Fungal Disease Prevention in Seedlings of Rice (Oryza sativa) and Other Grasses by Growth-Promoting Seed-Associated Endophytic Bacteria from Invasive Phragmites australis

Development and application of a novel suspension concentrate for seed coating of rice for controlling bakanae disease and seedling rot disease

The main rice planting areas in the middle and lower reaches of the Yangtze River are primarily affected by two types of rice seedling diseases: bakanae disease and seedling rot disease. These diseases lead to considerable losses. Seed coating technology effectively protects rice from these diseases and mitigates environmental pollution. We determined the antifungal activity of six fungicides, including phenamacril, azoxystrobin, fludioxonil, metconazole, thifluzamide and prothioconazole against Fusarium moniliforme Sheldon and Curvularia lunata in this study. In addition, the impact of fungicides and surfactants on rice seed germination were determined. Furthermore, phenamacril and fludioxonil were selected as the active components of suspension concentrate for seed coating. The antifungal activity of phenamacril against F. moniliforme Sheldon was 0.139 mg/L and fludioxonil against C. lunata was 0.110 mg/L. PEG-2000 was selected as the surfactant due to its promoting effect on rice seedling. Based on the above findings, 6% phenamacril fludioxonil FS was developed via the wet sand grinding method. The toxicity of 6% phenamacril fludioxonil FS to zebrafish was verified, and field experiments were conducted in five different regions of the Yangtze River Basin. The results indicated minimal toxicity of 6% phenamacril fludioxonil FS to zebrafish. Relative to the control agent consisting of 6.25% phenamacril metalaxyl-M FS, 6% phenamacril fludioxonil FS showed better control effect and exhibited superior efficacy in promoting growth and increasing yield in all five regions. Specifically, the control effect of 6% phenamacril fludioxonil FS on bakanae exceeded 84.83% with the highest yield increasing value recorded at 30.48%. Currently, the market offers a limited selection of suspension concentrate for seed coating of rice. The findings of this study may offer a viable alternative formulation and directions for further research concerning the application of suspension concentrate for seed coating of rice.

Biocontrol of plant pathogens in omics era-with special focus on endophytic bacilli

Nearly all plants and their organs are inhabited by endophytic microbes which play a crucial role in plant fitness and stress resilience. Harnessing endophytic services can provide effective solutions for a sustainable increase in agriculture productivity and can be used as a complement or alternative to agrochemicals. Shifting agriculture practices toward the use of nature-based solutions can contribute directly to the global challenges of food security and environmental sustainability. However, microbial inoculants have been used in agriculture for several decades with inconsistent efficacy. Key reasons of this inconsistent efficacy are linked to competition with indigenous soil microflora and inability to colonize plants. Endophytic microbes provide solutions to both of these issues which potentially make them better candidates for microbial inoculants. This article outlines the current advancements in endophytic research with special focus on endophytic bacilli. A better understanding of diverse mechanisms of disease control by bacilli is essential to achieve maximum biocontrol efficacy against multiple phytopathogens. Furthermore, we argue that integration of emerging technologies with strong theoretical frameworks have the potential to revolutionize biocontrol approaches based on endophytic microbes.

Seed-borne bacterial synthetic community resists seed pathogenic fungi and promotes plant growth

AIMS

In this study, the control effects of synthetic microbial communities composed of peanut seed bacteria against seed aflatoxin contamination caused by Aspergillus flavus and root rot by Fusarium oxysporum were evaluated.

METHODS AND RESULTS

Potentially conserved microbial synthetic communities (C), growth-promoting synthetic communities (S), and combined synthetic communities (CS) of peanut seeds were constructed after 16S rRNA Illumina sequencing, strain isolation, and measurement of plant growth promotion indicators. Three synthetic communities showed resistance to root rot and CS had the best effect after inoculating into peanut seedlings. This was achieved by increased defense enzyme activity and activated salicylic acid (SA)-related, systematically induced resistance in peanuts. In addition, CS also inhibited the reproduction of A. flavus on peanut seeds and the production of aflatoxin. These effects are related to bacterial degradation of toxins and destruction of mycelia.

CONCLUSIONS

Inoculation with a synthetic community composed of seed bacteria can help host peanuts resist the invasion of seeds by A. flavus and seedlings by F. oxysporum and promote the growth of peanut seedlings.

New report of endophytic bacterium Achromobacter xylosoxidans from root tissue of Musa spp

BACKGROUND

Cavendish (AAA) banana plant (Musa spp.) worldwide cultivated crop harbors many endophytic bacteria. Endophytic bacteria are those that live inside plant tissues without producing any visible symptoms of infection.

RESULTS

Endophytic bacterium (MRH 11), isolated from root tissue of Musa spp.was identified as Achromobacter xylosoxidans (ON955872) which showed positive effects in IAA production, phosphate solubilization, catalase production. A. xylosoxidans also showed in vitro antagonism against Curvularia lunata causing leaf spot disease of Cavendish (AAA) banana (G-9 variety). The GC-MS analysis of culture filtrate of A. xylosoxidans (ON955872) confirmed this finding. GC-MS analysis was carried by using two solvent etheyl acetate and chloroform and it showed several antifungal compounds. The identification of these bioactive secondary metabolites compounds was based on the peak area, retention time, molecular weight, molecular formula and antimicrobial actions. GC-MS analysis result revealed the presence of major components including Cyclododecane, 1-Octanol, Cetene, Diethyl phthalate. In vivo test to banana plants was carried out in separate field as well as in potted conditions. Appearance of leaf spots after foliar spray of spore of pathogen and reduction in leaf spots after application of bacterial suspension was found.

