Iftikhar Ahmed

SOIL BENEFICIAL BACTERIA AND THEIR ROLE IN PLANT GROWTH PROMOTION: A REVIEW

Soil bacteria are very important in biogeochemical cycles and have been used for crop production for decades. Plant–bacterial interactions in the rhizosphere are the determinants of plant health and soil fertility. Free-living soil bacteria beneficial to plant growth, usually referred to as plant growth promoting rhizobacteria (PGPR), are capable of promoting plant growth by colonizing the plant root. PGPR are also termed plant health promoting rhizobacteria (PHPR) or nodule promoting rhizobacteria (NPR). These are associated with the rhizosphere, which is an important soil ecological environment for plant–microbe interactions. Symbiotic nitrogen-fixing bacteria include the cyanobacteria of the genera Rhizobium, Bradyrhizobium, Azorhizobium, Allorhizobium, Sinorhizobium and Mesorhizobium. Free-living nitrogen-fixing bacteria or associative nitrogen fixers, for example bacteria belonging to the species Azospirillum, Enterobacter, Klebsiella and Pseudomonas, have been shown to attach to the root and efficiently colonize root surfaces. PGPR have the potential to contribute to sustainable plant growth promotion. Generally, PGPR function in three different ways: synthesizing particular compounds for the plants, facilitating the uptake of certain nutrients from the soil, and lessening or preventing the plants from diseases. Plant growth promotion and development can be facilitated both directly and indirectly. Indirect plant growth promotion includes the prevention of the deleterious effects of phytopathogenic organisms. This can be achieved by the production of siderophores, i.e. small metal-binding molecules. Biological control of soil-borne plant pathogens and the synthesis of antibiotics have also been reported in several bacterial species. Another mechanism by which PGPR can inhibit phytopathogens is the production of hydrogen cyanide (HCN) and/or fungal cell wall degrading enzymes, e.g., chitinase and ß-1,3-glucanase. Direct plant growth promotion includes symbiotic and non-symbiotic PGPR which function through production of plant hormones such as auxins, cytokinins, gibberellins, ethylene and abscisic acid. Production of indole-3-ethanol or indole-3-acetic acid (IAA), the compounds belonging to auxins, have been reported for several bacterial genera. Some PGPR function as a sink for 1-aminocyclopropane-1-carboxylate (ACC), the immediate precursor of ethylene in higher plants, by hydrolyzing it into α-ketobutyrate and ammonia, and in this way promote root growth by lowering indigenous ethylene levels in the micro-rhizo environment. PGPR also help in solubilization of mineral phosphates and other nutrients, enhance resistance to stress, stabilize soil aggregates, and improve soil structure and organic matter content. PGPR retain more soil organic N, and other nutrients in the plant–soil system, thus reducing the need for fertilizer N and P and enhancing release of the nutrients.

Lysinibacillus parviboronicapiens sp. nov., a low-boron-containing bacterium isolated from soil.

A spore-forming, Gram-positive-staining, motile, rod-shaped and low-boron-containing bacterium was isolated from soil. The strain, designated BAM-582(T), can tolerate 6 % (w/v) NaCl and 50 mM boron, but optimal growth was observed without addition of boron or NaCl. The optimum temperature and pH for growth were 30 degrees C (range 10-37 degrees C) and pH 7 (range pH 6-8). A comparative analysis of the 16S rRNA gene sequence demonstrated that the isolated strain was closely related to Lysinibacillus fusiformis DSM 2898(T) (97.7 % similarity) and Lysinibacillus sphaericus IAM 13420(T) (98.2 %). Levels of DNA-DNA relatedness were 33.9 % with L. fusiformis DSM 2898(T) and 29.5 % with L. sphaericus DSM 28(T). The genomic DNA G+C content of the novel strain was 38.7 mol%. The major respiratory quinone was MK-7 and the major fatty acids were iso-C(15 : 0) (37.4 %) and anteiso-C(15 : 0) (19.0 %). Analysis of cell-wall amino acids revealed that the strain contained peptidoglycan with lysine, aspartic acid, alanine and glutamic acid, as is the case with other species of the genus Lysinibacillus. Based upon its distinctive peptidoglycan composition, phylogenetic and genotypic analyses and physiological characteristics, the strain BAM-582(T) is concluded to represent a novel species in the genus Lysinibacillus, for which the name Lysinibacillus parviboronicapiens sp. nov. is proposed (type strain BAM-582(T) =NBRC 103144(T) =KCTC 13154(T)).

