Inoculation of Bacillus velezensis SD24 enhancing the accumulation of tea catechin secondary metabolites.

Synergistic effects of AMF and PGPR on improving saline-alkaline tolerance of Leymus chinensis by strengthening the link between rhizosphere metabolites and microbiomes

Among the biotic stresses, plant pathogens can reduce yield crop which affected potential loss to crop productivity. Plant growth-promoting rhizobacteria (PGPR) can help plants to be resistant against biotic stress via direct antagonism to pathogens or by induction of systemic resistance to pathogens. The presence of high levels of nutrients exuded from various roots of most plants can support bacterial growth and metabolism as well as maintain health of the plant in the growth process. PGPR promote plant growth due to their abilities in phytohormone production, nitrogen fixation, and phosphorus solubilization; produce several substances which are related to pathogen control, i.e., exhibiting competition with plant pathogens, synthesis of antibiotics, antifungal metabolites and defense enzymes, and secretion of iron-chelating siderophores; and trigger induced systemic resistance (ISR) via methyl jasmonate and methyl salicylate in plants. The ISR resembles pathogen-induced systemic acquired resistance (SAR) through the salicylic acid-dependent SAR pathway under conditions where the inducing bacteria and the challenging pathogen remain spatially separated. The use of PGPR combinations of different mechanisms of action, i.e., induced resistance and antagonistic PGPR, might be useful in formulating inoculants leading to a more efficient use for biological control strategies to improve crop productivity. Many PGPR have been isolated from the tissues of many plants, and various species of bacteria, i.e., Azotobacter, Azospirillum, Alcaligenes, Arthrobacter, Bacillus, Burkholderia, Enterobacter, Klebsiella, Pseudomonas, and Serratia, have been reported to control several diseases and enhance plant growth. PGPR belonging to the genera Pseudomonas and Bacillus are also well known for their antagonistic effects and their ability to trigger ISR. An increasingly successful study to reduce disease severity is the use of bacteria, namely, Bacillus subtilis, P. fluorescens, Serratia, and the fungus Trichoderma. Tea and rice plants are cultivated in Indonesia predominantly in Java and Sumatra islands. Major constraints of cultivation include low fertility of soils, poor input management, low germination, and high susceptibility to the diseases. The strategies employed by PGPR provide promising approaches to alter agricultural crops and plantation practices toward sustainable environmental development. Research has been conducted to know the effect of PGPR on tea plant growth that can work optimally as a biological fertilizer and plant-induced resistance to suppress blister blight (Exobasidium vexans Massee), a major disease in tea plantation that can decrease yield loss up to 50%. Individual PGPR strains for in vitro broad-spectrum pathogen suppression and production of several physiological/biochemical activities related to plant growth promotion have been screened. Numerous bacterial isolates have been found to function both as biofertilizers and biological control agents, namely, Chryseobacterium sp. AzII-1, Acinetobacter sp., Alcaligenes sp. E5, Bacillus E65, and Burkholderia E76. Study about synergism among bacteria has been carried out in the laboratory test using four combinations, i.e., (a) Chryseobacterium sp. AzII-1 + Acinetobacter sp., (b) Chryseobacterium sp. AzII-1 + Alcaligenes sp. E5, (c) Chryseobacterium sp. AzII-1 + Bacillus E65, and (d) Chryseobacterium sp. AzII-1 + Burkholderia E76. All bacterial combinations had a synergistic effect. It was shown that the bacterial population was not significantly different with the average of the total bacterial population (4.62 × 108 CFU/ml). The effect of bacterial combinations to blister blight and plant growth under a tea nursery trial revealed that combination of Chryseobacterium sp. AzII-1 75% + Alcaligenes sp. E5 25% could increase the growth of tea plant and suppress the intensity of blister blight up to 1.27%. The disease intensity of blister blight decreased in all treatments under field trial, while the Acinetobacter sp. treatment in tea shoots was 17.26% higher than the control. PGPR have also been isolated from cultivated rice. Serratia SKM, Burkholderia E76, and Bacillus E65 have the potential for controlling rice diseases and induce plant growth promotion. Under in vitro antagonistic assay, it was shown that these isolates could suppress effectively the growth of rice pathogens Xanthomonas oryzae pv. oryzae, the causal agent of bacterial blight (BB). Kaolin formulation of these three isolates was evaluated as a foliar application on rice. PGPR application under experimental plots resulted in enhancement of rice growth and yield, with the yield increment on cv. Sintanur being 12.8 percent higher compared with control (cv. Ciherang). Based on PGPR application technology which is demonstrated in farmers’ plots, the severity of BB disease was reduced to 76.8 percent compared with the untreated plot. The farmers were convinced with the beneficial effects of PGPR on both plant growth and yield and reduction of BB disease incidence. PGPR technologies have the potential to reduce agrochemical application. They can also be exploited as low in input and environmentally friendly for sustainable plant management. PGPR is highly diverse, and in this review, we focus on PGPR in plant growth promotion, as well as understanding the role of PGPR in crop protection.

