Improved grain yield and lowered arsenic accumulation in rice plants by inoculation with arsenite-oxidizing Achromobacter xylosoxidans GD03

Balancing application of plant growth-promoting bacteria and biochar in promoting selenium biofortification and remediating combined heavy metal pollution in paddy soil

Plant-growth-promoting bacteria (PGPB) and biochar have attracted increasing attention for remediating the combined pollution of arsenic (As) and cadmium (Cd) and promoting selenium (Se) biofortification. However, their differing effects on the bioavailability of As, Cd, and Se and their absorption by rice are still poorly understood. In this study, PGP Agrobacterium sp. T3F4 with Se- oxidizing capacity and corn straw biochar were applied to natively polluted paddy soil. Strain T3F4 reduced the bioavailability of As in soil but increased bioavailable Se, decreasing the As content in rice by 16.8% and improving the Se content of rice by 54.5% (p < .05). Application of 2.5% biochar stimulated iron (Fe) plaque formation of the root and immobilized As and Cd in the soil, decreasing the As and Cd absorption of rice by 14.7% and 40.3%, respectively (p < .05). Application of 5.0% biochar achieved similar mitigation effects for As and Cd but also decreased the Se content in rice by 60.6% by reducing bioavailability. This decrease in Se uptake was mitigated when 5.0% biochar was co-applied with strain T3F4. Notably, applying strain T3F4 also alleviated the oxidative stress on rice plants and enhanced soil enzyme activities, contributing to a substantial increase in grain yield in the polluted paddy soil. The adverse effects of 5.0% biochar on soil health and grain yield were mitigated by the co-application of strain T3F4. Our results provide new insights into applying PGPB and biochar for Se biofortification and As and Cd remediation in paddy soil.

Genome Deletions and Rewiring of the Transcriptome Underlying High Antimonite Resistance in Achromobacter sp. SMAs-55

Microbes have been shown to adapt to stressful or even lethal conditions through displaying genome plasticity. However, how bacteria utilize the ability of genomic plasticity to deal with high antimony (Sb) stress has remained unclear. In this study, the spontaneous mutant strain SMAs-55 of Achromobacter sp. As-55 was obtained under antimonite (Sb(III)) stress. SMAs-55 displayed significantly increased Sb(III) resistance, but it lost the ability to oxidize arsenite (As(III)) by deleting an entire gene island containing genes encoding functions involved in As(III) oxidation, arsenic (As)/Sb resistance and phosphate transport. This study suggests that genetic plasticity has played an important role in As-55 adaption to Sb(III) stress. Transcriptomic analysis found that genes encoding functions involved in capsule polysaccharide synthesis, as well as functions correlated to stress adaptation, ATP production, and metabolism were more strongly expressed in SMAs-55. In addition, a lower intracellular Sb(III) accumulation in SMAs-55 was observed. These findings indicate that reduced uptake through increased capsule biosynthesis was an effective way for SMAs-55 to adapt to an environment displaying high levels of Sb. This study helps us to better understand the evolutionary processes enabling survival of microbes and microbial community in contaminated environments.

Effects of the combined regulation of nitrogen, phosphorus, and potassium nutrients on the migration and transformation of arsenic species in paddy soil

Nitrogen (N), phosphorus (P) and potassium (K) are three macroelements in agriculture production, but their combined effects on arsenic (As) toxicity and its translocation in rice plants are not clear. In this study, an orthogonal rotation combination based on different N, P and K (NPK) concentration was first designed to examine their combined effect on the As toxicity, its transformation and migration in rice plants based on the hydroponic culture and pot soil culture. The results showed that 2.0 mg/L arsenite (As(III)) had obvious toxicity on the growth of indica LuYouMingZhan (LYMZ) and the optimal NPK concentration was 28.41, 6 and 50 mg/L based on the quadratic regression of the recovery rate of chlorophyll SPAD value of indica LYMZ. The optimal NPK combination significantly alleviated the physiological toxicity of As(III) on indica LYMZ rice seedling and decreased the accumulation of inorganic As in their roots and shoots by 23.8±1.8 % and 33.4±2.4 % respectively; further pot culture from different As(III) polluted soil showed that the optimal NPK combination significantly increased the dry weight of roots, stems, sheaths and leaves of indica LYMZ rice plants as well as yield indicators by 6.4 %-61.7 % and 7.1 %-89.8 % respectively, decreased the accumulation of As(III) and arsenate by 6.25 %-100 % and 12.36 %-100 % respectively in their roots, stems, sheaths, leaves, brans and kernels except As(III) concentration in their sheaths, decreased the accumulation of dimethylarsenate in their sheaths, leaves, brans and kernels, and had the best repair effect on the translocation of As species in 50 mg/kg As(III)-added soil. Our study provided a desirable strategy for alleviating As toxicity in paddy soil and reducing As pollution in rice plants.