Variovorax boronicumulans sp. nov., a boron- accumulating bacterium isolated from soil

A non-spore-forming, Gram-negative, motile, rod-shaped, boron-accumulating bacterium isolated from soil was characterized by polyphasic taxonomy. The strain, designated BAM-48(T), was positive for catalase and oxidase activities and grew at 4-37 degrees C, 0-1% NaCl and pH 5-9. Comparative analysis of the 16S rRNA gene sequence demonstrated that the novel isolate BAM-48(T) was closely related to Variovorax paradoxus IAM 12373(T) (99.3% sequence similarity), Variovorax soli GH9-3(T) (98.3%) and Variovorax dokdonensis DS-43(T) (97.0%). DNA-DNA hybridization values between strain BAM-48(T) and V. paradoxus NBRC 15149(T), V. soli KACC 11579(T) and V. dokdonensis KCTC 12544(T) were only 49.1, 25.4 and 24.6%, respectively. The major respiratory quinone was ubiquinone 8 (Q-8). The DNA G+C content was 71.2 mol%. Strain BAM-48(T) contained C(16:0) (36.1%), C(16:1)omega7c (21.4%) and C(17:0) cyclo (19.0%) as the major fatty acids. Based on phenotypic, chemotaxonomic and phylogenetic data, strain BAM-48(T) should be classified as a member of a novel species in the genus Variovorax, for which the name Variovorax boronicumulans sp. nov. is proposed. The type strain is BAM-48(T) (=NBRC 103145(T) =KCTC 22010(T)).

Physicochemical Characteristics, Functional Properties, and Nutritional Benefits of Peanut Oil: A Review

The legume Arachis hypogaea, commonly known as peanut or groundnut, is a very important food crop throughout the tropics and subtropics. Peanut is one of the most widely used legumes due to its nutrition and taste, and it occupies a rank of major oilseed crop in the world. It has been recognized as a functional food due to its role in a health promoting effect. Peanut oil contains a well-balanced fatty acid and antioxidant profile that provide protection against harmful substances especially free radicals. This paper gives an overview of scientific literature available on phytochemical and functional properties of peanut oil. Owing to its unique organoleptic properties associated with its cardioprotective and anti-inflammatory properties, peanut oil has found, recently, its place on the highly competitive international edible oil market.

Comparative effectiveness of Bacillus spp. possessing either dual or single growth-promoting traits for improving phosphorus uptake, growth and yield of wheat (Triticum aestivum L.)

The aim of this study was to compare the effectiveness of Bacillus spp. simultaneously carrying dual traits such as P solubilization and ACC deaminase activity with Bacillus spp. having any one of these traits for improving growth, yield and P uptake by wheat crop. Six Bacillus strains having predominantly either ACC deaminase activity (KA1 and KA2) or P solubilizing activity (KP3 and KP4) or simultaneously both of these traits (KAP5 and KAP6) were evaluated for improving growth of wheat cv. Bhakar-2002 using rock phosphate (RP) as an exclusive P-source. Under axenic conditions, the bacterial strains with dual plant growth-promoting activities were superior in improving growth of wheat as compared to the strains possessing single trait. Similarly, these dual traits bacterial strains were more effective than single trait strains under soil conditions (pot trial) in increasing root weight (up to 3.9-fold) and root elongation (up to 3.8-fold), dry shoot weight (up to 37.6%), number of tillers (up to 56%), grain yield (up to 38.5%) and P uptake in grain (up to 77.4%) of wheat grown in the presence of P applied as diammonium phosphate (DAP), RP (rock phosphate) or RP-enriched compost. An almost similar trend was observed when the same trial was repeated under field conditions. Inoculation in the presence of RP-enriched compost resulted in promoting various growth parameters almost comparable to that recorded in the case of DAP. It was concluded that the simultaneous presence of two superior plant growth-promoting traits in the bacteria could have an additive effect not only on growth and yield of wheat but also on P uptake. The performance of Bacillus strains possessing dual traits was distinctly superior to that of the single trait strains. These bacteria exhibited an excellent effectiveness in utilizing RP as the source of P in the growth medium as well as in soil.

