Improving Cold Tolerance of Asian Rice through Plant Growth Promoting Bacteria and Rice Gene Manipulation: Mechanisms of Pseudomonas Mosselli and OsMADS27

It is estimated that by the year 2050, the human population will extend to 9.7 billion and therefore the demand for food will increase. It is important to find ways to maintain production of critical crops, like rice, to match the demand. Climate change affects crop productivity as it is the reason for extreme warm or cold weather fluctuations. Asian rice (Oryza sativa L.) generally is grown in tropical and subtropical regions and thus, is sensitive to cold temperatures. This study hypothesized two strategies could improve growth and cold tolerance of rice plants: (1) use of plant growth promoting bacteria (PGPB), (2) gene manipulation of rice plants. To test the hypothesis concerning PGPB, a total of 140 bacteria were isolated and characterized from the root surface and inner tissues of roots and shoots of two-week old indica and japonica rice plants. Out of the 140, 5 PGPB were selected, based upon their characteristics, for testing their in vivo plant growth promoting capabilities to improve rice cold tolerance. Results showed that 4 of these PGPB, Pseudomonas mosselii, Paenibacillus rigui, Paenibacillus graminis and Microvirga sp. improved growth in a rice genotype-dependent manner but only P. mosselii, improved both indica and japonica varietal plants’ cold survival through increasing antioxidants such as reduced glutathione and proline, respectively. Additionally, P. mosselii showed antagonisms against phytopathogens, Fusarium fujikuroi and Talaromyces aurantiacus, and improved cold survival of japonica plants through either production of secondary metabolites or upregulation of defense genes. The data supported the hypothesis that P. mosselii contributes to cold tolerance of O. sativa through different mechanisms depending on the rice genotype. For the second hypothesis, OsMADS27 was chosen to evaluate its influence on cold tolerance and interactions with P. mosselii. Results indicated that OsMADS27 stimulated defense and peroxidase genes to detoxify excess amounts of reactive oxygen species (ROS) in rice plants as a response to cold stress. Furthermore, the presence of P. mosselii increased the cold survival of OsMADS27 overexpressed indica plants. Further studies need to be performed to understand the interactions of OsMADS27 overexpression with P. mosselii in improving cold tolerance of rice plants

Plant Growth-Promoting Activity of Bacteria Isolated from Asian Rice (\u3cem\u3eOryza sativa\u3c/em\u3e L.) Depends on Rice Genotype

Asian rice is one of the most important crops because it is a staple food for almost half of the world’s population. To have production of rice keep pace with a growing world population, it is anticipated that the use of fertilizers will also need to increase, which may cause environmental damage through runoff impacts. An alternative strategy to increase crop yield is the use of plant growth-promoting bacteria. Thousands of microbial species can exist in association with plant roots and shoots, and some are critical to the plant’s survival. We isolated 140 bacteria from two distantly related rice accessions and investigated whether their impact on the growth of four different rice accessions. The bacterial isolates were screened for their ability to solubilize phosphate, a known plant growth-promoting characteristic, and 25 isolates were selected for further analysis. These 25 phosphate-solubilizing isolates were also able to produce other potentially growth-promoting factors. Five of the most promising bacterial isolates were chosen for whole-genome sequencing. Four of these bacteria, isolates related to Pseudomonas mosselii, a Microvirga sp., Paenibacillus rigui, and Paenibacillus graminis, improved root and shoot growth in a rice genotype-dependent manner. This indicates that while bacteria have several known plant growth-promoting functions, their effects on growth parameters are rice genotype dependent and suggest a close relationship between plants and their microbial partners

Emerging Studies on Zataria multiflora Boiss L.: Pioneering the Antimicrobial and Antifungal Characteristics–A Systematic Review

