Search

The changed phenolic acids (PAs) allelochemicals exuded by the roots induced by interspecific interactions is related to intercropping alleviates soil-borne disease. However, the presence of PAs in roots and root exudations and their rhizodeposition under intercropping are still unclear. Hydroponic and soil experiments of wheat, faba bean, and wheat intercropped with faba bean were conducted, and the major compositions and contents of PAs in roots, root exudations, and rhizospheric soil were determined. The results showed that ρ-hydroxybenzoic, vanillic, and syringic acids were the major components of PAs in roots, root exudations, and rhizospheric soil in a wheat and faba bean intercropping system. The compositions and percentages of PAs in roots of faba bean were altered when faba bean intercropped with wheat. The total exudation rate of PAs in root exudations was decreased by 30%–60% under the wheat and faba bean intercropping (W//F) system as compared to mono-cropped faba bean (MF). ρ-hydroxybenzoic acid was identified in the root exudation of both MF and mono-cropped wheat (MW), but not detected in the intercropping on 60 days after transplanting. Vanillic acid was only detected in the root exudation of MF on 30 days after transplanting. The rhizodepostion of vanillic and cumaric acid were decreased at both branching and pod setting stages in W//F as compared to MF. In conclusion, interspecific interaction changed the compositions and contents of PAs in faba bean roots and root exudations. W//F constrained vanillic acid exuded by roots and decreased vanillic and coumaric acid rhizodeposition by faba bean, which provides insight into root-soil interactions in the intercropping systems.

Western Ghats are designated as world heritage sites and global biodiversity hotspots. Microbial diversity in this forest area has been largely neglected and is getting attention since the end of the last millennium. In this review, we have studied and organized various microorganisms from Western Ghats and their diversity, important characteristics and potential biotechnological applications. Microorganisms from Western Ghats have been explored individually for potential bioactive molecules. While most of the microorganisms were analyzed for antimicrobial activities, there have been studies on microbial promotion of plant growth. The microbes analyzed included from aquatics, soil, rhizosphere, phyllosphere and even as endophytes. There have been microorganisms which have shown antioxidant and anti-cancerous activities. There are microorganisms capable of degrading plant wastes and also xenobiotics. Microorganisms capable of producing industrially important enzymes have also been reported. The present review explores largely neglected microbial diversity with respect to their ability to produce potential bioactive biomolecules.

Nature-designed plant microbiomes may offer solutions to improve crop production and ecosystem restoration in less than optimum environments. Through a full exploration of metagenomic data, Camargo et al. showed that a previously unknown microbial diversity enhances nutrient mobilization in stress-adapted plants.

Environmental pollution with heavy metals continues to affect soil quality and crops yields. Among remediation solutions, biotechnology offers a number of environmentally friendly options, one of which is phytoremediation. The use of plants as hyperaccumulators for heavy metal ions is beneficial in terms of feasibility, costs, but has the disadvantage that plants may be affected by heavy metals toxicity. Also, heavy metals are often found in soil in less bioavailable forms to be extracted by plant roots. To overcome these shortcomings, various techniques have been proposed to intensify and accelerate the phytoremediation. They are analyzed and concisely described in this paper, emphasizing how these techniques can act to increase plant tolerance to the toxicity of heavy metal ions and can change the conditions in the rhizosphere area to favor heavy metals extraction and the transport in the roots and their translocation towards the aerial parts of the plant.

Phyllosphere is an important reservoir of antibiotic resistance genes (ARGs), but the transfer mechanism of ARGs from soil and air to phyllosphere remains unclear. This study demonstrated that soil-air-phyllosphere was the dominant ARG transfer pathway, and blocking it by film mulching can reduce typical phyllosphere ARGs in lettuce by 80.7% - 98.7% (89.5% on average). To further eliminate phyllosphere ARGs in lettuce grown with film mulching, the internal soil-endosphere-phyllosphere transfer pathway deserves more attention. We analyzed the ARG hosts and the resistome in lettuce rhizosphere and phyllosphere with film mulching via hybrid Illumina-Nanopore sequencing. Pseudomonas sp. 7SR1 was more abundant than other ARG hosts, accounting for 1.0% and 47.1% of the total bacteria in rhizosphere and phyllosphere, respectively. The species has flagella that can promote mobility and can excrete extracellular polymeric substances and/or surfactant-like microbial products, which benefits its colonization in the phyllosphere. Impeding the migration of Pseudomonas sp. 7SR1 via the soil-endosphere-phyllosphere pathway would be effective to further reduce ARGs in phyllosphere. Multidrug resistant genes were predominant in phyllosphere (40.3% of the total), and 87.6% of the phyllosphere ARGs were located on chromosomes, indicating relatively low horizontal gene transfer (HGT) potentials. This study provides insights into the transfer mechanism, hosts, and control strategies of phyllosphere ARGs in typical plants.

Plant root exudates serve pivotal roles in supporting plant development and interactions with the physicochemical and biological factors in the rhizosphere. Under stress conditions, root exudation is involved in enhancing plant resource-use efficiency and facilitating the crosstalk between plant and soil microbes to ameliorate stress. Although there are a large number of root exudates that remain to be characterized, recent technological advancements have allowed for the function of many exudate compounds to be elucidated. In this review, we discuss current knowledge about the key root exudates that modulate plant resource-use efficiency under various abiotic stresses including drought, aluminum toxicity, phosphorus, nitrogen, and iron deficiency. The role that key root exudates play in shaping microbial communities in the rhizosphere under stress conditions is also an important consideration addressed in this review.

Objective To find a suitable ecological cultivation measure to solve the problem of root-knot nematode disease of Panax quinquefolium (Panacis Quinquefolii Radix) and the heavy metals accumulating in its roots. Methods Three-year-old P. quinquefolium was treated with four different combinations of microbial inoculant (MI) and garbage fermentation liquid (GFL) [the joint application of ‘TuXiu’ MI and Fifty potassium MI (TF), the combination use of ‘No. 1’ MI and Fifty potassium MI (NF), ‘Gulefeng’ poly-γ-glutamic acid MI (PGA), GFL], and the untreated control (CK). Here, high-throughput sequencing, ICP-MS and UPLC were employed to systematically characterize changes of microbial diversity and structure composition, heavy metals (As, Cd and Pb) content and ginsenoside content among different treatments. Results The results revealed that different MIs and GFL could increase the root dry weight of P. quinquefolium, PGA enhanced it by 83.24%, followed by GFL (49.93%), meanwhile, PGA and GFL were able to lessen root-knot nematode disease incidence by 57.25% and 64.35%. The treatment of PGA and GFL can also effectively reduce heavy metals in roots. The As content in GFL and PGA was decreased by 52.17% and 43.48% respectively, while the Cd and Pb contents of GFL and PGA was decreased somewhat. Additionally, the content of total ginsenosides was increased by 42.14% and 42.07%, in response to TF and NF, respectively. Our metagenomic analysis showed that the relative abundance of particular soil microbial community members related to the biocontrol of root-knot nematode disease and plant pathogen (i.e., Chaetomium in NF, Xylari in GFL, and Microascus in PGA), heavy metal bioremediation (Hyphomacrobium in PGA and Xylaria in GFL), and nitrogen fixation (Nordella and Nitrospira in TF) was significantly increased; notably, potential harmful microflora, such as Plectosaphaerella and Rhizobacter, were more abundant in the control group. Conclusion MI and GFL could improve the quality of P. quinquefolium by modifying its rhizosphere microbial community structure and composition, both of them are beneficial to the development of ecological cultivation of P. quinquefolium.

s Plant-parasitic nematodes infect the roots of crops which bring rigorous economic loss to food industry across the globe. Several plant protection agents are being used but they cause severe negative environmental and health impacts. Recently, organic matter has become an important green alternative for several pesticides including nematicides. In the present study, identification and management of stylet bearing nematodes associated with Malus pumila from different locations of Khanpur, Pakistan, have been presented. Soil samples were collected from the rhizosphere of infected M. pumila and isolated using Baermann funnel extraction technique. Collected specimens were killed, fixed and mounted. After identification, cow dung (organic) and carbofuran (inorganic) were applied after taking the first soil samples and soil samples were recollected and analyzed after 3 months of applications. Ten species of nematodes; Helicotylenchus pseudorobustus, Helicotylenchus dihystera, Helicotylenchus vulgaris, Meloidogyne javanica, Meloidogyne incognita, Aphelenchus avenae, Pratylenchus penetrans, Filenchus sheri, Psilenchus hilarulus and Tylenchus semipenetrans were identified from different locations. Results of amendments revealed that carbofuran was found more effective because of its intense toxic properties, whereas nematode decline rate was slow in case of organic amendments. Being an insecticide, carbofuran killed maximum nematodes but it is highly toxic. If the time period is increased, comparable results can be achieved by applying cow dung, which makes it an environmentally friendly option for the protection of plants against nematodes.

