Faina Kamilova

Plant-Growth-Promoting Rhizobacteria

Several microbes promote plant growth, and many microbial products that stimulate plant growth have been marketed. In this review we restrict ourselves to bacteria that are derived from and exert this effect on the root. Such bacteria are generally designated as PGPR (plant-growth-promoting rhizobacteria). The beneficial effects of these rhizobacteria on plant growth can be direct or indirect. This review begins with describing the conditions under which bacteria live in the rhizosphere. To exert their beneficial effects, bacteria usually must colonize the root surface efficiently. Therefore, bacterial traits required for root colonization are subsequently described. Finally, several mechanisms by which microbes can act beneficially on plant growth are described. Examples of direct plant growth promotion that are discussed include (a) biofertilization, (b) stimulation of root growth, (c) rhizoremediation, and (d) plant stress control. Mechanisms of biological control by which rhizobacteria can promote plant growth indirectly, i.e., by reducing the level of disease, include antibiosis, induction of systemic resistance, and competition for nutrients and niches.

Organic acids, sugars, and L-tryptophane in exudates of vegetables growing on stonewool and their effects on activities of rhizosphere bacteria.

The influence of stonewool substrate on the exudation of the major soluble carbon nutrients and of the auxin precursor tryptophane for Pseudomonas biocontrol agents was studied. To this end, the composition of the organic acids and sugars, as well that of tryptophane, of axenically collected exudates of seed, seedlings, and roots of tomato, cucumber, and sweet pepper was determined. The major results were as follows. i) The total amount of organic acid is much higher than that of total sugar. ii) Exudation of both organic acids and sugars increases during plant growth. iii) Citric, succinic, and malic acids represent the major organic acids, whereas fructose and glucose are the major sugars. iv) Compared with glass beads as a neutral substrate, stonewool substantially stimulates exudation of organic acids and sugars. v) It appeared that enhanced root-tip-colonizing bacteria isolated previously from the rhizosphere of tomato and cucumber grow much better in minimal medium with citrate as the sole carbon source than other, randomly selected rhizobacteria do. This indicates that the procedure which selects for excellent root-tip colonizers enriches for strains which utilize the major exudate carbon source citrate. vi) The content of L-tryptophane, the direct precursor of auxin, is approximately 60-fold higher in seedling exudates of tomato and sweet pepper than in cucumber seedling exudates, indicating a higher possibility of plant growth stimulation after inoculation with auxin-producing rhizobacteria for tomato and sweet pepper crops than for cucumber. However, the biocontrol strain Pseudomonas fluorescens WCS365, which is able to convert tryptophane into auxin, did not stimulate growth of these three crops. In contrast, this strain did stimulate growth of roots of radish, a plant which exudes nine times more tryptophane than tomato does.

High incidence of plant growth-stimulating bacteria associated with the rhizosphere of wheat grown on salinated soil in Uzbekistan.

Soil salinization is increasing steadily in many parts of the world and causes major problems for plant productivity. Under these stress conditions, root-associated beneficial bacteria can help improve plant growth and nutrition. In this study, salt-tolerant bacteria from the rhizosphere of Uzbek wheat with potentially beneficial traits were isolated and characterized. Eight strains which initially positively affect the growth of wheat plants in vitro were investigated in detail. All eight strains are salt tolerant and have some of the following plant growth-beneficial properties: production of auxin, HCN, lipase or protease and wheat growth promotion. Using sequencing of part of the 16S rDNA, the eight new isolates were identified as Acinetobacter (two strains), Pseudomonas aeruginosa, Staphylococcus saprophyticus, Bacillus cereus, Enterobacter hormaechei, Pantoae agglomerans and Alcaligenes faecalis. All these strains are potential human pathogens. Possible reasons for why these bacteria present in the rhizosphere and establish there are discussed.

Effects of the tomato pathogen Fusarium oxysporum f. sp. radicis-lycopersici and of the biocontrol bacterium Pseudomonas fluorescens WCS365 on the composition of organic acids and sugars in tomato root exudate.

