Photosynthetic bacterium Rhodopseudomonas palustris GJ-22 induces systemic resistance against viruses

Selection and Effect of Plant Growth-Promoting Bacteria on Pine Seedlings (Pinus montezumae and Pinus patula)

Forest cover is deteriorating rapidly due to anthropogenic causes, making its restoration urgent. Plant growth-promoting bacteria (PGPB) could offer a viable solution to ensure successful reforestation efforts. This study aimed to select bacterial strains with mechanisms that promote plant growth and enhance seedling development. The bacterial strains used in this study were isolated from the rhizosphere and endophyte regions of Pinus montezumae Lamb. and Pinus patula Schl. et Cham., two Mexican conifer species commonly used for reforestation purposes. Sixteen bacterial strains were selected for their ability to produce auxins, chitinase, and siderophores, perform nitrogen fixation, and solubilize inorganic phosphates; they also harbored genes encoding antimicrobial production and ACC deaminase. The adhesion to seeds, germination rate, and seedling response of P. montezumae and P. patula were performed following inoculation with 10 bacterial strains exhibiting high plant growth-promoting potential. Some strains demonstrated the capacity to enhance seedling growth. The selected strains were taxonomically characterized and belonged to the genus Serratia, Buttiauxella, and Bacillus. These strains exhibited at least two mechanisms of action, including the production of indole-3-acetic acid, biological nitrogen fixation, and phosphate solubilization, and could serve as potential alternatives for the reforestation of affected areas.

Phyllosphere Microbiome in Plant Health and Disease

The phyllosphere refers to the aboveground surface of plants colonized by diverse microorganisms. Microbes inhabiting this environment play an important role in enhancing the host's genomic and metabolic capabilities, including defense against pathogens. Compared to the large volume of studies on rhizosphere microbiome for plant health and defense, our understanding of phyllosphere microbiome remains in its infancy. In this review, we aim to explore the mechanisms that govern the phyllosphere assembly and their function in host defence, as well as highlight the knowledge gaps. These efforts will help develop strategies to harness the phyllosphere microbiome toward sustainable crop production.

Characterization of the Pyrroloquinoline Quinone Producing Rhodopseudomonas palustris as a Plant Growth-Promoting Bacterium under Photoautotrophic and Photoheterotrophic Culture Conditions

Rhodopseudomonas palustris is a purple non-sulfide bacterium (PNSB), and some strains have been proven to promote plant growth. However, the mechanism underlying the effect of these PNSBs remains limited. Based on genetic information, R. palustris possesses the ability to produce pyrroloquinoline quinone (PQQ). PQQ is known to play a crucial role in stimulating plant growth, facilitating phosphorous solubilization, and acting as a reactive oxygen species scavenger. However, it is still uncertain whether growth conditions influence R. palustris's production of PQQ and other characteristics. In the present study, it was found that R. palustris exhibited a higher expression of genes related to PQQ synthesis under autotrophic culture conditions as compared to acetate culture conditions. Moreover, similar patterns were observed for phosphorous solubilization and siderophore activity, both of which are recognized to contribute to plant-growth benefits. However, these PNSB culture conditions did not show differences in Arabidopsis growth experiments, indicating that there may be other factors influencing plant growth in addition to PQQ content. Furthermore, the endophytic bacterial strains isolated from Arabidopsis exhibited differences according to the PNSB culture conditions. These findings imply that, depending on the PNSB's growing conditions, it may interact with various soil bacteria and facilitate their infiltration into plants.

The genome-scale metabolic model for the purple non-sulfur bacterium Rhodopseudomonas palustris Bis A53 accurately predicts phenotypes under chemoheterotrophic, chemoautotrophic, photoheterotrophic, and photoautotrophic growth conditions

The purple non-sulfur bacterium Rhodopseudomonas palustris is recognized as a critical microorganism in the nitrogen and carbon cycle and one of the most common members in wastewater treatment communities. This bacterium is metabolically extremely versatile. It is capable of heterotrophic growth under aerobic and anaerobic conditions, but also able to grow photoautotrophically as well as mixotrophically. Therefore R. palustris can adapt to multiple environments and establish commensal relationships with other organisms, expressing various enzymes supporting degradation of amino acids, carbohydrates, nucleotides, and complex polymers. Moreover, R. palustris can degrade a wide range of pollutants under anaerobic conditions, e.g., aromatic compounds such as benzoate and caffeate, enabling it to thrive in chemically contaminated environments. However, many metabolic mechanisms employed by R. palustris to breakdown and assimilate different carbon and nitrogen sources under chemoheterotrophic or photoheterotrophic conditions remain unknown. Systems biology approaches, such as metabolic modeling, have been employed extensively to unravel complex mechanisms of metabolism. Previously, metabolic models have been reconstructed to study selected capabilities of R. palustris under limited experimental conditions. Here, we developed a comprehensive metabolic model (M-model) for R. palustris Bis A53 (iDT1294) consisting of 2,721 reactions, 2,123 metabolites, and comprising 1,294 genes. We validated the model using high-throughput phenotypic, physiological, and kinetic data, testing over 350 growth conditions. iDT1294 achieved a prediction accuracy of 90% for growth with various carbon and nitrogen sources and close to 80% for assimilation of aromatic compounds. Moreover, the M-model accurately predicts dynamic changes of growth and substrate consumption rates over time under nine chemoheterotrophic conditions and demonstrated high precision in predicting metabolic changes between photoheterotrophic and photoautotrophic conditions. This comprehensive M-model will help to elucidate metabolic processes associated with the assimilation of multiple carbon and nitrogen sources, anoxygenic photosynthesis, aromatic compound degradation, as well as production of molecular hydrogen and polyhydroxybutyrate.

