- Open Access
Leaf-residing Methylobacterium species fix nitrogen and promote biomass and seed production in Jatropha curcas
Biotechnology for Biofuelsvolume 8, Article number: 222 (2015)
Jatropha curcas L. (Jatropha) is a potential biodiesel crop that can be cultivated on marginal land because of its strong tolerance to drought and low soil nutrient content. However, seed yield remains low. To enhance the commercial viability and green index of Jatropha biofuel, a systemic and coordinated approach must be adopted to improve seed oil and biomass productivity. Here, we present our investigations on the Jatropha-associated nitrogen-fixing bacteria with an aim to understand and exploit the unique biology of this plant from the perspective of plant–microbe interactions.
An analysis of 1017 endophytic bacterial isolates derived from different parts of Jatropha revealed that diazotrophs were abundant and diversely distributed into five classes belonging to α, β, γ-Proteobacteria, Actinobacteria and Firmicutes. Methylobacterium species accounted for 69.1 % of endophytic bacterial isolates in leaves and surprisingly, 30.2 % which were able to fix nitrogen that inhabit in leaves. Among the Methylobacterium isolates, strain L2-4 was characterized in detail. Phylogenetically, strain L2-4 is closely related to M. radiotolerans and showed strong molybdenum-iron dependent acetylene reduction (AR) activity in vitro and in planta. Foliar spray of L2-4 led to successful colonization on both leaf surface and in internal tissues of systemic leaves and significantly improved plant height, leaf number, chlorophyll content and stem volume. Importantly, seed production was improved by 222.2 and 96.3 % in plants potted in sterilized and non-sterilized soil, respectively. Seed yield increase was associated with an increase in female–male flower ratio.
The ability of Methylobacterium to fix nitrogen and colonize leaf tissues serves as an important trait for Jatropha. This bacteria–plant interaction may significantly contribute to Jatropha’s tolerance to low soil nutrient content. Strain L2-4 opens a new possibility to improve plant’s nitrogen supply from the leaves and may be exploited to significantly improve the productivity and Green Index of Jatropha biofuel.
Jatropha curcas L. (Jatropha) is a woody perennial, drought-tolerant shrub belonging to Euphorbiaceae and is widely distributed in tropical and subtropical regions. Jatropha seeds contain high level of triacylglyceride with a fatty composition well suited for biodiesel production . Jatropha is resistant to drought, able to thrive on marginal land under climate and soil conditions that are unsuitable for food crop plantation [2–5]. In addition to sequestrating CO2 and reducing the world’s reliance on fossil fuel, Jatropha helps control soil erosion  and detoxify polluted soil [7–9]. As a wild plant, however, Jatropha seed and oil productivity remains low, particularly when chemical fertilizer input is limited. Apart from breeding programs for high-yielding Jatropha varieties [10–12], agronomical practices, such as the application of inorganic fertilizer  and plant growth regulators, have also been reported to improve seed yield [14, 15]. As Jatropha is targeted to plant on marginal soil with low nutrient levels, fertilizer requirement would be higher than other crops. This would significantly affect the commercial viability of Jatropha and offset the Green Index of Jatropha biofuel.
It has been increasingly realized that plants form close association with a large population of diverse bacteria, which are either loosely associated with roots (rhizosphere bacteria), actively colonizing internal plants tissues (endophyte) and leaf surfaces (epiphyte) [16–21]. Plants often benefit from such interactions because of nitrogen fixation; production of plant growth hormones, such as auxin, cytokinin and gibberellin; delayed senescence through suppression of ethylene biosynthesis by secreting 1-aminocyclopropane-1-carboxylate (ACC) deaminase; alteration of sugar sensing mechanisms [22–24] and inhibiting pathogen attacks through production of hydrolytic enzymes , competition for space and nutrients [26, 27], and induction of systemic defence mechanisms [28–30]. Bacterial inoculations improved growth and development of switchgrass seedlings, significantly stimulated plant growth, and tiller number on the low fertility soil, and enhanced biomass accumulation on both poor and rich soils, with more effective stimulation of plant growth in low fertility soil than in high fertility soil . Our previous study also showed that Kosakonia species suitable for limited N-content soil and significantly promoted growth and seed yield of Jatropha . Here, we present an investigation on the diversity of culturable endophytic bacteria of Jatropha and a detailed study on the role of a novel leaf-colonizing diazotroph, Methylobacterium sp. strain L2-4, on Jatropha biomass and seed production.
Results and discussion
Culturable endophytic bacterial density in Jatropha tissues
We sampled Jatropha root, stem and leaf tissues from three different germplasm accessions. Endophytic bacterial colonies were established on six different solid media after thorough surface sterilization of the plant tissues. As expected, endophytic bacterial densities varied amongst tissue types and culture media employed. The highest density was seen in roots, followed by stems while leaves showed the lowest density irrespective of the isolation media used (Additional file 1: Figure S1). Similar to previous findings [33, 34], use of complete media, such as KB media and Medium 869, resulted in higher endophyte density while synthetic media, such as AMS with methanol as carbon source, Nfb or BAz media with malic acid or azelaic acid as the carbon source, yielded lower densities (Additional file 1: Figure S1). Canonical discriminant analysis (CDA) of the combined population data of 3 germplasm accessions showed that the origin of plant tissues and media employed for the isolation formed distinct groups (Additional file 2: Figure S2). These results suggest that the distribution of endophytic population vary within different parts of Jatropha and the bacterial population will be ill-presented if the investigation relies on a single medium.
Given the large endophytic bacterial population found in various types of tissues, we focused our studies on selected representatives of culturable species, which were selected randomly according to colony morphology, color and size. Amongst the 1017 isolates selected for analyses, 49.4 % was derived from the roots, 29.8 % from stems and 20.8 % from leaves. 16S rRNA gene analysis assigned 34.4 % of them to α-Proteobacteria, 31.1 % γ-Proteobacteria and 24.5 % Actinobacteria (Additional file 3: Table S1; Additional file 4: Table S2).