Rice planting (RP) is significant to methane (CH4) emissions from paddy fields, but its effect on the relative contribution of the acetoclastic methanogenesis to total CH4 production (Fac) and the fraction of CH4 oxidized (Fox) is poorly understood. To quantify the responses of the Fac and Fox to RP, we investigated CH4 fluxes, CH4 production and oxidation potentials, dissolved CH4 concentrations, and their stable carbon isotopes in a flooded paddy soil. The mcrA and pmoA gene copies were also determined by quantitative polymerase chain reaction (qPCR). Compared with the unplanted soil (control, CK), the seasonal CH4 emissions from the planted soil were significantly enhanced, 13.6 times, resulting in large decreases in the CH4 concentrations in the soil solution. This indicated that much more CH4 was released into the atmosphere by the RP than was stored in the soils. Acetoclastic methanogenesis became more important from the tillering stage (TS) to the ripening stage (RS) for the CK, with Fac values increased from 17%–20% to 46%–55%. With RP, the Fac values were enhanced by 10%–20%, and it significantly increased the copy numbers of the mcrA gene at the four rice stages (TS, booting stage (BS), grain-filling stage (GS), and RS). Furthermore, the effect of the RP on the abundance of the mcrA gene was highly concurrent with the effect on the Fac values. At the TS, the Fox values at the soil-water interface were around 50%–75% for the CK, being 15%–20% lower than those of the RP in the rhizosphere. It increased to 65%–100% at the GS, but was reduced by 20%–30% after the RP. These differences might be because the copy numbers of the pmoA gene were significantly raised at the TS while lowered at the GS by the RP. This was further demonstrated by the strong correlations between the effect of the RP on the abundance of the pmoA gene and the effect on the Fox values. These findings suggest that RP markedly impacts on the abundances of the mcrA and pmoA genes, affecting the pathway of CH4 production and the fraction of CH4 oxidization, respectively.

Nematode damage to coffee poses a serious threat to coffee production all over the world, including Vietnam. Accordingly, the nematode community composition could be a reliable indicator of ecological shifts that affect coffee plants' health. Here, we analysed the nematode communities in the rhizosphere of a monoculture Robusta coffee plantation in Dak Lak of the Central Highlands, Vietnam. We found changes in the community composition of nematodes in an age gradient of replanting coffee plants and revealed distinct patterns of nematode distribution in the soils of healthy and diseased plant groups. Further analyses indicate the impact of intensive farming and inefficient nematode controls, which caused disturbances and a gradual decrease of the nematode fauna diversity in the plantation soil. These results can add to a complete prediction model for plant fitness using nematode community composition.

The biostimulant BC204 is a commercially available biostimulant based on an extract from Citrus aurantium, comprising a mixture of bioflavonoids, other plant extracts and organic acids. In this study, the potential of BC204 to cause positive effects on plant growth and overall plant health by altering the rhizosphere microbial community of Solanum lycopersicum L. was investigated. Mycorrhizal colonization of plant roots was analysed by trypan blue-staining and light microscopy, followed by polymerase chain reaction (PCR) amplification of a region of the 18S rRNA gene conserved among arbuscular mycorrhizal fungi. No difference in mycorrhizal colonization of roots was observed between control and treated plants. The structural and functional diversity of rhizosphere bacteria between different treatment groups was assessed using 16S rRNA gene restriction fragment length polymorphism (RFLP) analysis and community-level physiological profiling (CLPP), respectively. Nearest sequence matches for three isolates from the rhizosphere of plants treated with BC204 as a soil drench in soil supplemented with Mycoroot™ revealed bacterial genera which play a role in promoting plant growth. Furthermore, the microbial community from this treatment group showed increased richness of substrate utilization on Biolog EcoPlates™. These results indicate some form of interaction between BC204 and Mycoroot™ which causes a shift in the structural and functional diversity of the rhizosphere bacterial community.

Harnessing the rhizospheric microbiome, including phosphorus mineralizing bacteria (PMB), is a promising technique for maintaining sustainability and productivity in intensive agricultural systems. However, it is unclear as to which beneficial taxonomic group populations in the rhizosphere are potentially associated with the changes in soil microbiomes shifted by fertilization regimes. Herein, we analyzed the diversity and community structure of total bacteria and PMB in the rhizosphere of maize (Zea mays L.) grown in soils under 25 years of four fertilization regimes (compost, biocompost, chemical, or non-fertilized) via selective culture and Illumina sequencing of the 16S rRNA genes. Plant development explained more variations (29 and 13%, respectively) in the composition of total bacteria and PMB in the rhizosphere of maize than the different fertilization regimes. Among those genera enriched in the rhizosphere of maize, the relative abundances of Oceanobacillus, Bacillus, Achromobacter, Ensifer, Paracoccus, Ramlibacter, and Luteimonas were positively correlated with those in the bulk soil. The relative abundance of Paracoccus was significantly higher in soils fertilized by compost or biocompost than the other soils. Similar results were also observed for PMB affiliated with Ensifer, Bacillus, and Streptomyces. Although plant development was the major factor in shaping the rhizospheric microbiome of maize, fertilization regimes might have modified beneficial rhizospheric microbial taxa such as Bacillus and Ensifer.

The rhizosphere microbial community is crucial to plant health. Many studies have explored the association between the rhizosphere microbiome and plant disease. However, few studies have focused on root rot in arecanut palm, a disease causing devastating effects and thus resulting in economic losses that considerably affect the development of the arecanut industry. Here, rhizosphere samples were collected from both healthy arecanut palm plants and root-rotted arecanut palm plants, and the microbial communities were analyzed using high-throughput sequencing. The root-rotted samples exhibited distinct microbial community richness, diversity, and composition compared with the healthy samples, which was associated with pH according to the Mantel test. Identified potential plant pathogens, including Proteobacteria, Bacteroidetes, Chytridiomycota, and Mortierellomycota, were significantly enriched in the root-rotted samples. In contrast, potentially beneficial plant microbes, such as Acidobacteria and Gemmatimonadetes, were significantly depleted in the root-rotted samples. Co-occurrence networks were constructed to further identify microbial relationships in the root-rotted samples. These findings revealed ecological imbalance among beneficial bacteria in the root-rotted samples. The present study therefore provides an integrated view of the association between the microbial community and root rot in arecanut palm.

Sesame (Sesamum indicum L.), the “Queen of oil seeds” is being infected with pathogens, i.e., fungi, bacteria, virus and nematodes. Fusarium oxysporum sp. sesami (Zap.), is one of the fiercest pathogens causing severe economic losses on sesame. This work aimed to evaluate the impact of the cultivation of some preceding crops and seed inoculation with antagonistic predominant rhizospheric bacteria and actinomycetes on the incidence and development of Fusarium damping-off and wilt disease. Results showed that the lowest pre and/or post-emergence damping-off and wilt of sesame were recorded after onion and garlic, followed by wheat compared to clover in both the 2019 and 2020 seasons. In vitro, soil extracts from plots where onion and garlic have been cultivated slightly decreased the conidia germination and mycelium radial growth of F. oxysporum. The numbers of sesame rhizospheric F. oxysporum and fungi were lower after the cultivation of onion and garlic than those after wheat and clover. However, the numbers of actinomycetes and bacteria were higher in the onion, garlic, and clover rhizosphere than wheat. Among all isolated bacteria and actinomycetes associated with sesame roots cultivated after preceding plants, the Tricoderma viride and Bacillus subtilis (isolate No.3) profoundly reduce F. oxysporum mycelial growth in vitro. When sesame seeds were inoculated with Tricoderma viride, Bacillus subtilis, Streptomyces rochei and Pseudomonas fluorescens, the disease incidence of damping-off and wilt significantly decreased in the greenhouse and field trials conducted in both tested growing seasons, also had highly significant on plant health and growth parameters. Therefore, the current study suggested that using the preceding onion and garlic plants could be used for eco-friendly reduction of damping-off and wilt disease of sesame.

