Rhizosphere Of Crop Plants Research Articles

Pseudomonas cucumis sp. nov., isolated from the rhizosphere of crop plants.

Two bacterial strains, FP1935T and FP1962, were isolated from the rhizosphere soil of cucumber and Chieh-qua plants, respectively, in Jilin Province, PR China. These strains were Gram-stain-negative, aerobic, rod-shaped and motile with one or two polar flagella. Analysis of the 16S rRNA gene sequences revealed that they represented members of the genus Pseudomonas, with the highest similarity to Pseudomonas silesiensis A3T (99.45 %), Pseudomonas frederiksbergensis JAJ28T (99.45 %), Pseudomonas mandelii NBRC 103147T (99.38 %), Pseudomonas piscium P50T (99.27 %) and Pseudomonas meliae CFBP 3225T (99.18 %). The DNA G+C contents of FP1935T and FP1962 were 58.99 mol% and 58.98 mol%, respectively. The results of in silico genome-based analyses indicated that these strains were distinct from other species in the genus Pseudomonas, as the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were below the recommended thresholds of 95 % (ANI) and 70 % (dDDH) for prokaryotic species delineation, with no values exceeding 94.1 and 55.8 %, respectively, compared with any other related species. The results of phenotypic and chemotaxonomic tests confirmed their differentiation from their closest relatives. The fatty acid profiles of both strains mainly consisted of summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C12 : 0 and C16 : 0. The predominant respiratory quinone was Q-9. Polar lipids include phosphatidylethanolamine, unidentified aminophospholipids, unidentified lipids and an unidentified phospholipid. On the basis of these phenotypic and genotypic results, we propose the name Pseudomonas cucumis sp. nov. for these novel strains. The type strain is FP1935T (=ACCC 62445T=JCM 35690T).

Fungi That Promote Plant Growth in the Rhizosphere Boost Crop Growth.

The fungi species dwelling in the rhizosphere of crop plants, revealing functions that endeavor sustainability of the plants, are commonly referred to as 'plant-growth-promoting fungi' (PGPF). They are biotic inducers that provide benefits and carry out important functions in agricultural sustainability. The problem encountered in the agricultural system nowadays is how to meet population demand based on crop yield and protection without putting the environment and human and animal health at risk based on crop production. PGPF including Trichoderma spp., Gliocladium virens, Penicillium digitatum, Aspergillus flavus, Actinomucor elegans, Podospora bulbillosa, Arbuscular mycorrhizal fungi, etc., have proven their ecofriendly nature to ameliorate the production of crops by improving the growth of the shoots and roots of crop plants, the germination of seeds, the production of chlorophyll for photosynthesis, and the abundant production of crops. PGPF's potential mode of action is as follows: the mineralization of the major and minor elements required to support plants' growth and productivity. In addition, PGPF produce phytohormones, induced resistance, and defense-related enzymes to inhibit or eradicate the invasion of pathogenic microbes, in other words, to help the plants while encountering stress. This review portrays the potential of PGPF as an effective bioagent to facilitate and promote crop production, plant growth, resistance to disease invasion, and various abiotic stresses.

Microbial expression profiles in the rhizosphere of two maize lines differing in N use efficiency

Study of the microbial expression profile in the rhizosphere of two contrasting maize lines, differing in the Nitrogen Use efficiency (NUE). The Lo5 and T250 inbred maize characterized by high and low NUE, respectively, were grown in rhizoboxes allowing precise sampling of rhizosphere and bulk soils. We conducted metatranscriptomic of rhizosphere and bulk soil by m-RNA sequencing. High activity of bacteria was observed compared to archaea and fungi in both rhizosphere and bulk soils of both maize lines. Proteobacteria and Actinobacteria were involved in all processes, while significant shifts occurred in the expression of Bacteroidetes, Chloroflexi, Firmicutes, Acidobacteria, Cyanobacteria, archaea and fungi, indicating their possible role in specific processes occurring in rhizosphere of two maize lines. Maize plants with different NUE induced changes in microbial processes, especially in N cycling, with high NUE maize favouring ammonification and nitrification processes and low NUE maize inducing expression of genes encoding for denitrifying process, likely favoured by longer N residence time in the rhizosphere. Overall our results showed that maize lines with different NUE shaped not only microbial communities but also conditioned the microbial functions and the N cycle in their rhizosphere. While the plant NUE is genetically determined and an inherent plant physiological trait, it also stimulates changes in the microbial community composition and gene expression in the rhizosphere, favouring microbial processes that mineralize and oxidize N in the high NUE maize. These results can improve our understanding on plant-microbe interaction in the rhizosphere of crop plants with potential applications for improving the management practices of the agro-ecosystems.

CuO and ZnO Nanoparticles Modify Interkingdom Cell Signaling Processes Relevant to Crop Production.