In leaves, α-Proteobacteria, particularly Methylobacterium genus clearly stood out in the population, while Sphingomonas, Pantoea, Kocuria, Microbacterium and Curtobacterium genera were also frequently isolated (Fig. 1; Additional file 4: Table S2). The stem population resembled that of leaves, with Curtobacterium, Methylobacterium and Sphingomonas being the top 3 genera (Additional file 5: Figure S3). In contrast, Pseudomonadaceae, Enterobacteriaceae and Rhizobiaceae dominated in roots (Additional file 6: Figure S4). The growth promoting role of Enterobacter in Jatropha has been demonstrated previously . Surprisingly, 31.2 % of the isolates potentially represent new taxa (Additional file 7: Figure S5).
Cell wall degrading endoglucanase activity was believed to be critical for endophytes to successfully colonize plants . We found that 253 strains (24.9 %) exhibited clear zones on CMC plates stained with Congo red, indicating production of endoglucanase in those strains (Table 1, Additional file 3: Table S1). Isolates from genera Cellulosimicrobium, Curtobacterium, Kosakonia and Pseudomonas were most frequently observed to produce endoglucanase. Unexpectedly, 55.9 % of the endophytic isolates did not show obvious endoglucanase activity. As it has been suggested previously, many of endophytes may passively entered the system from the root and spread to aerial parts in a systematic manner [36, 37].
Endophytic nitrogen-fixing bacteria
Among the 1017 isolates, 111 strains (11 %) were able to grow in nitrogen-free media. Members of the genus Pseudomonas (35.1 %), Curtobacterium (10.8 %), Methylobacterium (9.0 %), Sphingomonas (8.1 %) and Rhizobium (8.1 %) were the major taxa overall (Additional file 4: Table S2, Additional file 6: Table S3). To further confirm the diazotrophic nature of the strains, we analyzed the nifH gene encoding the dinitrogenase reductase subunit. nifH sequences were detected by PCR in 64.8 % of the strains that were able to grow in N-free medium . Notably, only 37.4 % nifH-positive strains displayed nitrogenase activity in vitro (Table 2; Additional file 3: Table S1). The discrepancy may be attributed to the presence of non-functional nifH gene. Alternatively, nitrogenases were not functional under the in vitro assay conditions. Therefore, the ability to grow on N-free medium and the presence of a nifH gene does not warrant nitrogenase activity in vitro. This is in accordance with several previous studies on nitrogen-fixing bacteria [39–41]. The majority of the nifH-positive isolates that failed to show in vitro nitrogenase activity belonged to the order Rhizobiales: e.g., Rhizobium, Ensifer, Sinorhizobium, Bradyrhizobium, and Mesorhizobium genera, which are known to fix nitrogen effectively only in root nodules [42, 43]. In contrast, isolates belonging to the genus Cellulomonas, Curtobacterium, Microbacterium, Mycobacterium, Chryseobacterium or Achromobacter showed AR activity. However, no nifH DNA sequences could be amplified under the conditions used, suggesting the nifH genes in those isolates was more divergent.
Our results demonstrated that Jatropha tissues are associated with an abundant and diverse population of diazotrophs. The differential pattern of diazotrophic population in different parts of Jatropha shared high similarity to those of soybean and potato [42, 44], but it was significantly different from that of switchgrass and wild rice .
Analyses of nifH genes
We sequenced the nifH PCR products from 42 strains that appeared to be unique species based on 16S rDNA sequences. All isolates showed AR activity in vitro culture except Rhizobium and Sinorhizobium groups. Alignment of the predicted NifH amino acid sequences formed 6 major clusters (A–F) (Fig. 2). It is noticeable that the NifH sequence homology does not consistently correlate with phylogenetic relationship. This suggests that multiple independent horizontal gene transfer events occurred in the evolution of nitrogen-fixing bacteria. Notably, cluster F include sequences from leaf isolates only, all belonging to the genus Methylobacterium. These sequences were highly divergent from NifH consensus sequence . In fact, they were more related to the Pfam NifH/frxC-family protein, i.e., chlorophyllide reductase iron protein subunit X involved in photosynthesis .
Nitrogenase activity of Methylobacterium species in vitro and in planta
Among 125 Methylobacterium isolates (Additional file 4: Table S2) characterized from Jatropha plant tissues, obvious AR activity was observed in 34 strains (20–634 nmol C2H4/bottle). 52 strains showed weak AR activity (<20 nmol C2H4/bottle) while 39 strains had no detectable activity although all strains had the nifH-like sequences (Additional file 3: Table S1, Additional file 4: Table S2). Phylogenetically, AR-positive strains were closely related to M. radiotolerans, M. populi, M. komagatae and M. aquaticum (Additional file 3: Table S1). Strain L2-4 can be classified as M. radiotolerans based on its rDNA sequence and was among the fastest grower in N-limiting conditions and showed distinct AR activity in vitro (Additional file 9: Figure S6). Assays of its AR activity in the presence or absence of iron (Fe2+), molybdenum (MoO4 2−) and vanadium (V) suggest that the L2-4 strain nitrogenase used Fe2+ and MoO4 2−) as co-factors. The highest AR activity was recorded in the presence of FeSO4 (10 mg/l) and Na2MoO4 (5 mg/l) (Fig. 3a). Vanadium showed weak inhibitory effect. As expected, ammonium ion strongly inhibited AR activity (Fig. 3b). The ability of L2-4 strain to fix nitrogen in planta was confirmed by inoculating the strain to Jatropha by foliar spraying and maintaining the plants under sterile condition. Seedlings treated with strain L2-4 showed strong AR activity (204.6 nmol C2H4 g−1 dry tissues day−1). Furthermore, L2-4 strain also displayed strong AR activity in planta in sorghum, rice, cotton, and caster plant (Fig. 3c). The association between Methylobacterium species and host plants varies from strong or symbiotic to weak or epiphytic and to intermediate or endophytic [48, 49]. Methylobacterium nodulans and M. radiotolerans have been reported to be involved in nitrogen fixation and nodule formation [50, 51], while other Methylobacterium species has been reported multiple plant growth promoting traits [52, 53].