Increased anthropogenic nitrogen (N) deposition is driving N-limited ecosystems towards phosphorus (P) limitation. Plants have evolved strategies to respond to P limitation which affect N cycling in plant‐soil systems. A comprehensive understanding of how plants with efficient P‐acquisition or ‐use strategies influence carbon (C) and N cycling remains elusive. We highlight how P‐acquisition/-use strategies, particularly the release of carboxylates into the rhizosphere, accelerate soil organic matter (SOM) decomposition and soil N mineralisation by destabilising aggregates and organic‐mineral associations. We advocate studying the effects of P-acquisition/-use strategies on SOM formation, directly or through microbial turnover.

Complex interactions based on host plant, rhizosphere microorganisms and soil microenvironment are presumed to be responsible for the suppressive properties of biochar against soil-borne diseases, although the underlying mechanisms are not well understood. This study is designed to evaluate the efficacy of biochar amendment for controlling tomato bacterial wilt caused by Ralstonia solanacearum, and to explore the interactions between biochar-induced changes in rhizosphere compound composition, the pathogen and tomato growth. The results showed that biochar amendment decreased disease incidence by 61–78% and simultaneously improved plant growth. The positive ‘biochar effect’ could be associated with enhanced microbial activity and alterations in the rhizosphere organic acid and amino acid composition. Specifically, elevated rhizosphere citric acid and lysine, but reduced salicylic acid, were induced by biochar which improved microbial activity and rendered the rhizosphere unsuitable for the development of R. solanacearum. In addition, nutrients which were either made more available by the stimulated microbial activity or supplied by the biochar could improve plant vigor and potentially enhance tomato resistance to diseases. Our findings highlight that biochar's ability to control tomato bacterial wilt could be associated with the alteration of the rhizosphere organic acid and amino acid composition, however, further research is required to verify these ‘biochar effects’ in field conditions.

Phosphorus (P) is an indispensable macronutrient required for plant growth and development. Natural phosphate (Pi) reserves are finite, and a better understanding of Pi utilization by crops is therefore vital for worldwide food security. Ammonium has long been known to enhance Pi acquisition efficiency in agriculture; however, the molecular mechanisms coordinating Pi nutrition and ammonium remains unclear. Here, we reveal that ammonium is a novel initiator that stimulates the accumulation of a key regulatory protein, STOP1, in the nuclei of Arabidopsis root cells under Pi deficiency. We show that Pi deficiency promotes ammonium uptake mediated by AMT1 transporters and causes rapid acidification of the root surface. Rhizosphere acidification-triggered STOP1 accumulation activates the excretion of organic acids, which help to solubilize Pi from insoluble iron or calcium phosphates. Ammonium uptake by AMT1 transporters is downregulated by a CIPK23 protein kinase whose expression is directly modulated by STOP1 when ammonium reaches toxic levels. Taken together, we have identified a STOP1-centered regulatory network that links external ammonium with efficient Pi acquisition from insoluble phosphate sources. These findings provide a framework for developing possible strategies to improve crop production by enhancing the utilization of non-bioavailable nutrients in soil.

Plants interact with a great variety of microorganisms that inhabit the rhizosphere playing critical roles in several aspects of plant growth and protection against abiotic and biotic diseases. In this study, we performed a screening of bacteria associated with the rhizosphere of Prunus domestica trees to identify bacterial strains with plant growth-promoting activity. Ten strains isolated from the rhizosphere of P. domestica showed multiple in vitro plant growth promoting rhizobacteria (PGPR) activity such as the production of indole acetic acid, hydrogen cyanide, ammonia, solubilization of phosphates and antifungal activity against Verticillium dalhiae and Fusarium oxysporum f.sp. melonis. In planta, they significantly increased the growth (stem length, number of leaflets, leaf area and root weight) and biochemical (nitrate reductase activity, proline and chlorophyll content) parameters of tomato, as well as the rate of seed germination. Two selected strains (Pr7 and Pr8) with higher antagonistic activity against V. dalhiae and F. oxysporum f.sp. melonis protected tomato plants against Verticillium wilt and salt stress. In addition, they enhanced acclimatization of Vitis vinifera cv. Pinot noir and the peach root stock GF305 from in vitro to the greenhouse. 16S rRNA sequencing identified strains Pr7 and Pr8 as Pseudomonas stutzeri and Bacillus toyonensis, respectively. Since these two PGPR inoculants exhibited multiple traits beneficial to the examined host plants, they may be applied in the development of safe, and effective seed treatments as an alternative to chemical fungicides and fertilization but also for successful acclimatization of micropropagated plants., Mohamed Faize was supported by funding from the ‘Ministère de l'Enseignement Supérieur, de la Recherche Scientifique de la Formation des Cadres’ (MERSFC, Morocco) within the framework of ARIMNet2 Project

Iron (Fe) toxicity is a major constraint to rice yields in much of the world due to the greater solubility of reduced ferrous Fe in paddy soils compared with ferric Fe in aerobic soils and resulting excess uptake into the plants. There is genotypic variation in tolerance in Oryza gene pools, but so far only weak-effect alleles have been identified, largely because multiple critical physiological processes determine the tolerance. Most past research has been done in nutrient solution screens at the seedling stage, and not under field conditions over the full life cycle. We investigated tolerance mechanisms in a diverse set of genotypes under field conditions in a highly iron toxic soil in the Central Highlands of Madagascar. We made repeated plant samplings of young and old tissues throughout the growth period until maturity. Multiple mechanisms were involved, and the importance of different mechanisms changed between growth stages. Higher grain yields were mainly due to healthy vegetative growth, achieved either by reducing Fe uptake (exclusion) or by minimizing the effect of excess uptake through compartmentalization in older tissues and tissue tolerance. Exclusion mechanisms were relaxed during reproductive growth, leading to increased Fe accumulation in shoots. But tolerant genotypes were nonetheless able to grow well through a combination of Fe compartmentalization and tissue tolerance, so that grain filling could proceed relatively unimpeded. Tissue phosphorus (P) and potassium (K) concentrations were close to or below deficiency limits throughout growth. Exclusion by ferrous Fe oxidation in the rhizosphere will impede access of P and K ions to roots, but the differences in their tissue concentrations were much smaller than differences in growth rates, so growth rates evidently drove the uptake differences and responses to Fe toxicity were the more important constraints. There was no relation between grain yield and visual symptoms. To identify useful donors and markers for breeding it is important to develop screening protocols that capture the individual tolerance mechanisms, allowing for the effects of growth stage on their relative importance and expression, and possible interactions with other factors such as mineral nutrition. Selection for tolerance based on visual symptoms, particularly at the seedling stage, is overly simplistic, though it can be useful in the study of specific tolerance mechanisms.

Drought stress is one of the main limiting factors in geographical distribution and production of Codonopsis pilosula. Understanding the biochemical and genetic information of the response of C. pilosula to drought stress is urgently needed for breeding tolerant varieties. Here, carbohydrates, namely trehalose, raffinose, maltotetraose, sucrose, and melezitose, significantly accumulated in C. pilosula roots under drought stress and thus served as biomarkers for drought stress response. Compared with those in the control group, the expression levels of key genes such as adenosine diphosphate glucose pyrophosphorylase, starch branching enzyme, granule-bound starch synthase, soluble starch synthase, galacturonate transferase, cellulose synthase A catalytic subunit, cellulase Korrigan in the carbohydrate biosynthesis pathway were markedly up-regulated in C. pilosula roots in the drought treatment group, some of them even exceeded 70%. Notably, and that of key genes including trehalose-6-phosphatase, trehalose-6-phosphate phosphatase, galactinol synthase, and raffinose synthase in the trehalose and raffinose biosynthesis pathways was improved by 12.6%-462.2% in C. pilosula roots treated by drought stress. The accumulation of carbohydrates in C. pilosula root or rhizosphere soil was correlated with microbiome variations. Analysis of exogenous trehalose and raffinose confirmed that increased carbohydrate content improved the drought tolerance of C. pilosula in a dose-dependent manner. This study provided solid foundation for breeding drought-tolerant C. pilosula varieties and developing drought-resistant microbial fertilizers.