Background and Objective: Zataria multiflora Boiss L., a medicinal herb, is addressed for its diverse biological characteristics, including antibacterial, antiviral, antifungal, antioxid-ant and pain-relieving characteristics. However, specific mechanisms and compounds responsible for these effects are still under investigation, particularly for their comparative efficacies. The aim of this study was to bridge this knowledge gaps by providing a focused novel analysis of the chemical composition and antimicrobial and antifungal effects of Zataria multiflora Boiss, highlighting its potential health benefits and therapeutic uses. Material and Methods: This review was carried out following standard protocols for systematic analyses. Comprehensive literature searches were carried out in multiple databases, including PubMed, EMBASE, CINAHL, Cochrane Library and Web of Science. Key search terms included "Zataria multiflora Boiss", "antibacterial", "antifungal", "chemical composition" and "biological activities". The review time period included 2003 to 2023 with 71 relevant articles selected based on predetermined inclusion and exclusion criteria. This approach ensured adherence to the journal formatting standards for systematic reviews. Results and Conclusion: The present analysis highlighted thymol and carvacrol as the primary compounds of interest in Zataria multiflora Boiss L. linked to its most potent antimicrobial and antifungal effects. Additionally, it was discovered that the antifungal characteristics of this herb were particularly pronounced, surpassing its other biological activities. However, the review included a limited evidence regarding the plant sedative and muscle relaxant characteristics, which fell outside the primary scope of this study on antimicrobial and antifungal effects. Conflict of interest: The authors declare no conflict of interest. 1.Introduction Use of medicinal plants and herbal medicines is still significant despite advances in synthetic drug develop-ment. In some countries, these natural remedies are critical parts of the healthcare system, often surpassing the trade of chemical drugs [1–3]. The World Health Organization (WHO) "Health for all by the year 2000" program emphas-ized importance of traditional medicine, leading to increased scientific and commercial interests in this field. Iran, with its diverse climate, is particularly addressed for its wealth of medicinal plants [4–7]. Shirazi thyme or Zataria (Z.) multiflora [8] is a significant example that is majorly detected in Iran, Pakistan and Afghanistan. This plant, as a part of the Lamiaceae family, grows up to 90-cm tall and is characterized by ovate circular leaves, dense tubercular mottling and white, hairy rounded buds in the leaf axils [9]. It is well-known for its culinary and medic-inal uses, particularly for its antiseptic, analgesic, anti-parasitic and antidiarrheal characteristics [10, 11]. Modern pharmacology verifies its therapeutic effects, including pain relief, spasm decrease and antiinflammatory effects. The Z. multiflora is used in various medicinal forms e.g. syrup and cream to treat a wide range of medical conditions, like inflammatory bowel disease (IBD), vagin-itis, dental pain, oral infections, respiratory and digestive diseases, pain, fever as well as common colds [9, 12–15]. The Z. multiflora essential oil (ZMEO) has been approved by the United States Food and Drug Administration (US FDA). Naturally, ZMEO contains phenolic oxygenated monoterpene compounds (carvacol, linalool and thymol) that act as free radical scavengers. Phenolic compounds are addressed as plant secondary metabolites, which are formed by the connection of an aromatic nucleus to one or more hydroxyl groups. These compounds are abundantly distributed in all parts of the Z. multiflora and include significant antioxidant activities. The antioxidant activity can be attributed to their redox characteristics and chemical structures [8, 17, 18]. A standard method for analysis of Z. multiflora secondary metabolites is gas chromatography (GC) coupled with mass spectrometry. Recently, methods such as mid-infrared spectroscopy, near-infrared spectroscopy and Raman spectroscopy have been used as chemical fingerprinting methods to analyze various secondary metabolites of plants [19]. Phenolic acids, poly-phenols and flavonoids are important compounds that include a wide range of biological activities. Their antioxidant activities are due to their polyphenolic natures. Their medicinal use includes a long history and are marketed as antispasmodic and anti-inflammatory drugs [20–22]. The study of yield efficiency and chemical compositions of Z. multiflora flowering branches essential oil (EO) showed that the highest and the lowest efficiencies of EO were associated to Zarghan (4%) and Sivand (2.91 %), respectively. Increasing global interests in medicinal plants, reinforced by WHO emphasis on traditional medicine, scores relevance of investigating less used natural remedies such as Z. multiflora [8]. Studies have shown medical uses