Isolation and Identification of Plant Growth Promoting Rhizobacteria from Cucumber Rhizosphere and Their Effect on Plant Growth Promotion and Disease Suppression

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

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

Differential Root Exudation and Architecture for Improved Growth of Wheat Mediated by Phosphate Solubilizing Bacteria

Phosphorous (P) deficiency is a major challenge faced by global agriculture. Phosphate-solubilizing bacteria (PSB) provide a sustainable approach to supply available phosphates to plants with improved crop productivity through synergistic interaction with plant roots. The present study demonstrates an insight into this synergistic P-solubilizing mechanism of PSB isolated from rhizosphere soils of major wheat-growing agro-ecological zones of Pakistan. Seven isolates were the efficient P solubilizers based on in vitro P-solubilizing activity (233-365 μg ml-1) with a concomitant decrease in pH (up to 3.5) by the production of organic acids, predominantly acetic acid (∼182 μg ml-1) and gluconic acid (∼117 μg ml-1). Amplification and phylogenetic analysis of gcd, pqqE, and phy genes of Enterobacter sp. ZW32, Ochrobactrum sp. SSR, and Pantoea sp. S1 showed the potential of these PSB to release orthophosphate from recalcitrant forms of phosphorus. Principal component analysis indicates the inoculation response of PSB consortia on the differential composition of root exudation (amino acids, sugars, and organic acids) with subsequently modified root architecture of three wheat varieties grown hydroponically. Rhizoscanning showed a significant increase in root parameters, i.e., root tips, diameter, and surface area of PSB-inoculated plants as compared to uninoculated controls. Efficiency of PSB consortia was validated by significant increase in plant P and oxidative stress management under P-deficient conditions. Reactive oxygen species (ROS)-induced oxidative damages mainly indicated by elevated levels of malondialdehyde (MDA) and H2O2 contents were significantly reduced in inoculated plants by the production of antioxidant enzymes, i.e., superoxide dismutase, catalase, and peroxidase. Furthermore, the inoculation response of these PSB on respective wheat varieties grown in native soils under greenhouse conditions was positively correlated with improved plant growth and soil P contents. Additionally, grain yield (8%) and seed P (14%) were significantly increased in inoculated wheat plants with 20% reduced application of diammonium phosphate (DAP) fertilizer under net house conditions. Thus, PSB capable of such synergistic strategies can confer P biofortification in wheat by modulating root morphophysiology and root exudation and can alleviate oxidative stress under P deficit conditions.

Prospect and Challenges for Sustainable Management of Climate Change-Associated Stresses to Soil and Plant Health by Beneficial Rhizobacteria

Climate change imposes biotic and abiotic stresses on soil and plant health all across the planet. Beneficial rhizobacterial genera, such as Bacillus, Pseudomonas, Paraburkholderia, Rhizobium, Serratia, and others, are gaining popularity due to their ability to provide simultaneous nutrition and protection of plants in adverse climatic conditions. Plant growth-promoting rhizobacteria are known to boost soil and plant health through a variety of direct and indirect mechanisms. However, various issues limit the wider commercialization of bacterial biostimulants, such as variable performance in different environmental conditions, poor shelf-life, application challenges, and our poor understanding on complex mechanisms of their interactions with plants and environment. This study focused on detecting the most recent findings on the improvement of plant and soil health under a stressful environment by the application of beneficial rhizobacteria. For a critical and systematic review story, we conducted a non-exhaustive but rigorous literature survey to assemble the most relevant literature (sorting of a total of 236 out of 300 articles produced from the search). In addition, a critical discussion deciphering the major challenges for the commercialization of these bioagents as biofertilizer, biostimulants, and biopesticides was undertaken to unlock the prospective research avenues and wider application of these natural resources. The advancement of biotechnological tools may help to enhance the sustainable use of bacterial biostimulants in agriculture. The perspective of biostimulants is also systematically evaluated for a better understanding of the molecular crosstalk between plants and beneficial bacteria in the changing climate towards sustainable soil and plant health.

Interactions Between Bacillus Spp., Pseudomonas Spp. and Cannabis sativa Promote Plant Growth

Plant growth-promoting rhizobacteria (PGPR) deploy several mechanisms to improve plant health, growth and yield. The aim of this study was to evaluate the efficacy of two Pseudomonas spp. strains and three Bacillus spp. strains used as single treatments and in consortia to improve the yield of Cannabis sativa and characterize the impact of these treatments on the diversity, structure and functions of the rhizosphere microbiome. Herein, we demonstrate a significant C. sativa yield increase up to 70% when inoculated with three different Pseudomonas spp./Bacillus spp. consortia but not with single inoculation treatments. This growth-promoting effect was observed in two different commercial soil substrates commonly used to grow cannabis: Promix and Canna coco. Marker-based genomic analysis highlighted Bacillus spp. as the main modulator of the rhizosphere microbiome diversity and Pseudomonas spp. as being strongly associated with plant growth promotion. We describe an increase abundance of predicted PGPR metabolic pathways linked with growth-promoting interactions in C. sativa.

Screening and Biocontrol Potential of Rhizobacteria Native to Gangetic Plains and Hilly Regions to Induce Systemic Resistance and Promote Plant Growth in Chilli against Bacterial Wilt Disease

Plant growth-promoting rhizobacteria (PGPR) is a microbial population found in the rhizosphere of plants that can stimulate plant development and restrict the growth of plant diseases directly or indirectly. In this study, 90 rhizospheric soil samples from five agro climatic zones of chilli (Capsicum annuum L.) were collected and rhizobacteria were isolated, screened and characterized at morphological, biochemical and molecular levels. In total, 38% of rhizobacteria exhibited the antagonistic capacity to suppress Ralstonia solanacearum growth and showed PGPR activities such as indole acetic acid production by 67.64% from total screened rhizobacteria isolates, phosphorus solubilization by 79.41%, ammonia by 67.75%, HCN by 58.82% and siderophore by 55.88%. We performed a principal component analysis depicting correlation and significance among plant growth-promoting activities, growth parameters of chilli and rhizobacterial strains. Plant inoculation studies indicated a significant increase in growth parameters and PDS1 strain showed maximum 71.11% biocontrol efficiency against wilt disease. The best five rhizobacterial isolates demonstrating both plant growth-promotion traits and biocontrol potential were characterized and identified as PDS1—Pseudomonas fluorescens (MN368159), BDS1—Bacillus subtilis (MN395039), UK4—Bacillus cereus (MT491099), UK2—Bacillus amyloliquefaciens (MT491100) and KA9—Bacillus subtilis (MT491101). These rhizobacteria have the potential natural elicitors to be used as biopesticides and biofertilizers to improve crop health while warding off soil-borne pathogens. The chilli cv. Pusa Jwala treated with Bacillus subtilis KA9 and Pseudomonas fluorescens PDS1 showed enhancement in the defensive enzymes PO, PPO, SOD and PAL activities in chilli leaf and root tissues, which collectively contributed to induced resistance in chilli plants against Ralstonia solanacearum. The induction of these defense enzymes was found higher in leave tissues (PO—4.87-fold, PP0—9.30-fold, SOD—9.49-fold and PAL—1.04-fold, respectively) in comparison to roots tissue at 48 h after pathogen inoculation. The findings support the view that plant growth-promoting rhizobacteria boost defense-related enzymes and limit pathogen growth in chilli plants, respectively, hence managing the chilli bacterial wilt.