We inoculated Tuber aestivum and Tuber sinoaestivum on Carya illinoinensis to explore the effects of inoculation on host plant growth, enzyme activities, the physicochemical properties of rhizosphere soil, the denitrifying bacterial community in the rhizosphere, and the distribution of mating type genes in the rhizosphere. We found that the Tuber spp. inoculation increased the height of the host plant and that the stem circumference of the host was greater two months after inoculation. Six months after inoculation, the peroxidase activity of the seedlings inoculated with T. sinoaestivum was higher than that of the control. At four and six months after inoculation, the superoxidase dismutase activities of the seedlings inoculated with T. aestivum were higher than those of the seedlings inoculated with T. sinoaestivum. Six months after inoculation, nitrate nitrogen content was lowest in the control and highest in the T. sinoaestivum treatment. Among the nirS-type denitrifying bacteria community, the relative abundances of Proteobacteria were high. T. aestivum and T. sinoaestivum inoculation did not affect the diversity of denitrifying bacteria. The mating type genes MAT1-1-1 and MAT1-2-1 were detected in the rhizosphere of C. illinoinensis inoculated with T. sinoaestivum and T. aestivum, and MAT1-1-1 dominated over MAT1-21. (c) 2021 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

The aim of the current study was to isolate, characterize, and assess the plant growth-promoting traits of bacterial isolates inhabiting the rhizosphere of the Ocimum basilicum (basil plant) in the Al-Ahsa region. Five bacterial isolates were isolated from the rhizosphere of the basil, and characterized morphologically, biochemically, and genotypically. Our isolates displayed multiple plant growth-stimulating features, such as nitrogen fixation, solubilization of inorganic phosphate, and production of phytohormones, ammonia, and acetoin. All bacterial isolates were able to grow under elevated NaCl concentrations of up to 3 %. Only FPW14 grew at 10% NaCl. Comparative sequence analysis of the 16S rRNA gene revealed that FPM11 and FPI13 belonged to Pseudomonas alcaliphila and Pseudomonas hunanensis, respectively, to which they showed 98.66% and 97.36% homology, respectively. Strains FCL6, FPK12, and FPW14 showed 16S rRNA gene sequences with 97.21%, 98.08%, and 98.37% identities with those of Streptomyces laurentii, Sinorhizobium sp., and Bacillus safensis, respectively. A neighbor-joining phylogenetic tree constructed using the 16S rRNA gene sequences clustered the bacterial isolates with their corresponding recognized bacterial species, providing robustness to the taxonomic affiliation of our strains. Bacterial inoculation significantly enhanced the root growth parameters of Phaseolus vulgaris L. In conclusion, all isolates belong to plant growth-promoting bacteria and can be used as biofertilizers to increase soil fertility and plant productivity in the Eastern region of Saudi Arabia.

A survey of plant parasitic nematodes (PPN) abundance and diversity was conducted in foothills of Western Ghats at Coimbatore and Nilgiris districts in Tamil Nadu, India. Our study pointed to evaluate the PPN association with weeds, shrubs, and herbs including some agricultural crop cover both agro and forest ecosystems. Soil samples were collected around the rhizosphere of the plants and nematodes were isolated, counted under a microscope and identified by morphological characters. We collected 415 soil samples around the rhizosphere of 84 major plant families. Among 84 plant families, we found 13 PPN genera those generally responsible for cash crop yield loss. The genus Helicotylenchus spp., and Meloidogyne spp., were found frequent (226,136 samples) and rarely Hemicycliophora spp.,. The PPN diversity was measured by Shannon diversity index which showed that the diversity of PPN found higher in plant species those from the families Rosaceae (2.20) and Rubiaceae (2.13). We also recorded the PPN richness was dominated in four plant families. This result reveals that the PPN diversity and richness are positively correlated with host plant species diversity and altitude. Further, our study concludes that a wild plant in the forest ecosystem behaves like a reservoir of PPN.

Amino acids are essential plant compounds serving as the building blocks of proteins, the predominant forms of nitrogen (N) distribution, and signaling molecules. Plant amino acids derive from root acquisition, nitrate reduction, and ammonium assimilation. Many amino acid transporters (AATs) mediating transfer processes of amino acids have been functionally characterized in Arabidopsis, whereas the function and regulation of the vast majority of AATs in rice (Oryza sativa L.) and other crops remain unknown. In this review, we summarize the current understanding of amino acids in the rhizosphere and in metabolism. We describe their function as signal molecules and in regulating plant architecture, flowering time, and defense against abiotic stress and pathogen attack. AATs not only function in root acquisition and translocation of amino acids from source to sink organs, regulating N uptake and use efficiency, but also as transporters of non-amino acid substrates or as amino acid sensors. Several AAT genes show natural variations in their promoter and coding regions that are associated with altered uptake rate of amino acids, grain N content, and tiller number. Development of an amino acid transfer model in plants will advance the manipulation of AATs for improving rice architecture, grain yield and quality, and N-use efficiency.

Trace metals such as manganese (Mn), copper (Cu), zinc (Zn), and iron (Fe) are essential for many biological processes in plant life cycles. However, in excess, they can be toxic and disrupt plant growth processes, which is economically undesirable for crop production. For this reason, processes such as homeostasis and transport control of these trace metals are of constant interest to scientists studying heavily contaminated habitats. Phytoremediation is a promising cleanup technology for soils polluted with heavy metals. However, this technique has some disadvantages, such as the slow growth rate of metal-accumulating plant species, low bioavailability of heavy metals, and long duration of remediation. Microbial-assisted phytoremediation is a promising strategy for hyperaccumulating, detoxifying, or remediating soil contaminants. Arbuscular mycorrhizal fungi (AMF) are found in association with almost all plants, contributing to their healthy performance and providing resistance against environmental stresses. They colonize plant roots and extend their hyphae to the rhizosphere region, assisting in mineral nutrient uptake and regulation of heavy metal acquisition. Endophytic fungi exist in every healthy plant tissue and provide enormous services to their host plants, including growth enhancement by nutrient acquisition, detoxification of heavy metals, secondary metabolite regulation, and enhancement of abiotic/biotic stress tolerance. The aim of the present work is to review the recent literature regarding the role of AMF and endophytic fungi in plant heavy metal tolerance in terms of its regulation in highly contaminated conditions.

In this study, the effects of three halotolerant rhizobacterial isolates AL, HR, and SB, which are able to grow at a salinity level of 1600 mM NaCl, with multiple plant growth promoting (PGP) traits on some seed and forage quality attributes, and vegetative, reproductive, biochemical and physiological characteristics of wheat plant irrigated with saline water (0, 40, 80, and 160 mM NaCl) were investigated. The ability of halotolerant bacterial isolates to produce PGP traits was affected by salinity levels, depending upon the bacterial isolates. Salinity stress significantly affected the yield, quality, and growth of wheat by modifying the morpho-physiological and biochemical traits of the exposed plants. However, all three bacterial isolates, especially isolate AL, significantly improved the biochemical (an increase in K+/Na+ ratio by 55%, plant P content by 50%, and plant Ca content by 31%), morphological (an increase in stem dry weight by 52%, root dry weight by 44%, spike dry weight by 34%, and grain dry weight by 43%), and physiological (an increase in leaf proline content by 50% and total phenol in leaf by 42%) attributes of wheat and aided the plant to tolerate salinity stress in contrast to un-inoculated plant. Plants inoculated with bacterial isolates showed significantly improved seed amylose by 36%, leaf crude protein by 30%, leaf metabolic energy by 37%, and leaf water-soluble sugar content by 34%. Among the measured PGP and plant attributes, bacterial auxin and plant K content were of key importance in increasing reproductive performance of wheat. The bacterial isolates AL, HR, and SB were identified as Bacillus safensis, B. pumilus, and Zhihengliuella halotolerans, respectively, based on 16 S rDNA sequence. The study reveals that application of halotolerant plant growth-promoting rhizobacteria isolated from halophytic rangeland plants can be a cost effective and ecological sustainable method to improve wheat productivity, especially the attributes related to seed and forage quality, under salinity stress conditions.