of Z. multiflora such as mouthwash for the treatment of aphthous stomatitis [9], IBD and vaginitis [23]. Originating from regions such as Iran, Pakistan and Afghanistan, Z. multiflora has long been recognized for its culinary and medicinal uses. While its antiseptic, analgesic, antiparasitic and antidiarrheal characteristics are well-documented, recent advancements in pharmacology include further validations of its broad therapeutic potentials. Therefore, the aim of this systematic review was to investigate less-studied dimensions of Z. multiflora, particularly focusing on its phenolic compounds such as carvacol, linalool and thymol, which are critical for their antioxidant activities. While the FDA has acknowledged benefits of ZMEO, significant scopes for the comparative studies on this EO with those of other medicinal plants and with investigation of its novel clinical uses are still available. The aim of the present study was to bridge this gap by providing a comprehensive analysis of Z. multiflora chemical composition and its various effects, especially in antimicrobial and antifungal fields. Furthermore, this review addressed phytochemical diversity of Z. multiflora, considering variations in its EO composition from various habitats. Such insights are important for cultivating Z. multiflora for industrial, food, pharmaceutical and cosmetic means. By investigating these novel aspects, this study developed understanding of Z. multiflora roles in healthy living, especially in modern medicine and therapy. 2. Materials and Methods 2.1. Search strategy and study selection Published research articles of 2003–2023 (last 20 years) in English were analyzed using relevant terms in Google Scholar, PubMed, EMBASE CINAHL, Cochrane Library and Web of Science databases. Search was carried out using the following keywords of "antibacterial activity", "anti-fungal", "chemical”, "Zataria multiflora", "biological act-ivities", "chemical composition", "Zataria multiflora Boiss", "antioxidant activity", "antioxidant" and "extract". Combinations of these words with the operators "and" and "or" were searched as well. 2.2. Inclusion and exclusion criteria Inclusion criteria included studies; in which, Z. multiflora Boiss L. and parameters associated to the extract and EO of this plant were assessed without limitations. Studies; in which, Z. multiflora Boiss L. was examined along with other plant species with no restrictions in terms of chemical characteristics included were investigated as well. Interventional studies exclusively assessing anti-fungal characteristics of Z. multiflora Boiss L. were selected for the present study. Exclusion criteria were extended for the studies involving plants other than Z. multiflora Boiss L. and those that did not primarily investigate antifungal attributes of Z. multiflora. Articles with no full texts were excluded from the study, as well as review articles, descriptive studies and manuscripts that were invalid, unassociated or did not meet the specific criteria of focusing on the antifungal aspects of Z. multiflora Boiss L. 2.3. Articles and screening selection protocol The primary search yielded 2912 citations. Removal of 941 duplicates resulted in 1971 citations. Titles and abstracts of 1971 articles were screened. Furthermore, 839 articles that did not meet inclusion criteria or were inappropriate due to indirect links with the subject were excluded. The rest of 1132 full-text articles were reviewed. of these articles, 1061 were excluded and 71 relevant studies were selected based on their relationships with the article goals, inclusion and exclusion criteria and their qualities. Method of analysis and interpretation included determining the study purpose and collecting findings based on preferred reporting items for the systematic review (PRISMA) (Figure 1). Quality of the final articles was assessed separately by an evaluating researcher with experience in systematic reviews and biological topics. Results and Discussion 3.1. Selection of articles In the primary search, 2912 records were identified. Totally, 941 articles were excluded due to duplication. By assessing texts of the articles based on the inclusion and exclusion criteria and topic relevance, a total of 71 articles were included in this review (Figure 2). Moreover, 48 articles assessed for antimicrobial and antifungal effects or pharmacological activities and 20 articles assessed for antimicrobial and antifungal effects. Antimicrobial and antifungal effects referred to the highlighted effects on patients’ symptoms or outcomes. Data regarding chemical composition were collected and reported as follows. 