Epiphytic and endophytic colonization by Methylobacterium
Methylobacterium species have been found in association with several species of plants, actively colonizing leaves, stem, branches and roots [54–60]. Methylobacterium cells were observed in intracellular space of the meristematic cells of Scots pine and tomato [61, 62]. Endophytic occurrence of Methylobacterium was confirmed in Medicago truncatula leaves . We found that strain L2-4 colonized on leaf surfaces (epiphytic) as well as inside leaf tissue of Jatropha grown under sterile conditions. On day 45 after leaf spraying, surface-sterilized leaf tissues had endophytic bacteria counts of 5.2 × 106 cfu/g leaf tissues. Epiphytic population based on leaf-imprinting assay was >100 cfu (cm2)−1 in treated leaves. As expected, pink color colonies were not detected in non-treated leaves of Jatropha seedlings grown under sterile conditions.
Inoculation of Methylobacterium improved production of biomass and seeds
To further confirm the growth promoting effect of strain L2-4, Jatropha seedlings were inoculated with the bacterial suspension through seed soaking and as foliage spray. Seed treatment by soaking seeds with L2-4 bacterial suspension for 2 h increased germination rate by 24 %, from 49.6 % in mock-inoculated seeds to 61.5 % in treated seeds. At 45 days after sowing, the average dry biomass of inoculated plants was 40.1 % higher than the mock-inoculated plants and this was associated with significantly increased leaf chlorophyll content and seedling vigor (Table 3). Several studies reported that Methylobacterium inoculation through seed imbibition and phyllosphere spray enhanced seed germination rate, storability, and seed vigor [64–66]. In another word, Methylobacterium has both nurturing and protecting roles for the plants . To demonstrate that nitrogen-fixing strain L2-4 is able to improve seed production of Jatropha, seedlings were inoculated by leaf spraying, planted in large pots and maintained in the open air. Again, L2-4 treated plants showed significant improvements in plant height, leaf counts, leaf chlorophyll content and stem volume compared with the untreated control plants (Fig. 4). At 120 DAI, treated plants recorded an increase of 11.5, 57.1, 11.4 and 56.2 % over the mock-inoculated controls in plant height, leaf counts, leaf chlorophyll content and stem volume, respectively (Fig. 4a–d). In consistence with the plant growth promotion, leaf-epiphytic and endophytic populations were found significantly higher in inoculated plants. Total leaf-associated methylotrophic bacterial density ranged from 7 to 7.5 log cfu g−1 of tissues in treated leaves compared to 6–6.7 log cfu g−1 of tissues in mock-treated plants at 60–120 DAP (Fig. 4e, f). Leaf-imprinting confirmed that strain L2-4 was an epiphyte, displaying 50–60 cfu (cm2)−1 in treated leaves compared to 8–11 cfu (cm2)−1 in non-treated leaves (Fig. 5). We analyzed the 16S rRNA sequence of 20 randomly picked colonies from the leaf-imprinting (Fig. 5a) and 15 of them (75 %) were identical to that of L2-4. These results indicate that L2-4 strain competed well with indigenous phyllosphere microflora under non-sterile conditions. As expected, pink-pigmented Methylobacterium were detected in low density in roots or stems irrespective of L2-4 treatments (data not shown).
In two independent long-term open-air growth experiments using sterilized and non-sterilized soil, the average seed set per tree was increased by approximately 213 and 84.3 %, respectively (Table 4). Student’s t test showed that the treated plants produced significantly more seed sets than mock-treated ones in both experiments (P < 0.05). The improvement in seed yield was associated with an increase of female-male flower ratio and fruit sets (Table 4). The average single seed weight was increased by 12.2 % in Trial I and 11.3 % in Trial II, both being very significant according to Student’s t test (P < 0.01). Cytokinin has been shown to improve female-to-male flower ratio  and Methylobacterium has been shown to change auxin and ethylene levels in plants due to secretion of 1-aminocyclopropane-1-carboxylate (ACC) deaminase . The cross-talk between cytokinin and ethylene pathways is well established. Methylobacterium strain L2-4 appears to promote Jatropha growth and seed setting via multiple mechanisms, including nitrogen fixation, modulating photosynthesis, leaf senescence and flower sex differentiation. The genome of strain L2-4 presents several genes involved in metabolic pathways that may contribute to promotion of plant growth and adaptation to plant surfaces . Methylobacterium on plant surfaces benefit from methanol produced by plants by means of methylotrophy [59, 69, 70]. However, methanol is not the only carbon substrate that these bacteria are able to consume in the phyllosphere .
We have provided strong evidence that the dominant leaf-associated Methylobacterium species were able to promote Jatropha growth and seed yield, at least in part due to nitrogen fixation. To the best of our knowledge, this is the first report of bacterial nitrogen fixation on leaf surface although strain L2-4 is also a competent endophyte in Jatropha. The abundance of endophytic nitrogen-fixing bacteria in Jatropha may contribute to Jatropha’s strong tolerance to poor soil nutrient. Our studies also suggest that strain L2-4 is able to promote growth and perform nitrogen fixation in a much wider range of crops.