Plant growth promoting endophyte Burkholderia contaminans NZ antagonizes phytopathogen Macrophomina phaseolina through melanin synthesis and pyrrolnitrin inhibition

The endophytic bacterium Burkholderia contaminans NZ was isolated from jute, which is an important fiber-producing plant. This bacterium exhibits significant growth promotion activity in in vivo pot experiments, and like other plant growth-promoting (PGP) bacteria fixes nitrogen, produces indole acetic acid (IAA), siderophore, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. B. contaminans NZ is considered to exert a promising growth inhibitory effect on Macrophomina phaseolina, a phytopathogen responsible for infecting hundreds of crops worldwide. This study aimed to identify the possibility of B. contaminans NZ as a safe biocontrol agent and assess its effectiveness in suppressing phytopathogenic fungi, especially M. phaseolina. Co-culture of M. phaseolina with B. contaminans NZ on both solid and liquid media revealed appreciable growth suppression of M. phaseolina and its chromogenic aberration in liquid culture. Genome mining of B. contaminans NZ using NaPDoS and antiSMASH revealed gene clusters that displayed 100% similarity for cytotoxic and antifungal substances, such as pyrrolnitrin. GC-MS analysis of B. contaminans NZ culture extracts revealed various bioactive compounds, including catechol; 9,10-dihydro-12'-hydroxy-2'-methyl-5'-(phenylmethyl)- ergotaman 3',6',18-trione; 2,3-dihydro-3,5- dihydroxy-6-methyl-4H-pyran-4-one; 1-(1,6-Dioxooctadecyl)- pyrrolidine; 9-Octadecenamide; and 2- methoxy- phenol. These compounds reportedly exhibit tyrosinase inhibitory, antifungal, and antibiotic activities. Using a more targeted approach, an RP-HPLC purified fraction was analyzed by LC-MS, confirming the existence of pyrrolnitrin in the B. contaminans NZ extract. Secondary metabolites, such as catechol and ergotaman, have been predicted to inhibit melanin synthesis in M. phaseolina. Thus, B. contaminans NZ appears to inhibit phytopathogens by apparently impairing melanin synthesis and other potential biochemical pathways, exhibiting considerable fungistatic activity.

Psychrotolerant Mesorhizobium sp. Isolated from Temperate and Cold Desert Regions Solubilizes Potassium and Produces Multiple Plant Growth Promoting Metabolites

Soil potassium (K) supplement depends intensively on the application of chemical fertilizers, which have substantial harmful environmental effects. However, some bacteria can act as inoculants by converting unavailable and insoluble K forms into plant-accessible forms. Such bacteria are an eco-friendly approach for enhancing plant K absorption and consequently reducing utilization of chemical fertilization. Therefore, the present research was undertaken to isolate, screen, and characterize the K solubilizing bacteria (KSB) from the rhizosphere soils of northern India. Overall, 110 strains were isolated, but only 13 isolates showed significant K solubilizing ability by forming a halo zone on solid media. They were further screened for K solubilizing activity at 0 °C, 1 °C, 3 °C, 5 °C, 7 °C, 15 °C, and 20 °C for 5, 10, and 20 days. All the bacterial isolates showed mineral K solubilization activity at these different temperatures. However, the content of K solubilization increased with the upsurge in temperature and period of incubation. The isolate KSB (Grz) showed the highest K solubilization index of 462.28% after 48 h of incubation at 20 °C. The maximum of 23.38 µg K/mL broth was solubilized by the isolate KSB (Grz) at 20 °C after 20 days of incubation. Based on morphological, biochemical, and molecular characterization (through the 16S rDNA approach), the isolate KSB (Grz) was identified as Mesorhizobium sp. The majority of the strains produced HCN and ammonia. The maximum indole acetic acid (IAA) (31.54 µM/mL) and cellulase (390 µM/mL) were produced by the isolate KSB (Grz). In contrast, the highest protease (525.12 µM/mL) and chitinase (5.20 µM/mL) activities were shown by standard strain Bacillus mucilaginosus and KSB (Gmr) isolate, respectively.

The Endophytic Pseudomonas sp. S57 for Plant-Growth Promotion and the Biocontrol of Phytopathogenic Fungi and Nematodes

Oregano from Socoroma (Atacama Desert) is characterized by its unique organoleptic properties and distinctive flavor and it is produced using ancestral pesticide-free agricultural practices performed by the Aymara communities. The cultivation in this zone is carried out under extreme conditions where the standard production of different crops is limited by several environmental factors, including aridity, high concentration of salts, and boron among others. However, oregano plants are associated with microorganisms that mitigate biotic and abiotic stresses present in this site. In this work, the S57 strain (member of the Pseudomonas genus that is closely related to Pseudomonas lini) was isolated from roots of oregano plants, which are grown in soils with high content of non-sodium salts and aluminum. This bacterium stimulates the growth of Micro-Tom tomato plants irrigated with saline-boric water. Moreover, it controls the growth of phytopathogenic fungi Fusarium oxysporum and Botrytis cinerea and the nematode Meloidogyne incognita under saline-boric conditions. Together with the high levels of bacterial biomass (~47 g/L), these results allow the establishment of the bases for developing a potential new agricultural bioproduct useful for arid and semiarid environments where commercial biological products show erratic behavior.

Deciphering the Bacillus amyloliquefaciens B9601-Y2 as a Potential Antagonist of Tobacco Leaf Mildew Pathogen During Flue-Curing

Tobacco leaf mildew caused by Rhizopus oryzae (Mucorales, Zygomycota) is an important and devastating post-harvest disease during flue-cured tobacco period, and also is known to cause diseases of fruits and vegetables. In this study, assessment of several candidate biological control agents were first tested in vitro to determine their antifungal activities and potential strains were further applied to tobacco leaves to prevent pathogen colonization during the tobacco-curing process. In vitro screening of 36 bacteria and the isolates of one fungus were performed for their antifungal activities against R. oryzae using dual culture method. Potential five isolates viz. Bacillus amyloliquefaciens B9601-Y2 (Y2), B. amyloliquefaciens YN201728 (YN28), Pseudomonas sp. (Pb), and B. amyloliquefaciens YN201732 (YN32) and T. harzianum B (Th-B) from total screened isolates have shown remarkable results for controlling the mycelial growth of R. oryzae. Finally, out of these five isolates, B. amyloliquefaciens B9601-Y2 potentially reduced the mycelial growth of fungal pathogen with great inhibitory effect. In order to get a better understanding of the biocontrol effect of B9601-Y2 in a flue-curing barn, various suspension density tests with two application methods involving spraying and soaking were examined. Two application methods of B. amyloliquefaciens B9601-Y2 had 98.60 and 98.15% control effects, respectively. In curing barn, the incidence in the treatment group was significantly reduced and tobacco leaves did not get mildew. Altogether, the study demonstrated that candidate bacterial strain B. amyloliquefaciens B9601-Y2 is a potential antagonist for the management of tobacco leaf mildew during flue-curing.

Phosphate solubilizing rhizobacteria isolated from jujube ziziphus lotus plant stimulate wheat germination rate and seedlings growth

Jujube plant (Ziziphus lotus (L.) Desf.) can survive in arid climates and tolerates both biotic and abiotic stresses. Here, we isolated, for the first time in Morocco, nine phosphate solubilizing bacteria strains from jujube rhizosphere, designated J10 to J13, J15, & J153 to J156. Genotypic identification based on 16S rDNA sequencing, revealed six strains that belong to Pseudomonas (J10, J12, J13, J15, J153 and J154), two to Bacillus (J11 and J156), and one to Paenibacillus J155. Siderophores were produced by all strains. Proteases activity was missing in Pseudomonas sp. J153 & J154, whereas cellulase was restricted only to Pseudomonas sp. J10, Paenibacillus xylanexedens J155 and Bacillus cereus J156. Indole-3- acetic acid and ammonia were also produced by all strains, with a maxima of 204.28 µg mL⁻¹ in Bacillus megaterium J11 and 0.33 µmol mL⁻¹ in Pseudomonas sp. J153, respectively. Pseudomonas sp. J10 and B. cereus J156 grew on plates containing 1,500 µg mL⁻¹ of nickel nitrate, while Pseudomonas sp. J153 withstood 1,500 µg mL⁻¹ of either copper sulfate or cadmium sulfate. Phenotypic analysis of the potential of the isolates to promote early plant growth showed that wheat seeds inoculated with either P. moraviensis J12 or B. cereus J156 remarkably increased germination rate and seedlings growth. Lastly, antibiotic resistance profiling revealed that except for Pseudomonas sp. J11 and B. cereus J156, remaining strains displayed resistance at least to one of tested antibiotics. Collectively, Pseudomonas sp. J10, P. moraviensis J12, Pseudomonas sp. J153 and B. cereus J156, represent potential biofertilizers suitable for soils that are poor in P, and/or heavy metals contaminated.