CONCLUSION

The present study has highlighted the role of endophytic bacterium as antagonist to the pathogen Curvularia lunata.

Synergistic biocontrol of Bacillus subtilis and Pseudomonas fluorescens against early blight disease in tomato

Early blight of tomato caused by Alternaria solani results in significant crop losses. In this study, Bacillus subtilis J3 and Pseudomonas fluorescens J8 were co-cultured as a synthetic microbial community (BCA) for synergistic biocontrol of A. solani, and the inhibition mechanism was investigated. BCA presented an inhibition ration against A. solani at 94.91%, which lowered the disease incidence by 38.26-42.87%; reduced peroxidase, catalase, superoxide dismutase activity of tomatoes by 73.11-90.22%; and promoted the biomass by 66.91-489.21%. With BCA protection, the relative expression of tomato resistance genes (including gPAL2, SWRKY, PR-10, and CHI) in roots and leaves was 12.83-90.70% lower than without protection. BCA also significantly altered the rhizosphere and phyllosphere microbial community. The abundance of potentially beneficial bacteria, including Bacillus, Pseudomonas, Arthrobacter, Lysobacter, and Rhizobium, elevated by 6.58-192.77%. They were negatively correlated with resistance gene expression, indicating their vital involvement in disease control. These results provided essential information on the synergistic biocontrol mechanism of bacteria against pathogens, which could contribute to developing novel biocontrol strategies. KEY POINTS: • Bacillus and Pseudomonas present a synergistic biocontrol effect against A. solani. • Biocontrol prevents pathogen damage and improves tomato growth and systemic resistance. • Beneficial bacteria thrive in the rhizosphere is the key to microbial regulation.

Screening, Identification, and Growth Promotion of Antagonistic Endophytes Associated with Chenopodium quinoa Against Quinoa Pathogens

Fungal disease is one of the important reasons for crop yield reduction. Isolation of important endophytes with biocontrol and growth-promoting effects is of great significance for the exploitation of beneficial microbial resources and the biological control of crop fungal diseases. In this study, endophytes from roots, stems, and leaves of quinoa at different growth and development stages were isolated and purified; then the antagonistic activity and growth-promoting characteristics of antagonistic endophytes were determined. Finally, the antagonistic endophytes were identified by morphological characteristics and ITS/16S rRNA sequence analysis. Our results showed that 122 endophytic fungi and 371 endophytic bacteria were isolated from quinoa, of which three endophytic fungi and seven endophytic bacteria were screened that had inhibitory activity against quinoa pathogenic fungi. Most of the antagonistic strains could produce indole-3 acetic acid and had the ability to dissolve organic phosphorus. In addition, the bacterial suspension of endophytic bacteria had the ability to promote the seed germination and plant growth of quinoa. The endophytic fungi with antagonistic activity were identified as Penicillium raperi and P. pulvillorum; the endophytic bacteria were identified as Bacillus paralicheniformis, B. tequilensis, and B. velezensis, respectively. The strains of quinoa endophytes in this study can provide rich microbial resources and a theoretical basis for biological control of plant fungal diseases and agricultural production.

Assembly and Function of Seed Endophytes in Response to Environmental Stress

Seeds are colonized by diverse microorganisms that can improve the growth and stress resistance of host plants. Although understanding the mechanisms of plant endophyte-host plant interactions is increasing, much of this knowledge does not come from seed endophytes, particularly under environmental stress that the plant host grows to face, including biotic (e.g., pathogens, herbivores and insects) and abiotic factors (e.g., drought, heavy metals and salt). In this article, we first provided a framework for the assembly and function of seed endophytes and discussed the sources and assembly process of seed endophytes. Following that, we reviewed the impact of environmental factors on the assembly of seed endophytes. Lastly, we explored recent advances in the growth promotion and stress resistance enhancement of plants, functioning by seed endophytes under various biotic and abiotic stressors.

Characterization of Growth-Promoting Activities of Consortia of Chlorpyrifos Mineralizing Endophytic Bacteria Naturally Harboring in Rice Plants-A Potential Bio-Stimulant to Develop a Safe and Sustainable Agriculture

Eighteen pesticide-degrading endophytic bacteria were isolated from the roots, stems, and leaves of healthy rice plants and identified through 16S rRNA gene sequencing. Furthermore, biochemical properties, including enzyme production, dye degradation, anti-bacterial activities, plant-growth-promoting traits, including N-fixation, P-solubilization, auxin production, and ACC-deaminase activities of these naturally occurring endophytic bacteria along with their four consortia, were characterized. Enterobacter cloacae HSTU-ABk39 and Enterobacter sp. HSTU-ABk36 displayed inhibition zones of 41.5 ± 1.5 mm, and 29 ± 09 mm against multidrug-resistant human pathogenic bacteria Staphylococcus aureus and Staphylococcus epidermidis, respectively. FT-IR analysis revealed that all eighteen isolates were able to degrade chlorpyrifos pesticide. Our study confirms that pesticide-degrading endophytic bacteria from rice plants play a key role in enhancing plant growth. Notably, rice plants grown in pots containing reduced urea (30%) mixed with either endophytic bacterial consortium-1, consortium-2, consortium-3, or consortia-4 demonstrated an increase of 17.3%, 38.6%, 18.2%, and 39.1% yields, respectively, compared to the control plants grown in pots containing 100% fertilizer. GC-MS/MS analysis confirmed that consortia treatment caused the degradation of chlorpyrifos into different non-toxic metabolites, including 2-Hydroxy-3,5,6 trichloropyridine, Diethyl methane phosphonate, Phorate sulfoxide, and Carbonochloridic. Thus, these isolates could be deployed as bio-stimulants to improve crop production by creating a sustainable biological system.