Arsenite Mediates Selenite Resistance and Reduction in Enterobacter sp. Z1, Thereby Enhancing Bacterial Survival in Selenium Environments

Arsenic (As) is widely present in the environment, and virtually all bacteria possess a conserved ars operon to resist As toxicity. High selenium (Se) concentrations tend to be cytotoxic. Se has an uneven regional distribution and is added to mitigate As contamination in Se-deficient areas. However, the bacterial response to exogenous Se remains poorly understood. Herein, we found that As(III) presence was crucial for Enterobacter sp. Z1 to develop resistance against Se(IV). Se(IV) reduction served as a detoxification mechanism in bacteria, and our results demonstrated an increase in the production of Se nanoparticles (SeNPs) in the presence of As(III). Tandem mass tag proteomics analysis revealed that the induction of As(III) activated the inositol phosphate, butanoyl-CoA/dodecanoyl-CoA, TCA cycle, and tyrosine metabolism pathways, thereby enhancing bacterial metabolism to resist Se(IV). Additionally, arsHRBC, sdr-mdr, purHD, and grxA were activated to participate in the reduction of Se(IV) into SeNPs. Our findings provide innovative perspectives for exploring As-induced Se biotransformation in prokaryotes.

Plant-Disease-Suppressive and Growth-Promoting Activities of Endophytic and Rhizobacterial Isolates Associated with Citrullus colocynthis

This study was conducted to investigate the antagonistic potential of endophytic and rhizospheric bacterial isolates obtained from Citrullus colocynthis in suppressing Fusarium solani and Pythium aphanidermatum and promoting the growth of cucumber. Molecular identification of bacterial strains associated with C. colocynthis confirmed that these strains belong to the Achromobacter, Pantoea, Pseudomonas, Rhizobium, Sphingobacterium, Bacillus, Sinorhizobium, Staphylococcus, Cupriavidus, and Exiguobacterium genera. A dual culture assay showed that nine of the bacterial strains exhibited antifungal activity, four of which were effective against both pathogens. Strains B27 (Pantoea dispersa) and B28 (Exiguobacterium indicum) caused the highest percentage of inhibition towards F. solani (48.5% and 48.1%, respectively). P. aphanidermatum growth was impeded by the B21 (Bacillus cereus, 44.7%) and B28 (Exiguobacterium indicum, 51.1%) strains. Scanning electron microscopy showed that the strains caused abnormality in phytopathogens' mycelia. All of the selected bacterial strains showed good IAA production (>500 ppm). A paper towel experiment demonstrated that these strains improved the seed germination, root/shoot growth, and vigor index of cucumber seedlings. Our findings suggest that the bacterial strains from C. colocynthis are suppressive to F. solani and P. aphanidermatum and can promote cucumber growth. This appears to be the first study to report the efficacy of these bacterial strains from C. colocynthis against F. solani and P. aphanidermatum.

As(III)-Oxidizing Bacteria Alleviate Arsenite Toxicity via Reducing As Accumulation, Elevating Antioxidative Activities and Modulating Ionome in Rice (Oryza sativa L.)

Paddy rice trends to accumulate more arsenic (As) from soils than other terrestrial crops. The toxicity and mobility of As mainly depend on its chemical species. Transformation of arsenite [As(III)] into arsenate [As(V)] would be a promising method to mitigate As toxicity. In the current study, As(III)-oxidizing strain SMS11 isolated from As-contaminated soils was employed for As remediation. Co-cultured with SMS11 alleviated As(III) stress to the rice plants by increasing the length and biomass of rice shoots up to 10% and 15%, respectively. Evaluation of oxidative stress indices showed that the activity of catalase in the rice shoots was weakened when exposed to As(III), increasing the risk of hydroxyl radical (·OH) formation. When co-cultivated with the bacteria, ·OH formation was significantly inhibited in the rice shoots. The ionomes of the rice plants were impacted by the external conditions. As(III) stress significantly disturbed ionome homeostasis in the rice plants. Uptake of As simultaneously elevated the levels of macro and nutrient elements such as Mg, P, K, Ca, and Zn in the rice shoots. The ionomic variation in the rice plants under As(III) stress was mitigated by inoculated with SMS11. The results represented that the As(III)-oxidizing bacteria alleviated external As(III) stress to the rice plants through elevating antioxidative activities and modulating ionome homeostasis.