Biological Control of Chili Damping-Off Disease, Caused by Pythium myriotylum

Pythium myriotylum is a notorious soil-borne oomycete that causes post-emergence damping-off in chili pepper. Of various disease management strategies, utilization of plant growth promoting rhizobacteria (PGPR) in disease suppression and plant growth promotion is an interesting strategy. The present study was performed to isolate and characterize PGPR indigenous to the chili rhizosphere in Pakistan, and to test the potential to suppress the damping-off and plant growth promotion in chili. Out of a total of 28 antagonists, eight bacterial isolates (4a2, JHL-8, JHL-12, 1C2, RH-24, 1D, 5C, and RH-87) significantly suppressed the colony growth of P. myriotylum in a dual culture experiment. All the tested bacterial isolates were characterized for biochemical attributes, and 16S rRNA sequence based phylogenetic analysis identified these isolates as Flavobacterium spp., Bacillus megaterium, Pseudomonas putida, Bacillus cereus, and Pseudomonas libanensis. All the tested bacterial isolates showed positive test results for ammonia production, starch hydrolase (except 4a2), and hydrogen cyanide production (except 4a2 and 1D). All the tested antagonists produced indole-3-acetic acid (13.4–39.0 μg mL^–1), solubilized inorganic phosphate (75–103 μg mL^–1), and produced siderophores (17.1–23.7%) in vitro. All the tested bacterial isolates showed varying levels of susceptibility and resistance response against different antibiotics and all these bacterial isolates were found to be non-pathogenic to chili seeds and notably enhanced percentage seed germination, plumule, redical length, and vigor index over un-inoculated control. Additionally, under pathogen pressure, bacterization increased the defense related enzymes such as Peroxidase (PO), polyphenol oxidase (PPO), and phenylalanine ammonia-lyase (PAL) activates. Moreover, the treatment of chili seeds with these bacterial isolates significantly suppressed the damping-off caused by P. myriotylum and improved PGP traits compared to the control. In addition, a positive correlation was noticed between shoot, root length, and dry shoot and root weight, and there was a negative correlation between dry shoot, root weight, and seedling percentage mortality. These results showed that native PGPR possesses multiple traits beneficial to the chili plants and can be used to develop eco-friendly and effective seed treatment formulation as an alternative to synthetic chemical fungicides.

Potential Role of Rhizobacteria Isolated from Citrus Rhizosphere for Biological Control of Citrus Dry Root Rot

Citrus trees face threats from several diseases that affect its production, in particular dry root rot (DRR). DRR is a multifactorial disease mainly attributed to Neocosmospora (Fusarium) solani and other several species of Neocosmospora and Fusarium spp. Nowadays, biological control holds a promising control strategy that showed its great potential as a reliable eco-friendly method for managing DRR disease. In the present study, antagonist rhizobacteria isolates were screened based on in vitro dual culture bioassay with N. solani. Out of 210 bacterial isolates collected from citrus rhizosphere, twenty isolates were selected and identified to the species level based on the 16S rRNA gene. Molecular identification based on 16S rRNA gene revealed nine species belonging to Bacillus, Stenotrophomonas, and Sphingobacterium genus. In addition, their possible mechanisms involved in biocontrol and plant growth promoting traits were also investigated. Results showed that pectinase, cellulose, and chitinase were produced by eighteen, sixteen, and eight bacterial isolates, respectively. All twenty isolates were able to produce amylase and protease, only four isolates produced hydrogen cyanide, fourteen isolates have solubilized tricalcium phosphate, and ten had the ability to produce indole-3-acetic acid (IAA). Surprisingly, antagonist bacteria differed substantially in their ability to produce antimicrobial substances such as bacillomycin (five isolates), iturin (ten isolates), fengycin (six isolates), surfactin (fourteen isolates), and bacteriocin (subtilosin A (six isolates)). Regarding the PGPR capabilities, an increase in the growth of the bacterial treated canola plants, used as a model plant, was observed. Interestingly, both bacterial isolates Bacillus subtilis K4-4 and GH3-8 appear to be more promising as biocontrol agents, since they completely suppressed the disease in greenhouse trials. Moreover, these antagonist bacteria could be used as bio-fertilizer for sustainable agriculture.

Systemic Resistance in Chilli Pepper against Anthracnose (Caused by Colletotrichum truncatum) Induced by Trichoderma harzianum, Trichoderma asperellum and Paenibacillus dendritiformis

In the present study, Paenibacillus dendritiformis, Trichoderma harzianum, and Trichoderma asperellum were appraised as potential biocontrol agents that induce resistance in chilli (Capsicum annuum) against the devastating pathogen Colletotrichum truncatum, which causes anthracnose. Bright-field and scanning electron micrographs showed the hyphal degradation, lysis, and abnormal swelling in C. truncatum against P. dendritiformis in a dual plate assay. Under greenhouse conditions, chilli seeds pretreated with P. dendritiformis, T. asperellum, T. harzianum, and T. asperellum + T. harzianum by soil soak method inflicted an induced systemic resistance (ISR) in chilli against a C. truncatum-challenged condition. In chilli, the disease index percentage was significantly reduced in the T. asperellum + T. harzianum-treated seeds, followed by the T. harzianum-, T. asperellum-, and P. dendritiformis-treated seeds as compared to the untreated and challenged, respectively. Chilli seeds were primed with T. asperellum + T. harzianum (78.67%), which revealed maximum disease protection under the challenged condition, followed by T. harzianum (70%), T. asperellum (64%), and P. dendritiformis (56%) as compared to untreated and C. truncatum-challenged (6%) condition served as control. The seeds that were pretreated with biocontrol agents (BCAs) inflicted ISR against C. truncatum by enhancing the activity of defence-related enzymes (superoxide dismutase (SOD), peroxidase (POX), polyphenol oxidase (PPO), catalase (CAT), ascorbate peroxidase (APX), guaiacol peroxidase (GPX) and phenylalanine ammonia-lyase (PAL)), accumulating phenolic compounds, and increasing the relative chlorophyll content in chilli. Nitroblue tetrazolium (NBT) and 3,3′-Diaminobenzidine (DAB) stains were used to detect the accumulation of superoxide anion and hydrogen peroxide that appeared nearby the fungal infection sites. The accumulation of reactive oxygen species (O₂⁻ and H₂O₂) in the pathogen-inoculated leaves was a maximum of 48 hpi, followed by P. dendritiformis, T. asperellum, T. harzianum, and T. asperellum + T. harzianum treated tissue upon C. truncatum-challenged condition as compared to the control. Overall, our results showed the potential of T. harzianum, T. asperellum, and P. dendritiformis as biocontrol agents that prevent infection by C. truncatum and inflict an induced systemic resistance in chilli by enhancing the biosynthesis of phenolic compounds, defence and antioxidative enzymes, and reducing the lesion development and reactive oxygen species accumulation. This is the first report of induced systemic resistance against anthracnose in chilli obtained by application of T. harzianum, T. asperellum and P. dendritiformis, through seed priming.

Rhizospheric Phosphate Solubilizing Bacillus atrophaeus GQJK17 S8 Increases Quinoa Seedling, Withstands Heavy Metals, and Mitigates Salt Stress

Introduction of quinoa (Chenopodium quinoa willd.), a gluten-free nutritious pseudo-cereal, outside its traditional growing areas exposed it to seedling damping-off. Here, we isolated eleven phosphate-solubilizing bacteria from the quinoa rhizosphere and assessed their effect on germination and seedlings growth. All isolates solubilized phosphate, produced indole3-acetic acid, hydrocyanic acid, siderophores, and ammonia. Genotypic analysis revealed that our strains are related to the genus of Bacillus, Pseudomonas, and Enterobacter. Strains Enterobacter asburiae (QD14, QE4, QE6, and QE16), Enterobacter sp. QE3, and Enterobacter hormaechei QE7 withstood 1.5 mg·L−1 of cadmium sulfate, 0.5 mg·mL−1 of nickel nitrate, and 1 mg·mL−1 of copper sulfate. Moreover, all strains solubilized zinc from ZnO; P. Stutzeri QD1 and E. asburiae QD14 did not solubilize Zn3(PO4)2 and CO3Zn, whereas CO3Zn was not solubilized by E. asburiae QE16. Bacillus atrophaeus S8 tolerated 11% NaCl. P. frederiksbergensis S6 and Pseudomonas sp. S7 induced biofilm formation. Anti-fusarium activity was demonstrated for E.asburiae QE16, P. stutzeri QD1, P. frederiksbergensis S6, Pseudomonas sp. S7, and B. atrophaeus S8. Lastly, inoculation of quinoa seeds with B. atrophaeus S8 and E. asburiae QB1 induced the best germination rate and seedling growth, suggesting their potential use as inoculants for salty and heavy metal or zinc contaminated soils.