Multifaceted Impacts of Plant-Beneficial Pseudomonas spp. in Managing Various Plant Diseases and Crop Yield Improvement

The modern agricultural system has issues with the reduction of agricultural productivity due to a wide range of abiotic and biotic stresses. It is also expected that in the future the entire world population may rapidly increase and will surely demand more food. Farmers now utilize a massive quantity of synthetic fertilizers and pesticides for disease management and to increase food production. These synthetic fertilizers badly affect the environment, the texture of the soil, plant productivity, and human health. However, agricultural safety and sustainability depend on an ecofriendly and inexpensive biological application. In contrast to synthetic fertilizers, soil inoculation with plant-growth-promoting rhizobacteria (PGPR) is one of the excellent alternative options. In this regard, we focused on the best PGPR genera, Pseudomonas, which exists in the rhizosphere as well as inside the plant's body and plays a role in sustainable agriculture. Many Pseudomonas spp. control plant pathogens and play an effective role in disease management through direct and indirect mechanisms. Pseudomonas spp. fix the amount of atmospheric nitrogen, solubilize phosphorus and potassium, and also produce phytohormones, lytic enzymes, volatile organic compounds, antibiotics, and secondary metabolites during stress conditions. These compounds stimulate plant growth by inducing systemic resistance and by inhibiting the growth of pathogens. Furthermore, pseudomonads also protect plants during different stress conditions like heavy metal pollution, osmosis, temperature, oxidative stress, etc. Now, several Pseudomonas-based commercial biological control products have been promoted and marketed, but there are a few limitations that hinder the development of this technology for extensive usage in agricultural systems. The variability among the members of Pseudomonas spp. draws attention to the huge research interest in this genus. There is a need to explore the potential of native Pseudomonas spp. as biocontrol agents and to use them in biopesticide development to support sustainable agriculture.

Biocontrol Efficacy of Endophyte Pseudomonas poae to Alleviate Fusarium Seedling Blight by Refining the Morpho-Physiological Attributes of Wheat

Some endophyte bacteria can improve plant growth and suppress plant diseases. However, little is known about the potential of endophytes bacteria to promote wheat growth and suppress the Fusarium seedling blight pathogen Fusarium graminearum. This study was conducted to isolate and identify endophytic bacteria and evaluate their efficacy for the plant growth promotion and disease suppression of Fusarium seedling blight (FSB) in wheat. The Pseudomonas poae strain CO showed strong antifungal activity in vitro and under greenhouse conditions against F. graminearum strain PH-1. The cell-free supernatants (CFSs) of P. poae strain CO were able to inhibit the mycelium growth, the number of colonies forming, spore germination, germ tube length, and the mycotoxin production of FSB with an inhibition rate of 87.00, 62.25, 51.33, 69.29, and 71.08%, respectively, with the highest concentration of CFSs. The results indicated that P. poae exhibited multifarious antifungal properties, such as the production of hydrolytic enzymes, siderophores, and lipopeptides. In addition, compared to untreated seeds, wheat plants treated with the strain showed significant growth rates, where root and shoot length increased by about 33% and the weight of fresh roots, fresh shoots, dry roots, and dry shoots by 50%. In addition, the strain produced high levels of indole-3-acetic acid, phosphate solubilization, and nitrogen fixation. Finally, the strain demonstrated strong antagonistic properties as well as a variety of plant growth-promoting properties. Thus, this result suggest that this strain could be used as an alternate to synthetic chemicals, which can serve as an effective method of protecting wheat from fungal infection.

Effect of Epichloë gansuensis Endophyte on Seed-Borne Microbes and Seed Metabolites in Achnatherum inebrians

The seed-borne microbiota and seed metabolites of the grass Achnatherum inebrians, either host to Epichloë gansuensis (endophyte infected [EI]) or endophyte free (EF), were investigated. This study determined the microbial communities both within the seed (endophytic) and on the seed surface (epiphytic) and of the protective glumes by using Illumina sequencing technology. Epichloë gansuensis decreased the richness of the seed-borne microbiota except for the epiphytic fungi of glumes and also decreased the diversity of seed-borne microbiota. In addition, metabolites of seeds and glumes were detected using liquid chromatography-mass spectrometry (LC-MS). Unlike with the seeds of EF plants, the presence of E. gansuensis resulted in significant changes in the content of 108 seed and 31 glume metabolites. A total of 319 significant correlations occurred between seed-borne microbiota and seed metabolites; these correlations comprised 163 (147 bacterial and 16 fungal) positive correlations and 156 (136 bacterial and 20 fungal) negative correlations. Meanwhile, there were 42 significant correlations between glume microbiota and metabolites; these correlations comprised 28 positive (10 bacterial and 18 fungal) and 14 negative (9 bacterial and 5 fungal) correlations. The presence of E. gansuensis endophyte altered the communities and diversities of seed-borne microbes and altered the composition and content of seed metabolites, and there were many close and complex relationships between microbes and metabolites. IMPORTANCE The present study was to investigate seed-borne microbiota and seed metabolites in Achnatherum inebrians using high-throughput sequencing and LC-MS technology. Epichloë gansuensis decreased the richness of the seed-borne microbiota except for the epiphytic fungi of glumes and also decreased the diversity of seed-borne microbiota. Compared with endophyte-free plants, the content of 108 seed and 31 glume metabolites of endophyte-infected plants was significantly changed. There were 319 significant correlations between seed-borne microbiota and seed metabolites and 42 significant correlations between glume microbiota and metabolites.