Effects of LPS from Rhodobacter sphaeroides, a Purple Non-Sulfur Bacterium (PNSB), on the Gene Expression of Rice Root

The effects of lipopolysaccharide (LPS) from Rhodobacter sphaeroides, a purple non-sulfur bacterium (PNSB), on the gene expression of the root of rice (Oryza sativa) were investigated by next generation sequencing (NGS) RNA-seq analysis. The rice seeds were germinated on agar plates containing 10 pg/mL of LPS from Rhodobacter sphaeroides NBRC 12203 (type culture). Three days after germination, RNA samples were extracted from the roots and analyzed by RNA-seq. The effects of dead (killed) PNSB cells of R. sphaeroides NBRC 12203^T at the concentration of 10¹ cfu/mL (ca. 50 pg cell dry weight/mL) were also examined. Clean reads of NGS were mapped to rice genome (number of transcript ID: 44785), and differentially expressed genes were analyzed by DEGs. As a result of DEG analysis, 300 and 128 genes, and 86 and 8 genes were significantly up- and down-regulated by LPS and dead cells of PNSB, respectively. The plot of logFC (fold change) values of the up-regulated genes of LPS and PNSB dead cells showed a significant positive relationship (r² = 0.6333, p < 0.0001), indicating that most of the effects of dead cell were attributed to those of LPS. Many genes related to tolerance against biotic (fungal and bacterial pathogens) and abiotic (cold, drought, and high salinity) stresses were up-regulated, and the most strikingly up-regulated genes were those involved in the jasmonate signaling pathway, and the genes of chalcone synthase isozymes, indicating that PNSB induced defense response against biotic and abiotic stresses via the jasmonate signaling pathway, despite the non-pathogenicity of PNSB.

Rhodopseudomonas palustris PSB06 agent enhance pepper yield and regulating the rhizosphere microecological environment

The Rhodopseudomonas palustris (R. palustris) PSB06 can promote crop growth, as it maybe regulates microbial communities in plant root soil, soil physicochemical properties, thus creating a favorable habitat for the crop growth. However, there are few studies on the yields and rhizosphere microbial community of R. palustris PSB06 agent. In the study, the high-throughput sequencing was used to study the changes of rhizosphere soil bacterial community after PSB06 treatment. The results indicated R. palustris PSB06 agent increased the pepper yield by 33.45% when compared to control group, with better effect than other treatments. And it also significantly increased soil nitrogen concentration. R. palustris PSB06 agent had improved pepper rhizosphere bacterial α diversity and changed the community structure. Acidobacteria, Proteobacteria, Actinomycetes and Firmicutes were dominant phyla in all the pepper rhizosphere soil samples. The results showed that soil bacterial community were significantly positively correlated with pH (R = 0.8537, P = 0.001) and total nitrogen (R = 0.4347, P = 0.003). The nine significantly enriched OTU in R.palustris PSB06 treatment (PB) group belong to Nitrososphaera (OTU_109, OTU_14, OTU_18, OTU_8), Lysobacter (OTU_2115, OTU_13), Arenimonas (OTU_26), Luteimonas (OTU_49), and Ramlibacter (OTU_70) were significantly positively correlated with the total yield of pepper (R &gt; 0.5, P &lt; 0.05). Overall, our results provide a theoretical basis for studying the microbial regulation of R.palustris PSB06 on rhizosphere soil.

Mechanisms of Microbial Plant Protection and Control of Plant Viruses

Plant viral diseases are major constraints causing significant yield losses worldwide in agricultural and horticultural crops. The commonly used methods cannot eliminate viral load in infected plants. Many unconventional methods are presently being employed to prevent viral infection; however, every time, these methods are not found promising. As a result, it is critical to identify the most promising and sustainable management strategies for economically important plant viral diseases. The genetic makeup of 90 percent of viral diseases constitutes a single-stranded RNA; the most promising way for management of any RNA viruses is through use ribonucleases. The scope of involving beneficial microbial organisms in the integrated management of viral diseases is of the utmost importance and is highly imperative. This review highlights the importance of prokaryotic plant growth-promoting rhizobacteria/endophytic bacteria, actinomycetes, and fungal organisms, as well as their possible mechanisms for suppressing viral infection in plants via cross-protection, ISR, and the accumulation of defensive enzymes, phenolic compounds, lipopeptides, protease, and RNase activity against plant virus infection.

Contributions of Beneficial Microorganisms in Soil Remediation and Quality Improvement of Medicinal Plants

Medicinal plants (MPs) are important resources widely used in the treatment and prevention of diseases and have attracted much attention owing to their significant antiviral, anti-inflammatory, antioxidant and other activities. However, soil degradation, caused by continuous cropping, excessive chemical fertilizers and pesticide residues and heavy metal contamination, seriously restricts the growth and quality formation of MPs. Microorganisms, as the major biota in soil, play a critical role in the restoration of the land ecosystem. Rhizosphere microecology directly or indirectly affects the growth and development, metabolic regulation and active ingredient accumulation of MPs. Microbial resources, with the advantages of economic efficiency, harmless to environment and non-toxic to organisms, have been recommended as a promising alternative to conventional fertilizers and pesticides. The introduction of beneficial microbes promotes the adaptability of MPs to adversity stress by enhancing soil fertility, inhibiting pathogens and inducing systemic resistance. On the other hand, it can improve the medicinal quality by removing soil pollutants, reducing the absorption and accumulation of harmful substances and regulating the synthesis of secondary metabolites. The ecological and economic benefits of the soil microbiome in agricultural practices are increasingly recognized, but the current understanding of the interaction between soil conditions, root exudates and microbial communities and the mechanism of rhizosphere microecology affecting the secondary metabolism of MPs is still quite limited. More research is needed to investigate the effects of the microbiome on the growth and quality of different medicinal species. Therefore, the present review summarizes the main soil issues in medicinal plant cultivation, the functions of microbes in soil remediation and plant growth promotion and the potential mechanism to further guide the use of microbial resources to promote the ecological cultivation and sustainable development of MPs.