BackgroundCatechins are the main polyphenol compounds in tea (Camellia sinensis). To understand the relationship between gene expression and product accumulation, the levels of catechins and relative expressions of key genes in tea leaves of different developmental stages were analyzed.ResultsThe amounts of catechins differed significantly in leaves of different stages, except for gallocatechin gallate. Close correlations between the expression of synthesis genes and the accumulation of catechins were identified. Correlation analysis showed that the expressions of chalcone synthase 1, chalcone synthase 3, anthocyanidin reductase 1, anthocyanidin reductase 2 and leucoanthocyanidin reductase genes were significantly and positively correlated with total catechin contents, suggesting their expression may largely affect total catechin accumulation. Anthocyanidin synthase was significantly correlated with catechin. While both ANRs and LAR were significantly and positively correlated with the contents of (−)-epigallocatechin gallate and (−)-epicatechin gallate.ConclusionOur results suggest synergistic changes between the expression of synthetic genes and the accumulation of catechins. Based on our findings, anthocyanidin synthase may regulate earlier steps in the conversion of catechin, while the anthocyanidin reductase and leucoanthocyanidin reductase genes may both play important roles in the biosynthesis of galloylated catechins.

One of the most important strategies to increase agricultural productivity and sustainability is to use a variety of local plant growth-promoting rhizobacteria (PGPB) and their improved consortium formulations. This study aimed to determine the effect of local PGPB on plant growth and rhizome development of Trachystemon orientalis, which has great potential as an alternative food source. Six different combined microbial consortia prepared from 11 different rhizobacteria isolated from tea rhizosphere, based on their multiple beneficial effects, were applied to the rhizomes of Trachystemon orientalis planted in 1:1 (v/v) peat: perlite medium. The experiment was set up according to the randomized complete block design with three replications, five rhizomes in each replication, and rhizomes not subjected to any treatment were used as controls. PGPB consortia were detected to be effective on 14 parameters examined related to rhizome development and plant growth. The correlation heatmap revealed a strong relationship between the applications and all the parameters examined. The best result was obtained from the P4 application containing a mixture of Pseudomonas putida and Bacillus spp. This microbial cocktail can be a good alternative to chemical fertilizers, as it is both beneficial and profitable, especially in seedling cultivation of Trachystemon orientalis.

Effect of UV-B irradiation time on accumulation of foliar catechins in two tea cultivars was investigated. Low influence rate and short term irradiation of UV-B stimulated accumulation of major tea catechins, resulting in an increase in level of total catechins. Excessive irradiation of UV-B supressed the accumulation of tea catechins. Epigallocatechin gallate (EGCG) increased more quickly than the other catechins under appropriate UV-B irradiation. The difference in response of different tea cultivars to UV-B is discussed.