Endophytic Pseudomonas sp. from Agave palmeri Participate in the Rhizophagy Cycle and Act as Biostimulants in Crop Plants

Plant growth-promoting bacteria are generating increasing interest in the agricultural industry as a promising alternative to traditional chemical fertilizers; however, much of the focus has been on rhizosphere bacteria. Bacterial endophytes are another promising source of plant growth-promoting bacteria, and though many plants have already been prospected for beneficial microbes, desert plants have been underrepresented in such studies. In this study, we show the growth-promoting potential of five strains of endophytic Pseudomonas sp. isolated from Agave palmeri, an agave from the Sonoran Desert. When inoculated onto Kentucky bluegrass, clover, carrot, coriander, and wheat, endophytic Pseudomonas sp. increased seedling root lengths in all hosts and seedling shoot lengths in Kentucky bluegrass, carrot, and wheat. Transformation of the Pseudomonas sp. strain P3AW to express the fluorescent protein mCherry revealed that Pseudomonas sp. becomes endophytic in non-native hosts and participates in parts of the rhizophagy cycle, a process by which endophytic bacteria cycle between the soil and roots, bringing in nutrients from the soil which are then extracted through reactive oxygen-mediated bacterial degradation in the roots. Tracking of the Pseudomonas sp. strain P3AW also provided evidence for a system of endophyte, or endophyte cell content, transport via the vascular bundle. These results provide further evidence of the rhizophagy cycle in plants and how it relates to growth promotion in plants by biostimulant bacteria.

The Effects of Temperature and Water on the Seed Germination and Seedling Development of Rapeseed (Brassica napus L.)

The seed germination and seedling growth of rapeseed are crucial stages in plant life, especially when facing abiotic stresses. In the present work, the effects of water and temperature on seed germination and seedling growth were investigated in a rapeseed crop (Brassica napus L.). The plants were examined under different temperature levels (5 °C, 10 °C, 15 °C, 20 °C, 25 °C, 30 °C, and 35 °C) and water levels (twenty-nine levels based on either one-milliliter intervals or as a percentage of the thousand-kernel weight (TKW)). Moreover, planting densities and antifungal application techniques were investigated in the study. The findings demonstrated substantial variations between all the growth parameters investigated at all the tested temperatures, and 20 °C was considered the optimum within a broad range of 15-25 °C. Water availability plays a significant role in germination, which can be initiated at 0.65 mL, corresponding to 500% of the TKW. The method of TKW is a more accurate aspect of water application because of the consideration of the seed weight and size. The optimal water range for the accumulation of dry weight, 3.85-5.9 mL (2900-4400% of TKW), was greater than that required for seedling growth, 1.45-3.05 mL (1100-2300% of TKW). Twenty to twenty-five seeds per 9 cm Petri dish exhibited the most outstanding values compared to the others, which provides an advantage in breeding programs, especially when there are seed limitations. Seed priming is a more effective antifungal application strategy. These data can be incorporated into future rapeseed germination in vitro studies, breeding programs, and sowing date predictions.

Cannabis Seedlings Inherit Seed-Borne Bioactive and Anti-Fungal Endophytic Bacilli

Throughout the hundreds of millions of years of co-evolution, plants and microorganisms have established intricate symbiotic and pathogenic relationships. Microbial communities associated with plants are in constant flux and can ultimately determine whether a plant will successfully reproduce or be destroyed by their environment. Inheritance of beneficial microorganisms is an adaptation plants can use to protect germinating seeds against biotic and abiotic stresses as seedlings develop. The interest in Cannabis as a modern crop requires research into effective biocontrol of common fungal pathogens, an area that has seen little research. This study examines the seed-borne endophytes present across 15 accessions of Cannabis grown to seed across Western Canada. Both hemp and marijuana seedlings inherited a closely related group of bioactive endophytic Bacilli. All Cannabis accessions possessed seed-inherited Paenibacillus mobilis with the capacity to solubilize mineral phosphate. Additionally, seeds were found to carry genera of fungal isolates known to be Cannabis pathogens and post-harvest molds: Alternaria, Penicillium, Cladosporium, Chaetomium, Aspergillus, Rhizopus, and Fusarium. Thirteen seed-borne endophytes showed antibiotic activity against Alternaria, Aspergillus, Penicillium, and Fusarium. This study suggests both fungal pathogens and bacterial endophytes that antagonize them are vectored across generations in Cannabis as they compete over this shared niche.

Discovery of a novel nucleoside immune signaling molecule 2'-deoxyguanosine in microbes and plants

INTRODUCTION

Beneficial microorganisms play essential roles in plant growth and induced systemic resistance (ISR) by releasing signaling molecules. Our previous study obtained the crude extract from beneficial endophyte Paecilomyces variotii, termed ZNC (ZhiNengCong), which significantly enhanced plant resistance to pathogen even at 100 ng/ml. However, the immunoreactive components of ZNC remain unclear. Here, we further identified one of the immunoreactive components of ZNC is a nucleoside 2'-deoxyguanosine (2-dG).

OBJECTIVES

This paper intends to reveal the molecular mechanism of microbial-derived 2'-deoxyguanosine (2-dG) in activating plant immunity, and the role of plant-derived 2-dG in plant immunity.

