Microbial communities play a pivotal role in the functioning of plants by influencing their physiology and development. While many members of the rhizosphere microbiome are beneficial to plant growth, also plant pathogenic microorganisms colonize the rhizosphere striving to break through the protective microbial shield and to overcome the innate plant defense mechanisms in order to cause disease. A third group of microorganisms that can be found in the rhizosphere are the true and opportunistic human pathogenic bacteria, which can be carried on or in plant tissue and may cause disease when introduced into debilitated humans. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, for the vast majority of rhizosphere microorganisms no knowledge exists. To enhance plant growth and health, it is essential to know which microorganism is present in the rhizosphere microbiome and what they are doing. Here, we review the main functions of rhizosphere microorganisms and how they impact on health and disease. We discuss the mechanisms involved in the multitrophic interactions and chemical dialogues that occur in the rhizosphere. Finally, we highlight several strategies to redirect or reshape the rhizosphere microbiome in favor of microorganisms that are beneficial to plant growth and health.

The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms

A variety of soil factors are known to increase nutrient availability and plant productivity. The most influential might be the organisms comprising the soil microbial community of the rhizosphere, which is the soil surrounding the roots of plants where complex interactions occur between the roots, soil, and microorganisms. Root exudates act as substrates and signaling molecules for microbes creating a complex and interwoven relationship between plants and the microbiome. While individual microorganisms such as endophytes, symbionts, pathogens, and plant growth promoting rhizobacteria are increasingly featured in the literature, the larger community of soil microorganisms, or soil microbiome, may have more far-reaching effects. Each microorganism functions in coordination with the overall soil microbiome to influence plant health and crop productivity. Increasing evidence indicates that plants can shape the soil microbiome through the secretion of root exudates. The molecular communication fluctuates according to the plant development stage, proximity to neighboring species, management techniques, and many other factors. This review seeks to summarize the current knowledge on this topic.

http://webdoc.agsci.colostate.edu/soilcrop/course/socr571_reading11.pdf

Manipulating the soil microbiome to increase soil health and plant fertility

Plant growth promoting rhizobacteria (PGPR) shows an important role in the sustainable agriculture industry. The increasing demand for crop production with a significant reduction of synthetic chemical fertilizers and pesticides use is a big challenge nowadays. The use of PGPR has been proven to be an environmentally sound way of increasing crop yields by facilitating plant growth through either a direct or indirect mechanism. The mechanisms of PGPR include regulating hormonal and nutritional balance, inducing resistance against plant pathogens, and solubilizing nutrients for easy uptake by plants. In addition, PGPR show synergistic and antagonistic interactions with microorganisms within the rhizosphere and beyond in bulk soil, which indirectly boosts plant growth rate. There are many bacteria species that act as PGPR, described in the literature as successful for improving plant growth. However, there is a gap between the mode of action (mechanism) of the PGPR for plant growth and the role of the PGPR as biofertilizer—thus the importance of nano-encapsulation technology in improving the efficacy of PGPR. Hence, this review bridges the gap mentioned and summarizes the mechanism of PGPR as a biofertilizer for agricultural sustainability.

https://www.mdpi.com/1420-3049/21/5/573/pdf

Role of Plant Growth Promoting Rhizobacteria in Agricultural Sustainability-A Review.

Root-colonizing non-pathogenic bacteria can increase plant resistance to biotic and abiotic stress factors. Bacterial inoculates have been applied as biofertilizers and can increase the effectiveness of phytoremediation. Inoculating plants with non-pathogenic bacteria can provide 'bioprotection' against biotic stresses, and some root-colonizing bacteria increase tolerance against abiotic stresses such as drought, salinity and metal toxicity. Systematic identification of bacterial strains providing cross-protection against multiple stressors would be highly valuable for agricultural production in changing environmental conditions. For bacterial cross-protection to be an effective tool, a better understanding of the underlying morphological, physiological and molecular mechanisms of bacterially mediated stress tolerance, and the phenomenon of cross-protection is critical. Beneficial bacteria-mediated plant gene expression studies under non-stress conditions or during pathogenic rhizobacteria-plant interactions are plentiful, but only few molecular studies on beneficial interactions under abiotic stress situations have been reported. Thus, here we attempt an overview of current knowledge on physiological impacts and modes of action of bacterial mitigation of abiotic stress symptoms in plants. Where available, molecular data will be provided to support physiological or morphological observations. We indicate further research avenues to enable better use of cross-protection capacities of root-colonizing non-pathogenic bacteria in agricultural production systems affected by a changing climate.

https://www.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-3040.2009.02028.x

Plant-rhizobacteria interactions alleviate abiotic stress conditions.

The role of mycorrhizae and plant growth promoting rhizobacteria (PGPR) in improving crop productivity under stressful environments.