Plant Associated Rhizobacteria for Biocontrol and Plant Growth Enhancement

Crop disease remains a major problem to global food production. Excess use of pesticides through chemical disease control measures is a serious problem for sustainable agriculture as we struggle for higher crop productivity. The use of plant growth promoting rhizobacteria (PGPR) is a proven environment friendly way of controlling plant disease and increasing crop yield. PGPR suppress diseases by directly synthesizing pathogen-antagonizing compounds, as well as by triggering plant immune responses. It is possible to identify and develop PGPR that both suppress plant disease and more directly stimulate plant growth, bringing dual benefit. A number of PGPR have been registered for commercial use under greenhouse and field conditions and a large number of strains have been identified and proved as effective biocontrol agents (BCAs) under environmentally controlled conditions. However, there are still a number of challenges before registration, large-scale application, and adoption of PGPR for the pest and disease management. Successful BCAs provide strong theoretical and practical support for application of PGPR in greenhouse production, which ensures the feasibility and efficacy of PGPR for commercial horticulture production. This could be pave the way for widespread use of BCAs in agriculture, including under field conditions, to assist with both disease management and climate change conditions.

Bacterial Plant Biostimulants: A Sustainable Way towards Improving Growth, Productivity, and Health of Crops

This review presents a comprehensive and systematic study of the field of bacterial plant biostimulants and considers the fundamental and innovative principles underlying this technology. Plant biostimulants are an important tool for modern agriculture as part of an integrated crop management (ICM) system, helping make agriculture more sustainable and resilient. Plant biostimulants contain substance(s) and/or microorganisms whose function when applied to plants or the rhizosphere is to stimulate natural processes to enhance plant nutrient uptake, nutrient use efficiency, tolerance to abiotic stress, biocontrol, and crop quality. The use of plant biostimulants has gained substantial and significant heed worldwide as an environmentally friendly alternative to sustainable agricultural production. At present, there is an increasing curiosity in industry and researchers about microbial biostimulants, especially bacterial plant biostimulants (BPBs), to improve crop growth and productivity. The BPBs that are based on PGPR (plant growth-promoting rhizobacteria) play plausible roles to promote/stimulate crop plant growth through several mechanisms that include (i) nutrient acquisition by nitrogen (N2) fixation and solubilization of insoluble minerals (P, K, Zn), organic acids and siderophores; (ii) antimicrobial metabolites and various lytic enzymes; (iii) the action of growth regulators and stress-responsive/induced phytohormones; (iv) ameliorating abiotic stress such as drought, high soil salinity, extreme temperatures, oxidative stress, and heavy metals by using different modes of action; and (v) plant defense induction modes. Presented here is a brief review emphasizing the applicability of BPBs as an innovative exertion to fulfill the current food crisis.

Multiple endogenous seed-born bacteria recovered rice growth disruption caused by Burkholderia glumae

Burkholderia glumae is a causal agent of bacterial grain and seedling rot in rice, and is a threat to stable global food supply. The virulence of B. glumae was suppressed when it was inoculated on budding seed rather than on non-budding seed. To clarify the phenomena, pathogen titer inside the rice plant was measured by serial dilution plating of lysates from budding rice seedlings. Surprisingly, morphologically different types of colonies were observed on the plates. These 'contaminated' rice seed-born bacteria (RSB) were identified by sequencing 16S rRNA genes as three strains of Pseudomonas putida (RSB1, RSB10, RSB15) and Stenotrophomonas maltophilia (RSB2). All bacteria and B. glumae were simultaneously inoculated onto rice seeds, and all three P. putida RSBs suppressed the growth disruption caused by B. glumae, whereas RSB2 had no effect. Thus, the virulence was synergistically suppressed when co-treated with RSBs. The effect could be dependent on the high biofilm formation ability of RSB2. By comprehensive microbiota analysis, endogenous rice flora were changed by RSBs treatment. These results suggest the possibility of novel pathogen control through pre-treatment with endogenous beneficial microorganisms. The method would contribute substantially to the implementation of sustainable agriculture stated in Sustainable Development Goals of United Nations.

Rhizosphere Engineering With Plant Growth-Promoting Microorganisms for Agriculture and Ecological Sustainability

The rhizosphere is undoubtedly the most complex microhabitat, comprised of an integrated network of plant roots, soil, and a diverse consortium of bacteria, fungi, eukaryotes, and archaea. The rhizosphere conditions have a direct impact on crop growth and yield. Nutrient-rich rhizosphere environments stimulate plant growth and yield and vice versa. Extensive cultivation exhaust most of the soils which need to be nurtured before or during the next crop. Chemical fertilizers are the major source of crop nutrients but their uncontrolled and widespread usage has posed a serious threat to the sustainability of agriculture and stability of an ecosystem. These chemicals are accumulated in the soil, drained in water, and emitted to the air where they persist for decades causing a serious threat to the overall ecosystem. Plant growth-promoting rhizobacteria (PGPR) present in the rhizosphere convert many plant-unavailable essential nutrients e.g., nitrogen, phosphorous, zinc, etc. into available forms. PGPR produces certain plant growth hormones (such as auxin, cytokinin, and gibberellin), cell lytic enzymes (chitinase, protease, hydrolases, etc.), secondary metabolites, and antibiotics, and stress alleviating compounds (e.g., 1-Aminocyclopropane-1- carboxylate deaminase), chelating agents (siderophores), and some signaling compounds (e.g., N-Acyl homoserine lactones) to interact with the beneficial or pathogenic counterparts in the rhizosphere. These multifarious activities of PGPR improve the soil structure, health, fertility, and functioning which directly or indirectly support plant growth under normal and stressed environments. Rhizosphere engineering with these PGPR has a wide-ranging application not only for crop fertilization but developing eco-friendly sustainable agriculture. Due to severe climate change effects on plants and rhizosphere biology, there is growing interest in stress-resilient PGPM and their subsequent application to induce stress (drought, salinity, and heat) tolerance mechanism in plants. This review describes the three components of rhizosphere engineering with an explicit focus on the broader perspective of PGPM that could facilitate rhizosphere engineering in selected hosts to serve as an efficient component for sustainable agriculture.

Microbes as Biofertilizers, a Potential Approach for Sustainable Crop Production

Continuous decline of earth’s natural resources and increased use of hazardous chemical fertilizers pose a great concern for the future of agriculture. Biofertilizers are a promising alternative to hazardous chemical fertilizers and are gaining importance for attaining sustainable agriculture. Biofertilizers play a key role in increasing crop yield and maintaining long-term soil fertility, which is essential for meeting global food demand. Microbes can interact with the crop plants and enhance their immunity, growth, and development. Nitrogen, phosphorous, potassium, zinc, and silica are the essential nutrients required for the proper growth of crops, but these nutrients are naturally present in insolubilized or complex forms. Certain microorganisms render them soluble and make them available to the plants. The potential microbes, their mode of action, along with their effect on crops, are discussed in this review. Biofertilizers, being cost effective, non-toxic, and eco-friendly, serve as a good substitute for expensive and harmful chemical fertilizers. The knowledge gained from this review can help us to understand the importance of microbes in agriculture and the ways to formulate these microbes as biofertilizers for sustainable crop production.

Plant Growth Promoting Rhizobacteria (PGPR) as Green Bioinoculants: Recent Developments, Constraints, and Prospects

The quest for enhancing agricultural yields due to increased pressure on food production has inevitably led to the indiscriminate use of chemical fertilizers and other agrochemicals. Biofertilizers are emerging as a suitable alternative to counteract the adverse environmental impacts exerted by synthetic agrochemicals. Biofertilizers facilitate the overall growth and yield of crops in an eco-friendly manner. They contain living or dormant microbes, which are applied to the soil or used for treating crop seeds. One of the foremost candidates in this respect is rhizobacteria. Plant growth promoting rhizobacteria (PGPR) are an important cluster of beneficial, root-colonizing bacteria thriving in the plant rhizosphere and bulk soil. They exhibit synergistic and antagonistic interactions with the soil microbiota and engage in an array of activities of ecological significance. They promote plant growth by facilitating biotic and abiotic stress tolerance and support the nutrition of host plants. Due to their active growth endorsing activities, PGPRs are considered an eco-friendly alternative to hazardous chemical fertilizers. The use of PGPRs as biofertilizers is a biological approach toward the sustainable intensification of agriculture. However, their application for increasing agricultural yields has several pros and cons. Application of potential biofertilizers that perform well in the laboratory and greenhouse conditions often fails to deliver the expected effects on plant development in field settings. Here we review the different types of PGPR-based biofertilizers, discuss the challenges faced in the widespread adoption of biofertilizers, and deliberate the prospects of using biofertilizers to promote sustainable agriculture.

