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Rhizobium Pongamiae Sp. Nov. from Root Nodules of Pongamia Pinnata

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Rhizobium Pongamiae Sp. Nov. from Root Nodules of Pongamia Pinnata Hindawi Publishing Corporation BioMed Research International Volume 2013, Article ID 165198, 9 pages http://dx.doi.org/10.1155/2013/165198 Research Article Rhizobium pongamiae sp. nov. from Root Nodules of Pongamia pinnata Vigya Kesari, Aadi Moolam Ramesh, and Latha Rangan Department of Biotechnology, Indian Institute of Technology Guwahati, Assam 781 039, India Correspondence should be addressed to Latha Rangan; latha [email protected] Received 27 April 2013; Accepted 6 June 2013 Academic Editor: Eldon R. Rene Copyright © 2013 Vigya Kesari et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Pongamia pinnata has an added advantage of N2-fixing ability and tolerance to stress conditions as compared with other biodiesel crops. It harbours “rhizobia” as an endophytic bacterial community on its root nodules. A gram-negative, nonmotile, fast-growing, ∘ rod-shaped, bacterial strain VKLR-01T wasisolatedfromrootnodulesofPongamia that grew optimal at 28 C, pH 7.0 in presence of 2% NaCl. Isolate VKLR-01 exhibits higher tolerance to the prevailing adverse conditions, for example, salt stress, elevated T T temperatures and alkalinity. Strain VKLR-01 hasthemajorcellularfattyacidasC18:1 7c (65.92%). Strain VKLR-01 was found to be a nitrogen fixer using the acetylene reduction assay and PCR detection ofa nif H gene. On the basis of phenotypic, phylogenetic distinctiveness and molecular data (16S rRNA, recA, and atpD gene sequences, G + C content, DNA-DNA hybridization etc.), strain VKLR-01T = (MTCC 10513T =MSCL1015T) is considered to represent a novel species of the genus Rhizobium for which the name Rhizobium pongamiae sp. nov. is proposed. Rhizobium pongamiae may possess specific traits that can be transferred to other rhizobia through biotechnological tools and can be directly used as inoculants for reclamation of wasteland; hence, they are very important from both economic and environmental prospects. 1. Introduction P. pinnata , which can be cultivated on marginal lands, has the potential to not only provide a renewable energy resource but Pongamia pinnata (L.) Pierre is a nonedible “pioneer” bio- in addition alleviate the competitive situation that exists with diesel and medicinal tree species of the family Leguminosae food crops as biofuels and associated arable land and water that grows in multiple geoclimatic conditions, ranging from use. It is also used in agriculture and environmental man- humid, tropical, subtropical regions to cooler and semiarid agement, due to its insecticidal and nematicidal properties zones [1–3]. Nitrogen is an important nutrient for plant [7]. Finally, Pongamia has been identified as a resource for growth and yield; however, its availability in soils is limited. agroforestry, urban landscaping to suspend the pollutants and Modern agriculture depends on chemically synthesized N the bioameloriation of degraded lands. fertilizers which are expensive and require fossil fuels for Isolation and identification of authentic and effective production, adding to greenhouse gas emissions. Biological rhizobiaisolatesarerequiredtosupportP. pinnata plantations nitrogen fixation is a useful and important alternative [4], in nitrogen-poor soils. Pongamia trees are purportedly able to especially in biofuel production [2, 5]. Pongamia can grow grow in a wide range of environments: in the tropics, with ∘ on low-fertility land due to its nodulation properties and temperatures from 13–45 C,salinesoils,andinsoilswith good N2-fixing symbiotic associations with “rhizobia” (a a range of pH including sodic soils, and they are an ideal polyphyletic assemblage of alphaproteobacteria family: Rhi- candidate for reforestation of marginal lands [3, 5]. The ability zobiaceae), thus minimizing competition with food crops or of rhizobia to grow in these diverse environmental condi- related fertilizer, water, and land resources needed for food tions will be important for the establishment and success and fodder production [6]. The sustainable production of of Pongamia plantations on these unfertile lands. It, thus, plant oils for biodiesel production from a tree crop such as satisfies all “sustainability criteria” expected from modern 2 BioMed Research International second- and third-generation biofuel crops. However, little described by Boyde and Wood [15]. A growth characteristic of attention has been paid to the occurrence of nitrogen-fixing isolate was recorded at different temperatures (4, 25, 28, 30, 37, ∘ endophytic bacteria in the rhizospheres of this biodiesel tree 42, and 50 C) in YEM broth and agar until 48 h of culture. The which is important