Iron (Fe) migration in soil-plants is a critical part of Fe biogeochemical cycling in the earth surface system. Fe isotope fractionation analysis in the soil-rice system is promising for quantitatively assessing various pathways and clarifying Fe transformation processes. However, the mechanisms of Fe isotope fractionation in the soil-rice system are not well understood. In this study, the Fe isotopic compositions (δ56Fe) of rhizosphere soils, pore water, Fe plaque, and rice plant tissues at the jointing and mature stages of the plants were determined. The rice plants were slightly enriched in heavier δ56Fe by ∼ 0.3‰ relative to the soil, and the stele and cortex showed similar δ56Fe values, indicating that the uptake of Fe by rice plants predominantly occurred via Fe(III)-phytosiderophores (Fe(III)-PS) chelation, but not Fe(III) reduction. Additionally, at both the jointing and mature stages, the rice plant tissues showed similar δ56Fe values. However, the Fe isotope fractionation between the roots and stems (Δ56Feroot−stem) was 1.39 ± 0.13‰, which is similar to the previously Ab initio-calculated values between Fe(III)-citrate and Fe(III)- 2-deoxymugineic acid (DMA), indicating that both the phloem and xylem have similar δ56Fe values, and the major Fe-chelating substances in the phloem of the rice plants are Fe(III)-DMA and Fe(II)- Nicotianamine (NA). Therefore, this study demonstrates that Fe isotope fractionation can be used as a signature for interpreting the Fe uptake and translocation mechanism in the soil-rice system.

Fusarium wilt of banana is considered one of the most destructive plant diseases. Bacillus subtilis R31 and TR21, isolated from Dendrobium sp. leaves, exhibit different phytobeneficial effects on banana Fusarium wilt bio-controlling. Here, we performed genome sequencing and comparative genomics analysis of R31 and TR21 to enhance our understanding of the different phytobeneficial traits. These results revealed that the strain-specific genes of R31 involved in sporulation , quorum sensing , and antibiotic synthesis allow R31 to present a better capacity of sporulation, rhizosphere adaptation, and quorum sensing than TR21. Selective pressure analysis indicated that the glycosylase and endo-alpha-(1- > 5)-L-arabinanase genes were strong positive selected, which may contribute to the TR21 to colonize well in banana's vascular bundles. Altogether, our findings presented here should advance further agricultural application of R31 and TR21 as two promising resources of plant growth promotion and biological control via genetic engineering.

Rhizosphere microbial communities play important roles in facilitating or inhibiting the establishment of exotic species. Since some invasive plants interact with soil microbial communities such as rhizosphere bacteria, changes triggered by rhizosphere bacteria may alter competitive interactions between exotic and native plants. This study compared the Bacillus cereus content in soils with different degrees of Ageratina adenophora invasion, and investigated the effects of A. adenophora allelochemicals on B. cereus growth and soil characteristics and the feedback effects of B. cereus on A. adenophora growth. Bacillus cereus content in the rhizosphere of A. adenophora increased with intensification of the invasion process, and newly invaded soil contained almost twice as much bacteria as noninvaded soil. When rhizosphere soil was added to the root exudates of A. adenophora, the contents of B. cereus were twice as much as the control, except on the first day. Certain soil parameters increased significantly, such as ammonium nitrogen (NH4+-N) and available phosphorus (AP), which were increased by 41 and 27%, respectively. Soil treatment with B. cereus promoted the degradation of two allelochemicals from the rhizosphere of A. adenophora, amorpha-4,7(11)-dien-8-one and 6-hydroxy-5-isopropy1-3,8-dimethyl-4a,5,6,7,8,8a-hexahydraphthalen-2(1H)-one, to varying degrees; and increased the germination rate by 50%, root length by 117%, shoot length by 48% and fresh weight by 81% for A. adenophora compared to those of untreated soil. Our results confirmed that the invasion of A. adenophora will promote an increase of B. cereus, a beneficial rhizosphere bacterium, which in turn induces a positive feedback effect on A. adenophora.

Plants establish symbioses with mutualistic fungi, such as arbuscular mycorrhizal (AM) fungi, and bacteria, such as rhizobia, to exchange key nutrients and thrive. Plants and symbionts have coevolved and represent vital components of terrestrial ecosystems. Plants employ an ancestral AM signaling pathway to establish intracellular symbioses, including the legume–rhizobia symbiosis, in their roots. Nevertheless, the relationship between the AM and rhizobial symbioses in native soil is poorly understood. Here, we examined how these distinct symbioses affect root-associated bacterial communities in Medicago truncatula by performing quantitative microbiota profiling (QMP) of 16S rRNA genes. We found that M. truncatula mutants that cannot establish AM or rhizobia symbiosis have an altered microbial load (quantitative abundance) in the rhizosphere and roots, and in particular that AM symbiosis is required to assemble a normal quantitative root-associated microbiota in native soil. Moreover, quantitative microbial co-abundance network analyses revealed that AM symbiosis affects Rhizobiales hubs among plant microbiota and benefits the plant holobiont. Through QMP of rhizobial rpoB and AM fungal SSU rRNA genes, we revealed a new layer of interaction whereby AM symbiosis promotes rhizobia accumulation in the rhizosphere of M. truncatula. We further showed that AM symbiosis-conditioned microbial communities within the M. truncatula rhizosphere could promote nodulation in different legume plants in native soil. Given that the AM and rhizobial symbioses are critical for crop growth, our findings might inform strategies to improve agricultural management. Moreover, our work sheds light on the co-evolution of these intracellular symbioses during plant adaptation to native soil conditions.

Highlights • Foliar application of 5.0–10.0 mg m−2 selenium was beneficial for the growth of Atractylodes macrocephala. • The selenium content of A. macrocephala rhizome was significantly positively correlated with the foliar Se level. • Foliar application of 2.5–20.0 mg m−2 selenium could decrease the pest damage to A. macrocephala leaves. • Specific Se level (e.g., 10.0 mg m-2) could change the bioavailability of organic matter, available nitrogen, available phosphorus, available potassium and alter the microbial community composition in A. macrocephala rhizosphere soil. • Bacterial diversity was positively correlated with A. macrocephala growth whereas fungal diversity was negatively correlated., Atractylodes macrocephala (A. macrocephala), a famous medicinal herb in China, is widely cultivated and consumed in China with various beneficial effects. Numerous studies have shown that selenium (Se) plays an important role in promoting plant growth, although Se has not been considered an essential element for higher plants. The objectives of this research were to determine the effects of foliar Se application (0, 2.5, 5.0, 10.0 and 20.0 mg m−2 Se in sodium selenite, sprayed monthly from May to August) on the growth and rhizospheric soil micro-ecological environment of A. macrocephala, and explore the possible mechanisms underlying plant response to foliar Se application through a field experiment. The results were: The foliar application of 5.0 mg m−2 Se significantly increased the survival rate of A. macrocephala compared to the control. The yield of A. macrocephala was increased when the Se level maintained belowed 10.0 mg m−2 but decreased when Se level reached 20.0 mg m−2. The Se content in the rhizome of A. macrocephala showed a significant positive correlation with the Se level, while the insect attack rate was significantly negatively correlated with the Se level. However, foliar Se application hardly affected the concentration of bioactive compound atractylenolide in the rhizome of A. macrocephala. Notably, the application of foliar Se changed the content of partial soil nutrients, microbial diversity and composition in the rhizosphere soil of A. macrocephala. Bacterial diversity was positively correlated with A. macrocephala growth whereas fungal diversity was negatively correlated, suggesting that microbial diversity in the rhizosphere soils is closely related to plant growth. Moreover, correlation analysis showed that available potassium, Burkholderia and Cupriavidus in rhizospheric soil might be critical factors for promoting the growth of A. macrocephala. Overall, the foliar application of Se at moderate concentration was beneficial for the growth of A. macrocephala, and 5.0-10.0 mg m−2 Se level was the optimum. Our findings revealed novel insights into the response of A. macrocephala to foliar Se application from plant growth, rhizospheric soil nutrient and microbial community composition .

Aflatoxin is a strong carcinogenic and toxic fungal toxin produced by Aspergillus flavus and other Aspergillus species, and can seriously threaten the health of consumers, thus becoming a global concern. Corn, as an important oil and economic crop, is highly susceptible contaminated by aflatoxin. In this study, antagonistic bacteria with strong inhibitory effect on aflatoxin were screened to provide support for the treatment aflatoxin contamination control in corn. Ten strains which have strong antagonistic effects against A. flavus were isolated from healthy corn from different corn producing areas in China. Among them, the antagonistic bacteria JTFM1001 through corn kernels in vivo and field experiment, the inhibition effect of aflatoxin contamination reached above 70% and 55%, respectively. And the strain was identified as Bacillus subtilis based on its morphological, physiological and biochemical characteristics and phylogenetic analysis of 16S rDNA. In addition, our data showed that it can colonize in the rhizosphere and survive for a long time, forming the dominant flora, with broad application prospect. Finally, we were surprised to find that the antibacterial metabolites secreted by the antagonistic bacteria was one of the mechanisms of its inhibition of A. flavus and aflatoxin. This will provide us with new ideas and perspectives on the effective prevention and control of aflatoxin contamination in corn and corn oil.