Combining the microbial agent Rhodopseudomonas palustris strain PSB-06 with fungicides for controlling rice blast

The rice blast disease caused by Magnaporthe oryzae threatens global rice production yields. Tricyclazole and isoprothiolane are widely used fungicides with high activity against rice blast, and our previous study indicated the photosynthetic bacterium Rhodopseudomonas palustris PSB-06 significantly antagonizes rice blast. However the effect of combining these two chemical fungicides with PSB-06 on rice blast control is unclear. Here we test the control effect of photosynthetic bacteria PSB-06 combined with isoprothiolane and tricyclazole on rice blast. The growth of PSB-06 was unaffected by up to 1.25 mg/L of tricyclazole and 0.3 mg/L of isoprothiolane in the photosynthetic medium, indicated the two fungicides have no inhibition on PSB-06. The control efficiency in the field test reached 76.06% when PSB-06 was combined with isoprothiolane. This value was significantly higher than the individual efficiency of PSB-06 (67.99%) and tricyclazole (65.46%) and the combined control efficiency (72.20%) of those two antifungal agents. Our current findings highlighted the potential of combining R. palustris strain PSB-06 with isoprothiolane to control rice blast, providing environmental protection and reducing the use of fungicides.

Effects of dazomet combined with Rhodopsesudomonas palustris PSB-06 on root-knot nematode, Meloidogyne incognita infecting ginger and soil microorganisms diversity

Root-knot nematode, Meloidogyne incognita is one of the most important nematodes affecting ginger crop. Rhodopseudomonas palustris PSB-06, as effective microbial fertilizer in increasing plant growth and suppressing soil-borne disease of many crops has been reported. The combination of R. palustris PSB-06 and dazomet treatments had been proved to inhibit root-knot nematode on ginger and increase ginger yield in our preliminary study. The field experiments were conducted to elucidate the reasons behind this finding, and followed by next-generation sequencing to determine the microbial population structures in ginger root rhizosphere. The results showed that combination of R. palustris PSB-06 and dazomet treatment had a synergetic effect by achieving of 80.00% reduction in root-knot nematode numbers less than soil without treatment, and also could increase 37.37% of ginger yield through increasing the contents of chlorophyll and total protein in ginger leaves. Microbiota composition and alpha diversity varied with treatments and growth stages, soil bacterial diversity rapidly increased after planting ginger. In addition, the combined treatment could increase diversity and community composition of probiotic bacteria, and decrease those of soil-borne pathogenic fungi comparing to the soil treated with dazomet alone. Meanwhile, it could also effectively increase soil organic matter, available phosphorus and available potassium. Analysis of correlation between soil microorganisms and physicochemical properties indicated that the soil pH value and available phosphorus content were important factors that could affect soil microorganisms structure at the harvest stage. The bacterial family was more closely correlated with the soil physicochemical properties than the fungal family. Therefore, the combination of R. palustris PSB-06 and dazomet was considered as an effective method to control root-knot nematode disease and improve ginger soil conditions.

Foliar Application of Rhodopseudomonas palustris Enhances the Rice Crop Growth and Yield under Field Conditions

Anthropogenic activities causing climate change and other environmental effects are lowering crop yield by deteriorating the growing environment for crops. Rice, a globally important cereal crop, is under production threat due to climate change and land degradation. This research aims to sustainably improve rice growth and yield by using Rhodopseudomonas palustris, a plant growth-promoting bacteria that has recently gained much attention in crop production. The experiment was set up in two fields, one as a control and the other as a PNSB-treated field. The foliar application of treatment was made fortnightly until the end of the vegetative stage. Data on the growth, yield, and antioxidant enzymes were collected weekly. The results of this experiment indicate no significant differences in the plant height, root volume, average grain per panicle, biological yield, grain fertility, and antioxidant enzyme activity between the PNSB-treated and untreated plants. However, a significant increase in the tiller number, leaf chlorophyll content and lodging resistance were noted with PNSB treatment. Likewise, PNSB-treatment significantly increased root length (25%), root dry weight (57%), productive tillers per plants (26%), average grains per plant (38%), grain yield (33%), 1000 grain weight (1.6%), and harvest index (41%). Hence, from this research, it can be concluded that foliar application of PNSB on rice crops under field conditions improves crop growth and yield, although it does not affect antioxidant enzyme activity.

