1s) are the primary plant AsV transporters. However, few PHT1s involved in AsV absorption have been identified in crops. In our previous study, TaPHT1;3, TaPHT1;6 and TaPHT1;9 were identified to function in phosphate absorption. Here, their AsV absorption capacities were evaluated using several experiments. Ectopic expression in yeast mutants indicated that TaPHT1;9 had the highest AsV absorption rates, followed by TaPHT1;6, while not for TaPHT1;3. Under AsV stress, further, BSMV-VIGS-mediated TaPHT1;9-silencing wheat plants exhibited higher AsV tolerance and lower As concentrations than TaPHT1;6-silenced plants, whereas TaPHT1;3-silencing plants had similar phenotype and AsV concentrations to control. These suggested that TaPHT1;9 and TaPHT1;6 possessed AsV absorption capacity with the former showing higher activities. Under hydroponic condition, furthermore, CRISPR-edited TaPHT1;9 wheat mutants showed the enhanced tolerance to AsV with decreased As distributions and concentrations, whereas TaPHT1;9 ectopic expression transgenic rice plants had the opposite results. Also, under AsV-contaminated soil condition, TaPHT1;9 transgenic rice plants exhibited depressed AsV tolerance with increased As concentrations in roots, straws and grains. Moreover, Pi addition alleviated the AsV toxicity. These suggested that TaPHT1;9 should be a candidate target gene for AsV phytoremediation.

Evaluating the efficacy and feasibility of post harvest methods for arsenic removal from rice grain and reduction of arsenic induced cancer risk from rice-based diet

Food-chain arsenic (As) contamination is a severe environmental and health problem worldwide, and its intake through rice affects billions of people. In this review, we have summarized the post harvest As removal methods from rice and their efficacy and feasibility. Rice grain subspecies (indica and japonica), size (short, medium and long), type (husked, parboiled or polished), soaking time, temperature and rice to water ratio (r/w) during washing and cooking are the major factors that affect the removal of total arsenic (tAs) from rice grain. The reduction in tAs was greater in japonica than indica rice and was directly proportional to As in husked rice. For the removal of As, a low water volume (1:2 r/w) was more effective during washing due to friction between rice grains, while high water (≥4 times water) during cooking was more effective. Up to 80 % As was removed by cooking in 1:10 (rice: water). Soaking rice in edible acids such as vinegar, acetic and ascorbic acid was not effective, except citric acid, which removes tAs up to 63 %. Human-health risk assessment showed that these post harvest and cooking methods reduce the non-carcinogenic and incremental lifetime cancer risk by up to 5-fold, as calculated on the basis of bioaccessible inorganic As. These post harvest methods also remove nutrient elements and vitamins. The recommended dietary intake (RDI) of Zn and Cu was particularly affected (up to 40 and 83 %). The levels of P, Mo, Mn and Co were still sufficient to meet the RDI through the rice-based diet, while rice is already poor in the RDI of Ca, K, Fe and Se, and their levels were further reduced by 0.22-44 %. In conclusion, these post harvest and cooking methods may significantly reduce As induced health risks; however, other dietary sources of nutrients need to be carefully evaluated and supplemented.

Mitigation of arsenic toxicity in rice by the co-inoculation of arsenate reducer yeast with multifunctional arsenite oxidizing bacteria

The study aimed to explicate the role of microbial co-inoculants for the mitigation of arsenic (As) toxicity in rice. Arsenate (AsV) reducer yeast Debaryomyces hansenii NBRI-Sh2.11 (Sh2.11) with bacterial strains of different biotransformation potential was attempted to develop microbial co-inoculants. An experiment to test their efficacy (yeast and bacterial strains) on plant growth and As uptake was conducted under a stressed condition of 20 mg kg-1 of arsenite (AsIII). A combination of Sh2.11 with an As(III)-oxidizer, Citrobacter sp. NBRI-B5.12 (B5.12), resulted in ∼90% decrease in grain As content as compared to Sh2.11 alone (∼40%). Reduced As accumulation in rice roots under co-treated condition was validated with SEM-EDS analysis. Enhanced As expulsion in the selected combination under in vitro conditions was found to be correlated with higher As content in the soil during their interaction with plants. Selected co-inoculant mediated enhanced nutrient uptake in association with better production of indole acetic acid (IAA) and gibberellic acid (GA) in shoot, support microbial co-inoculant mediated better biomass under stressful condition. Boosted defense response in association with enhanced glutathione-S-transferase (GST) and glutathione reductase (GR), activities under in vitro and in vivo conditions were observed. These results indicated that the As(III) oxidizer-B5.12 accelerated the As detoxification property of the As(V) reducer-Sh2.11. Henceforth, the results confer that the coupled reduction-oxidation process of the co-inoculant reduces the accumulation of As in rice grain. These co-inoculants can be further developed for field trials to achieve higher biomass with alleviated As toxicity in rice.

Bacillus amyloliquefaciens modulate sugar metabolism to mitigate arsenic toxicity in Oryza sativa L. var Saryu-52

In the current study, plant growth-promoting rhizobacterium Bacillus amyloliquefaciens SN13 (SN13) was evaluated for arsenic (As) toxicity amelioration potential under arsenate (AsV) and arsenite (AsIII) stress exposed to rice (Oryza sativa var Saryu-52) plants for 15 days. The PGPR-mediated alleviation of As toxicity was demonstrated by modulated measures such as proline, total soluble sugar, malondialdehyde content, enzymatic status, relative water content, and electrolytic leakage in treated rice seedlings under arsenic-stressed conditions as compared to the respective control. SN13 inoculation not only improved the agronomic traits but also modulated the micronutrient concentrations (Fe, Mo, Zn, Cu, and Co). The desirable results were obtained due to a significant decrease in the AsIII and AsV accumulation in the shoot (47 and 10 mg kg-1 dw), and the root (62 and 26 mg kg-1 dw) in B. amyloliquefaciens inoculated seedlings as compared to their uninoculated root (98 and 43 mg kg-1 dw) and shoot (57 and 12 mg kg-1 dw), respectively. Further, metabolome (GC-MS) analysis was performed to decipher the underlying PGPR-induced mechanisms under arsenic stress. A total of 67 distinct metabolites were identified, which influence the metabolic and physiological factors to modulate the As stress. The expression analysis of metabolism- and stress-responsive genes further proclaimed the involvement of SN13 through modulating the carbohydrate metabolism in rice seedlings, to enable improved growth and As stress tolerance.

Recent advances in arsenic mitigation in rice through biotechnological approaches

Arsenic (As) is a major threat to the environment and human health due to its toxicity and carcinogenicity. Occurrence of alarming concentrations of As in water and soil leads to its bioaccumulation in crops which is a major health concern globally. Rice (Oryza sativa) is a staple food for a large population staying in As contaminated areas so, it is of utmost importance to reduce As levels in rice, especially grains. Amongst several strategies in practice, biotechnology may provide an effective option to reduce As accumulation in rice grains. Genetic engineering can be a viable approach to exploit potential genes playing roles in As metabolism pathway in plants. Besides, developing low As accumulating rice varieties through breeding is also an important area. Identifying genotypic variation in rice is a crucial step toward the development of a safe rice cultivar for growing in As-affected areas. Significant genotypic variation has been found in rice varieties for As accumulation in grains and that is attributable to differential expression of transporters, radial oxygen loss, and other regulators of As stress. This review provides recent updates on the research advances leading to transgenic and breeding approaches adopted to reduce As levels in rice, especially grains.