3.2. Comprehensive pharmacological analysis of Zataria multiflora Boiss L. Table 1 provides a detailed analysis of the pharma-cological characteristics of Z. multiflora Boiss L. from 48 scholarly articles. This table extensively docum-ents the plant robust antifungal capabilities, with 25 studies corro-borating this attribute. Furthermore, it highlights the plant significant antibacterial characteristics, as identified in nine studies. The present study further includes investigation of Z. multiflora potentials in anti-cancer and antioxidant uses, each detailed in five studies. The table uniquely highlights studies assessing combined anti-bacterial and antioxidant effects of the plant, thereby enriching knowledge of its multifaceted pharmacological uses. This in-depth compilation of research scores Z. multiflora Boiss L. broad therapeutic potentials, illustrating its various uses in modern medicine. Results from studies on Z. multiflora Boiss L. can be translated into practical uses in medicine and therapeutics in various ways including antifungal and antibacterial treatments, cancer therapies and antioxidant benefits. The verified antifungal characteristics can lead to development of novel antifungal drugs, especially for drug-resistant fungal infections. Its anti-bacterial effects suggest potential uses in treating bacterial infections, possibly as an alternative to traditional antibiotics. Anti-cancer findings may contribute to novel approaches in cancer treatment, possibly as complementary therapies with conventional treatments. Antioxidant characteristics indicate uses of the plant in combating oxidative stress-related diseases, potentially as a dietary supplement. These potential uses demonstrate the therapeutic versatility of Z. multiflora, offering promising capabilities for future pharmaceutical developments. It is noteworthy that geographic origin and research methodology significantly affect results of studies on Z. multiflora Boiss L. Chemical com-position of plants can vary based on soil type, climate and other environ-mental factors. Studies from various regions may report variations in the concentration of active compounds, affecting their pharmacological efficacies. Moreover, selection of the extraction methods, experimental models and assay techniques can lead to various outcomes. For example, in-vitro studies may show various levels of efficacy, compared to those in-vivo studies may due to the complexity of biological systems. The reviewed studies show a wide range of pharmacological activities for Z. multiflora Boiss L., including antifungal, antibacterial, anti-cancer and antioxidant activities. This addresses potentials of this plant for various therapeutic uses. 3.3. Diverse pharmacological effects of Zataria multiflora The Z. multiflora, known for its antimicrobial and antifungal characteristics, has extensively been studied for various pharmacological effects. A comprehensive review of 20 articles has revealed a wide range of therapeutic potentials. These include relaxant effects in ten studies, which have shown significant improvements in conditions such as asthma and premenstrual syndrome. Three studies highlight its anti-parasitic efficacy, demonstrating effecti-veness against malaria vectors and Leishmania spp. Anal-gesic characteristics have been verified in two studies, showing decreased pain in conditions such as irritable bowel syndrome (IBS) and postpartum pain. Similarly, two articles have reported its anti-inflammatory effects, indicat-ing decreases in inflammatory cytokines and factors. Furthermore, a significant study has investigated its potential in nerve repair, particularly in a rat model of Alzheimer's disease, showing its neuroprotective charac-teristics. These diverse findings highlight the multifaceted pharmacological uses of Z. multiflora (Table 2). 3.4. Antifungal activity Antifungal effects of thyme extract and EO have been reported in various studies [24–27, 29–33]. Various studies have shown that Candida albicans is one of the most important causes of oral thrush and vaginal yeast infection and is strongly affected by the Z. multiflora extract and EO [24, 26, 32–34, 42–45, 48]. In 2015, Avaei et al. identified a total of 43 Z. multiflora compounds, whose major components included thymol, carvacrol, p-cymene, γ-terpinene and α-pinene. Other components make up less than 19.81% of the oil. Results of the antimicrobial analysis showed that Bacillus cereus was more resistant than the other two bacteria. Of the yeasts, Saccharomyces cervicii was more resistant than C. utilis. From the fungal species, growth of Penicillium digitatum and Aspergillus niger was inhibited by a similar oil concentration. Results of the present study showed that ZMEO included significant antimicrobial activity [30]. In a study, the lowest inhibitory concentration of EOs of 0.007–0.5 μg/ml was achieved [40]. In another study, it was detected that the antifungal effects of ethanolic and methanolic Z. multiflora extracts were significantly higher than its aqueous extract [47]. Further clinical studies in this field can help better understand antifungal characteristics of this plant. 