Unlocking the potential of plant growth-promoting rhizobacteria on soil health and the sustainability of agricultural systems

The concept of soil health refers to specific soil properties and the ability to support and sustain crop growth and productivity, while maintaining long-term environmental quality. The key components of healthy soil are high populations of organisms that promote plant growth, such as the plant growth promoting rhizobacteria (PGPR). PGPR plays multiple beneficial and ecological roles in the rhizosphere soil. Among the roles of PGPR in agroecosystems are the nutrient cycling and uptake, inhibition of potential phytopathogens growth, stimulation of plant innate immunity, and direct enhancement of plant growth by producing phytohormones or other metabolites. Other important roles of PGPR are their environmental cleanup capacities (soil bioremediation). In this work, we review recent literature concerning the diverse mechanisms of PGPR in maintaining healthy conditions of agricultural soils, thus reducing (or eliminating) the toxic agrochemicals dependence. In conclusion, this review provides comprehensive knowledge on the current PGPR basic mechanisms and applications as biocontrol agents, plant growth stimulators and soil rhizoremediators, with the final goal of having more agroecological practices for sustainable agriculture.

Mediation of induced systemic resistance by the plant growth-promoting rhizobacteria Bacillus pumilus S2-3-2

Plant-rhizobacteria interaction and co-evolution developed adaptive strategies which may help the plant survive in nature. Plant rhizosphere soil isolates were analyzed to investigated the effects of rhizobacteria for promoting plant growth and suppress plant disease. Bacterial strains which isolated from plant rhizosphere soil were screened for elicitation of induced systemic resistance (ISR) on tobacco. Strain S2-3-2 results in significant reduction of disease severity on tobacco, it was identified as Bacillus pumilus by multilocus sequence analysis (MLSA). Strain S2-3-2 was deeper studied for pepper plant growth promotion and biological control activity against pepper bacterial spot disease. It was found that the pepper disease severity was decreased when the roots were drenched with strain S2-3-2, and the pepper plants had a higher weight and chlorophyll content, as compared with the mock-treated plants. Transcriptional expression of pathogenesis-related (PR) protein genes in pepper was analyzed by real-time PCR, gene expressions of CaPR1, CaPR4, and CaPR10 were increased when the plants were treated with strain S2-3-2. Moreover, strain S2-3-2 was tested for the production of indole-3-acetic acid (IAA), and it was determined to emit volatiles that enhance the growth of the tobacco plants. Interesting, heat-killed S2-3-2 enhance the pepper root growth, increase the gene expressions of CaPR4 and CaPR10 after pathogen challenge for 6 h, but limited to suppress the pepper bacterial spot disease as compare to the mock-treated plants. Strain S2-3-2 can be a potential biological control agent on the plant root for plant growth promoting and disease suppression.

Soil microbes alter seedling performance and biotic interactions under plant competition and contrasting light conditions

BACKGROUND AND AIMS

Growing evidence suggests that the net effect of soil microbes on plants depends on both abiotic and biotic conditions, but the context-dependency of soil feedback effects remains poorly understood. Here we test for interactions between the presence of conspecific soil microbes, plant competition and light availability on tree seedling performance.

METHODS

Seedlings of two congeneric tropical tree species, Bauhinia brachycarpa and Bauhinia variegata, were grown in either sterilized soil or soil conditioned by conspecific soil microorganisms in a two-phase greenhouse feedback experiment. We examined the interactive effects of soil treatment (live, sterilized), light availability (low, high) and plant competition (no competition, intraspecific and interspecific competition) on tree seedling biomass. We also investigated the linkages between the outcomes of soil feedback effects and soil microbial community structure.

KEY RESULTS

The outcomes of soil feedback effects on seedling biomass varied depending on both competition treatment and light availability. Under low light conditions, soil feedback effects were neutral irrespective of competition treatment and plant species. Soil feedback effects were negative in high light for seedlings with interspecific competition, but positive for seedlings growing alone or with intraspecific competition. Soil feedback effects for seedlings were driven by variation in the Gram-positive:Gram-negative bacteria ratio. Light and conspecific soil microbes had interactive effects on the competitive environment experienced by tree species; in low light the presence of conspecific soil microbes decreased plant competition intensity, whereas in high light both the intensity and the importance of competition increased for seedlings in the presence of soil microbes, irrespective of plant species.

CONCLUSIONS

Our findings underline the importance of light and plant competition for the outcomes of soil feedback effects on young tree seedlings, and suggest that reduced light availability may reduce the influence of conspecific soil microbes on plant-plant interactions.

Bacillus velezensis 83 a bacterial strain from mango phyllosphere, useful for biological control and plant growth promotion

Bacillus velezensis 83 was isolated from mango tree phyllosphere of orchards located in El Rosario, Sinaloa, México. The assessment of this strain as BCA (biological control agent), as well as PGPB (plant growth-promoting bacteria), were demonstrated through in vivo and in vitro assays. In vivo assays showed that B. velezensis 83 was able to control anthracnose (Kent mangoes) as efficiently as chemical treatment with Captan 50 PH™ or Cupravit hidro™. The inoculation of B. velezensis 83 to the roots of maize seedlings yielded an increase of 12% in height and 45% of root biomass, as compared with uninoculated seedlings. In vitro co-culture assays showed that B. velezensis 83 promoted Arabidopsis thaliana growth (root and shoot biomass) while, under the same experimental conditions, B. velezensis FZB42 (reference strain) had a suppressive effect on plant growth. In order to characterize the isolated strain, the complete genome sequence of B. velezensis 83 is reported. Its circular genome consists of 3,997,902 bp coding to 3949 predicted genes. The assembly and annotation of this genome revealed gene clusters related with plant-bacteria interaction and sporulation, as well as ten secondary metabolites biosynthetic gene clusters implicated in the biological control of phytopathogens. Despite the high genomic identity (> 98%) between B. velezensis 83 and B. velezensis FZB42, they are phenotypically different. Indeed, in vitro production of compounds such as surfactin and bacillomycin D (biocontrol activity) and γ-PGA (biofilm component) is significantly different between both strains.

Deciphering the Omics of Plant-Microbe Interaction: Perspectives and New Insights

Introduction

Plants do not grow in isolation, rather they are hosts to a variety of microbes in their natural environments. While, few thrive in the plants for their own benefit, others may have a direct impact on plants in a symbiotic manner. Unraveling plant-microbe interactions is a critical component in recognizing the positive and negative impacts of microbes on plants. Also, by affecting the environment around plants, microbes may indirectly influence plants. The progress in sequencing technologies in the genomics era and several omics tools has accelerated in biological science. Studying the complex nature of plant-microbe interactions can offer several strategies to increase the productivity of plants in an environmentally friendly manner by providing better insights. This review brings forward the recent works performed in building omics strategies that decipher the interactions between plant-microbiome. At the same time, it further explores other associated mutually beneficial aspects of plant-microbe interactions such as plant growth promotion, nitrogen fixation, stress suppressions in crops and bioremediation; as well as provides better insights on metabolic interactions between microbes and plants through omics approaches. It also aims to explore advances in the study of Arabidopsis as an important avenue to serve as a baseline tool to create models that help in scrutinizing various factors that contribute to the elaborate relationship between plants and microbes. Causal relationships between plants and microbes can be established through systematic gnotobiotic experimental studies to test hypotheses on biologically derived interactions.

Conclusion

This review will cover recent advances in the study of plant-microbe interactions keeping in view the advantages of these interactions in improving nutrient uptake and plant health.