The effects of the pathogenic fungus Fusarium oxysporum f. sp. radicis-lycopersici and of the bacterial biocontrol strain Pseudomonas fluorescens WCS365, and of both microbes, on the amounts and composition of root exudate components of tomato plants grown in a gnotobiotic stonewool substrate system were studied. Conditions were selected under which introduction of F. oxysporum f. sp. radicis-lycopersici caused severe foot and root rot, whereas inoculation of the seed with P. fluorescens WCS365 decreased the percentage of diseased plants from 96 to 7%. This is a much better disease control level than was observed in potting soil. Analysis of root exudate revealed that the presence of F. oxysporum f. sp. radicis-lycopersici did not alter the total amount of organic acids, but that the amount of citric acid decreased and that of succinic acid increased compared with the nontreated control. In contrast, in the presence of the P. fluorescens biocontrol strain WCS365, the total amount of organic acid increased, mainly due to a strong increase of the amount of citric acid, whereas the amount of succinic acid decreased dramatically. Under biocontrol conditions, when both microbes are present, the content of succinic acid decreased and the level of citric acid was similar to that in the nontreated control. The amount of sugar was approximately half that of the control sample when either one of the microbes was present alone or when both were present. Analysis of the interactions between the two microbes grown together in sterile tomato root exudate showed that WCS365 inhibited multiplication of F. oxysporum f. sp. radicis-lycopersici, whereas the fungus did not affect the number of CFU of the bacterium.

Bacteria able to control foot and root rot and to promote growth of cucumber in salinated soils

The aim of the present work was to test known bacterial plant growth-promoting strains for their ability to promote cucumber plant growth in salinated soil and to improve cucumber fruit yield by protecting these plants against soil-borne pathogens. Fifty-two plant-beneficial bacterial strains were evaluated for their ability to protect plants against cucumber foot and root rot after bacterization of the seeds and infestation of salinated soil with the isolated Fusarium solani pathogen. Based on the results of initial screenings, five efficient strains were selected, namely Serratia plymuthica RR-2-5-10, Stenotrophomonas rhizophila e-p10, Pseudomonas fluorescens SPB2145, Pseudomonas extremorientalis TSAU20, and P. fluorescens PCL1751. All five strains are salt tolerant since they grow well in a medium to which 3% NaCl was added. Infestation of the soil with F. solani resulted in an increase of the percentage of diseased plants from 17 to 54. Priming of seedlings with the five selected bacterial strains reduced this proportion to as low as 10%. In addition, in the absence of an added pathogen, all five strains showed a significant stimulatory effect on cucumber plant growth, increasing the dry weight of whole cucumber plants up to 62% in comparison to the non-bacterized control. The strains also increased cucumber fruit yield in greenhouse varying from 9% to 32%. We conclude that seed priming with the selected microbes is a very promising approach for improving horticulture in salinated soils. Moreover, allochthonous strains isolated from non-salinated soil, from a moderate or even cold climate, and from other plants than cucumber, functioned as well as autochthonous strains as cucumber-beneficial bacteria in salinated Uzbek soils. These results show that these plant-beneficial strains are robust and they strongly suggest they can also be used successfully in case the climate gets warmer and the soils will become more salinated. Finally, the mechanisms by which they may exert their plant-beneficial action are discussed.

Selection of bacteria able to control Fusarium oxysporum f. sp. radicis-lycopersici in stonewool substrate

Aims:  Tomato foot and root rot (TFRR), caused by Fusariumoxysporum f. sp. radicis‐lycopersici (Forl), is an economically important disease of tomato. The aim of this study was to develop an efficient protocol for the isolation of bacteria, which controls TFRR based on selection of enhanced competitive root‐colonizing bacteria from total rhizosphere soil samples.

Characterization of Bacillus subtilis HC8, a novel plant‐beneficial endophytic strain from giant hogweed

Thirty endophytic bacteria were isolated from various plant species growing near Saint‐Petersburg, Russia. Based on a screening for various traits, including plant‐beneficial properties and DNA fragment patterns, potential siblings were removed. The remaining isolates were taxonomically identified using 16S rDNA sequences and potential human and plant pathogens were removed. The remaining strains were tested for their ability to promote radish root growth and to protect tomato plants against tomato foot and root rot. One strain, Bacillus subtilis HC8, isolated from the giant hogweed Heracleum sosnowskyi Manden, significantly promoted plant growth and protected tomato against tomato foot and root rot. Metabolites possibly responsible for these plant‐beneficial properties were identified as the hormone gibberellin and (lipo)peptide antibiotics respectively. The antibiotic properties of strain HC8 are similar to those of the commercially available plant‐beneficial strain Bacillus amyloliquefaciens FZB42. However, thin layer chromatography profiles of the two strains differ. It is speculated that endophytes such as B. subtilis HC8 contribute to the fast growth of giant hogweed.