To evaluate Ochrobactrum anthropi TRS-2 isolated from tea rhizosphere and its talc based formulation for growth promotion and management of brown root rot disease of tea. Ochrobactrum anthropi TRS-2, isolated from tea rhizosphere could solubilize phosphate, produce siderophore and IAA in vitro and also exhibited antifungal activity against six test pathogens. Application of an aqueous suspension of O. anthropi to the rhizosphere of nursery grown tea seedlings of five varieties of tea (TV-18, T-17, HV-39, S-449, UP-3 and) led to enhanced growth of the treated plants, as evidenced by increase in height, in the number of shoots and number of leaves per shoot. Treatment with O. anthropi also decreased brown root rot of tea, caused by Phellinus noxius. Multifold increase in activities of chitinase, beta-1,3-glucanase, peroxidase and phenylalanine ammonia lyase in tea plants was observed on application of O. anthropi to soil followed by inoculation with P. noxius. A concomitant increase in accumulation of phenolics was also obtained. Further, talc based formulation of O. anthropi was prepared and its survival determined every month up to a period of 12 months. Ochrobactrum anthropi could survive in the formulation up to a period of 9 months with a concentration of 7.0 log(10) CFU g(-1), after which there was a decline. Talc formulation was as effective as aqueous suspensions in both plant growth promotion and disease suppression. Ochrobactrum anthropi, either in aqueous suspension or as talc formulation induced growth of tea plants and suppressed brown root rot disease. It induced defense responses in tea plants. Ochrobactrum anthropi and its talc based formulation can be considered as an addition to available plant growth promoting rhizobacteria (PGPR) currently being used for field application. The present study offers a scope of utilizing this bacterium for growth promotion and disease management which would help in reduction of the use of chemicals in tea plantations.

Plant-environment interactions, particularly biotic stress, are increasingly essential for global food security due to crop losses in the dynamic environment. Therefore, understanding plant responses to biotic stress is vital to mitigate damage. Beneficial microorganisms and their association with plants can reduce the damage associated with plant pathogens. One such group is PGPR (Plant growth-promoting rhizobacteria), which influences plant immunity significantly by interacting with biotic stress factors and plant signalling compounds. This review explores the types, metabolism, and mechanisms of action of PGPR, including their enzyme pathways and the signalling compounds secreted by PGPR that modulate gene and protein expression during plant defence. Furthermore, the review will delve into the crosstalk between PGPR and other plant growth regulators and signalling compounds, elucidating the physiological, biochemical, and molecular insights into PGPR's impact on plants under multiple biotic stresses, including interactions with fungi, bacteria, and viruses. Overall, the review comprehensively adds to our knowledge about PGPR's role in plant immunity and its application for agricultural resilience and food security.

Soil salinization has been considered as a global problem in agriculture, which decreases crop productivity and threatens food security. Salt stress causes complex physiological damages in plants such as ionic imbalance, osmotic stress, and oxidative damage. However, plants have developed several genomic mechanisms to reduce these negative influences that are further supported by dynamic interactions with rhizosphere microbial communities. This review integrates current advances in understanding the interplay between plant genomes and the rhizosphere microbiome under salt stress. It highlights the role of plant-growth-promoting rhizobacteria (PGPR), arbuscular mycorrhizal fungi (AMF), and microbial volatiles in modulating gene expression and root architecture. Notably, PGPR such as Enterobacter sp. SA187 and Bacillus velezensis have been shown to upregulate key stress-related genes and increase antioxidant enzyme activities, which boost plant resilience under salinity. These microbes also influence stress signaling pathways such as SOS and ABA. Furthermore, this review also discusses the effect of root exudates on microbial communities, the application of synthetic microbial consortia, and genome-scale strategies such as transcriptomics, GWAS, and CRISPR. Our findings show that root exudation patterns shift significantly under salt stress, which enriches beneficial microbial taxa such as Sphingomonas and Streptomyces, while volatile compounds like benzenoids and ketones contribute to systemic stress responses. Understanding the synergistic plant–microbe interactions provides a foundation to engineer salt-resilient crops and for the advancement of sustainable agricultural practices in saline soils.