Endophytic bacterial communities in wild rice (Oryza officinalis) and their plant growth-promoting effects on perennial rice

Endophytic bacterial microbiomes of plants contribute to the physiological health of the host and its adaptive evolution and stress tolerance. Wild rice possesses enriched endophytic bacteria diversity, which is a potential resource for sustainable agriculture. Oryza officinalis is a unique perennial wild rice species in China with rich genetic resources. However, endophytic bacterial communities of this species and their plant growth-promoting (PGP) traits remain largely unknown. In this study, endophytic bacteria in the root, stem, and leaf tissues of O. officinalis were characterized using 16S rRNA gene Illumina sequencing. Culturable bacterial endophytes were also isolated from O. officinalis tissues and characterized for their PGP traits. The microbiome analysis showed a more complex structure and powerful function of the endophytic bacterial community in roots compared with those in other tissue compartments. Each compartment had its specific endophytic bacterial biomarkers, including Desulfomonile and Ruminiclostridium for roots; Lactobacillus, Acinetobacter, Cutibacterium and Dechloromonas for stems; and Stenotrophomonas, Chryseobacterium, Achromobacter and Methylobacterium for leaves. A total of 96 endophytic bacterial strains with PGP traits of phosphate solubilization, potassium release, nitrogen fixation, 1-aminocyclopropane-1-carboxylate (ACC) deaminase secretion, and siderophore or indole-3-acetic acid (IAA) production were isolated from O. officinalis. Among them, 11 strains identified as Enterobacter mori, E. ludwigii, E. cloacae, Bacillus amyloliquefaciens, B. siamensis, Pseudomonas rhodesiae and Kosakonia oryzae were selected for inoculation of perennial rice based on their IAA production traits. These strains showed promising PGP effects on perennial rice seedlings. They promoted plants to form a strong root system, stimulate biomass accumulation, and increase chlorophyll content and nitrogen uptake, which could fulfil the ecologically sustainable cultivation model of perennial rice. These results provide insights into the bacterial endosphere of O. officinalis and its application potential in perennial rice. There is the prospect of mining beneficial endophytic bacteria from wild rice species, which could rewild the microbiome of cultivated rice varieties and promote their growth.

Ionome profiling and arsenic speciation provide evidence of arsenite detoxification in rice by phosphate and arsenite-oxidizing bacteria

Arsenite (As(III)) as the most toxic and mobile form is the dominant arsenic (As) species in flooded paddy fields, resulting in higher accumulation of As in paddy rice than other terrestrial crops. Mitigation of As toxicity to rice plant is an important way to safeguard food production and safety. In the current study, As(III)-oxidizing bacteria Pseudomonas sp. strain SMS11 was inoculated with rice plants to accelerate conversion of As(III) into lower toxic arsenate (As(V)). Meanwhile, additional phosphate was supplemented to restrict As(V) uptake by the rice plants. Growth of rice plant was significantly inhibited under As(III) stress. The inhibition was alleviated by the introduction of additional P and SMS11. Arsenic speciation showed that additional P restricted As accumulation in the rice roots via competing common uptake pathways, while inoculation with SMS11 limited As translocation from root to shoot. Ionomic profiling revealed specific characteristics of the rice tissue samples from different treatment groups. Compared to the roots, ionomes of the rice shoots were more sensitive to environmental perturbations. Both extraneous P and As(III)-oxidizing bacteria SMS11 could alleviate As(III) stress to the rice plants through promoting growth and regulating ionome homeostasis.