Iron (Fe) is one of the essential nutrients for plant growth which is involved in several physiological functions. Hence, there are intensive efforts to improve plant tolerance to Fe deficiency, by genotypic screening and by the use of adapted physiological tools. The intend of the current study was to explore the seed priming effect with salicylic acid (SA 0.25 mM) and hydrogen peroxide (H2O2 20 mM), either separately applied or combined, on plant growth, nutritional elements status (Fe and potassium K), root acidification and photosynthetic activity in two S. carnosa cultivars (Sidi Khlif and Kalbia) with different tolerance to such constraint. Under unprimed conditions, Fe deficiency decreased plant growth, chlorophyll concentration, in addition to Fe and K contents. Moreover, it affected the photosynthetic activity by inhibiting the net CO2 assimilation rate and increasing the transpiration rate of both cultivars, following a reduced water use efficiency. The changes above described were much less pronounced in Sidi Khlif than in Kalbia. The stomatal conductance increased in Fe-deficient leaves of both cultivars, suggesting that the photosynthesis impairment should be attributed to non-stomatal factors. Interestingly, priming seeds with both agents significantly improved the growth performance and the rhizosphere acidification of deficient S. carnosa plants. However, the D + SA + H2O2 treatment had the most beneficial effect on S. carnosa plant growth. The degree of this stimulation may vary depending on the cultivar, the tissue and the priming agent applied. This could be owing to the photosynthetic performance modulation, leading to more efficient nutrient uptake.

Environmental pressure to reduce our reliance on agrochemicals and the necessity to increase crop production in a sustainable way have made the rhizosphere microbiome an untapped resource for combating challenges to agricultural sustainability. In recent years, substantial efforts to characterize the structural and functional diversity of rhizosphere microbiomes of the model plant Arabidopsis thaliana and various crops have demonstrated their importance for plant fitness. However, the plant benefiting mechanisms of the rhizosphere microbiome as a whole community rather than as an individual rhizobacterium have only been revealed in recent years. The underlying principle dominating the assembly of the rhizosphere microbiome remains to be elucidated, and we are still struggling to harness the rhizosphere microbiome for agricultural sustainability. In this review, we summarize the recent progress of the driving factors shaping the rhizosphere microbiome and provide community-level mechanistic insights into the benefits that the rhizosphere microbiome has for plant fitness. We then propose the functional compensatory principle underlying rhizosphere microbiome assembly. Finally, we suggest future research efforts to explore the rhizosphere microbiome for agricultural sustainability.

The connection between olive genetic responses to environmental and agro-climatic conditions and the composition, structure and functioning of host-associated, belowground microbiota has never been studied under the holobiont conceptual framework. Two groups of cultivars growing under the same environmental, pedological and agronomic conditions, and showing highest (AH) and lowest (AL) Actinophytocola relative abundances, were earlier identified. We aimed now to: i) compare the root transcriptome profiles of these two groups harboring significantly different relative abundances in the above-mentioned bacterial genus; ii) examine their rhizosphere and root-endosphere microbiota co-occurrence networks; and iii) connect the root host transcriptome pattern to the composition of the root microbial communities by correlation and co-occurrence network analyses. Significant differences in olive gene expression were found between the two groups. Co-occurrence networks of the root endosphere microbiota were clearly different as well. Pearson's correlation analysis enabled a first portray of the interaction occurring between the root host transcriptome and the endophytic community. To further identify keystone operational taxonomic units (OTUs) and genes, subsequent co-occurrence network analysis showed significant interactions between 32 differentially expressed genes (DEGs) and 19 OTUs. Overall, negative correlation was detected between all upregulated genes in the AH group and all OTUs except of Actinophytocola. While two groups of olive cultivars grown under the same conditions showed significantly different microbial profiles, the most remarkable finding was to unveil a strong correlation between these profiles and the differential gene expression pattern of each group. In conclusion, this study shows a holistic view of the plant-microbiome communication., Supported by grants AGL2016-75729-C2-1-R and AGL2016-75729-C2-2-R from the Spanish Ministerio de Economía, Industria y Competitividad/Agencia Estatal de Investigación, and grant PID2019-106283RB-I00 from the Spanish Ministerio de Ciencia e Innovación/Agencia Estatal de Investigación, all of them cofinanced by the European Regional Development Fund (ERDF). These funding sources had no involvement in this work preparation.

Root–soil interactions in the rhizosphere are central to resource acquisition and crop production in agricultural systems. However, apart from studies in idealized experimental systems, rhizosphere processes in real agricultural soils in situ are largely uncharacterized. This limits the contribution of rhizosphere science to agriculture and the ongoing Green Revolution. Here, we argue that understanding plant responses to soil heterogeneity is key to understanding rhizosphere processes. We highlight rhizosphere sensing and root-induced soil modification in the context of heterogeneous soil structure, resource distribution, and root–soil interactions. A deeper understanding of the integrated and dynamic root–soil interactions in the heterogeneously structured rhizosphere could increase crop production and resource use efficiency towards sustainable agriculture.

Aspalathus linearis is a commercially important plant species endemic to the Cape Floristic Region of South Africa and is used to produce a herbal tea known as rooibos tea. Symbiotic interactions between A. linearis and soil bacteria play an important role in the survival of Aspalathus plants in the highly nutrient-poor, acidic fynbos soil. The aim of this study was to characterize and compare rhizosphere and bulk soil bacterial communities associated with natural and commercially grown A. linearis, as well as the effect of seasonal changes on these communities. Bacterial communities were characterized using high throughput amplicon sequencing, and their correlations with soil chemical properties were investigated. The N-fixing bacterial community was characterized using terminal restriction fragment length polymorphism and real time quantitative polymerase chain reaction. Actinobacteria, Proteobacteria, and Acidobacteria were the most dominant bacterial phyla detected in this study. Highly similar bacterial communities were associated with natural and commercially grown plants. Significant differences in the bacterial community were observed between rhizosphere and bulk soils collected in the dry season, while no significant differences were detected in the wet season. This study provides insights into bacterial community structure and potential factors shaping bacterial community structure with commercially important A. linearis.

In this paper, a suitable and practical method to make bacterial concrete on a large and bulky scale is presented. In this method, first, bacteria compatible with concrete are extracted and identified. The bacteria are then added to the concrete in solution in a simple way. To find bacteria compatible with concrete, first, the soil near the roots of plants (rhizosphere) and two types of cement called Portland pozzolanic cement (PPC) for Darab city and Portland cement type 2 (PC2) for Hormozgan-Bandar Khamir were used. After extracting the cultured samples, it was observed that bacteria grew only in the soil sample and did not grow significantly in the cement samples. Therefore, the cultivation and reproduction of bacteria from concrete fragments were investigated. At this stage, concrete samples were prepared with two types of cement (PPC and PC2). Then, some concrete powder containing all the constituent materials was used to extract bacteria. The resulting bacteria were identified by the Deoxyribonucleic Acid (DNA) testing. Bacterial samples obtained from the concrete made of PPC with certainty exhibited the genus and species of Bacillus paralicheneniformis, but in the case of bacterial samples of concrete prepared with PC2 can only be bacterial Cited by Bacillus sp. Afterward, 4 mixing designs were designed to make concrete from the two abovementioned types of cement, with the addition of bacteria and without the addition of bacteria. In this mixing design, bacterial sediments were added to the solution and directly to the concrete mixing design. Finally, the compressive strength, water absorption and crack recovery in concrete samples were investigated. The results indicated that the presence of bacteria had slight effect on the compressive strength of concrete. The water absorption percentages of bacterial concrete samples with PPC and PC2 were 0.07 and 0.19% higher than those of non-bacterial samples, respectively. Both types of bacteria had the ability to repair cracks. Uncontrolled cracks in concrete samples were repaired to a width of at least 39.82 μm.