Previous decades have witnessed an exponential increase in the research and application of nanotechnology in agricultural sector. A diverse array of nanoparticles (NPs) are known to find usage in agricultural sector. Their functions can range from water storage to delivery of nutrients and fertilizers. In addition, the inherent possession of biocidal activity by different metal and metal oxide NPs have put forward their application to combat different bacterial and fungal pathogens. However, despite of several gains offered by the nanotechnological-interventions in agricultural systems, they are also known to possess inherent toxicity towards plant growth promoting rhizobacteria (PGPR) and beneficial fungi. The continuous exposure of NPs lead to induction of oxidative stress, production of reactive oxygen species, disruption of cell membrane and DNA damage in the beneficial soil microbiota and fungi associated to plant rhizosphere. The regular application of NPs marks their accrual in the soil systems and their concentration keeps on increasing with each crop cycle. In addition, they also keep on accumulating in different plant tissues, thus can be equally lethal for the consumers. Therefore, a critical assessment of their inherent toxicological attributes and off-target effects before their field application is strictly needed. In this chapter, we have summarized the toxicological attributes of different NPs towards the PGPR and beneficial soil fungi.

A dataset identifying plant growth-promoting rhizobacteria from the rhizosphere microbiome

Chapter17 - Plant growth promoting rhizobacteria from the perspectives of tea plantations and diseases

The tea plant is an economically important perennial crop whose yield and quality are severely constrained by cold stress. With the increasing frequency of extreme weather events, elucidating the molecular basis of cold tolerance is therefore essential for safeguarding tea production and its associated economic value. Catechins contribute to cold tolerance in tea plants, but the underlying regulatory mechanisms remain poorly understood. Here, we integrated transcriptomic, metabolomic, and physiological approaches to identify the CsMYB44-CsICE1 module, which regulates cold-induced flavonoid and catechin biosynthesis to enhance cold tolerance. Weighted gene co-expression network analysis (WGCNA) revealed that CsICE1 was strongly positively correlated with catechin accumulation and cold tolerance, whereas CsMYB44 was negatively correlated with these traits. Overexpression of CsICE1 in Arabidopsis improved cold tolerance by elevating flavonoid levels and upregulating antioxidant and cold-responsive genes, including AtSOD, AtPOD, and AtCBF1. Conversely, overexpression or silencing CsICE1 in tea plants significantly affected cold sensitivity. Overexpression of CsMYB44 reduced cold tolerance in Arabidopsis, while its silencing enhanced tolerance in tea plants. Yeast one-hybrid, electrophoretic mobility shift, and dual-luciferase assays demonstrated that CsMYB44 directly binds to the promoters of CsICE1, CsCHS (chalcone synthase), CsFLS (flavonol synthase), and CsANR (anthocyanidin reductase) to repress their expression. In contrast, CsICE1 activates the transcription of CsCHS, CsFLS, and CsANR. RT-qPCR analysis further indicated that short-term cold stress suppresses CsMYB44 expression, thereby releasing CsICE1, which subsequently upregulates CsCHS, CsFLS, and CsANR, promoting flavonoid and catechin accumulation and ultimately mitigating cold-induced damage. Collectively, these findings uncover a novel cold-tolerance mechanism in tea plants.

BackgroundThe rhizosphere is the narrow zone of soil immediately surrounding the root, and it is a critical hotspot of microbial activity, strongly influencing the physiology and development of plants. For analyzing the relationship between the microbiome and metabolome in the rhizosphere of tea (Camellia sinensis) plants, the bacterial composition and its correlation to soil metabolites were investigated under three different fertilization treatments (unfertilized, urea, cow manure) in different growing seasons (spring, early and late summer).ResultsThe bacterial phyla Proteobacteria, Bacteroidetes, Acidobacteria and Actinobacteria dominated the rhizosphere of tea plants regardless of the sampling time. These indicated that the compositional shift was associated with different fertilizer/manure treatments as well as the sampling time. However, the relative abundance of these enriched bacteria varied under the three different fertilizer regimes. Most of the enriched metabolic pathways stimulated by different fertilizer application were all related to sugars, amino acids fatty acids and alkaloids metabolism. Organic acids and fatty acids were potential metabolites mediating the plant-bacteria interaction in the rhizosphere. Bacteria in the genera Proteiniphilum, Fermentimonas and Pseudomonas in spring, Saccharimonadales and Gaiellales in early summer, Acidobacteriales and Gaiellales in late summer regulated relative contents of organic and fatty acids.ConclusionThis study documents the profound changes to the rhizosphere microbiome and bacterially derived metabolites under different fertilizer regimes and provides a conceptual framework towards improving the performance of tea plantations.