METHODS

The components of ZNC were separated using a high-performance liquid chromatography (HPLC), and 2-dG is identified using a HPLC-mass spectrometry system (LC-MS). Transcriptome analysis and genetic experiments were used to reveal the immune signaling pathway dependent on 2-dG activation of plant immunity.

RESULTS

This study identified 2'-deoxyguanosine (2-dG) as one of the immunoreactive components from ZNC. And 2-dG significantly enhanced plant pathogen resistance even at 10 ng/ml (37.42 nM). Furthermore, 2-dG-induced resistance depends on NPR1, pattern-recognition receptors/coreceptors, ATP receptor P2K1 (DORN1), ethylene signaling but not salicylic acid accumulation. In addition, we identified Arabidopsis VENOSA4 (VEN4) was involved in 2-dG biosynthesis and could convert dGTP to 2-dG, and vne4 mutant plants were more susceptible to pathogens.

CONCLUSION

In summary, microbial-derived 2-dG may act as a novel immune signaling molecule involved in plant-microorganism interactions, and VEN4 is 2-dG biosynthesis gene and plays a key role in plant immunity.

Production and Functionalities of Specialized Metabolites from Different Organic Sources

Medicinal plants are rich sources of specialized metabolites that are of great importance to plants, animals, and humans. The usefulness of active biological compounds cuts across different fields, such as agriculture, forestry, food processing and packaging, biofuels, biocatalysts, and environmental remediation. In recent years, research has shifted toward the use of microbes, especially endophytes (bacteria, fungi, and viruses), and the combination of these organisms with other alternatives to optimize the production and regulation of these compounds. This review reinforces the production of specialized metabolites, especially by plants and microorganisms, and the effectiveness of microorganisms in increasing the production/concentration of these compounds in plants. The study also highlights the functions of these compounds in plants and their applications in various fields. New research areas that should be explored to produce and regulate these compounds, especially in plants and microbes, have been identified. Methods involving molecular studies are yet to be fully explored, and next-generation sequencing possesses an interesting and reliable approach.

Production of Non-Volatile Metabolites from Sooty Molds and Their Bio-Functionalities

In the current study, eleven sooty mold isolates were collected from different tropical host plants. The isolates were identified under Capnodium, Leptoxyphium and Trichomerium, based on morphology and phylogeny. For the secondary metabolite analysis, the isolates were grown on Potato Dextrose Broth (PDB). The well-grown mycelia were filtered and extracted over methanol (MeOH). The metabolites in the growth medium (or filtrate) were extracted over ethyl acetate (EtOAc). The antifungal activities of each crude extract were tested over Alternaria sp., Colletotrichum sp., Curvularia sp., Fusarium sp. and Pestalotiopsis sp. The metabolites were further tested for their total phenolic, flavonoid and protein content prior to their antioxidant and anti-fungal potential evaluation. The MeOH extracts of sooty molds were enriched with proteins and specifically inhibited Curvularia sp. The total phenolic content and 2,2-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) activity was largely recovered from the filtrate corresponding to the inhibition of Alternaria sp.; while the flavonoid and free radical reduction suggested a relative induction of growth of the Fusarium sp., Colletotrichum sp. and Pestalotiopsis sp. Hence, this study reveals the diversity of sooty molds in Thailand by a modern phylogenetic approach. Furthermore, the preliminary screening of the isolates reveals the potential of finding novel compounds and providing insights for the future research on secondary metabolites of bio-trophic fungi and their potential usage on sustainable agriculture.

Epichloë Fungal Endophytes Influence Seed-Associated Bacterial Communities

Seeds commonly harbour diverse bacterial communities that can enhance the fitness of future plants. The bacterial microbiota associated with mother plant’s foliar tissues is one of the main sources of bacteria for seeds. Therefore, any ecological factor influencing the mother plant’s microbiota may also affect the diversity of the seed’s bacterial community. Grasses form associations with beneficial vertically transmitted fungal endophytes of genus Epichloë. The interaction of plants with Epichloë endophytes and insect herbivores can influence the plant foliar microbiota. However, it is unknown whether these interactions (alone or in concert) can affect the assembly of bacterial communities in the produced seed. We subjected Lolium multiflorum plants with and without its common endophyte Epichloë occultans (E+, E-, respectively) to an herbivory treatment with Rhopalosiphum padi aphids and assessed the diversity and composition of the bacterial communities in the produced seed. The presence of Epichloë endophytes influenced the seed bacterial microbiota by increasing the diversity and affecting the composition of the communities. The relative abundances of the bacterial taxa were more similarly distributed in communities associated with E+ than E- seeds with the latter being dominated by just a few bacterial groups. Contrary to our expectations, seed bacterial communities were not affected by the aphid herbivory experienced by mother plants. We speculate that the enhanced seed/seedling performance documented for Epichloë-host associations may be explained, at least in part, by the Epichloë-mediated increment in the seed-bacterial diversity, and that this phenomenon may be applicable to other plant-endophyte associations.