Metagenomic analysis of the dynamical conversion of photosynthetic bacterial communities in different crop fields over different growth periods

Photosynthetic bacteria are beneficial to plants, but knowledge of photosynthetic bacterial community dynamics in field crops during different growth stages is scarce. The factors controlling the changes in the photosynthetic bacterial community during plant growth require further investigation. In this study, 35 microbial community samples were collected from the seedling, flowering, and mature stages of tomato, cucumber, and soybean plants. 35 microbial community samples were assessed using Illumina sequencing of the photosynthetic reaction center subunit M (pufM) gene. The results revealed significant alpha diversity and community structure differences among the three crops at the different growth stages. Proteobacteria was the dominant bacterial phylum, and Methylobacterium, Roseateles, and Thiorhodococcus were the dominant genera at all growth stages. PCoA revealed clear differences in the structure of the microbial populations isolated from leaf samples collected from different crops at different growth stages. In addition, a dissimilarity test revealed significant differences in the photosynthetic bacterial community among crops and growth stages (P<0.05). The photosynthetic bacterial communities changed during crop growth. OTUs assigned to Methylobacterium were present in varying abundances among different sample types, which we speculated was related to the function of different Methylobacterium species in promoting plant growth development and enhancing plant photosynthetic efficiency. In conclusion, the dynamics observed in this study provide new research ideas for the detailed assessments of the relationship between photosynthetic bacteria and different growth stages of plants.

Characteristics and diversity of endophytic bacteria in Panax notoginseng under high temperature analysed using full-length 16S rRNA sequencing

Panax notoginseng is a traditional Chinese medicinal herb with diverse properties that is cultivated in a narrow ecological range because of its sensitivity to high temperatures. Endophytic bacteria play a prominent role in plant response to climate warming. However, the endophytic bacterial structures in P. notoginseng at high temperatures are yet unclear. In the present study, the diversity and composition of the endophytic bacterial community, and their relationships with two P. notoginseng plants with different heat tolerance capacities were compared using the full-length 16S rRNA PacBio sequencing system. The results revealed that the diversity and richness of endophytic bacteria were negatively associated with the heat tolerance of P. notoginseng. Beneficial Cyanobacteria, Rhodanobacter and Sphingomonas may be recruited positively by heat-tolerant plants, while higher amounts of adverse Proteobacteria such as Cellvibrio fibrivorans derived from soil destructed the cellular protective barriers of heat-sensitive plants and caused influx of pathogenic bacteria Stenotrophomonas maltophilia. Harmonious and conflicting bacterial community was observed in heat-tolerant and heat-sensitive P. notoginseng, respectively, based on the co-occurrence network. Using functional gene prediction of metabolism, endophytic bacteria have been proposed to be symbiotic with host plants; the bacteria improved primary metabolic pathways and secondary metabolite production of plants, incorporated beneficial endophytes, and combated adverse endophytes to prompt the adaptation of P. notoginseng to a warming environment. These findings provided a new perspective on the function of endophytes in P. notoginseng adaptation to high temperatures, and could pave the way for expanding the cultivable range of P. notoginseng.

Rhodopseudomonas palustris: A biotechnology chassis

Rhodopseudomonas palustris is an attractive option for biotechnical applications and industrial engineering due to its metabolic versatility and its ability to catabolize a wide variety of feedstocks and convert them to several high-value products. Given its adaptable metabolism, R. palustris has been studied and applied in an extensive variety of applications such as examining metabolic tradeoffs for environmental perturbations, biodegradation of aromatic compounds, environmental remediation, biofuel production, agricultural biostimulation, and bioelectricity production. This review provides a holistic summary of the commercial applications for R. palustris as a biotechnology chassis and suggests future perspectives for research and engineering.

Characteristics and Application of Rhodopseudomonas palustris as a Microbial Cell Factory

Rhodopseudomonas palustris, a purple nonsulfur bacterium, is a bacterium with the properties of extraordinary metabolic versatility, carbon source diversity and metabolite diversity. Due to its biodetoxification and biodegradation properties, R. palustris has been traditionally applied in wastewater treatment and bioremediation. R. palustris is rich in various metabolites, contributing to its application in agriculture, aquaculture and livestock breeding as additives. In recent years, R. palustris has been engineered as a microbial cell factory to produce valuable chemicals, especially photofermentation of hydrogen. The outstanding property of R. palustris as a microbial cell factory is its ability to use a diversity of carbon sources. R. palustris is capable of CO₂ fixation, contributing to photoautotrophic conversion of CO₂ into valuable chemicals. R. palustris can assimilate short-chain organic acids and crude glycerol from industrial and agricultural wastewater. Lignocellulosic biomass hydrolysates can also be degraded by R. palustris. Utilization of these feedstocks can reduce the industry cost and is beneficial for environment. Applications of R. palustris for biopolymers and their building blocks production, and biofuels production are discussed. Afterward, some novel applications in microbial fuel cells, microbial electrosynthesis and photocatalytic synthesis are summarized. The challenges of the application of R. palustris are analyzed, and possible solutions are suggested.

Structure and Function of Rhizosphere Soil and Root Endophytic Microbial Communities Associated With Root Rot of Panax notoginseng

Panax notoginseng (Burk.) F. H. Chen is a Chinese medicinal plant of the Araliaceae family used for the treatment of cardiovascular and cerebrovascular diseases in Asia. P. notoginseng is vulnerable to root rot disease, which reduces the yield of P. notoginseng. In this study, we analyzed the rhizosphere soil and root endophyte microbial communities of P. notoginseng from different geographical locations using high-throughput sequencing. Our results revealed that the P. notoginseng rhizosphere soil microbial community was more diverse than the root endophyte community. Rhodopseudomonas, Actinoplanes, Burkholderia, and Variovorax paradoxus can help P. notoginseng resist the invasion of root rot disease. Ilyonectria mors-panacis, Pseudomonas fluorescens, and Pseudopyrenochaeta lycopersici are pathogenic bacteria of P. notoginseng. The upregulation of amino acid transport and metabolism in the soil would help to resist pathogens and improve the resistance of P. notoginseng. The ABC transporter and gene modulating resistance genes can improve the disease resistance of P. notoginseng, and the increase in the number of GTs (glycosyltransferases) and GHs (glycoside hydrolases) families may be a molecular manifestation of P. notoginseng root rot. In addition, the complete genomes of two Flavobacteriaceae species and one Bacteroides species were obtained. This study demonstrated the microbial and functional diversity in the rhizosphere and root microbial community of P. notoginseng and provided useful information for a better understanding of the microbial community in P. notoginseng root rot. Our results provide insights into the molecular mechanism underlying P. notoginseng root rot and other plant rhizosphere microbial communities.