3.5. Antibacterial activity Various studies have shown effects of Z. multiflora extract and EO on various pathogenic bacteria [50, 51]. Results showed that the extract affected Gram-positive and Gram-negative bacteria [23, 49, 52]. Assessing the anti-bacterial and antioxidant characteristics of ZEO and Rhus coriaria L. hydroalcoholic extracts, Mojaddar Langroodi et al. showed that sumac extract included a stronger antioxidant activity than that the ZEO did. Based on antibacterial activity results, ZEO was more potent than sumac extract [67, 91]. Mansour et al. investigated antibacterial effects and physicochemical characteristics of ZMEO. Results showed that ZMEO was effective on pathogenic bacteria, especially Staphylococcus aureus. Investigating physicochemical characteristics such as effects of pH, temperature, detergents and enzymes on ZMEO activity showed that EO was completely stable against temperature and very stable in a wide range of pH. Antibacterial activity of EO is insensitive to all types of protein-denaturing detergents (e.g. Tween 80, Tween 20 and Triton 100) and enzymes (e.g. proteinase K, trypsin, lipase and lysozyme). Therefore, potential use of ZMEO is suggested. However, further studies including purification, mass spectrometry, nuclear magnetic resonance (NMR) and toxicity assessment are needed to verify this suggestion [92, 93]. 3.6. Antioxidant and antitumor activities Appropriate anti-cancer effects of Z. multiflora extract and EO were reported in five studies [57–61]. In several studies, it was detected that this plant could increase cell death in colon carcinoma, cervical cancer and breast cancer and this increase indicated toxicity caused by the plant extract [59–61]. In 2022, Saffari et al. investigated chem-ical composition, bioactive functional groups, antioxidant ability and cytotoxicity of Shirazi-thyme EO on HT29 cell line. Results showed that with increases in Shirazi-thyme EO concentration, effects on HT29 cell line increased and its survival rate decreased. Based on antioxidant power results, phenol and flavonoid of ZMEO, it is possible to use Z. multiflora as a natural preservative in the food industry [94]. 3.7. Anti-inflammatory and analgesic activities Based on the studies, blood inflammatory factor levels in the Zataria group were significantly improved [88, 89]. In addition, anti-inflammatory and analgesic effects of this plant have been observed in interventional studies. Ghorani et al. demonstrated that patients improved significantly in their blood inflammatory factors after two months of treat-ment [88]. Another study showed that gastrointestinal patients consuming Shirazi thyme experienced less pains [86]. These have verified anti-inflammatory and analgesic activities of Z. multiflora. 3.8. Antiparasitic activity Antiparasitic activity of plants has been identified during various investigations [83–85]. Based on a study, ZMEO could be effective against Anopheles mosquitos [84]. In another study, antiretroviral, antimalarial and anti-inflammatory roles of Betulinic (one of the important compounds of ablution) were reported [84, 95] in a study, nanoparticles containing extracts of several plants, including Shirazi thyme, inhibited major malaria vectors [83]. These findings show the importance of thyme as a complementary anti-parasitic treatment. 3.9. Relaxant effects Various therapeutic effects of Z. multiflora such as bronchial dilation and decreases in lung inflammation, common colds and women's disorders have been reported [72, 73]. Findings have shown that Z. multiflora includes good relaxing effects on smooth muscles. Relaxation can be therapeutically important, especially in respiratory obstructive disorders, high blood-pressure vasodilation and digestive disorders [75–79]. Possible mechanisms of Z. multiflora and its component relaxant effects (majorly carvacrol) on smooth muscles, including inhibitory effects on histamine (H1) and muscarinic receptors, blocking effects on calcium channels and stimulating effects on beta-adrenergic receptors, have been verified [96, 97]. Based on the findings, relaxant effect is one of the most important characteristics of carvacrol and thymol compounds, which are abundantly detected in this plant [98]. Several studies have verified these effects, indicating potential roles for this herb in smooth-muscle relaxation. 