Application of glutamic acid improved As tolerance in aromatic rice at early growth stage

To alleviate the arsenic (As) toxicity in aromatic rice, a hydroponic experiment of two As concentrations (0 and 100 μM sodium arsenite: A0, A1), three glutamic acid (Glu) concentrations (0, 100, and 500 μM l-glutamic acid: G0, G1, and G2) with Xiangyaxiangzhan and Meixiangzhan 2 was conducted. Results showed that the root As content were increased under A1G2 but reduced under A1G1 for Xiangyaxiangzhan as compared with A1G0. A decrement of As was transported from root to shoot caused by up-regulated OsABCC1 relative expression in Meixiangzhan 2. Likewise, As stress enhanced the H₂O₂ and malondialdehyde content, resulting in the impaired cell wall observed by transmission electron microscopy. However, compared with A1G0, the superoxide dismutase activity, ascorbic acid, glutathione, proline, and soluble sugar content were increased under A1G1. Additionally, arsenate reductase, monodehydroascorbate reductase activity, Glu, proline, and soluble sugar content were found positively associated with the As accumulation. Further, the metabolome analysis indicated that the pathway of amino acid and arginine biosynthesis were notably enriched after Glu application. Generally, 100 μM Glu application was the better treatment to enhance As tolerance in aromatic rice through up-regulating amino acid biosynthesis with increasing antioxidants and osmolytes to scavenge excessive reactive oxygen species.

Bacterial volatile organic compounds (VOCs) promote growth and induce metabolic changes in rice

Plant growth-promoting bacteria (PGPB) represent an eco-friendly alternative to reduce the use of chemical products while increasing the productivity of economically important crops. The emission of small gaseous signaling molecules from PGPB named volatile organic compounds (VOCs) has emerged as a promising biotechnological tool to promote biomass accumulation in model plants (especially Arabidopsis thaliana) and a few crops, such as tomato, lettuce, and cucumber. Rice (Oryza sativa) is the most essential food crop for more than half of the world's population. However, the use of VOCs to improve this crop performance has not yet been investigated. Here, we evaluated the composition and effects of bacterial VOCs on the growth and metabolism of rice. First, we selected bacterial isolates (IAT P4F9 and E.1b) that increased rice dry shoot biomass by up to 83% in co-cultivation assays performed with different durations of time (7 and 12 days). Metabolic profiles of the plants co-cultivated with these isolates and controls (without bacteria and non-promoter bacteria-1003-S-C1) were investigated via ¹H nuclear magnetic resonance. The analysis identified metabolites (e.g., amino acids, sugars, and others) with differential abundance between treatments that might play a role in metabolic pathways, such as protein synthesis, signaling, photosynthesis, energy metabolism, and nitrogen assimilation, involved in rice growth promotion. Interestingly, VOCs from IAT P4F9 displayed a more consistent promotion activity and were also able to increase rice dry shoot biomass in vivo. Molecular identification by sequencing the 16S rRNA gene of the isolates IAT P4F9 and E.1b showed a higher identity with Serratia and Achromobacter species, respectively. Lastly, volatilomes of these and two other non-promoter bacteria (1003-S-C1 and Escherichia coli DH5α) were evaluated through headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry. Compounds belonging to different chemical classes, such as benzenoids, ketones, alcohols, sulfide, alkanes, and pyrazines, were identified. One of these VOCs, nonan-2-one, was validated in vitro as a bioactive compound capable of promoting rice growth. Although further analyses are necessary to properly elucidate the molecular mechanisms, our results suggest that these two bacterial isolates are potential candidates as sources for bioproducts, contributing to a more sustainable agriculture.

Long term application of plant growth-promoting bacterium improved grain weight and reduced arsenic accumulation in rice grain: A comparison of 10 bacteria