GroEL protein from the potential biocontrol agent Rhodopseudomonas palustris enhances resistance to rice blast disease

BACKGROUND

GroEL, which is a chaperone, plays a key role in maintaining protein homeostasis and, among other functions, serves to prevent protein misfolding and aggregation. In addition, the GroEL protein also has a significant effect on enhancing plant resistance and inhibiting plant diseases. However, the function of the GroEL protein in the inhibition of rice blast remains unknown.

RESULTS

Field experiment results show that photosynthetic bacteria PSB-06 have a good control effect on Magnaporthe oryzae. PSB-06 also can promote rice growth and enhance stress resistance. A GroEL protein which was separated and purified from photosynthetic bacteria had a significant antagonistic effect on appressorial formation and pathogenicity of Magnaporthe oryzae, meanwhile transcriptional analysis demonstrated that the GroEL protein could improve the expression of defense gene of rice.

CONCLUSION

Our results show that the photosynthetic bacteria Rhodopseudomonas palustris significantly controls rice blast disease. Its action involves an extracellular GroEL protein, which inhibits appressoria formation, antagonizes the pathogenicity of Magnaporthe oryzae and promotes a host defense response. The research results provide evidence of the potential of this photosynthetic bacterium as a biocontrol agent at least for rice blast control. © 2021 Society of Chemical Industry.

From Lab to Farm: Elucidating the Beneficial Roles of Photosynthetic Bacteria in Sustainable Agriculture

Photosynthetic bacteria (PSB) possess versatile metabolic abilities and are widely applied in environmental bioremediation, bioenergy production and agriculture. In this review, we summarize examples of purple non-sulfur bacteria (PNSB) through biofertilization, biostimulation and biocontrol mechanisms to promote plant growth. They include improvement of nutrient acquisition, production of phytohormones, induction of immune system responses, interaction with resident microbial community. It has also been reported that PNSB can produce an endogenous 5-aminolevulinic acid (5-ALA) to alleviate abiotic stress in plants. Under biotic stress, these bacteria can trigger induced systemic resistance (ISR) of plants against pathogens. The nutrient elements in soil are significantly increased by PNSB inoculation, thus improving fertility. We share experiences of researching and developing an elite PNSB inoculant (Rhodopseudomonas palustris PS3), including strategies for screening and verifying beneficial bacteria as well as the establishment of optimal fermentation and formulation processes for commercialization. The effectiveness of PS3 inoculants for various crops under field conditions, including conventional and organic farming, is presented. We also discuss the underlying plant growth-promoting mechanisms of this bacterium from both microbial and plant viewpoints. This review improves our understanding of the application of PNSB in sustainable crop production and could inspire the development of diverse inoculants to overcome the changes in agricultural environments created by climate change.

Revealing the role of Plant Growth Promoting Rhizobacteria in suppressive soils against Fusarium oxysporum f.sp. cubense based on metagenomic analysis

Fusarium oxysporum f.sp. cubense (Foc) is a soil-borne pathogen causing fusarium wilt banana disease. Management of soil-borne disease generally required the application of toxic pesticides or fungicides strongly affect the soil microbiomes ecosystem. Suppressive soil is a promising method for controlling soil-borne pathogens in which soil microbiomes may affect the suppressiveness. The comparative analysis of microbial diversity was conducted from suppressive and conducive soils by analyzing whole shotgun metagenomic DNA data. Two suppressive soil samples and two conducive soil samples were collected from a banana plantation in Sukabumi, West Java, Indonesia. Each soil sample was prepared by mixing the soil samples collected from three points sampling sites with 20 cm depth. Analysis of microbial abundance, diversity, co-occurrence network using Metagenome Analyzer 6 (MEGAN6) and functional analysis using Kyoto Encyclopedia of Genes and Genomes (KEGG) was performed. Data showed the abundance of Actinobacteria, Betaproteobacteria, Rhizobiales, Burkholderiales, Bradyrhizobiaceae, Methylobacteriaceae, Rhodopseudomonas palustris, and Methylobacterium nodulans were higher in the suppressive than conducive soils. Interestingly, those bacteria groups are known functionally as members of Plant Growth Promoting Rhizobacteria (PGPR). The co-occurrence analysis showed Pseudomonas, Burkholderia, and Streptomyces were present in the suppressive soils, while Bacillus and more Streptomyces were found in the conducive soils. Furthermore, the relative abundance of Pseudomonas, Burkholderia, Bacillus, and Streptomyces was performed. The analysis showed that the relative abundance of Pseudomonas and Burkholderia was higher in the suppressive than conducive soils. Therefore, it assumed Pseudomonas and Burkholderia play a role in suppressing Foc based on co-occurrence and abundance analysis. Functional analysis of Pseudomonas and Burkholderia showed that the zinc/manganese transport system was higher in the suppressive than conducive soils. In contrast, the phosphate transport system was not found in conducive soils. Both functions are may be responsible for the synthesis of a siderophore and phosphate solubilization. In conclusion, this study provides information that PGPR may be contributing to Foc growth suppressing by releasing secondary metabolites.