Sampling and isolation of endophytic bacteria
Jatropha germplasm accessions collected in the form of seeds from Maluku Island, Indonesia; Yunnan Province, China; and Madurai, Tamil Nadu, India, and the plants were maintained at the Agrotechnology Experimental Station, Singapore. These natural germplasms accessions have been selected in the breeding program of JOil Company (http://www.joil.com.sg/) to generate hybrid plants on the basis of high productivity . Healthy, symptom-less leaves, stems and roots were collected from three individual plants of each germplasm and treated separately. Lateral roots of approximately 15 cm away from the primary stems with diameters from 0.5 to 1.5 cm were collected. Fully expanded leaves with no obvious pathogenic infections were collected. Similarly, uninfected stem segments of about 2.0–2.5 cm in diameter were sampled. All tissues were washed with 70 % ethanol at the cut sites and placed in plastic bags on ice during transportation. Subsequently, samples were subjected to a two-step surface sterilization procedure by washing for 5 min in 1 % (w/v) sodium hypochlorite supplemented with 1 drop of Tween 80 per 100 ml solution followed by three rinses in 70 % ethanol in sterilized distilled for 1 min each. To ensure complete surface sterilization, a second treatment was performed by washing the tissues for 15 min in 15 % H2O2, followed by 1 min in 70 % ethanol, and then rinsed in sterilized distilled water. A 100 µl sample of the water from the third rinse was plated on rich medium to verify the efficiency of sterilization. Surface-sterilized tissues were macerated by grinding in 50 ml 10 mM MgSO4 and serially diluted suspensions were plated on various solid media with 15 g/l agar or phytagel, including 869 medium , R2A medium , King’s B medium  and Ammonium Mineral Salt (AMS) medium , Nfb medium  and BAz medium . Nitrogen-fixing bacterial populations were estimated by the Most Probable Number (MPN) technique using five tubes per dilution with duplicate tubes per dilution , and incubated at 30 °C for 4–5 days. Bacterial growth as seen by a fine subsurface pellicle in the tubes were further purified by transferring to an N-free semi-solid medium, and single colonies were isolated by streaking on respective N-free agar plates. For N-free semi-solid medium, MPN counts were calculated at a level of 95 % confidence according to the method previously described .
16S rRNA gene amplification, sequencing, and strain identification
Phylogenetic positions of bacterial isolates were determined by sequence analysis of the complete 16S rRNA genes. Genomic DNAs were prepared as described previously . 16S rRNA genes were amplified by PCR using universal primers 27F and 1492R  (all primer sequences are shown in Additional file 10: Table S4) with the following cycling conditions: initial denaturation for 10 min at 95 °C; 30 cycles of 1.5 min at 95 °C, 1.5 min at 55 °C and 1.5 min at 72 °C; and a final extension for 10 min at 72 °C. PCR products were gel-purified and sequenced directly or cloned in pGEM-T Easy (Promega, Madison, USA) before sequencing with the Big-dye sequencing method (AB Applied Biosystems, Hitachi) using primers 27F, 1492R, 785F, 518R and 1100R. Sequences were aligned with the Megalign program of DNASTAR and analyzed against the EzTaxon-e Database (http://www.ezbiocloud.net/eztaxon) . Phylogenetic analyses were performed by the Neighbor-Joining , Maximum-Likelihood  and Maximum-Parsimony  methods using the MEGA version 5.05  with the bootstrap values set at 1000 replications .
Screening for cell wall degrading endoglucanase activity
Endoglucanase activity was determined as described previously  with some modifications. Plates containing Kim-Wimpenny solid medium with 0.2 % carboxymethyl cellulose (CMC) , with or without 0.5 % d-glucose, were spotted with 1 µl of grown cultures (OD600nm = 1.0), air-dried and incubated at 30 °C for 3 days. Cell colonies were flushed off plates with water and plates were stained with a 0.1 % Congo red solution for 30 min, followed by several washes with 1 M NaCl. The appearance of clear yellow halo around the colony in a red background indicates positive staining for endoglucanase activity.
Nitrogenase activity assay and nifH gene screening
Nitrogen-fixing capability of isolated strains was screened by testing their growth in 2 ml nitrogen-free liquid medium as described previously . Nitrogenase activity of selected strains was confirmed by acetylene reduction assay (ARA) in liquid cultures injected with purified acetylene gas (15 % v/v) in gas-tight bottles, which were incubated up to 96 h at 30 °C. Gas samples (0.5 ml) were extracted at regular intervals with a PTFE-syringe (Hewlett-Packard, USA) and analyzed in a Gas Chromatograph (GC 6890 N, Agilent Technologies Inc., USA) with an FID operated under the following conditions: carrier gas: He-35 ml/min; detector temperature: 200 °C; column: GS-Alumina (30 m × 0.53 mm I.D.); pressure: 4.0psi. Ethylene produced by the bacteria was quantified using standard ethylene (C2H4, Product Number: 00489, Sigma-Aldrich) curve prepared in duplicates in concentrations ranging from 1 to 1000 nmol. Protein concentration was determined with a modified Lowry method using BSA as the standard. For nitrogenase switch-off/switch-on assay, Methylobacterium cells were grown in N-free medium containing different levels (0–10 mM) of ammonium chloride and nitrogenase co-factors FeSO4 (10 mg l−1), Na2MoO4 (5 mg l−1) and VCl2 (18.1 mg l−1). Acetylene reduction activity in planta was performed as described previously . Briefly, samples from each replication were collected from the glass house and most of the adhering soil was removed by shaking. Seedlings were inserted into the 125 ml glass bottles, closed with a 20 mm red stopper sleeve. After removing an equivalent volume of air, acetylene was injected into these bottles to give a final concentration of 15 % and incubated at 30 °C for 24 h. In planta acetylene reduction activity was measured by GC and value is expressed in nmol C2H4 released day−1 seedlings−1 after subtracting plant’s background C2H4 emission.
PCR amplification of nifH gene fragments was performed using primers nif-Fo and nif-Re under stringent cycling conditions as described , i.e., 95 °C/5 min, 40 cycles of 94 °C/11 s, 92 °C/15 s, 54 °C/8 s, 56 °C/30 s, 74 °C/10 s and 72 °C/10 s, and final extension for 10 min/72 °C. PCR products were purified with QIAquick gel extraction kit (Qiagen, USA) and sequenced.
Leaf colonization by Methylobacterium
Surface sterilization of Jatropha seeds was done by washing coat-less seed kernels in 90 % ethanol (v/v) for 1 min and 10 % H2O2 (v/v) for 60 min followed by 3-5 rinses in sterilized distilled water. After soaking overnight at 28 °C in darkness, they were germinated on a hormone-free seed germination medium  in Petri dishes and incubated at 25 °C with 16/8 h light–dark cycles. After 10 days, healthy seedlings (10 seedlings/replica, n = 3) were transferred to Phytatrays (Sigma, USA) containing sterile sand (autoclaved) with 40 ml of plant nutrient solution . Jatropha leaves were sprayed with L2-4 suspension (108 cfu/ml) till completely wet. On day 45 and 60, epiphytic population was determined from leaves of inoculated plants were printed on an AMS agar plate supplemented with 0.5 % methanol (v/v) and incubated at 30 °C for 3–5 days. Endophytic colonization was determined from surface-sterilized leaves and homogenize with sterile pestle and mortar followed by serial dilution methods. Serially diluted samples were plated on an AMS agar plates, incubate at 30 °C for 3–5 days and pink-pigmented colonies counted from 10−3 to 10−4 dilutions.