PGPR-mediated induction of systemic resistance and physiochemical alterations in plants against the pathogens: Current perspectives

Plant growth-promoting rhizobacteria (PGPR) are diverse groups of plant-associated microorganisms, which can reduce the severity or incidence of disease during antagonism among bacteria and soil-borne pathogens, as well as by influencing a systemic resistance to elicit defense response in host plants. An amalgamation of various strains of PGPR has improved the efficacy by enhancing the systemic resistance opposed to various pathogens affecting the crop. Many PGPR used with seed treatment causes structural improvement of the cell wall and physiological/biochemical changes leading to the synthesis of proteins, peptides, and chemicals occupied in plant defense mechanisms. The major determinants of PGPR-mediated induced systemic resistance (ISR) are lipopolysaccharides, lipopeptides, siderophores, pyocyanin, antibiotics 2,4-diacetylphoroglucinol, the volatile 2,3-butanediol, N-alkylated benzylamine, and iron-regulated compounds. Many PGPR inoculants have been commercialized and these inoculants consequently aid in the improvement of crop growth yield and provide effective reinforcement to the crop from disease, whereas other inoculants are used as biofertilizers for native as well as crops growing at diverse extreme habitat and exhibit multifunctional plant growth-promoting attributes. A number of applications of PGPR formulation are needed to maintain the resistance levels in crop plants. Several microarray-based studies have been done to identify the genes, which are associated with PGPR-induced systemic resistance. Identification of these genes associated with ISR-mediating disease suppression and biochemical changes in the crop plant is one of the essential steps in understanding the disease resistance mechanisms in crops. Therefore, in this review, we discuss the PGPR-mediated innovative methods, focusing on the mode of action of compounds authorized that may be significant in the development contributing to enhance plant growth, disease resistance, and serve as an efficient bioinoculants for sustainable agriculture. The review also highlights current research progress in this field with a special emphasis on challenges, limitations, and their environmental and economic advantages.

Characterization of native plant growth promoting rhizobacteria and their anti-oomycete potential against Phytophthora capsici affecting chilli pepper (Capsicum annum L.)

Phytophthora capsici is a notorious fungus which infects many crop plants at their early and late growth stages. In the present study, twelve P. capsici isolates were morphologically characterized, and based on pathogenicity assays; two highly virulent isolates causing post-emergence damping-off on locally cultivated chilli pepper were screened. Two P. capsici isolates, HydPak1 (MF322868) and HydPk2 (MF322869) were identified based on internal transcribed spacer (ITS) sequence homology. Plant growth promoting rhizobacteria (PGPR) play a significant role in disease suppression and plant growth promotion in various crops. Out of fifteen bacterial strains recovered from chilli rhizosphere, eight were found potential antagonists to P. capsici in vitro. Bacterial strains with strong antifungal potential were subjected to biochemical and molecular analysis. All tested bacterial strains, were positive for hydrogen cyanide (HCN), catalase production and indole-3-acetic acid (IAA) production (ranging from 6.10 to 56.23 µg ml^-1), while siderophore production varied between 12.5 and 33.5%. The 16S rRNA sequence analysis of tested bacterial strains showed 98-100% identity with Pseudomonas putida, P. libanensis, P. aeruginosa, Bacillus subtilis, B. megaterium, and B. cereus sequences available in the National Center for Biotechnology Information (NCBI) GenBank nucleotide database. All sequences of identified bacteria were submitted to GenBank for accessions numbers (MH796347-50, MH796355-56, MH801129 and MH801071). Greenhouse studies concluded that all tested bacterial strains significantly suppressed the P. capsici infections (52.3-63%) and enhanced the plant growth characters in chilli pepper. Efficacy of many of these tested rhizobacteria is being first time reported against P. capsici from Pakistan. Plant growth promoting rhizobacteria (PGPR) exhibiting multiple traits may be used in the development of new, eco-friendly, and effective bioformulations as an alternative to synthetic fungicides.

Halo-tolerant plant growth promoting rhizobacteria for improving productivity and remediation of saline soils

Background

The collective impact of climate change and soil salinity is continuously increasing the degraded lands across the globe, bringing agricultural productivity and food security under stress. The high concentration of salts in saline soils impose osmotic, ionic, oxidative and water stress in plants. Biological solutions can be the most reliable and sustainable approach to ensure food security and limit the use of agro-chemicals.

Aim of Review

Halo-tolerant plant growth promoting rhizobacteria (HT-PGPR) are emerging as efficient biological tools to mitigate the toxic effects of high salt concentrations and improve the growth of plants, simultaneously remediating the degraded saline soils. The review explains the role of HT-PGPR in mitigating the salinity stress in plants through diverse mechanisms and concurrently leading to improvement of soil quality.

Key Scientific Concepts of Review

HT-PGPR are involved in alleviating the salinity stress in plants through a number of mechanisms evoking multipronged physiological, biochemical and molecular responses. These include changes in expression of defense-related proteins, exopolysaccharides synthesis, activation of antioxidant machinery, accumulation of osmolytes, maintaining the Na⁺ kinetics and improving the levels of phytohormones and nutrient uptake in plants. The modification of signaling by HT-PGPR inoculation under stress conditions elicits induced systemic resistance in plants which further prepares them against salinity stress. The role of microbial-mechanisms in remediating the saline soil through structural and compositional improvements is also important. Development of novel bioinoculants for saline soils based on the concepts presented in the review can be a sustainable approach in improving productivity of affected agro-ecosystems and simultaneously remediating them.

Microbiota in the Rhizosphere and Seed of Rice From China, With Reference to Their Transmission and Biogeography

Seeds play key roles in the acquisition of plant pioneer microbiota, including the transmission of microbes from parent plants to offspring. However, the issues about seed microbial communities are mostly unknown, especially for their potential origins and the factors influencing the structure and composition. In this study, samples of rice seed and rhizosphere were collected from northeast and central-south China in two harvest years and analyzed using a metabarcoding approach targeting 16S rRNA gene region. A higher level of vertical transmission (from parent seed microbiota to offspring) was revealed, as compared to the acquisition from the rhizosphere (25.5 vs 10.7%). The core microbiota of the rice seeds consisted of a smaller proportion of OTUs (3.59%) than that of the rice rhizosphere (7.54%). Among the core microbiota, species in Arthrobacter, Bacillus, Blastococcus, Curtobacterium, Pseudomonas, and Ramlibacter have been reported as potential pathogens and/or beneficial bacteria for plants. Both the seed and the rhizosphere of rice showed distance-decay of similarity in microbial communities. Seed moisture and winter mean annual temperature (WMAT) had significant impacts on seed microbiota, while WMAT, total carbon, available potassium, available phosphorus, aluminum, pH, and total nitrogen significantly determined the rhizosphere microbiota. Multiple functional pathways were found to be enriched in the seed or the rhizosphere microbiota, which, to some extent, explained the potential adaptation of bacterial communities to respective living habitats. The results presented here elucidate the composition and possible sources of rice seed microbiota, which is crucial for the health and productivity management in sustainable agriculture.

Plant Growth Enhancement using Rhizospheric Halotolerant Phosphate Solubilizing Bacterium Bacillus licheniformis QA1 and Enterobacter asburiae QF11 Isolated from Chenopodium quinoa Willd

Plant growth-promoting rhizobacteria represent a promising solution to enhancing agricultural productivity. Here, we screened phosphate solubilizing bacteria from the rhizospheric soil of Chenopodium quinoa Willd and assessed their plant-growth promoting rhizobacteria (PGPR) properties including production of indole-3-acetic acid (IAA), siderophores, hydrogen cyanide (HCN), ammonia and extracellular enzymes. We also investigated their tolerance to salt stress and their capacity to form biofilms. Two isolated strains, named QA1 and QF11, solubilized phosphate up to 346 mg/L, produced IAA up to 795.31 µg/mL, and tolerated up to 2 M NaCl in vitro. 16S rRNA and Cpn60 gene sequencing revealed that QA1 and QF11 belong to the genus Bacillus licheniformis and Enterobacter asburiae, respectively. In vivo, early plant growth potential showed that quinoa seeds inoculated either with QA1 or QF11 displayed higher germination rates and increased seedling growth. Under saline irrigation conditions, QA1 enhanced plant development/growth. Inoculation with QA1 increased leaf chlorophyll content index, enhanced P and K+ uptake and decreased plant Na+ uptake. Likewise, plants inoculated with QF11 strain accumulated more K+ and had reduced Na+ content. Collectively, our findings support the use of QA1 and QF11 as potential biofertilizers.

"ASURE": A multi-potential plant bioassay as a pre-determinative microbial efficiency testing tool for bioinoculant studies

Bioinoculant studies focusing on plant-microbe association hold immense importance for research in field of agriculture and plant science. Such plant-microbe associations are amongst the most complex and beneficial partnerships in nature. Research focused to explore favourable host-microbe relationship requires a contamination free, non-interceptive and easily manageable system where these interactions can be studied in real-time. Also a provision for efficient sample recovery to support a variety of analyses would be a definite advantage. The manuscript proposes a new multi-potential plant bioassay abbreviated “ASURE” inspired by hydroponics. ASURE is a robust system, providing a workable solution to challenges faced during in-vitro microcosm studies. Significance of this system is its plant growth supporting design, facilitating comparative assessment of PGPM treatment benefits to host plant while providing a closer real-time view of plant microbe association.