As the world population increases, strategies for sustainable agriculture are needed to fulfill the global need for plants for food and other commercial products. Nanoparticle formulations are likely to be part of the developing strategies. CuO and ZnO nanoparticles (NPs) offer potential as fertilizers, as they provide bioavailable essential metals, and as pesticides, because of dose-dependent toxicity. Effects of these metal oxide NPs on rhizosphere functions are the focus of this review. These NPs at doses of ≥10 mg metal/kg change the production of key metabolites involved in plant protection in a root-associated microbe, Pseudomonas chlororaphis O6. Altered synthesis occurs in the microbe for phenazines, which function in plant resistance to pathogens, the pyoverdine-like siderophore that enhances Fe bioavailability in the rhizosphere and indole-3-acetic acid affecting plant growth. In wheat seedlings, reprogramming of root morphology involves increases in root hair proliferation (CuO NPs) and lateral root formation (ZnO NPs). Systemic changes in wheat shoot gene expression point to altered regulation for metal stress resilience as well as the potential for enhanced survival under stress commonly encountered in the field. These responses to the NPs cross kingdoms involving the bacteria, fungi, and plants in the rhizosphere. Our challenge is to learn how to understand the value of these potential changes and successfully formulate the NPs for optimal activity in the rhizosphere of crop plants. These formulations may be integrated into developing practices to ensure the sustainability of crop production.

ACC deaminase and IAA producing growth promoting bacteria from the rhizosphere soil of tropical rice plants

Beneficial plant-associated bacteria play a key role in supporting and/or promoting plant growth and health. Plant growth promoting bacteria present in the rhizosphere of crop plants can directly affect plant metabolism or modulate phytohormone production or degradation. We isolated 355 bacteria from the rhizosphere of rice plants grown in the farmers' fields in the coastal rice field soil from five different locations of the Ganjam district of Odisha, India. Six bacteria producing both ACC deaminase (ranging from 603.94 to 1350.02 nmol α-ketobutyrate mg(-1) h(-1) ) and indole acetic acid (IAA; ranging from 10.54 to 37.65 μM ml(-1) ) in pure cultures were further identified using polyphasic taxonomy including BIOLOG((R)) , FAME analysis and the 16S rRNA gene sequencing. Phylogenetic analyses of the isolates resulted into five major clusters to include members of the genera Bacillus, Microbacterium, Methylophaga, Agromyces, and Paenibacillus. Seed inoculation of rice (cv. Naveen) by the six individual PGPR isolates had a considerable impact on different growth parameters including root elongation that was positively correlated with ACC deaminase activity and IAA production. The cultures also had other plant growth attributes including ammonia production and at least two isolates produced siderophores. Study indicates that presence of diverse rhizobacteria with effective growth-promoting traits, in the rice rhizosphere, may be exploited for a sustainable crop management under field conditions.

Selenium Mobilization by Pseudomonas aeruginosa (SNT-SG1) Isolated from Seleniferous Soils from India

Selenium (Se) is a metalloid required at trace concentrations for normal metabolic activities of the cell. The bioavailable forms viz., selenate and selenite have been found in localized high concentrations in seleniferous environments. Studies are in progress on bacterial strains that were isolated from one such location in the North-West region of Punjab, India. A facultative anaerobe, identified as Pseudomonas aeruginosa by 16S rRNA gene homology, was isolated from the rhizosphere of crop plants from this region and was examined for selenium mobilization potential in the presence of selenium oxyanions. The isolate was observed to reduce 53 and 21% of sodium selenite and selenate to elemental selenium, respectively, and volatilize 4.7 and 5.1% within 72-hour duration. This is one of the few selenium tolerant aerobic bacteria isolated and reported from tropical seleniferous soils from India, and the first to show volatilization potential. These organisms are being considered for bioaugmenting Se-impacted soils for enhanced Se mobilization and removal.

Small RNA-dependent Expression of Secondary Metabolism Is Controlled by Krebs Cycle Function in Pseudomonas fluorescens

Pseudomonas fluorescens CHA0, an antagonist of phytopathogenic fungi in the rhizosphere of crop plants, elaborates and excretes several secondary metabolites with antibiotic properties. Their synthesis depends on three small RNAs (RsmX, RsmY, and RsmZ), whose expression is positively controlled by the GacS-GacA two-component system at high cell population densities. To find regulatory links between primary and secondary metabolism in P. fluorescens and in the related species Pseudomonas aeruginosa, we searched for null mutations that affected central carbon metabolism as well as the expression of rsmY-gfp and rsmZ-gfp reporter constructs but without slowing down the growth rate in rich media. Mutation in the pycAB genes (for pyruvate carboxylase) led to down-regulation of rsmXYZ and secondary metabolism, whereas mutation in fumA (for a fumarase isoenzyme) resulted in up-regulation of the three small RNAs and secondary metabolism in the absence of detectable nutrient limitation. These effects required the GacS sensor kinase but not the accessory sensors RetS and LadS. An analysis of intracellular metabolites in P. fluorescens revealed a strong positive correlation between small RNA expression and the pools of 2-oxoglutarate, succinate, and fumarate. We conclude that Krebs cycle intermediates (already known to control GacA-dependent virulence factors in P. aeruginosa) exert a critical trigger function in secondary metabolism via the expression of GacA-dependent small RNAs.