Effect of Methylobacterium L2-4 on Jatropha seedling early growth
Seedling vigor test was performed with Jatropha to study effects of foliar spray with ACC deaminase producing Methylobacterium. Strain L2-4 was cultured in 2YT broth supplemented with 1 % methanol (v/v) until exponential growth phase and harvested by centrifugation. After washing once with sterile distilled water, inoculants were made by re-suspending the pellets in water to an OD600nm of 1.2 (~108 cfu ml−1). To assess the impact on seed germination and early growth of seedlings, imbibed seeds (50 seeds/replica, n = 3) were sown in plastic pots individually and allowed to develop into seedlings. Foliar application was done after seed germination and growth parameters were recorded at 45 DAS.
Effect of Methylobacterium on Jatropha growth and seed yield
Seeds of J. curcas cv. MD44 were used throughout the experiments. Surface sterilization of seeds was done by washing coat-less seed kernels in 75 % ethanol (v/v) for 1 min and 10 % H2O2 (v/v) for 60 min followed by 3–5 rinses in sterilized distilled water. After soaking overnight at 28 °C in darkness, they were germinated on a hormone-free seed germination medium (1/2 MS salt, B5 vitamins, 5 g l−1 sucrose, 0.5 g l−1 MES and 2.2 g l−1 phytagel, pH 5.6) in Phytatrays (Sigma, USA) in a tissue culture room with a temperature of 25 ± 2 °C and 16/8 h light–dark cycles. To assess the effects of bacterial inoculation on the growth and yield of Jatropha under natural conditions, two pot culture experiments were conducted with garden soil. Plants were planted in pots (one plant per pot) in sterilized soil (compost/sand mix at 1:1 ratio and in ɸ23 cm, 18 cm height pots; named as Trial I) or non-sterilized soil (nutrient poor clay soil in ɸ30 cm, 28 cm height pots; named as Trial II). Trial I and Trial II were maintained in different locations and started in different seasons. L2-4 cell suspension (1.2 OD600) was applied as foliar spray till wetting of the leaves at 21 days after seed germination. Commercial NPK Fertiliser was applied once in 15 days at about half of the recommended dose of approximately 50:30:30 g−1 plant−1 year−1. Biometric observations were recorded once in 30 days. After flowering, yield parameters were recorded once in 30 days. Seed set numbers per plant (n = 9 in Trial I and n = 12 in Trial II) were measured at 480 and 520 DAI in Trail I and Trail II, respectively, and single seed weight was calculated based on the average of 180 randomly selected seeds per treatment were measured.
Triplicate leaf samples were randomly picked from three plants on 30 DAI. For methylotrophic bacterial enumerations, homogenates were serially diluted using 1X PBS and plated on to AMS media with 0.5 % methanol to determine the methylotrophic population. Pink-pigmented colonies were counted after incubating the plates for 5 days at 30 °C. Further confirmation, 20 pink color colonies per replica were picked from 10−5 dilution and streaked on AMS agar plates and purified. Purified colonies were sequenced by 16S rRNA sequencing and identified using the EzTaxon server  on the basis of sequence data and sequencing results compared with pairwise identity of strain L2-4.
Nucleotide sequence accession numbers
All 16S rRNA gene sequences determined in this study have been submitted to NCBI under the accession numbers JQ659304 to JQ660320 and the numbers are also listed in Additional file 3: Table S1. nifH gene sequences have been submitted to NCBI under the accession numbers KR075947-KR075982, KC195919 and CP005991.
ammonium mineral salt medium
analysis of variance
acetylene reduction activity
canonical discriminant analysis
colony forming units
days after inoculation
Duncan’s multiple range test
least significant difference
most probable number
plant growth promotion
rate of germination
statistical analysis system
seedling vigor index
Openshaw K. A review of Jatropha curcas: an oil plant of unfulfilled promise. Biomass Bioenerg. 2000;19:1–15.
Achten WM, Trabucco A, Maes W, Verchot L, Aerts R, Mathijs E, et al. Global greenhouse gas implications of land conversion to biofuel crop cultivation in arid and semi-arid lands–Lessons learned from Jatropha. J Arid Environ. 2013;98:135–45.
Francis G, Edinger R, Becker K (eds.). A concept for simultaneous wasteland reclamation, fuel production, and socio‐economic development in degraded areas in India: Need, potential and perspectives of Jatropha plantations. Natural Resources Forum. Wiley Online Library; 2005.
Abou Kheira AA, Atta NM. Response of Jatropha curcas L. to water deficits: yield, water use efficiency and oilseed characteristics. Biomass Bioenerg. 2009;33:1343–50.
Berchmans HJ, Hirata S. Biodiesel production from crude Jatropha curcas L. seed oil with a high content of free fatty acids. Bioresour Technol. 2008;99:1716–21.
Reubens B, Achten WM, Maes W, Danjon F, Aerts R, Poesen J, et al. More than biofuel? Jatropha curcas root system symmetry and potential for soil erosion control. J Arid Environ. 2011;75:201–5.
Mangkoedihardjo S, Ratnawati R, Alfianti N. Phytoremediation of hexavalent chromium polluted soil using Pterocarpus indicus and Jatropha curcas L. World Appl Sci J. 2008;4:338–42.
Kumar G, Yadav S, Thawale P, Singh S, Juwarkar A. Growth of Jatropha curcas on heavy metal contaminated soil amended with industrial wastes and Azotobacter—a greenhouse study. Bioresour Technol. 2008;99:2078–82.