ACC deaminase producing Plant growth promoting rhizobacteria (PGPR) offers a great promise for ameliorating the negative impacts of salinity stress manifested on plants. In this context, 28 rhizospheric bacteria associated with ACC deaminase potential (198−1069 nmol α-ketobutyrate mg protein−1 h−1) were isolated from 5 different islands of Lakshadweep, union territory, India- Agatti, Kavaratti, Bangaram, Kadmat, and Thinnakara islands using DF-minimal medium. The diversity of cultivable ACC deaminase producing bacteria was analysed by PCR-RFLP (Restriction Fragment Length Polymorphism) method using three endonucleases AluI, MspI and HaeIII which led to the grouping of these isolates into six clusters at 80 % similarity index. Subsequently, isolates were functionally characterized for various PGP traits such that indole-3-acetic acid (IAA) production (∼10−80 μg mL−1); 16 isolates had phosphate solubilizing potential ranging from ∼19 to 88 P mg L−1 ; siderophore and ammonia production abilities were observed in 5 and 24 isolates, respectively while two strains tolerated up to 8% NaCl. Phylogenetic analysis of 16S rRNA gene sequences of representative strain from each cluster revealed that twenty-eight ACC deaminase producing PGPR belong to eight distinct genera: Pseudomonas, Bacillus, Azospirillum, Azotobacter, Escherichia, Paenibacillus, Burkholderia, and Klebsiella. Two isolates, CO1 (Pseudomonas putida) and CO8 (Bacillus paramycoides) were evaluated for plant growth promoting effects on French bean (Phaseolus vulgaris) under salinity (100 mM NaCl) stress. Both the selected isolates in consortium form significantly increased the root length, shoot length, root fresh and dry weight, shoot fresh and dry weight of French bean seedlings exposed to salinity stress, compared to non-inoculated control plants. The co-inoculation with selected strains CO1 and CO8 has significantly improved chlorophyll concentration, relative water content, membrane stability index, gas exchange parameters including net photosynthesis rate (PN), stomatal conductance (gs), transpiration rate (E) and water use efficiency of French bean plants by ∼100 %, ∼85 %, ∼40 %, ∼198 %, ∼80 %, ∼70 % and ∼75 %, respectively under saline conditions in comparison with non-inoculated plants. Moreover, the consortium treated French bean plants showed lower levels of stress-induced ethylene by 38 %, electrolyte leakage and Malondialdehyde (MDA) content by ∼15 % under salt stress compared to non-inoculated ones. This study unveiled the potential of halotolerant strains, Pseudomonas putida and Bacillus paramycoides as French bean biofertilizers in mitigating the adverse effects of salinity in plant growth in sustainable agriculture.

Heavy metals are the cause of one of the most significant biosphere contamination problems worldwide, as they can be highly reactive and toxic according to their oxidation levels. Their toxic effects are correlated with the elevated production of reactive oxygen species (ROS) and oxidative cellular damage occurring in plants. The aim of the present study was the investigation of the effects of three heavy metals (Ni, Cu, Zn) applied to the soil in biochemical defense-related responses and allergen production in the aromatic plant oregano (Origanum vulgare L.) from the Lamiaceae family. The concentrations of the three heavy metals used, were based on the 2002 Regulation of the Polish Ministry of the Environment on Soil Quality Standards [(i) agricultural land (group B): Ni 100 ppm, Ni 210 ppm, Cu 200 ppm, Cu 500 ppm, Zn 720 ppm and (ii) industrial land (group C): Ni 500 ppm, Cu 1000 ppm, Zn 1500 ppm, Zn 3000 ppm]. The investigated plants accumulated heavy metal ions in aerial parts to a variable extent. For plants grown in soil contaminated with Zn, phenotypic representation of the growth and development were strongly limited and dependent on zinc concentration. Phenotypic representation of plants grown in soil contaminated with Ni and Cu were characterized by normal growth, slightly lower or equal to that of the control plants. All tested metals (Ni, Cu, Zn) caused a concentration-dependent decrease in photosynthetic pigments especially in total chlorophyll content. Highest cellular damage levels were observed in plants treated with Cu and Zn. Increasing concentration of these metals (especially Zn) caused a further increase in cellular damage. 3000 ppm Zn caused highest increase in the concentration of proline compared with control plants, suggesting osmotic stress imposition. Treatment with 1000 ppm Cu led to increased concentration of the allergenic protein profilin in relation to control plants by profilin ELISA analysis, while increasing concentrations of Cu and Zn led to a decrease in the concentration of phenolic compounds and total antioxidant capacity. On the basis of these findings, Ni stress in oregano plants appears to be less damaging (in relation to Cu and Zn) and with lower allergenic potential, compared with 1000 ppm Cu. The present study provides novel biochemical insight in the defense and allergenic response of aromatic plants to metal ions present in the rhizosphere; however, more comprehensive research under realistic field conditions is needed to fully decipher this interaction.

The numerous bioactive components from Bacillus subtilis are commonly used as antimicrobial agents for reducing plant diseases caused by fungal pathovars. In this study, we isolated and identified B. subtilis SI-18 strain from twenty isolates of rhizosphere soil through morphological and molecular approaches, and explored its inhibitory activities against Rhizoctonia solani. According to morphological features and 16S rRNA and gyrB gene sequence analysis, B. subtilis SI-18 strain was identified. Additionally, the culture filtrate of B. subtilis SI-18 resulted in the suppression of R. solani mycelium growth and material leakage from the cells. Then, we have performed homology modelling and molecular docking study of S9 protein from R. solani where three potential compounds (D1, D2, and D3) were identified among 134 antimicrobial compounds derived from B. subtilis group based on higher binding energy and interaction at the active grove of the target protein. The D1 compound creates alkyl bond at Val48 whereas D2 also binds with Val48 by creating hydrogen bond. On the other hand, two hydrogen bonds were observed at Val48 and Ile52 by D3, which might be responsible for possible blocking of the target S9 protein of R. solani. To validate the docking study and understand the change in drug-ligand conformation, molecular dynamics simulation was assessed where rigid conformation was found for D1, D2 and D3 complexes. Moreover, ADMET study confirms that no toxicity and carcinogenicity were found for screened compounds. Based on our studies, we demonstrated that compounds D1, D2, and D3 derived from B. subtilis can be a potential inhibitor of S9 protein of R. solani that might be a possible strategy for fungal disease prevention.

Although roots are mainly embedded in the soil, recent studies revealed that light regulates mineral nutrient uptake by roots. However, it remains unclear whether the change in root system architecture in response to different rhizosphere nutrient statuses involves light signaling. Here, we report that blue light regulates primary root growth inhibition under phosphate-deficient conditions through the cryptochromes and their downstream signaling factors. We showed that the inhibition of root elongation by low phosphate requires blue light signal perception at the shoot and transduction to the root. In this process, SPA1 and COP1 play a negative role while HY5 plays a positive role. Further experiments revealed that HY5 is able to migrate from the shoot to root and that the shoot-derived HY5 autoactivates root HY5 and regulates primary root growth by directly activating the expression of LPR1, a suppressor of root growth under phosphate starvation. Taken together, our study reveals a regulatory mechanism by which blue light signaling regulates phosphate deficiency-induced primary root growth inhibition, providing new insights into the crosstalk between light and nutrient signaling.

Salinity represents a medium with high soluble salts where as sodicity represents a medium with high exchangeable sodium, low calcium and highly alkaline pH. Salinity and sodicity commonly occur together in salt-affected soils however physiological studies have mostly considered salinity alone ending up in poor field success of the selected genetic resources. Similarly, the role of root-mediated acidification in salt resistance is not known in wheat. Here six wheat genotypes were exposed to salinity (NaCl: 125 mM), low calcium (25% of non-treated control) and salinity + low calcium in solution culture. There were significant differences among the wheat genotypes for growth and leaf ionic composition under salinity, low calcium and salinity + low calcium treatments. The wheat genotypes SARC-1, 25-SAWSN-42 and Pasban-90 accumulated higher K+ and Ca2+ and lower Na+ and Cl− and were resistant to the combined stress of low calcium and salinity. These genotypes also showed higher root-mediated acidification under stress conditions. The wheat genotypes resistant to salinity + low calcium supply in solution culture also performed better in the saline-sodic soil in a lysimeter study. A genotype resistant to salinity alone accumulated lower Ca2+ and showed lower rhizosphere acidification potential and did not perform good in saline-sodic soil conditions. Therefore, root-mediated acidification potential and resistance to low calcium supply improves resistance of wheat to saline-sodic conditions. It is further suggested that screening of the wheat germplasm for saline-sodic soils should be carried out at salinity + low calcium to better simulate saline-sodic field conditions.