3.10. Chemical composition Table 3 comprehensively details chemical composition of Z. multiflora Boiss, as identified in various research studies within the last two decades. This table highlights that Z. multiflora Boiss is predominantly comprised of monoterpenes. Significantly, carvacrol is the predominant compound, with its concentration ranging 26.69–76.18% in 13 distinct studies. Another compound is closely thymol, with its concentration varying 19.89-71.40%. Other significant compounds such as p-cymene, γ-terpinene, linalool and myrcene have been reported. Presence of fatty acids, particularly β-sitosterol and Stigmasterol, has been addressed in two studies. Flavonoids, including 6-hydroxyluteolin, apigenin and luteolin were identified, each in two separate articles. This table provides an in-depth insight at the phytochemical diversity of Z. multiflora Boiss, underlining its potentials for various biological and therapeutic uses. 3.11. Chemical composition The most important compounds in this plant are monoterpenes with nearly 70% reported [54, 102]. Two researches have reported carvacrol, which is a type of monoterpene as the major compound of this plant extract [106, 107]. Thymol has been identified as the major compound in several research [101]. Various results have been reported regarding quantities of carvacrol and thymol. In a semi-experimental study, it was detected that 61% of the content included carvacrol and 25% included thymol [104]. In another similar study, it was detected that nearly 73% of thymol were present in fresh plants and nearly 63% of carvacrol were present in dried plants [105]. These two important substances in Z. multiflora plant include high anti-carcinogenic roles and environmental factors and plant stresses, stage of plant growth; geographical area is another important factor that affects their size [75, 108, 109]. Another major compound is p-cymene [110]. Based on a study, Z. multiflora contains flavonoids such as apigenin, luteolin and 6-hydroxyluteolin [111]. In a current systematic review, the most detected compound was carvacrol, which was reported as 26.69–76.18% followed by thymol as 19.89–71.40% in 13 studies. Based on the findings, thymol and carvacrol are phenolic monoterpenes that include positive effects on cellular functions and cellular and humoral immune responses [109, 112]. Older findings have shown that Z. multiflora contains small quantities of tannin, resin and saponins. Alkaloid compounds have not

\u3cem\u3ePseudomonas mosselii\u3c/em\u3e Improves Cold Tolerance of Asian Rice (\u3cem\u3eOryza sativa\u3c/em\u3e L.) in a Genotype-dependent Manner by Increasing Proline in \u3cem\u3ejaponica\u3c/em\u3e and Reduced Glutathione in \u3cem\u3eindica\u3c/em\u3e Varieties

Cold stress is an important factor limiting rice production and distribution. Identifying factors that contribute to cold tolerance in rice is of primary importance. While some plant specific genetic factors involved in cold tolerance have been identified, the role of the rice microbiome remains unexplored. In this study, we evaluated the influence of plant growth promoting bacteria (PGPB) with the ability of phosphate solubilization on rice cold tolerance and survival. To reach this goal, inoculated and uninoculated 2-week-old seedlings were cold stressed and evaluated for survival and other phenotypes such as electrolyte leakage (EL) and necessary elements for cold tolerance. The results of this study showed that of the five bacteria, Pseudomonas mosselii, improved both indica and japonica varietal plants’ survival and decreased EL, indicating increased membrane integrity. We observed different possible cold tolerance mechanisms in japonica and indica plants such as increases in proline and reduced glutathione levels, respectively. This bacterium also improved the shoot growth of cold exposed indica plants during the recovery period. This study confirmed the host genotype dependent activity of P. mosselii and indicated that there is an interaction between specific plant genes and bacterial genes that causes different plant responses to cold stress

Draft Genome Sequence of \u3cem\u3eStaphylococcus succinus\u3c/em\u3e Strain GN1, Isolated from a Basement Floor in Milwaukee, WI

A strain of Staphylococcus succinus was sampled from the floor of the basement of a house and isolated in an undergraduate classroom in Milwaukee, WI. Here, we report the draft genome sequence of this strain