Becker K, Wulfmeyer V, Berger T, Gebel J, Münch W. Carbon farming in hot, dry coastal areas: an option for climate change mitigation. Earth System Dyn. 2013;4:237–51.
Behera SK, Srivastava P, Tripathi R, Singh J, Singh N. Evaluation of plant performance of Jatropha curcas L. under different agro-practices for optimizing biomass—a case study. Biomass Bioenerg. 2010;34:30–41.
Liu P, Wang CM, Li L, Sun F, Yue GH. Mapping QTLs for oil traits and eQTLs for oleosin genes in jatropha. BMC Plant Biol. 2011;11:132.
Sun F, Liu P, Ye J, Lo LC, Cao S, Li L, et al. An approach for jatropha improvement using pleiotropic QTLs regulating plant growth and seed yield. Biotechnol Biofuels. 2012;5:1–10.
Yong J, Ng Y, Tan S, Chew A. Effect of fertilizer application on photosynthesis and oil yield of Jatropha curcas L. Photosynthetica. 2010;48:208–18.
Ghosh A, Chikara J, Chaudhary D, Prakash AR, Boricha G, Zala A. Paclobutrazol arrests vegetative growth and unveils unexpressed yield potential of Jatropha curcas. J Plant Growth Regul. 2010;29:307–15.
Pan B-Z, Xu Z-F. Benzyladenine treatment significantly increases the seed yield of the biofuel plant Jatropha curcas. J Plant Growth Regul. 2011;30:166–74.
Hunter PJ, Hand P, Pink D, Whipps JM, Bending GD. Both leaf properties and microbe-microbe interactions influence within-species variation in bacterial population diversity and structure in the lettuce (Lactuca species) phyllosphere. Appl Environ Microbiol. 2010;76:8117–25.
Hirano SS, Nordheim EV, Arny DC, Upper CD. Lognormal distribution of epiphytic bacterial populations on leaf surfaces. Appl Environ Microbiol. 1982;44:695–700.
Knief C, Ramette A, Frances L, Alonso-Blanco C, Vorholt JA. Site and plant species are important determinants of the Methylobacterium community composition in the plant phyllosphere. ISME J. 2010;4:719–28.
Ulrich A, Becker R. Soil parent material is a key determinant of the bacterial community structure in arable soils. FEMS Microbiol Ecol. 2006;56:430–43.
Ryan RP, Germaine K, Franks A, Ryan DJ, Dowling DN. Bacterial endophytes: recent developments and applications. FEMS Microbiol Lett. 2008;278:1–9.
van der Lelie D, Taghavi S, Monchy S, Schwender J, Miller L, Ferrieri R, et al. Poplar and its bacterial endophytes: coexistence and harmony. Crit Rev Plant Sci. 2009;28:346–58.
Lodewyckx C, Vangronsveld J, Porteous F, Moore ER, Taghavi S, Mezgeay M, et al. Endophytic bacteria and their potential applications. Crit Rev Plant Sci. 2002;21:583–606.
Sturz A, Christie B, Nowak J. Bacterial endophytes: potential role in developing sustainable systems of crop production. Criti Rev Plant Sci. 2000;19:1–30.
Kim S, Lowman S, Hou G, Nowak J, Flinn B, Mei C. Growth promotion and colonization of switchgrass (Panicum virgatum) cv. Alamo by bacterial endophyte Burkholderia phytofirmans strain PsJN. Biotechnol Biofuels. 2012;5:37.
Krechel A, Faupel A, Hallmann J, Ulrich A, Berg G. Potato-associated bacteria and their antagonistic potential towards plant-pathogenic fungi and the plant-parasitic nematode Meloidogyne incognita (Kofoid & White) Chitwood. Can J Microbiol. 2002;48:772–86.
Buyer JS, Wright JM, Leong J. Structure of pseudobactin A214, a siderophore from a bean-deleterious Pseudomonas. Biochemistry. 1986;25:5492–9.
O’sullivan DJ, O’Gara F. Traits of fluorescent Pseudomonas spp involved in suppression of plant root pathogens. Microbiol Rev. 1992;56:662–76.
Van Loon L, Bakker P, Pieterse C. Systemic resistance induced by rhizosphere bacteria. Ann Rev Phytopathol. 1998;36:453–83.
Ryu CM, Murphy JF, Mysore KS, Kloepper JW. Plant growth-promoting rhizobacteria systemically protect Arabidopsis thaliana against Cucumber mosaic virus by a salicylic acid and NPR1-independent and jasmonic acid-dependent signaling pathway. Plant J. 2004;39:381–92.
Zhang S, Reddy MS, Kloepper JW. Tobacco growth enhancement and blue mold disease protection by rhizobacteria: relationship between plant growth promotion and systemic disease protection by PGPR strain 90-166. Plant Soil. 2004;262:277–88.
Lowman JS, Lava-Chavez A, Kim-Dura S, Flinn B, Nowak J, Mei C. Switchgrass field performance on two soils as affected by bacterization of seedlings with Burkholderia phytofirmans strain PsJN. BioEnergy Res. 2015;8:440–9.
Madhaiyan M, Peng N, Te Si N, Hsin IC, Lin C, Lin F, et al. Improvement of plant growth and seed yield in Jatropha curcas by a novel nitrogen-fixing root associated Enterobacter species. Biotechnol Biofuels. 2013;6:140.
Barac T, Taghavi S, Borremans B, Provoost A, Oeyen L, Colpaert JV, et al. Engineered endophytic bacteria improve phytoremediation of water-soluble, volatile, organic pollutants. Nat Biotechnol. 2004;22:583–8.
Strobel G, Daisy B, Castillo U, Harper J. Natural products from endophytic microorganisms. J Nat Prod. 2004;67:257–68.
Hardoim PR, van Overbeek LS, van Elsas JD. Properties of bacterial endophytes and their proposed role in plant growth. Trends Microbiol. 2008;16:463–71.
Santi C, Bogusz D, Franche C. Biological nitrogen fixation in non-legume plants. Ann Bot. 2013;111:743–67.