Role of Bacillus licheniformis in Phytoremediation of Nickel Contaminated Soil Cultivated with Rice

Heavy metal contamination in soil is an important environmental problem and it has negative effect on agriculture. Bacteria play a major role in phytoremediation of heavy metals contaminated soil. In this study, the effect of Bacillus licheniformis NCCP-59, a halophilic bacterium isolated from salt mines near Karak, Pakistan, were determined on a three week old greenhouse grown seedling and germinating seeds of two rice varieties (Basmati-385 (B-385) and KSK-282) in soil contaminated with different concentrations (0, 100, 250, 500, and 1000 ppm) of Nickel. Nickel significantly reduced the germination rate and germination percentage mainly at 500 and 1000 ppm. Significant decrease in ion contents (Na, K, and Ca) was observed while Ni ion concentration in the plant tissues increases as the concentration of Ni applied increases. The photosynthetic pigments (chlorophyll a (chl a), chlorophyll b (chl b), and carotenoids) were also decreased by the application of different concentrations of Ni. Total protein and organic nitrogen were found to be reduced at higher concentrations of Nickel. Inoculation of Bacillus Licheniformis NCCP-59 improved seed germination and biochemical attribute of the plant under Ni stress. It is clear from the results that the Bacillus Licheniformis NCCP-59 strain has the ability to protect the plants from the toxic effects of nickel and can be used for the phytoremediation of Ni contaminated soil.

An Overview of Plant Growth Promoting Rhizobacteria (PGPR) for Sustainable Agriculture

Soil bacteria beneficial to plant growth usually referred to as plant growth promoting rhizobacteria (PGPR), are capable of promoting plant growth by colonizing the plant root. The mechanisms of PGPR-mediated enhancement of crop growth includes (i) a symbiotic and associative nitrogen fixation; (ii) solubilization and mineralization of other nutrients; (iii) production of hormones e.g. auxin i.e. indole acetic acid (IAA), abscisic acid (ABA), gibberellic acid and cytokinins; (iv) production of ACC-deaminase to reduce the level of ethylene in crop roots thus enhancing root length and density; (v) ability to produce antagonistic siderophores, s-1-3-glucanase, chitinases, antibiotics, fluorescent pigment and cyanide against pathogens and (vi) enhanced resistance to drought and oxidative stresses by producing water soluble vitamins niacin, thiamine, riboflavin, biotin and pantothenic acid. Increased crop production through biocontrol is an indirect mechanism of PGPR that results in suppression of soil born deleterious microorganisms. Biocontrol mechanisms involved in pathogen suppression by PGPR include substrate competition, antibiotic production, and induced systemic resistance in the host. PGPR can play an essential role in helping plants to establish and grow in nutrient deficient conditions. Their use in agriculture can favour a reduction in agro-chemical use and support ecofriendly crop production. Trials with rhizosphere-associated plant growth-promoting P-solubilizing and N2-fixing microorganisms indicated yield increase in rice, wheat, sugar cane, maize, sugar beet, legumes, canola, vegetables and conifer species. A range of beneficial bacteria including strains of Herbaspirillum, Azospirillum and Burkholderia are closely associated with rhizosphere of rice crops. Common bacteria found in the maize rhizosphere are Azospirillum sp., Klebsiella sp., Enterobacter sp., Rahnella aquatilis, Herbaspirillum seropedicae, Paenibacillus azotofixans, and Bacillus circulans. Similarly, strains of Azotobacter, Azorhizobium, Azospirillum, Herbaspirillum, Bacillus and Klebsiella can supplement the use of urea-N in wheat production either by BNF or growth promotion. The commonly present PGPR in sugarcane plants are Azospirillum brasilense, Azospirillum lipoferum, Azospirillum amazonense, Acetobacter diazotrophicus, Bacillus tropicalis, Bacillus borstelensis, Herbaspirillum rubrisubalbicans and Herbaspirillum seropedicae. Symbiotic N2-fixing bacteria collectively known as Rhizobia are currently classified into six genera; Rhizobium, Allorhizobium, Azorhizobium, Bradyrhizobium, Mesorhizobium and Sinorhizobium and 91 species. Their inoculation may increase nodulation and N2-fixation in legumes. All these Rhizobiumn spp. can minimize chemical N fertilizers by BNF, but only if conditions for expression of N2-fixing activity and subsequent transfer of N to plants are favourable. In this Chapter, PGPR role has been discussed in the process of crop growth promotion, their mechanisms of action and their importance in crop production on sustainable basis.