Pseudomonas spp. Mediate defense response in sugarcane through differential exudation of root phenolics

Pseudomonas spp., a ubiquitous biocontrol agent, protects the plants from phytopathogens by suppressing them directly by reinforcing the plant’s intrinsic defense mechanism. Root exudated phenolics play an important role in establishing the rhizobacteria population and cross the host boundaries in beneficial plant–microbe interaction. In this study, Pseudomonas spp. HU-8 & HU-9 antagonized the sugarcane red rot pathogen (C. falcatum) and showed a positive chemotactic response against different concentrations (10–30 µM) of synthetic phenolic acids like p-coumaric, vanillic, and 3,4 di-hydroxybenzoic acid. In a pot experiment, they effectively colonized the sugarcane rhizosphere and mediated defense response in sugarcane plants challenged with red rot pathogen C. falcatum by regulating the exudation of root phenolics under hydroponic conditions. They significantly induced the activity of the antioxidant enzymes CAT (1.24–1.64 fold), PO (0.78–1.61 fold), PAL (0.77–0.97 fold), and PPO (3.67–3.73 fold) over untreated plants in sugarcane. They also induced the total phenolic contents (TPC) in sugarcane in the presence (6.56–10.29 mg/g GAE) and absence (2.89–4.16 mg/g GAE) of the pathogen quantified through the Folin-Ciocalteu (FC) method. However, their effect was lower than that of the pathogen (4.34–8 mg/g GAE). The Pseudomonas spp. significantly colonized the sugarcane rhizosphere by maintaining a cell population of (1.0E + 07–1.3E + 08 CFU/mL). A significant positive Pearson’s correlation was observed between the root exudated total phenolic contents, antioxidant enzymatic activities, and rhizospheric population of inoculated bacteria. The 16S rRNA and rpoD gene analysis showed sequence conservation (C: 0.707), average number of nucleotide differences (k: 199.816), nucleotide diversity, (Pi): 0.09819), average number of informative nucleotide sites per site (Psi: 0.01275), GC content (0.57), and polymorphic sites (n = 656). These diverse Pseudomonas spp. could be an ideal bio-inoculants for a broad range of hosts especially graminaceous crops.

Bioprospecting Desert Plants for Endophytic and Biostimulant Microbes: A Strategy for Enhancing Agricultural Production in a Hotter, Drier Future

Simple Summary

Endophytes are microbes that live inside plants without causing negative effects in their hosts. All land plants are known to have endophytes, and these endophytes have the capacity to be transferred between plants. Taking endophytes from desert plants, which grow in low-nutrient, high-stress environments, and transferring them to crop plants may alleviate some of the challenges being faced by the agricultural industry, such as increasing drought frequency and rising opposition to chemical use in agriculture. Studies have shown that desert endophytes have the capacity to increase nutrient uptake and increase plant resistance to drought and heat stress, salt stress, and pathogen attack. Currently, the agricultural industry focuses on using irrigation, chemical fertilizers, and chemical pesticides to solve such issues, which can be extremely damaging to the environment. While there is still a lot that is unknown about endophytes, particularly desert plant endophytes, current research provides evidence that desert plant endophytes could be an environmentally friendly alternative to the conventional solutions being applied today.

Abstract

Deserts are challenging places for plants to survive in due to low nutrient availability, drought and heat stress, water stress, and herbivory. Endophytes—microbes that colonize and infect plant tissues without causing apparent disease—may contribute to plant success in such harsh environments. Current knowledge of desert plant endophytes is limited, but studies performed so far reveal that they can improve host nutrient acquisition, increase host tolerance to abiotic stresses, and increase host resistance to biotic stresses. When considered in combination with their broad host range and high colonization rate, there is great potential for desert endophytes to be used in a commercial agricultural setting, especially as croplands face more frequent and severe droughts due to climate change and as the agricultural industry faces mounting pressure to break away from agrochemicals towards more environmentally friendly alternatives. Much is still unknown about desert endophytes, but future studies may prove fruitful for the discovery of new endophyte-based biofertilizers, biocontrol agents, and abiotic stress relievers of crops.

Seed Treatment With Systemic Fungicides: Time for Review

Pre-sowing seed treatment with systemic fungicides is a firmly entrenched practice for most agricultural crops worldwide. The treatment is intended to protect the crop against seed- and soil-borne diseases. In recent years, there is increasing evidence that fungicidal applications to manage diseases might inadvertently also affect non-target organisms, such as endophytes. Endophytes are ubiquitously present in plants and contribute to plant growth and development besides offering resistance to biotic and abiotic stresses. In seeds, endophytes may play a role in seed development, seed germination, seedling establishment and crop performance. In this paper, we review the recent literature on non-target effects of fungicidal applications on endophytic fungal community and discuss the possible consequences of indiscriminate seed treatment with systemic fungicide on seed endophytes. It is now well recognized that endophytes are ubiquitously present in all parts of the plant, including the seeds. They may be transmitted vertically from seed to seed as in many grasses and/or acquired horizontally from the soil and the environment. Though the origins and evolution of these organisms in plants are a matter of conjecture, numerous studies have shown that they symbiotically aid in plant growth and development, in nutrient acquisition as well in protecting the plants from abiotic and biotic stresses. Against this background, it is reasonable to assume that the use of systemic fungicides in seed treatment may not only affect the seed endophytes but also their attendant benefits to seedling growth and establishment. While there is evidence to indicate that fungicidal applications to manage plant diseases also affect foliar endophytes, there are only few studies that have documented the effect of seed treatment on seed-borne endophytes. Some of the convincing examples of the latter come from studies on the effect of fungicide application on rye grass seed endophyte AR37. More recently, experiments have shown that removal of seed endophytes by treatment with systemic fungicides leads to significant loss of seedling vigour and that such losses could be partially restored by enriching the seedlings with the lost endophytes. Put together, these studies reinforce the importance of seed endophytes to seedling growth and establishment and draw attention on how to trade the balance between the benefits of seed treatments and the direct and indirect costs incurred due to loss of endophytes. Among several approaches, use of reduced-risk fungicides and identifying fungicide-resistant endophytes are suggested to sustain the endophyte contribution to early seedling growth.