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ASURE serves as a testing tool to pre-determine the efficiency of various plant friendly microbes to develop them as future bioinoculants.

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ASURE accommodates 16 individual samples in a 12 × 12 cm space, ensures homogenous micro environment and facilitates continuous and undisturbed (real-time) monitoring of root and shoot growth.

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ASURE enables efficient sample recovery with zero loss during harvesting and no interception from substrate.

Impacts of plant growth promoters and plant growth regulators on rainfed agriculture

Demand for agricultural crop continues to escalate in response to increasing population and damage of prime cropland for cultivation. Research interest is diverted to utilize soils with marginal plant production. Moisture stress has negative impact on crop growth and productivity. The plant growth promoting rhizobacteria (PGPR) and plant growth regulators (PGR) are vital for plant developmental process under moisture stress. The current study was carried out to investigate the effect of PGPR and PGRs (Salicylic acid and Putrescine) on the physiological activities of chickpea grown in sandy soil. The bacterial isolates were characterized based on biochemical characters including Gram-staining, P-solubilisation, antibacterial and antifungal activities and catalases and oxidases activities and were also screened for the production of indole-3-acetic acid (IAA), hydrogen cyanide (HCN) and ammonia (NH₃). The bacterial strains were identified as Bacillus subtilis, Bacillus thuringiensis and Bacillus megaterium based on the results of 16S-rRNA gene sequencing. Chickpea seeds of two varieties (Punjab Noor-2009 and 93127) differing in sensitivity to drought were soaked for 3 h before sowing in fresh grown cultures of isolates. Both the PGRs were applied (150 mg/L), as foliar spray on 20 days old seedlings of chickpea. Moisture stress significantly reduced the physiological parameters but the inoculation of PGPR and PGR treatment effectively ameliorated the adverse effects of moisture stress. The result showed that chickpea plants treated with PGPR and PGR significantly enhanced the chlorophyll, protein and sugar contents. Shoot and root fresh (81%) and dry weights (77%) were also enhanced significantly in the treated plants. Leaf proline content, lipid peroxidation and antioxidant enzymes (CAT, APOX, POD and SOD) were increased in reaction to drought stress but decreased due to PGPR. The plant height (61%), grain weight (41%), number of nodules (78%) and pod (88%), plant yield (76%), pod weight (53%) and total biomass (54%) were higher in PGPR and PGR treated chickpea plants grown in sandy soil. It is concluded from the present study that the integrative use of PGPR and PGRs is a promising method and eco-friendly strategy for increasing drought tolerance in crop plants.

Characterization of plant growth-promoting bacteria associated with avocado trees (Persea americana Miller) and their potential use in the biocontrol of Scirtothrips perseae (avocado thrips)

Plants interact with a great variety of microorganisms that inhabit the rhizosphere or the epiphytic and endophytic phyllosphere and that play critical roles in plant growth as well as the biocontrol of phytopathogens and insect pests. Avocado fruit damage caused by the thrips species Scirtothrips perseae leads to economic losses of 12–51% in many countries. In this study, a screening of bacteria associated with the rhizosphere or endophytic phyllosphere of avocado roots was performed to identify bacterial isolates with plant growth-promoting activity in vitro assays with Arabidopsis seedlings and to assess the biocontrol activity of the isolates against Scirtothrips perseae. The isolates with beneficial, pathogenic and/or neutral effects on Arabidopsis seedlings were identified. The plant growth-promoting bacteria were clustered in two different groups (G1 and G3B) based on their effects on root architecture and auxin responses, particularly bacteria of the Pseudomonas genus (MRf4-2, MRf4-4 and TRf2-7) and one Serratia sp. (TS3-6). Twenty strains were selected based on their plant growth promotion characteristics to evaluate their potential as thrips biocontrol agents. Analyzing the biocontrol activity of S. perseae, it was identified that Chryseobacterium sp. shows an entomopathogenic effect on avocado thrips survival. Through the metabolic profiling of compounds produced by bacteria with plant growth promotion activity, bioactive cyclodipeptides (CDPs) that could be responsible for the plant growth-promoting activity in Arabidopsis were identified in Pseudomonas, Serratia and Stenotrophomonas. This study unravels the diversity of bacteria from the avocado rhizosphere and highlights the potential of a unique isolate to achieve the biocontrol of S. perseae.

A potential antifungal and growth-promoting bacterium Bacillus sp. KTMA4 from tomato rhizosphere

Plant growth-promoting rhizobacteria are indigenous beneficial bacteria that will enhance plant growth as well as suppress phytopathogens. In the present study, the isolate KTMA4 showed the highest inhibition against major phytopathogens of tomato; Fusarium oxysporum (66%) and Alternaria solani (54%) after seven days of incubation. Analysis of the 16S rRNA gene sequence revealed that the isolate KTMA4 is Bacillus cereus (MG547975). The isolate produced in vitro plants growth-promoting factors such as Indole-3-acetic acid, ammonia, catalase, siderophore and 1-aminocyclopropane-1-carboxylate deaminase and it has nitrogen fixation ability. The bacterial strain has also produced lytic enzymes such as amylase, cellulase, xylanase, lipase, and protease. Moreover, the bacterium Bacillus cereus KTMA4 effectively produced biofilm, biosurfactants and salt-tolerant (5% NaCl). The bacterium exhibited intrinsic antibiotic resistance. The in vivo studies using tomato plants grown from seeds treated with the bacterial strain KTMA4 demonstrated an enhancement in seed germination percentage (86.66 ± 2.88) and vigour index (637.5 ± 21.65) over the uninoculated control (germination percentage- 28.33 ± 2.88 and vigour index- 42.5 ± 4.33). 60 days of greenhouse study revealed that the bacterial isolate enhanced the plant growth significantly (P ≤ 0.05) compared to the uninoculated control and the treated plants. Therefore the study suggests that the newly isolated rhizosphere bacterial strain can be used as a potential biocontrol agent against a multitude of fungal pathogens as well as a biofertilizer inoculant for tomato cultivation.

Co-existence of Leclercia adecarboxylata (LSE-1) and Bradyrhizobium sp. (LSBR-3) in nodule niche for multifaceted effects and profitability in soybean production

The present study was designed with the objective of improving growth and nodulation of soybean [Glycine max (L.) Merill] with co-inoculation of native Bradyrhizobium sp. (LSBR-3) (KF906140) and non-rhizobial nodule endophytic diazotroph Leclercia adecarboxylata (LSE-1) (KX925974) with multifunctional plant growth promoting (PGP) traits in cereal based cropping system (Rice-Wheat). A total of 40 endophytic bacteria from cultivated and wild sp. of soybean were screened for multifarious PGP traits and pathogenicity test. Based on PGP traits, antagonistic activities and bio-safety test; L. adecarboxylata (LSE-1) was identified with 16 S rRNA gene sequencing along with the presence of nifH (nitrogen fixation) and ipdc (IAA production) genes. Dual inoculant LSE-1 and LSBR-3 increased indole acetic acid (IAA), P & Zn-solubilization, 1-aminocyclopropane-1-carboxylate deaminase (ACCD) activity, siderophore, biofilm formation and exo-polysaccharides in contrast to single inoculation treatment. Further, assessment of dual inoculant LSBR-3 + LSE-1 improved growth parameters, nodulation, soil enzymes activities, nutrient accumulation and yield as compared to single as well as un-inoculated control treatment under field conditions. Single inoculant LSBR-3 improved yield by 8.84% over control. Further, enhancement of 4.15% grain yield was noticed with LSBR-3 + LSE-1 over LSBR-3 alone treatment. Application of LSBR-3 + LSE-1 gave superior B:C ratio (1.29) and additional income approximately 116 USD ha-1 in contrast to control treatment. The present results thus, is the first report of novel endophytic diazotroph L. adecarboxylata (LSE-1) as PGPR from Indian conditions particularly in Punjab region for exploiting as potential PGPR along with Bradyrhizobium sp. (LSBR-3) in soybean.