Olivares FL, Baldani VL, Reis VM, Baldani JI, Döbereiner J. Occurrence of the endophytic diazotrophs Herbaspirillum spp. in roots, stems, and leaves, predominantly of Gramineae. Biol Fertil Soils. 1996;21:197–200.
Ueda T, Suga Y, Yahiro N, Matsuguchi T. Remarkable N2-fixing bacterial diversity detected in rice roots by molecular evolutionary analysis of nifH gene sequences. J Bacteriol. 1995;177:1414–7.
Doty SL, Oakley B, Xin G, Kang JW, Singleton G, Khan Z, et al. Diazotrophic endophytes of native black cottonwood and willow. Symbiosis. 2009;47:23–33.
Videira SS, De Araujo JLS, da Silva Rodrigues L, Baldani VLD, Baldani JI. Occurrence and diversity of nitrogen-fixing Sphingomonas bacteria associated with rice plants grown in Brazil. FEMS Microbiol Lett. 2009;293:11–9.
Mirza BS, Rodrigues JL. Development of a direct isolation procedure for free-living diazotrophs under controlled hypoxic conditions. Appl Environ Microbiol. 2012;78:5542–9.
Kuklinsky-Sobral J, Araújo WL, Mendes R, Geraldi IO, Pizzirani-Kleiner AA, Azevedo JL. Isolation and characterization of soybean-associated bacteria and their potential for plant growth promotion. Environ Microbiol. 2004;6:1244–51.
Burbano CS, Liu Y, Rösner KL, Reis VM, Caballero-Mellado J, Reinhold-Hurek B, et al. Predominant nifH transcript phylotypes related to Rhizobium rosettiformans in field-grown sugarcane plants and in Norway spruce. Environ Microbiol Rep. 2011;3:383–9.
Sessitsch A, Reiter B, Pfeifer U, Wilhelm E. Cultivation-independent population analysis of bacterial endophytes in three potato varieties based on eubacterial and Actinomycetes-specific PCR of 16S rRNA genes. FEMS Microbiol Ecol. 2002;39:23–32.
Xia Y, Greissworth E, Mucci C, Williams MA, DeBolt S. Characterization of culturable bacterial endophytes of switchgrass (Panicum virgatum L.) and their capacity to influence plant growth. GCB Bioenergy. 2013;5:674–82.
Madhaiyan M, Chan KL, Ji L. Draft genome sequence of Methylobacterium sp. strain L2-4, a leaf-associated endophytic N-fixing bacterium isolated from Jatropha curcas L. Genome Announc. 2014;2:e01306–14.
Atamna-Ismaeel N, Finkel O, Glaser F, von Mering C, Vorholt JA, Koblížek M, et al. Bacterial anoxygenic photosynthesis on plant leaf surfaces. Env Microbiol Rep. 2012;4:209–16.
Jourand P, Giraud E, Béna G, Sy A, Willems A, Gillis M, et al. Methylobacterium nodulans sp. nov., for a group of aerobic, facultatively methylotrophic, legume root-nodule-forming and nitrogen-fixing bacteria. Int J Syst Evol Microbiol. 2004;54:2269–73.
Lacava P, Araújo W, Marcon J, Maccheroni W, Azevedo J. Interaction between endophytic bacteria from citrus plants and the phytopathogenic bacteria Xylella fastidiosa, causal agent of citrus-variegated chlorosis. Lett Appl Microbiol. 2004;39:55–9.
Menna P, Hungria M, Barcellos FG, Bangel EV, Hess PN, Martínez-Romero E. Molecular phylogeny based on the 16S rRNA gene of elite rhizobial strains used in Brazilian commercial inoculants. Syst Appl Microbiol. 2006;29:315–32.
Sy A, Giraud E, Jourand P, Garcia N, Willems A, de Lajudie P, et al. Methylotrophic Methylobacterium bacteria nodulate and fix nitrogen in symbiosis with legumes. J Bacteriol. 2001;183:214–20.
Koenig RL, Morris RO, Polacco JC. tRNA is the source of low-level trans-zeatin production in Methylobacterium spp. J Bacteriol. 2002;184:1832–42.
Madhaiyan M, Poonguzhali S, Ryu J, Sa T. Regulation of ethylene levels in canola (Brassica campestris) by 1-aminocyclopropane-1-carboxylate deaminase-containing Methylobacterium fujisawaense. Planta. 2006;224:268–78.
Andreote FD, Lacava PT, Gai CS, Araújo WL, Maccheroni J, Walter, vanOverbeek LS, et al. Model plants for studying the interaction between Methylobacterium mesophilicum and Xylella fastidiosa. Can J Microbiol. 2006;52:419–26.
Araújo WL, Marcon J, Maccheroni W, van Elsas JD, van Vuurde JW, Azevedo JL. Diversity of endophytic bacterial populations and their interaction with Xylella fastidiosa in citrus plants. Appl Environ Microbiol. 2002;68:4906–14.
Dourado MN, Ferreira A, Araújo WL, Azevedo JL, Lacava PT. The diversity of endophytic methylotrophic bacteria in an oil-contaminated and an oil-free mangrove ecosystem and their tolerance to heavy metals. Biotechnol Res Int. 2012;. doi:10.1155/2012/759865 (in press).
Pohjanen J, Koskimäki JJ, Sutela S, Ardanov P, Suorsa M, Niemi K, et al. Interaction with ectomycorrhizal fungi and endophytic Methylobacterium affects nutrient uptake and growth of pine seedlings in vitro. Tree Physiol. 2014;34:993–1005.
Andreote FD, Carneiro RT, Salles JF, Marcon J, Labate CA, Azevedo JL, et al. Culture-independent assessment of Rhizobiales-related Alphaproteobacteria and the diversity of Methylobacterium in the rhizosphere and rhizoplane of transgenic eucalyptus. Microb Ecol. 2009;57:82–93.
Abanda-Nkpwatt D, Müsch M, Tschiersch J, Boettner M, Schwab W. Molecular interaction between Methylobacterium extorquens and seedlings: growth promotion, methanol consumption, and localization of the methanol emission site. J Exp Bot. 2006;57:4025–32.