Bacterial communities associated with sugarcane under different agricultural management exhibit a diversity of plant growth-promoting traits and evidence of synergistic effect

Plant-associated microbiomes have been a target of interest for the prospection of microorganisms, which may be acting as effectors to increase agricultural productivity. For years, the search for beneficial microorganisms has been carried out from the characterization of functional traits of growth-promotion using tests with a few isolates. However, eventually, the expectations with positive results may not be realized when the evaluation is performed in association with plants. In our study, we accessed the cultivable sugarcane microbiome under two conditions of agronomic management: organic and conventional. From the use of a new customized culture medium, we recovered 944 endophytic and epiphytic bacterial communities derived from plant roots, stalks, leaves, and rhizospheric soil. This could be accomplished by using a large-scale approach, initially performing an in planta (Cynodon dactylon) screening process of inoculation to avoid early incompatibility. The inoculation was performed using the bacterial communities, considering that in this way, they could act synergistically. This process resulted in 38 candidate communities, 17 of which had higher Indole-3-acetic acid (IAA) production and phosphate solubilization activity and, were submitted to a new in planta test using Brachiaria ruziziensis and quantification of functional traits for growth-promotion and physiological tests. Enrichment analysis of selected communities has shown that they derived mainly from epiphytic populations of sugarcane stalks under conventional management. The sequencing of the V3-V4 region of the 16S rRNA gene revealed 34 genera and 24 species distributed among the phylum Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. We also observed a network of genera in these communities where the genus Chryseobacterium stands out with a greater degree of interaction, indicating a possible direct or indirect role as a keystone taxon in communities with plant-growth promotion capacities. From the results achieved, we can conclude that the approach is useful in the recovery of a set of sugarcane bacterial communities and that there is, evidence of synergistic action providing benefits to plants, and that they are compatible with plants of the same family (Poaceae). Thus, we are reporting the beneficial bacterial communities identified as suitable candidates with rated potential to be exploited as bioinoculants for crops.

The Endophytic Microbiome as a Hotspot of Synergistic Interactions, with Prospects of Plant Growth Promotion

The plant root is the primary site of interaction between plants and associated microorganisms and constitutes the main components of plant microbiomes that impact crop production. The endophytic bacteria in the root zone have an important role in plant growth promotion. Diverse microbial communities inhabit plant root tissues, and they directly or indirectly promote plant growth by inhibiting the growth of plant pathogens, producing various secondary metabolites. Mechanisms of plant growth promotion and response of root endophytic microorganisms for their survival and colonization in the host plants are the result of complex plant-microbe interactions. Endophytic microorganisms also assist the host to sustain different biotic and abiotic stresses. Better insights are emerging for the endophyte, such as host plant interactions due to advancements in 'omic' technologies, which facilitate the exploration of genes that are responsible for plant tissue colonization. Consequently, this is informative to envisage putative functions and metabolic processes crucial for endophytic adaptations. Detection of cell signaling molecules between host plants and identification of compounds synthesized by root endophytes are effective means for their utilization in the agriculture sector as biofertilizers. In addition, it is interesting that the endophytic microorganism colonization impacts the relative abundance of indigenous microbial communities and suppresses the deleterious microorganisms in plant tissues. Natural products released by endophytes act as biocontrol agents and inhibit pathogen growth. The symbiosis of endophytic bacteria and arbuscular mycorrhizal fungi (AMF) affects plant symbiotic signaling pathways and root colonization patterns and phytohormone synthesis. In this review, the potential of the root endophytic community, colonization, and role in the improvement of plant growth has been explained in the light of intricate plant-microbe interactions.

Genome Mining and Evaluation of the Biocontrol Potential of Pseudomonas fluorescens BRZ63, a New Endophyte of Oilseed Rape (Brassica napus L.) against Fungal Pathogens

Endophytic bacteria hold tremendous potential for use as biocontrol agents. Our study aimed to investigate the biocontrol activity of Pseudomonas fluorescens BRZ63, a new endophyte of oilseed rape (Brassica napus L.) against Rhizoctonia solani W70, Colletotrichum dematium K, Sclerotinia sclerotiorum K2291, and Fusarium avenaceum. In addition, features crucial for biocontrol, plant growth promotion, and colonization were assessed and linked with the genome sequences. The in vitro tests showed that BRZ63 significantly inhibited the mycelium growth of all tested pathogens and stimulated germination and growth of oilseed rape seedlings treated with fungal pathogens. The BRZ63 strain can benefit plants by producing biosurfactants, siderophores, indole-3-acetic acid (IAA), 1-aminocyclopropane-1-carboxylate (ACC) deaminase, and ammonia as well as phosphate solubilization. The abilities of exopolysaccharide production, autoaggregation, and biofilm formation additionally underline its potential to plant colonization and hence biocontrol. The effective colonization properties of the BRZ63 strain were confirmed by microscopy observations of EGFP-expressing cells colonizing the root surface and epidermal cells of Arabidopsis thaliana Col-0. Genome mining identified many genes related to the biocontrol process, such as transporters, siderophores, and other secondary metabolites. All analyses revealed that the BRZ63 strain is an excellent endophytic candidate for biocontrol of various plant pathogens and plant growth promotion.