Iron is one of the essential elements for a proper plant development. Providing plants with an accessible form of iron is crucial when it is scant or unavailable in soils. Chemical chelates are the only current alternative and are highly stable in soils, therefore, posing a threat to drinking water. The aim of this investigation was to quantify siderophores produced by two bacterial strains and to determine if these bacterial siderophores would palliate chlorotic symptoms of iron-starved tomato plants. For this purpose, siderophore production in MM9 medium by two selected bacterial strains was quantified, and the best was used for biological assay. Bacterial culture media free of bacteria (S) and with bacterial cells (BS), both supplemented with Fe were delivered to 12-week-old plants grown under iron starvation in hydroponic conditions; controls with full Hoagland solution, iron-free Hoagland solution and water were also conducted. Treatments were applied twice along the experiment, with a week in between. At harvest, plant yield, chlorophyll content and nutritional status in leaves were measured. Both the bacterial siderophore treatments significantly increased plant yield, chlorophyll and iron content over the positive controls with full Hoagland solution, indicating that siderophores are effective in providing Fe to the plant, either with or without the presence of bacteria. In summary, siderophores from strain Chryseobacterium C138 are effective in supplying Fe to iron-starved tomato plants by the roots, either with or without the presence of bacteria. Based on the amount of siderophores produced, an effective and economically feasible organic Fe chelator could be developed.

/pdf/bacterial-siderophores-efficiently-provide-iron-to-iron-4cf5yk9d7d.pdf

Bacterial siderophores efficiently provide iron to iron-starved tomato plants in hydroponics culture

The ability of four plant growth-promoting rhizobacteria, isolated in a previous study, to induce systemic resistance on Arabidopsis thaliana Col 0 against biotic and abiotic stress was evaluated All the bacteria enhanced protection against the foliar pathogen Pseudomonas syringae DC3000 and increased plant tolerance to salt stress (NaCl 60 mM) Bacillus sp strain L81 and Arthrobacter oxidans strain BB1 performed best with a decrease in the disease index of 612 and 523%, respectively, and a reduction in the mortality due to salt stress of 724 and 578%, respectively Additionally, significant differences were found in growth and photosynthesis, again, L81 and BB1 performed best either in normal or under stress conditions In order to elucidate the pathway elicited by these two strains to induce systemic resistance, experiments with the transgenic line of Arabidopsis thaliana NahG (defective in salicylic acid [SA]) and with the jar1 mutant (defective in jasmonic acid) were carried out Result

https://apsjournals.apsnet.org/doi/pdf/10.1094/PHYTO-98-6-0666

Protection Against Pathogen and Salt Stress by Four Plant Growth-Promoting Rhizobacteria Isolated from Pinus sp. on Arabidopsis thaliana

Use of two PGPR strains in the integrated management of blast disease in rice (Oryza sativa) in Southern Spain

A study of plant defensive systemic responses induced by three plant growth promoting rhizobacteria (PGPR) on Arabidopsis thaliana Col 0 against Pseudomonas syringae pv. tomato DC3000 at t...

https://apsjournals.apsnet.org/doi/pdf/10.1094/PHYTO-98-4-0451

Systemic disease protection elicited by plant growth promoting rhizobacteria strains: relationship between metabolic responses, systemic disease protection, and biotic elicitors.

Aims: In this study, 10 putative plant growth-promoting rhizobacteria (PGPR) were assayed for their ability to improve Pinus pinea growth and mycorrhization.



Methods and Results:  After an inoculation assay, except for two, all strains stimulated plant growth. All bacteria altered rhizosphere microbial communities as revealed by phospholipid fatty acid analysis; associating plant growth promotion with a decrease in biological diversity. Three strains were tested for their ability to enhance pine mycorrhization with wild fungi species. Only strain BB1 increased the total number of mycorrhizal root tips. Mycorrhizas present in the roots of each treatment were identified by ribosomal RNA sequencing and denaturing gradient gel electrophoresis analysis, detecting specificity between mycorrhizal species colonizing the roots and the inoculated PGPR.



Conclusions:  In conclusion, BB1 appears to be a good candidate to be developed into a biofertilizer directed to enhance pine growth and mycorrhization, which should result in a better establishment rate for plants used in reforestation.



Significance and Impact of the Study:  This study shows the potential of PGPR to improve fitness of forest tree specie. Moreover, the specificity between the bacteria inoculated and the mycorrhiza that the plant selects involve a potential biotechnological use in production of value-added fungi.

Effect of inoculation with putative plant growth‐promoting rhizobacteria isolated from Pinus spp. on Pinus pinea growth, mycorrhization and rhizosphere microbial communities

B. Ramos Solano

Papers

Bacterial siderophores efficiently provide iron to iron-starved tomato plants in hydroponics culture

Protection Against Pathogen and Salt Stress by Four Plant Growth-Promoting Rhizobacteria Isolated from Pinus sp. on Arabidopsis thaliana

Use of two PGPR strains in the integrated management of blast disease in rice (Oryza sativa) in Southern Spain

Systemic disease protection elicited by plant growth promoting rhizobacteria strains: relationship between metabolic responses, systemic disease protection, and biotic elicitors.

Effect of inoculation with putative plant growth‐promoting rhizobacteria isolated from Pinus spp. on Pinus pinea growth, mycorrhization and rhizosphere microbial communities