Dourado MN, Aparecida Camargo Neves A, Santos DS, Araújo WL. Biotechnological and agronomic potential of endophytic pink-pigmented methylotrophic Methylobacterium spp. BioMed Res Int. 2015;. doi:10.1155/2012/759865.
Koskimäki JJ, Pirttilä AM, Ihantola E-L, Halonen O, Frank AC. The intracellular scots pine shoot symbiont Methylobacterium extorquens DSM13060 aggregates around the host nucleus and encodes eukaryote-like proteins. MBio. 2015;6:e00039-15.
Poonguzhali S, Madhaiyan M, Yim W-J, Kim K-A, Sa T-M. Colonization pattern of plant root and leaf surfaces visualized by use of green-fluorescent-marked strain of Methylobacterium suomiense and its persistence in rhizosphere. Appl Microbiol Biotechnol. 2008;78:1033–43.
Sy A, Timmers AC, Knief C, Vorholt JA. Methylotrophic metabolism is advantageous for Methylobacterium extorquens during colonization of Medicago truncatula under competitive conditions. Appl Environ Microbiol. 2005;71:7245–52.
Holland M. Methylobacterium and plants. Rec Res Dev Plant Physiol. 1997;1:207–13.
Madhaiyan M, Poonguzhali S, Senthilkumar M, Seshadri S, Chung H, Jinchul Y et al. Growth promotion and induction of systemic resistance in rice cultivar Co-47 (Oryza sativa L.) by Methylobacterium spp. Bot Bull Acad Sin. 2004;45:315–24.
Madhaiyan M, Poonguzhali S, Lee H, Hari K, Sundaram S, Sa T. Pink-pigmented facultative methylotrophic bacteria accelerate germination, growth and yield of sugarcane clone Co86032 (Saccharum officinarum L.). Biol Fertil Soils. 2005;41(5):350–8.
Hollond MA, Long RLG, Polacco JC. Methylobacterium spp.: phylloplane bacteria involved in cross-talk with the plant host? In: Lindow SE, Hecht-Poinar EI, Elliot VJ, editors. Phyllosphere Microbiology. St. Paul, Minn: American Phytopathological Society; 2002. p. 125–35.
Madhaiyan M, Poonguzhali S, Sa T. Characterization of 1-aminocyclopropane-1-carboxylate (ACC) deaminase containing Methylobacterium oryzae and interactions with auxins and ACC regulation of ethylene in canola (Brassica campestris). Planta. 2007;226:867–76.
Chistoserdova L, Chen S-W, Lapidus A, Lidstrom ME. Methylotrophy in Methylobacterium extorquens AM1 from a genomic point of view. J Bacteriol. 2003;185(10):2980–7.
Kwak M-J, Jeong H, Madhaiyan M, Lee Y, Sa T-M, Oh TK, et al. Genome information of Methylobacterium oryzae, a plant-probiotic methylotroph in the phyllosphere. PLoS One. 2014;9(9):e106704.
Yi C, Reddy C, Varghese K, Bui TNH, Zhang S, Kallath M, et al. A new Jatropha curcas variety (JO S2) with improved seed productivity. Sustainability. 2014;6:4355–68.
Reasoner D, Geldreich E. A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol. 1985;49:1–7.
King EO, Ward MK, Raney DE. Two simple media for the demonstration of pyocyanin and fluorescin. J Lab Clin Med. 1954;44:301.
Whittenbury R, Phillips K, Wilkinson J. Enrichment, isolation and some properties of methane-utilizing bacteria. J Gen Microbiol. 1970;61:205–18.
Baldani VLD, Döbereiner J. Host-plant specificity in the infection of cereals with Azospirillum spp. Soil Biol Biochem. 1980;12:433–9.
Estrada-De Los Santos P, Bustillos-Cristales R, Caballero-Mellado J. Burkholderia, a genus rich in plant-associated nitrogen fixers with wide environmental and geographic distribution. Appl Environ Microbiol. 2001;67:2790–8.
Burdman S, Jurkevitch E, Schwartsburd B, Hampel M, Okon Y. Aggregation in Azospirillum brasilense: effects of chemical and physical factors and involvement of extracellular components. Microbiol. 1998;144:1989–99.
Hurley MA, Roscoe M. Automated statistical analysis of microbial enumeration by dilution series. J Appl Bacteriol. 1983;55:159–64.
Wilson K. Preparation of genomic DNA from bacteria. Curr Protoc Mol Biol. 1987:2.4.1–2.4.5.
DeLong EF. Archaea in coastal marine environments. Proc Natl Acad Sci USA. 1992;89:5685–9.
Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol. 2012;62:716–21.
Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406–25.
Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985:783–91.
Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol. 1971;20:406–16.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011;28:2731–9.
Reinhold-Hurek B, Hurek T, Claeyssens M, Van Montagu M. Cloning, expression in Escherichia coli, and characterization of cellulolytic enzymes of Azoarcus sp., a root-invading diazotroph. J Bacteriol. 1993;175:7056–65.
Kim B, Wimpenny J. Growth and cellulolytic activity of Cellulomonas flavigena. Can J Microbiol. 1981;27:1260–6.
Widmer F, Shaffer B, Porteous L, Seidler R. Analysis of nifH gene pool complexity in soil and litter at a Douglas fir forest site in the Oregon Cascade Mountain Range. Appl Environ Microbiol. 1999;65:374–80.
Iniguez AL, Dong Y, Triplett EW. Nitrogen fixation in wheat provided by Klebsiella pneumoniae 342. Mol Plant Microbe Int. 2004;17(10):1078–85.
MM and LJ conceived experiments and drafted the manuscript. MM performed strain isolation, characterization and bioassays for bacteria and plants. NST and THHA participated in plant inoculation experiments, data analysis and helped to revise the manuscript. BP participated in the bioinformatic, statistical analysis and helped to revise the manuscript. All authors read and approved the final manuscript.
This work was supported by the Temasek Foundation and the Singapore Economy Development Board (EDB).
The authors declare that they have no competing interests. Temasek Life Sciences Laboratory has an interest in using selected nitrogen-fixing strains for applications in agriculture.