Frankia is a mycelium-forming actinobacterial genus that is found in actinorhizal plants as a nitrogen-fixing facultative endo-symbiont. Frankia has been a commonly uncultured endophytic actinobacteria with very slow growth germination. In the present study, the root nodules from Casuarina spp. were collected at hyper-saline and terrestrial habitats in Tamil Nadu, South India. The root nodules were surface-sterilized, dried, homogenized, and inoculated on the DPM medium with sodium propionate as a carbon source and biotin as a vitamin source. A total of 11 Frankia isolates were obtained from the specified habitats in a solid and liquid medium. The larger number of isolates was recorded in the hyper-saline habitats compared to terrestrial habitats. Finally, 2 predominant growth occurrences of isolates were selected; from each habitat, unique isolates were molecularly characterized and identified as Frankia sp. DDNSF-01 and Frankia casuarinae DDNSF-02. The physico-chemical property analysis of Casuarina rhizosphere soil of hyper-saline habitat showed higher pH, salinity and micro-nutrients like Fe−, Mn−, Cu−, and Zn− than terrestrial habitats, which could be the major factors responsible for the distribution dynamics of Frankia in hyper-saline habitats. Similarly, the biologically active metabolites of Frankia spp. were extracted by the ethyl acetate extraction method and tested by MIC assay, which was performed against emerging multi-host pathogens like Pseudomonas sp. and Candida sp. Likewise, the antibiofilm activity assay was done against the above pathogens. The biofilm inhibition of live/dead cells was confirmed by CLSM microscopic analysis. The F. casuarinae was inhibited the high level of biofilm formation of both pathogens when compared with Frankia sp. The present findings conclude the F. casuarinae is efficient in the control of emerging multi-host pathogens in actinorhizal plants.

Phytoremediation is a promising approach for reclamation of salt-affected soil. Phytoextraction is the most commonly used process, which exploits plants to absorb, immobilize, and accumulate salt in their shoots. In this study, halotolerant plant growth-promoting rhizobacteria (PGPR) were isolated from the rhizosphere of wild grasses growing naturally in salt-affected areas of Lucknow, Uttar Pradesh (India) and were tested for their efficacies of salt-tolerance and plant growth-promoting (PGP) abilities. Based on 16S rRNA sequences, the most efficient halotolerant isolates possessing PGP traits were identified as Pseudomonas plecoglossicida (KM233646), Acinetobacter calcoaceticus (KM233647), Bacillus flexus (KM233648), and Bacillus safensis (KM233652). Application of these isolates as bio-inoculants significantly (P

Panax notoginseng (Araliaceae) is an important ginseng herb with various health benefits and a history of cultivation in southwestern China over 400 years. In recent years P. notoginseng has faced serious continuous-cropping obstacles due to its large-scale cultivation. In this study, we aim to explore the allelochemicals of P. notoginseng and their interactions with various plants and rhizosphere microorganisms. The chemical constituents of the soil cultivated with 3-year-old P. notoginseng were studied by column chromatography, spectroscopic and GC-MS analyses. We identified 13 volatile components and isolated six triterpenes (1–4, 6–7) and one anthraquinone (5). Compounds 1–7 were tested for their effects on seed germination and root elongation in P. notoginseng, corn, wheat, turnip, water spinach and Arabidopsis thaliana. We also examined the effect of compounds 1–7 on the growth of ten rhizosphere microorganisms of P. notoginseng. At a concentration of 1.0 μg mL−1, compounds 3 and 5–7 caused the death of P. notoginseng root cells and compounds 2, 6 and 7 induced the death of root cells of A. thaliana. Compounds 1–5 and 7 inhibited elongation of A. thaliana root tip cells at a concentration of 10.0 μg mL−1. Moreover, at a concentration of 0.1 mg mL−1, compounds 3, 4, 6 and 7 inhibited the growth of probiotics and promoted the growth of pathogens of P. notoginseng. These results suggest that these isolated ursane-type triterpenoid acids and anthraquinone are potential allelochemicals that contribute to continuous-cropping obstacles of P. notoginseng.

Exploration of native microbes is a feasible way to develop microbial agents for ecological restoration. This study was aimed to explore the impact of Bacillus amyloliquefaciens PDR1 from karst adaptive plant on the activity of root plasma membrane H+-ATPase in Arabidopsis thaliana. A. thaliana was cultured in presence or absence of B. amyloliquefaciens PDR1 and its effects on the growth were evaluated by measuring the taproot length and dry weight. The rhizosphere acidification capacity was detected by a pH indicator, a pH meter and non-invasive micro-test techniques (NMT). The nutrient uptake was performed using appropriate methods. A combination of transcriptome sequencing and real-time quantitative polymerase chain reaction (qRT-PCR) was used to measure the expression of functional genes that regulate the plasma membrane H+-ATPase activity in A. thaliana roots. Functional analysis was performed to understand how B. amyloliquefaciens regulates biological processes and metabolic pathways to strengthen A. thaliana resistance to alkaline stress. Here, we show that volatile organic compounds (VOCs) from B. amyloliquefaciens PDR1 promoted the growth and development of A. thaliana, enhanced the plasma membrane H+-ATPase activity, and affected ion absorption in Arabidopsis roots. Moreover, B. amyloliquefaciens PDR1 VOCs did not affect the expression of the gene coding for plasma membrane H+-ATPase, but affected the expression of genes regulating the activity of plasma membrane H+-ATPase. Our findings illuminate the mechanism by which B. amyloliquefaciens regulates the growth and alkaline stress resistance of A. thaliana, and lay a foundation for wide and efficient application for agricultural production and ecological protection.

Certain metal (loid)-resistant bacteria that inhabit the rhizosphere have shown to improve plant growth and tolerance under toxic metal stress. In this study, we tested if six native, arsenic-resistant and plant growth promoting bacteria (PGPB) were able to enhance soybean (Glycine max L.) growth and modulate arsenic (As) uptake. As a previous work, we tested all single isolates and all possible binary combinations without arsenic stress to identify the combinations that would have the greatest plant growth promoting effect. In this study, a screening assay was performed with only five inoculation options selected after first stage (Pseudomonas sp. AW4, Pseudomonas sp. AW6, AW4+AW6, Rhodococcus sp. AW3+Pseudomonas sp. AW5 and Enterobacter sp. AW1+AW6). In both stages, inoculation was implemented by imbibition of soybean seeds with bacterial suspensions, and plant growth was carried out in pots using perlite as substrate in a chamber with controlled conditions. In the third stage, we performed similar assays, under As stress, using the three most promising inoculation options (AW4, AW6 and AW3+AW5). Treatments were performed by irrigation with 25 μM arsenite (As3+), 25 μM arsenate (As5+), 25 μM equimolar As3+/As5+ solution or water (control). Biometric and biochemical parameters indicated that inoculation with Pseudomonas sp. AW4 significantly promoted soybean growth under As3+/As5+ treatment and did not modified As accumulation pattern. Further field studies are needed to determine if some of these inoculation options are useful to improve in situ soybean growth under arsenic stress and could become a tool for the development of sustainable agriculture in As-impacted environments.

Chemical potassium (K) fertilizer is commonly used in apple (Malus domestica L. Borkh) production but K is easily fixed by soil, resulting in reduced K fertilizer utilization and wasted resources. K-solubilizing bacteria (KSB) can cost-effectively increase the soluble K content in rhizosphere soil. Therefore, the objectives were to select high-efficiency KSB from apple orchards under various soil management models and evaluate their effects on apple seedling growth. Maize (Zea mays L.) straw mulching (MSM) increased the total carbon (TC), total nitrogen (TN) and available potassium (AK) in the rhizosphere and improved fruit quality. The number of KSB in the rhizosphere soil of MSM was 9.5×104 CFU g−1 soil, which was considerably higher than that in the other mulching models. Fourteen KSB strains were isolated with relative K solubilizing ability ranging from 17 to 30%, and five strains increased the dry weight per apple seedling. The most efficient strain was identified as Paenibacillus mucilaginosus through morphological observation and sequence analysis of 16S rDNA, named JGK. After inoculation, the colonization of JGK in soil decreased from 4.0 to 1.5×109 CFU g−1 soil within 28 d. The growth of the apple seedlings and the K accumulation in apple plants were promoted by irrigation with 50 mL JGK bacterial solution (1×109 CFU mL−1), but there was no significant increase in the AK content of rhizosphere soil. High-performance liquid phase analysis (HPLC) data showed that the JGK metabolites contained phytohormones and organic acids. Hence, the JGK strain promoted the growth of two-month-old apple seedlings by stimulating function of the produced phytohormones and enhanced K solubility by acidification for apple seedling uptake. This study enriches the understanding of KSB and provides an effective means to increase the K utilization efficiency of apple production.