VARIATION IN PHOSPHORUS EFFICIENCY AMONG BRASSICA CULTIVARS I: INTERNAL UTILIZATION AND PHOSPHORUS REMOBILIZATION

Plants have adapted a number of mechanisms to cope with widespread phosphorus (P) deficiency in arable lands. Crop species and even cultivars differ widely in one or more of these adaptive mechanisms hence, in P efficiency. Identification of these mechanisms is pre-requisite for long term breeding programs. Two independent experiments were conducted to study the possible mechanisms of P efficiency in Brassica cultivars. Eight Brassica cultivars (‘B.S.A.’, ‘Toria’, ‘Toria Selection’, ‘Brown Raya’, ‘Peela Raya’, ‘Dunkeld’, ‘Rainbow’, and ‘CON-1’) were selected on the basis of differences in growth under P deficiency from preliminary experiment. In the first experiment, cultivars were grown for 40 days in sand supplied either with sparingly soluble phosphate rock (PR) or soluble mono-ammonium phosphate (MAP). Cultivars differed significantly (P<0.05) for biomass production, P contents and P use efficiency. Low P availability in PR treatment resulted in significantly lower dry weights and P contents than those grown with MAP. The cultivars ‘Rainbow’, ‘Brown Raya’ and ‘Dunkeld’ accumulated more biomass (3.2 g/pot) and P contents (3.0 mg/pot) than other cultivars when grown with PR. Root dry weight was significantly correlated with shoot dry weight, shoot P content and total P content (r > 0.65) indicating significance of improved root growth for P acquisition. While in the second experiment cultivars were grown with adequate P for 30 days and then P was withdrawn from the nutrient solution by replacing fresh P free nutrient solution for 10 days. Induced P deficiency increased P contents in young leaves by two folds indicating remobilization of P from older leaves and shoot. Nonetheless cultivars varied for remobilization but differences in P remobilization could not explain the differences in P utilization efficiency among cultivars. Hence further experimentation to study root morphology, P uptake, and organic acid exudation by these cultivars in relation to P deficiency is recommended.

Rhodococcus baikonurensis BTM4c, a Boron-Tolerant Actinobacterial Strain Isolated from Soil

By screening a bacterial population from the soil in Tokyo, Japan, we isolated a boron-tolerant bacterium, strain BTM4c. Strain BTM4c grew under the boron excess conditions with 100 mM boric acid, which is generally toxic to bacteria. Molecular phylogenetic, chemotaxonomic, and physiological data showed that the strain belongs to the genus Rhodococcus, and is to be identified as Rhodococcus baikonurensis.

Biosorption of heavy metals by Pseudomonas species isolated from sugar industry

Heavy metal-resistant bacteria can be efficient bioremediators of metals and may provide an alternative or additional method to conventional methods of metal removal. In this study, 10 bacterial isolates were isolated from soil samples of a sugar industry, located at Peshawar, Pakistan. Morphological, physiological, and biochemical characteristics of these isolates were observed. Sequence analysis (16S ribosomal RNA) revealed that isolated strains were closely related to the species belonging to the genera Pseudomonas, Arthrobacter, Exiguobacterium, Citrobacter, and Enterobacter. Bacterial isolates were resistant with a minimum inhibitory concentration (500–900 ppm) to lead ion (Pb2+), (500–600 ppm) nickel ion (Ni2+), (500–800 ppm) copper ion (Cu2+), and (600–800 ppm) chromium ion (Cr3+) in solid media. Furthermore, biosorption of metals proved considerable removal of heavy metals by isolated metal-resistant strains. Pseudomonas sp. reduced 37% (Pb2+), 32% (Ni2+), 29% (Cu2+), and 32% (Cr3+) and was thus found to be most effective, whereas Enterobacter sp. reduced 19% (Pb2+), 7% (Ni2+), 14% (Cu2+), and 21% (Cr3+) and was found to be least effective. While average reduction of Pb2+, Ni2+, Cu2+, and Cr3+ by Citrobacter sp. was found to be 24%, 18%, 23%, and 27%, respectively, among recognized species. This study revealed that Pseudomonas sp. may provide a new microbial community that can be used for enhanced remediation of contaminated environment.