Rhodopseudomonas palustris Quorum Sensing Molecule pC-HSL Induces Systemic Resistance to TMV Infection via Upregulation of NbSIPK/NbWIPK Expressions in Nicotiana benthamiana

G-negative bacteria produce myriad N-acyl-homoserine lactones (AHLs) that can function as quorum sensing (QS) signaling molecules. AHLs are also known to regulate various plant biological activities. p-Coumaroyl-homoserine lactone (pC-HSL) is the only QS molecule produced by a photosynthetic bacterium, Rhodopseudomonas palustris. The role of pC-HSL in the interaction between R. palustris and plant has not been investigated. In this study, we investigated the effect of pC-HSL on plant immunity and found that this QS molecule can induce a systemic resistance to Tobacco mosaic virus (TMV) infection in Nicotiana benthamiana. The results show that pC-HSL treatment can prolong the activation of two mitogen-associated protein kinase genes (i.e., NbSIPK and NbWIPK) and increase the expression of transcription factor WRKY8 as well as immune response marker genes NbPR1 and NbPR10, leading to an increased accumulation of reactive oxygen species (ROS) in the TMV-infected plants. Our results also show that pC-HSL treatment can increase activities of two ROS-scavenging enzymes, peroxidase and superoxide dismutase. Knockdown of NbSIPK or NbWIPK expression in N. benthamiana plants through virus-induced gene silencing nullified or attenuated pC-HSL-induced systemic resistance, indicating that the functioning of pC-HSL relies on the activity of those two kinases. Meanwhile, pC-HSL-pretreated plants also showed a strong induction of kinase activities of NbSIPK and NbWIPK after TMV inoculation. Taken together, our results demonstrate that pC-HSL treatment increases plant resistance to TMV infection, which is helpful to uncover the outcome of interaction between R. palustris and its host plants.

An overview of anoxygenic phototrophic bacteria and their applications in environmental biotechnology for sustainable Resource recovery

Anoxygenic phototrophic bacteria (APB) are a phylogenetically diverse group of organisms that can harness solar energy for their growth and metabolism. These bacteria vary broadly in terms of their metabolism as well as the composition of their photosynthetic apparatus. Unlike oxygenic phototrophic bacteria such as algae and cyanobacteria, APB can use both organic and inorganic electron donors for light-dependent fixation of carbon dioxide without generating oxygen. Their versatile metabolism, ability to adapt in extreme conditions, low maintenance cost and high biomass yield make APB ideal for wastewater treatment, resource recovery and in the production of high value substances. This review highlights the advantages of APB over algae and cyanobacteria, and their applications in photo-bioelectrochemical systems, production of poly-β-hydroxyalkanoates, single-cell protein, biofertilizers and pigments. The ecology of ABP, their distinguishing factors, various physiochemical parameters governing the production of high-value substances and future directions of APB utilization are also discussed.

Structural characterization and functional activity of an exopolysaccharide secreted by Rhodopseudomonas palustris GJ-22

One water exopolysaccharide, designated G-EPS, was secreted by Rhodopseudomonas palustris GJ-22 culture media. The structure of G-EPS was characterized with HPGPC, GC-MS, methylation, 1D and 2D NMR, along with UV and FT-IR spectrum. The G-EPS molecular weight was 10.026 kilodalton, and is composed of D-mannose (92.8%) and d-glucose (7.2%). The purified G-EPS promoted plant growth and induced systemic resistance against TMV in Nicotiana benthamiana. These results suggested that G-EPS is an important active component of the bio-control capacity of GJ-22.

Purple non-sulphur bacteria and plant production: benefits for fertilization, stress resistance and the environment

Purple non-sulphur bacteria (PNSB) are phototrophic microorganisms, which increasingly gain attention in plant production due to their ability to produce and accumulate high-value compounds that are beneficial for plant growth. Remarkable features of PNSB include the accumulation of polyphosphate, the production of pigments and vitamins and the production of plant growth-promoting substances (PGPSs). Scattered case studies on the application of PNSB for plant cultivation have been reported for decades, yet a comprehensive overview is lacking. This review highlights the potential of using PNSB in plant production, with emphasis on three key performance indicators (KPIs): fertilization, resistance to stress (biotic and abiotic) and environmental benefits. PNSB have the potential to enhance plant growth performance, increase the yield and quality of edible plant biomass, boost the resistance to environmental stresses, bioremediate heavy metals and mitigate greenhouse gas emissions. Here, the mechanisms responsible for these attributes are discussed. A distinction is made between the use of living and dead PNSB cells, where critical interpretation of existing literature revealed the better performance of living cells. Finally, this review presents research gaps that remain yet to be elucidated and proposes a roadmap for future research and implementation paving the way for a more sustainable crop production.