The rhizosphere is the thin region of soil directly influenced by root secretions and microbes, known as the root microbiome. The rhizosphere associated with the roots of a plant contains numerous beneficial bacteria, fungi, and other microorganisms. Microbial constitution plays a vital role in a plant’s growth cycle by stimulating its morphology, physiology, and development. Several species in the soil rhizosphere are supportive of plant growth, development, and productivity. The beneficial plant-microbe relationship within the rhizosphere is the key determinant of soil health and plant growth. Plant growth-promoting rhizobacteria support the colonization of AM fungi within plant roots. In the current study, garlic plants were treated with six different biological strains treatment, a combination of specific PGPR (Azotobacter and Azospirillum), PSB, KSB, Bacillus, and AM fungal inoculums. The output from these treatments was considered in different parameters determining the quality and productivity of garlic crops. These microbes help the plants directly or indirectly through the acquisition of nutrients, overall improvement in growth by production of phytohormones, protection from pathogens and other abiotic stressors. Results showed a significant increase in several factors such as nutrient translocation, bulb size, bulb diameter, biological biomass, marketable yield, and AM fungi colonization in root systems in contrast with standard treatment (Control (100% RRF and 50% RRF). Treatment T7 Absolute consortium PGPR + AM fungi (Azotobacter, Azospirillum, Pseudomonas, Frateuria, Bacillus, and AM fungi) performed better than control and other combinations of biological ingredient’s utilization in different treatments and combinations. After harvest, garlic bulbs treated with Absolute consortium PGPR + AM fungi increased the Alliin content as well as the primary element responsible for garlic’s medicinal properties and its distinctive native taste. Maximum yield (137.15±1.45q ha- 1) was recorded in treatment T7, along with maximum values of dry matter (34.45±0.24), TSS (13.354%), starch (5.65%), reducing sugar (1.98%) and Alliin content (0.11 μg) as compared with control and other biological treatments. The best treatment in respect of projected yield was Absolute consortium PGPR + AM fungi) followed by control (50% RRF).

Bacillus velezensis strain WRN014 was isolated from banana fields in Hainan, China. Bacillus velezensis is an important member of the plant growth-promoting rhizobacteria (PGPR) which can enhance plant growth and control soil-borne disease. The complete genome of Bacillus velezensis WRN014 was sequenced by combining Illumina Hiseq 2500 system and Pacific Biosciences SMRT high-throughput sequencing technologies. Then, the genome of Bacillus velezensis WRN014, together with 45 other completed genome sequences of the Bacillus velezensis strains, were comparatively studied. The genome of Bacillus velezensis WRN014 was 4,063,541bp in length and contained 4,062 coding sequences, 9 genomic islands and 13 gene clusters. The results of comparative genomic analysis provide evidence that (i) The 46 Bacillus velezensis strains formed 2 obviously closely related clades in phylogenetic trees. (ii) The pangenome in this study is open and is increasing with the addition of new sequenced genomes. (iii) Analysis of single nucleotide polymorphisms (SNPs) revealed local diversification of the 46 Bacillus velezensis genomes. Surprisingly, SNPs were not evenly distributed throughout the whole genome. (iv) Analysis of gene clusters revealed that rich gene clusters spread over Bacillus velezensis strains and some gene clusters are conserved in different strains. This study reveals that the strain WRN014 and other Bacillus velezensis strains have potential to be used as PGPR and biopesticide.