Plant Growth-Promoting Bacteria: Fundamentals and Exploitation

Many plant-beneficial rhizobacteria have been described in the literature. These have been isolated from the plant root, where they usually live under conditions of nutrient starvation and at a low pH. In order to be beneficial, they usually need to colonize the root efficiently. Moreover, they have to multiply fast in order to be competitive with other organisms. To this end, traits such as chemotaxis to, and fast utilization of, the nutrients secreted by the root are required. These nutrients mainly consist of organic acids and sugars. Some plant-beneficial bacteria promote plant growth directly, e.g., by making nutrients available to the plant or by stimulating the growth of plants by production of hormones. Other plant-beneficial bacteria stimulate plant growth indirectly, e.g., by degrading environmental pollutants which inhibit plant growth or by controlling the growth of pathogens.

Biocontrol strain Pseudomonas fluorescens WCS365 inhibits germination of Fusarium oxysporum spores in tomato root exudate as well as subsequent formation of new spores.

Fusarium oxysporum f.sp.radicis-licopersici (Forl) is a soilborne pathogenic fungus which can cause tomato foot and root rot (TFRR). Tomato root exudate is a good source of nutrients for both Forl and the TFRR-suppressing biocontrol bacterium Pseudomonas fluorescens strain WCS365. Incubation of Forl microconidia in tomato root exudate stimulates their germination. This phenomenon is observed, to a lesser extent, upon incubation in plant nutrient solution supplemented with citrate or glucose, the major organic acid and sugar components, respectively, of tomato root exudate. Here we show that induction of germination of microconidia is significantly reduced in the presence of P. fluorescens WCS365 in all tested media. Scanning electron microscopy revealed that P. fluorescens WCS365 colonizes developing hyphae. Efficient colonization correlates with low nutrient availability. Eventually, new microconidia are formed. The presence of P. fluorescens WCS365 reduces the number of newly formed microconidia. This reduction does not depend on physical contact between bacteria and hyphae. We discuss that the ability of P. fluorescens WCS365 to slow down the processes of microconidia germination and development of new microconidia of the phytopathogen, and therefore the ability to reduce fungal dissemination, is likely to contribute to the biocontrol efficacy of this strain.

Genome Analysis of Pseudomonas fluorescens PCL1751: A Rhizobacterium that Controls Root Diseases and Alleviates Salt Stress for Its Plant Host.

Pseudomonas fluorescens PCL1751 is a rod-shaped Gram-negative bacterium isolated from the rhizosphere of a greenhouse-grown tomato plant in Uzbekistan. It controls several plant root diseases caused by Fusarium fungi through the mechanism of competition for nutrients and niches (CNN). This mechanism does not rely on the production of antibiotics, so it avoids the concerns of resistance development and is environmentally safe. Additionally, this bacterium promotes plant growth by alleviating salt stress for its plant host. To investigate the genetic mechanisms that may explain these observations, we determined the complete genome sequence of this bacterium, examined its gene content, and performed comparative genomics analysis with other Pseudomonas strains. The genome of P. fluorescens PCL1751 consisted of one circular chromosome that is 6,143,950 base-pairs (bp) in size; no plasmid was found. The annotation included 19 rRNA, 70 tRNA, and 5,534 protein-coding genes. The gene content analysis identified a large number of genes involved in chemotaxis and motility, colonization of the rhizosphere, siderophore biosynthesis, and osmoprotectant production. In contrast, the pathways involved in the biosynthesis of phytohormones or antibiotics were not found. Comparison with other Pseudomonas genomes revealed extensive variations in their genome size and gene content. The presence and absence of secretion system genes were highly variable. As expected, the synteny conservation among strains decreased as a function of phylogenetic divergence. The integration of prophages appeared to be an important driver for genome rearrangements. The whole-genome gene content analysis of this plant growth-promoting rhizobacterium (PGPR) provided some genetic explanations to its phenotypic characteristics. The extensive and versatile substrate utilization pathways, together with the presence of many genes involved in competitive root colonization, provided further support for the finding that this strain achieves biological control of pathogens through effective competition for nutrients and niches.