Exogenous Application of Harpin Protein Hpa1 onto Pinellia ternata Induces Systemic Resistance Against Tobacco Mosaic Virus

The harpin protein Hpa1 has various beneficial effects in plants, such as promoting plant growth and inducing pathogen resistance. Our previous study found that Hpa1 could significantly alleviate the mosaic symptoms of tobacco mosaic virus (TMV) in Pinellia ternata, indicating that Hpa1 can effectively stimulate resistance. Here, the potential mechanism of disease resistance and field applicability of Hpa1 against TMV in P. ternata were further investigated. The results showed that 15 µg ml-1 Hpa1 had stronger antiviral activity than the control, and its protective effect was better than its curative effect. Furthermore, Hpa1 could significantly induce an increase in defense-related enzyme activity, including polyphenol oxidase, peroxidase, catalase, and superoxide dismutase, as well as increase the expression of disease resistance-related genes (PR1, PR3, PR5, and PDF1.2). Concurrently, Hpa1 significantly increased the content of some disease resistance-related substances, including hydrogen peroxide, phenolics, and callose, whereas the content of malondialdehyde was reduced. In addition, field application analysis demonstrated that Hpa1 could effectively elicit a defense response against TMV in P. ternata. Our findings propose a mechanism by which Hpa1 can prevent TMV infection in Pinellia by inducing systemic resistance, thereby providing an environmentally friendly approach for the use of Hpa1 in large-scale applications to improve TMV resistance in Pinellia.

The importance of antimicrobial compounds produced by beneficial bacteria on the biocontrol of phytopathogens

Bacteria produce antimicrobial compounds to compete for nutrients and space in a particular habitat. Antagonistic interactions can be evaluated by several methodologies including the double-layer agar and simultaneous inhibition assays. Among the well-known inhibitory substances produced by bacteria are the broad-spectrum antibiotics, organic acids, siderophores, antifungal, and bacteriocins. The most studied bacterial genera able to produce these inhibitory substances are Enterococcus, Lactococcus, Streptomyces, Bacillus, Pseudomonas, Klebsiella, Escherichia, and Burkholderia. Some beneficial bacteria can promote plant growth and degrade toxic compounds in the environment representing an attractive solution to diverse issues in agriculture and soil pollution, particularly in fields with damaged soils where pesticides and fertilizers have been indiscriminately used. Beneficial bacteria may increase plant health by inhibiting pathogenic microorganisms; some examples include Gluconacetobacter diazotrophicus, Azospirullum brasilense, Pseudomonas fluorescens, Pseudomonas protegens, and Burkholderia tropica. However, most studies showing the antagonistic potential of these bacteria have been performed in vitro, and just a few of them have been evaluated in association with plants. Several inhibitory substances involved in pathogen antagonism have not been elucidated yet; in fact, we know only 1 % of the bacterial diversity in a natural environment leading us to assume that many other inhibitory substances remain unexplored. In this review, we will describe the characteristics of some antimicrobial compounds produced by beneficial bacteria, the principal methodologies performed to evaluate their production, modes of action, and their importance for biotechnological purposes.

Mechanisms of Plant Tolerance to RNA Viruses Induced by Plant-Growth-Promoting Microorganisms

Plant viruses are globally responsible for the significant crop losses of economically important plants. All common approaches are not able to eradicate viral infection. Many non-conventional strategies are currently used to control viral infection, but unfortunately, they are not always effective. Therefore, it is necessary to search for efficient and eco-friendly measures to prevent viral diseases. Since the genomic material of 90% higher plant viruses consists of single-stranded RNA, the best way to target the viral genome is to use ribonucleases (RNase), which can be effective against any viral disease of plants. Here, we show the importance of the search for endophytes with protease and RNase activity combined with the capacity to prime antiviral plant defense responses for their protection against viruses. This review discusses the possible mechanisms used to suppress a viral attack as well as the use of local endophytic bacteria for antiviral control in crops.

Characterization of Rhodopseudomonas palustris population dynamics on tobacco phyllosphere and induction of plant resistance to Tobacco mosaic virus

Although many biocontrol bacteria can be used to improve plant tolerance to stresses and to promote plant growth, the hostile environmental conditions on plant phyllosphere and the limited knowledge on bacterial colonization on plant phyllosphere minimized the beneficial effects produced by the biocontrol bacteria. Rhodopseudomonas palustris strain GJ-22 is known as a phyllosphere biocontrol agent. In this paper, we described detailed processes of strain GJ-22 colony establishment at various colonization stages. Four different types of bacterial colonies, Type 1, scattered single cells; Type 2, small cell clusters; Type 3, small cell aggregates; and Type 4, large cell aggregates, were observed in the course of bacterial colonization. We categorized bacterial colonization into four phases, which were, Phase I: bacterial colony exists as Type 1 and cell population reduced quickly; Phase II: Type 1 evolved into Type 2 and cell population remained steady; Phase III: Type 3 arose and replaced Type 2, and cell population expanded slowly; and Phase IV: Type 3 matured into Type 4 and cell population increased quickly. We have shown that the preferable location sites of bacterial aggregates on leaf phyllosphere are grooves between plant epidermal cells. Analyses of expressions of plant defence-related genes showed that, starting from Phase III, bacterial cells in the Type 3 and Type 4 colonies produced unidentified signals to induce host defence against Tobacco mosaic virus infection. In addition, we determined the crucial role of aggregates formation of GJ-22 cell on plant phyllosphere in terms of bacterial cell stress tolerance and ISR (induced systemic resistance) priming. To our knowledge, this is the first report focused on the colonization process of a phyllosphere biocontrol agent and gave a clear description on the morphological shift of bacterial colony on phyllosphere.