for their diverse applicabilities as well ability to grow in acid and alkaline media was also tested by as agronomic and ecological significances. In preliminary inoculating the isolate onto YEM broth and YEM agar plates studies, the effective nodulations of P. pinnata with three adjusted to various pH values (pH 4.0–11.0 at intervals of 1 pH strains of rhizobia (Bradyrhizobium japonicum strain CB1809, units)using1NHCl/1NNaOH.TheNaCltoleranceofthe Bradyrhizobium sp. strain CB564, and Rhizobia sp. strain isolate was tested by growing in YEM broth and YEM agar NGR234) were demonstrated [1]. plates containing 0%, 1%, 2%, 3%, 4%, and 5% (w/v) NaCl. The importance of characterizing indigenous rhizobia of Pongamia cannot be overemphasized. Still there has not 2.3. Gram Staining: Biochemical and Physiological Character- been any detailed study of phenotypic characteristics and istic. Gram reaction was determined with the bioMerieux´ symbiotic effectiveness of rhizobia isolates which naturally Gram-stain kit according to the manufacturer instructions. nodulate Pongamia considering its potential value in sus- Acid production from different carbohydrates was deter- tainable agriculture and role in agroforestry. Therefore, in mined by employing the API 50 CH system (bioMerieux)´ this work, we attempt to isolate the nitrogen-fixing rhizobial according to the manufacturers instructions. The ability of the symbiont strain from nodules of P. pinnata occurring in isolatetoutilizevariouscarbonandaminoacidscompounds North Guwahati, Assam, India. The objectives were to deter- as sole carbon and nitrogen source was investigated using the mine the exact taxonomic position of isolated and identified method described by Lindstrom¨ and Lehtomaki¨ [16]. Def 9 strain by using a polyphasic characterization that included (carbon source) and Def 8 (nitrogen source) agar mediums determination of phenotypic and biochemical properties, were used, and appropriate controls were maintained. Results ∘ phylogenetic investigations based on 16S rRNA, atpD, and were noted after 3 days of incubation at 28 C. A set of phys- recA gene sequences, and genetic analysis. Further investiga- iological characteristics including catalase and oxidase tests tions were also performed in order to verify the nodulation and nitrate reduction were assessed using protocols described and nitrogen-fixing property of the isolated bacterium strain. by Shieh et al. [17]. Gelatin hydrolysis and methyl red test were also performed using the methods of Smibert and Krieg 2. Materials and Methods [18]. The intrinsic antibiotic resistance tests for the isolate were performed by disc-diffusion assay in YEM agar against 2.1. Soil Sampling and Isolation of Rhizobia. P. pinnata sapl- 16 different antibiotics (Discs, HiMedia) of concentrations ings approximately 2-3 months old found in North Guwahati ranging from 2 to 100 g. Cell biomass for the analysis of ∘ ∘ isoprenoid quinones was obtained from the isolate grown on (26 14 6 N; 91 41 28 E),Assam,India,wereuprooted ∘ during April 2010 containing distinct nodules. Nodules yeast extract-mannitol broth (YEM) (12 h, 28 C, 180 rpm). excised from the roots were surface sterilized with 70% (v/v) ethanol for 1 min. Subsequently, nodules were treated with 2.4. FAME Analysis. Fattyacidmethylesters(FAMEs)ofthe 10%(w/v)sodiumhypochloritefor15minandwashedwith isolate were extracted and prepared according to the standard sterile distilled water (3x). Single surface-sterilized nodule protocol of the MIDI Sherlock/Hewlett Packard Microbial (approximately 2 mm) was opened into two halves with a Identification System as described by Sasser [19]. For cellular sterile blade, and the central parts of the nodule were scooped FAME analysis, isolate was grown on trypticase soy broth with blunt needle, macerated, and diluted in 500 Lofsaline agar (TSBA), which consists of 30 g trypticase soy broth and ∘ water (0.9%). Roughly 100 Loftheinoculumwasspread 15gofagar(BBL)for12hat28C under aerobic conditions on yeast extract-mannitol (YEM) and tryptone-yeast extract ∘ (180 rpm). The fatty acid methyl esters extracts were ana- (TYE) agar plates and incubated at 28 Cfor1–3days.The lyzed by Gas Chromatography MODEL 6850 (Agilent Gas purity of the culture was verified by repeated streaking of −1 Chromatography) equipped with an Agilent ultra 2 capillary single colony onto YEM agar [8]with25mgKg (w/v) congo column. red. Single purified isolate was maintained in YEM broth ∘ containing 20% (v/v) glycerol at −80 C. 2.5. DNA Extraction, PCR Amplification, and Sequencing. Cell biomass for DNA extraction was obtained from the 2.2. Growth and Phenotypic Characteristics. Cell size and isolate grown on yeast extract-mannitol (YEM) broth (12 h, ∘ morphology of the root nodule isolate
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