Evaluation of <i>Verticillium chlamydosporium</i> and <i>Arthrobotrys oligospora</i> for biological control of <i>Meloidogyne incognita</i> in celery and tomato

The ability of nematode trapping fungi and egg-parasitising fungi to colonize and persist in the rhizosphere of crop plants is thought to be an important factor influencing the success of biological control of root infecting nematodes. In this study, two strains of an egg parasitic fungus Verticillium chlamydosporium (Vc- 10 and Vc-2M) and one isolate of the nematode-trapping fungus Arthrobotrys oligospora were evaluated to determine their pathogenicity to Meloidogyne incognita and persistence in the rhizosphere of celery (Apium graveolus L.) and tomato(Lycopersicon esculentum L.) plants in a greenhouse experiment. The isolates tested differed significantly (P≤0.05) in their pathogenicity to M. incognita and survival in the rhizosphere. Isolate Vc-10 of V. chlamydosporium was the most virulent pathogen of the nematode. Root galling was lowest (P≤0.05) in tomato plants treated with the isolate Vc-10 (2.2); pots treated with this isolate had the lowest final soil population of infective juveniles; there was a 62.2% and 98.5% infections of eggs and egg-masses respectively by Vc-10 on tomato plants. Isolates Vc-10 and Vc-2M of V. chlamydosporium persisted in the soil and could be re-isolated from the rhizosphere and roots of tomato plants at least 16 weeks after soil infestation. The final inoculum density was, however, higher (P≤0.05) for Vc-10 (1.35×105 cfu/g soil) than Vc-2M (9.25×104 cfu/g soil). A. oligospora on the other hand did not give any significant (P≤0.05) control of the nematode on both crops, there was severe galling on the roots of celery plants (7.4) and tomato plants (6.3) treated with this biological control agent. A. oligospora could not be re-isolated from the plant rhizosphere sixteen weeks after soil infestation. Lack of nematode control on both crops by A. oligospora was attributed to its poor or no establishment in the plant rhizosphere. The fact that it could not be reisolated from the rhizosphere may imply that the fungus did not survive in the rhizosphere of the test plants. Keywords: Verticillium, Arthrobotrys, Meloidogyne, rhizosphere, persistence, root-knots, chlamydospores. J. Trop. Microbiol. Biotechnol. Vol. 3 (2) 2007: pp. 51-58

Stimulatory effects of compounds present in the rhizosphere on natural transformation of Acinetobacter sp. BD413 in soil

The stimulation of natural transformation of Acinetobacter sp. BD413(pFG4) cells by various organic compounds naturally found in the rhizosphere of crop plants was determined in sterile and non-sterile soil. Stimulation of bacterial competence by the organic acids, amino acids, sugars and inorganic fertilizers, was monitored by the transformation frequencies obtained with added cell lysates of Acinetobacter sp. carrying a kanamycin resistance gene ( nptII). Clear differences in the capability of the organic compounds to induce gene capture were detected. In sterile soil, most of the organic compounds used stimulated the appearance of transformants. Fewer compounds were able to induce transformation in non-sterile soil, and a high-P salt supplementation was found to be required for detectable gene transfer. The transformation frequencies in non-sterile soil were, however, if found, on average less than 10-fold reduced compared to those obtained under sterile soil conditions. Of the organic acids and amino acids applied in non-sterile soil, acetate, lactate and alanine gave the highest transformation frequencies, i.e. 1 to 2×10 −6. Of the sugars used, only glucose produced a few transformants in non-sterile soil (2.5×10 −7). Mixtures of the organic and amino acids, or the sugars, and the high-P salts produced the highest transformation frequencies in non-sterile soil, of 4.4 to 6.6×10 −6. The addition of fertilizers had a less pronounced effect on the transformation frequencies. We conclude that many of the compounds exuded into the rhizosphere of agriculturally grown plants are able to stimulate natural transformation of Acinetobacter sp. BD413(pFG4) cells in sterile silt loam soil, and that the presence of both carbon sources and inorganic salts is required for detectable gene transfer in non-sterile silt loam.

Microbial diversity in the rhizosphere of corn grown under conventional and low-input systems

Microbial processes within the rhizosphere of crop plants are crucial to agriculture. The relation of soil microbial community diversity to cropping system, yield, and soil quality are unclear at present. The Farming Systems Trial at the Rodale Institute Research Center, Kutztown, PA, is a 15-year study in which a conventional corn-soybean rotation has been compared with low-input systems (i.e. animal manure or legumes as nitrogen sources). The effects of the cropping systems on diversity of fast-growing, aerobic, culturable bacteria and fungi were conducted in 1994 by taking 84 cores in between corn plants in June, July, and August. Rhizosphere bacteria and fungi were extracted, plated, and counted. Approximately 6000 bacteria were identified by fatty acid methyl ester analysis, while 18000 fungi were identified by microscopic examination of spores. Microbial diversity and evenness were calculated using several different methods. Total counts, diversity, and evenness were not significantly different for the three cropping systems. These results suggest that conventional agricultural practices may maintain high indices of microbial diversity in the rhizosphere. The functional significance of this needs to be investigated.