Rice (Oryza sativa L.) is one of the main food crops, it plays an important role in the human diet. Arsenic (As) contamination in paddy soil inhibits rice growth and reduces rice yield seriously. In addition, As accumulated in rice grains was harmful to human health through the food chain. Using the exogenous method to alleviate As stress and reduce As accumulation in rice grain is one of the potential ways to achieve food safety in polluted farmland. In the present study, 10 bacteria was applied to evaluate the effects of plant growth-promoting bacteria (PGPBs) on rice growth and As accumulation in rice grain. The results showed higher levels of As inhibited PGPB growth, the most tolerant and sensitive bacteria were Bj05 and Ls09, with the growth reduction of 16.9% and 96.7% under 50 mM As, respectively. Most of 10 PGPBs enhanced rice growth and improved rice grain weight under As exposure, among them, Ts06 showed the most effective one. Six of 10 PGPBs reduced rice grain As levels significantly, the highest reduction of grain As was observed in Ts06 inoculated rice, with grain As deceasing to 46.3% of the control. Bj05 was the only one which caused the increase in grain As of Yangdao 6. The Pearson correlation analysis showed grain As concentration negatively correlated with leave As concentration, while did not correlated with total As accumulated in shoot, and soil available As and P. The present results indicated that some PGPBs inhibited As translocation from leave to grain, thus reduced As accumulation in rice grain. Ts06 was suggested to be a candidate as microbial amendments for As-contaminated paddy fields.

Characterization of Two Highly Arsenic-Resistant Caulobacteraceae Strains of Brevundimonas nasdae: Discovery of a New Arsenic Resistance Determinant

Arsenic (As), distributed widely in the natural environment, is a toxic substance which can severely impair the normal functions in living cells. Research on the genetic determinants conferring functions in arsenic resistance and metabolism is of great importance for remediating arsenic-contaminated environments. Many organisms, including bacteria, have developed various strategies to tolerate arsenic, by either detoxifying this harmful element or utilizing it for energy generation. More and more new arsenic resistance (ars) determinants have been identified to be conferring resistance to diverse arsenic compounds and encoded in ars operons. There is a hazard in mobilizing arsenic during gold-mining activities due to gold- and arsenic-bearing minerals coexisting. In this study, we isolated 8 gold enrichment strains from the Zijin gold and copper mine (Longyan, Fujian Province, China) wastewater treatment site soil, at an altitude of 192 m. We identified two Brevundimonas nasdae strains, Au-Bre29 and Au-Bre30, among these eight strains, having a high minimum inhibitory concentration (MIC) for As(III). These two strains contained the same ars operons but displayed differences regarding secretion of extra-polymeric substances (EPS) upon arsenite (As(III)) stress. B. nasdae Au-Bre29 contained one extra plasmid but without harboring any additional ars genes compared to B. nasdae Au-Bre30. We optimized the growth conditions for strains Au-Bre29 and Au-Bre30. Au-Bre30 was able to tolerate both a lower pH and slightly higher concentrations of NaCl. We also identified folE, a folate synthesis gene, in the ars operon of these two strains. In most organisms, folate synthesis begins with a FolE (GTP-Cyclohydrolase I)-type enzyme, and the corresponding gene is typically designated folE (in bacteria) or gch1 (in mammals). Heterologous expression of folE, cloned from B. nasdae Au-Bre30, in the arsenic-hypersensitive strain Escherichia coli AW3110, conferred resistance to As(III), arsenate (As(V)), trivalent roxarsone (Rox(III)), pentavalent roxarsone (Rox(V)), trivalent antimonite (Sb(III)), and pentavalent antimonate (Sb(V)), indicating that folate biosynthesis is a target of arsenite toxicity and increased production of folate confers increased resistance to oxyanions. Genes encoding Acr3 and ArsH were shown to confer resistance to As(III), Rox(III), Sb(III), and Sb(V), and ArsH also conferred resistance to As(V). Acr3 did not confer resistance to As(V) and Rox(V), while ArsH did not confer resistance to Rox(V).

Leveraging arsenic resistant plant growth-promoting rhizobacteria for arsenic abatement in crops

Arsenic is a toxic metalloid categorized under class 1 carcinogen and is detrimental to both plants and animals. Agricultural land in several countries is contaminated with arsenic, resulting in its accumulation in food grains. Increasing global food demand has made it essential to explore neglected lands like arsenic-contaminated lands for crop production. This has posed a severe threat to both food safety and security. Exploration of arsenic-resistant plant growth-promoting rhizobacteria (PGPR) is an environment-friendly approach that holds promise for both plant growth promotion and arsenic amelioration in food grains. However, their real-time performance is dependent upon several biotic and abiotic factors. Therefore, a detailed analysis of associated mechanisms and constraints becomes inevitable to explore the full potential of available arsenic-resistant PGPR germplasm. Authors in this review have highlighted the role and constraints of arsenic-resistant PGPR in reducing the arsenic toxicity in food crops, besides providing the details of arsenic transport in food grains.