Biocontrol of Rice Seedling Rot Disease Caused by Curvularia lunata and Helminthosporium oryzae by Epiphytic Yeasts from Plant Leaves

Seedling rot disease in rice leads to significant loss in the production of seedlings. This research was conducted to explore yeasts that could be used as biological control agents against rice seedling rot disease caused by Curvularia lunata and Helminthosporium oryzae. In total, 167 epiphytic yeast strains were evaluated, revealing that 13 of these yeast strains demonstrated antagonistic activities against fungal pathogens and either C. lunata DOAC 2313 or H. oryzae DOAC 2293. The volatile organic compounds (VOCs) and biofilm produced were possible antagonistic mechanisms in vitro for all the antagonistic yeast strains. Using nursery trays in a greenhouse, this study evaluated the control of rice seedling rot disease caused by these two fungal pathogens using antagonistic yeasts, identified in the present study and from our previous study. Torulaspora indica DMKU-RP31 and Wickerhamomyces anomalus YE-42 were found to completely control rice seedling rot disease caused by both of these fungal pathogens. Furthermore, W. anomalus DMKU-RP04 revealed 100% disease control when the disease was caused by H. oryzae. This is the first report on using antagonistic yeasts to control rice seedling rot disease caused by C. lunata and H. oryzae. These three antagonistic yeasts also showed promising potential for development as biocontrol agents against rice seedling rot disease caused by fungi.

Review: Endophytic microbes and their potential applications in crop management

Endophytes are microbes (mostly bacteria and fungi) present asymptomatically in plants. Endophytic microbes are often functional in that they may carry nutrients from the soil into plants, modulate plant development, increase stress tolerance of plants, suppress virulence in pathogens, increase disease resistance in plants, and suppress development of competitor plant species. Endophytic microbes have been shown to: (i) obtain nutrients in soils and transfer nutrients to plants in the rhizophagy cycle and other nutrient-transfer symbioses; (ii) increase plant growth and development; (iii) reduce oxidative stress of hosts; (iv) protect plants from disease; (v) deter feeding by herbivores; and (vi) suppress growth of competitor plant species. Because of the effective functions of endophytic microbes, we suggest that endophytic microbes may significantly reduce use of agrochemicals (fertilizers, fungicides, insecticides, and herbicides) in the cultivation of crop plants. The loss of endophytic microbes from crop plants during domestication and long-term cultivation could be remedied by transfer of endophytes from wild relatives of crops to crop species. Increasing atmospheric carbon dioxide levels could reduce the efficiency of the rhizophagy cycle due to repression of reactive oxygen used to extract nutrients from microbes in roots. © 2019 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Biosynthesis of silver nanoparticles using endophytic bacteria and their role in inhibition of rice pathogenic bacteria and plant growth promotion

The biosynthesis of silver nanoparticles (AgNPs) through the use of endophytic bacteria is a safe replacement for the chemical method. The study aimed to synthesize AgNPs using endophytic bacterium Bacillus siamensis strain C1, which was isolated from the medicinal plant Coriandrum sativum. The synthesized AgNPs with the size of 25 to 50 nm were further confirmed and characterized by UV-visible spectroscopy, Fourier transform infrared spectroscopy, X-ray diffraction, transmission electron microscopy and scanning electron microscopy with EDS profile. The synthesized AgNPs at 20 μg mL⁻¹ showed a strong antibacterial effect against the pathogen of rice bacterial leaf blight and bacterial brown stripe, while an inhibition zone of 17.3 and 16.0 mm was observed for Xanthomonas oryzae pv. oryzae (Xoo) strain LND0005 and Acidovorax oryzae (Ao) strain RS-1, respectively. Furthermore, the synthesized AgNPs significantly inhibited bacterial growth, biofilm formation and swimming motility of Xoo strain LND0005 and Ao strain RS-1. In addition, the synthesized AgNPs significantly increased root length, shoot length, fresh weight and dry weight of rice seedlings compared to the control. Overall, this study suggests that AgNPs have the potential to protect rice plants from bacterial infection and plant growth promotion.

The mechanism of silver nanoparticles (AgNPs) to inhibit rice pathogenic bacteria.

Rhizophagy Cycle: An Oxidative Process in Plants for Nutrient Extraction from Symbiotic Microbes

In this paper, we describe a mechanism for the transfer of nutrients from symbiotic microbes (bacteria and fungi) to host plant roots that we term the ‘rhizophagy cycle.’ In the rhizophagy cycle, microbes alternate between a root intracellular endophytic phase and a free-living soil phase. Microbes acquire soil nutrients in the free-living soil phase; nutrients are extracted through exposure to host-produced reactive oxygen in the intracellular endophytic phase. We conducted experiments on several seed-vectored microbes in several host species. We found that initially the symbiotic microbes grow on the rhizoplane in the exudate zone adjacent the root meristem. Microbes enter root tip meristem cells—locating within the periplasmic spaces between cell wall and plasma membrane. In the periplasmic spaces of root cells, microbes convert to wall-less protoplast forms. As root cells mature, microbes continue to be subjected to reactive oxygen (superoxide) produced by NADPH oxidases (NOX) on the root cell plasma membranes. Reactive oxygen degrades some of the intracellular microbes, also likely inducing electrolyte leakage from microbes—effectively extracting nutrients from microbes. Surviving bacteria in root epidermal cells trigger root hair elongation and as hairs elongate bacteria exit at the hair tips, reforming cell walls and cell shapes as microbes emerge into the rhizosphere where they may obtain additional nutrients. Precisely what nutrients are transferred through rhizophagy or how important this process is for nutrient acquisition is still unknown.