A genetic tool for production of GFP-expressing Rhodopseudomonas palustris for visualization of bacterial colonization

Development of a genetic tool for visualization of photosynthetic bacteria (PSB) is essential for understanding microbial function during their interaction with plant and microflora. In this study, Rhodopseudomonas palustris GJ-22-gfp harboring the vector pBBR1-pckA_PT-gfp was constructed using an electroporation transformation method and was used for dynamic tracing of bacteria in plants. The results showed that strain GJ-22-gfp was stable and did not affect the biocontrol function, and the Confocal Laser Scanning Microscopy (CLSM) results indicated it could successfully colonised on the surface of leaf and root of tobacco and rice. In tobacco leaves, cells formed aggregates on the mesophyll epidermal cells. While in rice, no aggregate was found. Instead, the fluorescent cells colonise the longitudinal intercellular spaces between epidermal cells. In addition, the results of strain GJ-22 on the growth promotion and disease resistance of tobacco and rice indicated that the different colonization patterns might be related to the bacteria could induce systemic resistance in tobacco.

Decoding Wheat Endosphere-Rhizosphere Microbiomes in Rhizoctonia solani-Infested Soils Challenged by Streptomyces Biocontrol Agents

The endosphere and the rhizosphere are pertinent milieus with microbial communities that perturb the agronomic traits of crop plants through beneficial or detrimental interactions. In this study, we challenged these communities by adding Streptomyces biocontrol strains to wheat seeds in soils with severe Rhizoctonia solani infestation. Wheat plants were grown in a glasshouse standardized system, and the bacterial and fungal microbiomes of 233 samples of wheat roots (endosphere) and rhizosphere soils were monitored for 20 weeks, from seed to mature plant stage. The results showed highly dynamic and diverse microbial communities that changed over time, with Sphingomonas bacteria and Aspergillus, Dipodascus, and Trichoderma fungi increasing over time. Application of biocontrol Streptomyces strains promoted plant growth and maturation of wheat heads and modulated the root microbiome, decreasing Paenibacillus and increasing other bacterial and fungal OTUs. The soils with the highest levels of R. solani had increased reads of Thanatephorus (Rhizoctonia anamorph) and increased root disease levels and increased Balneimonas, Massilia, Pseudomonas, and unclassified Micrococcaceae. As we enter the era of biologically sustainable agriculture, it may be possible to reduce and limit the effects of serious fungal infestations by promoting a beneficial microbiome through the application of biocontrol agents during different periods of plant development.

The impact of microbes in the orchestration of plants' resistance to biotic stress: a disease management approach

The struggle for survival is a natural and a continuous process. Microbes are struggling to survive by depending on plants for their nutrition while plants on the other hand are resisting the attack of microbes in order to survive. This interaction is a tug of war and the knowledge of microbe-plant relationship will enable farmers/agriculturists improve crop health, yield, sustain regular food supply, and minimize the use of agrochemicals such as fungicides and pesticides in the fight against plant pathogens. Although, these chemicals are capable of inhibiting pathogens, they also constitute an environmental hazard. However, certain microbes known as plant growth-promoting microbes (PGPM) aid in the sensitization and priming of the plant immune defense arsenal for it to conquer invading pathogens. PGPM perform this function by the production of elicitors such as volatile organic compounds, antimicrobials, and/or through competition. These elicitors are capable of inducing the expression of pathogenesis-related genes in plants through induced systemic resistance or acquired systemic resistance channels. This review discusses the current findings on the influence and participation of microbes in plants' resistance to biotic stress and to suggest integrative approach as a better practice in disease management and control for the achievement of sustainable environment, agriculture, and increasing food production.

Diversity of cultivable bacterial endophytes in Paullinia cupana and their potential for plant growth promotion and phytopathogen control

Endophytic bacteria occupy the same niche of phytopathogens and may produce metabolites that induce the host plant systemic resistance and growth. Host and environmental variables often determine the endophytic community's structure and composition. In this study, we addressed whether the plant genotype, organ, and geographic location influence the structure, composition, and functionality of endophytic bacterial communities in Paullinia cupana. To characterize the communities and identify strains with potential application in agriculture, we analyzed two P. cupana genotypes cultivated in two cities of the State of Amazonas, Brazil. Endophytic bacteria were isolated from surface-disinfested root, leaf, and seed tissues through the fragmentation and maceration techniques. The colonization rate, number of bacteria, richness, diversity, and functional traits were determined. The plant growth-promoting ability of selected bacterial strains was assessed in Sorghum bicolor. We identified 95 bacterial species distributed in 29 genera and 3 phyla (Proteobacteria, Actinobacteria, and Firmicutes). The colonization rate, richness, diversity, and species composition varied across the plant organs; the last parameter also varied across the plant genotype and location. Some strains exhibited relevant plant growth-promoting traits and antagonistic traits against the main phytopathogens of P. cupana, but they were not separated by functional traits. The main bacterial strains with plant growth-promoting traits induced S. bicolor growth. Altogether, our findings open opportunities to study the application of isolated endophytic bacterial strains in the bioprospection of processes and products.

Photosynthetic bacterium Rhodopseudomonas palustris GJ-22 induces systemic resistance against viruses

Photosynthetic bacteria (PSB) have been extensively used in agriculture to promote plant growth and to improve crop quality. Their potential application in plant disease management, however, is largely overlooked. In this study, the PSB strain Rhodopseudomonas palustris GJ-22 was investigated for its ability to induce resistance against a plant virus while promoting plant growth. In the field, a foliar spray of GJ-22 suspension protected tobacco plants against tobacco mosaic virus (TMV). Under axenic conditions, GJ-22 colonized the plant phyllosphere and induced resistance against TMV. Additionally, GJ-22 produced two phytohormones, indole-3-acetic acid and 5-aminolevulinic acid, which promote growth and germination in tobacco. Furthermore, GJ-22-inoculated plants elevated their immune response under subsequent TMV infection. This research may give rise to a novel biological agent with a dual function in disease management while promoting plant growth.