A wastewater bacterium Bacillus sp. KUJM2 acts as an agent for remediation of potentially toxic elements and promoter of plant (Lens culinaris) growth

This study investigated the role of an allochthonous Gram-positive wastewater bacterium (Bacillus sp. KUJM2) selected through rigorous screening, for the removal of potentially toxic elements (PTEs; As, Cd, Cu, Ni) and promotion of plant growth under PTE-stress conditions. The dried biomass of the bacterial strain removed PTEs (5 mg L^-1) from water by 90.17-94.75 and 60.4-81.41%, whereas live cells removed 87.15-91.69 and 57.5-78.8%, respectively, under single-PTE and co-contaminated conditions. When subjected to a single PTE, the bacterial production of indole-3-acetic acid (IAA) reached the maxima with Cu (67.66%) and Ni (64.33%), but Cd showed an inhibitory effect beyond 5 mg L^-1 level. The multiple-PTE treatment induced IAA production only up to 5 mg L^-1 beyond which inhibition ensued. Enhanced germination rate, germination index and seed production of lentil plant (Lens culinaris) under the bacterial inoculation indicated the plant growth promotion potential of the microbial strain. Lentil plants, as a result of bacterial inoculation, responded with higher shoot length (7.1-27.61%), shoot dry weight (18.22-36.3%) and seed production (19.23-29.17%) under PTE-stress conditions. The PTE uptake in lentil shoots decreased by 67.02-79.85% and 65.94-78.08%, respectively, under single- and multiple-PTE contaminated conditions. Similarly, PTE uptake was reduced in seeds up to 72.82-86.62% and 68.68-85.94%, respectively. The bacteria-mediated inhibition of PTE translocation in lentil plant was confirmed from the translocation factor of the respective PTEs. Thus, the selected bacterium (Bacillus sp. KUJM2) offered considerable potential as a PTE remediating agent, plant growth promoter and regulator of PTE translocation curtailing environmental and human health risks.

Identification of Klebsiella Variicola T29A Genes Involved In Tolerance To Desiccation

Introduction:

Several plant-beneficial bacteria have the capability to promote the growth of plants through different mechanisms. The survival of such bacteria could be affected by environmental abiotic factors compromising their capabilities of phytostimulation. One of the limiting abiotic factors is low water availability.

Materials and Methods:

In extreme cases, bacterial cells can suffer desiccation, which triggers harmful effects on cells. Bacteria tolerant to desiccation have developed different strategies to cope with these conditions; however, the genes involved in these processes have not been sufficiently explored.Klebsiella variicolaT29A is a beneficial bacterial strain that promotes the growth of corn plants and is highly tolerant to desiccation. In the present work, we investigated genes involved in desiccation tolerance.

Results & Discussion:

As a result, a library of 8974 mutants of this bacterial strain was generated by random mutagenesis with mini-Tn5 transposon, and mutants that lost the capability to tolerate desiccation were selected. We found 14 sensitive mutants; those with the lowest bacterial survival rate contained mini-Tn5 transposon inserted into genes encoding a protein domain related to BetR, putative secretion ATPase and dihydroorotase. The mutant in the betR gene had the lowest survival; therefore, the mutagenized gene was validated using specific amplification and sequencing.

Conclusion:

Trans complementation with the wild-type gene improved the survival of the mutant under desiccation conditions, showing that this gene is a determinant for the survival ofK. variicolaT29A under desiccation conditions.

Data on draft genome sequence of Bacillus sp. strain MHSD28, a bacterial endophyte isolated from Dicoma anomala

Here, we present the draft genome sequence of Bacillus sp. strain MHSD28 which was sequenced, and assembled with a total length of 5,571,729 bp. The genome has 43 contigs, the largest contig with 1,785,042 bp, N₅₀ of 1,474,247 bp, G + C% content of 35.23%. The strain was isolated from surface sterilized leaves of Dicoma anomala, obtained in Limpopo province, South Africa. The genome has 5792 total genes which include 5701 protein coding sequences (CDS), 192 pseudogenes, 7 rRNA genes with 3 operons (5S, 16S and 23S), 79 tRNA genes and 5 noncoding RNA (ncRNA) genes. This whole genome shotgun project has been deposited in DDBJ/ENA/GenBank under accession number VHIV00000000. The version described in this paper is version VHIV01000000.

Exopolysaccharide producing rhizobacteria and their impact on growth and drought tolerance of wheat grown under rainfed conditions

The demand for agricultural crops continues to escalate with an increasing population. To meet this demand, marginal land can be used as a sustainable source for increased plant productivity. However, moisture stress not only affects crop growth and productivity but also induces plants’ susceptibility to various diseases. The positive role of plant growth hormone, salicylic acid (SA), on the defence systems of plants has been well documented. With this in mind, a combination of plant growth promoting rhizobacteria (PGPR) and SA was used to evaluate its performance on wheat grown under rainfed conditions (average moisture 10–14%). The selected bacterial strains were characterized for proline production, indole-3-acetic acid (IAA), hydrogen cyanide (HCN), ammonia (NH₃), and exopolysaccharides (EPS). Wheat seeds of two genotypes, Inqilab-91 (drought tolerant) and Shahkar-2013 (drought sensitive), which differed in terms of their sensitivity to drought stress, were soaked for three hours prior to sowing in 24-hour old cultures of the bacterial strains Planomicrobium chinense strain P1 (accession no. MF616408) and Bacillus cereus strain P2 (accession no. MF616406). SA was applied (150 mg/L), as a foliar spray on one-month-old wheat seedlings. A significant reduction in the physiological parameters was noted in the plants grown in rainfed conditions but the PGPR and SA treatment effectively ameliorated the adverse effects of moisture stress. The wheat plants treated with PGPR and SA showed significant increases in leaf protein and sugar contents and maintained higher chlorophyll content, chlorophyll fluorescence (fv/fm) and performance index (PI) under rainfed conditions. Leaf proline content, lipid peroxidation, and antioxidant enzyme activity were higher in the non-inoculated plants grown in rainfed conditions but significantly reduced in the inoculated plants of both genotypes. Integrative use of a combination of PGPR strains and SA appears to be a promising and eco-friendly strategy for reducing moisture stress in plants.

A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application

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Microbiota are important for plant growth, health and stress resilience.

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Inoculation with key microbiota members can improve plant traits.

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Tailored selection and delivery of microbial strains or consortia is required.

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Microbiome improvement may be achieved by appropriate agro-management practices.

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Plant breeding for improved interaction with microbiota will be of benefit.

Plants have evolved with a plethora of microorganisms having important roles for plant growth and health. A considerable amount of information is now available on the structure and dynamics of plant microbiota as well as on the functional capacities of isolated community members. Due to the interesting functional potential of plant microbiota as well as due to current challenges in crop production there is an urgent need to bring microbial innovations into practice. Different approaches for microbiome improvement exist. On the one hand microbial strains or strain combinations can be applied, however, field success is often variable and improvement is urgently required. Smart, knowledge-driven selection of microorganisms is needed as well as the use of suitable delivery approaches and formulations. On the other hand, farming practices or the plant genotype can influence plant microbiota and thus functioning. Therefore, selection of appropriate farming practices and plant breeding leading to improved plant-microbiome interactions are avenues to increase the benefit of plant microbiota. In conclusion, different avenues making use of a new generation of inoculants as well as the application of microbiome-based agro-management practices and improved plant lines could lead to a better use of the plant microbiome. This paper reviews the importance and functionalities of the bacterial plant microbiome and discusses challenges and concepts in regard to the application of plant-associated bacteria.

Engineering root microbiomes for healthier crops and soils using beneficial, environmentally safe bacteria

The Green Revolution developed new crop varieties, which greatly improved food security worldwide. However, the growth of these plants relied heavily on chemical fertilizers and pesticides, which have led to an overuse of synthetic fertilizers, insecticides, and herbicides with serious environmental consequences and negative effects on human health. Environmentally friendly plant-growth-promoting methods to replace our current reliance on synthetic chemicals and to develop more sustainable agricultural practices to offset the damage caused by many agrochemicals are proposed herein. The increased use of bioinoculants, which consist of microorganisms that establish synergies with target crops and influence production and yield by enhancing plant growth, controlling disease, and providing critical mineral nutrients, is a potential solution. The microorganisms found in bioinoculants are often bacteria or fungi that reside within either external or internal plant microbiomes. However, before they can be used routinely in agriculture, these microbes must be confirmed as nonpathogenic strains that promote plant growth and survival. In this article, besides describing approaches for discovering plant-growth-promoting bacteria in various environments, including phytomicrobiomes and soils, we also discuss methods to evaluate their safety for the environment and for human health.